Ilya Shmulevich

Ilya Shmulevich

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Emergence of diversity in homogeneous coupled Boolean networks.

Phys Rev E 2018 May;97(5-1):052415

Institute for Systems Biology, Seattle, Washington 98109, USA.

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https://link.aps.org/doi/10.1103/PhysRevE.97.052415
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http://dx.doi.org/10.1103/PhysRevE.97.052415DOI Listing
May 2018

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Cell Rep 2018 04;23(1):227-238.e3

Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.03.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5916809PMC
April 2018

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Cell Rep 2018 04;23(1):270-281.e3

Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.03.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6055527PMC
April 2018

Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle.

PLoS Comput Biol 2017 Jun 19;13(6):e1005591. Epub 2017 Jun 19.

Institute for Systems Biology, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495484PMC
June 2017

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.

Sci Rep 2016 11 23;6:36812. Epub 2016 Nov 23.

Netherlands Cancer Institute, Amsterdam, and The Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1038/srep36812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120272PMC
November 2016

Combining dependent P-values with an empirical adaptation of Brown's method.

Bioinformatics 2016 09;32(17):i430-i436

Institute for Systems Biology, Seattle, WA 98109-5263, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013915PMC
September 2016

A multilevel pan-cancer map links gene mutations to cancer hallmarks.

Chin J Cancer 2015 Sep 14;34(10):439-49. Epub 2015 Sep 14.

Institute for Systems Biology, Seattle, WA, 98109, USA.

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http://dx.doi.org/10.1186/s40880-015-0050-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593384PMC
September 2015

Augmentation of response to chemotherapy by microRNA-506 through regulation of RAD51 in serous ovarian cancers.

J Natl Cancer Inst 2015 Jul 20;107(7). Epub 2015 May 20.

: Departments of Pathology (GL, DY, YS, XL, PJ, DC, LH, WZ), Experimental Therapeutics (CRA, GLB), and Gynecologic Oncology and Reproductive Medicine (RR, LSM, AKS), Division of Cancer Medicine (CVP), Center for RNAi and Non-Coding RNA (RR, CVP, LSM, CRA, GLB, AKS, WZ), the University of Texas MD Anderson Cancer Center, Houston, TX; Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China (GL, YW, FX); Department of Pathology (YS) and Epidemiology (KC), Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; Department of Biochemistry and Molecular Biology, State Key Laboratory of Cancer Biology, the Fourth Military Medical University, Xi'an, China (XL); Institute for Systems Biology, Seattle, WA (IS); Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy (LDC, DM).

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http://academic.oup.com/jnci/article/doi/10.1093/jnci/djv108
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http://dx.doi.org/10.1093/jnci/djv108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4554255PMC
July 2015

Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma.

JAMA Oncol 2015 Jul;1(4):486-94

Department of Pathology, University of Texas MD Anderson Cancer Center, Houston2Institute for Systems Biology/MD Anderson Cancer Center Genome Data Analysis Center, The Cancer Genome Atlas, Bethesda, Maryland.

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http://oncology.jamanetwork.com/article.aspx?doi=10.1001/jam
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http://dx.doi.org/10.1001/jamaoncol.2015.1432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608536PMC
July 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Key nodes of a microRNA network associated with the integrated mesenchymal subtype of high-grade serous ovarian cancer.

Chin J Cancer 2015 Jan;34(1):28-40

Departments of Pathology, The Key Laboratory of Tianjin Cancer Prevention and Treatment, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P. R. China.

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http://www.cjcsysu.com/ENpdf/2015/1/28.pdf
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http://www.cjcsysu.cn/abstract.asp?fr=doi&idno=21283
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http://dx.doi.org/10.5732/cjc.014.10284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302087PMC
January 2015

Biocellion: accelerating computer simulation of multicellular biological system models.

Bioinformatics 2014 Nov 26;30(21):3101-8. Epub 2014 Jul 26.

Computational Biology and Bioinformatics Group, High-performance Computing Group, Pacific Northwest National Laboratory, Richland, WA 99354, USA, Department of Computer Science, Utah State University, Logan, UT 84322, USA and Institute for Systems Biology, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609016PMC
November 2014

Clinical significance of CTNNB1 mutation and Wnt pathway activation in endometrioid endometrial carcinoma.

J Natl Cancer Inst 2014 Sep 10;106(9). Epub 2014 Sep 10.

Department of Pathology (YL, LP, RRB, WZ) and Department of Systems Biology (GBM) and Departments of Gynecologic Oncology and Reproductive Medicine and Cancer Biology (KHL, AKS), The University of Texas MD Anderson Cancer Center, Houston, TX; The Genome Institute, Washington University, St. Louis, MO (LD, ERM); Department of Genetics, Harvard Medical School, Boston, MA (RK); Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York City, NY (DAL); The Institute for Systems Biology, Seattle, WA (IS).

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http://jnci.oxfordjournals.org/content/106/9/dju245.full.pdf
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http://jnci.oxfordjournals.org/cgi/doi/10.1093/jnci/dju245
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http://dx.doi.org/10.1093/jnci/dju245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4200060PMC
September 2014

MiR-506 suppresses proliferation and induces senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer.

J Pathol 2014 Jul 21;233(3):308-18. Epub 2014 May 21.

Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, People's Republic of China.

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http://dx.doi.org/10.1002/path.4348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4144705PMC
July 2014

Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions.

J Hematol Oncol 2014 Mar 5;7:19. Epub 2014 Mar 5.

Department of Pathology, Unit 85, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.

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http://dx.doi.org/10.1186/1756-8722-7-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973872PMC
March 2014

Quantitative analysis of colony morphology in yeast.

Biotechniques 2014 Jan;56(1):18-27

Pacific Northwest Diabetes Research Institute, Seattle, WA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA.

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http://dx.doi.org/10.2144/000114123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3996921PMC
January 2014

POMO--Plotting Omics analysis results for Multiple Organisms.

BMC Genomics 2013 Dec 24;14:918. Epub 2013 Dec 24.

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg.

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http://dx.doi.org/10.1186/1471-2164-14-918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880012PMC
December 2013

The Cancer Genome Atlas Pan-Cancer analysis project.

Nat Genet 2013 Oct;45(10):1113-20

Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/ng.2764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919969PMC
October 2013

The somatic genomic landscape of glioblastoma.

Cell 2013 Oct;155(2):462-77

Human Oncology and Pathogenesis Program, Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, Department of Neurological Surgery, Weill Cornell Medical Center, New York, NY 10065, USA. Electronic address:

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https://www.genome.gov/Multimedia/Slides/TCGA2/27_Verhaak.pd
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http://linkinghub.elsevier.com/retrieve/pii/S009286741301208
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http://dx.doi.org/10.1016/j.cell.2013.09.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910500PMC
October 2013

Structure learning for Bayesian networks as models of biological networks.

Methods Mol Biol 2013 ;939:35-45

Department of Signal Processing, Tampere University of Technology, Tampere, Finland.

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http://dx.doi.org/10.1007/978-1-62703-107-3_4DOI Listing
June 2013

Gene-pair expression signatures reveal lineage control.

Nat Methods 2013 Jun 21;10(6):577-83. Epub 2013 Apr 21.

Life Sciences Research Unit, University of Luxembourg, Luxembourg, Luxembourg.

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http://dx.doi.org/10.1038/nmeth.2445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131748PMC
June 2013

On the limitations of biological knowledge.

Curr Genomics 2012 Nov;13(7):574-87

Department of Electrical and Computer Engineering, Texas A&M University ; Computational Biology Division, Translational Genomics Research Institute.

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http://dx.doi.org/10.2174/138920212803251445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468890PMC
November 2012

Differing clinical impact of BRCA1 and BRCA2 mutations in serous ovarian cancer.

Pharmacogenomics 2012 Oct;13(13):1523-35

Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.2217/pgs.12.137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603383PMC
October 2012

A regression model approach to enable cell morphology correction in high-throughput flow cytometry.

Mol Syst Biol 2011 Sep 27;7:531. Epub 2011 Sep 27.

Institute for Systems Biology, 401 Terry Avenue North, 1441 North 34th Street, Seattle, WA 98109-5234, USA.

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http://msb.embopress.org/cgi/doi/10.1038/msb.2011.64
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http://dx.doi.org/10.1038/msb.2011.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202802PMC
September 2011

Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues.

PLoS Comput Biol 2011 Jun 30;7(6):e1002091. Epub 2011 Jun 30.

Institute for Systems Biology, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127798PMC
June 2011

Probabilistic analysis of gene expression measurements from heterogeneous tissues.

Bioinformatics 2010 Oct 14;26(20):2571-7. Epub 2010 Jul 14.

Department of Signal Processing, Tampere University of Technology, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btq406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951082PMC
October 2010

Inference of Boolean networks using sensitivity regularization.

EURASIP J Bioinform Syst Biol 2008 :780541

Institute for Systems Biology, Seattle, WA 98103, USA.

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http://dx.doi.org/10.1155/2008/780541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171400PMC
June 2010

Steady-state analysis of genetic regulatory networks modelled by probabilistic boolean networks.

Comp Funct Genomics 2003 ;4(6):601-8

Cancer Genomics Laboratory, University of Texas, M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.

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http://dx.doi.org/10.1002/cfg.342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447305PMC
June 2010

An integrated study of aberrant gene copy number and gene expression in GIST and LMS.

Technol Cancer Res Treat 2010 Apr;9(2):171-8

Department of Pathology, Sarcoma Medical Oncology The University of Texas M. D. Anderson Cancer Center, Houston Texas, USA.

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http://dx.doi.org/10.1177/153303461000900206DOI Listing
April 2010

Biological Information as Set-Based Complexity.

IEEE Trans Inf Theory 2010 Feb 25;56(2):667-677. Epub 2010 Feb 25.

Institute for Systems Biology, Seattle, WA, USA.

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http://dx.doi.org/10.1109/TIT.2009.2037046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5110148PMC
February 2010

Deterministic and stochastic models of genetic regulatory networks.

Methods Enzymol 2009 ;467:335-356

Institute for Systems Biology, Seattle, Washington, USA.

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http://dx.doi.org/10.1016/S0076-6879(09)67013-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230268PMC
January 2010

Fewer permutations, more accurate P-values.

Bioinformatics 2009 Jun;25(12):i161-8

Institute for Systems Biology, Seattle, WA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687965PMC
June 2009

NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells.

Lab Invest 2009 May 23;89(5):531-48. Epub 2009 Mar 23.

Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1038/labinvest.2009.17DOI Listing
May 2009

Adaptable data management for systems biology investigations.

BMC Bioinformatics 2009 Mar 6;10:79. Epub 2009 Mar 6.

Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA.

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http://dx.doi.org/10.1186/1471-2105-10-79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2670281PMC
March 2009

Age-dependent signature of metallothionein expression in primary CD4 T cell responses is due to sustained zinc signaling.

Rejuvenation Res 2008 Dec;11(6):1001-11

Kathleen B and Mason I Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1089/rej.2008.0747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848531PMC
December 2008

Taming data.

Cell Host Microbe 2008 Oct;4(4):312-3

Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA.

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http://dx.doi.org/10.1016/j.chom.2008.09.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074406PMC
October 2008

Automated quantification of lymph node size and number in surgical specimens of stage II colorectal cancer.

Conf Proc IEEE Eng Med Biol Soc 2005 ;6:6313-6

Institute of Signal Processing, Tampere University of Technology, Tampere, Finland; The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA.

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http://dx.doi.org/10.1109/IEMBS.2005.1615941DOI Listing
September 2008

Critical dynamics in genetic regulatory networks: examples from four kingdoms.

PLoS One 2008 Jun 18;3(6):e2456. Epub 2008 Jun 18.

Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002456PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423472PMC
June 2008

Systems biology driven software design for the research enterprise.

BMC Bioinformatics 2008 Jun 25;9:295. Epub 2008 Jun 25.

Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA.

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http://dx.doi.org/10.1186/1471-2105-9-295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478690PMC
June 2008

Extraction of the number of peroxisomes in yeast cells by automated image analysis.

Conf Proc IEEE Eng Med Biol Soc 2006 ;1:2353-6

Institute of Signal Processing, Tampere University of Technology, Finland.

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http://dx.doi.org/10.1109/IEMBS.2006.259890DOI Listing
March 2008

A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy.

Conf Proc IEEE Eng Med Biol Soc 2007 ;2007:5559-62

Institute for Systems Biology, Seattle, Washington, USA.

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http://dx.doi.org/10.1109/IEMBS.2007.4353606DOI Listing
March 2008

Probabilistic inference of transcription factor binding from multiple data sources.

PLoS One 2008 Mar 26;3(3):e1820. Epub 2008 Mar 26.

Institute for Systems Biology, Seattle, Washington, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001820PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268002PMC
March 2008

Gene expression dynamics in the macrophage exhibit criticality.

Proc Natl Acad Sci U S A 2008 Feb 4;105(6):1897-900. Epub 2008 Feb 4.

Institute of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland.

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http://dx.doi.org/10.1073/pnas.0711525105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538855PMC
February 2008

Critical networks exhibit maximal information diversity in structure-dynamics relationships.

Phys Rev Lett 2008 Feb 4;100(5):058702. Epub 2008 Feb 4.

Institute of Signal Processing, Tampere University of Technology, Tampere, Finland.

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http://dx.doi.org/10.1103/PhysRevLett.100.058702DOI Listing
February 2008

ProbCD: enrichment analysis accounting for categorization uncertainty.

BMC Bioinformatics 2007 Oct 12;8:383. Epub 2007 Oct 12.

Institute for Systems Biology, 1441 North 34th street, Seattle, WA 98103-8904, USA.

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http://dx.doi.org/10.1186/1471-2105-8-383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2169266PMC
October 2007

Quantification of in vitro cell invasion through image analysis.

Conf Proc IEEE Eng Med Biol Soc 2004 ;3:1703-6

Institute of Signal Processing, Tampere University of Technology, Tampere, Finland.

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http://dx.doi.org/10.1109/IEMBS.2004.1403512DOI Listing
September 2007

Entropy of complex relevant components of Boolean networks.

Phys Rev E Stat Nonlin Soft Matter Phys 2007 Sep 27;76(3 Pt 2):036115. Epub 2007 Sep 27.

Institute for Systems Biology, Seattle, Washington 98103, USA.

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http://dx.doi.org/10.1103/PhysRevE.76.036115DOI Listing
September 2007

Biochemical and statistical network models for systems biology.

Curr Opin Biotechnol 2007 Aug 3;18(4):365-70. Epub 2007 Aug 3.

Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA.

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http://dx.doi.org/10.1016/j.copbio.2007.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034526PMC
August 2007

Simcluster: clustering enumeration gene expression data on the simplex space.

BMC Bioinformatics 2007 Jul 11;8:246. Epub 2007 Jul 11.

Institute for Systems Biology, 1441 North 34th street, Seattle, WA 98103-8904, USA.

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http://dx.doi.org/10.1186/1471-2105-8-246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2147035PMC
July 2007

Basin entropy in Boolean network ensembles.

Phys Rev Lett 2007 Apr 9;98(15):158701. Epub 2007 Apr 9.

Institute for Systems Biology, Seattle, Washington 98103, USA.

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http://dx.doi.org/10.1103/PhysRevLett.98.158701DOI Listing
April 2007

Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays.

Proteomics 2006 May;6(10):2964-71

Department of Pathology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.

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http://dx.doi.org/10.1002/pmic.200500555DOI Listing
May 2006

Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies.

Technol Cancer Res Treat 2006 Apr;5(2):177-82

Department of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA.

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http://dx.doi.org/10.1177/153303460600500209DOI Listing
April 2006

Analysis of angiogenesis using in vitro experiments and stochastic growth models.

Phys Rev E Stat Nonlin Soft Matter Phys 2005 Dec 16;72(6 Pt 1):062902. Epub 2005 Dec 16.

Institute of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland.

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http://dx.doi.org/10.1103/PhysRevE.72.062902DOI Listing
December 2005

Molecular voting for glioma classification reflecting heterogeneity in the continuum of cancer progression.

Oncol Rep 2005 Sep;14(3):651-6

Department of Pathology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.

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September 2005

Eukaryotic cells are dynamically ordered or critical but not chaotic.

Proc Natl Acad Sci U S A 2005 Sep 9;102(38):13439-44. Epub 2005 Sep 9.

Institute for Systems Biology, Seattle, WA 98103, USA.

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http://dx.doi.org/10.1073/pnas.0506771102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1224670PMC
September 2005

Robust quantification of in vitro angiogenesis through image analysis.

IEEE Trans Med Imaging 2005 Apr;24(4):549-53

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April 2005