Journal: Bioinformatics

Volume 39, Issue 9

0 -- 0Jackson Callaghan, Colleen H. Xu, Jiwen Xin, Marco Alvarado Cano, Anders Riutta, Eric Zhou, Rohan Juneja, Yao Yao, Madhumita Narayan, Kristina Hanspers, Ayushi Agrawal, Alexander R. Pico, Chunlei Wu, Andrew I. Su. BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs
0 -- 0Viktoria Schuster, Anders Krogh. The Deep Generative Decoder: MAP estimation of representations improves modelling of single-cell RNA data
0 -- 0Sophie Wharrie, Zhiyu Yang, Vishnu Raj, Remo Monti, Rahul Gupta, Ying Wang, Alicia Martin, Luke J. O'Connor, Samuel Kaski, Pekka Marttinen, Pier Francesco Palamara, Christoph Lippert, Andrea Ganna. HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes
0 -- 0Grzegorz Chojnowski, Rafal Zaborowski, Marcin Magnus, Sunandan Mukherjee, Janusz M. Bujnicki. RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints
0 -- 0Kyle Smith, Cheng Ye, Yatish Turakhia. Tracking and curating putative SARS-CoV-2 recombinants with RIVET
0 -- 0Anna Nadtochiy, Peter Luu, Scott E. Fraser, Thai V. Truong. VoDEx: a Python library for time annotation and management of volumetric functional imaging data
0 -- 0Jonathan Klonowski, Qianqian Liang, Zeynep H. Coban Akdemir, Cecilia Lo, Dennis Kostka. aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants
0 -- 0. Correction to: Online bias-aware disease module mining with ROBUST-Web
0 -- 0Saifur R. Khan, Andreea Obersterescu, Erica P. Gunderson, Babak Razani, Michael B. Wheeler, Brian J. Cox. metGWAS 1.0: an R workflow for network-driven over-representation analysis between independent metabolomic and meta-genome-wide association studies
0 -- 0Ronan M. T. Fleming, Hulda S. Haraldsdóttir, Le Hoai Minh, Phan Tu Vuong, Thomas Hankemeier, Ines Thiele. Cardinality optimization in constraint-based modelling: application to human metabolism
0 -- 0Bárbara Zita Peters Couto, Nicholas Robertson, Ellis Patrick, Shila Ghazanfar. MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor
0 -- 0Yan Zhu, Lingling Zhao, Naifeng Wen, Junjie Wang 0005, Chunyu Wang. DataDTA: a multi-feature and dual-interaction aggregation framework for drug-target binding affinity prediction
0 -- 0Yan Hu, Vipina Kuttichi Keloth, Kalpana Raja, Yong Chen, Hua Xu. Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach
0 -- 0David Teschner, David Gomez-Zepeda, Arthur Declercq, Mateusz K. Lacki, Seymen Avci, Konstantin Bob, Ute Distler, Thomas Michna, Lennart Martens, Stefan Tenzer, Andreas Hildebrandt 0001. Ionmob: a Python package for prediction of peptide collisional cross-section values
0 -- 0Mercedeh Movassagh, Steven J. Schiff, Joseph N. Paulson. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
0 -- 0Qijie Chen, Haotong Sun, Haoyang Liu, Yinghui Jiang, Ting Ran, Xurui Jin, Xianglu Xiao, Zhimin Lin, Hongming Chen, Zhangming Niu. An extensive benchmark study on biomedical text generation and mining with ChatGPT
0 -- 0Davide Cozzi, Massimiliano Rossi 0001, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni. μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data
0 -- 0Steven Grudman, J. Eduardo Fajardo, András Fiser. Optimal selection of suitable templates in protein interface prediction
0 -- 0Björn Wallner. AFsample: improving multimer prediction with AlphaFold using massive sampling
0 -- 0Manuel Huth, Jonas Arruda, Roy Gusinow, Lorenzo Contento, Evelina Tacconelli, Jan Hasenauer. Accessibility of covariance information creates vulnerability in Federated Learning frameworks
0 -- 0Nhan Ly-Trong, Giuseppe M. J. Barca, Bui Quang Minh. AliSim-HPC: parallel sequence simulator for phylogenetics
0 -- 0Pin Lyu, Yijie Zhai, Taibo Li, Jiang Qian. CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server
0 -- 0Anda Ramona Tanasie, Peter Kerpedjiev, Stefan Hammer, Stefan Badelt. DrForna: visualization of cotranscriptional folding
0 -- 0Sarah G. Ayton, Victor Treviño. MuTATE - an R package for comprehensive multi-objective molecular modeling
0 -- 0. Correction to: Python interfaces for the Smoldyn simulator
0 -- 0Jeffrey M. Dick, Xun Kang. chem16S: community-level chemical metrics for exploring genomic adaptation to environments
0 -- 0Wei Qu, Ronghui You, Hiroshi Mamitsuka, Shanfeng Zhu. DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction
0 -- 0Jun-Young Park, Jang Jae Lee, Younghwa Lee, Dongsoo Lee, Jungsoo Gim, Lindsay A. Farrer, Kun Ho Lee, Sungho Won. Machine learning-based quantification for disease uncertainty increases the statistical power of genetic association studies
0 -- 0Jace Webster, Hung Mai, Amy Ly, Christopher Maher. INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA
0 -- 0Gherard Batisti Biffignandi, Greta Bellinzona, Greta Petazzoni, Davide Sassera, Gianvincenzo Zuccotti, Claudio Bandi, Fausto Baldanti, Francesco Comandatore, Stefano Gaiarsa. P-DOR, an easy-to-use pipeline to reconstruct bacterial outbreaks using genomics
0 -- 0Bryce Kille, Erik Garrison, Todd J. Treangen, Adam M. Phillippy. Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
0 -- 0Jiani Ma, Chen Li, Yiwen Zhang, Zhikang Wang, Shanshan Li, Yuming Guo, Lin Zhang, Hui Liu, Xin Gao, Jiangning Song. MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning
0 -- 0Weiwen Wang, James Barbetti, Thomas Wong, Bryan Thornlow, Russell Corbett-Detig, Yatish Turakhia, Robert Lanfear, Bui Quang Minh. DecentTree: scalable Neighbour-Joining for the genomic era
0 -- 0Federico Bianca, Emilio Ispano, Ermanno Gazzola, Enrico Lavezzo, Paolo Fontana, Stefano Toppo. FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms
0 -- 0Matthew D. Smith 0004, Marshall A Case, Emily K. Makowski, Peter M. Tessier. Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data
0 -- 0Lechuan Li, Ruth Dannenfelser, Yu Zhu 0003, Nathaniel Hejduk, Santiago Segarra, Vicky Yao. Joint embedding of biological networks for cross-species functional alignment
0 -- 0Xinwei He, Kun Qian, Ziqian Wang, Shirou Zeng, Hongwei Li, Wei Vivian Li. scAce: an adaptive embedding and clustering method for single-cell gene expression data
0 -- 0. Correction to: Robust joint clustering of multi-omics single-cell data via multi-modal high-order neighborhood Laplacian matrix optimization
0 -- 0Tudor-Stefan Cotet, Andreas Agrafiotis, Victor Kreiner, Raphael Kuhn, Danielle Shlesinger, Marcos Manero-Carranza, Keywan Khodaverdi, Evgenios Kladis, Aurora Desideri Perea, Dylan Maassen-Veeters, Wiona Glänzer, Solène Massery, Lorenzo Guerci, Kai-Lin Hong, Jiami Han, Kostas Stiklioraitis, Vittoria Martinolli D'arcy, Raphael Dizerens, Samuel Kilchenmann, Lucas Stalder, Leon Nissen, Basil Vogelsanger, Stine Anzböck, Daria Laslo, Sophie Bakker, Melinda Kondorosy, Marco Venerito, Alejandro Sanz García, Isabelle Feller, Annette Oxenius, Sai T. Reddy, Alexander Yermanos. ePlatypus: an ecosystem for computational analysis of immunogenomics data
0 -- 0Pablo Millan Arias, Kathleen A. Hill, Lila Kari. iDeLUCS: a deep learning interactive tool for alignment-free clustering of DNA sequences
0 -- 0Johannes Smolander, Sini Junttila, Laura L. Elo. Cell-connectivity-guided trajectory inference from single-cell data
0 -- 0Seong Joon Park, Sunghwan Kim, Jaeho Jeong, Albert No, Jong-Seon No, Hosung Park. Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads
0 -- 0Boris Muzellec, Maria Telenczuk, Vincent Cabeli, Mathieu Andreux. PyDESeq2: a python package for bulk RNA-seq differential expression analysis
0 -- 0. Correction to: Optimal adjustment sets for causal query estimation in partially observed biomolecular networks
0 -- 0. Correction to: Clustering spatial transcriptomics data
0 -- 0Bhanwar Lal Puniya, Andreas Dräger. Advancements in computational modelling of biological systems: seventh annual SysMod meeting
0 -- 0Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Yaohang Li, Jianxin Wang 0001. MSDRP: a deep learning model based on multisource data for predicting drug response
0 -- 0Kleanthi Lakiotaki, Zacharias Papadovasilakis, Vincenzo Lagani, Stefanos Fafalios, Paulos Charonyktakis, Michail Tsagris, Ioannis Tsamardinos. Automated machine learning for genome wide association studies
0 -- 0Chuan-Yuan Wang, Shiyu Xu, Duanchen Sun, Zhi-Ping Liu. ActivePPI: quantifying protein-protein interaction network activity with Markov random fields
0 -- 0Daoyi Huang, Jianping Jiang, Tingting Zhao, Shengnan Wu, Pin Li, Yongfen Lyu, Jincai Feng, Mingyue Wei, Zhixing Zhu, Jianlei Gu, Yongyong Ren, Guangjun Yu, Hui Lu. diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype
0 -- 0Lin Wang, Chenhao Sun, Xianyu Xu, Jia Li, Wenjuan Zhang. A neighborhood-regularization method leveraging multiview data for predicting the frequency of drug-side effects
0 -- 0Megan L. Smith, Matthew W. Hahn. Phylogenetic inference using generative adversarial networks
0 -- 0Asmita Roy, Jun Chen, Xianyang Zhang. A general framework for powerful confounder adjustment in omics association studies
0 -- 0En-Yu Lai, Yen-Tsung Huang. Genome-wide multimediator analyses using the generalized Berk-Jones statistics with the composite test
0 -- 0Anna Paola Muntoni, Andrea Pagnani. DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors
0 -- 0Wuwei Tan, Yang Shen. Multimodal learning of noncoding variant effects using genome sequence and chromatin structure
0 -- 0. Correction to: "Retraction of: DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency"
0 -- 0Brian Johnson, Yubo Shuai, Jason Schweinsberg, Kit Curtius. cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory
0 -- 0Yuzhong Deng, Jianxiong Tang, Jiyang Zhang, Jianxiao Zou, Que Zhu, Shicai Fan. GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs
0 -- 0Xin He, Xianhui Huang, Yuexuan Long, Zhenping Liu, Xing Chang, Xianlong Zhang, Maojun Wang. Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms
0 -- 0Hui Yu, Limin Jiang, Chung-I Li, Scott Ness, Sara G. M. Piccirillo, Yan Guo. Somatic mutation effects diffused over microRNA dysregulation
0 -- 0Yiwei Liu, Changhuo Yang, Hong-Dong Li, Jianxin Wang. IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based method for predicting isoform functions
0 -- 0Adrià Fernández-Torras, Martina Locatelli, Martino Bertoni, Patrick Aloy. BQsupports: systematic assessment of the support and novelty of new biomedical associations