Journal: Bioinformatics

Volume 39, Issue 8

0 -- 0Jennifer Mattock, Marina Martínez-Álvaro, Matthew A Cleveland, Rainer Roehe, Mick Watson. KOunt: a reproducible KEGG orthologue abundance workflow
0 -- 0Lucas F. Voges, Lukas C. Jarren, Stephan Seifert. Exploitation of surrogate variables in random forests for unbiased analysis of mutual impact and importance of features
0 -- 0Göksel Misirli. libSBOLj3: a graph-based library for design and data exchange in synthetic biology
0 -- 0. Correction to: Joint registration of multiple point clouds for fast particle fusion in localization microscopy
0 -- 0Jianwen Fang. Predicting thermostability difference between cellular protein orthologs
0 -- 0Serene W. H. Wong, Chiara Pastrello, Max Kotlyar, Christos Faloutsos, Igor Jurisica. USNAP: fast unique dense region detection and its application to lung cancer
0 -- 0Guangzhi Xiong, Stefan Bekiranov, Aidong Zhang. ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq
0 -- 0Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Daisuke Kihara. Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling
0 -- 0Giovanni Madeo, Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio. CoCoNat: a novel method based on deep learning for coiled-coil prediction
0 -- 0Garrett M. Ginell, Aidan J. Flynn, Alex S. Holehouse. SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets
0 -- 0Lena Buck, Tobias Schmidt, Maren Feist, Philipp Schwarzfischer, Dieter Kube, Peter J. Oefner, Helena U. Zacharias, Michael Altenbuchinger, Katja Dettmer, Wolfram Gronwald, Rainer Spang. Anomaly detection in mixed high-dimensional molecular data
0 -- 0Anna Wierczeiko, Stefan Pastore, Stefan Mündnich, Anne M. Busch, Vincent Dietrich, Mark Helm, Tamer Butto, Susanne Gerber. NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis
0 -- 0Elena Krismer, Isabell Bludau, Maximilian T. Strauss, Matthias Mann. AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics
0 -- 0Kynon J. M. Benjamin, Tarun Katipalli, Apuã C. M. Paquola. dRFEtools: dynamic recursive feature elimination for omics
0 -- 0Joshua Barnett, Noori Sotudeh, Poorvi Rao, Jonah Silverman, Tamara Jafar, Liya Wang. AtlasXplore: a web platform for visualizing and sharing spatial epigenome data
0 -- 0Mercè Alemany-Chavarria, Jaime Rodríguez-Guerra, Jean-Didier Maréchal. TALAIA: a 3D visual dictionary for protein structures
0 -- 0Benjamin Hepp, Florence Lorieux, Augustin Degaugue, Jacques Oberto. VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes
0 -- 0Yuliang Pan, Yang Wang, Jihong Guan, Shuigeng Zhou. PCGAN: a generative approach for protein complex identification from protein interaction networks
0 -- 0Hamza Chegraoui, Vincent Guillemot, Amine Rebei, Arnaud Gloaguen, Jacques Grill, Cathy Philippe, Vincent Frouin. Integrating multiomics and prior knowledge: a study of the Graphnet penalty impact
0 -- 0Abbi Abdel-Rehim, Oghenejokpeme I. Orhobor, Hang Lou, Hao Ni, Ross D. King. Protein-ligand binding affinity prediction exploiting sequence constituent homology
0 -- 0Marteinn T. Hardarson, Gunnar Palsson, Bjarni V. Halldórsson. NCOurd: modelling length distributions of NCO events and gene conversion tracts
0 -- 0Yichen Cheng, Yusen Xia, Xinlei Wang 0001. Bayesian multitask learning for medicine recommendation based on online patient reviews
0 -- 0Ziqiao Zhang, Ailin Xie, Jihong Guan, Shuigeng Zhou. Molecular property prediction by semantic-invariant contrastive learning
0 -- 0Minghao Yang, Zhi-an Huang, Wei Zhou, Junkai Ji, Jun Zhang, Shan He, Zexuan Zhu. MIX-TPI: a flexible prediction framework for TCR-pMHC interactions based on multimodal representations
0 -- 0Jace Webster, Ha X. Dang, Pradeep S. Chauhan, WenJia Feng, Alex Shiang, Peter K. Harris, Russell K. Pachynski, Aadel A Chaudhuri, Christopher A. Maher. PACT: a pipeline for analysis of circulating tumor DNA
0 -- 0Eric H. Au, Christiana Fauci, Yanting Luo, Riley J. Mangan, Daniel A Snellings, Chelsea R. Shoben, Seth Weaver, Shae K. Simpson, Craig B. Lowe. Gonomics: uniting high performance and readability for genomics with Go
0 -- 0Richard Wilton, Alexander S. Szalay. Short-read aligner performance in germline variant identification
0 -- 0Fatemeh Rafiei, Hojjat Zeraati, Karim Abbasi, Jahan B. Ghasemi, Mahboubeh Parsaeian, Ali Masoudi-Nejad. DeepTraSynergy: drug combinations using multimodal deep learning with transformers
0 -- 0Bo-Wei Zhao, Xiao-Rui Su, Peng-Wei Hu, Yu-An Huang, Zhu-Hong You, Lun Hu. iGRLDTI: an improved graph representation learning method for predicting drug-target interactions over heterogeneous biological information network
0 -- 0Hans-Ulrich Klein. demuxmix: demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models
0 -- 0Feifei Wang, Dongzuo Liang, Yang Li, Shuangge Ma. Prior information-assisted integrative analysis of multiple datasets
0 -- 0Thaidy Moreno, Joaquin Magana, David A. Quigley. AARDVARK: an automated reversion detector for variants affecting resistance kinetics
0 -- 0Kim Philipp Jablonski, Niko Beerenwinkel. Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression
0 -- 0Ondrej Vavra, Jakub Beránek, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar. pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support
0 -- 0Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu. Chaining for accurate alignment of erroneous long reads to acyclic variation graphs
0 -- 0Apurva Kalia, Dilip Krishnan, Soha Hassoun. CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction
0 -- 0Gabriel Cretin, Charlotte Périn, Nicolas Zimmermann, Tatiana Galochkina, Jean-Christophe Gelly. ICARUS: flexible protein structural alignment based on Protein Units
0 -- 0Chen Wang, Harikumar Govindarajan, Panagiotis Katsonis, Olivier Lichtarge. B.subtilis
0 -- 0Anders Pitman, Xiaomeng Huang, Gabor T. Marth, Yi Qiao. quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics
0 -- 0Gang Wen, Limin Li. FGCNSurv: dually fused graph convolutional network for multi-omics survival prediction
0 -- 0Alexander Myronov, Giovanni Mazzocco, Paulina Król, Dariusz Plewczynski. BERTrand - peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing
0 -- 0Philip Hartout, Bojana Pocuca, Celia Méndez-García, Christian Schleberger. Investigating the human and nonobese diabetic mouse MHC class II immunopeptidome using protein language modeling
0 -- 0Bing-Xue Du, Yahui Long, Xiaoli Li, Min Wu, Jian-Yu Shi. CMMS-GCL: cross-modality metabolic stability prediction with graph contrastive learning
0 -- 0Chen Yang, Jiahao Mai, Xuan Cao, Aaron Burberry, Fabio Cominelli, LiangLiang Zhang. ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization
0 -- 0Tong Xin, Yanan Lv, Haoran Chen, Linlin Li, Lijun Shen, Guangcun Shan, Xi Chen 0031, Hua Han 0001. A novel registration method for long-serial section images of EM with a serial split technique based on unsupervised optical flow network
0 -- 0Daniel Liu, Martin Steinegger. Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices
0 -- 0Anton Zadorozhny, Anton Smirnov, Dmitry Filimonov, Alexey Lagunin. Prediction of pathogenic single amino acid substitutions using molecular fragment descriptors
0 -- 0Ruohua Shi, Keyan Bi, Kai Du, Lei Ma 0008, Fang Fang, Lingyu Duan, Tingting Jiang 0001, Tie-Jun Huang 0001. PS-Net: human perception-guided segmentation network for EM cell membrane
0 -- 0Jacob I Marsh, Jakob Petereit, Brady A Johnston, Philipp E. Bayer, Cassandria G. Tay Fernandez, Hawlader A Al-Mamun, Jacqueline Batley, David Edwards. crosshap: R package for local haplotype visualization for trait association analysis
0 -- 0Md Ashiqur Rahman, Abdullah Aman Tutul, Mahfuza Sharmin, Md. Shamsuzzoha Bayzid. BEENE: deep learning-based nonlinear embedding improves batch effect estimation
0 -- 0Russell B. Davidson, Mark Coletti, Mu Gao, Bryan Piatkowski, Avinash Sreedasyam, Farhan Quadir, David J. Weston, Jeremy Schmutz, Jianlin Cheng, Jeffrey Skolnick, Jerry M. Parks, Ada Sedova. Sphagnum divinum and proteome-scale annotation
0 -- 0Dmitry Penzar, Daria Nogina, Elizaveta Noskova, Arsenii Zinkevich, Georgy Meshcheryakov, Andrey Lando, Abdul Muntakim Rafi, Carl de Boer, Ivan V. Kulakovskiy. LegNet: a best-in-class deep learning model for short DNA regulatory regions
0 -- 0Zhenhuan Feng, Peiyang Fang, Hui Zheng, Xiaofei Zhang. DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data
0 -- 0Qunzhuo Wu, Zhaohong Deng, Wei Zhang, Xiaoyong Pan, Kup-Sze Choi, Yun Zuo, Hong-bin Shen, Dong-jun Yu. MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering
0 -- 0Longendri Aguilera-Mendoza, Sebastián Ayala-Ruano, Felix Martinez-Rios, Edgar Chávez, César R. García-Jacas, Carlos A. Brizuela, Yovani Marrero-Ponce. StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks
0 -- 0Amir Feizi, Kamalika Ray. otargen: GraphQL-based R package for tidy data accessing and processing from Open Targets Genetics
0 -- 0Xuhua Yan, Ruiqing Zheng, Jinmiao Chen, Min Li. scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization
0 -- 0Moctard Babatounde Oloulade, Jianliang Gao, Jiamin Chen, Raeed Al-Sabri, Zhenpeng Wu. Cancer drug response prediction with surrogate modeling-based graph neural architecture search
0 -- 0Yanli Wang, Zhiye Guo, Jianlin Cheng. Single-cell Hi-C data enhancement with deep residual and generative adversarial networks
0 -- 0Hyeongseon Jeon, Kyu-Sang Lim, Yet Nguyen, Dan Nettleton. Adjusting for gene-specific covariates to improve RNA-seq analysis
0 -- 0Eyal Mazuz, Guy Shtar, Nir Kutsky, Lior Rokach, Bracha Shapira. Pretrained transformer models for predicting the withdrawal of drugs from the market
0 -- 0Emanuel Cunha, Davide Lagoa, José P. Faria, Filipe Liu, Christopher S. Henry, Oscar Días. TranSyT, an innovative framework for identifying transport systems
0 -- 0Davor Orsolic, Tomislav Smuc. Dynamic applicability domain (dAD): compound-target binding affinity estimates with local conformal prediction
0 -- 0Andrea Mastropietro, Gianluca De Carlo, Aris Anagnostopoulos. XGDAG: explainable gene-disease associations via graph neural networks
0 -- 0Chen Li, Xiaoyang Chen, Shengquan Chen, Rui Jiang, Xuegong Zhang. simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data
0 -- 0Evangelos Karatzas, Fotis A. Baltoumas, Eleni Aplakidou, Panagiota I. Kontou, Panos Stathopoulos, Leonidas Stefanis, Pantelis G. Bagos, Georgios A. Pavlopoulos. Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources
0 -- 0Peng Chen, Jian Wang, Hongfei Lin, Di Zhao 0003, Zhihao Yang. Few-shot biomedical named entity recognition via knowledge-guided instance generation and prompt contrastive learning
0 -- 0Martin Wegner, Manuel Kaulich. co unting of single and combinatorial CRISPR gRNAs
0 -- 0Daniel T. Rademaker, Kevin J. van Geemen, Li C. Xue. GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations
0 -- 0Jack R. Leary, Yi Xu, Ashley B. Morrison, Chong Jin, Emily C. Shen, Peyton C. Kuhlers, Ye Su, Naim U. Rashid, Jen Jen Yeh, Xianlu Laura Peng. Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing
0 -- 0Sehi Park, Mobeen-ur-Rehman, Farman Ullah, Hilal Tayara, Kil To Chong 0001. iCpG-Pos: an accurate computational approach for identification of CpG sites using positional features on single-cell whole genome sequence data