Bioinformatics

plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data
Dmitry Antipov, Nolan Hartwick, Max Shen, Mikhail Raiko, Alla Lapidus, Pavel A. Pevzner

bioRxiv 048942; doi: https://doi.org/10.1101/048942

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Ten simple rules for managing high-throughput nucleotide sequencing data
Rutger A. Vos

bioRxiv 049338; doi: https://doi.org/10.1101/049338

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Impact of knowledge accumulation on pathway enrichment analysis
Lina Wadi, Mona Meyer, Joel Weiser, Lincoln D. Stein, Jüri Reimand

bioRxiv 049288; doi: https://doi.org/10.1101/049288

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Mash: fast genome and metagenome distance estimation using MinHash
Brian D. Ondov, Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren, Adam M. Phillippy

bioRxiv 029827; doi: https://doi.org/10.1101/029827

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AC-PCA: simultaneous dimension reduction and adjustment for confounding variation
Zhixiang Lin, Can Yang, Ying Zhu, John C. Duchi, Yao Fu, Yong Wang, Bai Jiang, Mahdi Zamanighomi, Xuming Xu, Mingfeng Li, Nenad Sestan, Hongyu Zhao, Wing Hung Wong

bioRxiv 040485; doi: https://doi.org/10.1101/040485

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Omics Discovery Index - Discovering and Linking Public ‘Omics’ Datasets
Yasset Perez-Riverol, Mingze Bai, Felipe da Veiga Leprevost, Silvano Squizzato, Young Mi Park, Kenneth Haug, Adam J. Carroll, Dylan Spalding, Justin Paschall, Mingxun Wang, Noemi del-Toro, Tobias Ternent, Peng Zhang, Nicola Buso, Nuno Bandeira, Eric W. Deutsch, David S Campbell, Ronald C. Beavis, Reza M. Salek, Alexey I. Nesvizhskii, Susanna-Assunta Sansone, Christoph Steinbeck, Rodrigo Lopez, Juan Antonio Vizcaíno, Peipei Ping, Henning Hermjakob

bioRxiv 049205; doi: https://doi.org/10.1101/049205

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Network-based Computational Drug Combination Prediction
Fuhai Li, Huang Lei, Jianting Sheng, Stephen Wong

bioRxiv 049015; doi: https://doi.org/10.1101/049015

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Convert Your Favorite Protein Modeling Program Into A Mutation Predictor: “MODICT”
Ibrahim Tanyalcin, Katrien Stouffs, Dorien Daneels, Carla Al Assaf, Willy Lissens, Anna Jansen, Alexander Gheldof

bioRxiv 038992; doi: https://doi.org/10.1101/038992

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Variance Adaptive Shrinkage (vash): Flexible Empirical Bayes estimation of variances
Mengyin Lu, Matthew Stephens

bioRxiv 048660; doi: https://doi.org/10.1101/048660

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Assembly of Long Error-Prone Reads Using de Bruijn Graphs
Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Pavel A. Pevzner

bioRxiv 048413; doi: https://doi.org/10.1101/048413

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Bioinformatics

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