Volume 40(4); 2024 Apr

Applications Note

Data and Text Mining

longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types

Jonas Hagenberg, Monika Budde, Teodora Pandeva, Ivan Kondofersky, Sabrina K Schaupp, Fabian J Theis, Thomas G Schulze, Nikola S Müller, Urs Heilbronner, Richa Batra, Janine Knauer-Arloth

Bioinformatics. 2024 Apr; 40(4): btae137. Published online 2024 Mar 14. doi: 10.1093/bioinformatics/btae137

PMCID:: PMC10994717

Article PDF–3.3M

GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data

Eric Odle, Samuel Kahng, Siratee Riewluang, Kyoko Kurihara, Kevin C Wakeman

Bioinformatics. 2024 Apr; 40(4): btae152. Published online 2024 Mar 19. doi: 10.1093/bioinformatics/btae152

PMCID:: PMC10987208

Article PDF–1.1M

Databases and Ontologies

PyCoM: a python library for large-scale analysis of residue–residue coevolution data

Philipp Bibik, Sabriyeh Alibai, Alessandro Pandini, Sarath Chandra Dantu

Bioinformatics. 2024 Apr; 40(4): btae166. Published online 2024 Mar 26. doi: 10.1093/bioinformatics/btae166

PMCID:: PMC11009027

Article PDF–1.1M

A machine-readable specification for genomics assays

Ali Sina Booeshaghi, Xi Chen, Lior Pachter

Bioinformatics. 2024 Apr; 40(4): btae168. Published online 2024 Apr 5. doi: 10.1093/bioinformatics/btae168

PMCID:: PMC11009023

Article PDF–2.5M

Gene Expression

ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells

Andrew Jiang, Russell G Snell, Klaus Lehnert

Bioinformatics. 2024 Apr; 40(4): btae167. Published online 2024 Mar 27. doi: 10.1093/bioinformatics/btae167

PMCID:: PMC11007236

Article PDF–1.6M

shinyExprPortal: a configurable ‘shiny’ portal for sharing analysis of molecular expression data

Rafael Henkin, Katriona Goldmann, Myles Lewis, Michael R Barnes

Bioinformatics. 2024 Apr; 40(4): btae172. Published online 2024 Mar 29. doi: 10.1093/bioinformatics/btae172

PMCID:: PMC11021805

Article PDF–1.2M

Genetics and Population Analysis

Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations

Kangcheng Hou, Stephanie Gogarten, Joohyun Kim, Xing Hua, Julie-Alexia Dias, Quan Sun, Ying Wang, Taotao Tan, Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working Group , Elizabeth G Atkinson, Alicia Martin, Jonathan Shortt, Jibril Hirbo, Yun Li, Bogdan Pasaniuc, Haoyu Zhang

Bioinformatics. 2024 Apr; 40(4): btae148. Published online 2024 Mar 15. doi: 10.1093/bioinformatics/btae148

PMCID:: PMC10980565

Article PDF–1.1M

Phylogenetics

AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss

Benoit Morel, Tom A Williams, Alexandros Stamatakis, Gergely J Szöllősi

Bioinformatics. 2024 Apr; 40(4): btae162. Published online 2024 Mar 21. doi: 10.1093/bioinformatics/btae162

PMCID:: PMC10990685

Article PDF–1.6M

Sequence Analysis

Icarust, a real-time simulator for Oxford Nanopore adaptive sampling

Rory Munro, Satrio Wibowo, Alexander Payne, Matthew Loose

Bioinformatics. 2024 Apr; 40(4): btae141. Published online 2024 Mar 13. doi: 10.1093/bioinformatics/btae141

PMCID:: PMC10980563

Article PDF–1.6M

Rapid multiple protein sequence search by parallel and heterogeneous computation

Jiefu Li, Ziyuan Wang, Xuwei Fan, Ruijie Yao, Guoqing Zhang, Rui Fan, Zefeng Wang

Bioinformatics. 2024 Apr; 40(4): btae151. Published online 2024 Mar 28. doi: 10.1093/bioinformatics/btae151

PMCID:: PMC11021808

Article PDF–1.7M

Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries

Jochen Weile, Gabrielle Ferra, Gabriel Boyle, Sriram Pendyala, Clara Amorosi, Chiann-Ling Yeh, Atina G Cote, Nishka Kishore, Daniel Tabet, Warren van Loggerenberg, Ashyad Rayhan, Douglas M Fowler, Maitreya J Dunham, Frederick P Roth

Bioinformatics. 2024 Apr; 40(4): btae182. Published online 2024 Apr 3. doi: 10.1093/bioinformatics/btae182

PMCID:: PMC11021806

Article PDF–488K

Structural Bioinformatics

CLAUDIO: automated structural analysis of cross-linking data

Alexander Röhl, Eugen Netz, Oliver Kohlbacher, Hadeer Elhabashy

Bioinformatics. 2024 Apr; 40(4): btae146. Published online 2024 Mar 18. doi: 10.1093/bioinformatics/btae146

PMCID:: PMC10994719

Article PDF–1.0M

Integrating physics in deep learning algorithms: a force field as a PyTorch module

Gabriele Orlando, Luis Serrano, Joost Schymkowitz, Frederic Rousseau

Bioinformatics. 2024 Apr; 40(4): btae160. Published online 2024 Mar 21. doi: 10.1093/bioinformatics/btae160

PMCID:: PMC11007235

Article PDF–598K

3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures

Victoria Ruiz-Serra, Samuel Valentini, Sergi Madroñero, Alfonso Valencia, Eduard Porta-Pardo

Bioinformatics. 2024 Apr; 40(4): btae171. Published online 2024 Apr 2. doi: 10.1093/bioinformatics/btae171

PMCID:: PMC11018535

Article PDF–2.0M

Systems Biology

PyCoMo: a python package for community metabolic model creation and analysis

Michael Predl, Marianne Mießkes, Thomas Rattei, Jürgen Zanghellini

Bioinformatics. 2024 Apr; 40(4): btae153. Published online 2024 Mar 26. doi: 10.1093/bioinformatics/btae153

PMCID:: PMC10990682

Article PDF–1.1M

Original Papers

Bioimage Informatics

A model-based hierarchical Bayesian approach to Sholl analysis

Erik VonKaenel, Alexis Feidler, Rebecca Lowery, Katherine Andersh, Tanzy Love, Ania Majewska, Matthew N McCall

Bioinformatics. 2024 Apr; 40(4): btae156. Published online 2024 Mar 21. doi: 10.1093/bioinformatics/btae156

PMCID:: PMC10985672

Article PDF–2.6M

Data and Text Mining

MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning

Ruochi Zhang, Chao Wu, Qian Yang, Chang Liu, Yan Wang, Kewei Li, Lan Huang, Fengfeng Zhou

Bioinformatics. 2024 Apr; 40(4): btae118. Published online 2024 Feb 29. doi: 10.1093/bioinformatics/btae118

PMCID:: PMC10984949

Article PDF–5.2M

CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis

Liang Wang, Chenyang Hong, Jiangning Song, Jianhua Yao

Bioinformatics. 2024 Apr; 40(4): btae130. Published online 2024 Mar 29. doi: 10.1093/bioinformatics/btae130

PMCID:: PMC10985676

Article PDF–10M

Advancing entity recognition in biomedicine via instruction tuning of large language models

Vipina K Keloth, Yan Hu, Qianqian Xie, Xueqing Peng, Yan Wang, Andrew Zheng, Melih Selek, Kalpana Raja, Chih Hsuan Wei, Qiao Jin, Zhiyong Lu, Qingyu Chen, Hua Xu

Bioinformatics. 2024 Apr; 40(4): btae163. Published online 2024 Mar 21. doi: 10.1093/bioinformatics/btae163

PMCID:: PMC11001490

Article PDF–2.1M

MoleMCL: a multi-level contrastive learning framework for molecular pre-training

Xinyi Zhang, Yanni Xu, Changzhi Jiang, Lian Shen, Xiangrong Liu

Bioinformatics. 2024 Apr; 40(4): btae164. Published online 2024 Mar 26. doi: 10.1093/bioinformatics/btae164

PMCID:: PMC11001485

Article PDF–1.5M

Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes

Weizhong Zhao, Junze Wu, Xingpeng Jiang, Tingting He, Xiaohua Hu

Bioinformatics. 2024 Apr; 40(4): btae180. Published online 2024 Apr 3. doi: 10.1093/bioinformatics/btae180

PMCID:: PMC11026140

Article PDF–1.2M

Genome Analysis

ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation

Irenaeus C C Chan, Alex Panchot, Evelyn Schmidt, Samantha McNulty, Brian J Wiley, Jie Liu, Kimberly Turner, Lea Moukarzel, Wendy S W Wong, Duc Tran, J Scott Beeler, Armel Landry Batchi-Bouyou, Mitchell J Machiela, Danielle M Karyadi, Benjamin J Krajacich, Junhua Zhao, Semyon Kruglyak, Bryan Lajoie, Shawn Levy, Minal Patel, Philip W Kantoff, Christopher E Mason, Daniel C Link, Todd E Druley, Konrad H Stopsack, Kelly L Bolton

Bioinformatics. 2024 Apr; 40(4): btae121. Published online 2024 Mar 14. doi: 10.1093/bioinformatics/btae121

PMCID:: PMC11014783

Article PDF–2.4M

Regional analysis to delineate intrasample heterogeneity with RegionalST

Yue Lyu, Chong Wu, Wei Sun, Ziyi Li

Bioinformatics. 2024 Apr; 40(4): btae186. Published online 2024 Apr 5. doi: 10.1093/bioinformatics/btae186

PMCID:: PMC11026142

Article PDF–5.0M

Phylogenetics

MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction

Fang Wang, Yibin Wang, Xiaofei Zeng, Shengcheng Zhang, Jiaxin Yu, Dongxi Li, Xingtan Zhang

Bioinformatics. 2024 Apr; 40(4): btae154. Published online 2024 Mar 28. doi: 10.1093/bioinformatics/btae154

PMCID:: PMC10990684

Article PDF–5.5M

Sequence Analysis

scPathoQuant: a tool for efficient alignment and quantification of pathogen sequence reads from 10× single cell sequencing datasets

Leanne S Whitmore, Jennifer Tisoncik-Go, Michael Gale, Jr

Bioinformatics. 2024 Apr; 40(4): btae145. Published online 2024 Mar 13. doi: 10.1093/bioinformatics/btae145

PMCID:: PMC10990681

Article PDF–4.6M

MINDG: a drug–target interaction prediction method based on an integrated learning algorithm

Hailong Yang, Yue Chen, Yun Zuo, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Dong-Jun Yu

Bioinformatics. 2024 Apr; 40(4): btae147. Published online 2024 Mar 14. doi: 10.1093/bioinformatics/btae147

PMCID:: PMC10997434

Article PDF–2.0M

CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing

Ali Osman Berk Şapcı, Eleonora Rachtman, Siavash Mirarab

Bioinformatics. 2024 Apr; 40(4): btae150. Published online 2024 Mar 16. doi: 10.1093/bioinformatics/btae150

PMCID:: PMC10985673

Article PDF–2.4M

TemStaPro: protein thermostability prediction using sequence representations from protein language models

Ieva Pudžiuvelytė, Kliment Olechnovič, Egle Godliauskaite, Kristupas Sermokas, Tomas Urbaitis, Giedrius Gasiunas, Darius Kazlauskas

Bioinformatics. 2024 Apr; 40(4): btae157. Published online 2024 Mar 20. doi: 10.1093/bioinformatics/btae157

PMCID:: PMC11001493

Article PDF–1.8M

EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery

Johanna Elena Schmitz, Nihit Aggarwal, Lukas Laufer, Jörn Walter, Abdulrahman Salhab, Sven Rahmann

Bioinformatics. 2024 Apr; 40(4): btae178. Published online 2024 Apr 2. doi: 10.1093/bioinformatics/btae178

PMCID:: PMC11026141

Article PDF–3.5M

Structural Bioinformatics

Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction

Saisai Sun, Lin Gao

Bioinformatics. 2024 Apr; 40(4): btae155. Published online 2024 Mar 20. doi: 10.1093/bioinformatics/btae155

PMCID:: PMC11007238

Article PDF–5.0M

Systems Biology

GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway–pathway interaction network

Teng Ma, Jianxin Wang

Bioinformatics. 2024 Apr; 40(4): btae165. Published online 2024 Mar 26. doi: 10.1093/bioinformatics/btae165

PMCID:: PMC11007237

Article PDF–1.7M

Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning

Fuqun Chen, Guanhua Zou, Yongxian Wu, Le Ou-Yang

Bioinformatics. 2024 Apr; 40(4): btae169. Published online 2024 Mar 28. doi: 10.1093/bioinformatics/btae169

PMCID:: PMC11015955

Article PDF–1.9M

DrugMGR: a deep bioactive molecule binding method to identify compounds targeting proteins

Xiaokun Li, Qiang Yang, Long Xu, Weihe Dong, Gongning Luo, Wei Wang, Suyu Dong, Kuanquan Wang, Ping Xuan, Xianyu Zhang, Xin Gao

Bioinformatics. 2024 Apr; 40(4): btae176. Published online 2024 Apr 1. doi: 10.1093/bioinformatics/btae176

PMCID:: PMC11015954

Article PDF–2.6M

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