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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Article PDF–851K

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

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

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

Article PDF–1.7M

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

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

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

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

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

Article PDF–2.0M

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

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

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

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

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

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

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

Article PDF–1.5M

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

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

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

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

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

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

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

Article PDF–1.8M

Sequence Analysis

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

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

Article PDF–1.8M

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

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

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

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

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

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

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

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

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

PMCID:: PMC10997052

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

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

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

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