| 0 | -- | 0 | Peishun Jiao, Beibei Wang, Xuan Wang, Bo Liu, Yadong Wang, Junyi Li. Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information |
| 0 | -- | 0 | Mario Fruzangohar, Paula Moolhuijzen, Nicolette Bakaj, Julian Taylor. CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes |
| 0 | -- | 0 | Cheng Zhong, Tian Tian, Zhi Wei 0001. Hidden Markov random field models for cell-type assignment of spatially resolved transcriptomics |
| 0 | -- | 0 | Fernando H. C. Dias, Manuel Cáceres, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu. A safety framework for flow decomposition problems via integer linear programming |
| 0 | -- | 0 | Serena Rosignoli, Luisa Di Paola, Alessandro Paiardini. PyPCN: protein contact networks in PyMOL |
| 0 | -- | 0 | Wenyi Yang, Pingping Wang, Meng Luo 0001, Yideng Cai, Chang Xu, Guangfu Xue, Xiyun Jin, Rui Cheng 0003, Jinhao Que, Fenglan Pang, Yuexin Yang, Huan Nie, Qinghua Jiang, Zhigang Liu, Zhaochun Xu. DeepCCI: a deep learning framework for identifying cell-cell interactions from single-cell RNA sequencing data |
| 0 | -- | 0 | Mohammad Nuwaisir Rahman, Abdullah Al Noman, Abir Mohammad Turza, Mohammed Abid Abrar, Md. Abul Hassan Samee, M. Saifur Rahman. ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data |
| 0 | -- | 0 | Junmin Wang, Steven Novick. DOSE-L1000: unveiling the intricate landscape of compound-induced transcriptional changes |
| 0 | -- | 0 | Luca R. Genz, Thomas Mulvaney, Sanjana Nair, Maya Topf. PICKLUSTER: a protein-interface clustering and analysis plug-in for UCSF ChimeraX |
| 0 | -- | 0 | Qiao Jin 0001, Won Kim 0003, Qingyu Chen 0001, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu. MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval |
| 0 | -- | 0 | Ping Han Hsieh, Camila Miranda Lopes-Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer. Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data |
| 0 | -- | 0 | Kamil Kaminski, Jan Ludwiczak, Kamil Pawlicki, Vikram Alva, Stanislaw Dunin-Horkawicz. pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models |
| 0 | -- | 0 | Grant Greenberg, Aditya Narayan Ravi, Ilan Shomorony. LexicHash: sequence similarity estimation via lexicographic comparison of hashes |
| 0 | -- | 0 | Ugo Bastolla, David Abia, Oscar Piette. PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score |
| 0 | -- | 0 | Gun Kaynar, Doruk Cakmakci, Caroline Bund, Julien Todeschi, Izzie-Jacques Namer, A. Ercüment Çiçek. PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas |
| 0 | -- | 0 | Luiz Felipe Piochi, António J. Preto, Irina S. Moreira. DELFOS - drug efficacy leveraging forked and specialized networks - benchmarking scRNA-seq data in multi-omics-based prediction of cancer sensitivity |
| 0 | -- | 0 | Zeeshan Abbas, Mobeen-ur-Rehman, Hilal Tayara, Kil To Chong 0001. ORI-Explorer: a unified cell-specific tool for origin of replication sites prediction by feature fusion |
| 0 | -- | 0 | Maria Theiss, Jean-Karim Hériché, Craig Russell, David Helekal, Alisdair Soppitt, Jonas Ries, Jan Ellenberg, Alvis Brazma, Virginie Uhlmann. Simulating structurally variable nuclear pore complexes for microscopy |
| 0 | -- | 0 | Jianting Gong, Lili Jiang, Yongbing Chen, Yixiang Zhang, Xue Li, Zhiqiang Ma, Zhiguo Fu, Fei He, Pingping Sun, Zilin Ren, Mingyao Tian. THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model |
| 0 | -- | 0 | Yuhang Liu, Hao Yuan, Qiang Zhang, Zixuan Wang, Shuwen Xiong, Naifeng Wen, Yongqing Zhang. Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding |
| 0 | -- | 0 | Ali Osman Berk Sapci, Shan Lu, Shuchen Yan, Ferhat Ay, Öznur Tastan, Sündüz Keles. MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing |
| 0 | -- | 0 | Huiling Liu, Wenxiu Ma. scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data |
| 0 | -- | 0 | Patrick Gohl, Jaume Bonet, Oriol Fornes, Joan Planas-Iglesias, Narcis Fernandez-Fuentes, Baldo Oliva. SBILib: a handle for protein modeling and engineering |
| 0 | -- | 0 | Dhaivat Joshi, Suhas N. Diggavi, Mark J. P. Chaisson, Sreeram Kannan. HQAlign: aligning nanopore reads for SV detection using current-level modeling |
| 0 | -- | 0 | Yi-Juan Hu, Glen A. Satten. Compositional analysis of microbiome data using the linear decomposition model (LDM) |
| 0 | -- | 0 | Richard A Schäfer, Qingxiang Guo, Rendong Yang. ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations |
| 0 | -- | 0 | Yujie Guo, Xiaowen Feng, Heng Li. Evaluation of haplotype-aware long-read error correction with hifieval |
| 0 | -- | 0 | Natália Teruel, Vinicius Magalhães Borges, Rafael Najmanovich. Surfaces: a software to quantify and visualize interactions within and between proteins and ligands |
| 0 | -- | 0 | Rachel Colquhoun, Ben Jackson, Áine Niamh O'toole, Andrew Rambaut. SCORPIO: a utility for defining and classifying mutation constellations of virus genomes |
| 0 | -- | 0 | Richard A. Schäfer, Dominik Rabsch, Guillaume E. Scholz, Peter F. Stadler, Wolfgang R. Hess, Rolf Backofen, Jörg Fallmann, Björn Voß. RNA interaction format: a general data format for RNA interactions |
| 0 | -- | 0 | Cyprien Plateau-Holleville, Simon Guionnière, Benjamin Boyer, Brian Jiménez-García, Guillaume Levieux, Stéphane Mérillou, Maxime Maria, Matthieu Montès. UDock2: interactive real-time multi-body protein-protein docking software |
| 0 | -- | 0 | Kevin Volkel, Kevin N. Lin, Paul W. Hook, Winston Timp, Albert J. Keung, James M. Tuck. FrameD: framework for DNA-based data storage design, verification, and validation |
| 0 | -- | 0 | Anowarul Kabir, Manish Bhattarai, Kim Ø. Rasmussen, Amarda Shehu, Anny Usheva, Alan R. Bishop, Boian S. Alexandrov. Examining DNA breathing with pyDNA-EPBD |
| 0 | -- | 0 | Noriaki Sato, Miho Uematsu, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto. ggkegg: analysis and visualization of KEGG data utilizing the grammar of graphics |
| 0 | -- | 0 | Roberto Malinverni, David Corujo, Bernat Gel, Marcus Buschbeck. regioneReloaded: evaluating the association of multiple genomic region sets |
| 0 | -- | 0 | Kwan-Ling Wu, Melisa A. Martinez-Paniagua, Kate Reichel, Prashant Menon, Shravani Deo, Badrinath Roysam, Navin Varadarajan. Automated detection of apoptotic bodies and cells in label-free time-lapse high-throughput video microscopy using deep convolutional neural networks |
| 0 | -- | 0 | Hyunjun Choi, Jay Moran, Nicholas Matsumoto, Miguel E. Hernandez, Jason H. Moore. Aliro: an automated machine learning tool leveraging large language models |
| 0 | -- | 0 | Andrea Gasparin, Federico Julian Camerota Verdù, Daniele Catanzaro, Lorenzo Castelli. An evolution strategy approach for the balanced minimum evolution problem |
| 0 | -- | 0 | Vijini Mallawaarachchi, Michael J. Roach 0001, Przemyslaw Decewicz, Bhavya Nalagampalli Papudeshi, Sarah K. Giles, Susanna R. Grigson, George Bouras, Ryan D. Hesse, Laura K. Inglis, Abbey L. K. Hutton, Elizabeth A. Dinsdale, Robert A. Edwards. Phables: from fragmented assemblies to high-quality bacteriophage genomes |
| 0 | -- | 0 | Jared G. Galloway, Kevin Sung, Samuel S. Minot, Meghan E. Garrett, Caitlin I Stoddard, Alexandra C. Willcox, Zak A. Yaffe, Ryan Yucha, Julie Overbaugh, Frederick A. Matsen. phippery: a software suite for PhIP-Seq data analysis |
| 0 | -- | 0 | Xiaoming Xu, Zekun Yin, Lifeng Yan, Huiguang Yi, Hua Wang, Bertil Schmidt, Weiguo Liu. RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures |
| 0 | -- | 0 | Felix Teufel, Jan C. Refsgaard, Christian T. Madsen, Carsten Stahlhut, Mads Grønborg, Ole Winther, Dennis Madsen. DeepPeptide predicts cleaved peptides in proteins using conditional random fields |
| 0 | -- | 0 | Thomas Naake, Johannes Rainer, Wolfgang Huber. MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data |
| 0 | -- | 0 | Ryo Yamamoto, Zhiheng Liu, Mudra Choudhury, Xinshu Xiao. in silico identification of dsRNA regions using long-read RNA-seq data |
| 0 | -- | 0 | Huaying Fang. gmcoda: Graphical model for multiple compositional vectors in microbiome studies |
| 0 | -- | 0 | KyungPyo Ham, Lee Sael. Evidential meta-model for molecular property prediction |
| 0 | -- | 0 | Haifan Gong, Yumeng Zhang, Chenhe Dong, Yue Wang, Guanqi Chen, Bilin Liang, Haofeng Li, Lanxuan Liu, Jie Xu, Guanbin Li. Unbiased curriculum learning enhanced global-local graph neural network for protein thermodynamic stability prediction |
| 0 | -- | 0 | Yiming Wu, Bing Qian, Anqi Wang, Heng Dong, Enqiang Zhu, Baoshan Ma. iLSGRN: inference of large-scale gene regulatory networks based on multi-model fusion |
| 0 | -- | 0 | Zerong Feng, Jiejie Feng, Baoyi Zhang, Yuhan Fei, Hongsheng Zhang, Ji Huang. PhasiHunter: a robust phased siRNA regulatory cascade mining tool based on multiple reference sequences |
| 0 | -- | 0 | Chih-Hsuan Wei, Ling Luo 0001, Rezarta Islamaj, Po-Ting Lai, Zhiyong Lu. GNorm2: an improved gene name recognition and normalization system |
| 0 | -- | 0 | Shihu Jiao, Xiucai Ye, Chunyan Ao, Tetsuya Sakurai, Quan Zou 0001, Lei Xu. Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites |
| 0 | -- | 0 | . Correction to: Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads |
| 0 | -- | 0 | Chen Li, Ting-Fung Chan, Can Yang, Zhixiang Lin. stVAE deconvolves cell-type composition in large-scale cellular resolution spatial transcriptomics |
| 0 | -- | 0 | Carlos Sequeiros, Manuel Pájaro, Carlos Vázquez 0002, Julio R. Banga, Irene Otero-Muras. IDESS: a toolbox for identification and automated design of stochastic gene circuits |
| 0 | -- | 0 | . Correction to: BIODICA: a computational environment for Independent Component Analysis of omics data |
| 0 | -- | 0 | Yevgeni Nogin, Daniella Bar-Lev, Dganit Hanania, Tahir Detinis Zur, Yuval Ebenstein, Eitan Yaakobi, Nir Weinberger, Yoav Shechtman. Design of optimal labeling patterns for optical genome mapping via information theory |
| 0 | -- | 0 | Michal Wlasnowolski, Pawel Z. Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski. cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling |
| 0 | -- | 0 | Neng Huang, Heng Li. compleasm: a faster and more accurate reimplementation of BUSCO |
| 0 | -- | 0 | Joshua Forrest, Vijay Rajagopal, Michael P. H. Stumpf, Michael Pan. BondGraphs.jl: composable energy-based modelling in systems biology |
| 0 | -- | 0 | Jun Liu, Dong Liu, Gui-jun Zhang. DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes |
| 0 | -- | 0 | Edgar E. Robles, Ye Jin, Padhraic Smyth, Richard H. Scheuermann, Jack D. Bui, Huan-You Wang, Jean Oak, Yu Qian. A cell-level discriminative neural network model for diagnosis of blood cancers |
| 0 | -- | 0 | Luis Francisco Hernández Sánchez, Bram Burger, Rodrigo Alexander Castro Campos, Stefan Johansson, Pål R. Njølstad, Harald Barsnes, Marc Vaudel. Extending protein interaction networks using proteoforms and small molecules |
| 0 | -- | 0 | Yanglan Gan, Xingyu Huang, Wenjing Guo, Cairong Yan, Guobing Zou. Predicting synergistic anticancer drug combination based on low-rank global attention mechanism and bilinear predictor |
| 0 | -- | 0 | Axel von Kamp, Steffen Klamt. Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis |
| 0 | -- | 0 | Woosub Shin, John H. Gennari, Joseph L. Hellerstein, Herbert M. Sauro. An automated model annotation system (AMAS) for SBML models |
| 0 | -- | 0 | Xinyue Wang, Leonard Dervishi, Wen-tao Li, Erman Ayday, Xiaoqian Jiang, Jaideep Vaidya. Privacy-preserving federated genome-wide association studies via dynamic sampling |
| 0 | -- | 0 | Romain Derelle, John Lees, Jody Phelan, Ajit Lalvani, Nimalan Arinaminpathy, Leonid Chindelevitch. Mycobacterium tuberculosis complex lineage typing |
| 0 | -- | 0 | Dmitriy Umerenkov, Fedor Nikolaev, Tatiana I Shashkova, Pavel V. Strashnov, Maria Sindeeva, Andrey Shevtsov, Nikita V. Ivanisenko, Olga L. Kardymon. PROSTATA: a framework for protein stability assessment using transformers |
| 0 | -- | 0 | Samuel Sledzieski, Kapil Devkota, Rohit Singh 0001, Lenore Cowen, Bonnie Berger. TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions |
| 0 | -- | 0 | Aakriti Jain, Neelja Singhal, Manish Kumar 0005. AFRbase: a database of protein mutations responsible for antifungal resistance |
| 0 | -- | 0 | Shabnam Sahay, Shishir Adhikari, Sahand Hormoz, Shaon Chakrabarti. An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells |
| 0 | -- | 0 | Nicolas Buton, François Coste, Yann Le Cunff. Predicting enzymatic function of protein sequences with attention |
| 0 | -- | 0 | Bastian Pfeifer, Hryhorii Chereda, Roman Martin, Anna Saranti, Sandra Clemens, Anne-Christin Hauschild, Tim Beißbarth, Andreas Holzinger, Dominik Heider. Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification |
| 0 | -- | 0 | Ruoyu Tang, Xinyu He, Ruiqi Wang. Constructing maps between distinct cell fates and parametric conditions by systematic perturbations |
| 0 | -- | 0 | Olli Sarala, Tanja Pyhäjärvi, Mikko J. Sillanpää. BELMM: Bayesian model selection and random walk smoothing in time-series clustering |
| 0 | -- | 0 | Vincenzo Laveglia, Milana Bazayeva, Claudia Andreini, Antonio Rosato. Hunting down zinc(II)-binding sites in proteins with distance matrices |
| 0 | -- | 0 | Anthony J. Aylward, Semar Petrus, Allen Mamerto, Nolan T. Hartwick, Todd P. Michael. k-mer-based and reference-free pangenome analysis |
| 0 | -- | 0 | Yao-zhong Zhang, Zeheng Bai, Seiya Imoto. Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings |
| 0 | -- | 0 | Megan M. Shuey, William W. Stead, Ida Aka, April L. Barnado, Lisa Bastarache, Elly Brokamp, Meredith Campbell, Robert J. Carroll, Jeffrey A. Goldstein, Adam Lewis, Beth A. Malow, Jonathan D. Mosley, Travis Osterman, Dolly A Padovani-Claudio, Andrea Ramirez, Dan M. Roden, Bryce A Schuler, Edward Siew, Jennifer Sucre, Isaac Thomsen, Rory J. Tinker, Sara Van Driest, Colin Walsh, Jeremy L. Warner, Quinn Stanton Wells, Lee E. Wheless. Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics |
| 0 | -- | 0 | Mhaned Oubounyt, Lorenz Adlung, Fabio Patroni, Nina Kerstin Wenke, Andreas Maier, Michael Hartung, Jan Baumbach, Maria L. Elkjaer. Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet |
| 0 | -- | 0 | Dong Pei, Rachel Griffard, Nanda Kumar Yellapu, Emily Nissen, Devin C. Koestler. optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis |
| 0 | -- | 0 | Ieva Kerseviciute, Juozas Gordevicius. aPEAR: an R package for autonomous visualization of pathway enrichment networks |
| 0 | -- | 0 | Michele Fontanesi, Alessio Micheli, Paolo Milazzo, Marco Podda. Exploiting the structure of biochemical pathways to investigate dynamical properties with neural networks for graphs |
| 0 | -- | 0 | Xinmeng Liao, Mehmet Ozcan, Mengnan Shi, Woonghee Kim, Han Jin, Xiangyu Li, Hasan Turkez, Adnane Achour, Mathias Uhlén, Adil Mardinoglu, Cheng Zhang 0002. Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy |
| 0 | -- | 0 | Dabin Jeong, Bonil Koo, Minsik Oh, Tae-Bum Kim, Sun Kim. GOAT: Gene-level biomarker discovery from multi-Omics data using graph ATtention neural network for eosinophilic asthma subtype |
| 0 | -- | 0 | Xiao Wang, Wei-Cheng Gu, Jie Li, Bin-Guang Ma. EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient |
| 0 | -- | 0 | Samuele Garda, Leon Weber-Genzel, Robert Martin, Ulf Leser. BELB: a biomedical entity linking benchmark |
| 0 | -- | 0 | Bilal Shaker, Jingyu Lee, Yunhyeok Lee, Myeong-Sang Yu, Hyang-Mi Lee, Eunee Lee, Hoon-Chul Kang, Kwang-Seok Oh, Hyung Wook Kim, Dokyun Na. A machine learning-based quantitative model (LogBB_Pred) to predict the blood-brain barrier permeability (logBB value) of drug compounds |
| 0 | -- | 0 | Thomas Weber, Marco Raffaele Cosenza, Jan Korbel. MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq |
| 0 | -- | 0 | Yang Hai, Jixiang Ma, Kaixin Yang, Yalu Wen. Bayesian linear mixed model with multiple random effects for prediction analysis on high-dimensional multi-omics data |
| 0 | -- | 0 | Palle Duun Rohde, Izel Fourie Sørensen, Peter Sørensen. Expanded utility of the R package, qgg, with applications within genomic medicine |
| 0 | -- | 0 | Luca Del Core, Danilo Pellin, Ernst C. Wit, Marco Grzegorczyk. Scalable inference of cell differentiation networks in gene therapy clonal tracking studies of haematopoiesis |
| 0 | -- | 0 | Xu Han, Wanli Wang, Li-Hua Ma, Ismael Ai-Ramahi, Juan Botas, Kevin Mackenzie, Genevera I. Allen, Damian W. Young, Zhandong Liu, Mirjana Maletic-Savatic. SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra |
| 0 | -- | 0 | Barbara Bodinier, Dragana Vuckovic, Sabrina Rodrigues, Sarah Filippi, Julien Chiquet, Marc Chadeau-Hyam. Automated calibration of consensus weighted distance-based clustering approaches using sharp |
| 0 | -- | 0 | Xiaoyang Hou, Yu Wang, Dongbo Bu, Yaojun Wang, Shiwei Sun. EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction |
| 0 | -- | 0 | Fabio Barteri, Alejandro Valenzuela, Xavier Farré, David de Juan, Gerard Muntané, Borja Esteve-Altava, Arcadi Navarro. CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions |
| 0 | -- | 0 | Marco Teixeira, Stephanie Pillay, Aysun Urhan, Thomas Abeel. SHIP: identifying antimicrobial resistance gene transfer between plasmids |
| 0 | -- | 0 | Ludvig Larsson, Lovisa Franzén, Patrik L. Ståhl, Joakim Lundeberg. Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization |
| 0 | -- | 0 | Kristian K. Ullrich, Nikoleta E. Glytnasi. oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data |
| 0 | -- | 0 | Dongze He, Rob Patro. simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry |
| 0 | -- | 0 | Zahed Khatooni, Navid Teymourian, Heather L. Wilson. Using a novel structure/function approach to select diverse swine major histocompatibility complex 1 alleles to predict epitopes for vaccine development |