Bioinformatics

High-throughput pipeline for the de novo viral genome assembly and the identification of minority variants from Next-Generation Sequencing of residual diagnostic samples
T Gallo Cassarino, D Frampton, R Sugar, E Charles, Z Kozlakidis, P Kellam

bioRxiv 035154; doi: https://doi.org/10.1101/035154

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Deconvolution model for cytometric microbial subgroups along a freshwater hydrologic continuum
Stefano Amalfitano, Stefano Fazi, Anna M. Romani, Butturini Andrea

bioRxiv 063164; doi: https://doi.org/10.1101/063164

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Boosting alignment accuracy through adaptive local realignment
Dan DeBlasio, John Kececioglu

bioRxiv 063131; doi: https://doi.org/10.1101/063131

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Reversible Polymorphism-Aware Phylogenetic Models and their Application to Tree Inference
Dominik Schrempf, Bui Quang Minh, Nicola De Maio, Arndt von Haeseler, Carolin Kosiol

bioRxiv 048496; doi: https://doi.org/10.1101/048496

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Combining multiple tools outperforms individual methods in gene set enrichment analyses
Monther Alhamdoosh, Milica Ng, Nicholas J. Wilson, Julie M. Sheridan, Huy Huynh, Michael J. Wilson, Matthew E. Ritchie

bioRxiv 042580; doi: https://doi.org/10.1101/042580

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Rapid and efficient analysis of 20,000 RNA-seq samples with Toil
John Vivian, Arjun Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian, Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, Melissa Cline, Brian O’Connor, Megan Hanna, Chet Birger, W. James Kent, David A. Patterson, Anthony D. Joseph, Jingchun Zhu, Sasha Zaranek, Gad Getz, David Haussler, Benedict Paten

bioRxiv 062497; doi: https://doi.org/10.1101/062497

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Assocplots: a python package for static and interactive visualization of multiple-group GWAS results
Ekaterina A Khramtsova, Barbara E. Stranger

bioRxiv 062737; doi: https://doi.org/10.1101/062737

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Modelling the transcription factor DNA-binding affinity using genome-wide ChIP-based data
Monther Alhamdoosh, Dianhui Wang

bioRxiv 061978; doi: https://doi.org/10.1101/061978

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An Empirical Analysis of Topic Modeling for Mining Cancer Clinical Notes
Katherine Redfield Chang, Xinghua Lou, Theofanis Karaletsos, Christopher Crosbie, Stuart Gardos, David Artz, Gunnar Rätsch

bioRxiv 062307; doi: https://doi.org/10.1101/062307

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cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK
Matthias König

bioRxiv 062091; doi: https://doi.org/10.1101/062091

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Bioinformatics

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