Bioinformatics

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Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning
Bo Wang, Junjie Zhu, Emma Pierson, Daniele Ramazzotti, Serafim Batzoglou

bioRxiv 052225; doi: https://doi.org/10.1101/052225

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GMPR: A novel normalization method for microbiome sequencing data
Li Chen, Jun Chen

bioRxiv 112565; doi: https://doi.org/10.1101/112565

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The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions
Yanli Wang, Bo Zhang, Lijun Zhang, Lin An, Jie Xu, Daofeng Li, Mayank NK Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang, Feng Yue

bioRxiv 112268; doi: https://doi.org/10.1101/112268

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Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity
Fengchao Yu, Ning Li, Weichuan Yu

bioRxiv 097089; doi: https://doi.org/10.1101/097089

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Post-selection Inference Following Aggregate Level Hypothesis Testing in Large Scale Genomic Data
Ruth Heller, Nilanjan Chatterjee, Abba Krieger, Jianxin Shi

bioRxiv 058404; doi: https://doi.org/10.1101/058404

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Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data
Sha Joe Zhu, Jacob Almagro-Garcia, Gil McVean

bioRxiv 099499; doi: https://doi.org/10.1101/099499

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MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data
David van Dijk, Juozas Nainys, Roshan Sharma, Pooja Kaithail, Ambrose J. Carr, Kevin R. Moon, Linas Mazutis, Guy Wolf, Smita Krishnaswamy, Dana Pe'er

bioRxiv 111591; doi: https://doi.org/10.1101/111591

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A recurrence based approach for validating structural variation using long-read sequencing technology
Xuefang Zhao, Alexandra M. Weber, Ryan E. Mills

bioRxiv 105817; doi: https://doi.org/10.1101/105817

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16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
Ruibang Luo, Michael C. Schatz, Steven L. Salzberg

bioRxiv 111393; doi: https://doi.org/10.1101/111393

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Conserved changes in secondary structure and aggregation properties of in vitro evolved proteins for thermo stability
Satyamurthy Kundharapu

bioRxiv 111443; doi: https://doi.org/10.1101/111443

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