Bioinformatics

PTRNAmark: an all-atomic distance-dependent knowledge-based potential for 3D RNA structure evaluation
Yi Yang, Qi Gu, Ya-Zhou Shi

bioRxiv 076000; doi: https://doi.org/10.1101/076000

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Genetic Information Relationship Network (GIRN): A Force-directed graphing tool for gene expression analysis
Gaelle Rondeau, John Welsh

bioRxiv 079590; doi: https://doi.org/10.1101/079590

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SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development
Robrecht Cannoodt, Wouter Saelens, Dorine Sichien, Simon Tavernier, Sophie Janssens, Martin Guilliams, Bart Lambrecht, Katleen De Preter, Yvan Saeys

bioRxiv 079509; doi: https://doi.org/10.1101/079509

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KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies
Daniel Mapleson, Gonzalo Garcia Accinelli, George Kettleborough, Jonathan Wright, Bernardo J. Clavijo

bioRxiv 064733; doi: https://doi.org/10.1101/064733

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Assessing Pathogens for Natural versus Laboratory Origins Using Genomic Data and Machine Learning
Tonia Korves, Christopher Garay, Heather A. Carleton, Ashley Sabol, Eija Trees, Matthew W. Peterson

bioRxiv 079541; doi: https://doi.org/10.1101/079541

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kWIP: The k-mer Weighted Inner Product, a de novo Estimator of Genetic Similarity
Kevin D. Murray, Christfried Webers, Cheng Soon Ong, Justin Borevitz, Norman Warthmann

bioRxiv 075481; doi: https://doi.org/10.1101/075481

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Computational prediction shines light on type III secretion origins
Tatyana Goldberg, Burkhard Rost, Yana Bromberg

bioRxiv 036251; doi: https://doi.org/10.1101/036251

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Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein
Eleisha L. Jackson, Stephanie J. Spielman, Claus O. Wilke

bioRxiv 079061; doi: https://doi.org/10.1101/079061

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Adaptive Somatic Mutations Calls with Deep Learning and Semi-Simulated Data
Remi Torracinta, Laurent Mesnard, Susan Levine, Rita Shaknovich, Maureen Hanson, Susan Levine

bioRxiv 079087; doi: https://doi.org/10.1101/079087

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Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change
Pejman Mohammadi, Stephane E Castel, Andrew A Brown, Tuuli Lappalainen

bioRxiv 078717; doi: https://doi.org/10.1101/078717

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Bioinformatics

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