Bioinformatics

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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Towards extracting supporting information about predicted protein-protein interactions
Adam Roth, Sandeep Subramanian, Madhavi K. Ganapathiraju

bioRxiv 031591; doi: https://doi.org/10.1101/031591

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DataJoint: managing big scientific data using MATLAB or Python
Dimitri Yatsenko, Jacob Reimer, Alexander S. Ecker, Edgar Y. Walker, Fabian Sinz, Philipp Berens, Andreas Hoenselaar, R. James Cotton, Athanassios S. Siapas, Andreas S. Tolias

bioRxiv 031658; doi: https://doi.org/10.1101/031658

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Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads
Ivan Sović, Krešimir Križanović, Karolj Skala, Mile Šikić

bioRxiv 030437; doi: https://doi.org/10.1101/030437

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Are all global alignment algorithms and implementations correct?
Tomáš Flouri, Kassian Kobert, Torbjørn Rognes, Alexandros Stamatakis

bioRxiv 031500; doi: https://doi.org/10.1101/031500 Contradictory Results

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Rapid Genotype Refinement for Whole-Genome Sequencing Data using Multi-Variate Normal Distributions
Rudy Arthur, Jared O’Connell, Ole Schulz-Trieglaff, Anthony J. Cox

bioRxiv 031484; doi: https://doi.org/10.1101/031484

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Bioinformatics

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