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ORCIDBioinformatics, Volume 39
Volume 39, Number 1, January 2023
- Hong Zhang
, Devan V. Mehrotra, Judong Shen:
AWOT and CWOT for genotype and genotype-by-treatment interaction joint analysis in pharmacogenetics GWAS. - Xuezhi Xie, Pedro A. Valiente, Philip M. Kim:
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures. - Xiaokun Hong, Ningshan Li, Jiyang Lv, Yan Zhang, Jing Li, Jian Zhang, Hai-Feng Chen:
PTMint database of experimentally verified PTM regulation on protein-protein interaction. - Alessandro Vinceti, Lucia Trastulla, Umberto Perron, Andrea Raiconi, Francesco Iorio:
A heuristic algorithm solving the mutual-exclusivity-sorting problem. - Nelle Varoquaux, William S. Noble, Jean-Philippe Vert:
Inference of 3D genome architecture by modeling overdispersion of Hi-C data. - Teresa De Jesus Martinez, Elliot A. Hershberg, Emma Guo, Garrett Stevens, Colin M. Diesh, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes:
JBrowse Jupyter: a Python interface to JBrowse 2. - Neda Shokraneh, Mariam Arab, Maxwell W. Libbrecht:
Integrative chromatin domain annotation through graph embedding of Hi-C data. - Shivam Kumar, Dipanka Sarmah, Shailendra Asthana, Samrat Chatterjee:
konnect2prot: a web application to explore the protein properties in a functional protein-protein interaction network. - Ngoc-Quang Nguyen, Gwanghoon Jang, Hajung Kim, Jaewoo Kang:
Perceiver CPI: a nested cross-attention network for compound-protein interaction prediction. - Manuel Glöckler, Andreas Dräger, Reihaneh Mostolizadeh:
Hierarchical modelling of microbial communities. - José Camacho, Raffaele Vitale, David Morales-Jiménez, Carolina Gómez-Llorente:
Variable-selection ANOVA Simultaneous Component Analysis (VASCA). - Filippo Grazioli, Pierre Machart, Anja Mösch, Kai Li, Leonardo V. Castorina, Nico Pfeifer, Martin Renqiang Min:
Attentive Variational Information Bottleneck for TCR-peptide interaction prediction. - Marcus T. Moen, Iain G. Johnston:
HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs. - Xingqi Wu, Yi Shi, Minghui Wang, Ao Li:
CAMR: cross-aligned multimodal representation learning for cancer survival prediction. - Jinding Liu, Yaru Zhang, Yapin Shi, Yiqing Zheng, Yali Zhu, Zhuoran Guan, Danyu Shen, Daolong Dou:
FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing. - Marija Stanojevic, Jovan Andjelkovic, Adrienne Kasprowicz, Louise A. Huuki, Jennifer Chao, S. Blair Hedges, Sudhir Kumar, Zoran Obradovic:
Discovering research articles containing evolutionary timetrees by machine learning. - Correction to: FASTRAL: improving scalability of phylogenomic analysis.
- Jonathan K. Vis, Mark A. Santcroos, Walter A. Kosters, Jeroen F. J. Laros:
A Boolean algebra for genetic variants. - Vamsi Nallapareddy, Nicola Bordin, Ian Sillitoe, Michael Heinzinger, Maria Littmann, Vaishali P. Waman, Neeladri Sen, Burkhard Rost, Christine A. Orengo:
CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models. - Chenxi Zhou, Shane A. McCarthy, Richard Durbin:
YaHS: yet another Hi-C scaffolding tool. - Correction to: Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms.
- Marek S. Wiewiórka, Agnieszka Szmurlo, Pawel Stankiewicz, Tomasz Gambin:
Cloud-native distributed genomic pileup operations. - Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf:
mOWL: Python library for machine learning with biomedical ontologies. - Dailin Gan, Jun Li:
SCIBER: a simple method for removing batch effects from single-cell RNA-sequencing data. - Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg:
GOThresher: a program to remove annotation biases from protein function annotation datasets. - Yufeng Liu, Ye Zhong, Xuan Zhao, Lijuan Liu, Liya Ding, Hanchuan Peng:
Tracing weak neuron fibers. - Yuwei Wang, Bin Lian, Haohui Zhang, Yuanke Zhong, Jie He, Fashuai Wu, Knut Reinert, Xuequn Shang, Hui Yang, Jialu Hu:
A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. - Abin Abraham, Abigail L. Labella, Mary Lauren Benton, Antonis Rokas, John A. Capra:
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. - Licai Huang, James P. Long, Ehsan Irajizad, James D. Doecke, Kim-Anh Do, Min Jin Ha:
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes. - Jialun Wu, Yuxin Dong, Zeyu Gao, Tieliang Gong, Chen Li:
Dual Attention and Patient Similarity Network for drug recommendation. - Wei Chen, Zhiwei Li, Hongyi Fang, Qianyuan Yao, Cheng Zhong, Jianye Hao, Qi Zhang, Xuanjing Huang, Jiajie Peng, Zhongyu Wei:
A benchmark for automatic medical consultation system: frameworks, tasks and datasets. - Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar:
Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. - Oluwadamilare Falola, Yagoub Adam, Olabode Ajayi, Judit Kumuthini, Suraju Adewale, Abayomi Mosaku, Chaimae Samtal, Glory O. Adebayo, Jerry Emmanuel, Milaine S. S. Tchamga, Udochukwu Erondu, Adebayo Nehemiah, Suraj Rasaq, Mary Ajayi, Bola Akanle, Olaleye Oladipo, Itunuoluwa Isewon, Marion O. Adebiyi, Jelili Oyelade, Ezekiel F. Adebiyi:
SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets. - Till Hartmann, Christopher Schröder, Elias Kuthe, David Laehnemann, Johannes Köster:
Insane in the vembrane: filtering and transforming VCF/BCF files. - Michael F. Adamer, Eljas Roellin, Lucie Bourguignon, Karsten M. Borgwardt:
SIMBSIG: similarity search and clustering for biobank-scale data. - Sergey Vilov, Matthias Heinig:
DeepSom: a CNN-based approach to somatic variant calling in WGS samples without a matched normal. - Correction to: Targeted metabolomics analyses for brain tumor margin assessment during surgery.
- Fabricio Almeida-Silva, Tao Zhao, Kristian K. Ullrich, M. Eric Schranz, Yves Van de Peer:
syntenet: an R/Bioconductor package for the inference and analysis of synteny networks. - Hannah Schriever, Dennis Kostka:
Vaeda computationally annotates doublets in single-cell RNA sequencing data. - Expression of Concern: Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking.
- Jin Xu, Jessie Jiang, Herbert M. Sauro:
SBMLDiagrams: a python package to process and visualize SBML layout and render. - Antonios Klonizakis, Christoforos Nikolaou, Thomas Graf:
SEGCOND predicts putative transcriptional condensate-associated genomic regions by integrating multi-omics data. - Yeonil Kim, Yueh-Yun Chi, Judong Shen, Fei Zou:
Robust genetic model-based SNP-set association test using CauchyGM. - Yohsuke T. Fukai, Kyogo Kawaguchi:
LapTrack: linear assignment particle tracking with tunable metrics. - Wei Shen, Hongyan Xiang, Tianquan Huang, Hui Tang, Mingli Peng, Dachuan Cai, Peng Hu, Hong Ren:
KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping. - Sudeep Sahadevan, Thileepan Sekaran, Nadia Ashaf, Marko Fritz, Matthias W. Hentze, Wolfgang Huber, Thomas Schwarzl:
htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets. - Renming Liu, Matthew J. Hirn, Arjun Krishnan:
Accurately modeling biased random walks on weighted networks using node2vec+. - Afshan Nabi, Berke Dilekoglu, Ogun Adebali, Öznur Tastan:
Discovering misannotated lncRNAs using deep learning training dynamics. - Yonghyun Nam, Sang-Hyuk Jung, Jae-Seung Yun, Vivek Sriram, Pankhuri Singhal, Marta Byrska-Bishop, Anurag Verma, Hyunjung Shin, Woong-Yang Park, Hong-Hee Won, Dokyoon Kim:
Discovering comorbid diseases using an inter-disease interactivity network based on biobank-scale PheWAS data. - Lewis Chinery, Newton Wahome, Iain Moal, Charlotte M. Deane:
Paragraph - antibody paratope prediction using graph neural networks with minimal feature vectors. - Robert Hanes, Pilar Ayuda-Durán, Leiv Rønneberg, Sigve Nakken, Eivind Hovig, Manuela Zucknick, Jorrit M. Enserink:
screenwerk: a modular tool for the design and analysis of drug combination screens. - John C. Braisted, Andrew Patt, Cole Tindall, Timothy Sheils, Jorge Neyra, Kyle Spencer, Tara Eicher, Ewy A. Mathé:
RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes. - Yanyan Diao, Feng Hu, Zihao Shen, Honglin Li:
MacFrag: segmenting large-scale molecules to obtain diverse fragments with high qualities. - Leonardo V. Castorina, Rokas Petrenas, Kartic Subr, Christopher W. Wood:
PDBench: evaluating computational methods for protein-sequence design. - Neng Huang, Minghua Xu, Fan Nie, Peng Ni, Chuan-Le Xiao, Feng Luo, Jianxin Wang:
NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data. - Nicola Apollonio, Daniel Blankenberg, Fabio Cumbo, Paolo Giulio Franciosa, Daniele Santoni:
Evaluating homophily in networks via HONTO (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks. - Thao Vu, Elizabeth Litkowski, Weixuan Liu, Katherine A. Pratte, Leslie Lange, Russell Bowler, Farnoush Banaei Kashani, Katerina J. Kechris:
NetSHy: network summarization via a hybrid approach leveraging topological properties. - Emmi Jokinen, Alexandru Dumitrescu, Jani Huuhtanen, Vladimir Gligorijevic, Satu Mustjoki, Richard Bonneau, Markus Heinonen, Harri Lähdesmäki:
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs. - Qing Mo, Zexin Xu, Hui Yan, Pin Chen, Yutong Lu:
VSTH: a user-friendly web server for structure-based virtual screening on Tianhe-2. - Sandra Díaz-Seoane, Xabier Rey-Barreiro, Alejandro F. Villaverde:
STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability. - Bayo Lau, Prashant S. Emani, Jackson Chapman, Lijing Yao, Tarsus Lam, Paul Merrill, Jonathan Warrell, Mark B. Gerstein, Hugo Y. K. Lam:
Insights from incorporating quantum computing into drug design workflows. - Heng Li:
Protein-to-genome alignment with miniprot. - Ke Yan, Hongwu Lv, Yichen Guo, Wei Peng, Bin Liu:
sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure. - Laura Luebbert, Lior Pachter:
Efficient querying of genomic reference databases with gget. - Caleb A. Class, Caiden J. Lukan, Christopher A. Bristow, Kim-Anh Do:
Easy NanoString nCounter data analysis with the NanoTube. - Xavier Didelot, David Helekal, Michelle Kendall, Paolo Ribeca:
Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease. - Benoit Morel, Tom A. Williams, Alexandros Stamatakis:
Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data. - Ha Vu, Zane Koch, Petko Fiziev, Jason Ernst:
A framework for group-wise summarization and comparison of chromatin state annotations. - Wanying Zhu, Hung-Hsin Chen, Alexander S. Petty, Lauren E. Petty, Hannah G. Polikowsky, Eric R. Gamazon, Jennifer E. Below, Heather M. Highland:
IMMerge: merging imputation data at scale. - Ege Ülgen, Ozan Ozisik, Osman Ugur Sezerman:
PANACEA: network-based methods for pharmacotherapy prioritization in personalized oncology. - Jiansi Gao, Michael R. May, Bruce Rannala, Brian R. Moore:
PrioriTree: a utility for improving phylodynamic analyses in BEAST. - Correction to: Biomedical evidence engineering for data-driven discovery.
- Diksha Bhalla, Marvin N. Steijaert, Eefje S. Poppelaars, Marc Teunis, Monique van der Voet, Marie Corradi, Elisabeth Dévière, Luke Noothout, Wilco Tomassen, Martijn Rooseboom, Richard A. Currie, Cyrille Krul, Raymond H. H. Pieters, Vera van Noort, Marjolein Wildwater:
DARTpaths, an in silico platform to investigate molecular mechanisms of compounds. - Heng Li, Mijuan Shi, Keyi Ren, Lei Zhang, Weidong Ye, Wanting Zhang, Yingyin Cheng, Xiaoqin Xia:
Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities. - Runzhou Yu, Dehan Cai, Yanni Sun:
AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data. - Andrea Vandelli, Magdalena Arnal Segura, Michele Monti, Jonathan Fiorentino, Laura Broglia, Alessio Colantoni, Natalia Sanchez de Groot, Marc Torrent Burgas, Alexandros Armaos, Gian Gaetano Tartaglia:
The PRALINE database: protein and Rna humAn singLe nucleotIde variaNts in condEnsates. - Rasmus Amund Henriksen, Lei Zhao, Thorfinn Sand Korneliussen:
NGSNGS: next-generation simulator for next-generation sequencing data. - Alexander Kramer, Theo Sanderson, Russell Corbett-Detig:
Treenome Browser: co-visualization of enormous phylogenies and millions of genomes. - Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu:
PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method. - Yu K. Mo, Robert Lanfear, Matthew W. Hahn, Bui Quang Minh:
Updated site concordance factors minimize effects of homoplasy and taxon sampling. - Qinhu Zhang, Pengrui Teng, Siguo Wang, Ying He, Zhen Cui, Zhenghao Guo, Yixin Liu, Changan Yuan, Qi Liu, De-Shuang Huang:
Computational prediction and characterization of cell-type-specific and shared binding sites. - Kaibin Huang, Shengyun Huang, Guojing Chen, Xue Li, Shawn Li, Ying Liang, Yi Gao:
An end-to-end multi-task system of automatic lesion detection and anatomical localization in whole-body bone scintigraphy by deep learning. - Iván Martín Hernández, Yves Dehouck, Ugo Bastolla, José Ramón López-Blanco, Pablo Chacón:
Predicting protein stability changes upon mutation using a simple orientational potential. - Tao Wang, Jinjin Yang, Yifu Xiao, Jingru Wang, Yuxian Wang, Xi Zeng, Yongtian Wang, Jiajie Peng:
DFinder: a novel end-to-end graph embedding-based method to identify drug-food interactions. - Micha Sam Brickman Raredon, Junchen Yang, Neeharika Kothapalli, Wesley Lewis, Naftali Kaminski, Laura E. Niklason, Yuval Kluger:
Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES. - Junhang Pan, Xiangchen Li, Mingwu Zhang, Yewei Lu, Yelei Zhu, Kunyang Wu, Yiwen Wu, Weixin Wang, Bin Chen, Zhengwei Liu, Xiaomeng Wang, Junshun Gao:
TransFlow: a Snakemake workflow for transmission analysis ofMycobacterium tuberculosiswhole-genome sequencing data. - Gavin M. Douglas, Sunu Kim, Morgan G. I. Langille, B. Jesse Shapiro:
Efficient computation of contributional diversity metrics from microbiome data with FuncDiv. - Ajay Anand Kumar, Bart Loeys, Gerarda Van De Beek, Nils Peeters, Wim Wuyts, Lut Van Laer, Geert Vandeweyer, Maaike Alaerts:
varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data. - Irbaz I Badshah, Pedro R. Cutillas:
Systematic identification of biochemical networks in cancer cells by functional pathway inference analysis. - Jaime Martínez de Villarreal, Mark Kalisz, Gabriel Piedrafita, Osvaldo Graña-Castro, Dafni Chondronasiou, Manuel Serrano, Francisco X. Real:
Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data. - Musu Yuan, Liang Chen, Minghua Deng:
Clustering single-cell multi-omics data with MoClust. - Samuel Martin, Martin Ayling, Livia Patrono, Mario Cáccamo, Pablo Murcia, Richard M. Leggett:
Capturing variation in metagenomic assembly graphs with MetaCortex. - Roshan Kulkarni, Yudi Zhang, Steven B. Cannon, Karin S. Dorman:
CAPG: comprehensive allopolyploid genotyper. - Marine Jeanmougin, Hans Petter Brodal, Heidi Dietrichson Pharo, Hege Marie Vedeld, Guro Elisabeth Lind:
PoDCall: positive droplet calling and normalization of droplet digital PCR DNA methylation data. - Kiran Javkar, Hugh Rand, Errol Strain, Mihai Pop:
PRAWNS: compact pan-genomic features for whole-genome population genomics. - Masaki Asada, Makoto Miwa, Yutaka Sasaki:
Integrating heterogeneous knowledge graphs into drug-drug interaction extraction from the literature. - Ángel Gálvez-Merchán, Kyung Hoi (Joseph) Min, Lior Pachter, A. Sina Booeshaghi:
Metadata retrieval from sequence databases with ffq. - Trevor Manz, Sehi L'Yi, Nils Gehlenborg:
Gos: a declarative library for interactive genomics visualization in Python. - Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker:
DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model. - Jaesub Park, Sangyeon Lee, Kwansoo Kim, Jaegyun Jung, Doheon Lee:
Large-scale prediction of adverse drug reactions-related proteins with network embedding. - Erik Garrison, Andrea Guarracino:
Unbiased pangenome graphs. - Philip C. Dishuck, Allison N. Rozanski, Glennis Logsdon, David Porubsky, Evan E. Eichler:
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads. - Henry Cousins, Taryn Hall, Yinglong Guo, Luke Tso, Kathy T. H. Tzeng, Le Cong, Russ B. Altman:
Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19. - Adam Platt, E. Josiah Lutton, Edward Offord, Till Bretschneider:
MiCellAnnGELo: annotate microscopy time series of complex cell surfaces with 3D virtual reality. - Chunyu Zhao, Boris Dimitrov, Miriam Goldman, Stephen Nayfach, Katherine S. Pollard:
MIDAS2: Metagenomic Intra-species Diversity Analysis System. - Philip T. L. C. Clausen:
Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining. - Xiaoyu Guan, Zhongnian Li, Yueying Zhou, Wei Shao, Daoqiang Zhang:
Active learning for efficient analysis of high-throughput nanopore data. - Lulu Yan, Xiaoqiang Sun:
Benchmarking and integration of methods for deconvoluting spatial transcriptomic data. - Correction to: ELIXIR biovalidator for semantic validation of life science metadata.
- Yojana Gadiya, Andrea Zaliani, Philip Gribbon, Martin Hofmann-Apitius:
PEMT: a patent enrichment tool for drug discovery. - Victor Wang, Ardalan Naseri, Shaojie Zhang, Degui Zhi:
Syllable-PBWT for space-efficient haplotype long-match query. - Yujie Wu, Boyu Ren, Prasad Patil:
A pairwise strategy for imputing predictive features when combining multiple datasets. - Riccardo Scandino, Federico Calabrese, Alessandro Romanel:
Synggen: fast and data-driven generation of synthetic heterogeneous NGS cancer data. - Priyanka Rana, Arcot Sowmya, Erik Meijering, Yang Song:
Imbalanced classification for protein subcellular localization with multilabel oversampling. - Zhirui Liao, Lei Xie, Hiroshi Mamitsuka, Shanfeng Zhu:
Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer. - Laura D. T. Vo Ngoc, Randy Osei, Katrin Dohr, Catharina Olsen, Sara Seneca, Alexander Gheldof:
EDIR: exome database of interspersed repeats. - Limin Jiang, Hui Yu, Jijun Tang, Yan Guo:
CoMutDB: the landscape of somatic mutation co-occurrence in cancers. - Swapnil Awasthi, Chia-Yen Chen, Max Lam, Hailiang Huang, Stephan Ripke, C. Anthony Altar:
GWAS quality score for evaluating associated regions in GWAS analyses. - Yuantao Tong, Fanglin Tan, Honglian Huang, Zeyu Zhang, Hui Zong, Yujia Xie, Danqi Huang, Shiyang Cheng, Ziyi Wei, Meng Fang, M. James C. Crabbe, Ying Wang, Xiaoyan Zhang:
ViMRT: a text-mining tool and search engine for automated virus mutation recognition. - Zhili Qiao, Elle Barnes, Susannah Tringe, Daniel P. Schachtman, Peng Liu:
Poisson hurdle model-based method for clustering microbiome features. - Thomas Binet, Bérangère Avalle, Miraine Dávila Felipe, Irene Maffucci:
AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures. - Xujun Liang, Ying Fu, Lingzhi Qu, Pengfei Zhang, Yongheng Chen:
Prediction of drug side effects with transductive matrix co-completion. - Timo Lassmann:
SAMStat 2: quality control for next generation sequencing data. - Justas Dapkunas, Mindaugas Margelevicius:
The COMER web server for protein analysis by homology. - Daniel Weilandt, Pierre Salvy, Maria Masid, Georgios Fengos, Robin Denhardt-Erikson, Zhaleh Hosseini, Vassily Hatzimanikatis:
Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models. - Nathan P. Williams, Carlos H. M. Rodrigues, Jia Truong, David B. Ascher, Jessica K. Holien:
DockNet: high-throughput protein-protein interface contact prediction. - Raulia Syrlybaeva, Eva-Maria Strauch:
Deep learning of protein sequence design of protein-protein interactions. - Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga:
Improving dynamic predictions with ensembles of observable models. - Shengquan Chen, Rongxiang Wang, Wenxin Long, Rui Jiang:
ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data. - Zuguang Gu, Daniel Hübschmann:
rGREAT: an R/bioconductor package for functional enrichment on genomic regions. - Max Franz, Christian Tannus Lopes, Dylan Fong, Mike Kucera, Manfred Cheung, Metin Can Siper, Gerardo Huck, Yue Dong, Selçuk Onur Sümer, Gary D. Bader:
Cytoscape.js 2023 update: a graph theory library for visualization and analysis. - Xiyu Peng, Karin S. Dorman:
Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers. - Jia-Juan Tu, Hui-Sheng Li, Hong Yan, Xiao-Fei Zhang:
EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning. - Yang Jiao, Lingkun Gu, Yingtao Jiang, Mo Weng, Mei Yang:
Digitally predicting protein localization and manipulating protein activity in fluorescence images using 4D reslicing GAN. - Jelena Banjac, Norbert Sprenger, Shaillay Kumar Dogra:
Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories. - Jianmei Zhao, Fengcui Qian, Xuecang Li, Zhengmin Yu, Jiang Zhu, Rui Yu, Yue Zhao, Ke Ding, Yanyu Li, Yongsan Yang, Qi Pan, Jiaxin Chen, Chao Song, Qiuyu Wang, Jian Zhang, Guohua Wang, Chunquan Li:
CanMethdb: a database for genome-wide DNA methylation annotation in cancers. - Jiangshan Liang, Luchen Deng, Shize Chen, Yimin Wang, Zongcai Ruan, Lingli Zhang:
Vaa3D-x for cross-platform teravoxel-scale immersive exploration of multidimensional image data. - Wei Chen, Cheng Zhong, Jiajie Peng, Zhongyu Wei:
DxFormer: a decoupled automatic diagnostic system based on decoder-encoder transformer with dense symptom representations. - Elias Ulrich, Stefan M. Pfister, Natalie Jäger:
Revana: a comprehensive tool for regulatory variant analysis and visualization of cancer genomes. - Trevor J. Chan, Xingjian Zhang, Michael Mak:
Biophysical informatics reveals distinctive phenotypic signatures and functional diversity of single-cell lineages. - Xiangning Xue, Wei Zong, Zhiguang Huo, Kyle D. Ketchesin, Madeline R. Scott, Kaitlyn A Petersen, Ryan W. Logan, Marianne L. Seney, Colleen A. Mcclung, George C. Tseng:
DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity. - Marie Denoulet, Mathilde Brulé, François Anquez, Audrey Vincent, Julie Schnipper, Eric Adriaenssens, Robert-Alain Toillon, Xuefen Le Bourhis, Chann Lagadec:
ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR. - George Bouras, Roshan Nepal, Ghais Houtak, Alkis James Psaltis, Peter-John Wormald, Sarah Vreugde:
Pharokka: a fast scalable bacteriophage annotation tool. - Ellie E. Armstrong, Michael G. Campana:
RatesTools: a Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data. - Jaromir Sant, Paul A. Jenkins, Jere Koskela, Dario Spanò:
EWF: simulating exact paths of the Wright-Fisher diffusion. - Lathan Liou, Milena Hornburg, David S. Robertson:
Global FDR control across multiple RNAseq experiments. - Changqing Su, Yuhan Gao, You Zhou, Yaoqi Sun, Chenggang Yan, Haibing Yin, Bo Xiong:
AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting. - Chit Tong Lio, Gordon Grabert, Zakaria Louadi, Amit Fenn, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy:
Systematic analysis of alternative splicing in time course data using Spycone. - Dingquan Yu, Grzegorz Chojnowski, Maria Rosenthal, Jan Kosinski:
AlphaPulldown - a python package for protein-protein interaction screens using AlphaFold-Multimer. - Minsoo Kim, Daniel D. Vo, Michi E. Kumagai, Connor T. Jops, Michael J. Gandal:
GeneticsMakie.jl: a versatile and scalable toolkit for visualizing locus-level genetic and genomic data. - Ciaran M. Welsh, Jin Xu, Lucian P. Smith, Matthias König, Kiri Choi, Herbert M. Sauro:
libRoadRunner 2.0: a high performance SBML simulation and analysis library. - Yekaterina Shulgina, Sean R. Eddy:
Codetta: predicting the genetic code from nucleotide sequence. - Lixin Cheng, Haonan Wu, Xubin Zheng, Ning Zhang, Pengfei Zhao, Ran Wang, Qiong Wu, Tao Liu, Xiaojun Yang, Qingshan Geng:
GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion. - Fandi Wu, Xiaoyang Jing, Xiao Luo, Jinbo Xu:
Improving protein structure prediction using templates and sequence embedding. - Zhuoqing Fang, Xinyuan Liu, Gary Peltz:
GSEApy: a comprehensive package for performing gene set enrichment analysis in Python. - Louis Faure, Ruslan Soldatov, Peter V. Kharchenko, Igor Adameyko:
scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data. - Amelia Villegas-Morcillo, Louis Robinson, Arthur Flajolet, Thomas D. Barrett:
ManyFold: an efficient and flexible library for training and validating protein folding models. - Manon Réau, Nicolas Renaud, Li C. Xue, Alexandre M. J. J. Bonvin:
DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces. - Kristiina Ausmees, Carl Nettelblad:
Achieving improved accuracy for imputation of ancient DNA. - Chen Chen, Xiao Chen, Alex Morehead, Tianqi Wu, Jianlin Cheng:
3D-equivariant graph neural networks for protein model quality assessment. - Aman Agarwal, Li Chen:
DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach. - Sugyun An, Soyeong Jang, Sang-Min Park, Chun-Kyung Lee, Hoon-Min Kim, Kwang-Hyun Cho:
Global stabilizing control of large-scale biomolecular regulatory networks. - Nick Strayer, Siwei Zhang, Lydia Yao, Tess Vessels, Cosmin Adrian Bejan, Ryan S. Hsi, Jana K. Shirey-Rice, Justin M. Balko, Douglas B. Johnson, Elizabeth J. Phillips, Alex Bick, Todd L. Edwards, Digna R. Velez Edwards, Jill M. Pulley, Quinn Stanton Wells, Michael R. Savona, Nancy J. Cox, Dan M. Roden, Douglas M. Ruderfer, Yaomin Xu:
Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs. - Nathan Edwards, Christian Dillard, N. M. Prashant, Liu Hongyu, Mia Yang, Evgenia Ulianova, Anelia Horvath:
SCExecute: custom cell barcode-stratified analyses of scRNA-seq data. - Pengcheng Zeng, Yuanyuan Ma, Zhixiang Lin:
scAWMV: an adaptively weighted multi-view learning framework for the integrative analysis of parallel scRNA-seq and scATAC-seq data. - Samantha Petti, Nicholas Bhattacharya, Roshan Rao, Justas Dauparas, Neil Thomas, Juannan Zhou, Alexander M. Rush, Peter K. Koo, Sergey Ovchinnikov:
End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. - Matteo Calgaro, Chiara Romualdi, Davide Risso, Nicola Vitulo:
benchdamic: benchmarking of differential abundance methods for microbiome data. - Jimeng Lei, Zongheng Cai, Xinyi He, Wanting Zheng, Jianxiao Liu:
An approach of gene regulatory network construction using mixed entropy optimizing context-related likelihood mutual information. - Jiaqian Yan, Ming Ma, Zhenhua Yu:
bmVAE: a variational autoencoder method for clustering single-cell mutation data. - José Pinto, Rafael S. Costa, Leonardo Alexandre, João Ramos, Rui Oliveira:
SBML2HYB: a Python interface for SBML compatible hybrid modeling. - Ross J. Burton, Simone M. Cuff, Matt P. Morgan, Andreas Artemiou, Matthias Eberl:
GeoWaVe: geometric median clustering with weighted voting for ensemble clustering of cytometry data. - Déborah Caucheteur, Zoë May Pendlington, Paola Roncaglia, Julien Gobeill, Luc Mottin, Nicolas Matentzoglu, Donat Agosti, David Osumi-Sutherland, Helen E. Parkinson, Patrick Ruch:
COVoc and COVTriage: novel resources to support literature triage. - Minhyuk Park, Stefan Ivanovic, Gillian Chu, Chengze Shen, Tandy J. Warnow:
UPP2: fast and accurate alignment of datasets with fragmentary sequences. - Zutan Li, Yuan Zhang, Jingya Fang, Zhihui Xu, Hao Zhang, Minfang Mao, Yuanyuan Chen, Liangyun Zhang, Cong Pian:
NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways. - Jessica A. Lavery, Samantha Brown, Michael Curry, Axel Martin, Daniel D. Sjoberg, Karissa Whiting:
A data processing pipeline for the AACR project GENIE biopharma collaborative data with the {genieBPC} R package. - Théophile Sanchez, Erik Madison Bray, Pierre Jobic, Jérémy Guez, Anne-Catherine Letournel, Guillaume Charpiat, Jean Cury, Flora Jay:
dnadna: a deep learning framework for population genetics inference. - Elisabeth Coudert, Sebastien Gehant, Edouard De Castro, Monica Pozzato, Delphine Baratin, Teresa Batista Neto, Christian J. A. Sigrist, Nicole Redaschi, Alan J. Bridge, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Béatrice A. Cuche, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Manuela Pruess, Catherine Rivoire, Karin Sonesson, Shyamala Sundaram, Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Hema Bye-A-Jee, Austra Cukura, Paul Denny, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Alok Mishra, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James D. Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang:
Annotation of biologically relevant ligands in UniProtKB using ChEBI. - Yiming Li, Min Zeng, Fuhao Zhang, Fang-Xiang Wu, Min Li:
DeepCellEss: cell line-specific essential protein prediction with attention-based interpretable deep learning. - James T. Robinson, Helga Thorvaldsdóttir, Douglass Turner, Jill P. Mesirov:
igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV).
Volume 39, Number 2, February 2023
- Andy Lin, Brooke L. Deatherage Kaiser, Janine R. Hutchison, Jeffrey A. Bilmes, William Stafford Noble:
MS1Connect: a mass spectrometry run similarity measure. - Xiang Cheng, Md Amanullah, Weigang Liu, Yi Liu, Xiaoqing Pan, Honghe Zhang, Haiming Xu, Pengyuan Liu, Yan Lu:
WMDS.net: a network control framework for identifying key players in transcriptome programs. - Kun Zhu, Hong Su, Zhenling Peng, Jianyi Yang:
A unified approach to protein domain parsing with inter-residue distance matrix. - Piotr Klukowski, Roland Riek, Peter Güntert:
NMRtist: an online platform for automated biomolecular NMR spectra analysis. - Xabier Rey-Barreiro, Alejandro F. Villaverde:
Benchmarking tools for a priori identifiability analysis. - Yunhe Wang, Zhuohan Yu, Shaochuan Li, Chuang Bian, Yanchun Liang, Ka-Chun Wong, Xiangtao Li:
scBGEDA: deep single-cell clustering analysis via a dual denoising autoencoder with bipartite graph ensemble clustering. - Erwan Moreau:
Literature-based discovery: addressing the issue of the subpar evaluation methodology. - Dan Guo, Melanie Christine Föll, Kylie A. Bemis, Olga Vitek:
A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images. - Samuel Neuenschwander, Diana I Cruz Dávalos, Lucas Anchieri, Bárbara Sousa da Mota, Davide Bozzi, Simone Rubinacci, Olivier Delaneau, Simon Rasmussen, Anna-Sapfo Malaspinas:
Mapache: a flexible pipeline to map ancient DNA. - Aman Agarwal, Fengdi Zhao, Yuchao Jiang, Li Chen:
TIVAN-indel: a computational framework for annotating and predicting non-coding regulatory small insertions and deletions. - Julien St-Pierre, Karim Oualkacha, Sahir Rai Bhatnagar:
Efficient penalized generalized linear mixed models for variable selection and genetic risk prediction in high-dimensional data. - Martin Kern, Sabrina Jaeger-Honz, Falk Schreiber, Björn Sommer:
APL@voro - interactive visualization and analysis of cell membrane simulations. - Daniel Chang, Vinod K. Gupta, Benjamin Hur, Kevin Cunningham, Jaeyun Sung:
GMWI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling. - Abhijit Mondal, Luiz Thibério Rangel, Jack G. Payette, Gregory Fournier, Mukul S. Bansal:
DaTeR: error-correcting phylogenetic chronograms using relative time constraints. - Christopher A. Mancuso, Renming Liu, Arjun Krishnan:
PyGenePlexus: a Python package for gene discovery using network-based machine learning. - Dhoha Abid, Michael R. Brent:
NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration. - Alexandru Oarga, Bridget Bannerman, Jorge Júlvez:
CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities. - CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells.
- Andrew Dickson, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad:
GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations. - Yan Zhu, Yuhuan Zhou, Yang Liu, Xuan Wang, Junyi Li:
SLGNN: synthetic lethality prediction in human cancers based on factor-aware knowledge graph neural network. - Jun Wen, Xiang Zhang, Everett Neil Rush, Vidul Ayakulangara Panickan, Xingyu Li, Tianrun Cai, Doudou Zhou, Yuk-Lam Ho, Lauren Costa, Edmon Begoli, Chuan Hong, J. Michael Gaziano, Kelly Cho, Junwei Lu, Katherine P. Liao, Marinka Zitnik, Tianxi Cai:
Multimodal representation learning for predicting molecule-disease relations. - Kangwei Wang, Zhengwei Li, Zhu-Hong You, Pengyong Han, Ru Nie:
Adversarial dense graph convolutional networks for single-cell classification. - Xinyi Yu, Jiashun Xiao, Mingxuan Cai, Yuling Jiao, Xiang Wan, Jin Liu, Can Yang:
PALM: a powerful and adaptive latent model for prioritizing risk variants with functional annotations. - Dennis Hecker, Fatemeh Behjati-Ardakani, Alexander Karollus, Julien Gagneur, Marcel H. Schulz:
The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data. - Pooya Borzou, Jafar Ghaisari, Iman Izadi, Yasin Eshraghi, Yousof Gheisari:
A novel strategy for dynamic modeling of genome-scale interaction networks. - Yanlei Kang, Arne Elofsson, Yunliang Jiang, Weihong Huang, Minzhe Yu, Zhong Li:
AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network. - Limin Li, Yameng Zhao, Huiran Li, Shuqin Zhang:
BLTSA: pseudotime prediction for single cells by branched local tangent space alignment. - Yang Hua, Xiaoning Song, Zhenhua Feng, Xiaojun Wu:
MFR-DTA: a multi-functional and robust model for predicting drug-target binding affinity and region. - Anton Zhiyanov, Narek Engibaryan, Stepan A. Nersisyan, Maxim U. Shkurnikov, Alexander G. Tonevitsky:
Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer. - Weijie Zhang, Yichu Shan, Lili Zhao, Zhen Liang, Chao Liu, Lihua Zhang, Yukui Zhang:
ComMap: a software to perform large-scale structure-based mapping for cross-linking mass spectrometry. - Santiago Marco-Sola, Jordan M. Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, Miquel Moretó:
Optimal gap-affine alignment in O(s) space. - John H. Morris, Karthik Soman, Rabia E. Akbas, Xiaoyuan Zhou, Brett Smith, Elaine C. Meng, Conrad C. Huang, Gabriel Cerono, Gundolf Schenk, Angela Rizk-Jackson, Adil Harroud, Lauren M. Sanders, Sylvain V. Costes, Krish Bharat, Arjun Chakraborty, Alexander R. Pico, Taline Mardirossian, Michael J. Keiser, Alice Tang, Josef Hardi, Yongmei Shi, Mark A. Musen, Sharat Israni, Sui Huang, Peter W. Rose, Charlotte A. Nelson, Sergio E. Baranzini:
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. - Dylan Feldner-Busztin, Panos Firbas Nisantzis, Shelley Jane Edmunds, Gergely Boza, Fernando Racimo, Shyam Gopalakrishnan, Morten Tønsberg Limborg, Leo Lahti, Gonzalo G. de Polavieja:
Dealing with dimensionality: the application of machine learning to multi-omics data. - Lu Chen, Liang Yu, Lin Gao:
Potent antibiotic design via guided search from antibacterial activity evaluations. - Seyed Amir Malekpour, Maryam Shahdoust, Rosa Aghdam, Mehdi Sadeghi:
wpLogicNet: logic gate and structure inference in gene regulatory networks. - Rockwell J. Weiner, Chirag M. Lakhani, David A. Knowles, Gamze Gürsoy:
LDmat: efficiently queryable compression of linkage disequilibrium matrices. - Paola Stolfi, Andrea Mastropietro, Giuseppe Pasculli, Paolo Tieri, Davide Vergni:
NIAPU: network-informed adaptive positive-unlabeled learning for disease gene identification. - Zhi Jin, Tingfang Wu, Taoning Chen, Deng Pan, Xuejiao Wang, Jingxin Xie, Lijun Quan, Qiang Lyu:
CAPLA: improved prediction of protein-ligand binding affinity by a deep learning approach based on a cross-attention mechanism. - Sehi L'Yi, Mark S. Keller, Ariaki Dandawate, Len Taing, Chen-Hao Chen, Myles Brown, Clifford A. Meyer, Nils Gehlenborg:
Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data. - Ziqi Chen, Baoyi Zhang, Hongyu Guo, Prashant S. Emani, Trevor Clancy, Chongming Jiang, Mark Gerstein, Xia Ning, Chao Cheng, Martin Renqiang Min:
Binding peptide generation for MHC Class I proteins with deep reinforcement learning. - Correction to: HOMELETTE: a unified interface to homology modelling software.
- Leopold Weidner, Daniel Hemmler, Michael Rychlik, Philippe Schmitt-Kopplin:
DBDIpy: a Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry. - Weiheng Liao, Xuelian Zhang:
Patpat: a public proteomics dataset search framework. - Martin C. Frith, Jim Shaw, John L. Spouge:
How to optimally sample a sequence for rapid analysis. - Zhongliang Zhou, Wayland Yeung, Nathan Gravel, Mariah Salcedo, Saber Soleymani, Sheng Li, Natarajan Kannan:
Phosformer: an explainable transformer model for protein kinase-specific phosphorylation predictions.
Volume 39, Number 3, March 2023
- Adam Streck, Tom L. Kaufmann, Roland F. Schwarz:
SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity. - Elisabet Munté, Lidia Feliubadaló, Marta Pineda, Eva Tornero, Maribel González, José Marcos Moreno-Cabrera, Carla Roca, Joan Bales Rubio, Laura Arnaldo, Gabriel Capellá, Jose Luis Mosquera, Conxi Lázaro:
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines. - Zhourun Wu, Mingyue Guo, Xiaopeng Jin, Junjie Chen, Bin Liu:
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction. - Arya R. Massarat, Michael Lamkin, Ciara Reeve, Amy L. Williams, Matteo D'Antonio, Melissa Gymrek:
Haptools: a toolkit for admixture and haplotype analysis. - Bianca A. Buchner, Tom J. Clement, Daan H. de Groot, Jürgen Zanghellini:
ecmtool: fast and memory-efficient enumeration of elementary conversion modes. - Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun:
VirBot: an RNA viral contig detector for metagenomic data. - Correction to: Improving annotation propagation on molecular networks through random walks: introducing ChemWalker.
- Xuhua Yan, Ruiqing Zheng, Fang-Xiang Wu, Min Li:
CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity. - Vladimir Porokhin, Li-Ping Liu, Soha Hassoun:
Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products. - Bin Huang, Tingwen Fan, Kaiyue Wang, Haicang Zhang, Chungong Yu, Shuyu Nie, Yangshuo Qi, Wei-Mou Zheng, Jian Han, Zheng Fan, Shiwei Sun, Sheng Ye, Huaiyi Yang, Dongbo Bu:
Accurate and efficient protein sequence design through learning concise local environment of residues. - Sanjay Kumar Srikakulam, Sebastian Keller, Fawaz Dabbaghie, Robert Bals, Olga V. Kalinina:
MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants. - Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, Ilana Barzilai, Onit Alalouf, Yuval Ebenstein, Yoav Shechtman:
DeepOM: single-molecule optical genome mapping via deep learning. - Amy Glen, Chunyu Ma, Luis Mendoza, Finn Womack, E. C. Wood, Meghamala Sinha, Liliana Acevedo, Lindsey G. Kvarfordt, Ross C. Peene, Shaopeng Liu, Andrew S. Hoffman, Jared C. Roach, Eric W. Deutsch, Stephen A. Ramsey, David Koslicki:
ARAX: a graph-based modular reasoning tool for translational biomedicine. - Tiago Cabral Borelli, Gabriel Santos Arini, Luís G. P. Feitosa, Pieter C. Dorrestein, Norberto Peporine Lopes, Ricardo Roberto da Silva:
Improving annotation propagation on molecular networks through random walks: introducing ChemWalker. - Qizhi Li, Xubin Zheng, Jize Xie, Ran Wang, Mengyao Li, Man Hon Wong, Kwong-Sak Leung, Shuai Li, Qingshan Geng, Lixin Cheng:
bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks. - Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B. Gasser, Anthony W. Purcell, Tatsuya Akutsu, Geoffrey I. Webb, Seiya Imoto, Jiangning Song:
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. - Weiming He, Jian Yang, Yi Jing, Lian Xu, Kang Yu, Xiaodong Fang:
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes. - Andrei Dmitrenko, Michelle Reid, Nicola Zamboni:
Regularized adversarial learning for normalization of multi-batch untargeted metabolomics data. - Correction to: On the feasibility of deep learning applications using raw mass spectrometry data.
- Correction to: SVJedi: genotyping structural variations with long reads.
- Sebastian Deorowicz, Agnieszka Danek, Heng Li:
AGC: compact representation of assembled genomes with fast queries and updates. - William Haese-Hill, Kathryn Crouch, Thomas D. Otto:
peaks2utr: a robust Python tool for the annotation of 3′ UTRs. - Huixi Zou, Tianli Sun, Bangqun Jin, Shengqin Wang:
sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome. - Jiawei Wu, Qingrui Liu, Min Li, Jiliang Xu, Chen Wang, Junyin Zhang, Minfeng Xiao, Yannan Bin, Junfeng Xia:
PhaGAA: an integrated web server platform for phage genome annotation and analysis. - Anupam Gautam, Wenhuan Zeng, Daniel H. Huson:
MeganServer: facilitating interactive access to metagenomic data on a server. - Zehao Xiong, Jiawei Luo, Wanwan Shi, Ying Liu, Zhongyuan Xu, Bo Wang:
scGCL: an imputation method for scRNA-seq data based on graph contrastive learning. - Gandhar Mahadeshwar, Rafael de Cesaris Araujo Tavares, Han Wan, Zion R. Perry, Anna Marie Pyle:
RSCanner: rapid assessment and visualization of RNA structure content. - Correction to: SBbadger: biochemical reaction networks with definable degree distributions.
- Correction to: Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome.
- Zhongshen Li, Junru Jin, Yu Wang, Wentao Long, Yuanhao Ding, Haiyan Hu, Leyi Wei:
ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides. - João Paulo Pereira Zanetti, Lucas Peres Oliveira, Leonid Chindelevitch, João Meidanis:
Generalizations of the genomic rank distance to indels. - Matti Pirinen:
linemodels: clustering effects based on linear relationships. - Rudolf T. Pillich, Jing Chen, Christopher Churas, Dylan Fong, Benjamin M. Gyori, Trey Ideker, Klas Karis, Sophie N. Liu, Keiichiro Ono, Alexander R. Pico, Dexter Pratt:
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. - Chirag Jain:
Coverage-preserving sparsification of overlap graphs for long-read assembly. - Iñaki Amatria-Barral, Jorge González-Domínguez, Juan Touriño:
PATO: genome-wide prediction of lncRNA-DNA triple helices. - Siebren Frölich, Maarten van der Sande, Tilman Schäfers, Simon J. van Heeringen:
genomepy: genes and genomes at your fingertips. - Karel J. van der Weg, Holger Gohlke:
TopEnzyme: a framework and database for structural coverage of the functional enzyme space. - Mohan Rakesh, Hélène Vézina, Catherine Laprise, Ellen E. Freeman, Kelly M. Burkett, Marie-Hélène Roy-Gagnon:
GENLIB: new function to simulate haplotype transmission in large complex genealogies. - Ludwig Geistlinger, Roger Vargas, Tyrone Lee, Joshua Pan, Edward L. Huttlin, Robert Gentleman:
BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions. - Jian Cheng, Christian Maltecca, Paul M. Vanraden, Jeffrey R. O'Connell, Li Ma, Jicai Jiang:
SLEMM: million-scale genomic predictions with window-based SNP weighting. - Omid Rohanian, Mohammadmahdi Nouriborji, Samaneh Kouchaki, David A. Clifton:
On the effectiveness of compact biomedical transformers. - Adrien Rougny, Irina Balaur, Augustin Luna, Alexander Mazein:
StonPy: a tool to parse and query collections of SBGN maps in a graph database. - Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Roger J. Daly, Jiangning Song:
Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. - Oleksandr Khoroshevskyi, Nathan Leroy, Vincent P. Reuter, Nathan C. Sheffield:
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA.
Volume 39, Number 4, April 2023
- Mingqian Zhang, Wenke Zhang, Yuzhu Chen, Jin Zhao, Shunyao Wu, Xiaoquan Su:
Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes. - Charles Tapley Hoyt, Amelia L. Hoyt, Benjamin M. Gyori:
Prediction and curation of missing biomedical identifier mappings with Biomappings. - Bansho Masutani, Riki Kawahara, Shinichi Morishita:
Decomposing mosaic tandem repeats accurately from long reads. - Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek:
Boolean network sketches: a unifying framework for logical model inference. - Correction to: Multi-omic integration by machine learning (MIMaL).
- Jing Xu, Aidi Zhang, Fang Liu, Xiujun Zhang:
STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data. - Jean-Pierre Borg, Jacques Colinge, Patrice Ravel:
Modular response analysis reformulated as a multilinear regression problem. - Correction to: Continuous chromatin state feature annotation of the human epigenome.
- Xiaoliang Ren, Yanwen Shao, Yiwen Zhang, Ying Ni, Yu Bi, Runsheng Li:
Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping. - Steven R. Shave, John C. Dawson, Abdullah M. Athar, Cuong Q. Nguyen, Richard Kasprowicz, Neil O. Carragher:
Phenonaut: multiomics data integration for phenotypic space exploration. - Lukas Heumos, Philipp Ehmele, Luis Kuhn Cuellar, Kevin Menden, Edmund Miller, Steffen Lemke, Gisela Gabernet, Sven Nahnsen:
mlf-core: a framework for deterministic machine learning. - Sheng Fu, Lu Deng, Han Zhang, William Wheeler, Jing Qin, Kai Yu:
Integrative analysis of individual-level data and high-dimensional summary statistics. - Michael Shaffer, Mikayla A. Borton, Ben Bolduc, José P. Faria, Rory M. Flynn, Parsa Ghadermazi, Janaka N. Edirisinghe, Elisha M. Wood-Charlson, Christopher S. Miller, Siu Hung Joshua Chan, Matthew B. Sullivan, Christopher S. Henry, Kelly C. Wrighton:
kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase. - Sean Upchurch, Emilio Palumbo, Jeremy Adams, David Bujold, Guillaume Bourque, Jared Nedzel, Keenan Graham, Meenakshi S. Kagda, Pedro Assis, Benjamin C. Hitz, Emilio Righi, Roderic Guigó, Barbara J. Wold, Alvis Brazma, Julia Burchard, Joe Capka, Michael Cherry, Laura Clarke, Brian Craft, Manolis Dermitzakis, Mark Diekhans, John Dursi, Michael Sean Fitzsimons, Zac Flaming, Romina Garrido, Alfred Gil, Paul Godden, Matt Green, Mitch Guttman, Brian Haas, Max Haeussler, Bo Li, Sten Linnarsson, Adam Lipski, David Liu, Simonne Longerich, David Lougheed, Jonathan Manning, John C. Marioni, Christopher Meyer, Stephen B. Montgomery, Alyssa Morrow, Alfonso Muñoz-Pomer Fuentes, Jared L. Nedzel, David Nguyen, Kevin Osborn, Francis Ouellette, Irene Papatheodorou, Dmitri D. Pervouchine, Arun K. Ramani, Jordi Rambla, Bashir Sadjad, David Steinberg, Jeremiah Talkar, Timothy Tickle, Kathy Tzeng, Saman Vaisipour, Sean Watford, Barbara Wold, Zhenyu Zhang, Jing Zhu:
RNAget: an API to securely retrieve RNA quantifications. - Daffodil M. Canson, Aimee L. Davidson, Miguel de la Hoya, Michael T. Parsons, Dylan M. Glubb, Olga Kondrashova, Amanda B. Spurdle:
SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion. - Yuxin Li, Xuhua Liu, Xueyan Jia, Tao Jiang, Jianghao Wu, Qianlong Zhang, Junhuai Li, Xiangning Li, Anan Li:
A high-performance deep-learning-based pipeline for whole-brain vasculature segmentation at the capillary resolution. - Mohamed Reda El Khili, Safyan Aman Memon, Amin Emad:
MARSY: a multitask deep-learning framework for prediction of drug combination synergy scores. - Shani Cohen, Eden Maximof, Shay Rokach, Mor Tadeski, Isana Veksler-Lublinsky:
sInterBase: a comprehensive database of Escherichia coli sRNA-mRNA interactions. - S. Taylor Head, Elizabeth J. Leslie, David J. Cutler, Michael P. Epstein:
POIROT: a powerful test for parent-of-origin effects in unrelated samples leveraging multiple phenotypes. - Hanyi Yu, Fusheng Wang, George Teodoro, Fan Chen, Xiaoyuan Guo, John Nickerson, Jun Kong:
Self-supervised semantic segmentation of retinal pigment epithelium cells in flatmount fluorescent microscopy images. - Gözde Yazici, Burcu Kurt Vatandaslar, Ilknur Aydin Canturk, Fatmagul I Aydinli, Ozge Arici Duz, Emre Karakoç, Bilal Ersen Kerman, Can Alkan:
Identification of protein-protein interaction bridges for multiple sclerosis. - Massimiliano Volpe, Jyotirmoy Das:
methylR: a graphical interface for comprehensive DNA methylation array data analysis. - Shulei Wang:
Multiscale adaptive differential abundance analysis in microbial compositional data. - Marie Mille, Julie Ripoll, Bastien Cazaux, Eric Rivals:
dipwmsearch: a Python package for searching di-PWM motifs. - André L. S. Meirelles, Tahsin M. Kurç, Jun Kong, Renato Ferreira, Joel H. Saltz, George Teodoro:
Effective and efficient active learning for deep learning-based tissue image analysis. - Guy Karlebach, Leigh Carmody, Jagadish Chandrabose Sundaramurthi, Elena Casiraghi, Peter Hansen, Justin T. Reese, Christopher J. Mungall, Giorgio Valentini, Peter N. Robinson:
An expectation-maximization framework for comprehensive prediction of isoform-specific functions. - Altay Yuzeir, David Alejandro Bejarano, Stephan Grein, Jan Hasenauer, Andreas Schlitzer, Jiangyan Yu:
IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line. - Chenyang Dong, Siqi Shen, Sündüz Keles:
AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver. - Fabio Fassetti, Simona E. Rombo, Cristina Serrao:
Discriminative pattern discovery for the characterization of different network populations. - Ke Yan, Yichen Guo, Bin Liu:
PreTP-2L: identification of therapeutic peptides and their types using two-layer ensemble learning framework. - Hannah M. Doherty, George Kritikos, Marco Galardini, Manuel Banzhaf, Danesh Moradigaravand:
ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling. - Can Chen, Scott T. Weiss, Yang-Yu Liu:
Graph convolutional network-based feature selection for high-dimensional and low-sample size data. - Benjamin B. Chu, Seyoon Ko, Jin J. Zhou, Aubrey Jensen, Hua Zhou, Janet S. Sinsheimer, Kenneth Lange:
Multivariate genome-wide association analysis by iterative hard thresholding. - Heather Marriott, Renata Kabiljo, Ahmad Al Khleifat, Richard J. B. Dobson, Ammar Al-Chalabi, Alfredo Iacoangeli:
DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for human next-generation sequencing data. - Signe Skog, Lovisa Örkenby, Unn Kugelberg, Anita Öst, Daniel Nätt:
Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts. - Jonathan D. Ogata, Wancen Mu, Eric S. Davis, Bingjie Xue, J. Chuck Harrell, Nathan C. Sheffield, Douglas H. Phanstiel, Michael I. Love, Mikhail G. Dozmorov:
excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies. - Diana F. Sousa, Francisco M. Couto:
K-RET: knowledgeable biomedical relation extraction system. - Ziang Zhang, Lei Sun:
The hidden factor: accounting for covariate effects in power and sample size computation for a binary trait. - Ruogu Wang, Alex A. Lemus, Colin M. Henneberry, Yiming Ying, Yunlong Feng, Alex M. Valm:
Unmixing biological fluorescence image data with sparse and low-rank Poisson regression. - Tiantian Ye, Yangyang Hu, Sydney Pun, Wenxiu Ma:
HiCube: interactive visualization of multiscale and multimodal Hi-C and 3D genome data. - Elisabetta C. Sciacca, Salvatore Alaimo, Gianmarco Silluzio, Alfredo Ferro, Vito Latora, Costantino Pitzalis, Alfredo Pulvirenti, Myles J. Lewis:
DEGGs: an R package with shiny app for the identification of differentially expressed gene-gene interactions in high-throughput sequencing data. - Yi Liu, Benjamin L. Elsworth, Tom R. Gaunt:
Using language models and ontology topology to perform semantic mapping of traits between biomedical datasets. - Natalia V. Loukachevitch, Suresh Manandhar, Elina Baral, Igor Rozhkov, Pavel Braslavski, Vladimir Ivanov, Tatiana Batura, Elena Tutubalina:
NEREL-BIO: a dataset of biomedical abstracts annotated with nested named entities. - Yuansong Zeng, Zhuoyi Wei, Qianmu Yuan, Sheng Chen, Weijiang Yu, Yutong Lu, Jianzhao Gao, Yuedong Yang:
Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model. - Liangrui Ren, Jun Wang, Zhao Li, Qingzhong Li, Guoxian Yu:
scMCs: a framework for single-cell multi-omics data integration and multiple clusterings. - Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li:
Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration. - René Staritzbichler, Nikola Ristic, Tülin Stapke, Peter W. Hildebrand:
SmoothT - a server constructing low-energy pathways from conformational ensembles for interactive visualization and enhanced sampling. - Petr Triska, Fabian Amman, Lukas Endler, Andreas Bergthaler:
WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) - a web application for visualization of wastewater pathogen sequencing results. - Conrad Leonard:
streammd: fast low-memory duplicate marking using a Bloom filter. - Lucas Prates, Renan B. Lemes, Tábita Hünemeier, Florencia G. Leonardi:
Population-based change-point detection for the identification of homozygosity islands. - Richard J. Packer, Alex T. Williams, William Hennah, Micaela T. Eisenberg, Nick Shrine, Katherine A Fawcett, Willow Pearson, Anna L. Guyatt, Ahmed Edris, Edward J. Hollox, Mikko Marttila, Balasubramanya S. Rao, John Raymond Bratty, Louise V. Wain, Frank Dudbridge, Martin D. Tobin:
DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies. - Olivier Mailhot, François Major, Rafael Najmanovich:
The DynaSig-ML Python package: automated learning of biomolecular dynamics-function relationships. - Can (sam) Chen, Jingbo Zhou, Fan Wang, Xue (Steve) Liu, Dejing Dou:
Structure-aware protein self-supervised learning. - Hyunbin Kim, Milot Mirdita, Martin Steinegger:
Foldcomp: a library and format for compressing and indexing large protein structure sets. - Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa:
Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres. - Deliang Bu, Xiao Wang, Qizhai Li:
Summary statistics-based association test for identifying the pleiotropic effects with set of genetic variants. - Saleh Riahi, Jae Hyeon Lee, Taylor Sorenson, Shuai Wei, Sven Jager, Reza Olfati-Saber, Yanfeng Zhou, Anna Park, Maria Wendt, Hervé Minoux, Yu Qiu:
Surface ID: a geometry-aware system for protein molecular surface comparison. - Yi Fang, Xiaoyong Pan, Hong-Bin Shen:
De novodrug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment. - Edin Salkovic, Mohammad Amin Sadeghi, Abdelkader Baggag, Ahmed Gamal Rashed Salem, Halima Bensmail:
OutSingle: a novel method of detecting and injecting outliers in RNA-Seq count data using the optimal hard threshold for singular values. - Min Yang, Bo Qiu, Guo-You He, Jian-Yuan Zhou, Hao-Jie Yu, Yu-Ying Zhang, Yan-Shang Li, Tai-Song Li, Jin-Cheng Guo, Xue-Cang Li, Jian-Jun Xie:
eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species. - Hyun Jae Cho, Mia Shu, Stefan Bekiranov, Chongzhi Zang, Aidong Zhang:
Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment.
Volume 39, Number 5, May 2023
- Yongxin Ji, Jiayu Shang, Xubo Tang, Yanni Sun:
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer. - Ran Wang, Xubin Zheng, Fangda Song, Man Hon Wong, Kwong-Sak Leung, Lixin Cheng:
Deciphering associations between gut microbiota and clinical factors using microbial modules. - Tianqi Wu, Zhiye Guo, Jianlin Cheng:
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer. - Kijin Kim, Kyungmin Park, Seonghyeon Lee, Seung-Hwan Baek, Tae-Hun Lim, Jongwoo Kim, Balachandran Manavalan, Jin-Won Song, Won-Keun Kim:
VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing. - Correction to: wpLogicNet: logic gate and structure inference in gene regulatory networks.
- Zixuan Wang, Shuwen Xiong, Yun Yu, Jiliu Zhou, Yongqing Zhang:
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency. - Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu:
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. - Masaki Tagashira:
ConsAlign: simultaneous RNA structural aligner based on rich transfer learning and thermodynamic ensemble model of alignment scoring. - Correction to: Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data.
- Ambuj Kumar, Burak T. Kaynak, Karin S. Dorman, Pemra Doruker, Robert L. Jernigan:
Predicting allosteric pockets in protein biological assemblages. - Pierre-Aurélien Gilliot, Thomas E. Gorochowski:
Effective design and inference for cell sorting and sequencing based massively parallel reporter assays. - Rui P. Ribeiro, Alejandro Giorgetti:
pyGOMoDo: GPCRs modeling and docking with python. - Linda Grob, Anne Bertolini, Matteo Carrara, Ulrike Lischetti, Aizhan Tastanova, Christian Beisel, Mitchell P. Levesque, Daniel J. Stekhoven, Franziska Singer:
gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis. - Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List:
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape. - Joung Min Choi, Ming Ji, Layne T. Watson, Liqing Zhang:
DeepMicroGen: a generative adversarial network-based method for longitudinal microbiome data imputation. - Weiyan Zhang, Chuang Chen, Jiacheng Wang, Jingping Liu, Tong Ruan:
A co-adaptive duality-aware framework for biomedical relation extraction. - Alfonso De Falco, Christophe M. Olinger, Barbara Klink, Michel Mittelbronn, Daniel Stieber:
Digital PCR cluster predictor: a universal R-package and shiny app for the automated analysis of multiplex digital PCR data. - Bowen Yang, Minal Khatri, Jinfang Zheng, Jitender S. Deogun, Yanbin Yin:
Genome mining for anti-CRISPR operons using machine learning. - Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani, Martina Ferri, Francesco Sassi, Luca Alessandrì, Dora Tortarolo, Raffaele A. Calogero, Livio Trusolino, Andrea Bertotti, Marco Beccuti, Martina Olivero, Francesca Cordero:
CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. - Roman Martin, Minh Kien Nguyen, Nick Lowack, Dominik Heider:
ODNA: identification of organellar DNA by machine learning. - Pétur Helgi Einarsson, Páll Melsted:
BUSZ: compressed BUS files. - Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj:
A framework for high-throughput sequence alignment using real processing-in-memory systems. - Wouter De Coster, Rosa Rademakers:
NanoPack2: population-scale evaluation of long-read sequencing data. - Yiyan Yang, Xiaofang Jiang:
Evolink: a phylogenetic approach for rapid identification of genotype-phenotype associations in large-scale microbial multispecies data. - Kyle Ferchen, Nathan Salomonis, H. Leighton Grimes:
pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells. - Lucas Robidou, Pierre Peterlongo:
fimpera: drastic improvement of Approximate Membership Query data-structures with counts. - Florin C. Walter, Oliver Stegle, Britta Velten:
FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution. - Francesco Monti, David Stewart, Anuradha Surendra, Irina Alecu, Thao Nguyen-Tran, Steffany A. L. Bennett, Miroslava Cuperlovic-Culf:
Signed Distance Correlation (SiDCo): an online implementation of distance correlation and partial distance correlation for data-driven network analysis. - Lingyu Li, Liangjie Sun, Guangyi Chen, Chi-Wing Wong, Wai-Ki Ching, Zhi-Ping Liu:
LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data. - Correction to: Integrative analysis of individual-level data and high-dimensional summary statistics.
- Eric S. Davis, Wancen Mu, Stuart Lee, Mikhail G. Dozmorov, Michael I. Love, Douglas H. Phanstiel:
matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling. - Niklas Philipp, Cedric K. Brinkmann, Jens Georg, Daniel Schindler, Bork A Berghoff:
DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria. - Boyan Zhou, Huilin Li:
STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data. - Thomas Büchler, Jannik Olbrich, Enno Ohlebusch:
Efficient short read mapping to a pangenome that is represented by a graph of ED strings. - Bin Wang, Kun Liu, Yaohang Li, Jianxin Wang:
DFHiC: a dilated full convolution model to enhance the resolution of Hi-C data. - Michal Zurkowski, Maciej Antczak, Marta Szachniuk:
High-quality, customizable heuristics for RNA 3D structure alignment. - Daniel Krefl, Alessandro Brandulas Cammarata, Sven Bergmann:
PascalX: a Python library for GWAS gene and pathway enrichment tests. - Sébastien Guizard, Katarzyna Miedzinska, Jacqueline Smith, Jonathan Smith, Richard I. Kuo, Megan Davey, Alan L. Archibald, Mick Watson:
nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing. - Alessio Del Conte, Alexander Miguel Monzon, Damiano Clementel, Giorgia F. Camagni, Giovanni Minervini, Silvio C. E. Tosatto, Damiano Piovesan:
RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics. - Dakota Y. Hawkins, Daniel T. Zuch, James Huth, Nahomie Rodriguez-Sastre, Kelley R. McCutcheon, Abigail Glick, Alexandra T. Lion, Christopher F. Thomas, Abigail E. Descoteaux, William Evan Johnson, Cynthia A Bradham:
ICAT: a novel algorithm to robustly identify cell states following perturbations in single-cell transcriptomes. - Ayush Noori, Michelle M. Li, Amelia L. M. Tan, Marinka Zitnik:
Metapaths: similarity search in heterogeneous knowledge graphs via meta-paths. - Julian Dosch, Holger Bergmann, Vinh Tran, Ingo Ebersberger:
FAS: assessing the similarity between proteins using multi-layered feature architectures. - Joshua A. M. Kaste, Yair Shachar-Hill:
Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling. - Jinjuan Wang, Mingya Long, Qizhai Li:
A maximum kernel-based association test to detect the pleiotropic genetic effects on multiple phenotypes. - Artyom A. Egorov, Gemma Catherine Atkinson:
uORF4u: a tool for annotation of conserved upstream open reading frames. - Tanja Holstein, Franziska Kistner, Lennart Martens, Thilo Muth:
PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores. - Nicholas A. G. Johnson, Liezel Tamon, Xin Liu, Aleksandr B. Sahakyan:
ROptimus: a parallel general-purpose adaptive optimization engine. - Robin Paul, Jian Wang, Colleen Reilly, Edgar Sioson, Jaimin Patel, Gavriel Matt, Aleksandar Acic, Xin Zhou:
ppBAM: ProteinPaint BAM track for read alignment visualization and variant genotyping. - Camille Juigné, Olivier Dameron, François Moreews, Florence Gondret, Emmanuelle Becker:
Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using semantic web technologies. - Niema Moshiri:
ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data. - Sergio Doria-Belenguer, Alexandros Xenos, Gaia Ceddia, Noël Malod-Dognin, Natasa Przulj:
A functional analysis of omic network embedding spaces reveals key altered functions in cancer. - Marie Macnee, Eduardo Pérez-Palma, Tobias Brünger, Chiara Klöckner, Konrad Platzer, Arthur Stefanski, Ludovica Montanucci, Allan Bayat, Maximilian Radtke, Ryan L. Collins, Michael E. Talkowski, Daniel Blankenberg, Rikke S. Møller, Johannes R. Lemke, Michael Nothnagel, Patrick May, Dennis Lal:
CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online. - Anjali Silva, Xiaoke Qin, Steven J. Rothstein, Paul D. McNicholas, Sanjeena Subedi:
Finite mixtures of matrix variate Poisson-log normal distributions for three-way count data. - Kimberly A. Dill-McFarland, Kiana Mitchell, Sashank Batchu, Richard Max Segnitz, Basilin Benson, Tomasz Janczyk, Madison S. Cox, Harriet Mayanja-Kizza, William Henry Boom, Penelope Benchek, Catherine M. Stein, Thomas R. Hawn, Matthew C. Altman:
Kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data. - Axel Schmidt, Sebastian Röner, Karola Mai, Hannah Klinkhammer, Martin Kircher, Kerstin U. Ludwig:
Predicting the pathogenicity of missense variants using features derived from AlphaFold2. - Mengbo Li, Gordon K. Smyth:
Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics. - Jinxian Wang, Jihong Guan, Shuigeng Zhou:
Molecular property prediction by contrastive learning with attention-guided positive sample selection. - Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen, Zhiyong Lu:
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. - Wancen Mu, Eric S. Davis, Stuart Lee, Mikhail G. Dozmorov, Douglas H. Phanstiel, Michael I. Love:
bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing. - Yunxiang Li, Yumeng Wei, Sheng Xu, Qingxiong Tan, Licheng Zong, Jiuming Wang, Yixuan Wang, Jiayang Chen, Liang Hong, Yu Li:
AcrNET: predicting anti-CRISPR with deep learning. - Ruimin Wang, Miaoshan Lu, Shaowei An, Jinyin Wang, Changbin Yu:
3D-MSNet: a point cloud-based deep learning model for untargeted feature detection and quantification in profile LC-HRMS data. - My-Diem Nguyen Pham, Thanh-Nhan Nguyen, Le Son Tran, Que-Tran Bui Nguyen, Thien-Phuc Hoang Nguyen, Thi Mong Quynh Pham, Hoai-Nghia Nguyen, Hoa Giang, Minh-Duy Phan, Vy Nguyen:
epiTCR: a highly sensitive predictor for TCR-peptide binding. - Xiaobin Zheng, Joseph R. Tran, Yixian Zheng:
CscoreTool-M infers 3D sub-compartment probabilities within cell population. - Szymon Grabowski, Wojciech Bieniecki:
copMEM2: robust and scalable maximum exact match finding. - Piotr Wlodzimierz, Michael Hong, Ian R. Henderson:
TRASH: Tandem Repeat Annotation and Structural Hierarchy. - Xueli Zhang, Lingcong Kong, Shunming Liu, Xiayin Zhang, Xianwen Shang, Zhuoting Zhu, Yu Huang, Shuo Ma, Jason Ha, Katerina V. Kiburg, Chunwen Zheng, Yunyan Hu, Cong Li, Guanrong Wu, Yingying Liang, Mengxia He, Yan Wang, Xiaohe Bai, Danli Shi, Wei Wang, Chi Zhang, Ke Zhao, Haining Yuan, Guang Hu, Yijun Hu, Huiying Liang, Honghua Yu, Lei Zhang, Mingguang He:
EBD: an eye biomarker database. - Xinran Wang, Zeyun Lu, Arjun Bhattacharya, Bogdan Pasaniuc, Nicholas Mancuso:
twas_sim, a Python-based tool for simulation and power analysis of transcriptome-wide association analysis. - Pietro Hiram Guzzi, Ugo Lomoio, Pierangelo Veltri:
GTExVisualizer: a web platform for supporting ageing studies. - Martin Larralde, Georg Zeller:
PyHMMER: a Python library binding to HMMER for efficient sequence analysis.
Volume 39, Number Supplement-1, June 2023
- Yann Ponty, Sushmita Roy:
ISMB/ECCB 2023 proceedings. 1-2 - Christiana N. Fogg, Diane E. Kovats, Martin Vingron:
2023 Outstanding Contributions to ISCB Award: Shoba Ranganathan. 3-4 - Christiana N. Fogg, Diane E. Kovats, Martin Vingron:
2023 ISCB Overton Prize: Jingyi Jessica Li. 5-6 - Christiana N. Fogg, Diane E. Kovats, Martin Vingron:
2023 ISCB innovator award: Dana Pe'er. 7-8 - Christiana N. Fogg, Diane E. Kovats, Martin Vingron:
2023 ISCB accomplishments by a senior scientist award: Mark Gerstein. 9-10 - Thomas Cokelaer, Sarah Cohen-Boulakia, Frédéric Lemoine:
Reprohackathons: promoting reproducibility in bioinformatics through training. 11-20 - Shaojun Pan, Xing-Ming Zhao, Luís Pedro Coelho:
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing. 21-29 - Jiayu Shang, Cheng Peng, Xubo Tang, Yanni Sun:
PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer. 30-39 - Mihir Mongia, Romel Baral, Abhinav Adduri, Donghui Yan, Yudong Liu, Yuying Bian, Paul Kim, Bahar Behsaz, Hosein Mohimani:
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes. 40-46 - Qi Wang, Michael Nute, Todd J. Treangen:
Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities. 47-56 - Wei Wei, Andrew Millward, David Koslicki:
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac. 57-65 - Andrew J. Mikalsen, Jaroslaw Zola:
Coriolis: enabling metagenomic classification on lightweight mobile devices. 66-75 - Jonas C. Ditz, Bernhard Reuter, Nico Pfeifer:
COmic: convolutional kernel networks for interpretable end-to-end learning on (multi-)omics data. 76-85 - Jonas C. Ditz, Jacqueline Wistuba-Hamprecht, Timo Maier, Rolf Fendel, Nico Pfeifer, Bernhard Reuter:
PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction. 86-93 - Aurélien Beaude, Milad Rafiee Vahid, Franck Augé, Farida Zehraoui, Blaise Hanczar:
AttOmics: attention-based architecture for diagnosis and prognosis from omics data. 94-102 - Alperen Dalkiran, Ahmet Atakan, Ahmet Süreyya Rifaioglu, Maria Jesus Martin, Rengül Çetin-Atalay, Aybar C. Acar, Tunca Dogan, Volkan Atalay:
Transfer learning for drug-target interaction prediction. 103-110 - Alice Lacan, Michèle Sebag, Blaise Hanczar:
GAN-based data augmentation for transcriptomics: survey and comparative assessment. 111-120 - Haoting Zhang, Carl Henrik Ek, Magnus Rattray, Marta Milo:
SynBa: improved estimation of drug combination synergies with uncertainty quantification. 121-130 - Eric Lee, Kevin Chern, Michael Nissen, Xuehai Wang, Chris Huang, Anita K. Gandhi, Alexandre Bouchard-Côté, Andrew P. Weng, Andrew Roth:
SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data. 131-139 - Monica T. Dayao, Alexandro Trevino, Honesty Kim, Matthew Ruffalo, H. Blaize D'angio, Ryan Preska, Umamaheswar Duvvuri, Aaron T. Mayer, Ziv Bar-Joseph:
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. 140-148 - Mohammad Al Olaimat, Jared Martinez, Fahad Saeed, Serdar Bozdag:
PPAD: a deep learning architecture to predict progression of Alzheimer's disease. 149-157 - Ke Zhang, Min Wu, Yong Liu, Yimiao Feng, Jie Zheng:
KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality. 158-167 - Leonard Dervishi, Wenbiao Li, Anisa Halimi, Xiaoqian Jiang, Jaideep Vaidya, Erman Ayday:
Privacy preserving identification of population stratification for collaborative genomic research. 168-176 - Siddhant Grover, Alexey Markin, Tavis K. Anderson, Oliver Eulenstein:
Phylogenetic diversity statistics for all clades in a phylogeny. 177-184 - Yasamin Tabatabaee, Chao Zhang, Tandy J. Warnow, Siavash Mirarab:
Phylogenomic branch length estimation using quartets. 185-193 - Hanqing Zhao, Matthijs Leon Souilljee, Pavlos Pavlidis, Nikolaos Alachiotis:
Genome-wide scans for selective sweeps using convolutional neural networks. 194-203 - Ziyun Guang, Matthew Smith-Erb, Layla Oesper:
A weighted distance-based approach for deriving consensus tumor evolutionary trees. 204-212 - Hartmut Häntze, Paul Horton:
Effects of spaced k-mers on alignment-free genotyping. 213-221 - Alexander J. Petri, Kristoffer Sahlin:
isONform: reference-free transcriptome reconstruction from Oxford Nanopore data. 222-231 - Xiang Li, Qian Shi, Ke Chen, Mingfu Shao:
Seeding with minimized subsequence. 232-241 - Marjan Hosseini, Aaron Palmer, William Manka, Patrick G. S. Grady, Venkata Patchigolla, Jinbo Bi, Rachel J. O'Neill, Zhiyi Chi, Derek Aguiar:
Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures. 242-251 - Camille Marchet, Antoine Limasset:
Scalable sequence database search using partitioned aggregated Bloom comb trees. 252-259 - Jarno N. Alanko, Jaakko Vuohtoniemi, Tommi Mäklin, Simon J. Puglisi:
Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes. 260-269 - Sandra Romain, Claire Lemaitre:
SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph. 270-278 - Timofey Prodanov, Vikas Bansal:
A multilocus approach for accurate variant calling in low-copy repeats using whole-genome sequencing. 279-287 - Aniket C. Mane, Mahsa Faizrahnemoon, Tomás Vinar, Brona Brejová, Cédric Chauve:
PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning. 288-296 - Can Firtina, Nika Mansouri-Ghiasi, Joël Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu:
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes. 297-307 - Xiao Chen, Alex Morehead, Jian Liu, Jianlin Cheng:
A gated graph transformer for protein complex structure quality assessment and its performance in CASP15. 308-317 - Frimpong Boadu, Hongyuan Cao, Jianlin Cheng:
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function. 318-325 - Jia-Ning Li, Guang Yang, Peng-Cheng Zhao, Xue-Xin Wei, Jian-Yu Shi:
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties. 326-336 - Md. Mahfuzur Rahaman, Nabila Shahnaz Khan, Shaojie Zhang:
RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families. 337-346 - Alexandru Dumitrescu, Emmi Jokinen, Anja Paatero, Juho Kellosalo, Ville O. Paavilainen, Harri Lähdesmäki:
TSignal: a transformer model for signal peptide prediction. 347-356 - Piyumi R. Amarasinghe, Lloyd Allison, Peter J. Stuckey, Maria Garcia de la Banda, Arthur M. Lesk, Arun Siddharth Konagurthu:
Getting 'ϕψχal' with proteins: minimum message length inference of joint distributions of backbone and sidechain dihedral angles. 357-367 - Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang:
CellBRF: a feature selection method for single-cell clustering using cell balance and random forest. 368-376 - Christopher Hill, Sanjarbek Hudaiberdiev, Ivan Ovcharenko:
ChromDL: a next-generation regulatory DNA classifier. 377-385 - Yanlin Zhang, Mathieu Blanchette:
Reference panel-guided super-resolution inference of Hi-C data. 386-393 - Cassandra Burdziak, Chujun Julia Zhao, Doron Haviv, Direna Alonso-Curbelo, Scott W. Lowe, Dana Pe'er:
scKINETICS: inference of regulatory velocity with single-cell transcriptomics data. 394-403 - Kirti Biharie, Lieke Michielsen, Marcel J. T. Reinders, Ahmed Mahfouz:
Cell type matching across species using protein embeddings and transfer learning. 404-412 - Ali Tugrul Balci, Mark Maher Ebeid, Panayiotis V. Benos, Dennis Kostka, Maria Chikina:
An intrinsically interpretable neural network architecture for sequence-to-function learning. 413-422 - Yueqi Sheng, Boaz Barak, Mor Nitzan:
Robust reconstruction of single-cell RNA-seq data with iterative gene weight updates. 423-430 - Asia Mendelevich, Saumya Gupta, Aleksei Pakharev, Athanasios Teodosiadis, Andrey A. Mironov, Alexander A. Gimelbrant:
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. 431-439 - Vincent Wagner, Nicole Radde:
The impossible challenge of estimating non-existent moments of the Chemical Master Equation. 440-447 - Mogan Gim, Junseok Choe, Seungheun Baek, Jueon Park, Chaeeun Lee, Minjae Ju, Sumin Lee, Jaewoo Kang:
ArkDTA: attention regularization guided by non-covalent interactions for explainable drug-target binding affinity prediction. 448-457 - Enio Gjerga, Isabel S. Naarmann-de Vries, Christoph Dieterich:
Characterizing alternative splicing effects on protein interaction networks with LINDA. 458-464 - Kerr Ding, Sheng Wang, Yunan Luo:
Supervised biological network alignment with graph neural networks. 465-474 - Zhijian Huang, Pan Zhang, Lei Deng:
DeepCoVDR: deep transfer learning with graph transformer and cross-attention for predicting COVID-19 drug response. 475-483 - Mihir Bafna, Hechen Li, Xiuwei Zhang:
CLARIFY: cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics. 484-493 - Sara Mohammad Taheri, Vartika Tewari, Rohan Kapre, Ehsan Rahiminasab, Karen Sachs, Charles Tapley Hoyt, Jeremy Zucker, Olga Vitek:
Optimal adjustment sets for causal query estimation in partially observed biomolecular networks. 494-503 - Addie Woicik, Mingxin Zhang, Hanwen Xu, Sara Mostafavi, Sheng Wang:
Gemini: memory-efficient integration of hundreds of gene networks with high-order pooling. 504-512 - Van-Giang Trinh, Belaid Benhamou, Thomas A. Henzinger, Samuel Pastva:
Trap spaces of multi-valued networks: definition, computation, and applications. 513-522 - Paolo Pellizzoni, Giulia Muzio, Karsten M. Borgwardt:
Higher-order genetic interaction discovery with network-based biological priors. 523-533 - Giulio Ermanno Pibiri, Yoshihiro Shibuya, Antoine Limasset:
Locality-preserving minimal perfect hashing of k-mers. 534-543 - Yasser Mohseni Behbahani, Elodie Laine, Alessandra Carbone:
Deep Local Analysis deconstructs protein-protein interfaces and accurately estimates binding affinity changes upon mutation. 544-552 - Muyu Yang, Jian Ma:
UNADON: transformer-based model to predict genome-wide chromosome spatial position. 553-562 - Tianshuo Zhou, Ning Dai, Sizhen Li, Max Ward, David H. Mathews, Liang Huang:
RNA design via structure-aware multifrontier ensemble optimization. 563-571
Volume 39, Number 8, August 2023
- Tong Xin, Yanan Lv, Haoran Chen, Linlin Li, Lijun Shen, Guangcun Shan, Xi Chen, Hua Han:
A novel registration method for long-serial section images of EM with a serial split technique based on unsupervised optical flow network. - Russell B. Davidson, Mark Coletti, Mu Gao, Bryan Piatkowski, Avinash Sreedasyam, Farhan Quadir, David J. Weston, Jeremy Schmutz, Jianlin Cheng, Jeffrey Skolnick, Jerry M. Parks, Ada Sedova:
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. - Abbi Abdel-Rehim, Oghenejokpeme I. Orhobor, Hang Lou, Hao Ni, Ross D. King:
Protein-ligand binding affinity prediction exploiting sequence constituent homology. - Jennifer Mattock, Marina Martínez-Álvaro, Matthew A Cleveland, Rainer Roehe, Mick Watson:
KOunt: a reproducible KEGG orthologue abundance workflow. - Feifei Wang, Dongzuo Liang, Yang Li, Shuangge Ma:
Prior information-assisted integrative analysis of multiple datasets. - Correction to: Joint registration of multiple point clouds for fast particle fusion in localization microscopy.
- Anna Wierczeiko, Stefan Pastore, Stefan Mündnich, Anne M. Busch, Vincent Dietrich, Mark Helm, Tamer Butto, Susanne Gerber:
NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis. - Evangelos Karatzas, Fotis A. Baltoumas, Eleni Aplakidou, Panagiota I. Kontou, Panos Stathopoulos, Leonidas Stefanis, Pantelis G. Bagos, Georgios A. Pavlopoulos:
Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources. - Longendri Aguilera-Mendoza, Sebastián Ayala-Ruano, Felix Martinez-Rios, Edgar Chávez, César R. García-Jacas, Carlos A. Brizuela, Yovani Marrero-Ponce:
StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks. - Chen Wang, Harikumar Govindarajan, Panagiotis Katsonis, Olivier Lichtarge:
ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis. - Eyal Mazuz, Guy Shtar, Nir Kutsky, Lior Rokach, Bracha Shapira:
Pretrained transformer models for predicting the withdrawal of drugs from the market. - Apurva Kalia, Dilip Krishnan, Soha Hassoun:
CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction. - Kim Philipp Jablonski, Niko Beerenwinkel:
Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression. - Yanli Wang, Zhiye Guo, Jianlin Cheng:
Single-cell Hi-C data enhancement with deep residual and generative adversarial networks. - Ondrej Vavra, Jakub Beránek, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar:
pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. - Gang Wen, Limin Li:
FGCNSurv: dually fused graph convolutional network for multi-omics survival prediction. - Yuliang Pan, Yang Wang, Jihong Guan, Shuigeng Zhou:
PCGAN: a generative approach for protein complex identification from protein interaction networks. - Qunzhuo Wu, Zhaohong Deng, Wei Zhang, Xiaoyong Pan, Kup-Sze Choi, Yun Zuo, Hong-Bin Shen, Dong-Jun Yu:
MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering. - Lucas F. Voges, Lukas C. Jarren, Stephan Seifert:
Exploitation of surrogate variables in random forests for unbiased analysis of mutual impact and importance of features. - Bo-Wei Zhao, Xiao-Rui Su, Peng-Wei Hu, Yu-An Huang, Zhu-Hong You, Lun Hu:
iGRLDTI: an improved graph representation learning method for predicting drug-target interactions over heterogeneous biological information network. - Garrett M. Ginell, Aidan J. Flynn, Alex S. Holehouse:
SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets. - Ziqiao Zhang, Ailin Xie, Jihong Guan, Shuigeng Zhou:
Molecular property prediction by semantic-invariant contrastive learning. - Peng Chen, Jian Wang, Hongfei Lin, Di Zhao, Zhihao Yang:
Few-shot biomedical named entity recognition via knowledge-guided instance generation and prompt contrastive learning. - Alexander Myronov, Giovanni Mazzocco, Paulina Król, Dariusz Plewczynski:
BERTrand - peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing. - Gabriel Cretin, Charlotte Périn, Nicolas Zimmermann, Tatiana Galochkina, Jean-Christophe Gelly:
ICARUS: flexible protein structural alignment based on Protein Units. - Anders Pitman, Xiaomeng Huang, Gabor T. Marth, Yi Qiao:
quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics. - Thaidy Moreno, Joaquin Magana, David A. Quigley:
AARDVARK: an automated reversion detector for variants affecting resistance kinetics. - Md Ashiqur Rahman, Abdullah Aman Tutul, Mahfuza Sharmin, Md. Shamsuzzoha Bayzid:
BEENE: deep learning-based nonlinear embedding improves batch effect estimation. - Babatounde Moctard Oloulade, Jianliang Gao, Jiamin Chen, Raeed Al-Sabri, Zhenpeng Wu:
Cancer drug response prediction with surrogate modeling-based graph neural architecture search. - Dmitry Penzar, Daria Nogina, Elizaveta Noskova, Arsenii Zinkevich, Georgy Meshcheryakov, Andrey Lando, Abdul Muntakim Rafi, Carl G. de Boer, Ivan V. Kulakovskiy:
LegNet: a best-in-class deep learning model for short DNA regulatory regions. - Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Daisuke Kihara:
Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling. - Elena Krismer, Isabell Bludau, Maximilian T. Strauss, Matthias Mann:
AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics. - Jacob I Marsh, Jakob Petereit, Brady A Johnston, Philipp E. Bayer, Cassandria G. Tay Fernandez, Hawlader A Al-Mamun, Jacqueline Batley, David Edwards:
crosshap: R package for local haplotype visualization for trait association analysis. - Sehi Park, Mobeen Ur Rehman, Farman Ullah, Hilal Tayara, Kil To Chong:
iCpG-Pos: an accurate computational approach for identification of CpG sites using positional features on single-cell whole genome sequence data. - Eric H. Au, Christiana Fauci, Yanting Luo, Riley J. Mangan, Daniel A Snellings, Chelsea R. Shoben, Seth Weaver, Shae K. Simpson, Craig B. Lowe:
Gonomics: uniting high performance and readability for genomics with Go. - Davor Orsolic, Tomislav Smuc:
Dynamic applicability domain (dAD): compound-target binding affinity estimates with local conformal prediction. - Philip Hartout, Bojana Pocuca, Celia Méndez-García, Christian Schleberger:
Investigating the human and nonobese diabetic mouse MHC class II immunopeptidome using protein language modeling. - Joshua Barnett, Noori Sotudeh, Poorvi Rao, Jonah Silverman, Tamara Jafar, Liya Wang:
AtlasXplore: a web platform for visualizing and sharing spatial epigenome data. - Jace Webster, Ha X. Dang, Pradeep S. Chauhan, Wenjia Feng, Alex Shiang, Peter K. Harris, Russell K. Pachynski, Aadel A Chaudhuri, Christopher A. Maher:
PACT: a pipeline for analysis of circulating tumor DNA. - Emanuel Cunha, Davide Lagoa, José P. Faria, Filipe Liu, Christopher S. Henry, Oscar Días:
TranSyT, an innovative framework for identifying transport systems. - Chen Li, Xiaoyang Chen, Shengquan Chen, Rui Jiang, Xuegong Zhang:
simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. - Fatemeh Rafiei, Hojjat Zeraati, Karim Abbasi, Jahan B. Ghasemi, Mahboubeh Parsaeian, Ali Masoudi-Nejad:
DeepTraSynergy: drug combinations using multimodal deep learning with transformers. - Mercè Alemany-Chavarria, Jaime Rodríguez-Guerra, Jean-Didier Maréchal:
TALAIA: a 3D visual dictionary for protein structures. - Lena Buck, Tobias Schmidt, Maren Feist, Philipp Schwarzfischer, Dieter Kube, Peter J. Oefner, Helena U. Zacharias, Michael Altenbuchinger, Katja Dettmer, Wolfram Gronwald, Rainer Spang:
Anomaly detection in mixed high-dimensional molecular data. - Benjamin Hepp, Florence Lorieux, Augustin Degaugue, Jacques Oberto:
VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes. - Hans-Ulrich Klein:
demuxmix: demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models. - Serene W. H. Wong, Chiara Pastrello, Max Kotlyar, Christos Faloutsos, Igor Jurisica:
USNAP: fast unique dense region detection and its application to lung cancer. - Yichen Cheng, Yusen Xia, Xinlei Wang:
Bayesian multitask learning for medicine recommendation based on online patient reviews. - Ruohua Shi, Keyan Bi, Kai Du, Lei Ma, Fang Fang, Lingyu Duan, Tingting Jiang, Tie-Jun Huang:
PS-Net: human perception-guided segmentation network for EM cell membrane. - Martin Wegner, Manuel Kaulich:
ReCo: automated NGS re ad- co unting of single and combinatorial CRISPR gRNAs. - Xuhua Yan, Ruiqing Zheng, Jinmiao Chen, Min Li:
scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization. - Jianwen Fang:
Predicting thermostability difference between cellular protein orthologs. - Göksel Misirli:
libSBOLj3: a graph-based library for design and data exchange in synthetic biology. - Kynon J. M. Benjamin, Tarun Katipalli, Apuã C. M. Paquola:
dRFEtools: dynamic recursive feature elimination for omics. - Amir Feizi, Kamalika Ray:
otargen: GraphQL-based R package for tidy data accessing and processing from Open Targets Genetics. - Anton Zadorozhny, Anton Smirnov, Dmitry Filimonov, Alexey Lagunin:
Prediction of pathogenic single amino acid substitutions using molecular fragment descriptors. - Daniel Liu, Martin Steinegger:
Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices. - Daniel-T. Rademaker, Kevin J. van Geemen, Li C. Xue:
GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations. - Giovanni Madeo, Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio:
CoCoNat: a novel method based on deep learning for coiled-coil prediction. - Hamza Chegraoui, Vincent Guillemot, Amine Rebei, Arnaud Gloaguen, Jacques Grill, Cathy Philippe, Vincent Frouin:
Integrating multiomics and prior knowledge: a study of the Graphnet penalty impact. - Hyeongseon Jeon, Kyu-Sang Lim, Yet Nguyen, Dan Nettleton:
Adjusting for gene-specific covariates to improve RNA-seq analysis. - Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu:
Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. - Andrea Mastropietro, Gianluca De Carlo, Aris Anagnostopoulos:
XGDAG: explainable gene-disease associations via graph neural networks. - Marteinn T. Hardarson, Gunnar Palsson, Bjarni V. Halldórsson:
NCOurd: modelling length distributions of NCO events and gene conversion tracts. - Minghao Yang, Zhi-An Huang, Wei Zhou, Junkai Ji, Jun Zhang, Shan He, Zexuan Zhu:
MIX-TPI: a flexible prediction framework for TCR-pMHC interactions based on multimodal representations. - Bing-Xue Du, Yahui Long, Xiaoli Li, Min Wu, Jian-Yu Shi:
CMMS-GCL: cross-modality metabolic stability prediction with graph contrastive learning. - Richard Wilton, Alexander S. Szalay:
Short-read aligner performance in germline variant identification. - Guangzhi Xiong, Stefan Bekiranov, Aidong Zhang:
ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq. - Jack R. Leary, Yi Xu, Ashley B. Morrison, Chong Jin, Emily C. Shen, Peyton C. Kuhlers, Ye Su, Naim U. Rashid, Jen Jen Yeh, Xianlu Laura Peng:
Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing. - Zhenhuan Feng, Peiyang Fang, Hui Zheng, Xiaofei Zhang:
DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data. - Chen Yang, Jiahao Mai, Xuan Cao, Aaron Burberry, Fabio Cominelli, Liangliang Zhang:
ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization.
Volume 39, Number 9, September 2023
- Hui Yu, Limin Jiang, Chung-I Li, Scott Ness, Sara G. M. Piccirillo, Yan Guo:
Somatic mutation effects diffused over microRNA dysregulation. - Lechuan Li, Ruth Dannenfelser, Yu Zhu, Nathaniel Hejduk, Santiago Segarra, Vicky Yao:
Joint embedding of biological networks for cross-species functional alignment. - Matthew D. Smith, Marshall A Case, Emily K. Makowski, Peter M. Tessier:
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data. - Pin Lyu, Yijie Zhai, Taibo Li, Jiang Qian:
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server. - Jeffrey M. Dick, Xun Kang:
chem16S: community-level chemical metrics for exploring genomic adaptation to environments. - Correction to: Python interfaces for the Smoldyn simulator.
- Jun Young Park, Jang Jae Lee, Younghwa Lee, Dongsoo Lee, Jungsoo Gim, Lindsay A. Farrer, Kun Ho Lee, Sungho Won:
Machine learning-based quantification for disease uncertainty increases the statistical power of genetic association studies. - Xin He, Xianhui Huang, Yuexuan Long, Zhenping Liu, Xing Chang, Xianlong Zhang, Maojun Wang:
Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms. - Manuel Huth, Jonas Arruda, Roy Gusinow, Lorenzo Contento, Evelina Tacconelli, Jan Hasenauer:
Accessibility of covariance information creates vulnerability in Federated Learning frameworks. - Correction to: Clustering spatial transcriptomics data.
- Ronan M. T. Fleming, Hulda S. Haraldsdóttir, Le Hoai Minh, Phan Tu Vuong, Thomas Hankemeier, Ines Thiele:
Cardinality optimization in constraint-based modelling: application to human metabolism. - Jiani Ma, Chen Li, Yiwen Zhang, Zhikang Wang, Shanshan Li, Yuming Guo, Lin Zhang, Hui Liu, Xin Gao, Jiangning Song:
MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning. - Daoyi Huang, Jianping Jiang, Tingting Zhao, Shengnan Wu, Pin Li, Yongfen Lyu, Jincai Feng, Mingyue Wei, Zhixing Zhu, Jianlei Gu, Yongyong Ren, Guangjun Yu, Hui Lu:
diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype. - Qijie Chen, Haotong Sun, Haoyang Liu, Yinghui Jiang, Ting Ran, Xurui Jin, Xianglu Xiao, Zhimin Lin, Hongming Chen, Zhangming Niu:
An extensive benchmark study on biomedical text generation and mining with ChatGPT. - Gherard Batisti Biffignandi, Greta Bellinzona, Greta Petazzoni, Davide Sassera, Gianvincenzo Zuccotti, Claudio Bandi, Fausto Baldanti, Francesco Comandatore, Stefano Gaiarsa:
P-DOR, an easy-to-use pipeline to reconstruct bacterial outbreaks using genomics. - Anda Ramona Tanasie, Peter Kerpedjiev, Stefan Hammer, Stefan Badelt:
DrForna: visualization of cotranscriptional folding. - Kyle Smith, Cheng Ye, Yatish Turakhia:
Tracking and curating putative SARS-CoV-2 recombinants with RIVET. - Grzegorz Chojnowski, Rafal Zaborowski, Marcin Magnus, Sunandan Mukherjee, Janusz M. Bujnicki:
RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints. - Jonathan Klonowski, Qianqian Liang, Zeynep H. Coban Akdemir, Cecilia Lo, Dennis Kostka:
aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants. - Xinwei He, Kun Qian, Ziqian Wang, Shirou Zeng, Hongwei Li, Wei Vivian Li:
scAce: an adaptive embedding and clustering method for single-cell gene expression data. - Yan Zhu, Lingling Zhao, Naifeng Wen, Junjie Wang, Chunyu Wang:
DataDTA: a multi-feature and dual-interaction aggregation framework for drug-target binding affinity prediction. - Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Yaohang Li, Jianxin Wang:
MSDRP: a deep learning model based on multisource data for predicting drug response. - Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni:
μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. - Sophie Wharrie, Zhiyu Yang, Vishnu Raj, Remo Monti, Rahul Gupta, Ying Wang, Alicia Martin, Luke J. O'Connor, Samuel Kaski, Pekka Marttinen, Pier Francesco Palamara, Christoph Lippert, Andrea Ganna:
HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes. - Yuzhong Deng, Jianxiong Tang, Jiyang Zhang, Jianxiao Zou, Que Zhu, Shicai Fan:
GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs. - Yiwei Liu, Changhuo Yang, Hong-Dong Li, Jianxin Wang:
IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based method for predicting isoform functions. - Lin Wang, Chenhao Sun, Xianyu Xu, Jia Li, Wenjuan Zhang:
A neighborhood-regularization method leveraging multiview data for predicting the frequency of drug-side effects. - Tudor-Stefan Cotet, Andreas Agrafiotis, Victor Kreiner, Raphael Kuhn, Danielle Shlesinger, Marcos Manero-Carranza, Keywan Khodaverdi, Evgenios Kladis, Aurora Desideri Perea, Dylan Maassen-Veeters, Wiona Glänzer, Solène Massery, Lorenzo Guerci, Kai-Lin Hong, Jiami Han, Kostas Stiklioraitis, Vittoria Martinolli D'arcy, Raphael Dizerens, Samuel Kilchenmann, Lucas Stalder, Leon Nissen, Basil Vogelsanger, Stine Anzböck, Daria Laslo, Sophie Bakker, Melinda Kondorosy, Marco Venerito, Alejandro Sanz García, Isabelle Feller, Annette Oxenius, Sai T. Reddy, Alexander Yermanos:
ePlatypus: an ecosystem for computational analysis of immunogenomics data. - Correction to: "Retraction of: DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency".