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ORCIDPLoS Computational Biology, Volume 20
Volume 20, Number 1, January 2024
- Marcus Kaiser
:
Ten simple rules for establishing an experimental lab. - Gabriel Reuben Smith, Carolina Bello, Lalasia Bialic-Murphy, Emily Clark, Camille S. Delavaux, Camille Fournier de Lauriere, Johan van den Hoogen, Thomas Lauber, Haozhi Ma, Daniel S. Maynard, Matthew Mirman, Lidong Mo, Dominic Rebindaine, Josephine Elena Reek, Leland K. Werden, Zhaofei Wu, Gayoung Yang, Qingzhou Zhao, Constantin M. Zohner, Thomas Ward Crowther:
Ten simple rules for using large language models in science, version 1.0.
- Alice Bruel, Ignacio Abadía, Thibault Collin, Icare Sakr, Henri Lorach, Niceto R. Luque, Eduardo Ros, Auke Jan Ijspeert:
The spinal cord facilitates cerebellar upper limb motor learning and control; inputs from neuromusculoskeletal simulation. - Enrique R. Sebastian, Julio Esparza, Liset M. De La Prida:
Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces. - Aakash Pandey, Abigail B. Feuka, Melinda Cosgrove, Megan Moriarty, Anthony Duffiney, Kurt C. Vercauteren, Henry Campa III, Kim M. Pepin:
Wildlife vaccination strategies for eliminating bovine tuberculosis in white-tailed deer populations. - Yoav Ger, Eliya Nachmani, Lior Wolf, Nitzan Shahar:
Harnessing the flexibility of neural networks to predict dynamic theoretical parameters underlying human choice behavior. - Jinchao Lv, Jin Wang, Chunhe Li:
Landscape quantifies the intermediate state and transition dynamics in ecological networks. - Yong-Jin Huang, Chun-Wei Chang, Chih-Hao Hsieh:
Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis. - Jiarui Feng, S. Peter Goedegebuure, Amanda Zeng, Ye Bi, Ting Wang, Philip R. O. Payne, Li Ding, David DeNardo, William Hawkins, Ryan C. Fields, Fuhai Li:
sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data. - Elizabeth Lawson-Keister, Tao Zhang, Fatemeh Nazari, François Fagotto, M. Lisa Manning:
Differences in boundary behavior in the 3D vertex and Voronoi models. - Lucas Castillo, Pablo León-Villagrá, Nick Chater, Adam Sanborn:
Explaining the flaws in human random generation as local sampling with momentum. - Haiqing Zhao, Hao Wu, Alex Guseman, Dulith Abeykoon, Christina M. Camara, Yamini Dalal, David Fushman, Garegin A. Papoian:
The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. - Florian G. Pflug, Deepak Bhat, Simone Pigolotti:
Genome replication in asynchronously growing microbial populations. - Paul F. Lang, David R. Penas, Julio R. Banga, Daniel Weindl, Béla Novák:
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. - Chin-Hsuan Sophie Lin, Trang Thuy Do, Lee Unsworth, Marta I. Garrido:
Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer. - Tijl Grootswagers, Amanda K. Robinson, Sophia M. Shatek, Thomas A. Carlson:
Mapping the dynamics of visual feature coding: Insights into perception and integration. - Michael J. Plank, Leighton M. Watson, Oliver J. Maclaren:
Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand. - Avik Mukherjee, Yu-Fang Chang, Yanqing Huang, Nina Catherine Benites, Leander Ammar, Jade Ealy, Mark Polk, Markus Basan:
Plasticity of growth laws tunes resource allocation strategies in bacteria. - Sjoerd Terpstra, Flavia Maria Darcie Marquitti, Vítor V. Vasconcelos:
Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change. - Christopher A. Mancuso, Kayla A. Johnson, Renming Liu, Arjun Krishnan:
Joint representation of molecular networks from multiple species improves gene classification. - Eric Elmoznino, Michael F. Bonner:
High-performing neural network models of visual cortex benefit from high latent dimensionality. - Jian Zou, Osama Shah, Yu-Chiao Chiu, Tianzhou Ma, Jennifer M. Atkinson, Steffi Oesterreich, Adrian V. Lee, George C. Tseng:
Systems approach for congruence and selection of cancer models towards precision medicine. - Eduardo Jardón-Valadez, Alfredo Ulloa-Aguirre:
Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations. - H. Robert Frost:
Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue. - Tyler S. Manning, Emma Alexander, Bruce G. Cumming, Gregory C. DeAngelis, Xin Huang, Emily A. Cooper:
Transformations of sensory information in the brain suggest changing criteria for optimality. - Karan Kabbur Hanumanthappa Manjunatha, Giorgia Baron, Danilo Benozzo, Erica Silvestri, Maurizio Corbetta, Alessandro Chiuso, Alessandra Bertoldo, Samir Suweis, Michele Allegra:
Controlling target brain regions by optimal selection of input nodes. - Kaiser J. Loell, Ryan Z. Friedman, Connie A. Myers, Joseph C. Corbo, Barak A. Cohen, Michael A. White:
Transcription factor interactions explain the context-dependent activity of CRX binding sites. - Hong An, J. Chris Pires, Gavin C. Conant:
Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. - Janne J. Luppi, Cornelis J. Stam, Philip Scheltens, Willem de Haan:
Virtual neural network-guided optimization of non-invasive brain stimulation in Alzheimer's disease. - Maki Sudo, Koichi Fujimoto:
Diffusive mediator feedbacks control the health-to-disease transition of skin inflammation. - Giovanni Lo Iacono, Alasdair J. C. Cook, Gianne Derks, Lora E. Fleming, Nigel French, Emma L. Gillingham, Laura C. Gonzalez Villeta, Clare Heaviside, Roberto La Ragione, Giovanni Leonardi, Christophe E. Sarran, Sotiris Vardoulakis, Francis Senyah, Arnoud H. M. van Vliet, Gordon Nichols:
A mathematical, classical stratification modeling approach to disentangling the impact of weather on infectious diseases: A case study using spatio-temporally disaggregated Campylobacter surveillance data for England and Wales. - Martin Grunnill, Julien Arino, Zachary McCarthy, Nicola Luigi Bragazzi, Laurent Coudeville, Edward W. Thommes, Amine Amiche, Abbas Ghasemi, Lydia Bourouiba, Mohammadali Tofighi, Ali Asgary, Mortaza Baky-Haskuee, Jianhong Wu:
Modelling disease mitigation at mass gatherings: A case study of COVID-19 at the 2022 FIFA World Cup. - Shunsuke Koseki, Mitsuhiro Hayashibe, Dai Owaki:
Identifying essential factors for energy-efficient walking control across a wide range of velocities in reflex-based musculoskeletal systems. - Virginia Dominguez-Garcia, Sonia Kéfi:
The structure and robustness of ecological networks with two interaction types. - Sebastian Idesis, Sebastián Geli, Joshua Faskowitz, Jakub Vohryzek, Yonatan Sanz Perl, Florian Pieper, Edgar E. Galindo-Leon, Andreas K. Engel, Gustavo Deco:
Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex. - Laura Schmid, Thomas Klotz, Oliver Röhrle, Randall K. Powers, Francesco Negro, Utku S. Yavuz:
Postinhibitory excitation in motoneurons can be facilitated by hyperpolarization-activated inward currents: A simulation study. - Anand Ramachandran, Steven S. Lumetta, Deming Chen:
PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning. - Chen Beer, Omri Barak:
Revealing and reshaping attractor dynamics in large networks of cortical neurons. - Sizhe Qiu, Xinlong Wan, Yueshan Liang, Cameron R. Lamoureux, Amir Akbari, Bernhard O. Palsson, Daniel C. Zielinski:
Inferred regulons are consistent with regulator binding sequences in E. coli. - Pablo Alvarez, Marouane El Mouss, Maxime Calka, Anca Belme, Gilles Berillon, Pauline Brige, Yohan Payan, Pascal Perrier, Amélie Vialet:
Predicting primate tongue morphology based on geometrical skull matching. A first step towards an application on fossil hominins. - Marine Louarn, Guillaume Collet, Ève Barré, Thierry Fest, Olivier Dameron, Anne Siegel, Fabrice Chatonnet:
Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints. - Javier Robles, Ananth Prakash, Juan Antonio Vizcaíno, J. Ignacio Casal:
Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation. - Bryan Shin, Gary An, Chase Cockrell:
Examining B-cell dynamics and responsiveness in different inflammatory milieus using an agent-based model. - Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar:
A genome-wide comprehensive analysis of nucleosome positioning in yeast. - Pascal P. Klamser, Adrian Zachariae, Benjamin F. Maier, Olga Baranov, Clara Jongen, Frank Schlosser, Dirk Brockmann:
Inferring country-specific import risk of diseases from the world air transportation network. - Andrea Papale, David Holcman:
Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories. - Kieran D. Lamb, Martha M. Luka, Megan Saathoff, Richard J. Orton, My V. T. Phan, Matthew Cotten, Ke Yuan, David L. Robertson:
Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. - Ian T. Ellwood:
Short-term Hebbian learning can implement transformer-like attention. - Raymond Copeland, Christopher Zhang, Brian K. Hammer, Peter J. Yunker:
Spatial constraints and stochastic seeding subvert microbial arms race. - Michiel van Boven, Christiaan H. van Dorp, Ilse Westerhof, Vincent Jaddoe, Valerie Heuvelman, Liesbeth Duijts, Elandri Fourie, Judith Sluiter-Post, Marlies A. van Houten, Paul Badoux, Sjoerd Euser, Bjorn Herpers, Dirk Eggink, Marieke de Hoog, Trisja Boom, Joanne Wildenbeest, Louis Bont, Ganna Rozhnova, Marc J. M. Bonten, Mirjam E. Kretzschmar, Patricia Bruijning-Verhagen:
Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study. - David L. Krongauz, Amir Ayali, Gal A. Kaminka:
Vision-based collective motion: A locust-inspired reductionist model. - Mehran Fazli, Richard Bertram:
Conversion of spikers to bursters in pituitary cell networks: Is it better to disperse for maximum exposure or circle the wagons? - Beatriz Ocaña-Tienda, Odelaisy León-Triana, Julián Pérez-Beteta, Juan Jiménez-Sánchez, Víctor M. Pérez-García:
Radiation necrosis after radiation therapy treatment of brain metastases: A computational approach. - Ata Kalirad, Ralf J. Sommer:
Spatial and temporal heterogeneity alter the cost of plasticity in Pristionchus pacificus. - Magdalena Kozielska, Franz J. Weissing:
A neural network model for the evolution of learning in changing environments. - Yaojia Chen, Jiacheng Wang, Chunyu Wang, Quan Zou:
AutoEdge-CCP: A novel approach for predicting cancer-associated circRNAs and drugs based on automated edge embedding. - Louis Yat Hin Chan, Gunnar Rø, Jørgen Eriksson Midtbø, Francesco Di Ruscio, Sara Sofie Viksmoen Watle, Lene Kristine Juvet, Jasper Littmann, Preben Aavitsland, Karin Maria Nygård, Are Stuwitz Berg, Geir Bukholm, Anja Bråthen Kristoffersen, Kenth Engø-Monsen, Solveig Engebretsen, David Swanson, Alfonso Diz-Lois Palomares, Jonas Christoffer Lindstrøm, Arnoldo Frigessi, Birgitte Freiesleben de Blasio:
Modeling geographic vaccination strategies for COVID-19 in Norway.
- Paul J. N. Brodersen, Hannah Alfonsa, Lukas B. Krone, Cristina Blanco-Duque, Angus S. Fisk, Sarah J. Flaherty, Mathilde C. C. Guillaumin, Yi-Ge Huang, Martin C. Kahn, Laura E. McKillop, Linus Milinski, Lewis Taylor, Christopher W. Thomas, Tomoko Yamagata, Russell G. Foster, Vladyslav V. Vyazovskiy, Colin J. Akerman:
Somnotate: A probabilistic sleep stage classifier for studying vigilance state transitions. - Rituparna Samanta, Jeffrey J. Gray:
Implicit model to capture electrostatic features of membrane environment. - Said el Bouhaddani, Matthias Höllerhage, Hae-Won Uh, Claudia Moebius, Marc Bickle, Günter U. Höglinger, Jeanine J. Houwing-Duistermaat:
Statistical integration of multi-omics and drug screening data from cell lines.
- Sebastian Himbert, Dorian Gaboo, Emre Brookes, John F. Nagle, Maikel C. Rheinstädter:
MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks. - Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu:
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing.
Volume 20, Number 2, February 2024
- Joachim Goedhart:
Studentsourcing - Aggregating and reusing data from a practical cell biology course.
- Helena Klara Jambor, Martin Bornhäuser:
Ten simple rules for designing graphical abstracts.
- Martijn A. de Jong, Esmée Adegeest, Noémie M. L. P. Bérenger-Currias, Maria Mircea, Roeland M. H. Merks, Stefan Semrau:
The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion. - Kameel Khabaz, Karen Yuan, Joseph Pugar, David Jiang, Seth Sankary, Sanjeev Dhara, Junsung Kim, Janet Kang, Nhung Nguyen, Kathleen Cao, Newell Washburn, Nicole Bohr, Cheong Jun Lee, Gordon Kindlmann, Ross Milner, Luka Pocivavsek:
The geometric evolution of aortic dissections: Predicting surgical success using fluctuations in integrated Gaussian curvature. - Jacob B. Roberts, Alberto A Nava, Allison N. Pearson, Matthew R. Incha, Luis E. Valencia, Melody Ma, Abhay Rao, Jay D. Keasling:
Foldy: An open-source web application for interactive protein structure analysis. - Sarah Percival, Joyce G. Onyenedum, Daniel H. Chitwood, Aman Y. Husbands:
Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae). - Matthijs Pals, Jakob H. Macke, Omri Barak:
Trained recurrent neural networks develop phase-locked limit cycles in a working memory task. - Jane Knöchel, Charlotte Kloft, Wilhelm Huisinga:
Index analysis: An approach to understand signal transduction with application to the EGFR signalling pathway. - Etienne Thoret, Thomas Andrillon, Caroline Gauriau, Damien Léger, Daniel Pressnitzer:
Sleep deprivation detected by voice analysis. - Sarvenaz Sarabipour, Karina Kinghorn, Kaitlyn M. Quigley, Anita Kovacs-Kasa, Brian H. Annex, Victoria L. Bautch, Feilim Mac Gabhann:
Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells. - Connor R. King, Casey-Tyler Berezin, Jean Peccoud:
Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production. - Te Liu, Sichao Huang, Qian Zhang, Yu Xia, Manjie Zhang, Bin Sun:
Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data. - Yu Feng, Nicolas Brunel:
Attractor neural networks with double well synapses. - Keith E. Kennedy, Nicole Kerlero de Rosbo, Antonio Uccelli, Maria Cellerino, Federico Ivaldi, Paola Contini, Raffaele De Palma, Hanne F. Harbo, Tone Berge, Steffan D. Bos, Einar A. Høgestøl, Synne Brune-Ingebretsen, Sigrid A. de Rodez Benavent, Friedemann Paul, Alexander U. Brandt, Priscilla Bäcker-Koduah, Janina Behrens, Joseph Kuchling, Susanna Asseyer, Michael Scheel, Claudia Chien, Hanna Zimmermann, Seyedamirhosein Motamedi, Josef Kauer-Bonin, Julio Saez-Rodriguez, Melanie Rinas, Leonidas G. Alexopoulos, Magí Andorrà, Sara Llufriu, Albert Saiz, Yolanda Blanco, Eloy Martinez-Heras, Elisabeth Solana, Irene Pulido-Valdeolivas, Elena H. Martinez-Lapiscina, Jordi García-Ojalvo, Pablo Villoslada:
Multiscale networks in multiple sclerosis. - Zhijie Feng, Robert Marsland III, Jason W. Rocks, Pankaj Mehta:
Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems. - Joe Hilton, Ian M. Hall:
A beta-Poisson model for infectious disease transmission. - Josepha Godivier, Elizabeth A. Lawrence, Mengdi Wang, Chrissy L. Hammond, Niamh C. Nowlan:
Compressive stress gradients direct mechanoregulation of anisotropic growth in the zebrafish jaw joint. - Linxing Preston Jiang, Rajesh P. N. Rao:
Dynamic predictive coding: A model of hierarchical sequence learning and prediction in the neocortex. - Xiang Liu, Nancy Gillis, Chang Jiang, Anthony McCofie, Timothy I. Shaw, Aik Choon Tan, Bo Zhao, Lixin Wan, Derek R. Duckett, Mingxiang Teng:
An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. - Meenal Datta, McCarthy Kennedy, Saeed Siri, Laura E. Via, James W. Baish, Lei Xu, Véronique Dartois, Clifton E. Barry 3rd, Rakesh K. Jain:
Mathematical model of oxygen, nutrient, and drug transport in tuberculosis granulomas. - Samuel H. A. von der Dunk, Paulien Hogeweg, Berend Snel:
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis. - Nathan LaPierre, Harold Pimentel:
Accounting for isoform expression increases power to identify genetic regulation of gene expression. - Kemin Zhu, Ling Yin, Kang Liu, Junli Liu, Yepeng Shi, Xuan Li, Hongyang Zou, Huibin Du:
Generating synthetic population for simulating the spatiotemporal dynamics of epidemics. - Carlos S. N. Brito, Wulfram Gerstner:
Learning what matters: Synaptic plasticity with invariance to second-order input correlations. - Zhenxing Guo, Daoyu Duan, Wen Tang, Julia Zhu, William S. Bush, Liangliang Zhang, Xiaofeng Zhu, Fulai Jin, Hao Feng:
magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing. - Lachlan Baer, Karissa Barthelson, John H. Postlethwait, David L. Adelson, Stephen M. Pederson, Michael Lardelli:
Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. - Jiao Zhao, Ke Chen, Bernhard O. Palsson, Laurence Yang:
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. - Li-Dunn Chen, Michael A. Caprio, Devin M. Chen, Andrew J. Kouba, Carrie K. Kouba:
Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians. - Jakub Köry, Vedang Narain, Bernadette J. Stolz, Jakob Kaeppler, Bostjan Markelc, Ruth J. Muschel, Philip K. Maini, Joe Pitt-Francis, Helen M. Byrne:
Enhanced perfusion following exposure to radiotherapy: A theoretical investigation. - András Zeke, Toby J. Gibson, Laszlo Dobson:
Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents. - Martin L. L. R. Barry, Wulfram Gerstner:
Fast adaptation to rule switching using neuronal surprise. - Sven Wientjes, Clay B. Holroyd:
The successor representation subserves hierarchical abstraction for goal-directed behavior. - Alexander D. Bird, Hermann Cuntz, Peter Jedlicka:
Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus. - Jose Gabriel Nino Barreat, Aris Katzourakis:
Ecological and evolutionary dynamics of cell-virus-virophage systems. - Natalie Schieferstein, Tilo Schwalger, Benjamin Lindner, Richard Kempter:
Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations. - Francesco Pinotti, José Lourenço, Sunetra Gupta, Suman Das Gupta, Joerg Henning, Damer Blake, Fiona Tomley, Tony Barnett, Dirk Pfeiffer, Md. Ahasanul Hoque, Guillaume Fournié:
EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks. - Quintessa Hay, Christopher Grubb, Sarah Minucci, Michael S. Valentine, Jennifer Van Mullekom, Rebecca L. Heise, Angela M. Reynolds:
Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis. - Juliette Cooke, Maxime Delmas, Cecilia Wieder, Pablo Rodríguez-Mier, Clément Frainay, Florence Vinson, Timothy M. D. Ebbels, Nathalie Poupin, Fabien Jourdan:
Genome scale metabolic network modelling for metabolic profile predictions. - Eshan S. King, Dagim Shiferaw Tadele, Beck Pierce, Michael Hinczewski, Jacob G. Scott:
Diverse mutant selection windows shape spatial heterogeneity in evolving populations. - Tom Van Wouwe, Jennifer L. Hicks, Scott L. Delp, C. Karen Liu:
A simulation framework to determine optimal strength training and musculoskeletal geometry for sprinting and distance running. - Tomas Barta, Lubomir Kostal:
Shared input and recurrency in neural networks for metabolically efficient information transmission. - Moritz Groden, Hannah M. Moessinger, Barbara Schaffran, Javier DeFelipe, Ruth Benavides-Piccione, Hermann Cuntz, Peter Jedlicka:
A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites. - Nicholas Tolley, Pedro L. C. Rodrigues, Alexandre Gramfort, Stephanie R. Jones:
Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference. - Paul Soulos, Leyla Isik:
Disentangled deep generative models reveal coding principles of the human face processing network. - Pan Li, Jae Kyoung Kim:
Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity. - Sangjeong Lee, Hyunwoo Kim:
Bidirectional de novo peptide sequencing using a transformer model. - R. Dustin Schaeffer, Jing Zhang, Kirill E. Medvedev, Lisa N. Kinch, Qian Cong, Nick V. Grishin:
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. - Chen Zhang, Junhui Gao, Hong-Yu Chen, Lingxin Kong, Guangshuo Cao, Xiangyu Guo, Wei Liu, Bin Ren, Dong-Qing Wei:
STGIC: A graph and image convolution-based method for spatial transcriptomic clustering. - Rui Wang, Zhilin Qu, Xiaodong Huang:
Dissecting the roles of calcium cycling and its coupling with voltage in the genesis of early afterdepolarizations in cardiac myocyte models. - Takahiro Kohsokabe, Shigeru Kuratanai, Kunihiko Kaneko:
Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory. - Denise Vlachou, Maria Veretennikova, Laura Usselmann, Vadim Vasilyev, Sascha Ott, Georg A. Bjarnason, Robert Dallmann, Francis Lévi, David A. Rand:
TimeTeller: A tool to probe the circadian clock as a multigene dynamical system. - Bonnie V. Dougherty, Connor J. Moore, Kristopher D. Rawls, Matthew L. Jenior, Bryan Chun, Sarbajeet Nagdas, Jeffrey J. Saucerman, Glynis L. Kolling, Anders Wallqvist, Jason A. Papin:
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. - Bastiaan J. R. Cockx, Tim Foster, Robert J. Clegg, Kieran Alden, Sankalp Arya, Dov J. Stekel, Barth F. Smets, Jan-Ulrich Kreft:
Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0. - Margaritis Voliotis, Ali Abbara, Julia K. Prague, Johannes D. Veldhuis, Waljit S. Dhillo, Krasimira Tsaneva-Atanasova:
HormoneBayes: A novel Bayesian framework for the analysis of pulsatile hormone dynamics.
- Daniele Dall'Olio, J. Eric Sträng, Amin T. Turki, Jesse M. Tettero, Martje Barbus, Renate Schulze-Rath, Javier Martinez Elicegui, Tommaso Matteuzzi, Alessandra Merlotti, Luciana Carota, Claudia Sala, Matteo G. Della Porta, Enrico Giampieri, Jesús María Hernández-Rivas, Lars Bullinger, Gastone C. Castellani:
Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology. - Yongtao Ye, Marcus H. Shum, Joseph L. Tsui, Guangchuang Yu, David K. Smith, Huachen Zhu, Joseph T. Wu, Yi Guan, Tommy Tsan-Yuk Lam:
Robust expansion of phylogeny for fast-growing genome sequence data. - Aaron L. Phillips, Scott Ferguson, Rachel A. Burton, Nathan S. Watson-Haigh:
CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data. - Luca Sesta, Andrea Pagnani, Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni:
Inference of annealed protein fitness landscapes with AnnealDCA. - Alexander Borst:
Connectivity Matrix Seriation via Relaxation. - Dennis Eschweiler, Rüveyda Yilmaz, Matisse Baumann, Ina Laube, Rijo Roy, Abin Jose, Daniel Brückner, Johannes Stegmaier:
Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets. - Lily Monnier, Paul-Henry Cournède:
A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization. - Martin H. P. Fernholz, Drago A. Guggiana Nilo, Tobias Bonhoeffer, Andreas M. Kist:
DeepD3, an open framework for automated quantification of dendritic spines.
- Tyson L. Swetnam, Parker B. Antin, Ryan Bartelme, Alexander Bucksch, David Camhy, Greg Chism, Illyoung Choi, Amanda M. Cooksey, Michele Cosi, Cindy Cowen, Michael Culshaw-Maurer, Robert Davey, Sean Davey, Upendra Devisetty, Tony Edgin, Andy Edmonds, Dmitry V. Fedorov, Jeremy Frady, John Fonner, Jeffrey K. Gillan, Iqbal Hossain, Blake Joyce, Konrad Lang, Tina Lee, Shelley Littin, Ian McEwen, Nirav C. Merchant, David Micklos, Andrew Nelson, Ashley Ramsey, Sarah Roberts, Paul Sarando, Edwin Skidmore, Jawon Song, Mary Margaret Sprinkle, Sriram Srinivasan, Dan Stanzione, Jonathan D. Strootman, Sarah Stryeck, Reetu Tuteja, Matthew Vaughn, Mojib Wali, Mariah Wall, Ramona Walls, Liya Wang, Todd Wickizer, Jason Williams, John Wregglesworth, Eric Lyons:
CyVerse: Cyberinfrastructure for open science. - Hong Seo Lim, Peng Qiu:
Quantifying the clusterness and trajectoriness of single-cell RNA-seq data.
Volume 20, Number 3, 2024
- Takehiro Ajioka, Nobuhiro Nakai, Okito Yamashita, Toru Takumi:
End-to-end deep learning approach to mouse behavior classification from cortex-wide calcium imaging. 1011074 - Kosaku Kitagawa, Kwang Su Kim, Masashi Iwamoto, Sanae Hayashi, Hyeongki Park, Takara Nishiyama, Naotoshi Nakamura, Yasuhisa Fujita, Shinji Nakaoka, Kazuyuki Aihara, Alan S. Perelson, Lena Allweiss, Maura Dandri, Koichi Watashi, Yasuhito Tanaka, Shingo Iwami:
Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers. 1011238 - Wencel Valega-Mackenzie, Marisabel Rodriguez Messan, Osman N. Yogurtçu, Ujwani Nukala, Zuben E. Sauna, Hong Yang:
Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine. 1011247 - Emma L. Davis, T. Déirdre Hollingsworth, Matt J. Keeling:
An analytically tractable, age-structured model of the impact of vector control on mosquito-transmitted infections. 1011440 - Tyler Cassidy, Kathryn E. Stephenson, Dan H. Barouch, Alan S. Perelson:
Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1. 1011518 - Matteo Martin, Morten Gram Pedersen:
Modelling and analysis of cAMP-induced mixed-mode oscillations in cortical neurons: Critical roles of HCN and M-type potassium channels. 1011559 - Yucai Shao, Andrew F. Magee, Tetyana I. Vasylyeva, Marc A. Suchard:
Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models. 1011640 - Siobhan Mackenzie Hall, Daniel Kochin, Carmel Carne, Patricia Herterich, Kristen Lenay Lewers, Mohamed Abdelhack, Arun Ramasubramanian, Juno Felecia Michael Alphonse, Visotheary Ung, Sara El-Gebali, Christopher Brian Currin, Esther Plomp, Rachel Thompson, Malvika Sharan:
Ten simple rules for pushing boundaries of inclusion at academic events. 1011797 - Cecilia Wieder, Juliette Cooke, Clément Frainay, Nathalie Poupin, Russell Bowler, Fabien Jourdan, Katerina J. Kechris, Rachel P. J. Lai, Timothy M. D. Ebbels:
PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration. 1011814 - Lauren A. Fromont, Mauricio Moldes, Michael Baudis, Anthony J. Brookes, Arcadi Navarro, Jordi Rambla:
Twelve quick tips for deploying a Beacon. 1011817 - Edgar Peña, Nicole A. Pelot, Warren M. Grill:
Computational models of compound nerve action potentials: Efficient filter-based methods to quantify effects of tissue conductivities, conduction distance, and nerve fiber parameters. 1011833 - Derek E. Moulton, Nathanaël Aubert-Kato, Axel A. Almet, Atsuko Sato:
A multiscale computational framework for the development of spines in molluscan shells. 1011835 - Benjamin S. M. Barlow, André Longtin, Béla Joós:
Impact on backpropagation of the spatial heterogeneity of sodium channel kinetics in the axon initial segment. 1011846 - Yu Toyoshima, Hirofumi Sato, Daiki Nagata, Manami Kanamori, Moon Sun Jang, Koyo Kuze, Suzu Oe, Takayuki Teramoto, Yuishi Iwasaki, Ryo Yoshida, Takeshi Ishihara, Yuichi Iino:
Ensemble dynamics and information flow deduction from whole-brain imaging data. 1011848 - Hendrik Reimann, Sjoerd M. Bruijn:
The condition for dynamic stability in humans walking with feedback control. 1011861 - Mari Kawakatsu, Sebastián Michel-Mata, Taylor A. Kessinger, Corina E. Tarnita, Joshua B. Plotkin:
When do stereotypes undermine indirect reciprocity? 1011862 - Elizabeth Seckel, Brandi Y. Stephens, Fátima Rodriguez:
Ten simple rules to leverage large language models for getting grants. 1011863 - Robert P. Gowers, Susanne Schreiber:
How neuronal morphology impacts the synchronisation state of neuronal networks. 1011874 - Tadeusz Satlawa, Mateusz Tarkowski, Sonia Wróbel, Pawel Dudzic, Tomasz Gawlowski, Tomasz Klaus, Marek Orlowski, Anna Kostyn, Sandeep Kumar, Andrew Buchanan, Konrad Krawczyk:
LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies. 1011881 - Chenyu Wu, Einar Bjarki Gunnarsson, Even Moa Myklebust, Alvaro Köhn-Luque, Dagim Shiferaw Tadele, Jorrit Martijn Enserink, Arnoldo Frigessi, Jasmine Foo, Kevin Leder:
Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data. 1011888 - András Ecker, Daniela Egas Santander, Sirio Bolaños-Puchet, James B. Isbister, Michael W. Reimann:
Cortical cell assemblies and their underlying connectivity: An in silico study. 1011891 - Nora S. Martin, Chico Q. Camargo, Ard A. Louis:
Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs. 1011893 - Kohei Ichikawa, Kunihiko Kaneko:
Bayesian inference is facilitated by modular neural networks with different time scales. 1011897 - Jonas Denk, Oskar Hallatschek:
Tipping points emerge from weak mutualism in metacommunities. 1011899 - Yang Jiang, Charlotte M. Deane, Garrett M. Morris, Edward P. O'Brien:
It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs. 1011901 - Maria Luisa Saggio, Viktor K. Jirsa:
Bifurcations and bursting in the Epileptor. 1011903 - Yang Ping Kuo, Oana Carja:
Evolutionary graph theory beyond pairwise interactions: Higher-order network motifs shape times to fixation in structured populations. 1011905 - Cera W. Hassinan, Scott C. Sterrett, Brennan Summy, Arnav Khera, Angie Wang, Jihong Bai:
Dimensionality of locomotor behaviors in developing C. elegans. 1011906 - Junjie Xia, Hoang Van Phan, Luke Vistain, Mengjie Chen, Aly A. Khan, Savas Tay:
Computational prediction of protein interactions in single cells by proximity sequencing. 1011915 - Nazanin Ahmadi Daryakenari, Mario De Florio, Khemraj Shukla, George Em Karniadakis:
AI-Aristotle: A physics-informed framework for systems biology gray-box identification. 1011916 - Jessica S. Yu, Neda Bagheri:
Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions. 1011917 - Nadin Haase, Wolf Holtkamp, Simon Christ, Dag Heinemann, Marina V. Rodnina, Sophia Rudorf:
Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation. 1011918 - Luís Pedro Coelho:
For long-term sustainable software in bioinformatics. 1011920 - Javier Galván Fraile, Franz Scherr, José J. Ramasco, Anton Arkhipov, Wolfgang Maass, Claudio R. Mirasso:
Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations. 1011921 - Minija Tamosiunaite, Christian Tetzlaff, Florentin Wörgötter:
Unsupervised learning of perceptual feature combinations. 1011926 - Søren D. Petersen, Lucas Levassor, Christine M. Pedersen, Jan Madsen, Lea G. Hansen, Jie Zhang, Ahmad K. Haidar, Rasmus John Normand Frandsen, Jay D. Keasling, Tilmann Weber, Nikolaus Sonnenschein, Michael K. Jensen:
teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering. 1011929 - Md Nurul Anwar, Lauren Smith, Angela Devine, Somya Mehra, Camelia R. Walker, Elizabeth Ivory, Eamon Conway, Ivo Mueller, James M. McCaw, Jennifer A. Flegg, Roslyn I. Hickson:
Mathematical models of Plasmodium vivax transmission: A scoping review. 1011931 - Cameron Zachreson, Julian Savulescu, Freya M. Shearer, Michael J. Plank, Simon Coghlan, Joel C. Miller, Kylie E. C. Ainslie, Nicholas Geard:
Ethical frameworks should be applied to computational modelling of infectious disease interventions. 1011933 - Sofía Jijón, Peter Czuppon, François Blanquart, Florence Débarre:
Using early detection data to estimate the date of emergence of an epidemic outbreak. 1011934 - Maximilian M. Mandl, Sabine Hoffmann, Sebastian Bieringer, Anna E. Jacob, Marie Kraft, Simon Lemster, Anne-Laure Boulesteix:
Raising awareness of uncertain choices in empirical data analysis: A teaching concept toward replicable research practices. 1011936 - Manuel Razo-Mejia, Madhav Mani, Dmitri Petrov:
Bayesian inference of relative fitness on high-throughput pooled competition assays. 1011937 - Moritz Ertelt, Vikram Khipple Mulligan, Jack B. Maguire, Sergey Lyskov, Rocco Moretti, Torben Schiffner, Jens Meiler, Clara T. Schoeder:
Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. 1011939 - Chaitanya Chintaluri, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski, Jakub M. Dzik, Joanna Jedrzejewska-Szmek, Daniel K. Wójcik:
kCSD-python, reliable current source density estimation with quality control. 1011941 - Hao-Ting Wang, Steven L. Meisler, Hanad Sharmarke, Natasha Clarke, Nicolas Gensollen, Christopher J. Markiewicz, François Paugam, Bertrand Thirion, Pierre Bellec:
Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn. 1011942 - Peng Liu, Ke Bo, Mingzhou Ding, Ruogu Fang:
Emergence of Emotion Selectivity in Deep Neural Networks Trained to Recognize Visual Objects. 1011943 - Pahala Gedara Jayathilake, Pedro Victori, Clara E. Pavillet, Chang Heon Lee, Dimitrios Voukantsis, Ana Miar, Anjali Arora, Adrian L. Harris, Karl J. Morten, Francesca M. Buffa:
Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study. 1011944 - Jaron T. Colas, John P. O'Doherty, Scott T. Grafton:
Active reinforcement learning versus action bias and hysteresis: control with a mixture of experts and nonexperts. 1011950 - Timothy Hasse, Esra Mantei, Rezvan Shahoei, Shristi Pawnikar, Jinan Wang, Yinglong Miao, Yu-ming M. Huang:
Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein. 1011955 - Büsra Atamer Balkan, You Chang, Martijn Sparnaaij, Berend Wouda, Doris Boschma, Yangfan Liu, Yufei Yuan, Winnie Daamen, Mart C. M. de Jong, Colin Teberg, Kevin Schachtschneider, Reina S. Sikkema, Linda van Veen, Dorine C. Duives, Quirine A. ten Bosch:
The multi-dimensional challenges of controlling respiratory virus transmission in indoor spaces: Insights from the linkage of a microscopic pedestrian simulation and SARS-CoV-2 transmission model. 1011956 - Rachael Pung, Timothy W. Russell, Adam J. Kucharski:
Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response. 1011967 - Nicholas Markarian, Kimberly M. Van Auken, Dustin Ebert, Paul W. Sternberg:
Enrichment on steps, not genes, improves inference of differentially expressed pathways. 1011968 - Jialiang Sun, Jun Guo, Jian Liu:
CRISPR-M: Predicting sgRNA off-target effect using a multi-view deep learning network. 1011972 - Sarah A. Vollert, Christopher C. Drovandi, Matthew P. Adams:
Unlocking ensemble ecosystem modelling for large and complex networks. 1011976 - Kati Hyvärinen, Katri Haimila, Camous Moslemi, Blood Service Biobank, Martin L. Olsson, Sisse R. Ostrowski, Ole B. Pedersen, Christian Erikstrup, Jukka Partanen, Jarmo Ritari:
A machine-learning method for biobank-scale genetic prediction of blood group antigens. 1011977 - Jonas Simoens, Tom Verguts, Senne Braem:
Learning environment-specific learning rates. 1011978 - Yitong Lv, He Gong, Xuechao Liu, Jia Hao, Lei Xu, Zhiwei Sun, Changyuan Yu, Lida Xu:
A dual computational and experimental strategy to enhance TSLP antibody affinity for improved asthma treatment. 1011984 - Ann Osi, Navid Ghaffarzadegan:
Parameter estimation in behavioral epidemic models with endogenous societal risk-response. 1011992 - Boaz Shvartzman, Yoav Ram:
Self-replicating artificial neural networks give rise to universal evolutionary dynamics. 1012004 - Jakub Svoboda, Soham Joshi, Josef Tkadlec, Krishnendu Chatterjee:
Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating. 1012008
Volume 20, Number 4, 2024
- Irena Balzekas, Joshua Trzasko, Grace Yu, Thomas J. Richner, Filip Mivalt, Vladimir Sladky, Nicholas M. Gregg, Jamie Van Gompel, Kai J. Miller, Paul E. Croarkin, Václav Kremen, Gregory A. Worrell:
Method for cycle detection in sparse, irregularly sampled, long-term neuro-behavioral timeseries: Basis pursuit denoising with polynomial detrending of long-term, inter-ictal epileptiform activity. 1011152 - Beren Millidge, Mufeng Tang, Mahyar Osanlouy, Nicol S. Harper, Rafal Bogacz:
Predictive coding networks for temporal prediction. 1011183 - Alice Geminiani, Claudia Casellato, Henk-Jan Boele, Alessandra Pedrocchi, Chris I. De Zeeuw, Egidio D'Angelo:
Mesoscale simulations predict the role of synergistic cerebellar plasticity during classical eyeblink conditioning. 1011277 - Chaoyue Sun, Ruogu Fang, Marco Salemi, Mattia Prosperi, Brittany Rife Magalis:
DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction. 1011351 - Rabea Link, Mona Jaggy, Martin Bastmeyer, Ulrich S. Schwarz:
Modelling cell shape in 3D structured environments: A quantitative comparison with experiments. 1011412 - Carolin Zitzmann, Ruian Ke, Ruy M. Ribeiro, Alan S. Perelson:
How robust are estimates of key parameters in standard viral dynamic models? 1011437 - Arco Bast, Rieke Fruengel, Christiaan P. J. de Kock, Marcel Oberländer:
Network-neuron interactions underlying sensory responses of layer 5 pyramidal tract neurons in barrel cortex. 1011468 - Vineeth Gutta, Satish Ranganathan Ganakammal, Sara Jones, Matthew Beyers, Sunita Chandrasekaran:
UNNT: A novel Utility for comparing Neural Net and Tree-based models. 1011504 - Yuhao Wang, Armin Lak, Sanjay G. Manohar, Rafal Bogacz:
Dopamine encoding of novelty facilitates efficient uncertainty-driven exploration. 1011516 - Anastasis Oulas, Kyriaki Savva, Nestoras Karathanasis, George M. Spyrou:
Ranking of cell clusters in a single-cell RNA-sequencing analysis framework using prior knowledge. 1011550 - Scott Boebinger, Aiden Payne, Giovanni Martino, Kennedy Kerr, Jasmine Mirdamadi, J. Lucas McKay, Michael Borich, Lena H. Ting:
Precise cortical contributions to sensorimotor feedback control during reactive balance. 1011562 - Judith A. Bouman, Anthony Hauser, Simon L. Grimm, Martin Wohlfender, Samir Bhatt, Elizaveta Semenova, Andrew Gelman, Christian L. Althaus, Julien Riou:
Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models. 1011575 - Alex D. Richardson, Tibor Antal, Richard A. Blythe, Linus J. Schumacher:
Learning spatio-temporal patterns with Neural Cellular Automata. 1011589 - Adam Husár, Mariam Ordyan, Guadalupe C. Garcia, Joel G. Yancey, Ali Sinan Saglam, James R. Faeder, Thomas M. Bartol, Mary B. Kennedy, Terrence J. Sejnowski:
MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface. 1011800 - Jinghao Chen, Jesse R. Holt, Elizabeth L. Evans, John S. Lowengrub, Medha M. Pathak:
PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration. 1011855 - Dong Ouyang, Yong Liang, Jinfeng Wang, Le Li, Ning Ai, Junning Feng, Shanghui Lu, Shuilin Liao, Xiaoying Liu, Shengli Xie:
HGCLAMIR: Hypergraph contrastive learning with attention mechanism and integrated multi-view representation for predicting miRNA-disease associations. 1011927 - Chang Liu, Kaimin Xiao, Cuinan Yu, Yipin Lei, Kangbo Lyu, Tingzhong Tian, Dan Zhao, Fengfeng Zhou, Haidong Tang, Jianyang Zeng:
A probabilistic knowledge graph for target identification. 1011945 - Tianhe Wang, Guy Avraham, Jonathan S. Tsay, Sabrina J. Abram, Richard B. Ivry:
Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation. 1011951 - Kenneth Kay, Natalie Biderman, Ramin Khajeh, Manuel Beiran, Christopher J. Cueva, Daphna Shohamy, Greg Jensen, Xue-Xin Wei, Vincent P. Ferrera, L. F. Abbott:
Emergent neural dynamics and geometry for generalization in a transitive inference task. 1011954 - Christian Donner, Julian Bartram, Philipp Hornauer, Taehoon Kim, Damian Roqueiro, Andreas Hierlemann, Guillaume Obozinski, Manuel S. Schröter:
Ensemble learning and ground-truth validation of synaptic connectivity inferred from spike trains. 1011964 - Danica Despotovic, Corentin Joffrois, Olivier Marre, Matthew Chalk:
Encoding surprise by retinal ganglion cells. 1011965 - Shiro Kato, Yukiko Himeno, Akira Amano:
Mathematical analysis of left ventricular elastance with respect to afterload change during ejection phase. 1011974 - Rui Meng, Kristofer E. Bouchard:
Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model. 1011975 - Bryce Morsky, Joshua B. Plotkin, Erol Akçay:
Indirect reciprocity with Bayesian reasoning and biases. 1011979 - Carla S. Griffiths, Jules M. Lebert, Joseph Sollini, Jennifer K. Bizley:
Gradient boosted decision trees reveal nuances of auditory discrimination behavior. 1011985 - Yixiao Zhai, Jiannan Chao, Yizheng Wang, Pinglu Zhang, Furong Tang, Quan Zou:
TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments. 1011988 - Yiyang Shi, Mingxiu He, Junheng Chen, Fangfang Han, Yongming Cai:
SubGE-DDI: A new prediction model for drug-drug interaction established through biomedical texts and drug-pairs knowledge subgraph enhancement. 1011989 - Yajas Shah, Scott Kulm, Jones T. Nauseef, Zhengming Chen, Olivier Elemento, Kevin H. Kensler, Ravi N. Sharaf:
Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort. 1011990 - Christopher N. Davis, Ronald E. Crump, Samuel A. Sutherland, Simon E. F. Spencer, Alice Corbella, Chansy Shampa, Junior Lebuki, Erick Mwamba Miaka, Kat S. Rock:
Comparison of stochastic and deterministic models for gambiense sleeping sickness at different spatial scales: A health area analysis in the DRC. 1011993 - Kje Hickman, Geoffrey Zahn:
Ten simple rules for leading a successful undergraduate-intensive research lab. 1011994 - Patrick Gemmell, Timothy B. Sackton, Scott V. Edwards, Jun S. Liu:
A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution. 1011995 - Adam Lampert:
Optimizing strategies for slowing the spread of invasive species. 1011996 - Alejandro Tlaie, Katharine Shapcott, Thijs L. van der Plas, James Rowland, Robert Lees, Joshua Keeling, Adam Packer, Paul Tiesinga, Marieke L. Schölvinck, Martha N. Havenith:
What does the mean mean? A simple test for neuroscience. 1012000 - Christian Cammarota, Nicole S. Dawney, Philip M. Bellomio, Maren Jüng, Alexander G. Fletcher, Tara M. Finegan, Dan T. Bergstralh:
The mechanical influence of densification on epithelial architecture. 1012001 - Florian E. C. Blanc, Anne Houdusse, Marco Cecchini:
A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis. 1012005 - Malek Senoussi, Thierry Artières, Paul Villoutreix:
Partial label learning for automated classification of single-cell transcriptomic profiles. 1012006 - Emma Beniston, Jordan P. Skittrall:
Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses. 1012009 - Hui Liu, Feng Wang, Jian Yu, Yong Pan, Chaoju Gong, Liang Zhang, Lin Zhang:
DBDNMF: A Dual Branch Deep Neural Matrix Factorization method for drug response prediction. 1012012 - Kamil Wolos, Leszek Pstras, Malgorzata Debowska, Wojciech Dabrowski, Dorota Siwicka-Gieroba, Jan Poleszczuk:
Non-invasive assessment of stroke volume and cardiovascular parameters based on peripheral pressure waveform. 1012013 - Kevin Zhang, Junhao Zhu, Dehan Kong, Zhaolei Zhang:
Modeling single cell trajectory using forward-backward stochastic differential equations. 1012015 - Satyaki Roy, Shehzad Z. Sheikh, Terrence S. Furey:
CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression. 1012016 - Jennifer A. Flegg, Sevvandi Kandanaarachchi, Philippe J. Guerin, Arjen M. Dondorp, Francois Nosten, Sabina Dahlström Otienoburu, Nick Golding:
Spatio-temporal spread of artemisinin resistance in Southeast Asia. 1012017 - Adrian Lison, Sam Abbott, Jana S. Huisman, Tanja Stadler:
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates. 1012021 - Luca Giudice, Ahmed Mohamed, Tarja Malm:
StellarPath: Hierarchical-vertical multi-omics classifier synergizes stable markers and interpretable similarity networks for patient profiling. 1012022 - Puranjan Ghimire, Mo Motamedi, Richard I. Joh:
Mathematical model for the role of multiple pericentromeric repeats on heterochromatin assembly. 1012027 - Marc D. Singleton, Michael B. Eisen:
Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation. 1012028 - Bingxian Xu, Dae-Sung Hwangbo, Sumit Saurabh, Clark Rosensweig, Ravi Allada, William L. Kath, Rosemary Braun:
Temperature-driven coordination of circadian transcriptional regulation. 1012029 - Sami Mollard, Catherine Wacongne, Sander M. Bohté, Pieter R. Roelfsema:
Recurrent neural networks that learn multi-step visual routines with reinforcement learning. 1012030 - Tracy J. Kuper, Mohammad Mazharul Islam, Shayn M. Peirce-Cottler, Jason A. Papin, Roseanne M. Ford:
Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment. 1012031 - Jesse Wheeler, Annaelaine Rosengart, Zhuoxun Jiang, Kevin Tan, Noah Treutle, Edward L. Ionides:
Informing policy via dynamic models: Cholera in Haiti. 1012032 - Florian G. Pflug, Simon Haendeler, Christopher Esk, Dominik Lindenhofer, Juergen A. Knoblich, Arndt von Haeseler:
Neutral competition explains the clonal composition of neural organoids. 1012054 - Lucy Lai, Samuel J. Gershman:
Human decision making balances reward maximization and policy compression. 1012057 - Sarah L. Master, Clayton E. Curtis, Peter Dayan:
Wagers for work: Decomposing the costs of cognitive effort. 1012060 - Robert Challen, Anastasia Chatzilena, George Qian, Glenda Oben, Rachel Kwiatkowska, Catherine Hyams, Adam Finn, Krasimira Tsaneva-Atanasova, Leon Danon:
Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error. 1012062 - Jong Hyuk Byun, Hye Seon Jeon, Hwi-yeol Yun, Jae Kyoung Kim:
Validity conditions of approximations for a target-mediated drug disposition model: A novel first-order approximation and its comparison to other approximations. 1012066 - Naiqian Zhang, Fubin Ma, Dong Guo, Yuxuan Pang, Chenye Wang, Yusen Zhang, Xiaoqi Zheng, Mingyi Wang:
A novel hypergraph model for identifying and prioritizing personalized drivers in cancer. 1012068 - Carla Alejandre, Jorge Calle-Espinosa, Jaime Iranzo:
Synergistic epistasis among cancer drivers can rescue early tumors from the accumulation of deleterious passengers. 1012081 - H. Robert Frost:
Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error. 1012084
Volume 20, Number 5, 2024
- Yifei Ren, Pouya Bashivan:
How well do models of visual cortex generalize to out of distribution samples? 1011145 - Velma K. Lopez, Estee Y. Cramer, Robert Pagano, John M. Drake, Eamon B. O'Dea, Madeline Adee, Turgay Ayer, Jagpreet Chhatwal, Ozden O. Dalgic, Mary A. Ladd, Benjamin P. Linas, Peter P. Mueller, Jade Xiao, Johannes Bracher, Alvaro J. Castro Rivadeneira, Aaron Gerding, Tilmann Gneiting, Yuxin Huang, Dasuni Jayawardena, Abdul H. Kanji, Khoa Le, Anja Mühlemann, Jarad Niemi, Evan L. Ray, Ariane Stark, Yijin Wang, Nutcha Wattanachit, Martha W. Zorn, Sen Pei, Jeffrey Shaman, Teresa K. Yamana, Samuel R. Tarasewicz, Daniel J. Wilson, Sid Baccam, Heidi Gurung, Steve Stage, Brad Suchoski, Lei Gao, Zhiling Gu, Myungjin Kim, Xinyi Li, Guannan Wang, Lily Wang, Yueying Wang, Shan Yu, Lauren Gardner, Sonia Jindal, Maximilian Marshall, Kristen Nixon, Juan Dent, Alison L. Hill, Joshua Kaminsky, Elizabeth C. Lee, Joseph Chadi Lemaitre, Justin Lessler, Claire P. Smith, Shaun Truelove, Matt Kinsey, Luke C. Mullany, Kaitlin Rainwater-Lovett, Lauren Shin, Katharine Tallaksen, Shelby Wilson, Dean Karlen, Lauren Castro, Geoffrey Fairchild, Isaac Michaud, Dave Osthus, Jiang Bian, Wei Cao, Zhifeng Gao, Juan Lavista Ferres, Chaozhuo Li, Tie-Yan Liu, Xing Xie, Shun Zhang, Shun Zheng, Matteo Chinazzi, Jessica T. Davis, Kunpeng Mu, Ana L. Pastore y Piontti, Alessandro Vespignani, Xinyue Xiong, Robert Walraven, Jinghui Chen, Quanquan Gu, Lingxiao Wang, Pan Xu, Weitong Zhang, Difan Zou, Graham Casey Gibson, Daniel Sheldon, Ajitesh Srivastava, Aniruddha Adiga, Benjamin Hurt, Gursharn Kaur, Bryan Lewis, Madhav V. Marathe, Akhil Sai Peddireddy, Przemyslaw J. Porebski, Srinivasan Venkatramanan, Lijing Wang, Pragati V. Prasad, Jo W. Walker, Alexander E. Webber, Rachel B. Slayton, Matthew Biggerstaff, Nicholas G. Reich, Michael A. Johansson:
Challenges of COVID-19 Case Forecasting in the US, 2020-2021. 1011200 - Paulina Clara Dagnino, Anira Escrichs, Ane López-González, Olivia Gosseries, Jitka Annen, Yonatan Sanz Perl, Morten L. Kringelbach, Steven Laureys, Gustavo Deco:
Re-awakening the brain: Forcing transitions in disorders of consciousness by external in silico perturbation. 1011350 - Sean M. Cascarina, Eric D. Ross:
Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life. 1011372 - Sanjeevani Choudhery, Michael A. DeJesus, Aarthi Srinivasan, Jeremy Rock, Dirk Schnappinger, Thomas R. Ioerger:
A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. 1011408 - Ariana Chriss, G. Valentin Börner, Shawn D. Ryan:
Agent-based modeling of nuclear chromosome ensembles identifies determinants of homolog pairing during meiosis. 1011416 - Eric R. Snyder, Alba Solsona-Berga, Simone Baumann-Pickering, Kait E. Frasier, Sean M. Wiggins, John A. Hildebrand:
Where's Whaledo: A software toolkit for array localization of animal vocalizations. 1011456 - Evan D. Gorman, Manuel E. Lladser:
Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance. 1011543 - Shoutik Mukherjee, Behtash Babadi:
Adaptive modeling and inference of higher-order coordination in neuronal assemblies: A dynamic greedy estimation approach. 1011605 - Luke Trinity, Ulrike Stege, Hosna Jabbari:
Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot. 1011787 - Moo K. Chung, Shih-Gu Huang, Ian C. Carroll, Vince D. Calhoun, H. Hill Goldsmith:
Topological state-space estimation of functional human brain networks. 1011869 - David Pastor-Alonso, Maxime Berg, Franck Boyer, Natalie Fomin-Thunemann, Michel Quintard, Yohan Davit, Sylvie Lorthois:
Modeling oxygen transport in the brain: An efficient coarse-grid approach to capture perivascular gradients in the parenchyma. 1011973 - Keiji Ota, Laurence T. Maloney:
Dissecting Bayes: Using influence measures to test normative use of probability density information derived from a sample. 1011999 - Andriana Manousidaki, Anna Little, Yuying Xie:
Clustering and visualization of single-cell RNA-seq data using path metrics. 1012014 - Ava M. Hoffman, Carrie Wright:
Ten simple rules for teaching an introduction to R. 1012018 - Hong Yang, Ying Shi, Anqi Lin, Chang Qi, Zaoqu Liu, Quan Cheng, Kai Miao, Jian Zhang, Peng Luo:
PESSA: A web tool for pathway enrichment score-based survival analysis in cancer. 1012024 - Fleur Zeldenrust, Niccolò Calcini, Xuan Yan, Ate Bijlsma, Tansu Celikel:
The tuning of tuning: How adaptation influences single cell information transfer. 1012043 - Raphael Sonabend, Hugo Gruson, Leo Wolansky, Agnes Kiragga, Daniel S. Katz:
FAIR-USE4OS: Guidelines for creating impactful open-source software. 1012045 - Héctor M. Sánchez C., David L. Smith, John M. Marshall:
MGSurvE: A framework to optimize trap placement for genetic surveillance of mosquito populations. 1012046 - Blox Bloxham, Hyunseok Lee, Jeff Gore:
Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches. 1012049 - Yves Dumont, Clélia F. Oliva:
On the impact of re-mating and residual fertility on the Sterile Insect Technique efficacy: Case study with the medfly, Ceratitis capitata. 1012052 - Benjamin Antin, Masato Sadahiro, Marta Gajowa, Marcus A. Triplett, Hillel Adesnik, Liam Paninski:
Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization. 1012053 - Santiago A. Cadena, Konstantin F. Willeke, Kelli Restivo, George H. Denfield, Fabian H. Sinz, Matthias Bethge, Andreas S. Tolias, Alexander S. Ecker:
Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks. 1012056 - Thirza Dado, Paolo Papale, Antonio Lozano, Lynn Le, Feng Wang, Marcel van Gerven, Pieter R. Roelfsema, Yagmur Güçlütürk, Umut Güçlü:
Brain2GAN: Feature-disentangled neural encoding and decoding of visual perception in the primate brain. 1012058 - Jason M. Müller, Katharina Moos, Till Baar, Kerstin C. Maier, Kristina Zumer, Achim Tresch:
Nuclear export is a limiting factor in eukaryotic mRNA metabolism. 1012059 - Richard Michael, Jacob Kæstel-Hansen, Peter Mørch Groth, Simon Bartels, Jesper Salomon, Pengfei Tian, Nikos S. Hatzakis, Wouter Boomsma:
A systematic analysis of regression models for protein engineering. 1012061 - Daniel L. Barton, Yow-Ren Chang, William Ducker, Jure Dobnikar:
Data-driven modelling makes quantitative predictions regarding bacteria surface motility. 1012063 - Nezar Abdennur, Sameer Abraham, Geoffrey Fudenberg, Ilya M. Flyamer, Aleksandra A. Galitsyna, Anton Goloborodko, Maxim Imakaev, Betul A. Oksuz, Sergey Venev, Yao Xiao:
Cooltools: Enabling high-resolution Hi-C analysis in Python. 1012067 - Charles Mullon, Jorge Peña, Laurent Lehmann:
The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance. 1012071 - Yuchao Li, Difan Deng, Chris Tina Höfer, Jihye Kim, Won Do Heo, Quanbin Xu, Xuedong Liu, Zhike Zi:
Liebig's law of the minimum in the TGF-β/SMAD pathway. 1012072 - Kanyarat Jitmana, Jason I. Griffiths, Sian Fereday, Anna Defazio, David Bowtell, Frederick R. Adler:
Mathematical modeling of the evolution of resistance and aggressiveness of high-grade serous ovarian cancer from patient CA-125 time series. 1012073 - Valdemar Kargård Olsen, Jonathan R. Whitlock, Yasser Roudi:
The quality and complexity of pairwise maximum entropy models for large cortical populations. 1012074 - James Ryu, Amin Nejatbakhsh, Mahdi Torkashvand, Sahana Gangadharan, Maedeh Seyedolmohadesin, Jinmahn Kim, Liam Paninski, Vivek Venkatachalam:
Versatile multiple object tracking in sparse 2D/3D videos via deformable image registration. 1012075 - Yasuhiro Mochizuki, Norihiro Harasawa, Mayank Aggarwal, Chong Chen, Haruaki Fukuda:
Foraging in a non-foraging task: Fitness maximization explains human risk preference dynamics under changing environment. 1012080 - An Qi Zhang, Martin R. Ralph, Adam R. Stinchcombe:
A mathematical model for the role of dopamine-D2 self-regulation in the production of ultradian rhythms. 1012082 - Udaysankar Chockanathan, Krishnan Padmanabhan:
Differential disruptions in population coding along the dorsal-ventral axis of CA1 in the APP/PS1 mouse model of Aβ pathology. 1012085 - Tianqi Wei, Qinghai Guo, Barbara Webb:
Learning with sparse reward in a gap junction network inspired by the insect mushroom body. 1012086 - David Mezey, Dominik Deffner, Ralf H. J. M. Kurvers, Pawel Romanczuk:
Visual social information use in collective foraging. 1012087 - Sébastien Benzekry, Michalis Mastri, Chiara Nicolò, John M. L. Ebos:
Machine-learning and mechanistic modeling of metastatic breast cancer after neoadjuvant treatment. 1012088 - Tanmoy Sarkar, Matej Krajnc:
Graph topological transformations in space-filling cell aggregates. 1012089 - Hazal Koptagel, Seong-Hwan Jun, Joanna Hård, Jens Lagergren:
Scuphr: A probabilistic framework for cell lineage tree reconstruction. 1012094 - Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji Kim, Olgica Milenkovic:
Interpretable online network dictionary learning for inferring long-range chromatin interactions. 1012095 - Phoebe Asplin, Matt J. Keeling, Rebecca Mancy, Edward M. Hill:
Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation. 1012096 - Tomas Ferreira Amaro Freire, Zhijian Hu, Kevin B. Wood, Erida Gjini:
Modeling spatial evolution of multi-drug resistance under drug environmental gradients. 1012098 - Alexander Kroll, Sahasra Ranjan, Martin J. Lercher:
A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships. 1012100 - Nikhil Phaniraj, Rahel K. Brügger, Judith M. Burkart:
Marmosets mutually compensate for differences in rhythms when coordinating vigilance. 1012104 - Tara Hameed, Natasha Motsi, Elaine Bignell, Reiko J. Tanaka:
Inferring fungal growth rates from optical density data. 1012105 - Martina Conte, Ryan T. Woodall, Margarita Gutova, Bihong T. Chen, Mark S. Shiroishi, Christine E. Brown, Jennifer M. Munson, Russell C. Rockne:
Structural and practical identifiability of contrast transport models for DCE-MRI. 1012106 - István Oszoli, István Zachar:
Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model. 1012107 - Albert Albesa-González, Claudia Clopath:
Learning with filopodia and spines: Complementary strong and weak competition lead to specialized, graded, and protected receptive fields. 1012110 - Claudia Pascovich, Diego Serantes, Alejo Rodriguez, Diego Mateos, Joaquín González, Diego Gallo, Mayda Rivas, Andrea Devera, Patricia Lagos, Nicolás Rubido, Pablo Torterolo:
Dorsal and median raphe neuronal firing dynamics characterized by nonlinear measures. 1012111 - Meng Wang, Xinyue Yan, Yanan Dong, Xiaoqin Li, Bin Gao:
Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment. 1012113 - Feng Jiao, Jing Li, Ting Liu, Yifeng Zhu, Wenhao Che, Leonidas Bleris, Chen Jia:
What can we learn when fitting a simple telegraph model to a complex gene expression model? 1012118 - Milena Rmus, Ti-Fen Pan, Liyu Xia, Anne G. E. Collins:
Artificial neural networks for model identification and parameter estimation in computational cognitive models. 1012119 - Alexander Massey, Corentin Boennec, Claudia Ximena Restrepo-Ortiz, Christophe Blanchet, Samuel Alizon, Mircea Sofonea:
Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model. 1012124 - Philippe Nguyen, Jinani Sooriyaarachchi, Qianyu Huang, Curtis L. Baker Jr.:
Estimating receptive fields of simple and complex cells in early visual cortex: A convolutional neural network model with parameterized rectification. 1012127 - Thomas Hladish, Alexander N. Pillai, Carl A. B. Pearson, Kok Ben Toh, Andrea C. Tamayo, Arlin Stoltzfus, Ira M. Longini:
Evaluating targeted COVID-19 vaccination strategies with agent-based modeling. 1012128 - Marko Sterk, Yaowen Zhang, Viljem Pohorec, Eva Paradiz Leitgeb, Jurij Dolensek, Richard K. P. Benninger, Andraz Stozer, Vira Kravets, Marko Gosak:
Network representation of multicellular activity in pancreatic islets: Technical considerations for functional connectivity analysis. 1012130 - Andre J. Faure, Ben Lehner, Verónica Miró Pina, Claudia Serrano Colome, Donate Weghorn:
An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity. 1012132 - Agastya Mondal, Héctor M. Sánchez C., John M. Marshall:
MGDrivE 3: A decoupled vector-human framework for epidemiological simulation of mosquito genetic control tools and their surveillance. 1012133 - Kerr Ding, Jiaqi Luo, Yunan Luo:
Leveraging conformal prediction to annotate enzyme function space with limited false positives. 1012135 - Tong Liu, Hao Zhu, Zheng Wang:
Learning Micro-C from Hi-C with diffusion models. 1012136 - Akseli Niemelä, Artturi Koivuniemi:
Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7. 1012137 - Zachary S. L. Foster, Andrew S. Tupper, Caroline M. Press, Niklaus J. Grünwald:
Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data. 1012139 - Maria J. Hagelaars, Milica M. Nikolic, Maud Vermeulen, Sylvia Dekker, Carlijn V. C. Bouten, Sandra Loerakker:
A computational analysis of the role of integrins and Rho-GTPases in the emergence and disruption of apical-basal polarization in renal epithelial cells. 1012140 - Thomas Rawson, Wes Hinsley, Raphael Sonabend, Elizaveta Semenova, Anne Cori, Neil M. Ferguson:
The impact of health inequity on spatial variation of COVID-19 transmission in England. 1012141 - Giacomo Janson, Michael Feig:
Transferable deep generative modeling of intrinsically disordered protein conformations. 1012144 - Xi Chen, Tamás I. Józsa, Danilo Cardim, Chiara Robba, Marek Czosnyka, Stephen J. Payne:
Modelling midline shift and ventricle collapse in cerebral oedema following acute ischaemic stroke. 1012145 - Lucy Lansch-Justen, Meriem El Karoui, Helen K. Alexander:
Estimating mutation rates under heterogeneous stress responses. 1012146 - Trini Nguyen, Babu Reddy Janakaloti Narayanareddy, Steven P. Gross, Christopher E. Miles:
Competition between physical search and a weak-to-strong transition rate-limits kinesin binding times. 1012158 - Amber Marijn Brands, Sasha Devore, Orrin Devinsky, Werner K. Doyle, Adeen Flinker, Daniel Friedman, Patricia Dugan, Jonathan Winawer, Iris Isabelle Anna Groen:
Temporal dynamics of short-term neural adaptation across human visual cortex. 1012161 - Nezar Abdennur, Geoffrey Fudenberg, Ilya M. Flyamer, Aleksandra A. Galitsyna, Anton Goloborodko, Maxim Imakaev, Sergey Venev:
Pairtools: From sequencing data to chromosome contacts. 1012164 - Garrick W. Bruening, Robert J. Courter, Shruthi Sukumar, Megan K. O'brien, Alaa A. Ahmed:
Disentangling the effects of metabolic cost and accuracy on movement speed. 1012169 - Franz Wurm, Benjamin Ernst, Marco Steinhauser:
Surprise-minimization as a solution to the structural credit assignment problem. 1012175 - Lulu Gong, Fabio Pasqualetti, Thomas Papouin, ShiNung Ching:
Astrocytes as a mechanism for contextually-guided network dynamics and function. 1012186
Volume 20, Number 6, 2024
- Jeremy Vanderdoes, Claire Marceaux, Kenta Yokote, Marie-Liesse Asselin-Labat, Gregory Rice, Jack D. Hywood:
Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments. 1011361 - Lu Zhang, Gang Xue, Xiaolin Zhou, Jiandong Huang, Zhiyuan Li:
A mathematical framework for understanding the spontaneous emergence of complexity applicable to growing multicellular systems. 1011882 - Jared Adolf-Bryfogle, Jason W. Labonte, John C. Kraft, Maxim Shapovalov, Sebastian Raemisch, Thomas Lütteke, Frank Dimaio, Christopher D. Bahl, Jesper Pallesen, Neil P. King, Jeffrey J. Gray, Daniel W. Kulp, William R. Schief:
Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design. 1011895 - Joshua M. Mitchell, Yuanye Chi, Maheshwor Thapa, Zhiqiang Pang, Jianguo Xia, Shuzhao Li:
Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline. 1011912 - Bartosz Ambrozy Gren, Maciej Antczak, Tomasz Zok, Joanna I. Sulkowska, Marta Szachniuk:
Knotted artifacts in predicted 3D RNA structures. 1011959 - Jakob Jordan, João Sacramento, Willem A. M. Wybo, Mihai A. Petrovici, Walter Senn:
Conductance-based dendrites perform Bayes-optimal cue integration. 1012047 - Joy M. O'Brien, Nathan Blais, Carmen Butler, Natalie White, Ash Bustead, Collin Figler, McKenna Wells, George Anderson, Anna Yuhas, Jessica Gilman Ernakovich:
Ten "simple" rules for non-Indigenous researchers engaging Indigenous communities in Arctic research. 1012093 - Pavel Sanda, Jaroslav Hlinka, Monica van den Berg, Antonín Skoch, Maxim Bazhenov, Georgios A. Keliris, Giri P. Krishnan:
Cholinergic modulation supports dynamic switching of resting state networks through selective DMN suppression. 1012099 - Xiaoman Xie, Saurabh Sinha:
Quantitative estimates of the regulatory influence of long non-coding RNAs on global gene expression variation using TCGA breast cancer transcriptomic data. 1012103 - Nikolaos M. Dimitriou, Salvador Flores-Torres, Maria Kyriakidou, Joseph Matthew Kinsella, Georgios D. Mitsis:
Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites. 1012112 - Devon J. Boland, Nicola M. Ayres:
Cracking AlphaFold2: Leveraging the power of artificial intelligence in undergraduate biochemistry curriculums. 1012123 - Ellie Mainou, Ruy M. Ribeiro, Jessica M. Conway:
Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection. 1012129 - Jacqueline Wistuba-Hamprecht, Bernhard Reuter, Rolf Fendel, Stephen L. Hoffman, Joseph J. Campo, Philip L. Felgner, Peter G. Kremsner, Benjamin Mordmüller, Nico Pfeifer:
Machine learning prediction of malaria vaccine efficacy based on antibody profiles. 1012131 - Christina M. P. Ray, Huilin Yang, Jamie B. Spangler, Feilim Mac Gabhann:
Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors. 1012157 - Seoyoung Ahn, Hossein Adeli, Gregory J. Zelinsky:
The attentive reconstruction of objects facilitates robust object recognition. 1012159 - Justin Bellavance, Linda Wang, Sarah A. Gagliano Taliun:
Eight quick tips for including chromosome X in genome-wide association studies. 1012160 - Mingyi Wang, Jacob G. Scott, Alexander Vladimirsky:
Threshold-awareness in adaptive cancer therapy. 1012165 - Roberto Efraín Díaz, Stephanie A. Wankowicz:
Ten recommendations for hosting a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club. 1012166 - Justine Vandendorpe, Beatrix Adam, Jeanne Wilbrandt, Birte Lindstädt, Konrad U. Förstner:
Ten simple rules for implementing electronic lab notebooks (ELNs). 1012170 - Genís Bayarri, Pau Andrio, Josep Lluis Gelpí, Adam Hospital, Modesto Orozco:
Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows. 1012173 - Mark D. Robinson, Peiying Cai, Martin Emons, Reto Gerber, Pierre-Luc Germain, Samuel Gunz, Siyuan Luo, Giulia Moro, Emanuel Sonder, Anthony Sonrel, Jiayi Wang, David Wissel, Izaskun Mallona:
Ten simple rules for computational biologists collaborating with wet lab researchers. 1012174 - Alexandra M. Proca, Fernando E. Rosas, Andrea I. Luppi, Daniel Bor, Matthew Crosby, Pedro A. M. Mediano:
Synergistic information supports modality integration and flexible learning in neural networks solving multiple tasks. 1012178 - Marisa Conte, Peter Boisvert, Philip D. Barrison, Farid Seifi, Zach Landis-Lewis, Allen J. Flynn, Charles P. Friedman:
Ten simple rules to make computable knowledge shareable and reusable. 1012179 - Mikhail Shubin, Hilde Kjelgaard Brustad, Jørgen Eriksson Midtbø, Felix Günther, Laura Alessandretti, Tapio Ala-Nissila, Gianpaolo Scalia Tomba, Mikko Kivelä, Louis Yat Hin Chan, Lasse Leskelä:
The influence of cross-border mobility on the COVID-19 epidemic in Nordic countries. 1012182 - Xiangting Li, Tom Chou:
Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies. 1012183 - Zijian Wang, Jan Hasenauer, Yannik Schälte:
Missing data in amortized simulation-based neural posterior estimation. 1012184 - Yuanchi Ha, Helena R. Ma, Feilun Wu, Andrea Weiss, Katherine Duncker, Helen Z. Xu, Jia Lu, Max Golovsky, Daniel Reker, Lingchong You:
Data-driven learning of structure augments quantitative prediction of biological responses. 1012185 - Lindsey Perry, Rebecca L. Kelble, Valerie N. Brewer, Cara E. Christensen, Mark Kerstens, Terrah Owens, Megan A. Sampognaro, Dorothy L. Zahor, Rachel A. Zitomer, Suzanne Austin, Jamie Cornelius, Jonathan Dinkins, Sarah J. K. Frey, Cecelia E. Frisinger, Stephanie M. Lequier, Carl G. Lundblad, Jamie Oskowski, Hallie R. Perlman, William J. Price, Richard Rich, Kayla Ruth, Vanessa Schroeder, Shawn B. Szabo, James W. Rivers:
Ten simple rules for implementing a successful field season. 1012189 - Caleb J. Holt, Kenneth D. Miller, Yashar Ahmadian:
The stabilized supralinear network accounts for the contrast dependence of visual cortical gamma oscillations. 1012190 - Apolline Louvet, Clément Mantoux, Nathalie Machon:
Assessing the extinction risk of the spontaneous flora in urban tree bases. 1012191 - Sebastian Salwig, Jakob Drefs, Jörg Lücke:
Zero-shot denoising of microscopy images recorded at high-resolution limits. 1012192 - Yu Zhu, Babak Momeni:
Revisiting the invasion paradox: Resistance-richness relationship is driven by augmentation and displacement trends. 1012193 - Md Zulfikar Ali, Sunil Guharajan, Vinuselvi Parisutham, Robert C. Brewster:
Regulatory properties of transcription factors with diverse mechanistic function. 1012194 - Matthew C. Perrone, Michael G. Lerner, Matthew Dunworth, Andrew J. Ewald, Joel S. Bader:
Prioritizing drug targets by perturbing biological network response functions. 1012195 - Kris Sankaran, Pratheepa Jeganathan:
mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics. 1012196 - Roseline Dzekem Dine, Lamis Yahia Mohamed Elkheir, Morufu Olalekan Raimi, Micheal Alemayehu, Salem Youssef Mohamed, Justice Kwadwo Turzin, Femi Qudus Arogundade, Elizabeth Akinyi Ochola, Alex Mukungu Nasiyo, Raziah Quallatein Mwawanga, Yahaya Abubakar Yabo:
Ten simple rules for successful and sustainable African research collaborations. 1012197 - Florian Bolenz, Thorsten Pachur:
Older adults select different but not simpler strategies than younger adults in risky choice. 1012204 - Seolah Shin, Seok Joo Chae, Seunggyu Lee, Jae Kyoung Kim:
Beyond homogeneity: Assessing the validity of the Michaelis-Menten rate law in spatially heterogeneous environments. 1012205 - Diego Andrés Contreras, Giulia Cencetti, Alain Barrat:
Infection patterns in simple and complex contagion processes on networks. 1012206 - Lionel Rigoux, Klaas E. Stephan, Frederike Petzschner:
Beliefs, compulsive behavior and reduced confidence in control. 1012207 - Lakshmipuram S. Swapna, Grant C. Stevens, Aline Sardinha-Silva, Lucas Zhongming Hu, Verena Brand, Daniel D. Fusca, Cuihong Wan, Xuejian Xiong, Jon P. Boyle, Michael E. Grigg, Andrew Emili, John Parkinson:
ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii. 1012208 - Jente Willaert, Kaat Desloovere, Anja Van Campenhout, Lena H. Ting, Friedl De Groote:
Combined translational and rotational perturbations of standing balance reveal contributions of reduced reciprocal inhibition to balance impairments in children with cerebral palsy. 1012209 - Jack M. O'shea, Peter Doerner, Annis Richardson, Christopher W. Wood:
Computational design of Periplasmic binding protein biosensors guided by molecular dynamics. 1012212 - Edward M. Hill, Stavros Petrou, Simon de Lusignan, Ivelina Yonova, Matt J. Keeling:
Correction: Seasonal influenza: Modelling approaches to capture immunity propagation. 1012213 - Shaked Bergman, Tamir Tuller:
Strong association between genomic 3D structure and CRISPR cleavage efficiency. 1012214 - Roberth Anthony Rojas Chávez, Mohammad Fili, Changze Han, Syed A. Rahman, Isaiah G. L. Bicar, Sullivan Gregory, Annika Helverson, Guiping Hu, Benjamin W. Darbro, Jishnu Das, Grant D. Brown, Hillel Haim:
Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics. 1012215 - Jannik Jauch, Moritz Becker, Christian Tetzlaff, Michael Fauth:
Differences in the consolidation by spontaneous and evoked ripples in the presence of active dendrites. 1012218 - Lars D'Hondt, Friedl De Groote, Maarten Afschrift:
A dynamic foot model for predictive simulations of human gait reveals causal relations between foot structure and whole-body mechanics. 1012219 - Lara S. Burchardt, Yana van de Sande, Mounia Kehy, Marco Gamba, Andrea Ravignani, Wim T. J. L. Pouw:
A toolkit for the dynamic study of air sacs in siamang and other elastic circular structures. 1012222 - Audrey Duval, Quentin J. Leclerc, Didier Guillemot, Laura Temime, Lulla Opatowski:
An algorithm to build synthetic temporal contact networks based on close-proximity interactions data. 1012227 - Chengwei Ai, Hongpeng Yang, Xiaoyi Liu, Ruihan Dong, Yijie Ding, Fei Guo:
MTMol-GPT: De novo multi-target molecular generation with transformer-based generative adversarial imitation learning. 1012229 - Tina Yao, Endrit Pajaziti, Michael Quail, Silvia Schievano, Jennifer Anne Steeden, Vivek Muthurangu:
Image2Flow: A proof-of-concept hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data. 1012231 - Soraya Mirzaei, Mojtaba Tefagh:
GEM-based computational modeling for exploring metabolic interactions in a microbial community. 1012233 - Leopold Zehetner, Diana Széliová, Barbara Kraus, Juan A. Hernandez Bort, Jürgen Zanghellini:
Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways. 1012236 - Hyeonuk Woo, Yubeen Kim, Chaok Seok:
Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling. 1012239 - Qince Li, Zheng Yan, Zhen Wang, Cuiping Liang, Xiqian Wang, Xianghu Wu, Wei Wang, Yongfeng Yuan, Kuanquan Wang:
A simulation study on the antiarrhythmic mechanisms of established agents in myocardial ischemia and infarction. 1012244 - Youcheng Li, Leann Lac, Qian Liu, Pingzhao Hu:
ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning. 1012254
Volume 20, Number 7, 2024
- Bin Liu, Bodo Rosenhahn, Thomas Illig, David S. DeLuca:
A variational autoencoder trained with priors from canonical pathways increases the interpretability of transcriptome data. 1011198 - Maud Delattre, Yusuke Toda, Jessica Tressou, Hiroyoshi Iwata:
Modeling soybean growth: A mixed model approach. 1011258 - Jesper J. Madsen, Y. Zenmei Ohkubo:
Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM. 1011421 - Paul Schmidt-Barbo, Gabriel Kalweit, Mehdi Naouar, Lisa Paschold, Edith Willscher, Christoph Schultheiß, Bruno Märkl, Stefan Dirnhofer, Alexandar Tzankov, Mascha Binder, Maria Kalweit:
Detection of disease-specific signatures in B cell repertoires of lymphomas using machine learning. 1011570 - Florian Borse, Dovydas Kiciatovas, Teemu Kuosmanen, Mabel Vidal, Guillermo Cabrera-Vives, Johannes Cairns, Jonas Warringer, Ville Mustonen:
Quantifying massively parallel microbial growth with spatially mediated interactions. 1011585 - Gustavo Magaña López, Laurence Calzone, Andrei Yu. Zinovyev, Loïc Paulevé:
scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics. 1011620 - David R. Penas, Meysam Hashemi, Viktor K. Jirsa, Julio R. Banga:
Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers. 1011642 - Ghazaleh Ostovar, James Q. Boedicker:
Phenotypic memory in quorum sensing. 1011696 - Jonas Verhellen, Kosio Beshkov, Sebastian Amundsen, Torbjørn V. Ness, Gaute T. Einevoll:
Multitask learning of a biophysically-detailed neuron model. 1011728 - Haocheng Zhu, Ulrik R. Beierholm, Ladan Shams:
BCI Toolbox: An open-source python package for the Bayesian causal inference model. 1011791 - Wilfredo Blanco, Joël Tabak, Richard Bertram:
Population bursts in a modular neural network as a mechanism for synchronized activity in KNDy neurons. 1011820 - Thomas Couppey, Louis Regnacq, Roland Giraud, Olivier Romain, Yannick Bornat, Florian Kölbl:
NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies. 1011826 - Matthieu Bouguéon, Vincent Legagneux, Octave Hazard, Jérémy Bomo, Anne Siegel, Jérôme Feret, Nathalie Théret:
A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression. 1011858 - Vivienne Leech, Fiona N. Kenny, Stefania Marcotti, Tanya J. Shaw, Brian Stramer, Angelika Manhart:
Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment. 1011879 - Harry Saxton, Xu Xu, Torsten Schenkel, Richard H. Clayton, Ian Halliday:
Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis. 1011946 - Lu Hong, Tanja Kortemme:
An integrative approach to protein sequence design through multiobjective optimization. 1011953 - Nathan J. Doyle, Fergus Cumming, Robin N. Thompson, Michael J. Tildesley:
When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty. 1012010 - Wentao Li, Han Chen, Xiaoqian Jiang, Arif Ozgun Harmanci:
FedGMMAT: Federated generalized linear mixed model association tests. 1012142 - Samuel E. Hoff, F. Emil Thomasen, Kresten Lindorff-Larsen, Massimiliano Bonomi:
Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference. 1012180 - Robyn M. Stuart, Jamie A. Cohen, Cliff C. Kerr, Prashant Mathur, Romesh G. Abeysuriya, Marita Zimmermann, Darcy W. Rao, Mariah C. Boudreau, Serin Lee, Luojun Yang, Daniel J. Klein:
HPVsim: An agent-based model of HPV transmission and cervical disease. 1012181 - Xiaoyu Yang, Giancarlo La Camera:
Co-existence of synaptic plasticity and metastable dynamics in a spiking model of cortical circuits. 1012220 - Luka Maisuradze, Megan C. King, Ivan V. Surovtsev, Simon G. J. Mochrie, Mark D. Shattuck, Corey S. O'Hern:
Identifying topologically associating domains using differential kernels. 1012221 - Pascal Grobecker, Thomas Sakoparnig, Erik van Nimwegen:
Identifying cell states in single-cell RNA-seq data at statistically maximal resolution. 1012224 - Sarah Schwöbel, Dimitrije Markovic, Michael N. Smolka, Stefan J. Kiebel:
Joint modeling of choices and reaction times based on Bayesian contextual behavioral control. 1012228 - Sara Stoudt, Yacine Jernite, Brandeis Marshall, Ben Marwick, Malvika Sharan, Kirstie Whitaker, Valentin Danchev:
Ten simple rules for building and maintaining a responsible data science workflow. 1012232 - Vinoth Manivannan, Mandar M. Inamdar, Ranjith Padinhateeri:
Role of diffusion and reaction of the constituents in spreading of histone modification marks. 1012235 - Mahshid Fardadi, James Leiter, Daniel C. Lu, Tetsuya Iwasaki:
Model-based analysis of the acute effects of transcutaneous magnetic spinal cord stimulation on micturition after spinal cord injury in humans. 1012237 - Chrysovalantou Kalaitzidou, Georgios Grekas, Andreas Zilian, Charalambos G. Makridakis, Phoebus Rosakis:
Compressive instabilities enable cell-induced extreme densification patterns in the fibrous extracellular matrix: Discrete model predictions. 1012238 - Simone Blanco Malerba, Aurora Micheli, Michael Woodford, Rava Azeredo da Silveira:
Jointly efficient encoding and decoding in neural populations. 1012240 - Andrew A. Chen, Kelly Clark, Blake E. Dewey, Anna Duval, Nicole Pellegrini, Govind Nair, Youmna Jalkh, Samar Khalil, Jon Zurawski, Peter A. Calabresi, Daniel S. Reich, Rohit Bakshi, Haochang Shou, Russell T. Shinohara:
PARE: A framework for removal of confounding effects from any distance-based dimension reduction method. 1012241 - Ulrik Hvid, Namiko Mitarai:
Competitive advantages of T-even phage lysis inhibition in response to secondary infection. 1012242 - Xun Fu, Jack Withers, Juri A. Miyamae, Talia Y. Moore:
ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture. 1012243 - Brianna Marsh, M. Gabriela Navas-Zuloaga, Burke Q. Rosen, Yury Sokolov, Jean Erik Delanois, Oscar C. Gonzalez, Giri P. Krishnan, Eric Halgren, Maxim Bazhenov:
Emergent effects of synaptic connectivity on the dynamics of global and local slow waves in a large-scale thalamocortical network model of the human brain. 1012245 - Marcus Ghosh, Gabriel Béna, Volker Bormuth, Dan F. M. Goodman:
Nonlinear fusion is optimal for a wide class of multisensory tasks. 1012246 - Simon K. S. Chu, Kush Narang, Justin B. Siegel:
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset. 1012248 - David Moreau, Kristina Wiebels:
Nine quick tips for open meta-analyses. 1012252 - Patrick Bryant, Frank Noé:
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile. 1012253 - Shihan Ma, Irene Mendez Guerra, Arnault H. Caillet, Jiamin Zhao, Alexander Kenneth Clarke, Kostiantyn Maksymenko, Samuel Deslauriers-Gauthier, Xinjun Sheng, Xiangyang Zhu, Dario Farina:
NeuroMotion: Open-source platform with neuromechanical and deep network modules to generate surface EMG signals during voluntary movement. 1012257 - Matthew Beauregard Smith, Kent Vandervelden, Thomas Blom, Heather D. Stout, James H. Mapes, Tucker M. Folsom, Christopher Martin, Angela M. Bardo, Edward M. Marcotte:
Estimating error rates for single molecule protein sequencing experiments. 1012258 - Pau Clusella, Linus Manubens-Gil, Jordi García-Ojalvo, Mara Dierssen:
Modeling the impact of neuromorphological alterations in Down syndrome on fast neural oscillations. 1012259 - Kanishk Chauhan, Alexander B. Neiman, Peter A. Tass:
Synaptic reorganization of synchronized neuronal networks with synaptic weight and structural plasticity. 1012261 - Elias Rosenblatt, Jonathan D. Cook, Graziella V. Direnzo, Evan H. Campbell Grant, Fernando Arce, Kim M. Pepin, F. Javiera Rudolph, Michael C. Runge, Susan Shriner, Daniel P. Walsh, Brittany A. Mosher:
Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission. 1012263 - Thomas Williams, James M. McCaw, James M. Osborne:
Spatial information allows inference of the prevalence of direct cell-to-cell viral infection. 1012264 - Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole G. Jensen, David Ladd, Mark Polster, Friederike Hanssen, Simon Heumos, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein:
nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. 1012265 - Alexa Petrucciani, Alexis Hoerter, Leigh Kotze, Nelita Du Plessis, Elsje Pienaar:
Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma. 1012266 - Andres J. Nevarez, Anusorn Mudla, Sabrina A. Diaz, Nan Hao:
Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome. 1012271 - Pierre Le Denmat, Tom Verguts, Kobe Desender:
A low-dimensional approximation of optimal confidence. 1012273 - Ziyan Guo, Jialu Yu, Wenxin Wang, Patricia Lockwood, Zhen Wu:
Reinforcement learning of altruistic punishment differs between cultures and across the lifespan. 1012274 - Virgile Andréani, Eric J. South, Mary J. Dunlop:
Generating information-dense promoter sequences with optimal string packing. 1012276 - Hsun Chiang, Chih-Ang Chung:
Simulation of Soluble and Bound VEGF-stimulated in vitro Capillary-like Network Formation on Deformed Substrate. 1012281 - Botond B. Antal, Anthony G. Chesebro, Helmut H. Strey, Lilianne R. Mujica-Parodi, Corey Weistuch:
Achieving Occam's razor: Deep learning for optimal model reduction. 1012283 - Yingjun Ma, Yuanyuan Ma:
Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations. 1012287 - David A. Brewster, Martin A. Nowak, Josef Tkadlec:
Fixation times on directed graphs. 1012299 - Diogo Melo, Luisa F. Pallares, Julien F. Ayroles:
Reassessing the modularity of gene co-expression networks using the Stochastic Block Model. 1012300 - Noah B. Herrington, Yan Chak Li, David Stein, Gaurav Pandey, Avner Schlessinger:
A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures. 1012302 - Eric Tatara, Qinyun Lin, Jonathan Ozik, Marynia Kolak, Nicholson T. Collier, Dylan Halpern, Luc Anselin, Harel Dahari, Basmattee Boodram, John A. Schneider:
Spatial inequities in access to medications for treatment of opioid use disorder highlight scarcity of methadone providers under counterfactual scenarios. 1012307 - Beth M. Tuschhoff, David A. Kennedy:
Detecting and quantifying heterogeneity in susceptibility using contact tracing data. 1012310 - Yiu Chung Lau, Songwei Shan, Dong Wang, Dongxuan Chen, Zhanwei Du, Eric H. Y. Lau, Daihai He, Linwei Tian, Peng Wu, Benjamin J. Cowling, Sheikh Taslim Ali:
Forecasting of influenza activity and associated hospital admission burden and estimating the impact of COVID-19 pandemic on 2019/20 winter season in Hong Kong. 1012311 - Nan Wu, Isabel Valera, Fabian H. Sinz, Alexander S. Ecker, Thomas Euler, Yongrong Qiu:
Probabilistic neural transfer function estimation with Bayesian system identification. 1012354
Volume 20, Number 8, 2024
- Priscilla E. Greenwood, Lawrence M. Ward:
Attentional selection and communication through coherence: Scope and limitations. 1011431 - Ayooluwa J. Bolaji, Ana T. Duggan:
In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences. 1011539 - William F. Dean, Tomasz J. Nawara, Rose M. Albert, Alexa L. Mattheyses:
OOPS: Object-Oriented Polarization Software for analysis of fluorescence polarization microscopy images. 1011723 - Mahraz Behbood, Louisiane Lemaire, Jan-Hendrik Schleimer, Susanne Schreiber:
The Na+/K+-ATPase generically enables deterministic bursting in class I neurons by shearing the spike-onset bifurcation structure. 1011751 - Robby Concha-Eloko, Michiel Stock, Bernard De Baets, Yves Briers, Rafael Sanjuán, Pilar Domingo-Calap, Dimitri Boeckaerts:
DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models. 1011831 - Fengdi Zhao, Xin Ma, Bing Yao, Qing Lu, Li Chen:
scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data. 1011854 - Rachael Stentiford, James C. Knight, Thomas Nowotny, Andrew Philippides, Paul Graham:
Estimating orientation in natural scenes: A spiking neural network model of the insect central complex. 1011913 - Daniel Seeler, Nastasja Grdseloff, Claudia Jasmin Rödel, Charlotte Kloft, Salim Abdelilah-Seyfried, Wilhelm Huisinga:
Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos. 1011924 - Catherine M. Byrne, Ana Citlali Márquez, Bing Cai, Daniel Coombs, Soren Gantt:
Spatial kinetics and immune control of murine cytomegalovirus infection in the salivary glands. 1011940 - Simon Syga, Harish P. Jain, Marcus Krellner, Haralampos Hatzikirou, Andreas Deutsch:
Evolution of phenotypic plasticity leads to tumor heterogeneity with implications for therapy. 1012003 - Janani Ravi, Kewalin Samart, Jason Zwolak:
Modeling the START transition in the budding yeast cell cycle. 1012048 - Alex T. Keeley, Jeffrey M. Lotthammer, Jacqueline F. Pelham:
Rhythmidia: A modern tool for circadian period analysis of filamentous fungi. 1012167 - Chadi M. Saad-Roy, Sinead E. Morris, Mike Boots, Rachel E. Baker, Bryan L. Lewis, Jeremy Farrar, Madhav V. Marathe, Andrea L. Graham, Simon A. Levin, Caroline E. Wagner, C. Jessica E. Metcalf, Bryan T. Grenfell:
Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy. 1012211 - Einar Bjarki Gunnarsson, Seungil Kim, Brandon Choi, J. Karl Schmid, Karn Kaura, Heinz-Josef Lenz, Shannon M. Mumenthaler, Jasmine Foo:
Understanding patient-derived tumor organoid growth through an integrated imaging and mathematical modeling framework. 1012256 - Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning. 1012260
- Teemu J. Rintala, Vittorio Fortino:
COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms. 1012275 - Rune Höper, Daria Komkova, Tomás Zavrel, Ralf Steuer:
A quantitative description of light-limited cyanobacterial growth using flux balance analysis. 1012280 - Hiroto Murata, Kazuma Toko, George Chikenji:
Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel β-sheet topologies. 1012282 - Ulysse Rançon, Timothée Masquelier, Benoit R. Cottereau:
A general model unifying the adaptive, transient and sustained properties of ON and OFF auditory neural responses. 1012288 - Pras Pathmanathan, Kenneth I. Aycock, Andreu Badal, Ramin Bighamian, Jeff Bodner, Brent A. Craven, Steven A. Niederer:
Credibility assessment of in silico clinical trials for medical devices. 1012289 - Iratxe Puebla, Giorgio A. Ascoli, Jeffrey Blume, John Chodacki, Joshua Finnell, David N. Kennedy, Bernard Mair, Maryann E. Martone, Jamie Wittenberg, Jean-Baptiste Poline:
Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure. 1012296 - Ye Chen, Peter Beech, Ziwei Yin, Shanshan Jia, Jiayi Zhang, Zhaofei Yu, Jian K. Liu:
Decoding dynamic visual scenes across the brain hierarchy. 1012297 - Jiayi Lin, Hrayer Aprahamian, George Golovko:
A proactive/reactive mass screening approach with uncertain symptomatic cases. 1012308 - Ioana Bouros, Edward M. Hill, Matt J. Keeling, Sam Moore, Robin N. Thompson:
Prioritising older individuals for COVID-19 booster vaccination leads to optimal public health outcomes in a range of socio-economic settings. 1012309 - Honghan Li, Shiyou Liu, Shinji Deguchi, Daiki Matsunaga:
Diffusion model predicts the geometry of actin cytoskeleton from cell morphology. 1012312 - Jose L. Alejo, Dylan Girodat, Michael J. Hammerling, Jessica A. Willi, Michael C. Jewett, Aaron E. Engelhart, Katarzyna P. Adamala:
Alternate conformational trajectories in ribosome translocation. 1012319 - Ksenia Guseva, Moritz Mohrlok, Lauren Alteio, Hannes Schmidt, Shaul Pollak, Christina Kaiser:
Bacteria face trade-offs in the decomposition of complex biopolymers. 1012320 - Andrew A. Schmidt, Alexander Y. Grosberg, Anna Grosberg:
A novel kinetic model to demonstrate the independent effects of ATP and ADP/Pi concentrations on sarcomere function. 1012321 - Alireza Zaeemzadeh, Giulio Tononi:
Upper bounds for integrated information. 1012323 - Jiaping Liu, Zhenglun Cai, Paul Gustafson, Daniel J. McDonald:
rtestim: Time-varying reproduction number estimation with trend filtering. 1012324 - Jonathan S. Ramos, Ivo Henrique Provensi Vieira, Wan Song Rocha, Rosimar Pires Esquerdo, Carolina Yukari Veludo Watanabe, Fernando Berton Zanchi:
A transfer learning approach to identify Plasmodium in microscopic images. 1012327 - Lies Zandberg, Veronica Morfi, Julia M. George, David Clayton, Dan Stowell, Robert F. Lachlan:
Bird song comparison using deep learning trained from avian perceptual judgments. 1012329 - Christoph Koch, Ondrej Zika, Rasmus Bruckner, Nicolas W. Schuck:
Influence of surprise on reinforcement learning in younger and older adults. 1012331 - David G. Pina:
Ten simple rules for successfully managing EU research grants. 1012335 - Anubha Dey, Suresh Mudunuri, Manjari Kiran:
MAGICAL: A multi-class classifier to predict synthetic lethal and viable interactions using protein-protein interaction network. 1012336 - Anton Suvorov, Daniel R. Schrider:
Reliable estimation of tree branch lengths using deep neural networks. 1012337 - Michael B. Sohn, Cynthia Monaco, Steven R. Gill:
An optimal normalization method for high sparse compositional microbiome data. 1012338 - Yuqing Qian, Quan Zou, Mengyuan Zhao, Yi Liu, Fei Guo, Yijie Ding:
scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization. 1012339 - Vasyl V. Mykuliak, Rolle Rahikainen, Neil J. Ball, Giovanni Bussi, Benjamin T. Goult, Vesa P. Hytönen:
Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force. 1012341 - Ján Antolík, Rémy Cagnol, Tibor Rózsa, Cyril Monier, Yves Frégnac, Andrew P. Davison:
A comprehensive data-driven model of cat primary visual cortex. 1012342 - Seth Commichaux, Tu Luan, Harihara Subrahmaniam Muralidharan, Mihai Pop:
Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes. 1012343 - Yicheng Tao, Fan Feng, Xin Luo, Conrad V. Reihsmann, Alexander L. Hopkirk, Jean-Philippe Cartailler, Marcela Brissova, Stephen C. J. Parker, Diane C. Saunders, Jie Liu:
CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images. 1012344 - Yunfeng Xiong, Chuntian Wang, Yuan Zhang:
Interacting particle models on the impact of spatially heterogeneous human behavioral factors on dynamics of infectious diseases. 1012345 - Lucas Rudelt, Daniel González Marx, F. Paul Spitzner, Benjamin Cramer, Johannes Zierenberg, Viola Priesemann:
Signatures of hierarchical temporal processing in the mouse visual system. 1012355 - Easwaran Ramamurthy, Snigdha Agarwal, Noelle Toong, Heather Sestili, Irene M. Kaplow, Ziheng Chen, BaDoi N. Phan, Andreas R. Pfenning:
Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease. 1012356 - Gerardo J. Félix-Martínez, Diana Osorio-Londoño, J. Rafael Godínez-Fernández:
Impact of oxygen and glucose availability on the viability and connectivity of islet cells: A computational study of reconstructed avascular human islets. 1012357 - Scott L. Nuismer, Andrew J. Basinski, Courtney L. Schreiner, Evan A. Eskew, Elisabeth Fichet-Calvet, Christopher H. Remien:
Quantifying the risk of spillover reduction programs for human health. 1012358 - Daniel Schirmacher, Ümmünur Armagan, Yang Zhang, Tobias Kull, Markus Auler, Timm Schroeder:
aiSEGcell: User-friendly deep learning-based segmentation of nuclei in transmitted light images. 1012361 - Keyvan Mahjoory, Andreas Bahmer, Molly J. Henry:
Convolutional neural networks can identify brain interactions involved in decoding spatial auditory attention. 1012376 - Efrat Cohen-Davidi, Isana Veksler-Lublinsky:
Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions. 1012385 - Diogo L. Pires, Mark Broom:
The rules of multiplayer cooperation in networks of communities. 1012388 - Peiting Shi, Junmin Han, Yinghao Zhang, Guanpu Li, Xionghui Zhou:
IMI-driver: Integrating multi-level gene networks and multi-omics for cancer driver gene identification. 1012389 - Lin Yuan, Ling Zhao, Jinling Lai, Yufeng Jiang, Qinhu Zhang, Zhen Shen, Chun-Hou Zheng, De-Shuang Huang:
iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites. 1012399 - Tao Wang, Linlin Zhuo, Yifan Chen, Xiangzheng Fu, Xiangxiang Zeng, Quan Zou:
ECD-CDGI: An efficient energy-constrained diffusion model for cancer driver gene identification. 1012400 - Alexander Ney, Nuno R. Nené, Eva Sedlak, Pilar Acedo, Oleg Blyuss, Harry J. Whitwell, Eithne Costello, Aleksandra Gentry-Maharaj, Norman R. Williams, Usha Menon, Giuseppe K. Fusai, Alexey Zaikin, Stephen P. Pereira:
Identification of a serum proteomic biomarker panel using diagnosis specific ensemble learning and symptoms for early pancreatic cancer detection. 1012408
Volume 20, Number 9, 2024
- Joseph Shingleton, David Mustard, Steven Dyke, Hannah Williams, Emma Bennett, Thomas Finnie:
Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases. 1010817 - Annika Schmidt, Marion Forano, Arne Sachtler, Davide Calzolari, Bernhard M. Weber, David W. Franklin, Alin Albu-Schäffer:
Finding the rhythm: Humans exploit nonlinear intrinsic dynamics of compliant systems in periodic interaction tasks. 1011478 - Carlos Albors, Jordi Mill, Andy L. Olivares, Xavier Iriart, Hubert Cochet, Oscar Camara:
Impact of occluder device configurations in in-silico left atrial hemodynamics for the analysis of device-related thrombus. 1011546 - Monica Golumbeanu, Olivier Briët, Clara Champagne, Jeanne Lemant, Munir Winkel, Barnabas Zogo, Maximilian Gerhards, Marianne Sinka, Nakul Chitnis, Melissa Penny, Emilie Pothin, Thomas A. Smith:
AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact. 1011609 - Cécile Le Sueur, Magnus Rattray, Mikhail Savitski:
GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments. 1011632 - G. Eric Bastien, Rachel N. Cable, Cecelia Batterbee, A. J. Wing, Luis Zaman, Melissa Beth Duhaime:
Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks. 1011649 - Silja Tammi, Satu Koskela, Kati Hyvärinen, Jukka Partanen, Jarmo Ritari:
Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data. 1011718 - Janice Yang, Neil J. Daily, Taylor K. Pullinger, Tetsuro Wakatsuki, Eric A. Sobie:
Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. 1011806 - Israel Luis, Maarten Afschrift, Elena M. Gutierrez-Farewik:
Springs vs. motors: Ideal assistance in the lower limbs during walking at different speeds. 1011837 - Anis Ur Rahman, Gleb Tikhonov, Jari Oksanen, Tuomas Rossi, Otso Ovaskainen:
Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting. 1011914 - Ilaria Granata, Lucia Maddalena, Mario Manzo, Mario Rosario Guarracino, Maurizio Giordano:
HELP: A computational framework for labelling and predicting human common and context-specific essential genes. 1012076 - Nicola Dietler, Alia Abbara, Subham Choudhury, Anne-Florence Bitbol:
Impact of phylogeny on the inference of functional sectors from protein sequence data. 1012091 - Adrielli Tina Lopes Rego, Joshua Snell, Martijn Meeter:
Language models outperform cloze predictability in a cognitive model of reading. 1012117 - Kath Nicholls, Paul D. W. Kirk, Chris Wallace:
Bayesian clustering with uncertain data. 1012301 - Yann Le Cunff, Laurent Chesneau, Sylvain Pastezeur, Xavier Pinson, Nina Soler, Danielle Fairbrass, Benjamin Mercat, Ruddi Rodriguez-Garcia, Zahraa Alayan, Ahmed Abdouni, Gary de Neidhardt, Valentin Costes, Mélodie Anjubault, Hélène Bouvrais, Christophe Héligon, Jacques Pécréaux:
Unveiling inter-embryo variability in spindle length over time: Towards quantitative phenotype analysis. 1012330 - Yanpeng Yang, Yanyi Zheng, Quan Zou, Jian Li, Hailin Feng:
Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model. 1012340 - Artemy Bakulin, Noam B. Teyssier, Martin Kampmann, Matvei Khoroshkin, Hani Goodarzi:
pyPAGE: A framework for Addressing biases in gene-set enrichment analysis - A case study on Alzheimer's disease. 1012346 - Hannah Zoller, Carlos Garcia Perez, Javier Betel Geijo Fernández, Wolfgang zu Castell:
Measuring and understanding information storage and transfer in a simulated human gut microbiome. 1012359 - Gustavo Menesse, Joaquín J. Torres:
Information dynamics of in silico EEG Brain Waves: Insights into oscillations and functions. 1012369 - Steffen Krüppel, Mohammad H. Khani, Helene M. Schreyer, Shashwat Sridhar, Varsha Ramakrishna, Sören J. Zapp, Matthias Mietsch, Dimokratis Karamanlis, Tim Gollisch:
Applying Super-Resolution and Tomography Concepts to Identify Receptive Field Subunits in the Retina. 1012370 - Ariel Rokem:
Ten simple rules for scientific code review. 1012375 - Yujin Goto, Keiichi Kitajo:
Selective consistency of recurrent neural networks induced by plasticity as a mechanism of unsupervised perceptual learning. 1012378 - Hamza Giaffar, Sergey Shuvaev, Dmitry Rinberg, Alexei A. Koulakov:
The primacy model and the structure of olfactory space. 1012379 - Laura Collesano, Marta Luksza, Michael Lässig:
Energy landscapes of peptide-MHC binding. 1012380 - Seema B. Plaisier, Danielle O. Alarid, Joelle A. Denning, Sara E. Brownell, Kenneth H. Buetow, Katelyn M. Cooper, Melissa A. Wilson:
Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics. 1012384 - Breanne Sparta, Timothy Hamilton, Gunalan Natesan, Samuel D. Aragones, Eric J. Deeds:
Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing. 1012386 - Caterina Millevoi, Damiano Pasetto, Massimiliano Ferronato:
A Physics-Informed Neural Network approach for compartmental epidemiological models. 1012387 - Olav N. L. Aga, Morten Brun, Kazeem Adesina Dauda, Ramón Díaz-Uriarte, Konstantinos Giannakis, Iain G. Johnston:
HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures. 1012393 - Zhichao Zhu, Yang Qi, Wenlian Lu, Jianfeng Feng:
Learning to integrate parts for whole through correlated neural variability. 1012401 - Wilson Wen Bin Goh, Mohammad Neamul Kabir, Sehwan Yoo, Limsoon Wong:
Ten quick tips for ensuring machine learning model validity. 1012402 - Clémence Bergerot, Wolfram Barfuss, Pawel Romanczuk:
Moderate confirmation bias enhances decision-making in groups of reinforcement-learning agents. 1012404 - Hao Duan, Qingchen Zhang, Feifei Cui, Quan Zou, Zilong Zhang:
MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks. 1012409 - Kit Gallagher, Richard Creswell, Ben Lambert, Martin Robinson, Chon Lok Lei, Gary R. Mirams, David J. Gavaghan:
Ten simple rules for training scientists to make better software. 1012410 - Israel Luis, Maarten Afschrift, Friedl De Groote, Elena M. Gutierrez-Farewik:
Insights into muscle metabolic energetics: Modelling muscle-tendon mechanics and metabolic rates during walking across speeds. 1012411 - Jiaxin Jiang, Xiaona Meng, Yibo Wang, Ziqian Zhuang, Ting Du, Jing Yan:
Effect of aberrant fructose metabolism following SARS-CoV-2 infection on colorectal cancer patients' poor prognosis. 1012412 - Dong Yu, Tianyu Li, Qianming Ding, Yong Wu, Ziying Fu, Xuan Zhan, Lijian Yang, Ya Jia:
Maintenance of delay-period activity in working memory task is modulated by local network structure. 1012415 - Kirstin I. Oliveira Roster, Stephen M. Kissler, Enoma Omoregie, Jade C. Wang, Helly Amin, Steve Di Lonardo, Scott Hughes, Yonatan H. Grad:
Surveillance strategies for the detection of new pathogen variants across epidemiological contexts. 1012416 - Daniel Steiert, Corey Wittig, Priyanka Banerjee, Robert Preissner, Robert Szulcek:
An exploration into CTEPH medications: Combining natural language processing, embedding learning, in vitro models, and real-world evidence for drug repurposing. 1012417 - Travis M. Blimkie, Andy An, Robert E. W. Hancock:
Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR. 1012422 - Adrian J. Green, Lisa Truong, Preethi Thunga, Connor Leong, Melody Hancock, Robyn L. Tanguay, David M. Reif:
Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies. 1012423 - Alia Abbara, Lisa Pagani, Celia García-Pareja, Anne-Florence Bitbol:
Mutant fate in spatially structured populations on graphs: Connecting models to experiments. 1012424 - Michiel Stock, Wim Van Criekinge, Dimitri Boeckaerts, Steff Taelman, Maxime Van Haeverbeke, Pieter Dewulf, Bernard De Baets:
Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data. 1012426 - Justin Lin, Julia Fukuyama:
Calibrating dimension reduction hyperparameters in the presence of noise. 1012427 - Nafiseh Atapour, Marcello G. P. Rosa, Shi Bai, Sylwia Bednarek, Agata Kulesza, Gabriela Saworska, Sadaf Teymornejad, Katrina H. Worthy, Piotr Majka:
Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex. 1012428 - Katharina Duecker, Marco Idiart, Marcel van Gerven, Ole Jensen:
Oscillations in an artificial neural network convert competing inputs into a temporal code. 1012429 - Aakash Agrawal, Stanislas Dehaene:
Cracking the neural code for word recognition in convolutional neural networks. 1012430 - Diego A. Forero, Walter H. Curioso, Wei Wang:
Ten simple rules for successfully carrying out funded research projects. 1012431 - Maansi Desai, Alyssa M. Field, Liberty S. Hamilton:
A comparison of EEG encoding models using audiovisual stimuli and their unimodal counterparts. 1012433 - Bharadwaj Vemparala, Vincent Madelain, Caroline Passaes, Antoine Millet, Véronique Avettand-Fenoel, Ramsès Djidjou-Demasse, Nathalie Dereuddre-Bosquet, Roger Le Grand, Christine Rouzioux, Bruno Vaslin, Asier Sáez-Cirión, Jérémie Guedj, Narendra M. Dixit:
Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection: Learning in vivo dynamics using ex vivo data. 1012434 - Ahmadou Sylla, Christine Chevillon, Ramsès Djidjiou-Demasse, Ousmane Seydi, Carlos A. Vargas Campos, Magdalene Dogbe, Kayla M. Fast, Jennifer L. Pechal, Alex Rakestraw, Matthew E. Scott, Michael W. Sandel, Heather Jordan, Mark Eric Benbow, Jean-François Guégan:
Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model. 1012435 - Elena Miu, Luke Rendell, Sam Bowles, Rob Boyd, Daniel Cownden, Magnus Enquist, Kimmo Eriksson, Marcus W. Feldman, Timothy P. Lillicrap, Richard McElreath, Stuart Murray, James Ounsley, Kevin N. Lala:
The refinement paradox and cumulative cultural evolution: Complex products of collective improvement favor conformist outcomes, blind copying, and hyper-credulity. 1012436 - Jason A. Papin, Feilim Mac Gabhann, Virginia E. Pitzer:
Celebrating a body of work. 1012441 - Eslam Abousamra, Marlin Figgins, Trevor Bedford:
Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency. 1012443 - Shuo Wang, Shanjin Wang, Wei Pan, Yuyang Yi, Junyan Lu:
Construct prognostic models of multiple myeloma with pathway information incorporated. 1012444 - Tobias Pfennig, Elena Kullmann, Tomás Zavrel, Andreas Nakielski, Oliver Ebenhöh, Jan Cervený, Gábor Bernát, Anna Matuszynska:
Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803. 1012445 - Constance Creux, Farida Zehraoui, François Radvanyi, Fariza Tahi:
Comparison and benchmark of deep learning methods for non-coding RNA classification. 1012446 - Juan Pablo Franco, Peter Bossaerts, Carsten Murawski:
The neural dynamics associated with computational complexity. 1012447 - Mario Grassi, Barbara Tarantino:
SEMbap: Bow-free covariance search and data de-correlation. 1012448 - Matt J. Keeling, Louise Dyson:
A retrospective assessment of forecasting the peak of the SARS-CoV-2 Omicron BA.1 wave in England. 1012452 - Kiesha Prem, Kevin van Zandvoort, Petra Klepac, Rosalind M. Eggo, Nicholas G. Davies:
Correction: Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era. 1012454 - Jolanda Malamud, Sinan Guloksuz, Ruud van Winkel, Philippe Delespaul, Marc A. F. De Hert, Catherine Derom, Evert Thiery, Nele Jacobs, Bart P. F. Rutten, Quentin J. M. Huys:
Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter. 1012457 - Brian C. O'Meara, Jeremy M. Beaulieu:
Noise leads to the perceived increase in evolutionary rates over short time scales. 1012458 - Anibal S. Amaral, Damien P. Devos:
The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes. 1012459 - Margherita Molaro, Sakshi Mohan, Bingling She, Martin Chalkley, Tim Colbourn, Joseph H. Collins, Emilia Connolly, Matthew M. Graham, Eva Janousková, Ines Li Lin, Gerald Manthalu, Emmanuel Mnjowe, Dominic Nkhoma, Pakwanja D. Twea, Andrew N. Phillips, Paul Revill, Asif U. Tamuri, Joseph Mfutso-Bengo, Tara D. Mangal, Timothy B. Hallett:
A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi. 1012462 - Ke Li, Chrispin Chaguza, Julian Stamp, Yi Ting Chew, Nicholas F. G. Chen, David Ferguson, Sameer Pandya, Nick Kerantzas, Wade Schulz, Anne M. Hahn, C. Brandon Ogbunugafor, Virginia E. Pitzer, Lorin Crawford, Daniel M. Weinberger, Nathan D. Grubaugh:
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. 1012469 - Carlos A. Velazquez-Vargas, Nathaniel D. Daw, Jordan A. Taylor:
The role of training variability for model-based and model-free learning of an arbitrary visuomotor mapping. 1012471 - Ylva Katarina Wedmark, Jon Olav Vik, Ove Øyås:
A hierarchy of metabolite exchanges in metabolic models of microbial species and communities. 1012472 - Yutaro Kumagai:
BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks. 1012480 - Jacopo Pasqualini, Sonia Facchin, Andrea Rinaldo, Amos Maritan, Edoardo Savarino, Samir Suweis:
Emergent ecological patterns and modelling of gut microbiomes in health and in disease. 1012482 - Julien Roche, Mathieu Besson, François Allal, Pierrick Haffray, Pierre Patrice, Marc Vandeputte, Florence Phocas:
GenoTriplo: A SNP genotype calling method for triploids. 1012483 - Helder Veras Ribeiro filho, Gabriel Ernesto Jara, João Victor da Silva Guerra, Melyssa Cheung, Nathaniel R. Felbinger, José Geraldo de Carvalho Pereira, Brian G. Pierce, Paulo Sérgio Lopes-de-Oliveira:
Exploring the potential of structure-based deep learning approaches for T cell receptor design. 1012489 - Kevin Tsai, Zhen Zhou, Jiadong Yang, Zhiliang Xu, Shixin Xu, Roya Zandi, Nan Hao, Weitao Chen, Mark S. Alber:
Study of impacts of two types of cellular aging on the yeast bud morphogenesis. 1012491 - Biao Tang, Kexin Ma, Yan Liu, Xia Wang, Sanyi Tang, Yanni Xiao, Robert A. Cheke:
Managing spatio-temporal heterogeneity of susceptibles by embedding it into an homogeneous model: A mechanistic and deep learning study. 1012497 - Mengze Zhang, Xia Wang, Sanyi Tang:
Integrating dynamic models and neural networks to discover the mechanism of meteorological factors on Aedes population. 1012499 - Ron Zeira, Leon Anavy, Zohar Yakhini, Ehud Rivlin, Daniel Freedman:
HIPI: Spatially resolved multiplexed protein expression inferred from H&E WSIs. 1012501
Volume 20, Number 10, 2024
- Michele Gentili, Kimberly Glass, Enrico Maiorino, Brian D. Hobbs, Zhonghui Xu, Peter J. Castaldi, Michael H. Cho, Craig P. Hersh, Dandi Qiao, Jarrett D. Morrow, Vincent J. Carey, John Platig, Edwin K. Silverman:
Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals. 1011079 - Abhishek Ranjan, Jaya Kumari Swain, Balpreet Singh Ahluwalia, Frank Melandsø:
3-D Visualization of Atlantic salmon skin through Ultrasound and Photoacoustic Microscopy. 1011709 - Cecilia de Vicariis, Vinil T. Chackochan, Laura Bandini, Eleonora Ravaschio, Vittorio Sanguineti:
Computational joint action: Dynamical models to understand the development of joint coordination. 1011948 - Felix Ezequiel Gerbaldo, Emanuel Sonder, Vincent Fischer, Selina Frei, Jiayi Wang, Katharina Gapp, Mark D. Robinson, Pierre-Luc Germain:
On the identification of differentially-active transcription factors from ATAC-seq data. 1011971 - Marie-Cécile Dupas, Francesco Pinotti, Chaitanya Joshi, Madhvi Joshi, Weerapong Thanapongtharm, Madhur S. Dhingra, Damer Blake, Fiona Tomley, Marius Gilbert, Guillaume Fournié:
Spatial distribution of poultry farms using point pattern modelling: A method to address livestock environmental impacts and disease transmission risks. 1011980 - Jessica L. Gaines, Kwang S. Kim, Benjamin Parrell, Vikram Ramanarayanan, Alvincé L. Pongos, Srikantan S. Nagarajan, John F. Houde:
Bayesian inference of state feedback control parameters for fo perturbation responses in cerebellar ataxia. 1011986 - Yushi Yang, Abdelwahab Kawafi, Qiao Tong, Erika Kague, Chrissy L. Hammond, C. Patrick Royall:
Tuning collective behaviour in zebrafish with genetic modification. 1012034 - Xubin Zheng, Dian Meng, Duo Chen, Wan-Ki Wong, Ka-Ho To, Lei Zhu, Jiafei Wu, Yining Liang, Kwong-Sak Leung, Man Hon Wong, Lixin Cheng:
scCaT: An explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing. 1012083 - Malin Ramne, Jon W. Sensinger:
A Computational Framework for Understanding the Impact of Prior Experiences on Pain Perception and Neuropathic Pain. 1012097 - Amanda Craine, Adarsh Krishnamurthy, Christopher T. Villongco, Kevin Vincent, David E. Krummen, Sanjiv M. Narayan, Roy C. P. Kerckhoffs, Jeffrey H. Omens, Francisco Contijoch, Andrew D. McCulloch:
Successful cardiac resynchronization therapy reduces negative septal work in patient-specific models of dyssynchronous heart failure. 1012150 - Haolin Jiang, Yulian Xu, Yunguang Tong, Dong Zhang, Ruhong Zhou:
IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation. 1012293 - Raúl A. Reyes Hueros, Rodrigo A. Gier, Sydney M. Shaffer:
Non-genetic differences underlie variability in proliferation among esophageal epithelial clones. 1012360 - Ted Moskovitz, Kevin J. Miller, Maneesh Sahani, Matthew M. Botvinick:
Understanding dual process cognition via the minimum description length principle. 1012383 - Jan Lause, Philipp Berens, Dmitry Kobak:
The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense. 1012403 - Colby Fronk, Jaewoong Yun, Prashant Singh, Linda R. Petzold:
Bayesian polynomial neural networks and polynomial neural ordinary differential equations. 1012414 - Nicolai Kraus, Michael Aichem, Karsten Klein, Etienne Lein, Alex Jordan, Falk Schreiber:
TIBA: A web application for the visual analysis of temporal occurrences, interactions, and transitions of animal behavior. 1012425 - Ruipeng Wei, Masahiro Hitomi, Tammy Sadler, Lamis Yehia, Daniela Calvetti, Jacob G. Scott, Charis Eng:
Quantitative evaluation of DNA damage repair dynamics to elucidate predictors of autism vs. cancer in individuals with germline PTEN variants. 1012449 - Francesco Poli, Maran Koolen, Carlos A. Velázquez-Vargas, Jessica Ramos-Sanchez, Marlene Meyer, Rogier B. Mars, Nanda Rommelse, Sabine Hunnius:
Autistic traits foster effective curiosity-driven exploration. 1012453 - Ankur Kamboj, Rajiv Ranganathan, Xiaobo Tan, Vaibhav Srivastava:
Human motor learning dynamics in high-dimensional tasks. 1012455 - Dephney Mathebula, Abigail Amankwah, Kossi Amouzouvi, Kétévi Adiklè Assamagan, Somiealo Azote, Jesutofunmi Ayo Fajemisin, Jean Baptiste Fankam Fankame, Aluwani Guga, Moses Kamwela, Mulape Mutule Kanduza, Toivo Samuel Mabote, Francisco Fenias Macucule, Azwinndini Muronga, Ann Njeri, Michael Olusegun Oluwole, Cláudio Moisés Paulo:
Modelling the impact of vaccination on COVID-19 in African countries. 1012456 - Alexis Bénichou, Jean-Baptiste Masson, Christian L. Vestergaard:
Compression-based inference of network motif sets. 1012460 - Safiye Celik, Jan-Christian Hütter, Sandra Melo Carlos, Nathan H. Lazar, Rahul Mohan, Conor Tillinghast, Tommaso Biancalani, Marta M. Fay, Berton Earnshaw, Imran S. Haque:
Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data. 1012463 - Lani Fox, William C. Miller, Dionne Gesink, Irene A. Doherty, Marc L. Serre:
Enhancing insights in sexually transmitted infection mapping: Syphilis in Forsyth County, North Carolina, a case study. 1012464 - Philip Greulich:
Emergent order in epithelial sheets by interplay of cell divisions and cell fate regulation. 1012465 - Diana C. de Oliveira, Hani Cheikh Sleiman, Kelly Payette, Jana Hutter, Lisa Story, Joseph V. Hajnal, Daniel C. Alexander, Rebecca J. Shipley, Paddy J. Slator:
A flexible generative algorithm for growing in silico placentas. 1012470 - Adam M. Roth, John H. Buggeln, Joanna E. Hoh, Jonathan M. Wood, Seth R. Sullivan, Truc T. Ngo, Jan A. Calalo, Rakshith Lokesh, Susanne M. Morton, Stephen Grill, John J. Jeka, Michael J. Carter, Joshua G. A. Cashaback:
Roles and interplay of reinforcement-based and error-based processes during reaching and gait in neurotypical adults and individuals with Parkinson's disease. 1012474 - Brandon J. Thio, Nathan D. Titus, Nicole A. Pelot, Warren M. Grill:
Reverse-engineered models reveal differential membrane properties of autonomic and cutaneous unmyelinated fibers. 1012475 - Dmitry R. Lyamzin, Andrea Alamia, Mohammad Abdolrahmani, Ryo Aoki, Andrea Benucci:
Regularizing hyperparameters of interacting neural signals in the mouse cortex reflect states of arousal. 1012478 - Elin K. Falla, Nik J. Cunniffe:
Why aphid virus retention needs more attention: Modelling aphid behaviour and virus manipulation in non-persistent plant virus transmission. 1012479 - Chenxi Liao, Masataka Sawayama, Bei Xiao:
Probing the link between vision and language in material perception using psychophysics and unsupervised learning. 1012481 - Nick Schafstall, Xavier Benito, Sandra O. Brugger, Althea L. Davies, Erle C. Ellis, Sergi Pla-Rabes, Alicja Bonk, M. Jane Bunting, Frank M. Chambers, Suzette G. A. Flantua, Tamara L. Fletcher, Caroline Greiser, Armand Hernández, Benjamin Gwinneth, Gerbrand Koren, Katarzyna Marcisz, Encarni Montoya, Adolfo Quesada-Román, Amila S. Ratnayake, Pierre Sabatier, John P. Smol, Nancy Y. Suárez-Mozo:
Ten simple rules to bridge ecology and palaeoecology by publishing outside palaeoecological journals. 1012487 - Bertram Klinger, Isabel Rausch, Anja Sieber, Helmut Kutz, Vanessa Kruse, Marieluise Kirchner, Philipp Mertins, Arnd Kieser, Nils Blüthgen, Dieter Kube:
Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network. 1012488 - Lianghong Chen, Zi Huai Huang, Yan Sun, Mike Domaratzki, Qian Liu, Pingzhao Hu:
Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer. 1012490 - George Gabriel, Faisal Mushtaq, J. Ryan Morehead:
De novo sensorimotor learning through reuse of movement components. 1012492 - Fan Xia, Yanni Xiao, Junling Ma:
The optimal spatially-dependent control measures to effectively and economically eliminate emerging infectious diseases. 1012498 - Marta Mackowiak, Bartosz Adamczyk, Marta Szachniuk, Tomasz Zok:
RNAtango: Analysing and comparing RNA 3D structures via torsional angles. 1012500 - Jaspreet Ishar, Yee Man Tam, Simon Mages, Johanna Klughammer:
BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images. 1012504 - Anika T. Löwe, Léo Touzo, Paul S. Muhle-Karbe, Andrew M. Saxe, Christopher Summerfield, Nicolas W. Schuck:
Abrupt and spontaneous strategy switches emerge in simple regularised neural networks. 1012505 - Marta Sampaio, Miguel Rocha, Oscar Dias:
A diel multi-tissue genome-scale metabolic model of Vitis vinifera. 1012506 - Carrisa Cocuzza, Ruben Sanchez-Romero, Takuya Ito, Ravi D. Mill, Brian P. Keane, Michael W. Cole:
Distributed network flows generate localized category selectivity in human visual cortex. 1012507 - Richard D. J. G. Ho, Kasumi Kishi, Maciej Majka, Anna Kicheva, Marcin Zagórski:
Dynamics of morphogen source formation in a growing tissue. 1012508 - Emmanouil Giannakakis, Oleg Vinogradov, Victor Buendia, Anna Levina:
Structural influences on synaptic plasticity: The role of presynaptic connectivity in the emergence of E/I co-tuning. 1012510 - Wei Liu, Huaqin He, Davide Chicco:
Gene signatures for cancer research: A 25-year retrospective and future avenues. 1012512 - Kelly Charniga, Sang Woo Park, Andrei R. Akhmetzhanov, Anne Cori, Jonathan Dushoff, Sebastian Funk, Katelyn M. Gostic, Natalie M. Linton, Adrian Lison, Christopher E. Overton, Juliet R. C. Pulliam, Thomas Ward, Simon Cauchemez, Sam Abbott:
Best practices for estimating and reporting epidemiological delay distributions of infectious diseases. 1012520 - Giacomo Barzon, Ettore Ambrosini, Antonino Vallesi, Samir Suweis:
EEG microstate transition cost correlates with task demands. 1012521 - Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni, Kévin Ricard, Francesca Anselmi, Clément Nizak, Andrea Pagnani, Olivier Rivoire:
Inference and design of antibody specificity: From experiments to models and back. 1012522 - Alessio Andronico, Juliette Paireau, Simon Cauchemez:
Integrating information from historical data into mechanistic models for influenza forecasting. 1012523 - Yujie Zhang, Mark Mao, Robert Zhang, Yen-Te Liao, Vivian C. H. Wu:
DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle. 1012525 - Shaojun Yu, Junjie Wu, Yumeng Shao, Deqiang Qiu, Zhaohui S. Qin:
A novel classification framework for genome-wide association study of whole brain MRI images using deep learning. 1012527 - Ashima Keshava, Farbod Nosrat Nezami, Henri Neumann, Krzysztof Izdebski, Thomas Schüler, Peter König:
Just-in-time: Gaze guidance in natural behavior. 1012529 - Ulisses Nunes da Rocha, Jonas Coelho Kasmanas, Rodolfo Toscan, Danilo Sipoli Sanches, Stefanía Magnúsdóttir, João Pedro Saraiva:
Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery. 1012530 - Gaspard Oliviers, Rafal Bogacz, Alexander Meulemans:
Learning probability distributions of sensory inputs with Monte Carlo predictive coding. 1012532 - Natchapon Srinak, Porntip Chiewchankaset, Saowalak Kalapanulak, Pornpan Panichnumsin, Treenut Saithong:
Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters. 1012533 - Lachlan Webb, Andrew J. K. Phillips, James A. Roberts:
Mapping the physiological changes in sleep regulation across infancy and young childhood. 1012541 - Yun Zuo, Xingze Fang, Jiayong Wan, Wenying He, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng:
PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites. 1012544 - Olga A. Nev, Elena Zamaraeva, Romain De Oliveira, Ilia Ryzhkov, Lucian Duvenage, Wassim Abou-Jaoudé, Djomangan Adama Ouattara, Jennifer Claire Hoving, Ivana Gudelj, Alistair J. P. Brown:
Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium. 1012545 - Anand V. Sastry, Yuan Yuan, Saugat Poudel, Kevin Rychel, Reo Yoo, Cameron R. Lamoureux, Gaoyuan Li, Joshua T. Burrows, Siddharth Chauhan, Zachary B. Haiman, Tahani Al Bulushi, Yara Seif, Bernhard O. Palsson, Daniel C. Zielinski:
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. 1012546 - Mark C. W. van Rossum, Aaron Pache:
Competitive plasticity to reduce the energetic costs of learning. 1012553 - Jiamu Jiang, Emilie Foyard, Mark C. W. van Rossum:
Reinforcement learning when your life depends on it: A neuro-economic theory of learning. 1012554 - Saishi Cui, Sina Nassiri, Issa Zakeri:
Mcadet: A feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection. 1012560 - Lingxia Qiao, Michael Getz, Ben Gross, Brian Tenner, Jin Zhang, Padmini Rangamani:
Spatiotemporal orchestration of calcium-cAMP oscillations on AKAP/AC nanodomains is governed by an incoherent feedforward loop. 1012564 - Gabriel A. A. Silva, Avril M. Harder, Kenneth B. Kirksey, Samarth Mathur, Janna R. Willoughby:
Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history. 1012566
Volume 20, Number 11, 2024
- Christian Jarvers, Heiko Neumann:
Teaching deep networks to see shape: Lessons from a simplified visual world. 1012019 - Jonathan Eden, Ekaterina Ivanova, Etienne Burdet:
During haptic communication, the central nervous system compensates distinctly for delay and noise. 1012037 - Martina Bukac, Suncica Canic, Boris Muha, Yifan Wang:
A computational algorithm for optimal design of a bioartificial organ scaffold architecture. 1012079 - Marte J. Sætra, Yoichiro Mori:
An electrodiffusive network model with multicompartmental neurons and synaptic connections. 1012114 - Hong Yan Huang, Fu Wei Zhang, Jie Yu, Yan Hong Xiao, Di Zhu, Xiaolin Yi, Xiaohua Lin, Ming Jin, Hai Yun Jin, Yong Sheng Huang, Shu Wei Ren:
A computational analysis of the oncogenic and anti-tumor immunity role of P4HA3 in human cancers. 1012284 - John H. Tay, Arthur Kocher, Sebastián Duchêne:
Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal. 1012371 - Qing Wu, Eric M. Morrow, Ece D. Gamsiz Uzun:
A deep learning model for prediction of autism status using whole-exome sequencing data. 1012468 - Michael Alexander Ramirez Sierra, Thomas R. Sokolowski:
AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis. 1012473 - Fabian Santiago, Amandeep Kaur, Shannon Bride, Dougald Monroe, Karin Leiderman, Suzanne S. Sindi:
A new look at TFPI inhibition of factor X activation. 1012509 - Hugh O'Brien, Max Salm, Laura T. Morton, Maciej Szukszto, Felix O'farrell, Charlotte Boulton, Laurence King, Supreet Kaur Bola, Pablo D. Becker, Andrew Craig, Morten Nielsen, Yardena Samuels, Charles Swanton, Marc R. Mansour, Sine Reker Hadrup, Sergio A. Quezada:
A modular protein language modelling approach to immunogenicity prediction. 1012511 - Alexandria M. Jensen, Peter Dewitt, Brianne M. Bettcher, Julia Wrobel, Katerina J. Kechris, Debashis Ghosh:
Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics. 1012524 - Boyan Xu, Alois Cerbu, Christopher J. Tralie, Daven Lim, Ksenia Krasileva:
Structure-aware annotation of leucine-rich repeat domains. 1012526 - Ciara E. Judge, Timothy G. Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill:
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering. 1012528 - David Kappel, Christian Tetzlaff:
Synapses learn to utilize stochastic pre-synaptic release for the prediction of postsynaptic dynamics. 1012531 - Toshihito Umegaki, Hisashi Moriizumi, Fumiko Ogushi, Mutsuhiro Takekawa, Takashi Suzuki:
Molecular dynamics simulations of a multicellular model with cell-cell interactions and Hippo signaling pathway. 1012536 - Andrew Anderson, Chris Davis, Edmund C. Lalor:
Deep-learning models reveal how context and listener attention shape electrophysiological correlates of speech-to-language transformation. 1012537 - Robert van Dijk, John Arevalo, Mehrtash Babadi, Anne E. Carpenter, Shantanu Singh:
Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning. 1012547 - Alireza Rezvani-Sharif, Hadi Lioe, Steven K. Dower, Matthias Pelzing, Con Panousis, Dalton J. E. Harvie, Ineke L. Muir:
A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors. 1012552 - Rym Ben Boubaker, Daniel Henrion, Marie Chabbert:
Mechanical stress and anionic lipids synergistically stabilize an atypical structure of the angiotensin II type 1 receptor (AT1). 1012559 - Jørgen Ankill, Zhi Zhao, Xavier Tekpli, Elin H. Kure, Vessela N. Kristensen, Anthony Mathelier, Thomas Fleischer:
Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation. 1012565 - J. Roadnight Sheehan, Astrid S. de Wijn, Thales Souza Freire, Ran Friedman:
Beyond IC50 - A computational dynamic model of drug resistance in enzyme inhibition treatment. 1012570 - Sven B. Gould, Jonas Magiera, Carolina García García, Parth K. Raval:
Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing. 1012575 - Zahra Razaghi-Moghadam, Fayaz Soleymani Babadi, Zoran Nikoloski:
Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes. 1012576 - Baptiste Ruiz, Arnaud Belcour, Samuel Blanquart, Sylvie Buffet-Bataillon, Isabelle Le Huërou-Luron, Anne Siegel, Yann Le Cunff:
SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects. 1012577 - Medha Shekhar, Dobromir Rahnev:
Human-like dissociations between confidence and accuracy in convolutional neural networks. 1012578 - Beren Millidge, Yuhang Song, Armin Lak, Mark E. Walton, Rafal Bogacz:
Reward Bases: A simple mechanism for adaptive acquisition of multiple reward types. 1012580 - Lin Lin, Rachel L. Spreng, Kelly E. Seaton, S. Moses Dennison, Lindsay C. Dahora, Daniel J. Schuster, Sheetal Sawant, Peter B. Gilbert, Youyi Fong, Neville Kisalu, Andrew J. Pollard, Georgia D. Tomaras, Jia Li:
GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies. 1012581 - Marta Kryven, Suhyoun Yu, Max Kleiman-Weiner, Tomer D. Ullman, Joshua B. Tenenbaum:
Approximate planning in spatial search. 1012582 - Yuanchen Zhao, Otto X. Cordero, Mikhail Tikhonov:
Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function. 1012590 - Aylin Bircan, Nurdan Kuru, Onur Dereli, Berkay Selçuk, Ogun Adebali:
Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations. 1012591 - Evandro Konzen, Richard J. Delahay, Dave J. Hodgson, Robbie A. McDonald, Ellen Brooks Pollock, Simon E. F. Spencer, Trevelyan J. McKinley:
Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers. 1012592 - Anna K. Leinheiser, Colleen C. Mitchell, Ethan Rooke, Stefan Strack, Chad E. Grueter:
A dynamical systems model for the total fission rate in Drp1-dependent mitochondrial fission. 1012596 - Dan Liu, Francesca Young, Kieran D. Lamb, David L. Robertson, Ke Yuan:
Prediction of virus-host associations using protein language models and multiple instance learning. 1012597 - Salah Bazzi, Stephan Stansfield, Neville Hogan, Dagmar Sternad:
Simplified internal models in human control of complex objects. 1012599 - Aaron R. Allred, Caroline R. Austin, Lanna Klausing, Nicholas Boggess, Torin K. Clark:
Human perception of self-motion and orientation during galvanic vestibular stimulation and physical motion. 1012601 - Qiangwei Peng, Xiaojie Qiu, Tiejun Li:
Storm: Incorporating transient stochastic dynamics to infer the RNA velocity with metabolic labeling information. 1012606 - Chao Wang, Quan Zou:
MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm. 1012607 - Fei Cai, Yuehua Wei, Daniel Kirchhofer, Andrew Chang, Yingnan Zhang:
Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds. 1012609
Volume 20, Number 12, 2024
- Atle E. Rimehaug, Anders M. Dale, Anton Arkhipov, Gaute T. Einevoll:
Uncovering population contributions to the extracellular potential in the mouse visual system using Laminar Population Analysis. 1011830 - Anna N. Osiecka, Przemyslaw Bryndza, Elodie F. Briefer, Katarzyna Wojczulanis-Jakubas:
Long distance calls: Negligible information loss of little auk social vocalisations due to high frequency propagation losses. 1011961 - Marko Sostar, Maja Marinovic, Vedrana Filic, Nenad Pavin, Igor Weber:
Oscillatory dynamics of Rac1 activity in Dictyostelium discoideum amoebae. 1012025 - Máté Mohácsi, Márk Patrik Török, Sára Sáray, Luca Tar, Gábor Farkas, Szabolcs Káli:
Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software framework. 1012039 - Nyall Jamieson, Christiana Charalambous, David M. Schultz, Ian Hall:
The Burr distribution as a model for the delay between key events in an individual's infection history. 1012041 - Kathrin Pabst, Evripidis Gkanias, Barbara Webb, Uwe Homberg, Dominik Endres:
A computational model for angular velocity integration in a locust heading circuit. 1012155 - Bethan Cracknell Daniels, Darunee Buddhari, Taweewun Hunsawong, Sopon Iamsirithaworn, Aaron R. Farmer, Derek A. T. Cummings, Kathryn B. Anderson, Ilaria Dorigatti:
Predicting the infecting dengue serotype from antibody titre data using machine learning. 1012188 - Katherine Levandosky, Calina A. Copos:
Model supports asymmetric regulation across the intercellular junction for collective cell polarization. 1012216 - Jorin Overwiening, Federico Tesler, Domenico Guarino, Alain Destexhe:
A multi-scale study of thalamic state-dependent responsiveness. 1012262 - Karolina Tlalka, Harry Saxton, Ian Halliday, Xu Xu, Andrew J. Narracott, Daniel J. Taylor, Maciej Malawski:
Sensitivity analysis of closed-loop one-chamber and four-chamber models with baroreflex. 1012377 - Giuseppe Benagiano, Andrea R. Genazzani, Giovanni Grandi, Sun-Wei Guo, Marwan Habiba:
Comment on: Toward an optimal contraception dosing strategy. 1012398 - Nathan R. Zuniga, Noah E. Earls, Ariel E. A. Denos, Jared M. Elison, Benjamin S. Jones, Ethan G. Smith, Noah G. Moran, Katie L. Broce, Gerome M. Romero, Chad D. Hyer, Kimberly B. Wagstaff, Haifa M. Almughamsi, Mark K. Transtrum, John C. Price:
Quantitative and Kinetic Proteomics Reveal ApoE Isoform-dependent Proteostasis Adaptations in Mouse Brain. 1012407 - Maciej Majka, Nils B. Becker, Pieter Rein ten Wolde, Marcin Zagórski, Thomas R. Sokolowski:
Stable developmental patterns of gene expression without morphogen gradients. 1012555 - Nan Zhang, Linan Zhuang, Marco-Felipe King, Hua Qian, Min Zhu:
Public surface disinfection every 2 hours can reduce the infection risk of norovirus in airports up to 83%. 1012561 - Renata Retkute, William Thurston, Keith Cressman, Christopher A. Gilligan:
A framework for modelling desert locust population dynamics and large-scale dispersal. 1012562 - Victor Geadah, Stefan Horoi, Giancarlo Kerg, Guy Wolf, Guillaume Lajoie:
Neural networks with optimized single-neuron adaptation uncover biologically plausible regularization. 1012567 - Hind Zaaraoui, Clarisse Schumer, Xavier Duval, Bruno Hoen, Lulla Opatowski, Jérémie Guedj:
Modelling the effectiveness of antiviral treatment strategies to prevent household transmission of acute respiratory viruses. 1012573 - Janez Demsar, Blaz Zupan:
Hands-on training about data clustering with orange data mining toolbox. 1012574 - Faye Orcales, Lucy Moctezuma Tan, Meris Johnson-Hagler, John Matthew Suntay, Jameel Ali, Kristiene Recto, Phelan Glenn, Pleuni S. Pennings:
Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper. 1012579 - Jan Stasinski, Halgurd Taher, Jil Mona Meier, Michael Schirner, Dionysios Perdikis, Petra Ritter:
Homeodynamic feedback inhibition control in whole-brain simulations. 1012595 - Lalit Pandey, Donsuk Lee, Samantha M. W. Wood, Justin N. Wood:
Parallel development of object recognition in newborn chicks and deep neural networks. 1012600 - Mark A. Orloff, Dongil Chung, Xiaosi Gu, Xingchao Wang, Zhixian Gao, Guiding Song, Chandana Tatineni, Shuai Xu, Brooks Casas, Pearl H. Chiu:
Social conformity is a heuristic when individual risky decision-making is disrupted. 1012602 - Yuqian Liu, Yan Chen, Huanwen Wu, Xuanping Zhang, Yuqi Wang, Xin Yi, Zhiyong Liang, Jiayin Wang:
scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum. 1012608 - Max Grogan, Kyle P. Blum, Yufei Wu, John Alexander Harston, Lee E. Miller, A. Aldo Faisal:
Predicting proprioceptive cortical anatomy and neural coding with topographic autoencoders. 1012614 - Meng Yuan, Seppe Goovaerts, Michiel Vanneste, Harold S. Matthews, Hanne Hoskens, Stephen Richmond, Ophir D. Klein, Richard A. Spritz, Benedikt Hallgrímsson, Susan Walsh, Mark D. Shriver, John R. Shaffer, Seth M. Weinberg, Hilde Peeters, Peter Claes:
Mapping genes for human face shape: Exploration of univariate phenotyping strategies. 1012617 - Ryohei Shibue, Tomoharu Iwata:
Marked point process variational autoencoder with applications to unsorted spiking activities. 1012620 - Nisha A. Viswan, Alexandre Tribut, Manvel Gasparyan, Ovidiu Radulescu, Upinder S. Bhalla:
Mathematical basis and toolchain for hierarchical optimization of biochemical networks. 1012624 - Xavier Escriba-Montagut, Yannick Marcon, Augusto Anguita-Ruiz, Demetris Avraam, Jose Urquiza, Andrei S. Morgan, Rebecca C. Wilson, Paul R. Burton, Juan R. González:
Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform. 1012626 - Camille Champion, Raphaëlle Momal, Emmanuelle Le Chatelier, Mathilde Sola, Mahendra Mariadassou, Magali Berland:
OneNet - One network to rule them all: Consensus network inference from microbiome data. 1012627 - Adrián Fernández Amil, Albert Albesa-González, Paul F. M. J. Verschure:
Theta oscillations optimize a speed-precision trade-off in phase coding neurons. 1012628 - Michiel Vanslambrouck, Wim Thiels, Jef Vangheel, Casper van Bavel, Bart Smeets, Rob Jelier:
Image-based force inference by biomechanical simulation. 1012629 - Henrik Zunker, René Schmieding, David Kerkmann, Alain Schengen, Sophie Diexer, Rafael Mikolajczyk, Michael Meyer-Hermann, Martin J. Kühn:
Novel travel time aware metapopulation models and multi-layer waning immunity for late-phase epidemic and endemic scenarios. 1012630 - Henri Schmidt, Benjamin J. Raphael:
A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors. 1012631 - Qi Song, Alex Singh, John E. McDonough, Taylor Sterling Adams, Robin Vos, Ruben De Man, Greg Myers, Laurens J. Ceulemans, Bart M. Vanaudenaerde, Wim A. Wuyts, Xiting Yan, Jonas Schupp, James S. Hagood, Naftali Kaminski, Ziv Bar-Joseph:
Predicting lung aging using scRNA-Seq data. 1012632 - Gene J. Yu, Federico Ranieri, Vincenzo Di Lazzaro, Marc A. Sommer, Angel V. Peterchev, Warren M. Grill:
Circuits and mechanisms for TMS-induced corticospinal waves: Connecting sensitivity analysis to the network graph. 1012640 - Emine Celiker, Charlie Woodrow, Òscar Guadayol, Leonidas-Romanos Davranoglou, Christian M. Schlepütz, Beth Mortimer, Graham K. Taylor, Stuart Humphries, Fernando Montealegre-Z:
Mechanical network equivalence between the katydid and mammalian inner ears. 1012641 - Yutong Sun, Peng Qiu:
Hierarchical marker genes selection in scRNA-seq analysis. 1012643 - Nikoleta E. Glynatsi, Vincent A. Knight, Marc Harper:
Properties of winning Iterated Prisoner's Dilemma strategies. 1012644 - Masami Iwamoto, Satoko Hirabayashi, Noritoshi Atsumi:
In-silico simultaneous respiratory and circulatory measurement during voluntary breathing, exercise, and mental stress: A computational approach. 1012645 - Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane:
Large scale paired antibody language models. 1012646 - Michael Forrester, Sammy Petros, Oliver Cattell, Yi Ming Lai, Reuben D. O'Dea, Stamatios Sotiropoulos, Stephen Coombes:
Whole brain functional connectivity: Insights from next generation neural mass modelling incorporating electrical synapses. 1012647 - Kenneth Y. Wertheim, Robert Chisholm, Paul Richmond, Dawn C. Walker:
Multicellular model of neuroblastoma proposes unconventional therapy based on multiple roles of p53. 1012648 - Brenda Lyn A. Gavina, Aurelio A. de los Reyes V., Mette S. Olufsen, Suzanne Lenhart, Johnny T. Ottesen:
Response to comment on: Toward an optimal contraception dosing strategy. 1012649 - Ikram Mahmoudi, Chloé Quignot, Carla Martins, Jessica Andreani:
Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts. 1012650 - Niloufar Abhari, Caroline Colijn, Arne Mooers, Paul F. Tupper:
Measuring genetic diversity across populations. 1012651 - Andrea L. Graham, Roland R. Regoes:
Dose-dependent interaction of parasites with tiers of host defense predicts "wormholes" that prolong infection at intermediate inoculum sizes. 1012652 - Ethan Kulman, Rui Kuang, Quaid Morris:
Orchard: Building large cancer phylogenies using stochastic combinatorial search. 1012653 - Ahmed Akib Jawad Karim, Muhammad Zawad Mahmud, Riasat Khan:
Advanced vision transformers and open-set learning for robust mosquito classification: A novel approach to entomological studies. 1012654 - Jiyoung Kang, Hae-Jeong Park:
Integration of partially observed multimodal and multiscale neural signals for estimating a neural circuit using dynamic causal modeling. 1012655 - Asier Ortega-Legarreta, Sara Palomino-Echeverria, Estefania Huergo, Vincenzo Lagani, Narsis A. Kiani, Pierre-Emmanuel Rautou, Nuria Planell-Picola, Jesper Tegnér, David Gomez-Cabrero:
ClustAll: An R package for patient stratification in complex diseases. 1012656 - George E. Kapellos, Hermann J. Eberl, Nicolas Kalogerakis, Patrick S. Doyle, Christakis A. Paraskeva:
Bacterial clustering amplifies the reshaping of eutrophic plumes around marine particles: A hybrid data-driven model. 1012660 - Lucille Calmon, Elisabetta Colosi, Giulia Bassignana, Alain Barrat, Vittoria Colizza:
Preserving friendships in school contacts: An algorithm to construct synthetic temporal networks for epidemic modelling. 1012661 - Sarah E. Baum, Daniele M. Pelissari, Fernanda Dockhorn Costa, Luiza O. Harada, Mauro Sanchez, Patricia Bartholomay, Ted Cohen, Marcia C. Castro, Nicolas A. Menzies:
Surveillance for TB drug resistance using routine rapid diagnostic testing data: Methodological development and application in Brazil. 1012662 - Armaan A. Abraham, Zhixin Cyrillus Tan, Priyanka Shrestha, Emily R. Bozich, Aaron S. Meyer:
A multivalent binding model infers antibody Fc species from systems serology. 1012663 - Simone Ciccolella, Davide Cozzi, Gianluca Della Vedova, Stephen Njuguna Kuria, Paola Bonizzoni, Luca Denti:
Differential quantification of alternative splicing events on spliced pangenome graphs. 1012665 - Elif Köksal Ersöz, Pascal Benquet, Fabrice Wendling:
Expansion of epileptogenic networks via neuroplasticity in neural mass models. 1012666 - Juliana Chase, Liyu Xia, Lung-Hao Tai, Wan Chen Lin, Anne G. E. Collins, Linda Wilbrecht:
Adolescent and adult mice use both incremental reinforcement learning and short term memory when learning concurrent stimulus-action associations. 1012667 - Abel Bernadou, Raphaël Jeanson:
Randomness as a driver of inactivity in social groups. 1012668 - Pengyu Liu, Jacob Lusk, Natasa Jonoska, Mariel Vázquez:
Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding. 1012669 - Karim Habashy, Benjamin D. Evans, Dan F. M. Goodman, Jeffrey S. Bowers:
Adapting to time: Why nature may have evolved a diverse set of neurons. 1012673 - Moritz Grosse-Wentrup, Akshey Kumar, Anja Meunier, Manuel Zimmer:
Neuro-cognitive multilevel causal modeling: A framework that bridges the explanatory gap between neuronal activity and cognition. 1012674 - Amit Basak, Supratim Sengupta:
Evolution of cooperation in multichannel games on multiplex networks. 1012678 - Wei Lan, Tongsheng Ling, Qingfeng Chen, Ruiqing Zheng, Min Li, Yi Pan:
scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis. 1012679 - Philip Cherian, Jayanta Kshirsagar, Bhavesh Neekhra, Gaurav Deshkar, Harshal Hayatnagarkar, Kshitij Kapoor, Chandrakant Kaski, Ganesh Kathar, Swapnil Khandekar, Saurabh Mookherjee, Praveen Ninawe, Riz Fernando Noronha, Pranjal Ranka, Vaibhhav Sinha, Tina Vinod, Chhaya Yadav, Debayan Gupta, Gautam I. Menon:
BharatSim: An agent-based modelling framework for India. 1012682 - Roukayatou R. Ouedraogo, Hannah K. Sowers, Spencer R. Lynch, Nathan E. Hudson, Brittany E. Bannish:
A mathematical model of plasmin-mediated fibrinolysis of single fibrin fibers. 1012684 - Tal Gutman, Tamir Tuller:
Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding. 1012685 - Oscar Fajardo-Fontiveros, Mattia Mattei, Giulio Burgio, Clara Granell, Sergio Gómez, Alex Arenas, Marta Sales-Pardo, Roger Guimerà:
Machine learning mathematical models for incidence estimation during pandemics. 1012687 - Thiago Ohno Bezerra, Antonio Carlos Roque:
Dopamine facilitates the response to glutamatergic inputs in astrocyte cell models. 1012688 - Annie G. Bryant, Kevin M. Aquino, Linden Parkes, Alex Fornito, Ben D. Fulcher:
Extracting interpretable signatures of whole-brain dynamics through systematic comparison. 1012692 - Alexandre Guet-McCreight, Frank Mazza, Thomas D. Prevot, Etienne Sibille, Etay Hay:
Therapeutic dose prediction of α5-GABA receptor modulation from simulated EEG of depression severity. 1012693 - Xin-Yu Zhang, Lan-Lan Yu, Wei-Yi Wang, Gui-Quan Sun, Jian-Cheng Lv, Tao Zhou, Quan-Hui Liu:
Estimating the time-varying effective reproduction number via Cycle Threshold-based Transformer. 1012694 - Jessica James, Sebastian Towers, Jakob N. Foerster, Harrison Steel:
Optimisation strategies for directed evolution without sequencing. 1012695 - Hyeontae Jo, Sung Woong Cho, Hyung Ju Hwang:
Estimating the distribution of parameters in differential equations with repeated cross-sectional data. 1012696 - Rosalind Wenshan Pan, Tom Röschinger, Kian Faizi, Hernan G. Garcia, Rob Phillips:
Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns. 1012697 - Yongqi Bu, Jiaxuan Liang, Zhen Li, Jianbo Wang, Jun Wang, Guoxian Yu:
Cancer molecular subtyping using limited multi-omics data with missingness. 1012710 - Akash Bahai, Chee Keong Kwoh, Yuguang Mu, Yinghui Li:
Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction. 1012715
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