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Frontiers in Bioinformatics, Volume 4
Volume 4, 2024
- Shubham Choudhury
, Nisha Bajiya, Sumeet Patiyal, Gajendra P. S. Raghava:
MRSLpred - a hybrid approach for predicting multi-label subcellular localization of mRNA at the genome scale. - Marin Truchi, Caroline Lacoux, Cyprien Gille
Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network. - Samuel D. Chorlton:
Ten common issues with reference sequence databases and how to mitigate them. - Shamini Hemandhar Kumar, Ines Tapken
bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses. - Alexander G. Lucaci, William E. Brew, Jason Lamanna, Avery Selberg, Vincenzo Carnevale, Anna R. Moore, Sergei L. Kosakovsky Pond:
The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders. - Xihaier Luo, Seyednami Niyakan, Patrick R. Johnstone, Sean McCorkle, Gilchan Park
Pathway-based analyses of gene expression profiles at low doses of ionizing radiation. - Neta Zadok, Gil Ast, Roded Sharan:
A network-based method for associating genes with autism spectrum disorder. - Isaac Filella-Merce, Vincent Mallet, Eric Durand, Michael Nilges, Guillaume Bouvier, Riccardo Pellarin:
AlignScape, displaying sequence similarity using self-organizing maps. - Lajoyce Mboning, Liudmilla Rubbi, Michael Thompson, Louis-S. Bouchard, Matteo Pellegrini:
BayesAge: A maximum likelihood algorithm to predict epigenetic age. - Rang Li
Computational identification of antibody-binding epitopes from mimotope datasets. - Brona Brejová, Travis Gagie, Eva Herencsárová, Tomás Vinar:
Maximum-scoring path sets on pangenome graphs of constant treewidth. - Ruofan Cao, Yide Zhang, Jessica Houston:
Editorial: Phasor analysis for fluorescence lifetime data. - Kai O. Kreissner, Benjamin Faller, Ivan Talucci, Hans M. Maric
MARTin - an open-source platform for microarray analysis. - Aimer Gutierrez-Diaz
Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells. - Fengyuan Huang, Robert S. Welner, Jake Y. Chen, Zongliang Yue
PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis. - Michaël Vacher, Rodrigo Cánovas
A comprehensive multi-omics analysis reveals unique signatures to predict Alzheimer's disease. - Michael S. Rosenberg:
MetaWin 3: open-source software for meta-analysis. - Lieke Michielsen
Predicting cell population-specific gene expression from genomic sequence. - Kevan Baker, Nathaniel Hughes, Sutanu Bhattacharya:
An interactive visualization tool for educational outreach in protein contact map overlap analysis. - Pietro Di Lena, Christine Nardini, Matteo Pellegrini:
Editorial: Computational methods for analysis of DNA methylation data, volume II. - Jannes Peeters, Daniël M. Bot, Gustavo Alberto Rovelo Ruiz
Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs. - A. L. Swan, A. Broadbent, Prakash Singh Gaur, A. Mishra, Kim T. Gurwitz, A. Mithani, Sarah L. Morgan, G. Malhotra, Catherine Brooksbank:
Making bioinformatics training FAIR: the EMBL-EBI training portal. - Hayet Belghit, Mariano Spivak, Manuel Dauchez, Marc Baaden, Jessica Prévoteau-Jonquet:
From complex data to clear insights: visualizing molecular dynamics trajectories. - Gennaro Calendo, Dara Kusic, Jozef Madzo, Neda Gharani, Laura Scheinfeldt:
ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole-genome sequencing data. - Sarah von Löhneysen, Mario Mörl
Limits of experimental evidence in RNA secondary structure prediction. - Michael Olbrich, Lennart Bartels, Inken Wohlers:
Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research. - Joshua Zhang, Mary E. Sehl, Roger Shih, Elizabeth Crabb Breen, Fengxue Li, Ake T. Lu, Jay H. Bream, Priya Duggal, Jeremy Martinson, Steven M. Wolinsky, Otoniel Martinez-Maza, Christina M. Ramirez, Steve Horvath, Beth D. Jamieson:
Effects of highly active antiretroviral therapy initiation on epigenomic DNA methylation in persons living with HIV. - Claudia Sala, Pietro Di Lena, Danielle Fernandes Durso, Ìtalo Faria do Valle, Maria Giulia Bacalini, Daniele Dall'Olio
Where are we in the implementation of tissue-specific epigenetic clocks? - Wouter-Michiel A. M. Vierdag
A perspective on FAIR quality control in multiplexed imaging data processing. - Alban Obel Slabowska, Charles Pyke, Henning Hvid, Leon Eyrich Jessen
A systematic evaluation of state-of-the-art deconvolution methods in spatial transcriptomics: insights from cardiovascular disease and chronic kidney disease. - Ashraf Akintayo Akintola, Abdullahi Tunde Aborode, Muhammed Taofiq Hamza, Augustine Amakiri, Benjamin Moore
Bioinformatics proficiency among African students. - Phillip J. Tomezsko, Colby T. Ford, Avery E. Meyer, Adam M. Michaleas, Rafael Jaimes:
Human cytokine and coronavirus nucleocapsid protein interactivity using large-scale virtual screens. - Mary E. Sehl, Elizabeth Crabb Breen, Roger Shih, Fengxue Li, Joshua Zhang, Peter Langfelder, Steve Horvath, Jay H. Bream, Priya Duggal, Jeremy Martinson, Steven M. Wolinsky, Otoniel Martinez-Maza, Christina M. Ramirez, Beth D. Jamieson:
Decreased but persistent epigenetic age acceleration is associated with changes in T-cell subsets after initiation of highly active antiretroviral therapy in persons living with HIV. - Trudy M. Wassenaar, Terry Harville, Jonathan Chastain, Visanu Wanchai, David Wayne Ussery:
DNA structural features and variability of complete MHC locus sequences.
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