| 0 | -- | 0 | Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, Ilana Barzilai, Onit Alalouf, Yuval Ebenstein, Yoav Shechtman. DeepOM: single-molecule optical genome mapping via deep learning |
| 0 | -- | 0 | Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao 0001, Roger J. Daly, Jiangning Song. Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification |
| 0 | -- | 0 | . Correction to: On the feasibility of deep learning applications using raw mass spectrometry data |
| 0 | -- | 0 | Amy Glen, Chunyu Ma, Luis Mendoza, Finn Womack, E. C. Wood, Meghamala Sinha, Liliana Acevedo, Lindsey G. Kvarfordt, Ross C. Peene, Shaopeng Liu, Andrew S. Hoffman, Jared C. Roach, Eric W. Deutsch, Stephen A. Ramsey, David Koslicki. ARAX: a graph-based modular reasoning tool for translational biomedicine |
| 0 | -- | 0 | Arya R. Massarat, Michael Lamkin, Ciara Reeve, Amy L. Williams, Matteo D'Antonio, Melissa Gymrek. Haptools: a toolkit for admixture and haplotype analysis |
| 0 | -- | 0 | Ludwig Geistlinger, Roger Vargas, Tyrone Lee, Joshua Pan, Edward L. Huttlin, Robert Gentleman. BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions |
| 0 | -- | 0 | Mohan Rakesh, Hélène Vézina, Catherine Laprise, Ellen E. Freeman, Kelly M. Burkett, Marie-Hélène Roy-Gagnon. GENLIB: new function to simulate haplotype transmission in large complex genealogies |
| 0 | -- | 0 | Iñaki Amatria-Barral, Jorge González-Domínguez, Juan Touriño. PATO: genome-wide prediction of lncRNA-DNA triple helices |
| 0 | -- | 0 | Anupam Gautam, Wenhuan Zeng, Daniel H. Huson. MeganServer: facilitating interactive access to metagenomic data on a server |
| 0 | -- | 0 | Huixi Zou, Tianli Sun, Bangqun Jin, Shengqin Wang. sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome |
| 0 | -- | 0 | . Correction to: SVJedi: genotyping structural variations with long reads |
| 0 | -- | 0 | Jiawei Wu, Qingrui Liu, Min Li, Jiliang Xu, Chen Wang, Junyin Zhang, Minfeng Xiao, Yannan Bin, Junfeng Xia. PhaGAA: an integrated web server platform for phage genome annotation and analysis |
| 0 | -- | 0 | Gandhar Mahadeshwar, Rafael de Cesaris Araujo Tavares, Han Wan, Zion R. Perry, Anna Marie Pyle. RSCanner: rapid assessment and visualization of RNA structure content |
| 0 | -- | 0 | . M. tuberculosis genome |
| 0 | -- | 0 | Tong Pan, Chen Li 0021, Yue Bi, Zhikang Wang, Robin B. Gasser, Anthony W. Purcell, Tatsuya Akutsu, Geoffrey I. Webb, Seiya Imoto, Jiangning Song. PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships |
| 0 | -- | 0 | Zhourun Wu, Mingyue Guo, Xiaopeng Jin, Junjie Chen 0004, Bin Liu 0014. CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction |
| 0 | -- | 0 | Weiming He, Jian Yang, Yi Jing, Lian Xu, Kang Yu, Xiaodong Fang. NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes |
| 0 | -- | 0 | Zehao Xiong, Jiawei Luo 0001, Wanwan Shi, Ying Liu, Zhongyuan Xu, Bo Wang. scGCL: an imputation method for scRNA-seq data based on graph contrastive learning |
| 0 | -- | 0 | Xuhua Yan, Ruiqing Zheng, Fang-Xiang Wu, Min Li 0007. CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity |
| 0 | -- | 0 | Andrei Dmitrenko, Michelle Reid, Nicola Zamboni. Regularized adversarial learning for normalization of multi-batch untargeted metabolomics data |
| 0 | -- | 0 | . Correction to: SBbadger: biochemical reaction networks with definable degree distributions |
| 0 | -- | 0 | Tiago Cabral Borelli, Gabriel Santos Arini, Luís G. P. Feitosa, Pieter C. Dorrestein, Norberto Peporine Lopes, Ricardo R. da Silva. Improving annotation propagation on molecular networks through random walks: introducing ChemWalker |
| 0 | -- | 0 | Adrien Rougny, Irina Balaur, Augustin Luna, Alexander Mazein. StonPy: a tool to parse and query collections of SBGN maps in a graph database |
| 0 | -- | 0 | Karel J. van der Weg, Holger Gohlke. TopEnzyme: a framework and database for structural coverage of the functional enzyme space |
| 0 | -- | 0 | . Correction to: Improving annotation propagation on molecular networks through random walks: introducing ChemWalker |
| 0 | -- | 0 | Qizhi Li, Xubin Zheng, Jize Xie, Ran Wang, Mengyao Li, Man Hon Wong 0001, Kwong-Sak Leung, Shuai Li 0010, Qingshan Geng, Lixin Cheng. bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks |
| 0 | -- | 0 | Bin Huang, Tingwen Fan, Kaiyue Wang, Haicang Zhang, Chungong Yu, Shuyu Nie, Yangshuo Qi, Wei-Mou Zheng, Jian Han, Zheng Fan, Shiwei Sun, Sheng Ye, Huaiyi Yang, Dongbo Bu. Accurate and efficient protein sequence design through learning concise local environment of residues |
| 0 | -- | 0 | Adam Streck, Tom L. Kaufmann, Roland F. Schwarz. SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity |
| 0 | -- | 0 | Zhongshen Li, Junru Jin, Yu Wang, Wentao Long, Yuanhao Ding, Haiyan Hu, Leyi Wei. ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides |
| 0 | -- | 0 | Vladimir Porokhin, Li-Ping Liu 0001, Soha Hassoun. Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products |
| 0 | -- | 0 | Matti Pirinen. linemodels: clustering effects based on linear relationships |
| 0 | -- | 0 | Sebastian Deorowicz, Agnieszka Danek, Heng Li. AGC: compact representation of assembled genomes with fast queries and updates |
| 0 | -- | 0 | Rudolf T. Pillich, Jing Chen, Christopher Churas, Dylan Fong, Benjamin M. Gyori, Trey Ideker, Klas Karis, Sophie N. Liu, Keiichiro Ono, Alexander R. Pico, Dexter Pratt. NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange |
| 0 | -- | 0 | William Haese-Hill, Kathryn Crouch, Thomas D. Otto. peaks2utr: a robust Python tool for the annotation of 3′ UTRs |
| 0 | -- | 0 | João Paulo Pereira Zanetti, Lucas Peres Oliveira, Leonid Chindelevitch, João Meidanis. Generalizations of the genomic rank distance to indels |
| 0 | -- | 0 | Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun. VirBot: an RNA viral contig detector for metagenomic data |
| 0 | -- | 0 | Sanjay K. Srikakulam, Sebastian Keller, Fawaz Dabbaghie, Robert Bals, Olga V. Kalinina. MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants |
| 0 | -- | 0 | Elisabet Munté, Lidia Feliubadaló, Marta Pineda, Eva Tornero, Maribel González, José Marcos Moreno-Cabrera, Carla Roca, Joan Bales Rubio, Laura Arnaldo, Gabriel Capellá, Jose Luis Mosquera, Conxi Lázaro. vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines |
| 0 | -- | 0 | Bianca A. Buchner, Tom J. Clement, Daan H. de Groot, Jürgen Zanghellini. ecmtool: fast and memory-efficient enumeration of elementary conversion modes |
| 0 | -- | 0 | Chirag Jain. Coverage-preserving sparsification of overlap graphs for long-read assembly |
| 0 | -- | 0 | Omid Rohanian, Mohammadmahdi Nouriborji, Samaneh Kouchaki, David A. Clifton. On the effectiveness of compact biomedical transformers |
| 0 | -- | 0 | Jian Cheng, Christian Maltecca, Paul M. Vanraden, Jeffrey R. O'Connell, Li Ma, Jicai Jiang. SLEMM: million-scale genomic predictions with window-based SNP weighting |
| 0 | -- | 0 | Siebren Frölich, Maarten van der Sande, Tilman Schäfers, Simon J. van Heeringen. genomepy: genes and genomes at your fingertips |
| 0 | -- | 0 | Oleksandr Khoroshevskyi, Nathan Leroy, Vincent P. Reuter, Nathan C. Sheffield. GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA |