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ORCIDBioinformatics, Volume 40
Volume 40, Number 1, January 2024
- Zongquan Li, Pengxuan Ren, Hao Yang
, Jie Zheng, Fang Bai:
TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug-target affinities. - Ting Liu, K. Anton Feenstra, Zhisheng Huang, Jaap Heringa:
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph. - Jeffrey K. Ng, Tychele Turner:
HAT: de novo variant calling for highly accurate short-read and long-read sequencing data. - Chunyue Feng, Kok Haur Ong, David M. Young, Bingxian Chen, Longjie Li, Xinmi Huo, Haoda Lu, Weizhong Gu, Fei Liu, Hongfeng Tang, Manli Zhao, Min Yang, Kun Zhu, Limin Huang, Qiang Wang, Gabriel Pik Liang Marini, Kun Gui, Hao Han, Stephan J. Sanders, Lin Li, Weimiao Yu, Jianhua Mao:
Artificial intelligence-assisted quantification and assessment of whole slide images for pediatric kidney disease diagnosis. - Pinglu Zhang, Huan Liu, Yanming Wei, Yixiao Zhai, Qinzhong Tian, Quan Zou:
FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets. - T. J. Sego:
SimService: a lightweight library for building simulation services in Python. - Aditi Shenoy, Yogesh Kalakoti, Durai Sundar, Arne Elofsson:
M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings. - Xuejiao Wang, Tingfang Wu, Yelu Jiang, Taoning Chen, Deng Pan, Zhi Jin, Jingxin Xie, Lijun Quan, Qiang Lyu:
RPEMHC: improved prediction of MHC-peptide binding affinity by a deep learning approach based on residue-residue pair encoding. - Zsolt Balázs, Todor Gitchev, Ivna Ivankovic, Michael Krauthammer:
Fragmentstein - facilitating data reuse for cell-free DNA fragment analysis. - Timothy G. Vaughan:
ReMASTER: improved phylodynamic simulation for BEAST 2.7. - Seyedmohsen Hosseini, Geoffrey Brian Golding, Lucian Ilie:
Seq-InSite: sequence supersedes structure for protein interaction site prediction. - Parsa Ghadermazi, Siu Hung Joshua Chan:
Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution. - Felix M. Weidner, Nensi Ikonomi, Silke D. Werle, Julian D. Schwab, Hans A. Kestler:
GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks. - Tareian A. Cazares, Richard E. Higgs, Jibo Wang, Hatice Gulcin Ozer:
SeedMatchR: identify off-target effects mediated by siRNA seed regions in RNA-seq experiments. - Seungjun Ahn, Somnath Datta:
SOHPIE: statistical approach via pseudo-value information and estimation for differential network analysis of microbiome data. - Alexander Peltzer, Christopher Mohr, Kai Bernd Stadermann, Matthias Zwick, Ramona Schmid:
nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis. - Rui Cao, Evan Olawsky, Edward McFowland, Erin Marcotte, Logan Spector, Tianzhong Yang:
Subset scanning for multi-trait analysis using GWAS summary statistics. - Lorenzo Pantolini, Gabriel Studer, Joana Pereira, Janani Durairaj, Gerardo Tauriello, Torsten Schwede:
Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone. - Daniel Ji, Robert Aboukhalil, Niema Moshiri:
ViralWasm: a client-side user-friendly web application suite for viral genomics. - Sebastian Staab, Anny Cardénas, Raquel Silva Peixoto, Falk Schreiber, Christian R. Voolstra:
Coracle - a machine learning framework to identify bacteria associated with continuous variables. - Vince Buffalo:
SciDataFlow: a tool for improving the flow of data through science. - Xinliang Sun, Xiao Jia, Zhangli Lu, Jing Tang, Min Li:
Drug repositioning with adaptive graph convolutional networks. - Robert W. Gregg, Panayiotis V. Benos:
CellularPotts.jl: simulating multiscale cellular models in Julia. - Patiphan Wongklaew, Sira Sriswasdi, Ekapol Chuangsuwanich:
MHCSeqNet2 - improved peptide-class I MHC binding prediction for alleles with low data. - Hannelore Longin, Nand Broeckaert, Maarten Langen, Roshan Hari, Anna Kramarska, Kasper Oikarinen, Hanne Hendrix, Rob Lavigne, Vera van Noort:
FLAMS: Find Lysine Acylations and other Modification Sites. - Yasin Tepeli, Colm Seale, Joana P. Gonçalves:
ELISL: early-late integrated synthetic lethality prediction in cancer. - Teng Liu, Zhaoyu Fang, Xin Li, Lining Zhang, Dong-Sheng Cao, Min Li, Mingzhu Yin:
Assembling spatial clustering framework for heterogeneous spatial transcriptomics data with GRAPHDeep. - Hu Cang, Yang Liu, Jianhua Xing:
Mosaic-PICASSO: accurate crosstalk removal for multiplex fluorescence imaging. - Carles Pons, Caroline Mauvezin:
QATS: an ImageJ plugin for the quantification of toroidal nuclei in biological images. - Xiran Liu, Naama M. Kopelman, Noah A. Rosenberg:
Clumppling: cluster matching and permutation program with integer linear programming. - Huang Xu, Tian Wang, Yuqi Miao, Min Qian, Yaning Yang, Shuang Wang:
MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification. - Zikun Yang, Xin Li, Lele Sheng, Ming Zhu, Xun Lan, Fei Gu:
Multiomics-integrated deep language model enables in silico genome-wide detection of transcription factor binding site in unexplored biosamples. - Gustavo S. Jeuken, Lukas Käll:
Pathway analysis through mutual information. - Joren Sebastian Retel, Andreas Poehlmann, Josh Chiou, Andreas Steffen, Djork-Arné Clevert:
A fast machine learning dataloader for epigenetic tracks from BigWig files. - Zachary A. Szpiech:
selscan 2.0: scanning for sweeps in unphased data. - Charlotte Collins, Simon Baker, Jason Brown, Huiyuan Zheng, Adelyne Chan, Ulla Stenius, Masashi Narita, Anna Korhonen:
Text mining for contexts and relationships in cancer genomics literature. - Colin Brown, Anuradha Agarwal, Antoni Luque:
pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells. - Yan Zhou, Ying Zhang, Minjiao Peng, Yaru Zhang, Chenghao Li, Lianjie Shu, Yaohua Hu, Jianzhong Su, Jinfeng Xu:
scDMV: a zero-one inflated beta mixture model for DNA methylation variability with scBS-seq data. - Anna Plaksienko, Pietro Di Lena, Christine Nardini, Claudia Angelini:
methyLImp2: faster missing value estimation for DNA methylation data. - Zhaoyu Fang, Ruiqing Zheng, Min Li:
scMAE: a masked autoencoder for single-cell RNA-seq clustering. - Uxía Veleiro, Jesus de la Fuente, Guillermo Serrano, Marija Pizurica, Mikel Casals, Antonio Pineda-Lucena, Silve Vicent, Idoia Ochoa, Olivier Gevaert, Mikel Hernaez:
Ge N Nius : an ultrafast drug-target interaction inference method based on graph neural networks. - Louise Ryan, Colleen Lawless, Graham M. Hughes:
Sensommatic: an efficient pipeline to mine and predict sensory receptor genes in the era of reference-quality genomes. - Eric Lee, Dongkyu Lee, Wayne Fan, Andrew Lytle, Yuxiang Fu, David W. Scott, Christian Steidl, Samuel Aparicio, Andrew Roth:
ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images. - Jon-Michael Beasley, Daniel R. Korn, Nyssa N. Tucker, Erick T. M. Alves, Eugene N. Muratov, Chris Bizon, Alexander Tropsha:
ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining. - Jackson Barth, Yuqiu Yang, Guanghua Xiao, Xinlei Wang:
MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data. - Azam Hussain, Charles L. Brooks III:
Guiding discovery of protein sequence-structure-function modeling. - Chao Cao, Chunyu Wang, Shuhong Yang, Quan Zou:
CircSI-SSL: circRNA-binding site identification based on self-supervised learning. - James M. Holt, Christopher T. Saunders, William J. Rowell, Zev N. Kronenberg, Aaron M. Wenger, Michael A. Eberle:
HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing. - Dmitry Meleshko, Andrey D. Prjbelski, Mikhail Raiko, Alexandru I. Tomescu, Hagen U. Tilgner, Iman Hajirasouliha:
cloudrna SP Ades : isoform assembly using bulk barcoded RNA sequencing data. - Momoko Hamano, Toru Nakamura, Ryoku Ito, Yuki Shimada, Michio Iwata, Jun-ichi Takeshita, Ryohei Eguchi, Yoshihiro Yamanishi:
DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion. - Fatih Karaoglanoglu, Baraa Orabi, Ryan Flannigan, Cédric Chauve, Faraz Hach:
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator. - Giulio Genovese, Nicole B. Rockweiler, Bryan R. Gorman, Tim B. Bigdeli, Michelle T. Pato, Carlos N. Pato, Kiku Ichihara, Steven A. McCarroll:
BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies. - Zhongliang Zhou, Wayland Yeung, Saber Soleymani, Nathan Gravel, Mariah Salcedo, Sheng Li, Natarajan Kannan:
Using explainable machine learning to uncover the kinase-substrate interaction landscape. - Daniel Brunnsåker, Filip Kronström, Ievgeniia A. Tiukova, Ross D. King:
Interpreting protein abundance in Saccharomyces cerevisiae through relational learning. - Zilong Li:
vcfpp: a C++ API for rapid processing of the variant call format. - Danielle Miller, Ofir Arias, David Burstein:
GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function. - Correction to: USNAP: fast unique dense region detection and its application to lung cancer.
- Chenxu Pan, Knut Reinert:
A simple refined DNA minimizer operator enables 2-fold faster computation. - Hagai Levi, Ran Elkon, Ron Shamir:
The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population. - Chih-Yuan Hsu, Chia-Jung Chang, Qi Liu, Yu Shyr:
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data. - Laura Luebbert, Chi Hoang, Manjeet Kumar, Lior Pachter:
Fast and scalable querying of eukaryotic linear motifs with gget elm. - Ragnar Groot Koerkamp, Pesho Ivanov:
Exact global alignment using A* with chaining seed heuristic and match pruning. - Chitrasen Mohanty, Aman Prasad, Lingxin Cheng, Lisa M. Arkin, Bridget E. Shields, Beth Drolet, Christina Kendziorski:
SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments. - Zhi Zhao, John Zobolas, Manuela Zucknick, Tero Aittokallio:
Tutorial on survival modeling with applications to omics data. - Jiahan Liu, Chaochao Yan, Yang Yu, Chan Lu, Junzhou Huang, Le Ou-Yang, Peilin Zhao:
MARS: a motif-based autoregressive model for retrosynthesis prediction. - Xuncai Zhang, Baonan Qi, Ying Niu:
A dual-rule encoding DNA storage system using chaotic mapping to control GC content. - Jung Kim, Ammar S. Naqvi, Ryan J. Corbett, Rebecca S. Kaufman, Zalman Vaksman, Miguel A. Brown, Daniel P. Miller, Saksham Phul, Zhuangzhuang Geng, Phillip B. Storm, Adam C. Resnick, Douglas R. Stewart, Jo Lynne Rokita, Sharon J. Diskin:
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification. - Yuting Chen, Haoling Zhang, Wen Wang, Yue Shen, Zhi Ping:
Rapid generation of high-quality structure figures for publication with PyMOL-PUB. - Jorge Carrasco Muriel, Nicholas Cowie, Shannara Taylor Parkins, Marjan Mansouvar, Teddy Groves, Lars Keld Nielsen:
Shu: visualization of high-dimensional biological pathways. - Xingyu Bi, Wenbin Ye, Xin Cheng, Ning Yang, Xiaohui Wu:
vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data. - Mikko Rautiainen:
Ribotin: automated assembly and phasing of rDNA morphs. - Markus Wenzel, Erik Grüner, Nils Strodthoff:
Insights into the inner workings of transformer models for protein function prediction. - Jonas Cordes, Thomas Enzlein, Carsten Hopf, Ivo Wolf:
pyM2aia: Python interface for mass spectrometry imaging with focus on deep learning. - Yan Sun, Yan Yi Li, Carson K. Leung, Pingzhao Hu:
iNGNN-DTI: prediction of drug-target interaction with interpretable nested graph neural network and pretrained molecule models. - Liandong Li, Haoyi Fu, Wentai Ma, Mingkun Li:
PySNV for complex intra-host variation detection. - Michael D. Linderman, Jacob Wallace, Alderik van der Heyde, Eliza Wieman, Daniel Brey, Yiran Shi, Peter Hansen, Zahra Shamsi, Jeremiah Liu, Bruce D. Gelb, Ali Bashir:
NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data. - Fahu Ji, Qian Zhou, Jue Ruan, Zexuan Zhu, Xianming Liu:
A compressive seeding algorithm in conjunction with reordering-based compression. - Orit Adato, Anna Sloutskin, Hodaya Komemi, Ian Brabb, Sascha Duttke, Philipp Bucher, Ron Unger, Tamar Juven-Gershon:
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements. - Jakob Woerner, Vivek Sriram, Yonghyun Nam, Anurag Verma, Dokyoon Kim:
Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network. - William D. Lees, Swati Saha, Gur Yaari, Corey T. Watson:
Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies. - David R. Lougheed, Hanshi Liu, Katherine A. Aracena, Romain Grégoire, Alain Pacis, Tomi Pastinen, Luis B. Barreiro, Yann Joly, David Bujold, Guillaume Bourque:
EpiVar Browser: advanced exploration of epigenomics data under controlled access. - Lauren Theunissen, Thomas Mortier, Yvan Saeys, Willem Waegeman:
Uncertainty-aware single-cell annotation with a hierarchical reject option. - Jason Y. Cain, Jacob I. Evarts, Jessica S. Yu, Neda Bagheri:
Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence. - Shengli Zhang, Ya Zhao, Yunyun Liang:
AACFlow: an end-to-end model based on attention augmented convolutional neural network and flow-attention mechanism for identification of anticancer peptides. - Hao Wang, Yumou Qiu, Hongqing Guo, Yanhai Yin, Peng Liu:
Information-incorporated gene network construction with FDR control. - Haochen Wang, Qixiu Du, Ye Wang, Hanwen Xu, Zheng Wei, Xiaowo Wang:
GPro: generative AI-empowered toolkit for promoter design. - Hannes Hauswedell, Sara Hetzel, Simon Gottlieb, Helene Kretzmer, Alexander Meissner, Knut Reinert:
Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. - Erhu Liu, Hongqiang Lyu, Yuan Liu, Laiyi Fu, Xiaoliang Cheng, Xiaoran Yin:
Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection. - Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng:
CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs. - Lucile Massenet-Regad, Vassili Soumelis:
ICELLNET v2: a versatile method for cell-cell communication analysis from human transcriptomic data.
Volume 40, Number 2, February 2024
- Diogo A. C. Narciso, Ana Pereira, Nuno O. Dias, Manuel Monteiro, Luis F. Melo, Fernando Gomes Martins:
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties. - Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko:
Statistical framework to determine indel-length distribution. - Jinyu Yu, Junxi Mu, Ting Wei, Hai-Feng Chen:
Multi-indicator comparative evaluation for deep learning-based protein sequence design methods. - Arnaud Chol, Roman Sarrazin-Gendron, Eric Lécuyer, Mathieu Blanchette, Jérôme Waldispühl:
PERFUMES: pipeline to extract RNA functional motifs and exposed structures. - David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov:
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. - Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A. Matsen IV, Marc A. Suchard:
Many-core algorithms for high-dimensional gradients on phylogenetic trees. - Gabriel Loyer, Vladimir Reinharz:
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework. - Loïc Lannelongue, Michael Inouye:
Pitfalls of machine learning models for protein-protein interaction networks. - Ping Xuan, Jing Gu, Hui Cui, Shuai Wang, Toshiya Nakaguchi, Cheng Liu, Tiangang Zhang:
Multi-scale topology and position feature learning and relationship-aware graph reasoning for prediction of drug-related microbes. - Yue Zhuo, Heng Du, Chenguang Diao, Weining Li, Lei Zhou, Li Jiang, Jicai Jiang, Jianfeng Liu:
MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems. - Xin Liu, Jieni Hu, Jie Zheng:
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality. - Bjarne Daenekas, Eilís Pérez, Fabio Boniolo, Sabina Stefan, Salvatore Benfatto, Martin Sill, Dominik Sturm, David T. W. Jones, David Capper, Marc Zapatka, Volker Hovestadt:
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice. - Kuan Xie, Yuying Hou, Xionghui Zhou:
Deep centroid: a general deep cascade classifier for biomedical omics data classification. - Haohui Zhang, Yuwei Wang, Bin Lian, Yiran Wang, Xingyi Li, Tao Wang, Xuequn Shang, Hui Yang, Ahmad Aziz, Jialu Hu:
Scbean: a python library for single-cell multi-omics data analysis. - Peiying Cai, Mark D. Robinson, Simone Tiberi:
DESpace: spatially variable gene detection via differential expression testing of spatial clusters. - Zeyu Chen, Yuxin Miao, Zhiyuan Tan, Qifan Hu, Yanhong Wu, Xinqi Li, Wenbo Guo, Jin Gu:
scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution. - Huangqingbo Sun, Jiayi Li, Robert F. Murphy:
Expanding the coverage of spatial proteomics: a machine learning approach. - Xiao Wang, Ziyi Chai, Shaohua Li, Yan Liu, Chen Li, Yu Jiang, Quanzhong Liu:
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data. - Juanru Guo, Wenjin Zhang, Xuhua Chen, Allen Yen, Lucy Chen, Christian A. Shively, Daofeng Li, Ting Wang, Joseph D. Dougherty, Robi D. Mitra:
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data. - Yash Patel, Chenghao Zhu, Takafumi N. Yamaguchi, Yuan Zhe Bugh, Mao Tian, Aaron Holmes, Sorel T. Fitz-Gibbon, Paul C. Boutros:
NFTest: automated testing of Nextflow pipelines. - Fabrizio Pucci, Mehari B. Zerihun, Marianne Rooman, Alexander Schug:
pycofitness - Evaluating the fitness landscape of RNA and protein sequences. - Correction to: GTExVisualizer: a web platform for supporting ageing studies.
- Xiaoshu Zhu, Shuang Meng, Gaoshi Li, Jian-Xin Wang, Xiaoqing Peng:
AGImpute: imputation of scRNA-seq data based on a hybrid GAN with dropouts identification. - Anna Sintsova, Hans-Joachim Ruscheweyh, Christopher M. Field, Lilith Feer, Bidong D. Nguyen, Benjamin Daniel, Wolf-Dietrich Hardt, Julia A. Vorholt, Shinichi Sunagawa:
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations. - Lap Sum Chan, Gen Li:
Zero is not absence: censoring-based differential abundance analysis for microbiome data. - Lu Yang, Pei Wang, Jun Chen:
2dGBH: Two-dimensional group Benjamini-Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data. - Haixiang Zhang, Xiumei Hong, Yinan Zheng, Lifang Hou, Cheng Zheng, Xiaobin Wang, Lei Liu:
High-dimensional quantile mediation analysis with application to a birth cohort study of mother-newborn pairs. - Kexin Shi, Yuanpeng Xiong, Yu Wang, Yifan Deng, Wenjia Wang, Bingyi Jing, Xin Gao:
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction. - Zongyang Du, Zhenling Peng, Jianyi Yang:
RNA threading with secondary structure and sequence profile. - Niek van Hilten, Nino Verwei, Jeroen Methorst, Carsten Nase, Andrius Bernatavicius, Herre Jelger Risselada:
PMIpred: a physics-informed web server for quantitative protein-membrane interaction prediction. - Diego Mañanes, Inés Rivero-García, Carlos Relaño, Miguel Torres, David Sancho, Daniel Jimenez-Carretero, Carlos Torroja Fungairino, Fátima Sánchez-Cabo:
SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks. - Jun Wang, Marc Horlacher, Lixin Cheng, Ole Winther:
DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning. - Yash Patel, Arpi Beshlikyan, Madison Jordan, Gina Kim, Aaron Holmes, Takafumi N. Yamaguchi, Paul C. Boutros:
PipeVal: light-weight extensible tool for file validation. - Xinyuan Huang, Xiujuan Gao, Ling Fu:
BINGO: a blind unmixing algorithm for ultra-multiplexing fluorescence images. - Chenglin Yin, Ruheng Wang, Jianbo Qiao, Hua Shi, Hongliang Duan, Xinbo Jiang, Saisai Teng, Leyi Wei:
NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection. - Ioan Ieremie, Rob M. Ewing, Mahesan Niranjan:
Protein language models meet reduced amino acid alphabets. - Junchi Ma, Xiaoyu Zhao, Enfeng Qi, Renmin Han, Ting Yu, Guojun Li:
Highly efficient clustering of long-read transcriptomic data with GeLuster. - Carson M. Andorf, Olivia C. Haley, Rita K. Hayford, John L. Portwood II, Stephen Harding, Shatabdi Sen, Ethalinda K. S. Cannon, Jack M. Gardiner, Hye-Seon Kim, Margaret Woodhouse:
PanEffect: a pan-genome visualization tool for variant effects in maize. - Nezar Abdennur, Geoffrey Fudenberg, Ilya M. Flyamer, Aleksandra A. Galitsyna, Anton Goloborodko, Maxim Imakaev, Sergey Venev:
Bioframe: operations on genomic intervals in Pandas dataframes. - Jue Yang, Weiwen Wang, Xiwen Zhang:
scSemiGCN: boosting cell-type annotation from noise-resistant graph neural networks with extremely limited supervision. - Nicole Pradas, Federico Jurado-Ruiz, Carles Onielfa, Pere Arús, Maria José Aranzana:
PERSEUS: an interactive and intuitive web-based tool for pedigree visualization. - Mikaela Koutrouli, Katerina C. Nastou, Pau Piera Líndez, Robbin Bouwmeester, Simon Rasmussen, Lennart Martens, Lars Juhl Jensen:
FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data. - Alex Morehead, Jianlin Cheng:
Geometry-complete perceptron networks for 3D molecular graphs. - Ding Wang, Junru Jin, Zhongshen Li, Yu Wang, Mushuang Fan, Sirui Liang, Ran Su, Leyi Wei:
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides. - Yuzhen Mao, Yen-Yi Lin, Nelson K. Y. Wong, Stanislav Volik, Funda Sar, Colin C. Collins, Martin Ester:
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks. - Yongtao Guan, Daniel Levy:
Estimation of inbreeding and kinship coefficients via latent identity-by-descent states. - Xiaoyu Guan, Wei Shao, Daoqiang Zhang:
T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition. - Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu:
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information. - Philippe Charron, Mingsong Kang:
VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs. - Kemal Demirtas, Burak Erman, Türkan Haliloglu:
Dynamic correlations: exact and approximate methods for mutual information.
Volume 40, Number 3, March 2024
- David Ferreiro, Catarina Branco, Miguel Arenas:
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation. - Zuher Jahshan, Leonid Yavits:
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment. - Jiqing Wu, Viktor H. Koelzer:
SST-editing: in silico spatial transcriptomic editing at single-cell resolution. - Oliver Cheng, Min Hao Ling, Changqing Wang, Shuyi Wu, Matthew E. Ritchie, Jonathan Göke, Noorul Amin, Nadia M. Davidson:
Flexiplex: a versatile demultiplexer and search tool for omics data. - Correction to: OncoThreads: visualization of large-scale longitudinal cancer molecular data.
- Jun Xue, Bingyi Wang, Hongchao Ji, Weihua Li:
RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification. - Yiyang Yu, Shivani Muthukumar, Peter K. Koo:
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. - Hamza Biyuzan, Mohamed-Akram Masrour, Lucas Grandmougin, Frédéric Payan, Dominique Douguet:
SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space. - Hannah-Marie Martiny, Nikiforos Pyrounakis, Thomas Nordahl Petersen, Oksana Lukjancenko, Frank Aarestrup, Philip T. L. C. Clausen, Patrick Munk:
ARGprofiler - a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets. - J. Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas Matentzoglu, Hyeongsik Kim, Sierra A. T. Moxon, Justin T. Reese, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. - Chiung-Ting Wu, Dongping Du, Lulu Chen, Rujia Dai, Chunyu Liu, Guoqiang Yu, Saurabh Bhardwaj, Sarah J. Parker, Zhen Zhang, Robert Clarke, David M. Herrington, Yue Wang:
CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution. - Arik Ermshaus, Michael Piechotta, Gina Rüter, Ulrich Keilholz, Ulf Leser, Manuela Benary:
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology. - Emese I Végh, Katerina Douka:
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS. - Guillermo Dufort y Álvarez, Martí Xargay-Ferrer, Alba Pagès-Zamora, Idoia Ochoa:
EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization. - Kristofer Sandås, Jacob Lewerentz, Edvin Karlsson, Linda Karlsson, David Sundell, Kotryna Simonyté-Sjödin, Andreas Sjödin:
Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification. - Xiangxin Zhan, Yanbin Yin, Han Zhang:
BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework. - Florian J. Gisdon, Mariella Zunker, Jan Niclas Wolf, Kai Prüfer, Jörg Ackermann, Christoph Welsch, Ina Koch:
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes. - Jaroslaw Chilimoniuk, Krystyna Grzesiak, Jakub Kala, Dominik Nowakowski, Adam Kretowski, Rafal Kolenda, Michal Ciborowski, Michal Burdukiewicz:
imputomics: web server and R package for missing values imputation in metabolomics data. - Shreyas Arvindekar, Aditi S. Pathak, Kartik Majila, Shruthi Viswanath:
Optimizing representations for integrative structural modeling using Bayesian model selection. - Zhengyang Guo, Yang Wang, Guangshuo Ou:
Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison. - Melpomeni Kasapi, Kexin Xu, Timothy M. D. Ebbels, Declan P. O'Regan, James S. Ware, Joram M. Posma:
LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies. - Haoliang Xue, Mélina Gallopin, Camille Marchet, Ha N. Nguyen, Yunfeng Wang, Antoine Lainé, Chloé Bessière, Daniel Gautheret:
KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction. - Milind Misra, Jeffy Jeffy, Charis Liao, Stephanie Pickthorn, Kshitij Wagh, Alon Herschhorn:
HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies. - Woosung Jeon, Dongsup Kim:
AbFlex: designing antibody complementarity determining regions with flexible CDR definition. - Jose L. Figueroa III, Eliza Dhungel, Madeline Bellanger, Cory R. Brouwer, Richard Allen White III:
MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life.
Volume 40, Number 4, 2024
- Ruochi Zhang, Chao Wu, Qian Yang, Chang Liu, Yan Wang, Kewei Li, Lan Huang, Fengfeng Zhou:
MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning. - Bogeum Seo, Dohee Lee, Heungjin Jeon, Junhyoung Ha, SeungBeum Suh:
MotGen: a closed-loop bacterial motility control framework using generative adversarial networks. - Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov:
Effect of tokenization on transformers for biological sequences. - Ruohan Wang, Yen Kaow Ng, Xianglilan Zhang, Jianping Wang, Shuai Cheng Li:
Coding genomes with gapped pattern graph convolutional network. - Martin Hölzer:
POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy. - Jakub Galgonek, Jirí Vondrásek:
The IDSM mass spectrometry extension: searching mass spectra using SPARQL. - Jonathan L. Price, Omer Ziv, Malte L. Pinckert, Andrew Lim, Eric A. Miska:
rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments. - Xinyi Zhang, Yanni Xu, Changzhi Jiang, Lian Shen, Xiangrong Liu:
MoleMCL: a multi-level contrastive learning framework for molecular pre-training. - Haohua Wang, Kai Lin, Qiang Zhang, Jinlong Shi, Xinyu Song, Jue Wu, Chenghui Zhao, Kunlun He:
HyperTMO: a trusted multi-omics integration framework based on hypergraph convolutional network for patient classification. - Xiaokun Li, Qiang Yang, Long Xu, Weihe Dong, Gongning Luo, Wei Wang, Suyu Dong, Kuanquan Wang, Ping Xuan, Xianyu Zhang, Xin Gao:
DrugMGR: a deep bioactive molecule binding method to identify compounds targeting proteins. - Irenaeus C. C. Chan, Alex Panchot, Evelyn Schmidt, Samantha N. McNulty, Brian J. Wiley, Jie Liu, Kimberly Turner, Lea Moukarzel, Wendy S. W. Wong, Duc Tran, J. Scott Beeler, Armel Landry Batchi-Bouyou, Mitchell J. Machiela, Danielle M. Karyadi, Benjamin J. Krajacich, Junhua Zhao, Semyon Kruglyak, Bryan R. Lajoie, Shawn E. Levy, Minal Patel, Philip W. Kantoff, Christopher E. Mason, Daniel C. Link, Todd E. Druley, Konrad H. Stopsack, Kelly L. Bolton:
ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation. - Jochen Weile, Gabrielle Ferra, Gabriel Boyle, Sriram Pendyala, Clara J. Amorosi, Chiann-Ling C. Yeh, Atina G. Coté, Nishka Kishore, Daniel Tabet, Warren van Loggerenberg, Ashyad Rayhan, Douglas M. Fowler, Maitreya J. Dunham, Frederick P. Roth:
Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries. - Weizhong Zhao, Junze Wu, Xingpeng Jiang, Tingting He, Xiaohua Hu:
Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes. - Amy Francis, Colin Campbell, Tom R. Gaunt:
DrivR-Base: a feature extraction toolkit for variant effect prediction model construction. - Zhaohui Zhan, Lusheng Wang:
Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra. - Yue Lyu, Chong Wu, Wei Sun, Ziyi Li:
Regional analysis to delineate intrasample heterogeneity with RegionalST. - Andrew G. Duncan, Jennifer A Mitchell, Alan M. Moses:
Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation. - Philipp E. Glass, Sabriyeh Alibai, Alessandro Pandini, Sarath Chandra Dantu:
PyCoM: a python library for large-scale analysis of residue-residue coevolution data. - Jingqi Duan, Audrey P. Gasch, Sündüz Keles:
Integrative annotation scores of variants for impact on RNA binding protein activities. - Artuur Couckuyt, Benjamin Rombaut, Yvan Saeys, Sofie Van Gassen:
Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools. - Divya Sharma, Wendy Lou, Wei Xu:
phylaGAN: data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data. - Erik Vonkaenel, Alexis Feidler, Rebecca Lowery, Katherine Andersh, Tanzy Love, Ania Majewska, Matthew N. McCall:
A model-based hierarchical Bayesian approach to Sholl analysis. - Eric Odle, Samuel Kahng, Siratee Riewluang, Kyoko Kurihara, Kevin C. Wakeman:
GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data. - Sijing An, Jinhui Shi, Runyan Liu, Yaowen Chen, Jing Wang, Shuofeng Hu, Xinyu Xia, Guohua Dong, Xiaochen Bo, Zhen He, Xiaomin Ying:
scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model. - Wenliang Pan, Yue Shan, Chuang Li, Shuai Huang, Tengfei Li, Yun Li, Hongtu Zhu:
FPLS-DC: functional partial least squares through distance covariance for imaging genetics. - Leanne S. Whitmore, Jennifer Tisoncik-Go, Michael Gale:
scPathoQuant: a tool for efficient alignment and quantification of pathogen sequence reads from 10× single cell sequencing datasets. - Andrew Jiang, Russell G. Snell, Klaus Lehnert:
ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells. - Fuqun Chen, Guanhua Zou, Yongxian Wu, Le Ou-Yang:
Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning. - Hailong Yang, Yue Chen, Yun Zuo, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Dong-Jun Yu:
MINDG: a drug-target interaction prediction method based on an integrated learning algorithm. - Barbara Gravel, Alexandre Renaux, Sofia Papadimitriou, Guillaume Smits, Ann Nowé, Tom Lenaerts:
Prioritization of oligogenic variant combinations in whole exomes. - Yurui Chen, Louxin Zhang:
Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction. - Federica De Paoli, Silvia Berardelli, Ivan Limongelli, Ettore Rizzo, Susanna Zucca:
VarChat: the generative AI assistant for the interpretation of human genomic variations. - Teng Ma, Jianxin Wang:
GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway-pathway interaction network. - Benoit Morel, Tom A. Williams, Alexandros Stamatakis, Gergely J. Szöllosi:
AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss. - Rafael Henkin, Katriona Goldmann, Myles J. Lewis, Michael R. Barnes:
shinyExprPortal: a configurable 'shiny' portal for sharing analysis of molecular expression data. - Ieva Pudziuvelyte, Kliment Olechnovic, Egle Godliauskaite, Kristupas Sermokas, Tomas Urbaitis, Giedrius Gasiunas, Darius Kazlauskas:
TemStaPro: protein thermostability prediction using sequence representations from protein language models. - Lucas Paulo de Lima Camillo:
pyaging : a Python-based compendium of GPU-optimized aging clocks. - Sijie Li, Yuxi Li, Yu Sun, Yaru Li, Xiaoyang Chen, Songming Tang, Shengquan Chen:
EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data. - Fang Wang, Yibin Wang, Xiaofei Zeng, Shengcheng Zhang, Jiaxin Yu, Dongxi Li, Xingtan Zhang:
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction. - Priyadarshini Rai, Atishay Jain, Shivani Kumar, Divya Sharma, Neha Jha, Smriti Chawla, Abhijit Raj, Apoorva Gupta, Sarita Poonia, Angshul Majumdar, Tanmoy Chakraborty, Gaurav Ahuja, Debarka Sengupta:
Literature mining discerns latent disease-gene relationships. - Moein Karami, Aryan Soltani Mohammadi, Marcel Martin, Baris Ekim, Wei Shen, Lidong Guo, Mengyang Xu, Giulio Ermanno Pibiri, Rob Patro, Kristoffer Sahlin:
Designing efficient randstrobes for sequence similarity analyses. - Liang Wang, Chenyang Hong, Jiangning Song, Jianhua Yao:
CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis. - Jonas Hagenberg, Monika Budde, Teodora Pandeva, Ivan Kondofersky, Sabrina K. Schaupp, Fabian J. Theis, Thomas G. Schulze, Nikola S. Müller, Urs Heilbronner, Richa Batra, Janine Knauer-Arloth:
longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types. - Ali Osman Berk Sapci, Eleonora Rachtman, Siavash Mirarab:
CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing. - A. Sina Booeshaghi, Xi Chen, Lior Pachter:
A machine-readable specification for genomics assays. - Saisai Sun, Lin Gao:
Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction. - Donghyung Lee, Silviu-Alin Bacanu:
GAUSS: a summary-statistics-based R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation, and TWAS analysis of cosmopolitan cohorts. - Jiefu Li, Ziyuan Wang, Xuwei Fan, Ruijie Yao, Guoqing Zhang, Rui Fan, Zefeng Wang:
Rapid multiple protein sequence search by parallel and heterogeneous computation. - Michael Predl, Marianne Mießkes, Thomas Rattei, Jürgen Zanghellini:
PyCoMo: a python package for community metabolic model creation and analysis. - Alexander Röhl, Eugen Netz, Oliver Kohlbacher, Hadeer Elhabashy:
CLAUDIO: automated structural analysis of cross-linking data. - Victoria Ruiz-Serra, Samuel Valentini, Sergi Madroñero, Alfonso Valencia, Eduard Porta-Pardo:
3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures. - Johanna Elena Schmitz, Nihit Aggarwal, Lukas Laufer, Jörn Walter, Abdulrahman Salhab, Sven Rahmann:
EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery. - Gabriele Orlando, Luis Serrano, Joost Schymkowitz, Frederic Rousseau:
Integrating physics in deep learning algorithms: a force field as a PyTorch module. - Kangcheng Hou, Stephanie M. Gogarten, Joohyun Kim, Xing Hua, Julie-Alexia Dias, Quan Sun, Ying Wang, Taotao Tan, Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working Group, Elizabeth G. Atkinson, Alicia Martin, Jonathan Shortt, Jibril Hirbo, Yun Li, Bogdan Pasaniuc, Haoyu Zhang:
Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations. - Correction to: Rapid generation of high-quality structure figures for publication with PyMOL-PUB.
- Nicolas Ruffini, Saleh Altahini, Stephan Weißbach, Nico Weber, Jonas Milkovits, Anna Wierczeiko, Hendrik Backhaus, Albrecht Stroh:
ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface. - Zuohan Zhao, Lijuan Liu, Yufeng Liu:
NIEND: neuronal image enhancement through noise disentanglement. - Vipina Kuttichi Keloth, Yan Hu, Qianqian Xie, Xueqing Peng, Yan Wang, Andrew Zheng, Melih Selek, Kalpana Raja, Chih-Hsuan Wei, Qiao Jin, Zhiyong Lu, Qingyu Chen, Hua Xu:
Advancing entity recognition in biomedicine via instruction tuning of large language models. - Rory Munro, Satrio Wibowo, Alexander Payne, Matthew Loose:
Icarust, a real-time simulator for Oxford Nanopore adaptive sampling. - Guangchen Liu, Xun Chen, Yihui Luan, Dawei Li:
VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.
Volume 40, Number 5, 2024
- Wenmin Zhang, Tianyuan Lu, Robert Sladek, Yue Li, Hamed S. Najafabadi, Josée Dupuis:
SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals. - Feng Pan, Chong Yin, Si-Qi Liu, Tao Huang, Zhaoxiang Bian, Pong Chi Yuen:
BindingSiteDTI: differential-scale binding site modelling for drug-target interaction prediction. - Shihu Jiao, Xiucai Ye, Tetsuya Sakurai, Quan Zou, Ruijun Liu:
Integrated convolution and self-attention for improving peptide toxicity prediction. - Yushan Qiu, Lingfei Yang, Hao Jiang, Quan Zou:
scTPC: a novel semisupervised deep clustering model for scRNA-seq data. - Hang Wei, Lin Gao, Shuai Wu, Yina Jiang, Bin Liu:
DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity. - Pawel Pratyush, Soufia Bahmani, Suresh Pokharel, Hamid D. Ismail, Dukka B. KC:
LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model. - Johanna Galvis, Joris Guyon, Benjamin Dartigues, Helge Hecht, Björn A. Grüning, Florian Specque, Hayssam Soueidan, Slim Karkar, Thomas Daubon, Macha Nikolski:
DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data. - Antonio Di Maria, Lorenzo Bellomo, Fabrizio Billeci, Alfio Cardillo, Salvatore Alaimo, Paolo Ferragina, Alfredo Ferro, Alfredo Pulvirenti:
NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph. - Ryan Green, Xufeng Qu, Jinze Liu, Tingting Yu:
BTR: a bioinformatics tool recommendation system. - Christian Carrizosa, Dag E. Undlien, Magnus Dehli Vigeland:
shinyseg: a web application for flexible cosegregation and sensitivity analysis. - Semih Kurt, Mandi Chen, Hosein Toosi, Xinsong Chen, Camilla Engblom, Jeff E. Mold, Johan Hartman, Jens Lagergren:
CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics. - Correction to: kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase.
- Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti, Xavier Didelot, Davide Cesare Monti, Yuri Pirola:
RecGraph: recombination-aware alignment of sequences to variation graphs. - Rodolphe Loubaton, Nicolas Champagnat, Pierre Vallois, Laurent Vallat:
MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions. - Simone Caligola, Luca Giacobazzi, Stefania Canè, Antonio Vella, Annalisa Adamo, Stefano Ugel, Rosalba Giugno, Vincenzo Bronte:
GateMeClass: Gate Mining and Classification of cytometry data. - Sheikh Nizamuddin, H. Th. Marc Timmers:
greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets. - Telmo Blasco, Francesco Balzerani, Luis Vitores Valcarcel, Pedro Larrañaga, Concha Bielza, María Pilar Francino, José Ángel Rufián-Henares, Francisco J. Planes, Sergio Pérez-Burillo:
BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities. - Halil Ibrahim Kuru, A. Ercüment Çiçek, Öznur Tastan:
From cell lines to cancer patients: personalized drug synergy prediction. - Bangyi Zhao, Weixia Xu, Jihong Guan, Shuigeng Zhou:
Molecular property prediction based on graph structure learning. - Yanglan Gan, Jiacheng Yu, Guangwei Xu, Cairong Yan, Guobing Zou:
Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding. - Joseph A. Zoller, Steve Horvath:
MammalMethylClock R package: software for DNA methylation-based epigenetic clocks in mammals. - Junmin Wang, Steven Novick:
Peptide set test: a peptide-centric strategy to infer differentially expressed proteins. - Hui Sun, Yingfeng Zheng, Haonan Xie, Huidong Ma, Cheng Zhong, Meng Yan, Xiaoguang Liu, Gang Wang:
PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping. - Samuel J. Peccoud, Casey-Tyler Berezin, Sarah I. Hernandez, Jean Peccoud:
PlasCAT: Plasmid Cloud Assembly Tool. - Shen Zhang, Huaying Fang, Tao Hu:
fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data. - Charlotte Crauwels, Sophie-Luise Heidig, Adrián Díaz, Wim F. Vranken:
Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper. - Nikolaos N. Louros, Frederic Rousseau, Joost Schymkowitz:
CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences. - Yuanyuan Li, Chuxiao Lai, Meng Wang, Jun Wu, Yongbin Li, Hanchuan Peng, Lei Qu:
Automated segmentation and recognition of C. elegans whole-body cells. - Jeremy P. Gygi, Anna Konstorum, Shrikant Pawar, Edel Aron, Steven H. Kleinstein, Leying Guan:
A supervised Bayesian factor model for the identification of multi-omics signatures. - Hubert Sokolowski, Marcin Czajkowski, Anna Czajkowska, Krzysztof Jurczuk, Marek Kretowski:
ITree: a user-driven tool for interactive decision-making with classification trees. - Jonathan Parkinson, Wei Wang:
For antibody sequence generative modeling, mixture models may be all you need. - Zongli Xu, Liang Niu, Jacob K. Kresovich, Jack A. Taylor:
methscore: a comprehensive R function for DNA methylation-based health predictors. - Kailing Tu, Xuemei Li, Qilin Zhang, Wei Huang, Dan Xie:
A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing. - Jicai Jiang:
MPH: fast REML for large-scale genome partitioning of quantitative genetic variation. - Ian G. Brennan, Sonal Singhal, Ziad Al Bkhetan:
pipesnake : generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci. - Rahul Nikam, Sherlyn Jemimah, M. Michael Gromiha:
DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein-protein complexes upon mutation. - Remi Trimbour, Ina Maria Deutschmann, Laura Cantini:
Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS. - Andreas Wagner:
Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape. - Zulema Rodriguez-Hernandez, Mathias Gorski, Maria Tellez-Plaza, Pascal Schlosser, Matthias Wuttke:
metaGWASmanager: a toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia. - Sebastian Höpfl, Mohamed Albadry, Uta Dahmen, Karl-Heinz Herrmann, Eva Marie Kindler, Matthias König, Jürgen Rainer Reichenbach, Hans-Michael Tautenhahn, Weiwei Wei, Wan-Ting Zhao, Nicole Radde:
Bayesian modelling of time series data (BayModTS) - a FAIR workflow to process sparse and highly variable data. - Yanguang Liu, Hailong Yu, Xinya Duan, Xiaomin Zhang, Ting Cheng, Feng Jiang, Hao Tang, Yao Ruan, Miao Zhang, Hongyu Zhang, Qingye Zhang:
TransGEM: a molecule generation model based on Transformer with gene expression data. - Jude Wells, Alex Hawkins-Hooker, Nicola Bordin, Ian Sillitoe, Brooks Paige, Christine A. Orengo:
Chainsaw: protein domain segmentation with fully convolutional neural networks. - Bryce Kille, Michael G. Nute, Victor Huang, Eddie Kim, Adam M. Phillippy, Todd J. Treangen:
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. - Matee Ullah, Shahid Akbar, Ali Raza, Quan Zou:
DeepAVP-TPPred: identification of antiviral peptides using transformed image-based localized descriptors and binary tree growth algorithm. - Valentina Giansanti, Francesca Giannese, Oronza A. Botrugno, Giorgia Gandolfi, Chiara Balestrieri, Marco Antoniotti, Giovanni Tonon, Davide Cittaro:
Scalable integration of multiomic single-cell data using generative adversarial networks. - Corrado Pancotti, Cesare Rollo, Francesco Codicè, Giovanni Birolo, Piero Fariselli, Tiziana Sanavia:
MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification. - Lingyi Cai, Dimitris Anastassiou:
CASCC: a co-expression-assisted single-cell RNA-seq data clustering method. - Hongzhen Ding, Xue Li, Peifu Han, Xu Tian, Fengrui Jing, Shuang Wang, Tao Song, Hanjiao Fu, Na Kang:
MEG-PPIS: a fast protein-protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network. - Roni Gurvich, Gal Markel, ZiaurRehman Tanoli, Tomer Meirson:
Peptriever: a Bi-Encoder approach for large-scale protein-peptide binding search. - Anja Mösch, Filippo Grazioli, Pierre Machart, Brandon Malone:
NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population. - Marco Stock, Niclas Popp, Jonathan Fiorentino, Antonio Scialdone:
Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data. - Zhecheng Zhou, Qingquan Liao, Jinhang Wei, Linlin Zhuo, Xiaonan Wu, Xiangzheng Fu, Quan Zou:
Revisiting drug-protein interaction prediction: a novel global-local perspective. - Xiaofan Liu, Yuhuan Tao, Zilin Cai, Pengfei Bao, Hongli Ma, Kexing Li, Mengtao Li, Yunping Zhu, Zhi John Lu:
Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data. - Maximilian Mordig, Gunnar Rätsch, André Kahles:
SimReadUntil for benchmarking selective sequencing algorithms on ONT devices. - Azza Althagafi, Fernando Zhapa-Camacho, Robert Hoehndorf:
Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning. - Dvir Ben Shabat, Adar Hadad, Avital Boruchovsky, Eitan Yaakobi:
GradHC: highly reliable gradual hash-based clustering for DNA storage systems. - Hengchi Chen, Arthur Zwaenepoel, Yves Van de Peer:
wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication. - Qun Jiang, Shengquan Chen, Xiaoyang Chen, Rui Jiang:
scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism. - Zachary A. Rollins, Talal Widatalla, Andrew B. Waight, Alan C. Cheng, Essam Metwally:
AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictions.
Volume 40, Number 6, 2024
- Xingjian Chen, Jiecong Lin, Yuchen Wang, Weitong Zhang, Weidun Xie, Zetian Zheng, Ka-Chun Wong:
HE2Gene: image-to-RNA translation via multi-task learning for spatial transcriptomics data. - Aditya K. Mishra, Iqbal Mahmud, Philip L. Lorenzi, Robert R. Jenq, Jennifer A Wargo, Nadim J. Ajami, Christine B. Peterson:
TARO: tree-aggregated factor regression for microbiome data integration. - Yueyu Jiang, Daniel McDonald, Daniela Perry, Rob Knight, Siavash Mirarab:
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. - Xiying Chen, Jinsha Huang, Tianqiao Shen, Houjin Zhang, Li Xu, Min Yang, Xiaoman Xie, Yunjun Yan, Jinyong Yan:
DEAttentionDTA: protein-ligand binding affinity prediction based on dynamic embedding and self-attention. - Delaney K. Sullivan, Lior Pachter:
Flexible parsing, interpretation, and editing of technical sequences with splitcode. - Jiangmei Xiong, Harsimran Kaur, Cody N. Heiser, Eliot T. McKinley, Joseph T. Roland, Robert J. Coffey, Martha J. Shrubsole, Julia Wrobel, Siyuan Ma, Ken S. Lau, Simon N. Vandekar:
GammaGateR: semi-automated marker gating for single-cell multiplexed imaging. - Xiaopeng Xu, Chencheng Xu, Wenjia He, Lesong Wei, Haoyang Li, Juexiao Zhou, Ruochi Zhang, Yu Wang, Yuanpeng Xiong, Xin Gao:
HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer. - Jonathan Chacko, Hakan Özadam, Can Cenik:
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution. - Uthra Balaji, Juan Rodríguez-Alcázar, Preetha Balasubramanian, Cynthia Smitherman, Jeanine Baisch, Virginia Pascual, Jinghua Gu:
Ragas: integration and enhanced visualization for single cell subcluster analysis. - Giulia Di Teodoro, Martin Pirkl, Francesca Incardona, Ilaria Vicenti, Anders Sönnerborg, Rolf Kaiser, Laura Palagi, Maurizio Zazzi, Thomas Lengauer:
Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy's outcome for HIV-1. - Mohd Imran Khan, Sheetal Pathania, Mohammed W. Al-Rabia, Abdul S. Ethayathulla, Mohammad Imran Khan, Khaled S. Allemailem, Mohd Azam, Gururao Hariprasad, Mohammad Azhar Imran:
MolDy: molecular dynamics simulation made easy. - Etienne Sollier, Jessica Heilmann, Clarissa Gerhauser, Michael Scherer, Christoph Plass, Pavlo Lutsik:
Figeno: multi-region genomic figures with long-read support. - Lexiang Wang, Jingli Zhou, Xuan Wang, Yadong Wang, Junyi Li:
MCDHGN: heterogeneous network-based cancer driver gene prediction and interpretability analysis. - Yonghui Dong, Sergey Malitsky:
MetaboReport: from metabolomics data analysis to comprehensive reporting. - Yueming Yin, Haifeng Hu, Jitao Yang, Chun Ye, Wilson Wen Bin Goh, Adams Wai-Kin Kong, Jiansheng Wu:
OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs. - Peng Ni, Jinrui Xu, Zeyu Zhong, Feng Luo, Jianxin Wang:
RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads. - Alexander Gerniers, Siegfried Nijssen, Pierre Dupont:
scCross: efficient search for rare subpopulations across multiple single-cell samples. - Marjan Faizi, Ryan T. Fellers, Dan Lu, Bryon S. Drown, Ashwini Jambhekar, Galit Lahav, Neil L. Kelleher, Jeremy Gunawardena:
MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data. - Manoj M. Wagle, Siqu Long, Carissa Chen, Chunlei Liu, Pengyi Yang:
Interpretable deep learning in single-cell omics. - Siang Chen, Hao Wang, Dongdong Zhang, Runsheng Chen, Jianjun Luo:
Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data. - Yi Fu, Yingzhou Lu, Yizhi Wang, Bai Zhang, Zhen Zhang, Guoqiang Yu, Chunyu Liu, Robert Clarke, David M. Herrington, Yue Wang:
DDN3.0: determining significant rewiring of biological network structure with differential dependency networks. - Nicholas Matsumoto, Jay Moran, Hyunjun Choi, Miguel E. Hernandez, Mythreye Venkatesan, Zhiping Paul Wang, Jason H. Moore:
KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models. - Ho Yeung Chim, Arne Elofsson:
MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2. - Ziheng Duan, Dylan Riffle, Ren Li, Junhao Liu, Martin Renqiang Min, Jing Zhang:
Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation. - Maxime Branger, Sébastien O. Leclercq:
GenoFig: a user-friendly application for the visualization and comparison of genomic regions. - Correction to: For antibody sequence generative modeling, mixture models may be all you need.
- Ketrin Gjoni, Katherine S. Pollard:
SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. - Wei Song, Lewen Xu, Chenguang Han, Zhen Tian, Quan Zou:
Drug-target interaction predictions with multi-view similarity network fusion strategy and deep interactive attention mechanism. - Eric S. Davis, Sarah M. Parker, Nicole E. Kramer, J. P. Flores, Manjari Kiran, Douglas H. Phanstiel:
Mariner: explore the Hi-Cs. - G. Maria Jakobsdottir, Stefan C. Dentro, Robert G. Bristow, David C. Wedge:
AmplificationTimeR: an R package for timing sequential amplification events. - Nianqiao Ju, Jiawei Liu, Qixin He:
SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts. - Qi Zhang, Le Zuo, Ying Ren, Siyuan Wang, Wenfa Wang, Lerong Ma, Jing Zhang, Bisheng Xia:
FMCA-DTI: a fragment-oriented method based on a multihead cross attention mechanism to improve drug-target interaction prediction. - Alexander Grentner, Eliot Ragueneau, Chuqiao Gong, Adrian Prinz, Sabina Gansberger, Inigo Oyarzun, Henning Hermjakob, Johannes Griss:
ReactomeGSA: new features to simplify public data reuse. - Carlos J. Rodriguez-Flores, Naroa Barrena, Danel Olaverri-Mendizabal, Idoia Ochoa, Luis Vitores Valcarcel, Francisco J. Planes:
gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python. - Philipp Eberhard, Martin Kern, Michael Aichem, Hanna Borlinghaus, Karsten Klein, Johannes Delp, Ilinca Suciu, Benjamin Moser, Daniel Dietrich, Marcel Leist, Falk Schreiber:
PathwayNexus: a tool for interactive metabolic data analysis. - Francesco Gualdi, Baldomero Oliva, Janet Piñero:
Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases. - Jack D. Huey, Nezar Abdennur:
Bigtools: a high-performance BigWig and BigBed library in Rust. - Dylan Barth, Richard Van, Jonathan Cardwell, Mira V. Han:
Supervised learning of enhancer-promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning. - Noriaki Sato, Yao-zhong Zhang, Zuguang Gu, Seiya Imoto:
biotextgraph: graphical summarization of functional similarities from textual information. - Gizem Tas, Timo Westerdijk, Eric O. Postma, Project MinE ALS GWAS Consortium, Jan H. Veldink, Alexander Schönhuth, Marleen Balvert:
Computing linkage disequilibrium aware genome embeddings using autoencoders. - Sebastian Bittrich, Joan Segura, Jose M. Duarte, Stephen K. Burley, Yana Rose:
RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments. - Minzhu Xie, Yabin Kuang, Mengyun Song, Ergude Bao:
Subtype-MGTP: a cancer subtype identification framework based on multi-omics translation. - Philipp Spohr, Max Ried, Laura C. Kühle, Alexander T. Dilthey:
SWGTS - a platform for stream-based host DNA depletion. - Enzo Battistella, Susan Dina Ghiassian, Albert-László Barabási:
Improving the performance and interpretability on medical datasets using graphical ensemble feature selection. - Daiki Tagami, Gertjan Bisschop, Jerome Kelleher:
tstrait : a quantitative trait simulator for ancestral recombination graphs. - Noah Liguori-Bills, Michael L. Blinov:
bnglViz: online visualization of rule-based models. - Marco Guazzini, Alexander G. Reisach, Sebastian Weichwald, Christof Seiler:
spillR : spillover compensation in mass cytometry data. - Teng-Yu Lin, Szu-Chi Chung:
CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm. - Kim L. Vertacnik, Oksana V. Vernygora, Julian R. Dupuis:
snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics. - Aysun Urhan, Bianca-Maria Cosma, Ashlee M. Earl, Abigail L. Manson, Thomas Abeel:
SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings. - Heng Li, Maximillian G. Marin, Maha R. Farhat:
Exploring gene content with pangene graphs. - Marco Pegoraro, Clémentine C. J. Dominé, Emanuele Rodolà, Petar Velickovic, Andreea Deac:
Geometric epitope and paratope prediction. - Oufan Zhang, Shubhankar A. Naik, Zi Hao Liu, Julie D. Forman-Kay, Teresa Head-Gordon:
A curated rotamer library for common post-translational modifications of proteins. - Yingxi Zhang, Zhuohan Yu, Ka-Chun Wong, Xiangtao Li:
Unraveling spatial domain characterization in spatially resolved transcriptomics with robust graph contrastive clustering. - Océane Cassan, Charles-Henri Lecellier, Antoine Martin, Laurent Bréhélin, Sophie Lèbre:
Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana. - Tudor Groza, Dylan Gration, Gareth Baynam, Peter N. Robinson:
FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology. - Zhiming Zhang, Jing Ren, Lili Ren, Lanying Zhang, Qubo Ai, Haixin Long, Yi Ren, Kun Yang, Huiying Feng, Sabrina Li, Xu Li:
MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species. - Fabien Mareuil, Alexandra Moine-Franel, Anuradha Kar, Michael Nilges, Constantin Bogdan Ciambur, Olivier Sperandio:
Protein interaction explorer (PIE): a comprehensive platform for navigating protein-protein interactions and ligand binding pockets. - Davide Cenzato, Zsuzsanna Lipták:
A survey of BWT variants for string collections. - Yan Zhong, Siwei Cui, Yongjian Yang, James J. Cai:
Controlled noise: evidence of epigenetic regulation of single-cell expression variability. - Maria Janina Sarol, Shufan Ming, Shruthan Radhakrishna, Jodi Schneider, Halil Kilicoglu:
Assessing citation integrity in biomedical publications: corpus annotation and NLP models. - Dandan Zheng, Siyu Zhou, Lihong Chen, Guansong Pang, Jian Yang:
A deep learning method to predict bacterial ADP-ribosyltransferase toxins. - Mayank Baranwal, Abram Magner, Paolo Elvati, Jacob Saldinger, Angela Violi, Alfred O. Hero III:
A deep learning architecture for metabolic pathway prediction. - Correction to: The 2024 ISCB Innovator Award - Dr Su-In Lee.
- Wei Tian, Wubin Ding, Jiawei Shen, Daofeng Li, Ting Wang, Joseph R. Ecker:
BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data. - Simon J. Goodman, Ian M. Carr:
Drawing mitochondrial genomes with circularMT. - Zhanhe Chang, Yunfan Xu, Xin Dong, Yawei Gao, Chenfei Wang:
Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro. - Tatiana Novikova, Alexey Ovchinnikov, Gleb Pogudin, Jessica C. Ramella-Roman:
Time-efficient filtering of imaging polarimetric data by checking physical realizability of experimental Mueller matrices. - Dario Simionato, Antonio Collesei, Federica Miglietta, Fabio Vandin:
ALLSTAR: inference of reliAble causaL ruLes between Somatic muTAtions and canceR phenotypes. - Mengying Hu, Maria Chikina:
InstaPrism: an R package for fast implementation of BayesPrism. - Sarah Samorodnitsky, Katie Campbell, Antoni Ribas, Michael C. Wu:
A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data. - Brian H. Chen, Wanding Zhou:
mLiftOver: harmonizing data across Infinium DNA methylation platforms. - Yongjie Wang, Fengfan Zhou, Jinting Guan:
SFINN: inferring gene regulatory network from single-cell and spatial transcriptomic data with shared factor neighborhood and integrated neural network. - François Laurent, Alexandre Blanc, Lilly May, Lautaro Gándara, Benjamin T. Cocanougher, Benjamin M. W. Jones, Peter Hague, Chloé Barré, Christian L. Vestergaard, Justin M. Crocker, Marta Zlatic, Tihana Jovanic, Jean-Baptiste Masson:
LarvaTagger: manual and automatic tagging of Drosophila larval behaviour. - Xinqian Ma, Xiangzheng Fu, Tao Wang, Linlin Zhuo, Quan Zou:
GraphADT: empowering interpretable predictions of acute dermal toxicity with multi-view graph pooling and structure remapping. - Priyansh Srivastava, Marta Benegas Coll, Stefan Götz, María José Nueda, Ana Conesa:
scMaSigPro: differential expression analysis along single-cell trajectories. - Colin G. Cess, Laleh Haghverdi:
Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization. - Vadim A. Pisarenco, Joel Vizueta, Julio Rozas:
GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes. - Retraction and replacement of: A deep learning architecture for metabolic pathway prediction.
- Maxell L. Neal, Nandini Shukla, Fred D. Mast, Jean-Claude Farré, Therese M. Pacio, Katelyn E. Raney-Plourde, Sumedh Prasad, Suresh Subramani, John D. Aitchison:
Automated, image-based quantification of peroxisome characteristics with perox-per-cell. - Brendan Daisley, Sarah J. Vancuren, Dylan J. L. Brettingham, Jacob Wilde, Simone Renwick, Christine V. Macpherson, David A. Good, Alexander J. Botschner, Sandi Yen, Janet E. Hill, Matthew T. Sorbara, Emma Allen-Vercoe:
isolateR: an R package for generating microbial libraries from Sanger sequencing data. - Daniel Pirak, Roded Sharan:
D'or: deep orienter of protein-protein interaction networks. - Ziqing Wang, Michael Cassidy, Danielle A. Wallace, Tamar Sofer:
MethParquet: an R package for rapid and efficient DNA methylation association analysis adopting Apache Parquet. - Roberto Rossini, Jonas Paulsen:
hictk: blazing fast toolkit to work with .hic and .cool files. - Richard D. Paul, Johann F. Jadebeck, Anton Stratmann, Wolfgang Wiechert, Katharina Nöh:
hopsy - a methods marketplace for convex polytope sampling in Python. - Francesca Cuturello, Marco Celoria, Alessio Ansuini, Alberto Cazzaniga:
Enhancing predictions of protein stability changes induced by single mutations using MSA-based language models. - Stephanie Dolenz, Tom van der Valk, Chenyu Jin, Jonas Oppenheimer, Muhammad Bilal Sharif, Ludovic Orlando, Beth Shapiro, Love Dalén, Peter D. Heintzman:
Unravelling reference bias in ancient DNA datasets. - Zhuoyang Chen, Qiong Luo:
DualNetGO: a dual network model for protein function prediction via effective feature selection.
Volume 40, Number 7, 2024
- Yichi Zhang, Chenghui Hu, Xiaohui Wu, Jian Song:
Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data. - Cedric Landerer, Maxim Scheremetjew, HongKee Moon, Lena Hersemann, Ágnes Tóth-Petróczy:
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets. - Guangzhi Xiong, Nathan Leroy, Stefan Bekiranov, Nathan C. Sheffield, Aidong Zhang:
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data. - Thang V. Pham, Alex A. Henneman, Nam X. Truong, Connie R. Jimenez:
msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease. - Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F. Miller, Rahul Satija, John W. Hickey, Jean Fan:
SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis. - Sebastian Deorowicz, Adam Gudys:
Efficient protein structure archiving using ProteStAr. - Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joseph C. Wu, Rabindra V. Shivnaraine, James Zou:
ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries. - Hamed Vasei, Mohammad-Hadi Foroughmand-Araabi, Amir Daneshgar:
Weighted centroid trees: a general approach to summarize phylogenies in single-labeled tumor mutation tree inference. - Mo Li, Xing Hua, Shuai Li, Michael C. Wu, Ni Zhao:
A multi-bin rarefying method for evaluating alpha diversities in TCR sequencing data. - Zilin Ren, Lili Jiang, Yaxin Di, Dufei Zhang, Jianli Gong, Jianting Gong, Qiwei Jiang, Zhiguo Fu, Pingping Sun, Bo Zhou, Ming Ni:
CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism. - Sabhay Jain, Xingjian Li, Min Xu:
Knowledge transfer from macro-world to micro-world: enhancing 3D Cryo-ET classification through fine-tuning video-based deep models. - Rinaldo W. Montalvão, William R. Pitt, Vitor Bernardes Pinheiro, Tom L. Blundell:
Melodia: a Python library for protein structure analysis. - Jose Manuel Martí, Chloe Hsu, Charlotte Rochereau, Chenling Xu, Tomasz Blazejewski, Hunter Nisonoff, Sean P. Leonard, Christina S. Kang-Yun, Jennifer Chlebek, Dante P. Ricci, Dan Park, Harris Wang, Jennifer Listgarten, Yongqin Jiao, Jonathan E. Allen:
GENTANGLE: integrated computational design of gene entanglements. - Liting Zhang, Xin Maizie Zhou, Xian F. Mallory:
SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data. - Wan-Yu Lin:
Detecting gene-environment interactions from multiple continuous traits. - Jayamini C. Liyanage, Luke Prendergast, Robert G. Staudte, Alysha M. De Livera:
MetaHD: a multivariate meta-analysis model for metabolomics data. - Zheng-Dao Yang, Hsuan-Yu Kuo, Po-Wei Hsieh, Jui-Hung Hung:
Efficient construction and utilization of k-ordered FM-indexes with kISS for ultra-fast read mapping in large genomes. - Ali Gharizadeh, Karim Abbasi, Amin Ghareyazi, Mohammad R. K. Mofrad, Hamid R. Rabiee:
HGTDR: Advancing drug repurposing with heterogeneous graph transformers. - Fei Wang, Xianglong Cheng, Xin Xia, Chunhou Zheng, Yansen Su:
Adaptive space search-based molecular evolution optimization algorithm. - Qi Qi, Yunhe Wang, Yujian Huang, Yi Fan, Xiangtao Li:
PredGCN: a Pruning-enabled Gene-Cell Net for automatic cell annotation of single cell transcriptome data. - Ana Mendes, Jesper Foged Havelund, Jonas Lemvig, Veit Schwämmle, Nils J. Færgeman:
MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data. - Kristen Nader, Misra Tasci, Aleksandr Ianevski, Andrew Erickson, Emmy W. Verschuren, Tero Aittokallio, Mitro Miihkinen:
ScType enables fast and accurate cell type identification from spatial transcriptomics data. - Saeed Moayedpour, Jonathan Broadbent, Saleh Riahi, Michael Bailey, Hoa V. Thu, Dimitar A. Dobchev, Akshay Balsubramani, Ricardo N. D. Santos, Lorenzo Kogler-Anele, Alejandro Corrochano-Navarro, Sizhen Li, Fernando U. Montoya, Vikram Agarwal, Ziv Bar-Joseph, Sven Jager:
Representations of lipid nanoparticles using large language models for transfection efficiency prediction. - Jiating Yu, Jiacheng Leng, Fan Yuan, Duanchen Sun, Ling-Yun Wu:
Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks. - Michael Payne, Dalong Hu, Qinning Wang, Geraldine Sullivan, Rikki M. Graham, Irani U. Rathnayake, Amy V. Jennison, Vitali Sintchenko, Ruiting Lan:
DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance. - Shiyu Xu, Lian Shen, Menglong Zhang, Changzhi Jiang, Xinyi Zhang, Yanni Xu, Juan Liu, Xiangrong Liu:
Surface-based multimodal protein-ligand binding affinity prediction. - Simon Heumos, Andrea Guarracino, Jan-Niklas Schmelzle, Jiajie Li, Zhiru Zhang, Jörg Hagmann, Sven Nahnsen, Pjotr Prins, Erik Garrison:
Pangenome graph layout by Path-Guided Stochastic Gradient Descent. - Weihong Xu, Po-Kai Hsu, Niema Moshiri, Shimeng Yu, Tajana Rosing:
HyperGen: compact and efficient genome sketching using hyperdimensional vectors. - Jianyuan Yuan, Fengyu Zhang, Yimeng Qiu, Hongfei Lin, Yijia Zhang:
Document-level biomedical relation extraction via hierarchical tree graph and relation segmentation module.
Volume 40, Number 8, 2024
- Andrew Dickson, Mohammad R. K. Mofrad:
Fine-tuning protein embeddings for functional similarity evaluation. - Samson Weiner, Bingjun Li, Sheida Nabavi:
Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing. - Yuelei Hao, Xuyang Liu, Haohao Fu, Xueguang Shao, Wensheng Cai:
PGAT-ABPp: harnessing protein language models and graph attention networks for antibacterial peptide identification with remarkable accuracy. - Aditya J. Sethi, Pablo Acera Mateos, Rippei Hayashi, Nikolay E. Shirokikh, Eduardo Eyras:
R2Dtool: integration and visualization of isoform-resolved RNA features. - Nuwan Goonasekera, Alexandru Mahmoud, Keith Suderman, Enis Afgan:
Galaxy Helm chart: a standardized method for deploying production Galaxy servers. - Mauro Silberberg, Henning Hermjakob, Rahuman S. Malik-Sheriff, Hernán E. Grecco:
Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems. - Can Firtina, Melina Soysal, Joël Lindegger, Onur Mutlu:
RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization. - Arijit Panda, Milovan Suvakov, Helga Thorvaldsdóttir, Jill P. Mesirov, James T. Robinson, Alexej Abyzov:
Genome-wide analysis and visualization of copy number with CNVpytor in igv.js. - Yunxiang Yu, Mengyun Gu, Hai Guo, Yabo Deng, Danna Chen, Jianwei Wang, Caixia Wang, Xia Liu, Wenjin Yan, Jinqi Huang:
MuCoCP: a priori chemical knowledge-based multimodal contrastive learning pre-trained neural network for the prediction of cyclic peptide membrane penetration ability. - Osamu Gotoh:
Spaln3: improvement in speed and accuracy of genome mapping and spliced alignment of protein query sequences. - Eric Weine, Peter Carbonetto, Matthew Stephens:
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. - Daniel H. Huson, Joana C. Xavier, Mike A. Steel:
CatReNet: interactive analysis of (auto-) catalytic reaction networks. - Shilin Yu, Guanqun Meng, Wen Tang, Wenjing Ma, Rui Wang, Xiongwei Zhu, Xiaobo Sun, Hao Feng:
cypress: an R/Bioconductor package for cell-type-specific differential expression analysis power assessment. - Johanna Lena Geist, Chop Yan Lee, Joelle Morgan Strom, José de Jesús Naveja, Katja Luck:
Generation of a high confidence set of domain-domain interface types to guide protein complex structure predictions by AlphaFold. - Awan Afiaz, Andrey Ivanov, John Chamberlin, David Hanauer, Candace Savonen, Mary J. Goldman, Martin Morgan, Michael Reich, Alexander Getka, Aaron Holmes, Sarthak Pati, Dan Knight, Paul C. Boutros, Spyridon Bakas, J. Gregory Caporaso, Guilherme Del Fiol, Harry Hochheiser, Brian Haas, Patrick D. Schloss, James A. Eddy, Jake Albrecht, Andrey Fedorov, Levi Waldron, Ava M. Hoffman, Richard L. Bradshaw, Jeffrey T. Leek, Carrie Wright:
Best practices to evaluate the impact of biomedical research software - metric collection beyond citations. - Ha Young Kim, Sungsik Kim, Woong-Yang Park, Dongsup Kim:
TSpred: a robust prediction framework for TCR-epitope interactions using paired chain TCR sequence data. - Hiruna Samarakoon, Kisaru Liyanage, James M. Ferguson, Sri Parameswaran, Hasindu Gamaarachchi, Ira W. Deveson:
Interactive visualization of nanopore sequencing signal data with Squigualiser. - Lucas Czech, Jeffrey P. Spence, Moisés Expósito-Alonso:
grenedalf: population genetic statistics for the next generation of pool sequencing. - Anqi Wang, Peixin Tian, Yan Dora Zhang:
TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference. - Fuyi Li, Yue Bi, Xudong Guo, Xiaolan Tan, Cong Wang, Shirui Pan:
Advancing mRNA subcellular localization prediction with graph neural network and RNA structure. - James Krieger, Frane Doljanin, Anthony T. Bogetti, Feng Zhang, Thiliban Manivarma, Ivet Bahar, Karolina Mikulska-Ruminska:
WatFinder: a ProDy tool for protein-water interactions. - Loïc Le Grégam, Yann Guitton, Floriant Bellvert, Stéphanie Heux, Fabien Jourdan, Jean-Charles Portais, Pierre Millard:
PhysioFit: a software to quantify cell growth parameters and extracellular fluxes. - Aarushi Sehgal, Helyaneh Ziaei Jam, Andrew Shen, Melissa Gymrek:
Genome-wide detection of somatic mosaicism at short tandem repeats. - Jacques Serizay, Romain Koszul:
Epigenomics coverage data extraction and aggregation in R with tidyCoverage. - Becca Bonham-Carter, Geoffrey Schiebinger:
Cellular proliferation biases clonal lineage tracing and trajectory inference. - Guangyao Mao, Yi Yang, Zhuojuan Luo, Chengqi Lin, Peng Xie:
SpatialQC: automated quality control for spatial transcriptome data. - Áine Niamh O'toole, Ammar Aziz, Daniel Maloney:
Publication-ready single nucleotide polymorphism visualization with snipit. - James V. Talwar, Adam R. Klie, Meghana S. Pagadala, Hannah Carter:
GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies. - Pallavi Surana, Pratik Dutta, Ramana V. Davuluri:
TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups. - Douyue Li, Zhuochao Min, Jia Guo, Yubin Chen, Wenliang Zhang:
ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities. - Lars Berling, Lena Collienne, Alex Gavryushkin:
Estimating the mean in the space of ranked phylogenetic trees. - Hanyu Luo, Li Tang, Min Zeng, Rui Yin, Pingjian Ding, Lingyun Luo, Min Li:
BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model. - Samuele Garda, Ulf Leser:
BELHD: improving biomedical entity linking with homonym disambiguation. - Harto Saarinen, Mark Goldsmith, Rui-Sheng Wang, Joseph Loscalzo, Sabrina Maniscalco:
Disease gene prioritization with quantum walks. - Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Ignacio Carvajal, Sarah Bailey, Susan Thomson, Cecilia H. Deng:
AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality. - Xinmeng Li, Yan Zhou Chen, Apurva Kalia, Hao Zhu, Liping Liu, Soha Hassoun:
An Ensemble Spectral Prediction (ESP) model for metabolite annotation. - Julián Montoto-Louzao, Alberto Gómez-Carballa, Xabier Bello, Jacobo Pardo-Seco, Alba Camino-Mera, Sandra Viz-Lasheras, María J. Martín, Federico Martinón-Torres, Antonio Salas:
GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization. - German P. Barletta, Rika Tandiana, Miguel A. Soler, Sara Fortuna, Walter Rocchia:
Locuaz: an in silico platform for protein binders optimization. - Hanbin Lee, Buhm Han:
Pseudobulk with proper offsets has the same statistical properties as generalized linear mixed models in single-cell case-control studies. - Alexander P. Sweeten, Michael C. Schatz, Adam M. Phillippy:
ModDotPlot - rapid and interactive visualization of tandem repeats. - Shai Elkayam, Ido Tziony, Yaron Orenstein:
DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 on-target editing efficiency in specific cellular contexts. - Aron Schulman, Juho Rousu, Tero Aittokallio, ZiaurRehman Tanoli:
Attention-based approach to predict drug-target interactions across seven target superfamilies. - Nicholas S. Edmunds, Ahmet G. Genc, Liam J. McGuffin:
Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes. - Kwan-Ling Wu, Melisa Montalvo, Prashant Menon, Badrinath Roysam, Navin Varadarajan:
PostFocus: automated selective post-acquisition high-throughput focus restoration using diffusion model for label-free time-lapse microscopy. - Eva Martín del Pico, Josep Lluís Gelpí, Salvador Capella-Gutiérrez:
FAIRsoft - a practical implementation of FAIR principles for research software. - Rachel J. House, James P. Eapen, Hui Shen, Carrie R. Graveel, Matthew R. Steensma:
ceas: an R package for Seahorse data analysis and visualization. - Jiahao Gao, Mark Gerstein:
Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks. - Kimia Yazdani, Reza Mousapour, Wayne B. Hayes:
New GO-based measures in multiple network alignment. - Teer Ba, Hao Miao, Lirong Zhang, Caixia Gao, Yong Wang:
ClusterMatch aligns single-cell RNA-sequencing data at the multi-scale cluster level via stable matching. - Sergey Oreshkov, Kaido Lepik, Federico A. Santoni:
pyTWMR: transcriptome-wide Mendelian randomization in python. - Maria K. Janowska, Katherine Reiter, Pearl Magala, Miklos Guttman, Rachel E. Klevit:
HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen-Deuterium Exchange Mass-Spectrometry datasets of different protein states.
Volume 40, Number 9, 2024
- Yue Lyu, Steven H. Lin, Hao Wu, Ziyi Li:
SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric. - Helena B. Conceição, Rafael L. V. Mercuri, Matheus P. M. de Castro, Daniel T. Ohara, Gabriela D. A. Guardia, Pedro A. F. Galante:
RCPedia: a global resource for studying and exploring retrocopies in diverse species. - Ziad Al Bkhetan, Sen Wang:
mgikit: demultiplexing toolkit for MGI fastq files. - Valérie Marot-Lassauzaie, Sergi Beneyto-Calabuig, Benedikt Obermayer, Lars Velten, Dieter Beule, Laleh Haghverdi:
Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data. - Karthik Soman, Peter W. Rose, John H. Morris, Rabia E. Akbas, Brett Smith, Braian Peetoom, Catalina Villouta-Reyes, Gabriel Cerono, Yongmei Shi, Angela Rizk-Jackson, Sharat Israni, Charlotte A. Nelson, Sui Huang, Sergio E. Baranzini:
Biomedical knowledge graph-optimized prompt generation for large language models. - William R. Boulton, Fatma Rabia Fidan, Hubert Denise, Nicola De Maio, Nick Goldman:
SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes. - Prawin Rimal, Shailesh Kumar Panday, Wang Xu, Yunhui Peng, Emil Alexov:
SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein-protein complexes. - Antoine Passemiers, Stefania Tuveri, Dhanya Sudhakaran, Tatjana Jatsenko, Tina Laga, Kevin Punie, Sigrid Hatse, Sabine Tejpar, An Coosemans, Els Van Nieuwenhuysen, Dirk Timmerman, Giuseppe Floris, Anne-Sophie Van Rompuy, Xavier Sagaert, Antonia C. Testa, Daniela Ficherova, Daniele Raimondi, Frederic Amant, Liesbeth Lenaerts, Yves Moreau, Joris Robert Vermeesch:
MetDecode: methylation-based deconvolution of cell-free DNA for noninvasive multi-cancer typing. - Jinbo Zhang, Shunling Yuan, Wen Cao, Xianrui Jiang, Cheng Yang, Chenchao Jiang, Runhui Liu, Wei Yang, Saisai Tian:
Signature Search Polestar: a comprehensive drug repurposing method evaluation assistant for customized oncogenic signature. - Jiayu Shang, Cheng Peng, Yongxin Ji, Jiaojiao Guan, Dehan Cai, Xubo Tang, Yanni Sun:
Accurate and efficient protein embedding using multi-teacher distillation learning. - Mehrshad Sadria, Thomas M. Bury:
FateNet: an integration of dynamical systems and deep learning for cell fate prediction. - Dhruv Khatri, Shivani A. Yadav, Chaitanya A. Athale:
KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs. - Zheni Zeng, Bangchen Yin, Shipeng Wang, Jiarui Liu, Cheng Yang, Haishen Yao, Xingzhi Sun, Maosong Sun, Guotong Xie, Zhiyuan Liu:
ChatMol: interactive molecular discovery with natural language. - Chih-Yuan Hsu, Qi Liu, Yu Shyr:
A distribution-free and analytic method for power and sample size calculation in single-cell differential expression. - Sam Boshar, Evan Trop, Bernardo P. de Almeida, Liviu Copoiu, Thomas Pierrot:
Are genomic language models all you need? Exploring genomic language models on protein downstream tasks. - Xiangyong Tan, Xiao Zhang, Yuehua Cui, Xu Liu:
Uncertainty quantification in high-dimensional linear models incorporating graphical structures with applications to gene set analysis. - Raúl Fernández-Díaz, Rodrigo Cossio-Pérez, Clement Agoni, Hoang Thanh Lam, Vanessa López, Denis C. Shields:
AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors. - Xin Ma, Sai Ritesh Thela, Fengdi Zhao, Bing Yao, Zhexing Wen, Peng Jin, Jinying Zhao, Li Chen:
Deep5hmC: predicting genome-wide 5-hydroxymethylcytosine landscape via a multimodal deep learning model. - Jan Velecký, Matej Berezný, Milos Musil, Jirí Damborský, David Bednar, Stanislav Mazurenko:
BenchStab: a tool for automated querying of web-based stability predictors. - Xingyu Pan, Siyuan Pan, Murong Du, Jinlei Yang, Huan Yao, Xinrong Zhang, Sichun Zhang:
SCMeTA: a pipeline for single-cell metabolic analysis data processing. - Krzysztof Polanski, Raquel Bartolomé-Casado, Ioannis Sarropoulos, Chuan Xu, Nick England, Frode L. Jahnsen, Sarah A. Teichmann, Nadav Yayon:
Bin2cell reconstructs cells from high resolution Visium HD data. - Peter De Rijk, Tijs Watzeels, Fahri Küçükali, Jasper Van Dongen, Júlia Faura, Patrick Willems, Lara De Deyn, Lena Duchateau, Carolin Grones, Thomas Eekhout, Tim De Pooter, Geert Joris, Stephane Rombauts, Bert De Rybel, Rosa Rademakers, Frank Van Breusegem, Mojca Strazisar, Kristel Sleegers, Wouter De Coster:
Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing. - Barry Ryan, Riccardo E. Marioni, T. Ian Simpson:
Multi-Omic Graph Diagnosis (MOGDx): a data integration tool to perform classification tasks for heterogeneous diseases. - Khandakar Tanvir Ahmed, Md. Istiaq Ansari, Wei Zhang:
DTI-LM: language model powered drug-target interaction prediction. - Xiaoyi Liu, Chengwei Ai, Hongpeng Yang, Ruihan Dong, Jijun Tang, Shuangjia Zheng, Fei Guo:
RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representation. - Tümay Capraz, Wolfgang Huber:
Feature selection by replicate reproducibility and non-redundancy. - Mena Soliman Asaad Kamel, Amrut Sarangi, Pavel Senin, Sergio Villordo, Sunaal Mathew, Het Barot, Seqian Wang, Ana Solbas, Luis Cano Ayestas, Marion Classe, Ziv Bar-Joseph, Albert Pla Planas:
SpatialOne: end-to-end analysis of visium data at scale. - Yi Liu, Tom R. Gaunt:
Triangulating evidence in health sciences with Annotated Semantic Queries. - Jose Gavaldá-García, Adrián Díaz, Wim F. Vranken:
bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties. - Sara Mohammad Taheri, Pruthvi Prakash Navada, Charles Tapley Hoyt, Jeremy Zucker, Karen Sachs, Benjamin M. Gyori, Olga Vitek:
Eliater: a Python package for estimating outcomes of perturbations in biomolecular networks. - Steven B. Cannon, Hyunoh Lee, Nathan T. Weeks, Joel Berendzen:
Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications. - David Wissel, Nikita Janakarajan, Julius Schulte, Daniel Rowson, Xintian Yuan, Valentina Boeva:
sparsesurv: a Python package for fitting sparse survival models via knowledge distillation. - Ping Xuan, Zelong Xu, Hui Cui, Jing Gu, Cheng Liu, Tiangang Zhang, Peiliang Wu:
Dynamic category-sensitive hypergraph inferring and homo-heterogeneous neighbor feature learning for drug-related microbe prediction. - Joel Hellewell, Samuel T. Horsfield, Johanna von Wachsmann, Tatiana A. Gurbich, Robert D. Finn, Zamin Iqbal, Leah W. Roberts, John A. Lees:
CELEBRIMBOR: core and accessory genes from metagenomes. - Soel Micheletti, Daniel Schlauch, John Quackenbush, Marouen Ben Guebila:
Higher-order correction of persistent batch effects in correlation networks. - Erpai Luo, Minsheng Hao, Lei Wei, Xuegong Zhang:
scDiffusion: conditional generation of high-quality single-cell data using diffusion model. - Tao Jiang, Zuji Zhou, Zhendong Zhang, Shuqi Cao, Yadong Wang, Yadong Liu:
MEHunter: transformer-based mobile element variant detection from long reads. - Zeyu Xia, Weiming Xiang, Qingzhe Wang, Xingze Li, Yilin Li, Junyu Gao, Tao Tang, Canqun Yang, Yingbo Cui:
CSV-Filter: a deep learning-based comprehensive structural variant filtering method for both short and long reads. - Dawei Jiang, Binbin Xi, Wenchong Tan, Zixi Chen, Jinfen Wei, Meiling Hu, Xiaoyun Lu, Dong Chen, Hongmin Cai, Hongli Du:
NeoaPred: a deep-learning framework for predicting immunogenic neoantigen based on surface and structural features of peptide-human leukocyte antigen complexes. - Jana M. Braunger, Britta Velten:
Guide assignment in single-cell CRISPR screens using crispat. - Farrokh Mehryary, Katerina C. Nastou, Tomoko Ohta, Lars Juhl Jensen, Sampo Pyysalo:
STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature.
Volume 40, Number 10, 2024
- Oliver Pain, Ammar Al-Chalabi, Cathryn M. Lewis:
The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring. - Kevin Mildau, Christoph Bueschl, Jürgen Zanghellini, Justin J. J. van der Hooft:
Combined LC-MS/MS feature grouping, statistical prioritization, and interactive networking in msFeaST. - Yilan Bai, Haochen Zhong, Taiwei Wang, Zhi John Lu:
OligoFormer: an accurate and robust prediction method for siRNA design. - Benjamin B. Chu, Jiaqi Gu, Zhaomeng Chen, Tim Morrison, Emmanuel J. Candès, Zihuai He, Chiara Sabatti:
Second-order group knockoffs with applications to genome-wide association studies. - Correction to: AgIn: measuring the landscape of CpG methylation of individual repetitive elements.
- Sayan Ghosal, Michael C. Schatz, Archana Venkataraman:
BEATRICE: Bayesian fine-mapping from summary data using deep variational inference. - Correction to: Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students.
- Ramisa Alam, Sazan Mahbub, Md. Shamsuzzoha Bayzid:
Pair-EGRET: enhancing the prediction of protein-protein interaction sites through graph attention networks and protein language models. - Yilin Zhu, Guowei Chen, Yanni Sun:
VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation. - Marco Giulini, Constantin Schneider, Daniel Cutting, Nikita Desai, Charlotte M. Deane, Alexandre M. J. J. Bonvin:
Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking. - Weijia Jin, Yi Xia, Javlon Nizomov, Yunlong Liu, Zhigang Li, Qing Lu, Li Chen:
MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants. - Kathryn Lande, April E. Williams:
PCBS: an R package for fast and accurate analysis of bisulfite sequencing data. - Anindita Nath, Savannah Mwesigwa, Yulin Dai, Xiaoqian Jiang, Zhongming Zhao:
GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console. - Jan Beránek, Ales Krenek, Vojtech Spiwok:
Analysis of metadynamics simulations by metadynminer.py. - Maxwell Murphy, Bryan Greenhouse:
MOIRE: a software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data. - Ruipeng Lu, Tim Dumonceaux, Muhammad Anzar, Athanasios Zovoilis, Kym Antonation, Dillon Barker, Cindi Corbett, Celine Nadon, James Robertson, Shannon H. C. Eagle, Oliver Lung, Josip Rudar, Om Surujballi, Chad Laing:
MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification. - Koichiro Majima, Yasuhiro Kojima, Kodai Minoura, Ko Abe, Haruka Hirose, Teppei Shimamura:
LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors. - Tianjiao Zhang, Hongfei Zhang, Jixiang Ren, Zhenao Wu, Zhongqian Zhao, Guohua Wang:
scDRMAE: integrating masked autoencoder with residual attention networks to leverage omics feature dependencies for accurate cell clustering. - Chenyu Zhang, Honglin Wang, Yeonsoo Chung, Seung-Hyun Hong, Merissa Olmer, Hannah Swahn, Martin Lotz, Peter F. Maye, David W. Rowe, Dong-Guk Shin:
vSPACE: exploring virtual spatial representation of articular chondrocytes at the single-cell level. - Tao Tang, Tianyang Li, Weizhuo Li, Xiaofeng Cao, Yuansheng Liu, Xiangxiang Zeng:
Anti-symmetric framework for balanced learning of protein-protein interactions. - Zihuan Liu, Yan Sun, Xin Huang:
BioPred: an R package for biomarkers analysis in precision medicine. - András Gézsi, Péter Antal:
GNN4DM: a graph neural network-based method to identify overlapping functional disease modules. - Xueliang Li, Bihan Shen, Fangyoumin Feng, Kunshi Li, Zhixuan Tang, Liangxiao Ma, Hong Li:
Dual-view jointly learning improves personalized drug synergy prediction. - Hegang Chen, Yuyin Lu, Yanghui Rao:
A self-training interpretable cell type annotation framework using specific marker gene. - Baixue Qiao, Shuda Wang, Mingjun Hou, Haodi Chen, Zhengwenyang Zhou, Xueying Xie, Shaozi Pang, Chunxue Yang, Fenglong Yang, Quan Zou, Shanwen Sun:
Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network. - Wenqian Yu, Hongwu Yu, Jingjing Zhao, Hena Zhang, Kalam Ke, Zhixiang Hu, Shenglin Huang:
NeoDesign: a computational tool for optimal selection of polyvalent neoantigen combinations. - Jiaxing Huang, Yaoru Luo, Yuanhao Guo, Wenjing Li, Zichen Wang, Guole Liu, Ge Yang:
Accurate segmentation of intracellular organelle networks using low-level features and topological self-similarity. - Ying Li, Teresa Lee, Kai Marin, Xing Hua, Sujatha Srinivasan, David N. Fredricks, John R. Lee, Wodan Ling:
SurvBal: compositional microbiome balances for survival outcomes. - Claudio Mirabello, Björn Wallner:
DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules. - Rajalakshmi Viswanathan, Moshe Carroll, Alexandra Roffe, Jorge E. Fajardo, András Fiser:
Computational prediction of multiple antigen epitopes. - Richard Mayne, Shannah Secret, Cyndi Geoghegan, Amy Trebes, Kai Kean, Kaitlin Reid, Gu-Lung Lin, M. Azim Ansari, Mariateresa de Cesare, David G. Bonsall, Ivo Elliott, Paolo Piazza, Anthony Brown, James Bray, Julian C. Knight, Heli Harvala, Judith Breuer, Peter Simmonds, Rory J. Bowden, Tanya Golubchik:
Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data. - Jipeng Huang, Chang Sun, Minglei Li, Rong Tang, Bin Xie, Shuqin Wang, Jin-Mao Wei:
Structure-inclusive similarity based directed GNN: a method that can control information flow to predict drug-target binding affinity. - Joshua T. Davis, Alyssa N. Obermayer, Alex C. Soupir, Rebecca S. Hesterberg, Thac Duong, Ching-Yao Yang, Ken Phong Dao, Brandon J. Manley, G. Daniel Grass, Dorina Avram, Paulo C. Rodriguez, Brooke L. Fridley, Xiaoqing Yu, Mingxiang Teng, Xuefeng Wang, Timothy I. Shaw:
BatchFLEX: feature-level equalization of X-batch. - Guanyu Qiao, Guohua Wang, Yang Li:
Causal enhanced drug-target interaction prediction based on graph generation and multi-source information fusion. - Fanjun Meng, Xiaobo Li, Xiaodi Hou, Mingyu Lu, Yijia Zhang:
MGRN: toward robust drug recommendation via multi-view gating retrieval network. - Honghao Wang, Acong Zhang, Yuan Zhong, Junlei Tang, Kai Zhang, Ping Li:
Chain-aware graph neural networks for molecular property prediction. - Chao Hou, Guihua Duan, Cheng Yan:
MSDAFL: molecular substructure-based dual attention feature learning framework for predicting drug-drug interactions. - Hang Yang, Xiaoxin Lu, Jiaxing Chang, Qing Chang, Wen Zheng, Zehua Chen, Huiguang Yi:
Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique. - Lu Meng, Xiaoran Wang:
TAWFN: a deep learning framework for protein function prediction. - Peng Chen, Jian Wang, Ling Luo, Hongfei Lin, Zhihao Yang:
Learning to explain is a good biomedical few-shot learner. - Kanami Yagimoto, Shion Hosoda, Miwa Sato, Michiaki Hamada:
Prediction of antibiotic resistance mechanisms using a protein language model. - Sofia Mongardi, Silvia Cascianelli, Marco Masseroli:
Biologically weighted LASSO: enhancing functional interpretability in gene expression data analysis. - Oliver Hunewald, Agnieszka Demczuk, Joseph Longworth, Markus Ollert:
CyCadas: accelerating interactive annotation and analysis of clustered cytometry data. - Henry Kenlay, Frédéric A. Dreyer, Daniel Cutting, Daniel A. Nissley, Charlotte M. Deane:
ABodyBuilder3: improved and scalable antibody structure predictions. - Long Zhao, Hongmei Wang, Shaoping Shi:
PocketDTA: an advanced multimodal architecture for enhanced prediction of drug-target affinity from 3D structural data of target binding pockets. - Eva Brombacher, Clemens Kreutz:
RTF: an R package for modelling time course data. - Mario Sänger, Samuele Garda, Xing David Wang, Leon Weber-Genzel, Pia Droop, Benedikt Fuchs, Alan Akbik, Ulf Leser:
HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools. - Brad T. Sherman, Ganesh Panzade, Tomozumi Imamichi, Weizhong Chang:
DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs. - Cong Zhou, Chuipu Cai, Xiao-Tian Huang, Song Wu, Jun-Lin Yu, Jing-Wei Wu, Jiansong Fang, Guo-Bo Li:
TarKG: a comprehensive biomedical knowledge graph for target discovery. - Yanfang Li, Shihua Zhang:
Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics. - Xiao Liang, Pei Liu, Li Xue, Baiyun Chen, Wei Liu, Wanwan Shi, Yongwang Wang, Xiangtao Chen, Jiawei Luo:
A multi-modality and multi-granularity collaborative learning framework for identifying spatial domains and spatially variable genes. - Anchen Li, Elena Casiraghi, Juho Rousu:
Chemical reaction enhanced graph learning for molecule representation.
Volume 40, Number 11, 2024
- Remco L. van den Broek, Xabier Bello, Rebecca V. Küpper, Gerard J. P. van Westen, Willem Jespers, Hugo Gutiérrez-de-Terán:
Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell. - Brendan O'Fallon, Ashini Bolia, Jacob Durtschi, Luobin Yang, Eric Fredrickson, Hunter Best:
Generative haplotype prediction outperforms statistical methods for small variant detection in next-generation sequencing data. - Esmaeil Nourani, Mikaela Koutrouli, Yijia Xie, Danai Vagiaki, Sampo Pyysalo, Katerina C. Nastou, Søren Brunak, Lars Juhl Jensen:
Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition. - Subash Chandra Pakhrin, Neha Chauhan, Salman Khan, Jamie Upadhyaya, Moriah Rene Beck, Eduardo Blanco:
Prediction of human O-linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model. - Juan C. Muñoz-Sánchez, María J. Olmo-Uceda, José Ángel Oteo, Santiago F. Elena:
Quantifying defective and wild-type viruses from high-throughput RNA sequencing. - Céline Marquet, Julius Schlensok, Marina Abakarova, Burkhard Rost, Elodie Laine:
Expert-guided protein language models enable accurate and blazingly fast fitness prediction. - Zelin Li, Dongying Xie, Yiming Ma, Cunming Zhao, Sicheng You, Hong Yan, Zhongying Zhao:
Deep learning-based enhancement of fluorescence labeling for accurate cell lineage tracing during embryogenesis. - Mukai Wang, Simon Fontaine, Hui Jiang, Gen Li:
ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models. - Norbert Deutsch, Zsuzsanna Dosztányi, István Csabai, Anna Medgyes-Horváth, Orsolya Pipek, József Stéger, Krisztián Papp, Dávid Visontai, Gábor Erdös, Anikó Mentes:
ViralPrimer: a web server to monitor viral nucleic acid amplification tests' primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox. - Brandon H. Bergsneider, Orieta Celiku:
PRONA: an R-package for Patient Reported Outcomes Network Analysis. - Haoyu Chao, Zhuojin Li, Dijun Chen, Ming Chen:
iSeq: an integrated tool to fetch public sequencing data. - Michael K. B. Ford, Ananth Hari, Qinghui Zhou, Ibrahim Numanagic, S. Cenk Sahinalp:
Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool. - Robert C. Edgar:
Protein structure alignment by Reseek improves sensitivity to remote homologs. - Simon Heumos, Michael L. Heuer, Friederike Hanssen, Lukas Heumos, Andrea Guarracino, Peter Heringer, Philipp Ehmele, Pjotr Prins, Erik Garrison, Sven Nahnsen:
Cluster-efficient pangenome graph construction with nf-core/pangenome. - Rosario Astaburuaga-García, Thomas Sell, Samet Mutlu, Anja Sieber, Kirsten Lauber, Nils Blüthgen:
RUCova: Removal of Unwanted Covariance in mass cytometry data. - Congcong Hu, Yunxiao Li, Longhui Li, Naiqian Zhang, Xiaoqi Zheng:
BS-clock, advancing epigenetic age prediction with high-resolution DNA methylation bisulfite sequencing data. - Matthew McFee, Jisun Kim, Philip M. Kim:
EuDockScore: Euclidean graph neural networks for scoring protein-protein interfaces. - Kristine Bilgrav Saether, Jesper Eisfeldt:
Detecting transposable elements in long-read genomes using sTELLeR. - Quanyu Chen, Chentao Yang, Guojie Zhang, Dongya Wu:
GCI: a continuity inspector for complete genome assembly. - Jun Hyeong Kim, Bonil Koo, Sun Kim:
PONYTA: prioritization of phenotype-related genes from mouse KO events using PU learning on a biological network. - Seyedeh Fatemeh Khezri, Ali Ebrahimi, Changiz Eslahchi:
Target controllability: a feed-forward greedy algorithm in complex networks, meeting Kalman's rank condition. - Benjamin S. Strope, Katherine E. Pendleton, William Z. Bowie, Gloria V. Echeverria, Qian Zhu:
Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments. - Alejandro Alonso-Marín, Ivan Fernandez, Quim Aguado-Puig, Juan Gómez-Luna, Santiago Marco-Sola, Onur Mutlu, Miquel Moretó:
BIMSA: accelerating long sequence alignment using processing-in-memory. - Bruno Sousa, Maria Bessa, Filipa L. de Mendonça, Pedro G. Ferreira, Alexandra Moreira, Isabel Pereira-Castro:
APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data. - Sri Devan Appasamy, Craig L. Zirbel:
R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species. - Javier González-Delgado, Pau Bernadó, Pierre Neuvial, Juan Cortés:
Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins. - Tasbiraha Athaya, Xiaoman Li, Haiyan Hu:
A deep learning method to integrate extracelluar miRNA with mRNA for cancer studies. - Benjamin Jean-Marie Tremblay, Julia I. Qüesta:
quaqc: efficient and quick ATAC-seq quality control and filtering. - Hiromu Hayashi, Toshiyuki Ko, Zhehao Dai, Kanna Fujita, Seitaro Nomura, Hiroki Kiyoshima, Shinya Ishihara, Momoko Hamano, Issei Komuro, Yoshihiro Yamanishi:
TRAITER: transformer-guided diagnosis and prognosis of heart failure using cell nuclear morphology and DNA damage marker.