Using individual barcodes to increase quantification power of massively parallel reporter assays
BMC Bioinformatics
by Pia Keukeleire, Jonathan D. Rosen, Angelina Göbel-Knapp, Kilian Salomon, Max Schubach and Martin Kircher
1d ago
Massively parallel reporter assays (MPRAs) are an experimental technology for measuring the activity of thousands of candidate regulatory sequences or their variants in parallel, where the activity of individu ..read more
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CoMIT: a bioinformatic pipeline for risk-based prediction of COVID-19 test inclusivity
BMC Bioinformatics
by Diane M. Walker, Wendy A. Smith, Lia Gale, Jacob T. Wolff, Connor P. Healy, Hannah F. Van Hollebeke, Ashlie Stephenson and Marianne Kim
1d ago
The global Coronavirus Disease 2019 (COVID-19) pandemic highlighted the need to quickly diagnose infections to identify and prevent viral spread in the population. In response to the pandemic, BioFire Defense ..read more
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Mammalian piRNA target prediction using a hierarchical attention model
BMC Bioinformatics
by Tianjiao Zhang, Liang Chen, Haibin Zhu and Garry Wong
1d ago
Piwi-interacting RNAs (piRNAs) are well established for monitoring and protecting the genome from transposons in germline cells. Recently, numerous studies provided evidence that piRNAs also play important rol ..read more
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HarmonizR: blocking and singular feature data adjustment improve runtime efficiency and data preservation
BMC Bioinformatics
by Simon Schlumbohm, Julia E. Neumann and Philipp Neumann
4d ago
Data adjustment is an essential tool for increasing statistical power during analysis, for example in case of complex multi-experiment data from (single-cell) RNA, proteomics and other omics data. Despite its ..read more
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A hybrid machine learning framework for functional annotation of mitochondrial glutathione transport and metabolism proteins in cancers
BMC Bioinformatics
by Luke Kennedy, Jagdeep K. Sandhu, Mary-Ellen Harper and Miroslava Cuperlovic-Culf
4d ago
Alterations of metabolism, including changes in mitochondrial metabolism as well as glutathione (GSH) metabolism are a well appreciated hallmark of many cancers. Mitochondrial GSH (mGSH) transport is a poorly ..read more
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SEGT-GO: a graph transformer method based on PPI serialization and explanatory artificial intelligence for protein function prediction
BMC Bioinformatics
by Yansong Wang, Yundong Sun, Baohui Lin, Haotian Zhang, Xiaoling Luo, Yumeng Liu, Xiaopeng Jin and Dongjie Zhu
4d ago
A massive amount of protein sequences have been obtained, but their functions remain challenging to discern. In recent research on protein function prediction, Protein-Protein Interaction (PPI) Networks have p ..read more
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Conditional similarity triplets enable covariate-informed representations of single-cell data
BMC Bioinformatics
by Chi-Jane Chen, Haidong Yi and Natalie Stanley
4d ago
Single-cell technologies enable comprehensive profiling of diverse immune cell-types through the measurement of multiple genes or proteins per individual cell. In order to translate immune signatures assayed f ..read more
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TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis
BMC Bioinformatics
by Masahiro Ono
6d ago
Fluorescent Timer proteins, which display time-dependent changes in their emission spectra, are invaluable for analyzing the temporal dynamics of cellular events at the single-cell level. We previously develop ..read more
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Correction: HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes
BMC Bioinformatics
by Thomas M. Adams, Moray Smith, Yuhan Wang, Lynn H. Brown, Micha M. Bayer and Ingo Hein
6d ago
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Direct coupling analysis and the attention mechanism
BMC Bioinformatics
by Francesco Caredda and Andrea Pagnani
6d ago
Proteins are involved in nearly all cellular functions, encompassing roles in transport, signaling, enzymatic activity, and more. Their functionalities crucially depend on their complex three-dimensional arran ..read more
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