Journal Issue: Bioinform Adv Volume 4(1);  2024

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Journal List

Volume 4(1);  2024

Application Notes

Proteomics and Metabolomics

DIAgui: a Shiny application to process the output from DIA-NN
Marc-Antoine Gerault, Luc Camoin, Samuel Granjeaud
Bioinform Adv. 2024; 4(1): vbae001. Published online 2024 Jan 13. doi: 10.1093/bioadv/vbae001
PMCID:
PMC10799745
Abstract Article PDF–683K

Software

RespirAnalyzer: an R package for analyzing data from continuous monitoring of respiratory signals
Teng Zhang, Xinzheng Dong, Dandan Wang, Chen Huang, Xiaohua Douglas Zhang
Bioinform Adv. 2024; 4(1): vbae003. Published online 2024 Jan 13. doi: 10.1093/bioadv/vbae003
PMCID:
PMC10807906
Abstract Article PDF–1.1M
mvlearnR and Shiny App for multiview learning
Elise F Palzer, Sandra E Safo
Bioinform Adv. 2024; 4(1): vbae005. Published online 2024 Jan 16. doi: 10.1093/bioadv/vbae005
PMCID:
PMC10833139
Abstract Article PDF–1.0M

Sequence Analysis

ClusterV-Web: a user-friendly tool for profiling HIV quasispecies and generating drug resistance reports from nanopore long-read data
Junhao Su, Shumin Li, Zhenxian Zheng, Tak-Wah Lam, Ruibang Luo
Bioinform Adv. 2024; 4(1): vbae006. Published online 2024 Jan 13. doi: 10.1093/bioadv/vbae006
PMCID:
PMC10812873
Abstract Article PDF–881K

Databases and Ontologies

HIVseqDB: a portable resource for NGS and sample metadata integration for HIV-1 drug resistance analysis
Alfred Ssekagiri, Daudi Jjingo, Nicholas Bbosa, Daniel L Bugembe, David P Kateete, I King Jordan, Pontiano Kaleebu, Deogratius Ssemwanga
Bioinform Adv. 2024; 4(1): vbae008. Published online 2024 Jan 14. doi: 10.1093/bioadv/vbae008
PMCID:
PMC10834361
Abstract Article PDF–1015K

Genome Analysis

ZygosityPredictor
Marco Rheinnecker, Martina Fröhlich, Marc Rübsam, Nagarajan Paramasivam, Christoph E Heilig, Stefan Fröhling, Richard F Schlenk, Barbara Hutter, Daniel Hübschmann
Bioinform Adv. 2024; 4(1): vbae017. Published online 2024 Feb 6. doi: 10.1093/bioadv/vbae017
PMCID:
PMC10980564
Abstract Article PDF–743K

Software

CMAT: ClinVar Mapping and Annotation Toolkit
April Shen, Marcos Casado Barbero, Baron Koylass, Kirill Tsukanov, Tim Cezard, Thomas M Keane
Bioinform Adv. 2024; 4(1): vbae018. Published online 2024 Feb 7. doi: 10.1093/bioadv/vbae018
PMCID:
PMC10879749
Abstract Article PDF–1.2M

Immunoinformatics

ExpoSeq: simplified analysis of high-throughput sequencing data from antibody discovery campaigns
Christoffer V Sørensen, Nils Hofmann, Puneet Rawat, Frederik V Sørensen, Anne Ljungars, Victor Greiff, Andreas H Laustsen, Timothy P Jenkins
Bioinform Adv. 2024; 4(1): vbae020. Published online 2024 Feb 10. doi: 10.1093/bioadv/vbae020
PMCID:
PMC10902677
Abstract Article PDF–692K

Software

BioModME for building and simulating dynamic computational models of complex biological systems
Justin A Womack, Viren Shah, Said H Audi, Scott S Terhune, Ranjan K Dash
Bioinform Adv. 2024; 4(1): vbae023. Published online 2024 Feb 20. doi: 10.1093/bioadv/vbae023
PMCID:
PMC10918630
Abstract Article PDF–716K

Systems Biology

CloudProteoAnalyzer: scalable processing of big data from proteomics using cloud computing
Jiancheng Li, Yi Xiong, Shichao Feng, Chongle Pan, Xuan Guo
Bioinform Adv. 2024; 4(1): vbae024. Published online 2024 Feb 23. doi: 10.1093/bioadv/vbae024
PMCID:
PMC10942798
Abstract Article PDF–1.0M

Software

OMEinfo: global geographic metadata for -omics experiments
Matthew Crown, Matthew Bashton
Bioinform Adv. 2024; 4(1): vbae025. Published online 2024 Feb 21. doi: 10.1093/bioadv/vbae025
PMCID:
PMC10918632
Abstract Article PDF–1000K
TrajPy: empowering feature engineering for trajectory analysis across domains
Maurício Moreira-Soares, Eduardo Mossmann, Rui D M Travasso, José Rafael Bordin
Bioinform Adv. 2024; 4(1): vbae026. Published online 2024 Feb 23. doi: 10.1093/bioadv/vbae026
PMCID:
PMC11032726
Abstract Article PDF–779K

Genome Analysis

Trackplot: a fast and lightweight R script for epigenomic enrichment plots
Anand Mayakonda, Frank Westermann
Bioinform Adv. 2024; 4(1): vbae031. Published online 2024 Feb 28. doi: 10.1093/bioadv/vbae031
PMCID:
PMC10932608
Abstract Article PDF–801K

Immunoinformatics

Making mouse transcriptomics deconvolution accessible with immunedeconv
Lorenzo Merotto, Gregor Sturm, Alexander Dietrich, Markus List, Francesca Finotello
Bioinform Adv. 2024; 4(1): vbae032. Published online 2024 Feb 28. doi: 10.1093/bioadv/vbae032
PMCID:
PMC10924280
Abstract Article PDF–1.1M

Systems Biology

dingo: a Python package for metabolic flux sampling
Apostolos Chalkis, Vissarion Fisikopoulos, Elias Tsigaridas, Haris Zafeiropoulos
Bioinform Adv. 2024; 4(1): vbae037. Published online 2024 Mar 22. doi: 10.1093/bioadv/vbae037
PMCID:
PMC10997433
Abstract Article PDF–469K
Extending BioMASS to construct mathematical models from external knowledge
Kiwamu Arakane, Hiroaki Imoto, Fabian Ormersbach, Mariko Okada
Bioinform Adv. 2024; 4(1): vbae042. Published online 2024 Apr 4. doi: 10.1093/bioadv/vbae042
PMCID:
PMC11007111
Abstract Article PDF–1.2M

Software

CAFA-evaluator: a Python tool for benchmarking ontological classification methods
Damiano Piovesan, Davide Zago, Parnal Joshi, M Clara De Paolis Kaluza, Mahta Mehdiabadi, Rashika Ramola, Alexander Miguel Monzon, Walter Reade, Iddo Friedberg, Predrag Radivojac, Silvio C E Tosatto
Bioinform Adv. 2024; 4(1): vbae043. Published online 2024 Mar 14. doi: 10.1093/bioadv/vbae043
PMCID:
PMC10965419
Abstract Article PDF–496K

Data and Text Mining

ExplaineR: an R package to explain machine learning models
Ramtin Zargari Marandi
Bioinform Adv. 2024; 4(1): vbae049. Published online 2024 Mar 26. doi: 10.1093/bioadv/vbae049
PMCID:
PMC10994716
Abstract Article PDF–854K

Genome Analysis

OpenAnnotateApi: Python and R packages to efficiently annotate and analyze chromatin accessibility of genomic regions
Zijing Gao, Rui Jiang, Shengquan Chen
Bioinform Adv. 2024; 4(1): vbae055. Published online 2024 Apr 10. doi: 10.1093/bioadv/vbae055
PMCID:
PMC11031356
Abstract Article PDF–851K

Proteomics and Metabolomics

FlexStat: combinatory differentially expressed protein extraction
Senuri De Silva, Asfa Alli-Shaik, Jayantha Gunaratne
Bioinform Adv. 2024; 4(1): vbae056. Published online 2024 Apr 11. doi: 10.1093/bioadv/vbae056
PMCID:
PMC11055397
Abstract Article PDF–1.4M

Software

GLIMMERS: glioma molecular markers exploration using long-read sequencing
Wichayapat Thongrattana, Tantip Arigul, Bhoom Suktitipat, Manop Pithukpakorn, Sith Sathornsumetee, Thidathip Wongsurawat, Piroon Jenjaroenpun
Bioinform Adv. 2024; 4(1): vbae058. Published online 2024 Apr 15. doi: 10.1093/bioadv/vbae058
PMCID:
PMC11087932
Abstract Article PDF–755K

Data and Text Mining

Syntactic sugars: crafting a regular expression framework for glycan structures
Alexander R Bennett, Daniel Bojar
Bioinform Adv. 2024; 4(1): vbae059. Published online 2024 Apr 19. doi: 10.1093/bioadv/vbae059
PMCID:
PMC11069104
Abstract Article PDF–1.3M

Software

scX: a user-friendly tool for scRNAseq exploration
Tomás V Waichman, M L Vercesi, Ariel A Berardino, Maximiliano S Beckel, Damiana Giacomini, Natalí B Rasetto, Magalí Herrero, Daniela J Di Bella, Paola Arlotta, Alejandro F Schinder, Ariel Chernomoretz
Bioinform Adv. 2024; 4(1): vbae062. Published online 2024 May 2. doi: 10.1093/bioadv/vbae062
PMCID:
PMC11109472
Abstract Article PDF–822K

Databases and Ontologies

rNMPID: a database for riboNucleoside MonoPhosphates in DNA
Jingcheng Yang, Mo Sun, Zihan Ran, Taehwan Yang, Deepali L Kundnani, Francesca Storici, Penghao Xu
Bioinform Adv. 2024; 4(1): vbae063. Published online 2024 May 8. doi: 10.1093/bioadv/vbae063
PMCID:
PMC11088741
Abstract Article PDF–918K

Gene Regulation

danRerLib: a Python package for zebrafish transcriptomics
Ashley V Schwartz, Karilyn E Sant, Uduak Z George
Bioinform Adv. 2024; 4(1): vbae065. Published online 2024 May 6. doi: 10.1093/bioadv/vbae065
PMCID:
PMC11105952
Abstract Article PDF–952K

Genome Analysis

COSGAP: COntainerized Statistical Genetics Analysis Pipelines
Bayram Cevdet Akdeniz, Oleksandr Frei, Espen Hagen, Tahir Tekin Filiz, Sandeep Karthikeyan, Joëlle Pasman, Andreas Jangmo, Jacob Bergstedt, John R Shorter, Richard Zetterberg, Joeri Meijsen, Ida Elken Sønderby, Alfonso Buil, Martin Tesli, Yi Lu, Patrick Sullivan, Ole A Andreassen, Eivind Hovig
Bioinform Adv. 2024; 4(1): vbae067. Published online 2024 May 9. doi: 10.1093/bioadv/vbae067
PMCID:
PMC11132817
Abstract Article PDF–833K

Systems Biology

Microbial Abundances Retrieved from Sequencing data—automated NCBI Taxonomy (MARS): a pipeline to create relative microbial abundance data for the Microbiome Modelling Toolbox and utilizing homosynonyms for efficient mapping to resources
Tim Hulshof, Bram Nap, Filippo Martinelli, Ines Thiele
Bioinform Adv. 2024; 4(1): vbae068. Published online 2024 May 10. doi: 10.1093/bioadv/vbae068
PMCID:
PMC11193099
Abstract Article PDF–539K

Database and Ontologies

ASpedia-R: a package to retrieve junction-incorporating features and knowledge-based functions of human alternative splicing events
Daejin Hyung, Soo Young Cho, Kyubin Lee, Namhee Yu, Sehwa Hong, Charny Park
Bioinform Adv. 2024; 4(1): vbae071. Published online 2024 May 11. doi: 10.1093/bioadv/vbae071
PMCID:
PMC11142624
Abstract Article PDF–1.9M

Genome Analysis

DeGeCI 1.1: a web platform for gene annotation of mitochondrial genomes
Lisa Fiedler, Matthias Bernt, Martin Middendorf
Bioinform Adv. 2024; 4(1): vbae072. Published online 2024 May 13. doi: 10.1093/bioadv/vbae072
PMCID:
PMC11116735
Abstract Article PDF–1.0M

Genetics and Population Analysis

Hapsolutely: a user-friendly tool integrating haplotype phasing, network construction, and haploweb calculation
Miguel Vences, Stefanos Patmanidis, Jan-Christopher Schmidt, Michael Matschiner, Aurélien Miralles, Susanne S Renner
Bioinform Adv. 2024; 4(1): vbae083. Published online 2024 Jun 5. doi: 10.1093/bioadv/vbae083
PMCID:
PMC11184345
Abstract Article PDF–957K

Genome Analysis

racoon_clip—a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data
Melina Klostermann, Kathi Zarnack
Bioinform Adv. 2024; 4(1): vbae084. Published online 2024 Jun 26. doi: 10.1093/bioadv/vbae084
PMCID:
PMC11213630
Abstract Article PDF–670K

Data and Text Mining

A customizable secure DIY web application for accessing, sharing, and browsing aggregate experimental results and metadata
Jaewoo Lee, Mehita Achuthan, Lucas Chen, Paulina Carmona-Mora
Bioinform Adv. 2024; 4(1): vbae087. Published online 2024 Jun 28. doi: 10.1093/bioadv/vbae087
PMCID:
PMC11257709
Abstract Article PDF–488K

Gene Regulation

Evergene: an interactive webtool for large-scale gene-centric analysis of primary tumours
Anna Kennedy, Ella Richardson, Jonathan Higham, Panagiotis Kotsantis, Richard Mort, Barbara Bo-Ju Shih
Bioinform Adv. 2024; 4(1): vbae092. Published online 2024 Jun 18. doi: 10.1093/bioadv/vbae092
PMCID:
PMC11213629
Abstract Article PDF–2.0M

Genetics and Population Analysis

loco-pipe: an automated pipeline for population genomics with low-coverage whole-genome sequencing
Zehua T Zhou, Gregory L Owens, Wesley A Larson, Runyang Nicolas Lou, Peter H Sudmant
Bioinform Adv. 2024; 4(1): vbae098. Published online 2024 Jul 11. doi: 10.1093/bioadv/vbae098
PMCID:
PMC11246161
Abstract Article PDF–1.0M

Systems Biology

INCAWrapper: a Python wrapper for INCA for seamless data import, -export, and -processing
Matthias Mattanovich, Viktor Hesselberg-Thomsen, Annette Lien, Dovydas Vaitkus, Victoria Sara Saad, Douglas McCloskey
Bioinform Adv. 2024; 4(1): vbae100. Published online 2024 Jul 4. doi: 10.1093/bioadv/vbae100
PMCID:
PMC11245311
Abstract Article PDF–490K

Software

TWCOM: an R package for inference of cell–cell communication on spatially resolved transcriptomics data
Dongyuan Wu, Susmita Datta
Bioinform Adv. 2024; 4(1): vbae101. Published online 2024 Jul 16. doi: 10.1093/bioadv/vbae101
PMCID:
PMC11262461
Abstract Article PDF–864K
consICA: an R package for robust reference-free deconvolution of multi-omics data
Maryna Chepeleva, Tony Kaoma, Andrei Zinovyev, Reka Toth, Petr V Nazarov
Bioinform Adv. 2024; 4(1): vbae102. Published online 2024 Jul 13. doi: 10.1093/bioadv/vbae102
PMCID:
PMC11257712
Abstract Article PDF–678K

Systems Biology

ScyNet: Visualizing interactions in community metabolic models
Michael Predl, Kilian Gandolf, Michael Hofer, Thomas Rattei
Bioinform Adv. 2024; 4(1): vbae104. Published online 2024 Jul 17. doi: 10.1093/bioadv/vbae104
PMCID:
PMC11315608
Abstract Article PDF–1.4M

Data and Text Mining

survivalContour: visualizing predicted survival via colored contour plots
Yushu Shi, Liangliang Zhang, Kim-Anh Do, Robert R Jenq, Christine B Peterson
Bioinform Adv. 2024; 4(1): vbae105. Published online 2024 Jul 25. doi: 10.1093/bioadv/vbae105
PMCID:
PMC11290613
Abstract Article PDF–854K

Structural Bioinformatics

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration
Jhih-Siang Lai, Stephen K Burley, Jose M Duarte
Bioinform Adv. 2024; 4(1): vbae111. Published online 2024 Jul 25. doi: 10.1093/bioadv/vbae111
PMCID:
PMC11297494
Abstract Article PDF–585K

Genetics and Population Analysis

PaintorPipe: a pipeline for genetic variant fine-mapping using functional annotations
Zoé Gerber, Michel Fisun, Hugues Aschard, Sarah Djebali
Bioinform Adv. 2024; 4(1): vbad188. Published online 2023 Dec 21. doi: 10.1093/bioadv/vbad188
PMCID:
PMC10783948
Abstract Article PDF–1.1M

Original Articles

Gene Regulation

Predicting evolutionary targets and parameters of gene deletion from expression data
Andre Luiz Campelo dos Santos, Michael DeGiorgio, Raquel Assis
Bioinform Adv. 2024; 4(1): vbae002. Published online 2024 Jan 17. doi: 10.1093/bioadv/vbae002
PMCID:
PMC10812876
Abstract Article PDF–1.7M

Software

DeepRegFinder: deep learning-based regulatory elements finder
Aarthi Ramakrishnan, George Wangensteen, Sarah Kim, Eric J Nestler, Li Shen
Bioinform Adv. 2024; 4(1): vbae007. Published online 2024 Jan 14. doi: 10.1093/bioadv/vbae007
PMCID:
PMC10858349
Abstract Article PDF–1.7M

Data and Text Mining

Non-Negative matrix factorization combined with kernel regression for the prediction of adverse drug reaction profiles
Yezhao Zhong, Cathal Seoighe, Haixuan Yang
Bioinform Adv. 2024; 4(1): vbae009. Published online 2024 Jan 23. doi: 10.1093/bioadv/vbae009
PMCID:
PMC11087822
Abstract Article PDF–2.0M

Systems Biology

MMDRP: drug response prediction and biomarker discovery using multi-modal deep learning
Farzan Taj, Lincoln D Stein
Bioinform Adv. 2024; 4(1): vbae010. Published online 2024 Jan 20. doi: 10.1093/bioadv/vbae010
PMCID:
PMC10872075
Abstract Article PDF–1.9M

Gene Regulation

SPREd: a simulation-supervised neural network tool for gene regulatory network reconstruction
Zijun Wu, Saurabh Sinha
Bioinform Adv. 2024; 4(1): vbae011. Published online 2024 Jan 23. doi: 10.1093/bioadv/vbae011
PMCID:
PMC10913396
Abstract Article PDF–844K

Proteomics and Metabolomics

RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein composition that occur during biological processes
William Edwin Hackett, Deborah Chang, Luis Carvalho, Joseph Zaia
Bioinform Adv. 2024; 4(1): vbae012. Published online 2024 Jan 25. doi: 10.1093/bioadv/vbae012
PMCID:
PMC10879752
Abstract Article PDF–4.0M

Systems Biology

PM-CNN: microbiome status recognition and disease detection model based on phylogeny and multi-path neural network
Qiangqiang Wang, Xiaoqian Fan, Shunyao Wu, Xiaoquan Su
Bioinform Adv. 2024; 4(1): vbae013. Published online 2024 Jan 27. doi: 10.1093/bioadv/vbae013
PMCID:
PMC10873578
Abstract Article PDF–1.3M

Phylogenetics

Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants
Zhaoxing Wu, Claudia Solís-Lemus
Bioinform Adv. 2024; 4(1): vbae014. Published online 2024 Feb 8. doi: 10.1093/bioadv/vbae014
PMCID:
PMC10879748
Abstract Article PDF–2.0M

Genome Analysis

iCluF: an unsupervised iterative cluster-fusion method for patient stratification using multiomics data
Sushil K Shakyawar, Balasrinivasa R Sajja, Jai Chand Patel, Chittibabu Guda
Bioinform Adv. 2024; 4(1): vbae015. Published online 2024 Jan 30. doi: 10.1093/bioadv/vbae015
PMCID:
PMC11063539
Abstract Article PDF–1.4M

Metagenomics

HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads
Bhavish Verma, John Parkinson
Bioinform Adv. 2024; 4(1): vbae016. Published online 2024 Feb 1. doi: 10.1093/bioadv/vbae016
PMCID:
PMC10873905
Abstract Article PDF–1.3M

Phylogenetics

Novel symmetry-preserving neural network model for phylogenetic inference
Xudong Tang, Leonardo Zepeda-Nuñez, Shengwen Yang, Zelin Zhao, Claudia Solís-Lemus
Bioinform Adv. 2024; 4(1): vbae022. Published online 2024 Feb 19. doi: 10.1093/bioadv/vbae022
PMCID:
PMC11026143
Abstract Article PDF–1.4M

Genetics and Population Analysis

MetaQuad: shared informative variants discovery in metagenomic samples
Sheng Xu, Daniel C Morgan, Gordon Qian, Yuanhua Huang, Joshua W K Ho
Bioinform Adv. 2024; 4(1): vbae030. Published online 2024 Feb 24. doi: 10.1093/bioadv/vbae030
PMCID:
PMC10932609
Abstract Article PDF–1.4M

Immunoinformatics

nanoBERT: a deep learning model for gene agnostic navigation of the nanobody mutational space
Johannes Thorling Hadsund, Tadeusz Satława, Bartosz Janusz, Lu Shan, Li Zhou, Richard Röttger, Konrad Krawczyk
Bioinform Adv. 2024; 4(1): vbae033. Published online 2024 Mar 6. doi: 10.1093/bioadv/vbae033
PMCID:
PMC10978573
Abstract Article PDF–1.7M

Gene Regulation

Inference of differential gene regulatory networks using boosted differential trees
Gihanna Galindez, Markus List, Jan Baumbach, Uwe Völker, Ulrike Mäder, David B Blumenthal, Tim Kacprowski
Bioinform Adv. 2024; 4(1): vbae034. Published online 2024 Feb 29. doi: 10.1093/bioadv/vbae034
PMCID:
PMC10948285
Abstract Article PDF–3.5M

Databases and Ontologies

MERITS: a web-based integrated Mycobacterial PE/PPE protein database
Zhijie He, Cong Wang, Xudong Guo, Heyun Sun, Yue Bi, Miranda E Pitt, Chen Li, Jiangning Song, Lachlan J M Coin, Fuyi Li
Bioinform Adv. 2024; 4(1): vbae035. Published online 2024 Mar 2. doi: 10.1093/bioadv/vbae035
PMCID:
PMC10973932
Abstract Article PDF–1.6M

Systems Biology

Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning
Luca Cappelletti, Lauren Rekerle, Tommaso Fontana, Peter Hansen, Elena Casiraghi, Vida Ravanmehr, Christopher J Mungall, Jeremy J Yang, Leonard Spranger, Guy Karlebach, J Harry Caufield, Leigh Carmody, Ben Coleman, Tudor I Oprea, Justin Reese, Giorgio Valentini, Peter N Robinson
Bioinform Adv. 2024; 4(1): vbae036. Published online 2024 Mar 4. doi: 10.1093/bioadv/vbae036
PMCID:
PMC10994718
Abstract Article PDF–1.5M

Disease Bioinformatics/Translational Medicine

Mapping drug biology to disease genetics to discover drug impacts on the human phenome
Mamoon Habib, Panagiotis Nikolaos Lalagkas, Rachel D Melamed
Bioinform Adv. 2024; 4(1): vbae038. Published online 2024 Mar 9. doi: 10.1093/bioadv/vbae038
PMCID:
PMC11087821
Abstract Article PDF–2.2M

Cheminformatics

Prediction of bitterness based on modular designed graph neural network
Yi He, Kaifeng Liu, Yuyang Liu, Weiwei Han
Bioinform Adv. 2024; 4(1): vbae041. Published online 2024 Mar 13. doi: 10.1093/bioadv/vbae041
PMCID:
PMC10987211
Abstract Article PDF–2.9M

Sequence Analysis

DeGenPrime provides robust primer design and optimization unlocking the biosphere
Bryan Fulghum, Sophie H Tanker, Richard Allen White, III
Bioinform Adv. 2024; 4(1): vbae044. Published online 2024 Mar 14. doi: 10.1093/bioadv/vbae044
PMCID:
PMC11001487
Abstract Article PDF–1.4M

Data and Text Mining

Data-driven information extraction and enrichment of molecular profiling data for cancer cell lines
Ellery Smith, Rahel Paloots, Dimitris Giagkos, Michael Baudis, Kurt Stockinger
Bioinform Adv. 2024; 4(1): vbae045. Published online 2024 Mar 16. doi: 10.1093/bioadv/vbae045
PMCID:
PMC10978572
Abstract Article PDF–1.8M

Systems Biology

BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering
Richard Oliver Matzko, Savas Konur
Bioinform Adv. 2024; 4(1): vbae046. Published online 2024 Mar 20. doi: 10.1093/bioadv/vbae046
PMCID:
PMC10990683
Abstract Article PDF–2.7M

Cancer

Text-mining-based feature selection for anticancer drug response prediction
Grace Wu, Arvin Zaker, Amirhosein Ebrahimi, Shivanshi Tripathi, Arvind Singh Mer
Bioinform Adv. 2024; 4(1): vbae047. Published online 2024 Mar 26. doi: 10.1093/bioadv/vbae047
PMCID:
PMC11009020
Abstract Article PDF–1.8M

Software

CATD: a reproducible pipeline for selecting cell-type deconvolution methods across tissues
Anna Vathrakokoili Pournara, Zhichao Miao, Ozgur Yilimaz Beker, Nadja Nolte, Alvis Brazma, Irene Papatheodorou
Bioinform Adv. 2024; 4(1): vbae048. Published online 2024 Mar 23. doi: 10.1093/bioadv/vbae048
PMCID:
PMC11023940
Abstract Article PDF–3.3M

Data and Text Mining

Adjusting for covariates and assessing modeling fitness in machine learning using MUVR2
Yingxiao Yan, Tessa Schillemans, Viktor Skantze, Carl Brunius
Bioinform Adv. 2024; 4(1): vbae051. Published online 2024 Apr 4. doi: 10.1093/bioadv/vbae051
PMCID:
PMC11031361
Abstract Article PDF–1.8M

Sequence Analysis

WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences
George Glidden-Handgis, Travis J Wheeler
Bioinform Adv. 2024; 4(1): vbae052. Published online 2024 Apr 8. doi: 10.1093/bioadv/vbae052
PMCID:
PMC11099658
Abstract Article PDF–11M
Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages
Anže Božič, Rudolf Podgornik
Bioinform Adv. 2024; 4(1): vbae053. Published online 2024 Apr 8. doi: 10.1093/bioadv/vbae053
PMCID:
PMC11031363
Abstract Article PDF–1.6M

Databases and Ontologies

Single-cell type annotation with deep learning in 265 cell types for humans
Sherry Dong, Kaiwen Deng, Xiuzhen Huang
Bioinform Adv. 2024; 4(1): vbae054. Published online 2024 Apr 8. doi: 10.1093/bioadv/vbae054
PMCID:
PMC11031354
Abstract Article PDF–1.8M

Data and Text Mining

Deep IDA: a deep learning approach for integrative discriminant analysis of multi-omics data with feature ranking—an application to COVID-19
Jiuzhou Wang, Sandra E Safo
Bioinform Adv. 2024; 4(1): vbae060. Published online 2024 Apr 24. doi: 10.1093/bioadv/vbae060
PMCID:
PMC11256945
Abstract Article PDF–1.9M

Metagenomics

MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data
Jose L Figueroa, III, Andrew Redinbo, Ajay Panyala, Sean Colby, Maren L Friesen, Lisa Tiemann, Richard Allen White, III
Bioinform Adv. 2024; 4(1): vbae061. Published online 2024 Apr 24. doi: 10.1093/bioadv/vbae061
PMCID:
PMC11090762
Abstract Article PDF–1.5M

Systems Biology

Uncover spatially informed variations for single-cell spatial transcriptomics with STew
Nanxi Guo, Juan Vargas, Samantha Reynoso, Douglas Fritz, Revanth Krishna, Chuangqi Wang, Fan Zhang
Bioinform Adv. 2024; 4(1): vbae064. Published online 2024 May 29. doi: 10.1093/bioadv/vbae064
PMCID:
PMC11142628
Abstract Article PDF–2.4M
Network depth affects inference of gene sets from bacterial transcriptomes using denoising autoencoders
Willow Kion-Crosby, Lars Barquist
Bioinform Adv. 2024; 4(1): vbae066. Published online 2024 May 8. doi: 10.1093/bioadv/vbae066
PMCID:
PMC11256956
Abstract Article PDF–1.2M

Genome Analysis

WGCCRR: a web-based tool for genome-wide screening of convergent indels and substitutions of amino acids
Zheng Dong, Chen Wang, Qingming Qu
Bioinform Adv. 2024; 4(1): vbae070. Published online 2024 May 24. doi: 10.1093/bioadv/vbae070
PMCID:
PMC11132816
Abstract Article PDF–1.0M

Data and Text Mining

Assessing the validity of driver gene identification tools for targeted genome sequencing data
Felipe Rojas-Rodriguez, Marjanka K Schmidt, Sander Canisius
Bioinform Adv. 2024; 4(1): vbae073. Published online 2024 May 23. doi: 10.1093/bioadv/vbae073
PMCID:
PMC11132814
Abstract Article PDF–1.2M

Genome Analysis

Predmoter—cross-species prediction of plant promoter and enhancer regions
Felicitas Kindel, Sebastian Triesch, Urte Schlüter, Laura Alexandra Randarevitch, Vanessa Reichel-Deland, Andreas P M Weber, Alisandra K Denton
Bioinform Adv. 2024; 4(1): vbae074. Published online 2024 May 24. doi: 10.1093/bioadv/vbae074
PMCID:
PMC11150885
Abstract Article PDF–2.8M

Systems Biology

The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell
Sergio Doria-Belenguer, Alexandros Xenos, Gaia Ceddia, Noël Malod-Dognin, Nataša Pržulj
Bioinform Adv. 2024; 4(1): vbae075. Published online 2024 May 23. doi: 10.1093/bioadv/vbae075
PMCID:
PMC11142626
Abstract Article PDF–1.3M

Sequence Analysis

Improve-RRBS: a novel tool to correct the 3′ trimming of reduced representation sequencing reads
Ábel Fóthi, Hongbo Liu, Katalin Susztak, Tamas Aranyi
Bioinform Adv. 2024; 4(1): vbae076. Published online 2024 May 24. doi: 10.1093/bioadv/vbae076
PMCID:
PMC11154647
Abstract Article PDF–1.1M

Bioimage Informatics

OM2Seq: learning retrieval embeddings for optical genome mapping
Yevgeni Nogin, Danielle Sapir, Tahir Detinis Zur, Nir Weinberger, Yonatan Belinkov, Yuval Ebenstein, Yoav Shechtman
Bioinform Adv. 2024; 4(1): vbae079. Published online 2024 Jun 5. doi: 10.1093/bioadv/vbae079
PMCID:
PMC11194751
Abstract Article PDF–2.1M

Genome Analysis

Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates
Franziska Lang, Patrick Sorn, Martin Suchan, Alina Henrich, Christian Albrecht, Nina Köhl, Aline Beicht, Pablo Riesgo-Ferreiro, Christoph Holtsträter, Barbara Schrörs, David Weber, Martin Löwer, Ugur Sahin, Jonas Ibn-Salem
Bioinform Adv. 2024; 4(1): vbae080. Published online 2024 May 29. doi: 10.1093/bioadv/vbae080
PMCID:
PMC11165244
Abstract Article PDF–2.1M

Software

CellsFromSpace: a fast, accurate, and reference-free tool to deconvolve and annotate spatially distributed omics data
Corentin Thuilliez, Gaël Moquin-Beaudry, Pierre Khneisser, Maria Eugenia Marques Da Costa, Slim Karkar, Hanane Boudhouche, Damien Drubay, Baptiste Audinot, Birgit Geoerger, Jean-Yves Scoazec, Nathalie Gaspar, Antonin Marchais
Bioinform Adv. 2024; 4(1): vbae081. Published online 2024 May 30. doi: 10.1093/bioadv/vbae081
PMCID:
PMC11194756
Abstract Article PDF–41M

Phylogenetics

Differentiable phylogenetics via hyperbolic embeddings with Dodonaphy
Matthew Macaulay, Mathieu Fourment
Bioinform Adv. 2024; 4(1): vbae082. Published online 2024 Jun 19. doi: 10.1093/bioadv/vbae082
PMCID:
PMC11310108
Abstract Article PDF–1.1M

Gene Regulation

scVIC: deep generative modeling of heterogeneity for scRNA-seq data
Jiankang Xiong, Fuzhou Gong, Liang Ma, Lin Wan
Bioinform Adv. 2024; 4(1): vbae086. Published online 2024 Jun 13. doi: 10.1093/bioadv/vbae086
PMCID:
PMC11256938
Abstract Article PDF–2.1M

Sequence Analysis

Sensitive and error-tolerant annotation of protein-coding DNA with BATH
Genevieve R Krause, Walt Shands, Travis J Wheeler
Bioinform Adv. 2024; 4(1): vbae088. Published online 2024 Jun 14. doi: 10.1093/bioadv/vbae088
PMCID:
PMC11223822
Abstract Article PDF–2.9M

Genome Analysis

Discovering genomic islands in unannotated bacterial genomes using sequence embedding
Priyanka Banerjee, Oliver Eulenstein, Iddo Friedberg
Bioinform Adv. 2024; 4(1): vbae089. Published online 2024 Jun 17. doi: 10.1093/bioadv/vbae089
PMCID:
PMC11193100
Abstract Article PDF–2.0M

Data and Text Mining

Optimal linear ensemble of binary classifiers
Mehmet Eren Ahsen, Robert Vogel, Gustavo Stolovitzky
Bioinform Adv. 2024; 4(1): vbae093. Published online 2024 Jun 25. doi: 10.1093/bioadv/vbae093
PMCID:
PMC11249386
Abstract Article PDF–1.4M

Data Visualization

SlowMoMan: a web app for discovery of important features along user-drawn trajectories in 2D embeddings
Kiran Deol, Griffin M Weber, Yun William Yu
Bioinform Adv. 2024; 4(1): vbae095. Published online 2024 Jun 21. doi: 10.1093/bioadv/vbae095
PMCID:
PMC11220466
Abstract Article PDF–2.2M

Sequence Analysis

TemBERTure: advancing protein thermostability prediction with deep learning and attention mechanisms
Chiara Rodella, Symela Lazaridi, Thomas Lemmin
Bioinform Adv. 2024; 4(1): vbae103. Published online 2024 Jul 13. doi: 10.1093/bioadv/vbae103
PMCID:
PMC11262459
Abstract Article PDF–1.5M

Data and Text Mining

Mining drug–target interactions from biomedical literature using chemical and gene descriptions-based ensemble transformer model
Jehad Aldahdooh, Ziaurrehman Tanoli, Jing Tang
Bioinform Adv. 2024; 4(1): vbae106. Published online 2024 Jul 22. doi: 10.1093/bioadv/vbae106
PMCID:
PMC11293871
Abstract Article PDF–1.9M

Genetics and Population Analysis

Genotype imputation in F2 crosses of inbred lines
Saul Pierotti, Bettina Welz, Mireia Osuna-López, Tomas Fitzgerald, Joachim Wittbrodt, Ewan Birney
Bioinform Adv. 2024; 4(1): vbae107. Published online 2024 Jul 23. doi: 10.1093/bioadv/vbae107
PMCID:
PMC11286293
Abstract Article PDF–1.3M

Gene Regulation

Systematic analysis on the horse-shoe-like effect in PCA plots of scRNA-seq data
Najeebullah Shah, Qiuchen Meng, Ziheng Zou, Xuegong Zhang
Bioinform Adv. 2024; 4(1): vbae109. Published online 2024 Jul 29. doi: 10.1093/bioadv/vbae109
PMCID:
PMC11316618
Abstract Article PDF–1.5M

Genome Analysis

Marker discovery in the large
Beatriz Vieira Mourato, Ivan Tsers, Svenja Denker, Fabian Klötzl, Bernhard Haubold
Bioinform Adv. 2024; 4(1): vbae113. Published online 2024 Jul 27. doi: 10.1093/bioadv/vbae113
PMCID:
PMC11310107
Abstract Article PDF–840K

Systems Biology

BannMI deciphers potential n-to-1 information transduction in signaling pathways to unravel message of intrinsic apoptosis
Bettina Schmidt, Christine Sers, Nadja Klein
Bioinform Adv. 2024; 4(1): vbad175. Published online 2023 Nov 29. doi: 10.1093/bioadv/vbad175
PMCID:
PMC10769817
Abstract Article PDF–1.3M

Sequence Analysis

Quantifying orthogonal barcodes for sequence census assays
A Sina Booeshaghi, Kyung Hoi (Joseph) Min, Jase Gehring, Lior Pachter
Bioinform Adv. 2024; 4(1): vbad181. Published online 2023 Dec 20. doi: 10.1093/bioadv/vbad181
PMCID:
PMC10783946
Abstract Article PDF–1023K

Systems Biology

Batch correction of single-cell sequencing data via an autoencoder architecture
Reut Danino, Iftach Nachman, Roded Sharan
Bioinform Adv. 2024; 4(1): vbad186. Published online 2023 Dec 28. doi: 10.1093/bioadv/vbad186
PMCID:
PMC10781938
Abstract Article PDF–2.5M

Sequence Analysis

Seq2Phase: language model-based accurate prediction of client proteins in liquid–liquid phase separation
Kazuki Miyata, Wataru Iwasaki
Bioinform Adv. 2024; 4(1): vbad189. Published online 2023 Dec 22. doi: 10.1093/bioadv/vbad189
PMCID:
PMC10777356
Abstract Article PDF–2.8M

Systems Biology

Comparison of multiple modalities for drug response prediction with learning curves using neural networks and XGBoost
Nikhil Branson, Pedro R Cutillas, Conrad Bessant
Bioinform Adv. 2024; 4(1): vbad190. Published online 2023 Dec 23. doi: 10.1093/bioadv/vbad190
PMCID:
PMC10812874
Abstract Article PDF–1.1M

Structural Bioinformatics

DeepRank-GNN-esm: a graph neural network for scoring protein–protein models using protein language model
Xiaotong Xu, Alexandre M J J Bonvin
Bioinform Adv. 2024; 4(1): vbad191. Published online 2024 Jan 5. doi: 10.1093/bioadv/vbad191
PMCID:
PMC10782804
Abstract Article PDF–964K

Genome Analysis

Joint regression analysis of multiple traits based on genetic relationships
Ann-Sophie Buchardt, Xiang Zhou, Claus Thorn Ekstrøm
Bioinform Adv. 2024; 4(1): vbad192. Published online 2024 Jan 4. doi: 10.1093/bioadv/vbad192
PMCID:
PMC10805347
Abstract Article PDF–1.3M

Discovery Note

Data and Text Mining

Optimizer’s dilemma: optimization strongly influences model selection in transcriptomic prediction
Jake Crawford, Maria Chikina, Casey S Greene
Bioinform Adv. 2024; 4(1): vbae004. Published online 2024 Jan 24. doi: 10.1093/bioadv/vbae004
PMCID:
PMC10822580
Abstract Article PDF–1.5M

Review

Genome Analysis

Quantitative transcriptomic and epigenomic data analysis: a primer
Louis Coussement, Wim Van Criekinge, Tim De Meyer
Bioinform Adv. 2024; 4(1): vbae019. Published online 2024 Feb 10. doi: 10.1093/bioadv/vbae019
Correction in:
Bioinform Adv. 2024; 4(1): vbae091.
PMCID:
PMC10997052
Abstract Article PDF–1.4M

Original Papers

Data and Text Mining

TOSCCA: a framework for interpretation and testing of sparse canonical correlations
Nuria Senar, Mark van de Wiel, Aeilko H Zwinderman, Michel H Hof
Bioinform Adv. 2024; 4(1): vbae021. Published online 2024 Feb 21. doi: 10.1093/bioadv/vbae021
PMCID:
PMC10919946
Abstract Article PDF–1.3M

Sequence Analysis

Tackling reference bias in genotyping by using founder sequences with PanVC 3
Tuukka Norri, Veli Mäkinen
Bioinform Adv. 2024; 4(1): vbae027. Published online 2024 Mar 4. doi: 10.1093/bioadv/vbae027
PMCID:
PMC10924279
Abstract Article PDF–1.7M

Genome Analysis

The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues
Daniel Cerdán-Vélez, Michael Liam Tress
Bioinform Adv. 2024; 4(1): vbae029. Published online 2024 Feb 28. doi: 10.1093/bioadv/vbae029
PMCID:
PMC10924726
Abstract Article PDF–2.3M

Features

Community Report

Adapting beyond borders: Insights from the 19th Student Council Symposium (SCS2023), the first hybrid ISCB Student Council global event
Syed Muktadir Al Sium, Estefania Torrejón, Sanjana Fatema Chowdhury, Rubaiat Ahmed, Aakriti Jain, Mirko Treccani, Laura Veschetti, Arsalan Riaz, Pradeep Eranti, Gabriel J Olguín-Orellana
Bioinform Adv. 2024; 4(1): vbae028. Published online 2024 Apr 3. doi: 10.1093/bioadv/vbae028
PMCID:
PMC11007116
Abstract Article PDF–1.5M

Genome Analysis

Yves Moreau has received the 2023 Einstein Foundation Individual Award for Promoting Quality in Research
Thomas Lengauer
Bioinform Adv. 2024; 4(1): vbae039. Published online 2024 Mar 29. doi: 10.1093/bioadv/vbae039
PMCID:
PMC10985674
Article PDF–357K

Community Report

ISMB/ECCB 2023 organization benefited from the strengths of the French bioinformatics community
Anna-Sophie Fiston-Lavier, Sandra Dérozier, Guy Perrière, Marie-France Sagot
Bioinform Adv. 2024; 4(1): vbae040. Published online 2024 May 3. doi: 10.1093/bioadv/vbae040
PMCID:
PMC11076915
Article PDF–792K
Advancements in bioinformatics and computational biology: 15th annual Polish Bioinformatic Society Symposium
Joanna Zyla, Joanna Tobiasz, Justyna Mika, Paweł P Łabaj, Aleksandra Gruca
Bioinform Adv. 2024; 4(1): vbad187. Published online 2024 Jan 13. doi: 10.1093/bioadv/vbad187
PMCID:
PMC10796173
Abstract Article PDF–1.6M

Perspective

Databases and Ontologies

Perspectives on tracking data reuse across biodata resources
Karen E Ross, Frederic B Bastian, Matt Buys, Charles E Cook, Peter D’Eustachio, Melissa Harrison, Henning Hermjakob, Donghui Li, Phillip Lord, Darren A Natale, Bjoern Peters, Paul W Sternberg, Andrew I Su, Matthew Thakur, Paul D Thomas, Alex Bateman, and the UniProt Consortium
Bioinform Adv. 2024; 4(1): vbae057. Published online 2024 Apr 25. doi: 10.1093/bioadv/vbae057
PMCID:
PMC11076920
Abstract Article PDF–953K

Data and Text Mining

Biology’s transformation: from observation through experiment to computation
Christos A Ouzounis
Bioinform Adv. 2024; 4(1): vbae069. Published online 2024 May 22. doi: 10.1093/bioadv/vbae069
PMCID:
PMC11127110
Abstract Article PDF–663K

Systems Biology

Perspectives on computational modeling of biological systems and the significance of the SysMod community
Bhanwar Lal Puniya, Meghna Verma, Chiara Damiani, Shaimaa Bakr, Andreas Dräger
Bioinform Adv. 2024; 4(1): vbae090. Published online 2024 Jun 26. doi: 10.1093/bioadv/vbae090
PMCID:
PMC11213628
Abstract Article PDF–888K

Opinion

Cancer

Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction
Jiaying Lai, Yi Yang, Yunzhou Liu, Robert B Scharpf, Rachel Karchin
Bioinform Adv. 2024; 4(1): vbae094. Published online 2024 Jun 26. doi: 10.1093/bioadv/vbae094
PMCID:
PMC11213631
Abstract Article PDF–2.0M

Corrections

Correction to: wTSA-CRAFT: an open-access web server for rapid analysis of thermal shift assay experiments
Bioinform Adv. 2024; 4(1): vbae050. Published online 2024 Apr 9. doi: 10.1093/bioadv/vbae050
Corrects:
Bioinform Adv. 2023; 3(1): vbad136.
PMCID:
PMC11004552
Correction PDF–204K
Correction to: Quantitative transcriptomic and epigenomic data analysis: a primer
Bioinform Adv. 2024; 4(1): vbae091. Published online 2024 Jul 18. doi: 10.1093/bioadv/vbae091
Corrects:
Bioinform Adv. 2024; 4(1): vbae019.
PMCID:
PMC11257713
Correction PDF–185K
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