Bioinformatics

PEDLA: predicting enhancers with a deep learning-based algorithmic framework
Feng Liu, Hao Li, Chao Ren, Xiaochen Bo, Wenjie Shu

bioRxiv 036129; doi: https://doi.org/10.1101/036129

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Protein complex prediction for large protein protein interaction networks with the Core&Peel Method
Marco Pellegrini, Miriam Baglioni, Filippo Geraci

bioRxiv 053876; doi: https://doi.org/10.1101/053876

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EGAD: Ultra-fast functional analysis of gene networks
Sara Ballouz, Melanie Weber, Paul Pavlidis, Jesse Gillis

bioRxiv 053868; doi: https://doi.org/10.1101/053868

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Algorithmic methods to infer the evolutionary trajectories in cancer progression
Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti, Rebeca Sanz-Pamplona, Luca De Sano, Giancarlo Mauri, Victor Moreno, Marco Antoniotti, Bud Mishra

bioRxiv 027359; doi: https://doi.org/10.1101/027359

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AlmostSignificant: Simplifying quality control of high-throughput sequencing data
Joseph Ward, Christian Cole, Melanie Febrer, Geoffrey Barton

bioRxiv 053702; doi: https://doi.org/10.1101/053702

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Accuracy, speed and error tolerance of short DNA sequence aligners
Mark Ziemann

bioRxiv 053686; doi: https://doi.org/10.1101/053686

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gmos: Rapid detection of genome mosaicism over short evolutionary distances
Mirjana Domazet-Lošo, Tomislav Domazet-Lošo

bioRxiv 053694; doi: https://doi.org/10.1101/053694

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Synthesizer: Expediting synthesis studies from context-free data with natural language processing
Lisa Gandy, Jordan Gumm, Benjamin Fertig, Michael J. Kennish, Sameer Chavan, Ann Thessen, Luigi Marchionni, Xiaoxan Xia, Shambhavi Shankrit, Elana J Fertig

bioRxiv 053629; doi: https://doi.org/10.1101/053629

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VERSE: a versatile and efficient RNA-Seq read counting tool
Qin Zhu, Stephen A Fisher, Jamie Shallcross, Junhyong Kim

bioRxiv 053306; doi: https://doi.org/10.1101/053306

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Ten Simple Rules for Taking Advantage of git and GitHub
Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J Pollard, Alexander Konovalov, Robert M. Flight, Kai Blin, Juan Antonio Vizcaino

bioRxiv 048744; doi: https://doi.org/10.1101/048744

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Bioinformatics

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