| 0 | -- | 0 | Jonathan D. Ogata, Wancen Mu, Eric S. Davis, Bingjie Xue, J. Chuck Harrell, Nathan C. Sheffield, Douglas H. Phanstiel, Michael I. Love, Mikhail G. Dozmorov. excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies |
| 0 | -- | 0 | Massimiliano Volpe, Jyotirmoy Das. methylR: a graphical interface for comprehensive DNA methylation array data analysis |
| 0 | -- | 0 | Natalia V. Loukachevitch, Suresh Manandhar, Elina Baral, Igor Rozhkov, Pavel Braslavski, Vladimir Ivanov 0001, Tatiana Batura, Elena Tutubalina. NEREL-BIO: a dataset of biomedical abstracts annotated with nested named entities |
| 0 | -- | 0 | Min Yang, Bo Qiu, Guo-You He, Jian-Yuan Zhou, Hao-Jie Yu, Yu-Ying Zhang, Yan-Shang Li, Tai-Song Li, Jin-Cheng Guo, Xue-Cang Li, Jian-Jun Xie. eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species |
| 0 | -- | 0 | René Staritzbichler, Nikola Ristic, Tülin Stapke, Peter W. Hildebrand. SmoothT - a server constructing low-energy pathways from conformational ensembles for interactive visualization and enhanced sampling |
| 0 | -- | 0 | Saleh Riahi, Jae-Hyeon Lee, Taylor Sorenson, Shuai Wei, Sven Jager, Reza Olfati-Saber, Yanfeng Zhou, Anna Park, Maria Wendt, Hervé Minoux, Yu Qiu. Surface ID: a geometry-aware system for protein molecular surface comparison |
| 0 | -- | 0 | Xiaoliang Ren, Yanwen Shao, Yiwen Zhang, Ying Ni, Yu Bi, Runsheng Li. Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping |
| 0 | -- | 0 | Elisabetta C. Sciacca, Salvatore Alaimo, Gianmarco Silluzio, Alfredo Ferro, Vito Latora, Costantino Pitzalis, Alfredo Pulvirenti, Myles J. Lewis. DEGGs: an R package with shiny app for the identification of differentially expressed gene-gene interactions in high-throughput sequencing data |
| 0 | -- | 0 | Can (sam) Chen, Jingbo Zhou, Fan Wang, Xue (Steve) Liu, Dejing Dou. Structure-aware protein self-supervised learning |
| 0 | -- | 0 | Ziang Zhang, Lei Sun. The hidden factor: accounting for covariate effects in power and sample size computation for a binary trait |
| 0 | -- | 0 | Hannah M. Doherty, George Kritikos, Marco Galardini, Manuel Banzhaf, Danesh Moradigaravand. ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling |
| 0 | -- | 0 | Benjamin B. Chu, Seyoon Ko, Jin J. Zhou, Aubrey Jensen, Hua Zhou 0001, Janet S. Sinsheimer, Kenneth Lange. Multivariate genome-wide association analysis by iterative hard thresholding |
| 0 | -- | 0 | Can Chen, Scott T. Weiss, Yang-Yu Liu. Graph convolutional network-based feature selection for high-dimensional and low-sample size data |
| 0 | -- | 0 | Bansho Masutani, Riki Kawahara, Shinichi Morishita. Decomposing mosaic tandem repeats accurately from long reads |
| 0 | -- | 0 | Diana F. Sousa, Francisco M. Couto. K-RET: knowledgeable biomedical relation extraction system |
| 0 | -- | 0 | Marie Mille, Julie Ripoll, Bastien Cazaux, Eric Rivals. dipwmsearch: a Python package for searching di-PWM motifs |
| 0 | -- | 0 | Petr Triska, Fabian Amman, Lukas Endler, Andreas Bergthaler. WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) - a web application for visualization of wastewater pathogen sequencing results |
| 0 | -- | 0 | Signe Skog, Lovisa Örkenby, Unn Kugelberg, Anita Öst, Daniel Nätt. Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts |
| 0 | -- | 0 | Tiantian Ye, Yangyang Hu, Sydney Pun, Wenxiu Ma. HiCube: interactive visualization of multiscale and multimodal Hi-C and 3D genome data |
| 0 | -- | 0 | Sheng Fu, Lu Deng, Han Zhang 0003, William Wheeler, Jing Qin, Kai Yu. Integrative analysis of individual-level data and high-dimensional summary statistics |
| 0 | -- | 0 | Guy Karlebach, Leigh Carmody, Jagadish Chandrabose Sundaramurthi, Elena Casiraghi, Peter Hansen, Justin T. Reese, Christopher J. Mungall, Giorgio Valentini, Peter N. Robinson. An expectation-maximization framework for comprehensive prediction of isoform-specific functions |
| 0 | -- | 0 | Steven Shave, John C. Dawson, Abdullah M. Athar, Cuong Q. Nguyen, Richard Kasprowicz, Neil O. Carragher. Phenonaut: multiomics data integration for phenotypic space exploration |
| 0 | -- | 0 | Yi Fang, Xiaoyong Pan, Hong-bin Shen. De novodrug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment |
| 0 | -- | 0 | Olivier Mailhot, François Major, Rafael Najmanovich. The DynaSig-ML Python package: automated learning of biomolecular dynamics-function relationships |
| 0 | -- | 0 | Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek. Boolean network sketches: a unifying framework for logical model inference |
| 0 | -- | 0 | Conrad Leonard. streammd: fast low-memory duplicate marking using a Bloom filter |
| 0 | -- | 0 | . Correction to: Multi-omic integration by machine learning (MIMaL) |
| 0 | -- | 0 | Altay Yuzeir, David Alejandro Bejarano, Stephan Grein, Jan Hasenauer, Andreas Schlitzer, Jiangyan Yu. IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line |
| 0 | -- | 0 | Michael Shaffer, Mikayla A. Borton, Ben Bolduc, José P. Faria, Rory M. Flynn, Parsa Ghadermazi, Janaka N. Edirisinghe, Elisha M. Wood-Charlson, Christopher S. Miller, Siu Hung Joshua Chan, Matthew B. Sullivan, Christopher S. Henry, Kelly C. Wrighton. kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase |
| 0 | -- | 0 | Lukas Heumos, Philipp Ehmele, Luis Kuhn Cuellar, Kevin Menden, Edmund Miller, Steffen Lemke 0003, Gisela Gabernet, Sven Nahnsen. mlf-core: a framework for deterministic machine learning |
| 0 | -- | 0 | Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa. Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres |
| 0 | -- | 0 | Yuxin Li, Xuhua Liu, Xueyan Jia, Tao Jiang, Jianghao Wu, Qianlong Zhang, Junhuai Li, Xiangning Li, Anan Li. A high-performance deep-learning-based pipeline for whole-brain vasculature segmentation at the capillary resolution |
| 0 | -- | 0 | Ke Yan 0003, Yichen Guo, Bin Liu. PreTP-2L: identification of therapeutic peptides and their types using two-layer ensemble learning framework |
| 0 | -- | 0 | Jing Xu, Aidi Zhang, Fang Liu, Xiujun Zhang. STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data |
| 0 | -- | 0 | Daffodil M. Canson, Aimee L. Davidson, Miguel de la Hoya, Michael T. Parsons, Dylan M. Glubb, Olga Kondrashova, Amanda B. Spurdle. SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion |
| 0 | -- | 0 | Yi Liu 0058, Benjamin L. Elsworth, Tom R. Gaunt. Using language models and ontology topology to perform semantic mapping of traits between biomedical datasets |
| 0 | -- | 0 | Chenyang Dong, Siqi Shen, Sündüz Keles. AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver |
| 0 | -- | 0 | Lucas Prates, Renan B. Lemes, Tábita Hünemeier, Florencia G. Leonardi. Population-based change-point detection for the identification of homozygosity islands |
| 0 | -- | 0 | Liangrui Ren, Jun Wang, Zhao Li, Qingzhong Li, Guoxian Yu. scMCs: a framework for single-cell multi-omics data integration and multiple clusterings |
| 0 | -- | 0 | Hanyi Yu, Fusheng Wang 0001, George Teodoro, Fan Chen, Xiaoyuan Guo, John Nickerson, Jun Kong. Self-supervised semantic segmentation of retinal pigment epithelium cells in flatmount fluorescent microscopy images |
| 0 | -- | 0 | Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li. Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration |
| 0 | -- | 0 | Richard J. Packer, Alex T. Williams, William Hennah, Micaela T. Eisenberg, Nick Shrine, Katherine A Fawcett, Willow Pearson, Anna L. Guyatt, Ahmed Edris, Edward J. Hollox, Mikko Marttila, Balasubramanya S. Rao, John Raymond Bratty, Louise V. Wain, Frank Dudbridge, Martin D. Tobin. DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies |
| 0 | -- | 0 | Mohamed Reda El Khili, Safyan Aman Memon, Amin Emad. MARSY: a multitask deep-learning framework for prediction of drug combination synergy scores |
| 0 | -- | 0 | Sean Upchurch, Emilio Palumbo, Jeremy Adams, David Bujold, Guillaume Bourque, Jared Nedzel, Keenan Graham, Meenakshi S. Kagda, Pedro Assis, Benjamin Hitz, Emilio Righi, Roderic Guigó, Barbara J. Wold, Alvis Brazma, Julia Burchard, Joe Capka, Michael Cherry, Laura Clarke, Brian Craft, Manolis Dermitzakis, Mark Diekhans, John Dursi, Michael Sean Fitzsimons, Zac Flaming, Romina Garrido, Alfred Gil, Paul Godden, Matt Green, Mitch Guttman, Brian Haas, Max Haeussler, Bo Li, Sten Linnarsson, Adam Lipski, David Liu, Simonne Longerich, David Lougheed, Jonathan Manning, John C. Marioni, Christopher Meyer, Stephen B. Montgomery, Alyssa Morrow, Alfonso Muñoz-Pomer Fuentes, Jared L. Nedzel, David Nguyen, Kevin Osborn, Francis Ouellette, Irene Papatheodorou, Dmitri D. Pervouchine, Arun K. Ramani, Jordi Rambla, Bashir Sadjad, David Steinberg, Jeremiah Talkar, Timothy Tickle, Kathy Tzeng, Saman Vaisipour, Sean Watford, Barbara Wold, Zhenyu Zhang, Jing Zhu. RNAget: an API to securely retrieve RNA quantifications |
| 0 | -- | 0 | Yuansong Zeng, Zhuoyi Wei, Qianmu Yuan, Sheng Chen, Weijiang Yu, Yutong Lu, Jianzhao Gao, Yuedong Yang. Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model |
| 0 | -- | 0 | . Correction to: Continuous chromatin state feature annotation of the human epigenome |
| 0 | -- | 0 | Mingqian Zhang, Wenke Zhang, Yuzhu Chen, Jin Zhao, Shunyao Wu, Xiaoquan Su. Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes |
| 0 | -- | 0 | Shulei Wang. Multiscale adaptive differential abundance analysis in microbial compositional data |
| 0 | -- | 0 | Hyun Jae Cho, Mia Shu, Stefan Bekiranov, Chongzhi Zang, Aidong Zhang. Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment |
| 0 | -- | 0 | Shani Cohen, Eden Maximof, Shay Rokach, Mor Tadeski, Isana Veksler-Lublinsky. Escherichia coli sRNA-mRNA interactions |
| 0 | -- | 0 | Jean-Pierre Borg, Jacques Colinge, Patrice Ravel. Modular response analysis reformulated as a multilinear regression problem |
| 0 | -- | 0 | Charles Tapley Hoyt, Amelia L. Hoyt, Benjamin M. Gyori. Prediction and curation of missing biomedical identifier mappings with Biomappings |
| 0 | -- | 0 | Ruogu Wang, Alex A. Lemus, Colin M. Henneberry, Yiming Ying, Yunlong Feng, Alex M. Valm. Unmixing biological fluorescence image data with sparse and low-rank Poisson regression |
| 0 | -- | 0 | Deliang Bu, Xiao Wang, Qizhai Li. Summary statistics-based association test for identifying the pleiotropic effects with set of genetic variants |
| 0 | -- | 0 | Fabio Fassetti, Simona E. Rombo, Cristina Serrao. Discriminative pattern discovery for the characterization of different network populations |
| 0 | -- | 0 | Gözde Yazici, Burcu Kurt Vatandaslar, Ilknur Aydin Canturk, Fatmagul I Aydinli, Ozge Arici Duz, Emre Karakoç, Bilal Ersen Kerman, Can Alkan. Identification of protein-protein interaction bridges for multiple sclerosis |
| 0 | -- | 0 | S. Taylor Head, Elizabeth J. Leslie, David J. Cutler, Michael P. Epstein. POIROT: a powerful test for parent-of-origin effects in unrelated samples leveraging multiple phenotypes |
| 0 | -- | 0 | André L. S. Meirelles, Tahsin M. Kurç, Jun Kong, Renato Ferreira, Joel H. Saltz, George Teodoro. Effective and efficient active learning for deep learning-based tissue image analysis |
| 0 | -- | 0 | Hyunbin Kim, Milot Mirdita, Martin Steinegger. Foldcomp: a library and format for compressing and indexing large protein structure sets |
| 0 | -- | 0 | Heather Marriott, Renata Kabiljo, Ahmad Al Khleifat, Richard J. Dobson, Ammar Al-Chalabi, Alfredo Iacoangeli. DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for human next-generation sequencing data |
| 0 | -- | 0 | Edin Salkovic, Mohammad Amin Sadeghi, Abdelkader Baggag, Ahmed Gamal Rashed Salem, Halima Bensmail. OutSingle: a novel method of detecting and injecting outliers in RNA-Seq count data using the optimal hard threshold for singular values |