Bioinformatics

BioJS-HGV Viewer: Genetic Variation Visualizer
Saket Choudhary, Leyla Garcia, Andrew Nightingale, Maria Martin

bioRxiv 032573; doi: https://doi.org/10.1101/032573

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ASAP: A Machine-Learning Framework for Local Protein Properties
Nadav Brandes, Dan Ofer, Michal Linial

bioRxiv 032532; doi: https://doi.org/10.1101/032532

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BRANE Cut: Biologically-Related A priori Network Enhancement with Graph cuts for Gene Regulatory Network Inference
Aurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent Duval, Jean-Christophe Pesquet

bioRxiv 032383; doi: https://doi.org/10.1101/032383

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From raw reads to trees: Whole genome SNP phylogenetics across the tree of life
Sanaa A. Ahmed, Chien-Chi Lo, Po-E Li, Karen W. Davenport, Patrick S. G. Chain

bioRxiv 032250; doi: https://doi.org/10.1101/032250

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Wikidata as a semantic framework for the Gene Wiki initiative
Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim Putman, Justin Leong, Paul Pavlidis, Lynn Schriml, Benjamin M. Good, Andrew I. Su

bioRxiv 032144; doi: https://doi.org/10.1101/032144

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XMRF: An R package to Fit Markov Networks to High-Throughput Genetics Data
Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Zhandong Liu

bioRxiv 032219; doi: https://doi.org/10.1101/032219

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Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls
Yi-Juan Hu, Peizhou Liao, H. Richard Johnston, Andrew S. Allen, Glen A. Satten

bioRxiv 032037; doi: https://doi.org/10.1101/032037

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Learning structure in gene expression data using deep architectures, with an application to gene clustering
Aman Gupta, Haohan Wang, Madhavi Ganapathiraju

bioRxiv 031906; doi: https://doi.org/10.1101/031906

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Wikidata: A platform for data integration and dissemination for the life sciences and beyond
Elvira Mitraka, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, Lynn M. Schriml, Andrew I. Su, Benjamin M. Good

bioRxiv 031971; doi: https://doi.org/10.1101/031971

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Mass graphs and their applications in top-down proteomics
Qiang Kou, Si Wu, Nikola Tolić, Ljiljana Pasa-Tolić, Xiaowen Liu

bioRxiv 031997; doi: https://doi.org/10.1101/031997

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Bioinformatics

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