The COMBREX project: design, methodology, and initial results.

Autor: Brian P Anton, Yi-Chien Chang, Peter Brown, Han-Pil Choi, Lina L Faller, Jyotsna Guleria, Zhenjun Hu, Niels Klitgord, Ami Levy-Moonshine, Almaz Maksad, Varun Mazumdar, Mark McGettrick, Lais Osmani, Revonda Pokrzywa, John Rachlin, Rajeswari Swaminathan, Benjamin Allen, Genevieve Housman, Caitlin Monahan, Krista Rochussen, Kevin Tao, Ashok S Bhagwat, Steven E Brenner, Linda Columbus, Valérie de Crécy-Lagard, Donald Ferguson, Alexey Fomenkov, Giovanni Gadda, Richard D Morgan, Andrei L Osterman, Dmitry A Rodionov, Irina A Rodionova, Kenneth E Rudd, Dieter Söll, James Spain, Shuang-Yong Xu, Alex Bateman, Robert M Blumenthal, J Martin Bollinger, Woo-Suk Chang, Manuel Ferrer, Iddo Friedberg, Michael Y Galperin, Julien Gobeill, Daniel Haft, John Hunt, Peter Karp, William Klimke, Carsten Krebs, Dana Macelis, Ramana Madupu, Maria J Martin, Jeffrey H Miller, Claire O'Donovan, Bernhard Palsson, Patrick Ruch, Aaron Setterdahl, Granger Sutton, John Tate, Alexander Yakunin, Dmitri Tchigvintsev, Germán Plata, Jie Hu, Russell Greiner, David Horn, Kimmen Sjölander, Steven L Salzberg, Dennis Vitkup, Stanley Letovsky, Daniel Segrè, Charles DeLisi, Richard J Roberts, Martin Steffen, Simon Kasif

Publikováno v: PLoS Biology, Vol 11, Iss 8, p e1001638 (2013)

Externí odkaz: https://doaj.org/article/08400167d9dc4fa29d1dc69cd0f6756f

Comprehensive comparative analysis of 5'-end RNA-sequencing methods

Autor: Xi Shi, Madeline A. Lancaster, Zhe Ji, Adam L. Haber, Michele Busby, Xian Adiconis, Joshua Z. Levin, Jen Q. Pan, Justin Jacques, Sean Simmons, Ami Levy Moonshine, Aviv Regev

Publikováno v: Nature methods

RNA-Seq is an effective method to study the transcriptome, but specialized methods are required to identify 5’ ends of transcripts. Several published strategies exist for this specific purpose, but their relative merits have not been systematically

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::38ca0ebc5ceec0d73c652cdfbd12f4e2
https://pubmed.ncbi.nlm.nih.gov/30459407

Analysis of protein-coding genetic variation in 60,706 humans

Autor: Jack A. Kosmicki, Mark A. DePristo, Mark I. McCarthy, Patrick F. Sullivan, Laramie E. Duncan, Ryan Poplin, David Neil Cooper, Mitja I. Kurki, Aarno Palotie, Hong-Hee Won, Dermot P.B. McGovern, John Danesh, Jose C. Florez, Grace Tiao, Anne H. O’Donnell-Luria, Timothy Fennell, Gad Getz, Douglas M. Ruderfer, Joanne Berghout, Mark J. Daly, Monkol Lek, Daniel P. Howrigan, Stacey Gabriel, Daniel P. Birnbaum, Ami Levy Moonshine, Michael Boehnke, Ben Weisburd, Ruth McPherson, Christine Stevens, Dongmei Yu, Sekar Kathiresan, Andrew J. Hill, James G. Wilson, James S. Ware, Hugh Watkins, Benjamin M. Neale, Khalid Shakir, David Altshuler, María Teresa Tusié-Luna, Lorena Orozco, James Zou, Samuel A. Rose, Menachem Fromer, Jeremiah M. Scharf, Daniel G. MacArthur, Namrata Gupta, Pamela Sklar, Eric Vallabh Minikel, Steven A. McCarroll, Jaakko Tuomilehto, Jackie Goldstein, Ming T. Tsuang, Stacey Donnelly, Konrad J. Karczewski, Fengmei Zhao, Stephen J. Glatt, Ron Do, Nicole A. Deflaux, Adam Kiezun, Emma Pierce-Hoffman, Markku Laakso, Beryl B. Cummings, Pradeep Natarajan, Danish Saleheen, Karol Estrada, Peter D. Stenson, Manuel A. Rivas, Diego Ardissino, Kaitlin E. Samocha, Gina M. Peloso, Laura D. Gauthier, Eric Banks, Brett Thomas, Shaun Purcell, Taru Tukiainen, Valentin Ruano-Rubio, Christina M. Hultman, Jason Flannick, Roberto Elosua

Publikováno v: Lek, M, Karczewski, K J, Minikel, E V, Samocha, K E, Posthuma, D & Exome Aggregation Consortium, U 2016, ' Analysis of protein-coding genetic variation in 60,706 humans ', Nature, vol. 536, no. 7616, pp. 285-291 . https://doi.org/10.1038/nature19057
Nature, 536(7616), 285-291. Nature Publishing Group
Nature, vol 536, iss 7616

SummaryLarge-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) sequence

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d62da66cab8b3012619459d5ee3a67d5
https://doi.org/10.1038/nature19057

Tools and best practices for data processing in allelic expression analysis

Autor: Tuuli Lappalainen, Pejman Mohammadi, Ami Levy-Moonshine, Stephane E. Castel, Eric Banks

Publikováno v: Genome Biology

Allelic expression analysis has become important for integrating genome and transcriptome data to characterize various biological phenomena such as cis-regulatory variation and nonsense-mediated decay. We analyze the properties of allelic expression

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c300b418915aa7ebc4cb68c9f799758
https://pubmed.ncbi.nlm.nih.gov/26381377

The COMBREX project: design, methodology, and initial results

Autor: Kimmen Sjölander, Jyotsna Guleria, Donald J. Ferguson, Giovanni Gadda, John F. Hunt, Almaz Maksad, Maria Jesus Martin, Revonda M. Pokrzywa, Charles DeLisi, Linda Columbus, David Horn, John Tate, Dieter Söll, Rajeswari Swaminathan, Jeffrey H Miller, Lina L. Faller, Alexander F. Yakunin, Bernhard O. Palsson, Martin Steffen, Granger G. Sutton, Daniel Segrè, Kenneth E. Rudd, Krista Rochussen, Peter D. Karp, Mark G. McGettrick, Alexey Fomenkov, Han-Pil Choi, Ramana Madupu, Robert Blumenthal, Manuel Ferrer, Jim C. Spain, Claire O'Donovan, Russell Greiner, J. Martin Bollinger, Ami Levy-Moonshine, Richard J. Roberts, William Klimke, Shuang-yong Xu, Kevin R. Tao, Yi Chien Chang, Caitlin Monahan, Julien Gobeill, Germán Plata, Varun Mazumdar, Aaron T. Setterdahl, Dmitri Tchigvintsev, Genevieve Housman, Jie Hu, John Rachlin, Woo Suk Chang, Ashok S. Bhagwat, Michael Y. Galperin, Irina A. Rodionova, Zhenjun Hu, Lais Osmani, Carsten Krebs, Dennis Vitkup, Brian P. Anton, Daniel H. Haft, Iddo Friedberg, Simon Kasif, Steven E. Brenner, Steven L. Salzberg, Stanley Letovsky, Niels Klitgord, Dana Macelis, Alex Bateman, Richard D. Morgan, Peter Brown, Valérie de Crécy-Lagard, Andrei L. Osterman, Benjamin L. Allen, Dmitry A. Rodionov, Patrick Ruch

Publikováno v: PLoS Biology
Digital.CSIC. Repositorio Institucional del CSIC
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PLoS Biology, Vol 11, Iss 8, p e1001638 (2013)

© 2013 Brian P. et al.
Prior to the “genomic era,” when the acquisition of DNA sequence involved significant labor and expense, the sequencing of genes was strongly linked to the experimental characterization of their products. Sequencing a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::14ac19c12ba81148df7af8775c6d2d4b
http://doc.rero.ch/record/208905/files/Ruch2013_Combrex_project.pdf