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Genomics

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  • Genomic architecture of codfishes featured by expansions of innate immune genes and short tandem repeats
    Ole K. Tørresen, Marine S. O. Brieuc, Monica H. Solbakken, Elin Sørhus, Alexander J. Nederbragt, Kjetill S. Jakobsen, Sonnich Meier, Rolf B. Edvardsen, Sissel Jentoft
    bioRxiv 163949; doi: https://doi.org/10.1101/163949
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  • Duplex Proximity Sequencing (Pro-Seq): A method to improve DNA sequencing accuracy without the cost of molecular barcoding redundancy
    Joel Pel, Wendy W. Y. Choi, Amy O. Leung, Gosuke Shibahara, Laura Gelinas, Milenko Despotovic, W. Lloyd Ung, Andre Marziali
    bioRxiv 163444; doi: https://doi.org/10.1101/163444
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  • Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism
    Robert Stewart, Marc D. Auffret, Amanda Warr, Tim Snelling, Richard Dewhurst, Alan W. Walker, Rainer Roehe, Mick Watson
    bioRxiv 162578; doi: https://doi.org/10.1101/162578
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  • Resequencing the Escherichia coli genome by GenoCare single molecule sequencing platform
    Luyang Zhao, Liwei Deng, Gailing Li, Huan Jin, Jinsen Cai, Huan Shang, Yan Li, Andrew X. Yang, Fang Chen, Zhi Zhao, Guanjie Xu, Wuxing Liu, Siyu Liu, Guobing Xiang, Bin Liu, Weibin Xu, Lidong Zeng, Renli Zhang, Huan Zhao, Ping Wu, Zhiliang Zhou, Jiao Zheng, Pierre Ezanno, Weiyue Chen, Qin Yan, Michael W. Deem, Jun Yu, Jiankui He
    bioRxiv 163089; doi: https://doi.org/10.1101/163089
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  • Toward Rapid Sequenced-Based Detection and Characterization of Causative Agents of Bacteremia
    F. Curtis Hewitt, Stephanie L. Guertin, Krista L. Ternus, Kathleen Schulte, Dana R. Kadavy
    bioRxiv 162735; doi: https://doi.org/10.1101/162735
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  • 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages
    Chun-Xiao Song, Senlin Yin, Li Ma, Amanda Wheeler, Yu Chen, Yan Zhang, Bin Liu, Junjie Xiong, Weihan Zhang, Jiankun Hu, Zongguang Zhou, Biao Dong, Zhiqi Tian, Stefanie S. Jeffrey, Mei-Sze Chua, Samuel So, Weimin Li, Yuquan Wei, Jiajie Diao, Dan Xie, Stephen R. Quake
    bioRxiv 162081; doi: https://doi.org/10.1101/162081
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  • Genome-wide analysis of the association of transposable elements with gene regulation suggests that Alu elements have the largest overall regulatory impact
    Lu Zeng, Stephen M. Pederson, Danfeng Cao, Zhipeng Qu, Zhiqiang Hu, David L. Adelson, Chaochun Wei
    bioRxiv 142018; doi: https://doi.org/10.1101/142018
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  • The Nuclear And Mitochondrial Genomes Of The Facultatively Eusocial Orchid Bee Euglossa dilemma
    Philipp Brand, Nicholas Saleh, Hailin Pan, Cai Li, Karen M. Kapheim, Santiago R. Ramírez
    bioRxiv 123687; doi: https://doi.org/10.1101/123687
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  • Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments
    Christina K. Yung, Brian D. O’Connor, Sergei Yakneen, Junjun Zhang, Kyle Ellrott, Kortine Kleinheinz, Naoki Miyoshi, Keiran M. Raine, Romina Royo, Gordon B. Saksena, Matthias Schlesner, Solomon I. Shorser, Miguel Vazquez, Joachim Weischenfeldt, Denis Yuen, Adam P. Butler, Brandi N. Davis-Dusenbery, Roland Eils, Vincent Ferretti, Robert L. Grossman, Olivier Harismendy, Youngwook Kim, Hidewaki Nakagawa, Steven J. Newhouse, David Torrents, Lincoln D. Stein, on behalf of the PCAWG Technical Working Group, Javier Bartolomé Rodriguez, Keith A. Boroevich, Rich Boyce, Angela N. Brooks, Alex Buchanan, Ivo Buchhalter, Niall J. Byrne, Andy Cafferkey, Peter J. Campbell, Zhaohong Chen, Sunghoon Cho, Wan Choi, Peter Clapham, Francisco M. De La Vega, Jonas Demeulemeester, Michelle T. Dow, Lewis J. Dursi, Juergen Eils, Claudiu Farcas, Francesco Favero, Nodirjon Fayzullaev, Paul Flicek, Nuno A. Fonseca, Josep L.l. Gelpi, Gad Getz, Bob Gibson, Michael C. Heinold, Julian M. Hess, Oliver Hofmann, Jongwhi H. Hong, Thomas J. Hudson, Daniel Huebschmann, Barbara Hutter, Carolyn M. Hutter, Seiya Imoto, Sinisa Ivkovic, Seung-Hyup Jeon, Wei Jiao, Jongsun Jung, Rolf Kabbe, Andre Kahles, Jules Kerssemakers, Hyunghwan Kim, Hyung-Lae Kim, Jihoon Kim, Jan O. Korbel, Michael Koscher, Antonios Koures, Milena Kovacevic, Chris Lawerenz, Ignaty Leshchiner, Dimitri G. Livitz, George L. Mihaiescu, Sanja Mijalkovic, Ana Mijalkovic Lazic, Satoru Miyano, Hardeep K. Nahal, Mia Nastic, Jonathan Nicholson, David Ocana, Kazuhiro Ohi, Lucila Ohno-Machado, Larsson Omberg, B.F. Francis Ouellette, Nagarajan Paramasivam, Marc D. Perry, Todd D. Pihl, Manuel Prinz, Montserrat Puiggròs, Petar Radovic, Esther Rheinbay, Mara W. Rosenberg, Charles Short, Heidi J. Sofia, Jonathan Spring, Adam J. Struck, Grace Tiao, Nebojsa Tijanic, Peter Van Loo, David Vicente, Jeremiah A. Wala, Zhining Wang, Johannes Werner, Ashley Williams, Youngchoon Woo, Adam J. Wright, Qian Xiang, the PCAWG Network
    bioRxiv 161638; doi: https://doi.org/10.1101/161638
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  • Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells
    Robin M. Meyers, Jordan G. Bryan, James M. McFarland, Barbara A. Weir, Ann E. Sizemore, Han Xu, Neekesh V. Dharia, Phillip G. Montgomery, Glenn S. Cowley, Sasha Pantel, Amy Goodale, Yenarae Lee, Levi D. Ali, Guozhi Jiang, Rakela Lubonja, William F. Harrington, Matthew Strickland, Ting Wu, Derek C. Hawes, Victor A. Zhivich, Meghan R. Wyatt, Zohra Kalani, Jaime J. Chang, Michael Okamoto, Todd R. Golub, Jesse S. Boehm, Francisca Vazquez, David E. Root, William C. Hahn, Aviad Tsherniak
    bioRxiv 160861; doi: https://doi.org/10.1101/160861
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