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Institution

Institute for Systems Biology

Nonprofit•Seattle, Washington, United States•
About: Institute for Systems Biology is a nonprofit organization based out in Seattle, Washington, United States. It is known for research contribution in the topics: Population & Proteomics. The organization has 1277 authors who have published 2777 publications receiving 353165 citations.
Topics: Population, Proteomics, Proteome, Systems biology, Gene
Papers published on a yearly basis
Papers
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Journal Article•DOI•
An Essential Switch in Subunit Composition of a Chromatin Remodeling Complex during Neural Development

[...]

Julie Lessard1, Jiang Wu1, Jeffrey A. Ranish2, Mimi Wan1, Monte M. Winslow1, Brett T. Staahl1, Hai Wu1, Ruedi Aebersold2, Isabella A. Graef1, Gerald R. Crabtree1 •
Howard Hughes Medical Institute1, Institute for Systems Biology2
19 Jul 2007-Neuron
TL;DR: It is suggested that SWI/SNF-like complexes in vertebrates achieve biological specificity by combinatorial assembly of their subunits by preventing the subunit switch impairs neuronal differentiation.

674 citations

Journal Article•DOI•
Analysis and validation of proteomic data generated by tandem mass spectrometry.

[...]

Alexey I. Nesvizhskii1, Olga Vitek2, Ruedi Aebersold3, Ruedi Aebersold4•
University of Michigan1, Purdue University2, Institute for Systems Biology3, École Polytechnique Fédérale de Lausanne4
01 Oct 2007-Nature Methods
TL;DR: This review discusses critical issues related to data processing and analysis in proteomics and describes available methods and tools and places special emphasis on the elaboration of results that are supported by sound statistical arguments.
Abstract: The analysis of the large amount of data generated in mass spectrometry-based proteomics experiments represents a significant challenge and is currently a bottleneck in many proteomics projects. In this review we discuss critical issues related to data processing and analysis in proteomics and describe available methods and tools. We place special emphasis on the elaboration of results that are supported by sound statistical arguments.

664 citations

Journal Article•DOI•
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.

[...]

Joel H. Saltz1, Rajarsi Gupta1, Le Hou1, Tahsin Kurc1, Pankaj Singh2, Vu Nguyen1, Dimitris Samaras1, Kenneth R. Shroyer1, Tianhao Zhao1, Rebecca Batiste1, John Van Van Arnam3, Ilya Shmulevich4, Arvind Rao2, Alexander J. Lazar2, Ashish Sharma5, Vesteinn Thorsson4 •
Stony Brook University1, University of Texas MD Anderson Cancer Center2, University of Pennsylvania3, Institute for Systems Biology4, Emory University5
03 Apr 2018-Cell Reports
TL;DR: Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment.

655 citations

Journal Article•DOI•
Genome analysis of the platypus reveals unique signatures of evolution

[...]

Wesley C. Warren1, LaDeana W. Hillier1, Jennifer A. Marshall Graves2, Ewan Birney, Chris P. Ponting3, Frank Grützner4, Katherine Belov5, Webb Miller6, Laura Clarke7, Asif T. Chinwalla1, Shiaw Pyng Yang1, Andreas Heger3, Devin P. Locke1, Pat Miethke2, Paul D. Waters2, Frédéric Veyrunes2, Frédéric Veyrunes8, Lucinda Fulton1, Bob Fulton1, Tina Graves1, John W. Wallis1, Xose S. Puente9, Carlos López-Otín9, Gonzalo R. Ordóñez9, Evan E. Eichler10, Lin Chen10, Ze Cheng10, Janine E. Deakin2, Amber E. Alsop2, Katherine Thompson2, Patrick J. Kirby2, Anthony T. Papenfuss11, Matthew Wakefield11, Tsviya Olender12, Doron Lancet12, Gavin A. Huttley2, Arian F.A. Smit13, Andrew J Pask14, Peter Temple-Smith15, Peter Temple-Smith14, Mark A. Batzer16, Jerilyn A. Walker16, Miriam K. Konkel16, Robert S. Harris6, Camilla M. Whittington5, Emily S. W. Wong5, Neil J. Gemmell17, Emmanuel Buschiazzo17, Iris M. Vargas Jentzsch17, Angelika Merkel17, Juergen Schmitz18, Anja Zemann18, Gennady Churakov18, Jan Ole Kriegs18, Juergen Brosius18, Elizabeth P. Murchison19, Ravi Sachidanandam19, Carly Smith19, Gregory J. Hannon19, Enkhjargal Tsend-Ayush4, Daniel McMillan2, Rosalind Attenborough2, Willem Rens8, Malcolm A. Ferguson-Smith8, Christophe Lefevre14, Christophe Lefevre20, Julie A. Sharp14, Kevin R. Nicholas14, David A. Ray21, Michael Kube, Richard Reinhardt, Thomas H. Pringle, James Taylor22, Russell C. Jones, Brett Nixon, Jean Louis Dacheux23, Hitoshi Niwa, Yoko Sekita, Xiaoqiu Huang24, Alexander Stark25, Pouya Kheradpour25, Manolis Kellis25, Paul Flicek, Yuan Chen, Caleb Webber3, Ross C. Hardison, Joanne O. Nelson1, Kym Hallsworth-Pepin1, Kim D. Delehaunty1, Chris Markovic1, Patrick Minx1, Yucheng Feng1, Colin Kremitzki1, Makedonka Mitreva1, Jarret Glasscock1, Todd Wylie1, Patricia Wohldmann1, Prathapan Thiru1, Michael N. Nhan1, Craig Pohl1, Scott M. Smith1, Shunfeng Hou1, Marilyn B. Renfree14, Elaine R. Mardis1, Richard K. Wilson1 •
Washington University in St. Louis1, Australian National University2, University of Oxford3, University of Adelaide4, University of Sydney5, Pennsylvania State University6, Wellcome Trust Sanger Institute7, University of Cambridge8, University of Oviedo9, University of Washington10, Walter and Eliza Hall Institute of Medical Research11, Weizmann Institute of Science12, Institute for Systems Biology13, University of Melbourne14, Hudson Institute of Medical Research15, Louisiana State University16, University of Canterbury17, University of Münster18, Howard Hughes Medical Institute19, Monash University20, West Virginia University21, New York University22, Institut national de la recherche agronomique23, Iowa State University24, Broad Institute25
08 May 2008-Nature
TL;DR: It is found that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypUS biology.
Abstract: We present a draft genome sequence of the platypus, Ornithorhynchus anatinus This monotreme exhibits a fascinating combination of reptilian and mammalian characters For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles Analysis of the first monotreme genome aligned these features with genetic innovations We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation

653 citations

Journal Article•DOI•
The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC)

[...]

Daniela S. Gerhard1, Lukas Wagner1, Elise A. Feingold1, Carolyn M. Shenmen1, Lynette H. Grouse1, Greg Schuler1, Steven L. Klein1, Susan Old1, Rebekah S. Rasooly1, Peter J. Good1, Mark S. Guyer1, Allison M. Peck1, Jeffery G. Derge2, David J. Lipman1, Francis S. Collins1, Wonhee Jang1, Steven Sherry1, Mike Feolo1, Leonie Misquitta1, Eduardo Lee1, Kirill Rotmistrovsky1, Susan F. Greenhut1, Carl F. Schaefer1, Kenneth H. Buetow1, Tom I. Bonner1, David Haussler3, Jim Kent3, Mark Diekhans3, Terry Furey3, Michael R. Brent4, Christa Prange5, Kirsten Schreiber5, Nicole Shapiro5, Narayan K. Bhat2, Ralph F. Hopkins2, Florence Hsie, Tom Driscoll, M. Bento Soares6, Maria de Fatima Bonaldo6, Thomas L. Casavant6, Todd E. Scheetz6, Michael J. Brownstein1, Ted B. Usdin1, Shiraki Toshiyuki, Piero Carninci, Yulan Piao1, Dawood B. Dudekula1, Minoru S.H. Ko1, Koichi Kawakami7, Yutaka Suzuki8, Sumio Sugano8, C. E. Gruber, M. R. Smith, Blake A. Simmons, Troy Moore, Richard C. Waterman4, Stephen L. Johnson4, Yijun Ruan9, Chia-Lin Wei9, Sinnakaruppan Mathavan9, Preethi H. Gunaratne10, Jia Qian Wu10, Angela M. Garcia10, Stephen W. Hulyk10, Edwin Fuh10, Ye Yuan10, Anna Sneed10, Carla Kowis10, Anne Hodgson10, Donna M. Muzny10, John Douglas Mcpherson10, Richard A. Gibbs10, Jessica Fahey6, Jessica Fahey11, Erin Helton11, Mark Ketteman11, Anuradha Madan11, Anuradha Madan6, Stephanie Rodrigues6, Stephanie Rodrigues11, Amy Sanchez11, Michelle Whiting11, Anup Madan6, Anup Madan11, Alice C. Young1, Keith Wetherby1, Steven J. Granite1, Peggy N. Kwong1, Charles P. Brinkley1, Russell L. Pearson1, Gerard G. Bouffard1, Robert W. Blakesly1, Eric D. Green1, Mark Dickson12, Alex Rodriguez12, Jane Grimwood12, Jeremy Schmutz12, Richard M. Myers12, Yaron S.N. Butterfield13, Malachi Griffith13, Obi L. Griffith13, Martin Krzywinski13, Nancy Y. Liao13, Ryan Morrin13, Diana L. Palmquist13, Anca Petrescu13, Ursula Skalska13, Duane E. Smailus13, Jeff M. Stott13, Angelique Schnerch13, Jacqueline E. Schein13, Steven J.M. Jones13, Robert A. Holt13, Agnes Baross13, Marco A. Marra13, Sandra W. Clifton4, Kathryn A. Makowski, Stephanie Bosak, Joel A. Malek •
National Institutes of Health1, Science Applications International Corporation2, University of California, Santa Cruz3, Washington University in St. Louis4, Lawrence Livermore National Laboratory5, University of Iowa6, National Institute of Genetics7, University of Tokyo8, Agency for Science, Technology and Research9, Baylor College of Medicine10, Institute for Systems Biology11, Stanford University12, University of British Columbia13
01 Oct 2004-Genome Research
TL;DR: Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors.
Abstract: The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline

641 citations

Authors

Showing all 1292 results

NameH-indexPapersCitations
Younan Xia216943175757
Ruedi Aebersold182879141881
David Haussler172488224960
Steven P. Gygi172704129173
Nahum Sonenberg167647104053
Leroy Hood158853128452
Mark H. Ellisman11763755289
Wei Zhang112118993641
John Ralph10944239238
Eric H. Davidson10645447058
James R. Heath10342558548
Alan Aderem9924646682
Anne-Claude Gingras9733640714
Trey Ideker9730672276
Michael H. Gelb9450634714
Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
20233
202260
2021216
2020204
2019188
2018168