Bioinformatics

Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies
Jie Liu, John T. Halloran, Jeffrey A. Bilmes, Riza M. Daza, Choli Lee, Elisabeth M. Mahen, Donna Prunkard, Chaozhong Song, Sibel Blau, Michael O. Dorschner, Vijayakrishna K. Gadi, Jay Shendure, C. Anthony Blau, William S. Noble

bioRxiv 125138; doi: https://doi.org/10.1101/125138

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The value of prior knowledge in machine learning of complex network systems
David Craft, Dana Ferranti, David Krane

bioRxiv 094151; doi: https://doi.org/10.1101/094151

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Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition
Laurent Guéguen, Laurent Duret

bioRxiv 124925; doi: https://doi.org/10.1101/124925

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SOMSC: Self-Organization-Map for High-Dimensional Single-Cell Data of Cellular States and Their Transitions
Tao Peng, Qing Nie

bioRxiv 124735; doi: https://doi.org/10.1101/124735

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Literature Evidence in Open Targets – a target validation platform
Şenay Kafkas, Ian Dunham, Johanna McEntyre

bioRxiv 124719; doi: https://doi.org/10.1101/124719

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MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures
Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlić, Peter W. Rose

bioRxiv 122689; doi: https://doi.org/10.1101/122689

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DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
Sneha Mitra, Anushua Biswas, Leelavati Narlikar

bioRxiv 122325; doi: https://doi.org/10.1101/122325

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HadoopCNV: A dynamic programming imputation algorithm to detect copy number variants from sequencing data
Hui Yang, Gary Chen, Leandro Lima, Han Fang, Laura Jimenez, Mingyao Li, Gholson J Lyon, Max He, Kai Wang

bioRxiv 124339; doi: https://doi.org/10.1101/124339

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Evidence-based gene models for structural and functional annotations of the oil palm genome
Chan Kuang Lim, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy, Leslie Low Eng Ti

bioRxiv 111120; doi: https://doi.org/10.1101/111120

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PREDICTD: PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition
Timothy J. Durham, Maxwell W. Libbrecht, J. Jeffry Howbert, Jeff Bilmes, William Stafford Noble

bioRxiv 123927; doi: https://doi.org/10.1101/123927

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Bioinformatics

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