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ORCIDFrontiers 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, Julien Fassy, Virginie Magnone, Rafael Lopes Goncalves, Cédric Girard Riboulleau, Iris Manosalva-Pena, Marine Gautier-Isola, Kevin Lebrigand, Pascal Barbry, Salvatore Spicuglia, Georges Vassaux, Roger Rezzonico, Michel Barlaud, Bernard Mari:
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, Daniela Kuhn, Peter Claus, Klaus Jung:
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, Vanessa López-Marrero, Shinjae Yoo, Edward R. Dougherty, Xiaoning Qian, Francis J. Alexander, Shantenu Jha, Byung-Jun Yoon:
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, Sabrina Wilderotter, Madison Stoddard, Debra Van Egeren, Arijit Chakravarty, Diane Joseph-McCarthy:
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, Steve Hoffmann, Juan Carlos Gallego-Gómez, Clara Bermudez-Santana:
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, Simon M. Laws, James D. Doecke:
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, Marcel J. T. Reinders, Ahmed Mahfouz:
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, Jan Aerts:
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, Peter F. Stadler:
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, Claudio Franceschi, Gastone C. Castellani, Paolo Garagnani, Christine Nardini:
Where are we in the implementation of tissue-specific epigenetic clocks? - Wouter-Michiel A. M. Vierdag, Sinem K. Saka:
A perspective on FAIR quality control in multiplexed imaging data processing. - Alban Obel Slabowska, Charles Pyke, Henning Hvid, Leon Eyrich Jessen, Simon J. Baumgart, Vivek Das:
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, Suliat Abdulai, Oluyinka Ajibola Iyiola, Lateef Adegboyega Sulaimon, Effiong Effiong, Adedeji Ogunyemi, Boluwatife Dosunmu, Abdulkadir Yusif Maigoro, Opeyemi Lawal, Kayode Raheem, Ui Wook Hwang:
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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