Nathan D Price

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Nathan D Price

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100Publications

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Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate.

Cell Stem Cell 2019 May 14;24(5):812-820.e5. Epub 2019 Mar 14.

Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Medicine, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.02.006DOI Listing
May 2019

OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.

PLoS Comput Biol 2019 03 8;15(3):e1006835. Epub 2019 Mar 8.

Bio-X Institutes, Key laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.

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http://dx.plos.org/10.1371/journal.pcbi.1006835
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http://dx.doi.org/10.1371/journal.pcbi.1006835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426274PMC
March 2019

Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders.

Cell Syst 2019 Feb 13;8(2):122-135.e7. Epub 2019 Feb 13.

Institute for Systems Biology, Seattle, WA, USA; Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.01.002DOI Listing
February 2019

Motor neuron loss and neuroinflammation in a model of α-synuclein-induced neurodegeneration.

Neurobiol Dis 2018 12 6;120:98-106. Epub 2018 Sep 6.

Department of Neuroscience, University of Florida, Gainesville, FL 32610, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32610, USA; McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA. Electronic address:

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http://dx.doi.org/10.1016/j.nbd.2018.09.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6190709PMC
December 2018

Distinct communication patterns of trophoblastic miRNA among the maternal-placental-fetal compartments.

Placenta 2018 12 22;72-73:28-35. Epub 2018 Oct 22.

Magee-Womens Research Institute, USA; Department of Obstetrics and Gynecology and Reproductive Science, University of Pittsburgh, Pittsburgh, PA, 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213, USA. Electronic address:

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http://dx.doi.org/10.1016/j.placenta.2018.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329371PMC
December 2018

Reply to "Precision medicine in the clouds".

Nat Biotechnol 2018 08;36(8):680-682

Arivale, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nbt.4211DOI Listing
August 2018

Reply.

Am J Obstet Gynecol 2018 07 28;219(1):123-124. Epub 2018 Mar 28.

Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ajog.2018.03.022DOI Listing
July 2018

Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus.

Neuron 2018 07 21;99(1):64-82.e7. Epub 2018 Jun 21.

Departments of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute of Genomic Sciences and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85287-5001, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2018.05.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551233PMC
July 2018

The building blocks of successful translation of proteomics to the clinic.

Curr Opin Biotechnol 2018 06 7;51:123-129. Epub 2018 Feb 7.

Institute for Systems Biology, Seattle, WA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2017.12.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091638PMC
June 2018

Editorial overview: Systems biology: Data, discovery, delivery.

Curr Opin Biotechnol 2018 06;51:vii-viii

Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2018.05.002DOI Listing
June 2018

Enhanced retinal responses in Huntington's disease patients.

J Huntingtons Dis 2017 ;6(3):237-247

Department of Neurology, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.3233/JHD-170255DOI Listing
May 2018

Digitizing omics profiles by divergence from a baseline.

Proc Natl Acad Sci U S A 2018 05 16;115(18):4545-4552. Epub 2018 Apr 16.

Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218;

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http://dx.doi.org/10.1073/pnas.1721628115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5939095PMC
May 2018

Taking Systems Medicine to Heart.

Circ Res 2018 Apr;122(9):1276-1289

From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.).

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http://dx.doi.org/10.1161/CIRCRESAHA.117.310999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5926821PMC
April 2018

Comparative analysis of gene expression in maternal peripheral blood and monocytes during spontaneous preterm labor.

Am J Obstet Gynecol 2018 03 2;218(3):345.e1-345.e30. Epub 2018 Jan 2.

Program in Development and Fetal Health, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ajog.2017.12.234DOI Listing
March 2018

Comparative transcriptomic analysis of human placentae at term and preterm delivery.

Biol Reprod 2018 01;98(1):89-101

Division of Human Genetics, Center for Prevention of Preterm Birth, Cincinnati Children's, Hospital Medical Center, Cincinnati, Ohio, USA.

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http://dx.doi.org/10.1093/biolre/iox163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5803773PMC
January 2018

Genomic, Transcriptional, and Phenotypic Analysis of the Glucose Derepressed Clostridium beijerinckii Mutant Exhibiting Acid Crash Phenotype.

Biotechnol J 2017 Nov 9;12(11). Epub 2017 Oct 9.

Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

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http://dx.doi.org/10.1002/biot.201700182DOI Listing
November 2017

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease.

Authors:
Rebecca Sims Sven J van der Lee Adam C Naj Céline Bellenguez Nandini Badarinarayan Johanna Jakobsdottir Brian W Kunkle Anne Boland Rachel Raybould Joshua C Bis Eden R Martin Benjamin Grenier-Boley Stefanie Heilmann-Heimbach Vincent Chouraki Amanda B Kuzma Kristel Sleegers Maria Vronskaya Agustin Ruiz Robert R Graham Robert Olaso Per Hoffmann Megan L Grove Badri N Vardarajan Mikko Hiltunen Markus M Nöthen Charles C White Kara L Hamilton-Nelson Jacques Epelbaum Wolfgang Maier Seung-Hoan Choi Gary W Beecham Cécile Dulary Stefan Herms Albert V Smith Cory C Funk Céline Derbois Andreas J Forstner Shahzad Ahmad Hongdong Li Delphine Bacq Denise Harold Claudia L Satizabal Otto Valladares Alessio Squassina Rhodri Thomas Jennifer A Brody Liming Qu Pascual Sánchez-Juan Taniesha Morgan Frank J Wolters Yi Zhao Florentino Sanchez Garcia Nicola Denning Myriam Fornage John Malamon Maria Candida Deniz Naranjo Elisa Majounie Thomas H Mosley Beth Dombroski David Wallon Michelle K Lupton Josée Dupuis Patrice Whitehead Laura Fratiglioni Christopher Medway Xueqiu Jian Shubhabrata Mukherjee Lina Keller Kristelle Brown Honghuang Lin Laura B Cantwell Francesco Panza Bernadette McGuinness Sonia Moreno-Grau Jeremy D Burgess Vincenzo Solfrizzi Petra Proitsi Hieab H Adams Mariet Allen Davide Seripa Pau Pastor L Adrienne Cupples Nathan D Price Didier Hannequin Ana Frank-García Daniel Levy Paramita Chakrabarty Paolo Caffarra Ina Giegling Alexa S Beiser Vilmantas Giedraitis Harald Hampel Melissa E Garcia Xue Wang Lars Lannfelt Patrizia Mecocci Gudny Eiriksdottir Paul K Crane Florence Pasquier Virginia Boccardi Isabel Henández Robert C Barber Martin Scherer Lluis Tarraga Perrie M Adams Markus Leber Yuning Chen Marilyn S Albert Steffi Riedel-Heller Valur Emilsson Duane Beekly Anne Braae Reinhold Schmidt Deborah Blacker Carlo Masullo Helena Schmidt Rachelle S Doody Gianfranco Spalletta W T Longstreth Thomas J Fairchild Paola Bossù Oscar L Lopez Matthew P Frosch Eleonora Sacchinelli Bernardino Ghetti Qiong Yang Ryan M Huebinger Frank Jessen Shuo Li M Ilyas Kamboh John Morris Oscar Sotolongo-Grau Mindy J Katz Chris Corcoran Melanie Dunstan Amy Braddel Charlene Thomas Alun Meggy Rachel Marshall Amy Gerrish Jade Chapman Miquel Aguilar Sarah Taylor Matt Hill Mònica Díez Fairén Angela Hodges Bruno Vellas Hilkka Soininen Iwona Kloszewska Makrina Daniilidou James Uphill Yogen Patel Joseph T Hughes Jenny Lord James Turton Annette M Hartmann Roberta Cecchetti Chiara Fenoglio Maria Serpente Marina Arcaro Carlo Caltagirone Maria Donata Orfei Antonio Ciaramella Sabrina Pichler Manuel Mayhaus Wei Gu Alberto Lleó Juan Fortea Rafael Blesa Imelda S Barber Keeley Brookes Chiara Cupidi Raffaele Giovanni Maletta David Carrell Sandro Sorbi Susanne Moebus Maria Urbano Alberto Pilotto Johannes Kornhuber Paolo Bosco Stephen Todd David Craig Janet Johnston Michael Gill Brian Lawlor Aoibhinn Lynch Nick C Fox John Hardy Roger L Albin Liana G Apostolova Steven E Arnold Sanjay Asthana Craig S Atwood Clinton T Baldwin Lisa L Barnes Sandra Barral Thomas G Beach James T Becker Eileen H Bigio Thomas D Bird Bradley F Boeve James D Bowen Adam Boxer James R Burke Jeffrey M Burns Joseph D Buxbaum Nigel J Cairns Chuanhai Cao Chris S Carlson Cynthia M Carlsson Regina M Carney Minerva M Carrasquillo Steven L Carroll Carolina Ceballos Diaz Helena C Chui David G Clark David H Cribbs Elizabeth A Crocco Charles DeCarli Malcolm Dick Ranjan Duara Denis A Evans Kelley M Faber Kenneth B Fallon David W Fardo Martin R Farlow Steven Ferris Tatiana M Foroud Douglas R Galasko Marla Gearing Daniel H Geschwind John R Gilbert Neill R Graff-Radford Robert C Green John H Growdon Ronald L Hamilton Lindy E Harrell Lawrence S Honig Matthew J Huentelman Christine M Hulette Bradley T Hyman Gail P Jarvik Erin Abner Lee-Way Jin Gyungah Jun Anna Karydas Jeffrey A Kaye Ronald Kim Neil W Kowall Joel H Kramer Frank M LaFerla James J Lah James B Leverenz Allan I Levey Ge Li Andrew P Lieberman Kathryn L Lunetta Constantine G Lyketsos Daniel C Marson Frank Martiniuk Deborah C Mash Eliezer Masliah Wayne C McCormick Susan M McCurry Andrew N McDavid Ann C McKee Marsel Mesulam Bruce L Miller Carol A Miller Joshua W Miller John C Morris Jill R Murrell Amanda J Myers Sid O'Bryant John M Olichney Vernon S Pankratz Joseph E Parisi Henry L Paulson William Perry Elaine Peskind Aimee Pierce Wayne W Poon Huntington Potter Joseph F Quinn Ashok Raj Murray Raskind Barry Reisberg Christiane Reitz John M Ringman Erik D Roberson Ekaterina Rogaeva Howard J Rosen Roger N Rosenberg Mark A Sager Andrew J Saykin Julie A Schneider Lon S Schneider William W Seeley Amanda G Smith Joshua A Sonnen Salvatore Spina Robert A Stern Russell H Swerdlow Rudolph E Tanzi Tricia A Thornton-Wells John Q Trojanowski Juan C Troncoso Vivianna M Van Deerlin Linda J Van Eldik Harry V Vinters Jean Paul Vonsattel Sandra Weintraub Kathleen A Welsh-Bohmer Kirk C Wilhelmsen Jennifer Williamson Thomas S Wingo Randall L Woltjer Clinton B Wright Chang-En Yu Lei Yu Fabienne Garzia Feroze Golamaully Gislain Septier Sebastien Engelborghs Rik Vandenberghe Peter P De Deyn Carmen Muñoz Fernadez Yoland Aladro Benito Hakan Thonberg Charlotte Forsell Lena Lilius Anne Kinhult-Stählbom Lena Kilander RoseMarie Brundin Letizia Concari Seppo Helisalmi Anne Maria Koivisto Annakaisa Haapasalo Vincent Dermecourt Nathalie Fievet Olivier Hanon Carole Dufouil Alexis Brice Karen Ritchie Bruno Dubois Jayanadra J Himali C Dirk Keene JoAnn Tschanz Annette L Fitzpatrick Walter A Kukull Maria Norton Thor Aspelund Eric B Larson Ron Munger Jerome I Rotter Richard B Lipton María J Bullido Albert Hofman Thomas J Montine Eliecer Coto Eric Boerwinkle Ronald C Petersen Victoria Alvarez Fernando Rivadeneira Eric M Reiman Maura Gallo Christopher J O'Donnell Joan S Reisch Amalia Cecilia Bruni Donald R Royall Martin Dichgans Mary Sano Daniela Galimberti Peter St George-Hyslop Elio Scarpini Debby W Tsuang Michelangelo Mancuso Ubaldo Bonuccelli Ashley R Winslow Antonio Daniele Chuang-Kuo Wu Oliver Peters Benedetta Nacmias Matthias Riemenschneider Reinhard Heun Carol Brayne David C Rubinsztein Jose Bras Rita Guerreiro Ammar Al-Chalabi Christopher E Shaw John Collinge David Mann Magda Tsolaki Jordi Clarimón Rebecca Sussams Simon Lovestone Michael C O'Donovan Michael J Owen Timothy W Behrens Simon Mead Alison M Goate Andre G Uitterlinden Clive Holmes Carlos Cruchaga Martin Ingelsson David A Bennett John Powell Todd E Golde Caroline Graff Philip L De Jager Kevin Morgan Nilufer Ertekin-Taner Onofre Combarros Bruce M Psaty Peter Passmore Steven G Younkin Claudine Berr Vilmundur Gudnason Dan Rujescu Dennis W Dickson Jean-François Dartigues Anita L DeStefano Sara Ortega-Cubero Hakon Hakonarson Dominique Campion Merce Boada John Keoni Kauwe Lindsay A Farrer Christine Van Broeckhoven M Arfan Ikram Lesley Jones Jonathan L Haines Christophe Tzourio Lenore J Launer Valentina Escott-Price Richard Mayeux Jean-François Deleuze Najaf Amin Peter A Holmans Margaret A Pericak-Vance Philippe Amouyel Cornelia M van Duijn Alfredo Ramirez Li-San Wang Jean-Charles Lambert Sudha Seshadri Julie Williams Gerard D Schellenberg

Nat Genet 2017 09 17;49(9):1373-1384. Epub 2017 Jul 17.

Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1038/ng.3916DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669039PMC
September 2017

Network reconstruction and systems analysis of plant cell wall deconstruction by .

Biotechnol Biofuels 2017 21;10:225. Epub 2017 Sep 21.

Energy Biosciences Institute, University of California Berkeley, Berkeley, CA 94704 USA.

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http://biotechnologyforbiofuels.biomedcentral.com/articles/1
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http://dx.doi.org/10.1186/s13068-017-0901-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609067PMC
September 2017

The P4 Health Spectrum - A Predictive, Preventive, Personalized and Participatory Continuum for Promoting Healthspan.

Prog Cardiovasc Dis 2017 Mar - Apr;59(5):506-521. Epub 2016 Aug 18.

College of Applied Health Sciences, University of Illinois at Chicago, Chicago, IL, USA; SARENA Clinic, Medical Center and Research Institute.

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http://dx.doi.org/10.1016/j.pcad.2016.08.002DOI Listing
June 2017

Relative stability of network states in Boolean network models of gene regulation in development.

Biosystems 2016 Apr-May;142-143:15-24. Epub 2016 Mar 7.

Institute for Systems Biology, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.biosystems.2016.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5149109PMC
January 2017

Emerging Proteomic Technologies Provide Enormous and Underutilized Potential for Brain Cancer Research.

Mol Cell Proteomics 2016 Feb 25;15(2):362-7. Epub 2015 Sep 25.

From the ‡Institute for Systems Biology, Seattle, WA 98109

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http://dx.doi.org/10.1074/mcp.R115.053884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739660PMC
February 2016

Personalized nutrition through big data.

Nat Biotechnol 2016 Feb;34(2):152-4

Institute for Systems Biology, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nbt.3476DOI Listing
February 2016

Measuring the effect of inter-study variability on estimating prediction error.

PLoS One 2014 17;9(10):e110840. Epub 2014 Oct 17.

Institute for Systems Biology, Seattle, Washington, United States of America; Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois, United States of America; Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110840PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201588PMC
December 2015

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis.

Sci Data 2015 31;2:150010. Epub 2015 Mar 31.

Institute for Systems Biology , Seattle, Washington 98109, USA ; Molecular and Cellular Biology Program, University of Washington , Seattle, Washington 98195, USA ; Departments of Biology and Microbiology, University of Washington , Seattle, Washington 98195, USA ; Lawrence Berkeley National Lab , Berkeley, California 94720, USA.

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http://dx.doi.org/10.1038/sdata.2015.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413241PMC
December 2015

Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.

Biotechnol Biofuels 2015 2;8:207. Epub 2015 Dec 2.

Institute for Systems Biology, 401 Terry Ave N, Seattle, 98109 WA USA ; Departments of Biology and Microbiology, University of Washington, Seattle, WA USA ; Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA ; Lawrence Berkeley National Lab, Berkeley, CA USA.

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http://dx.doi.org/10.1186/s13068-015-0391-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667458PMC
December 2015

Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction.

PLoS Comput Biol 2015 Nov 13;11(11):e1004530. Epub 2015 Nov 13.

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

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http://dx.doi.org/10.1371/journal.pcbi.1004530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643975PMC
November 2015

Isoforms of RNA-Editing Enzyme ADAR1 Independently Control Nucleic Acid Sensor MDA5-Driven Autoimmunity and Multi-organ Development.

Immunity 2015 Nov;43(5):933-44

Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2015.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654992PMC
November 2015

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis.

PLoS Comput Biol 2015 Nov 30;11(11):e1004543. Epub 2015 Nov 30.

Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664399PMC
November 2015

Transparency in metabolic network reconstruction enables scalable biological discovery.

Curr Opin Biotechnol 2015 Aug 3;34:105-9. Epub 2015 Jan 3.

Institute for Systems Biology, Seattle, WA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2014.12.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4490137PMC
August 2015

Fostering synergy between cell biology and systems biology.

Trends Cell Biol 2015 Aug 23;25(8):440-5. Epub 2015 May 23.

Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tcb.2015.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758507PMC
August 2015

SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis.

IEEE Life Sci Lett 2015 Aug 28;1(2):22-25. Epub 2015 Aug 28.

Institute for Systems Biology, Seattle, WA 98109.

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http://dx.doi.org/10.1109/LLS.2015.2465870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736311PMC
August 2015

An argument for mechanism-based statistical inference in cancer.

Hum Genet 2015 May 9;134(5):479-95. Epub 2014 Nov 9.

Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, 21210, USA,

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http://dx.doi.org/10.1007/s00439-014-1501-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612627PMC
May 2015

Genome-scale modeling for metabolic engineering.

J Ind Microbiol Biotechnol 2015 Mar 13;42(3):327-38. Epub 2015 Jan 13.

Institute for Systems Biology, 401 Terry Avenue, North Seattle, WA, 98109, USA,

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http://dx.doi.org/10.1007/s10295-014-1576-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455951PMC
March 2015

Integrating big data and actionable health coaching to optimize wellness.

BMC Med 2015 Jan 9;13. Epub 2015 Jan 9.

Institute for Systems Biology, 401 Terry Avenue North, Seattle 98109, WA, USA.

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http://dx.doi.org/10.1186/s12916-014-0238-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288554PMC
January 2015

The DNA-binding network of Mycobacterium tuberculosis.

Nat Commun 2015 Jan 12;6:5829. Epub 2015 Jan 12.

1] Seattle Biomedical Research Institute, Seattle, Washington 98109, USA [2] Interdisciplinary Program of Pathobiology, Department of Global Health, University of Washington, Seattle, Washington 98195, USA.

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http://search.proquest.com/openview/b7ab9294cd40174c628302e5
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http://www.nature.com/doifinder/10.1038/ncomms6829
Publisher Site
http://dx.doi.org/10.1038/ncomms6829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301838PMC
January 2015

Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models.

PLoS Comput Biol 2014 Oct 16;10(10):e1003882. Epub 2014 Oct 16.

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America; Institute for Systems Biology, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199484PMC
October 2014

Systems approach to neurodegenerative disease biomarker discovery.

Annu Rev Pharmacol Toxicol 2014 23;54:457-81. Epub 2013 Oct 23.

Institute for Systems Biology, Seattle, Washington 98109; email: , , , , , ,

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http://dx.doi.org/10.1146/annurev-pharmtox-011613-135928DOI Listing
September 2014

Transcriptional analysis of aggressiveness and heterogeneity across grades of astrocytomas.

PLoS One 2013 11;8(10):e76694. Epub 2013 Oct 11.

Institute for Systems Biology, Seattle, Washington, United States of America ; Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076694PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795736PMC
August 2014

Metabolic constraint-based refinement of transcriptional regulatory networks.

PLoS Comput Biol 2013 5;9(12):e1003370. Epub 2013 Dec 5.

Institute for Systems Biology, Seattle, Washington, United States of America ; Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3857774PMC
August 2014

Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir.

Environ Microbiol 2014 Jun 12;16(6):1695-708. Epub 2013 Dec 12.

Energy Biosciences Institute, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Institute for Genomic Biology, University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Department of Geology, University of Illinois Urbana-Champaign, 1301 W. Green Street, Urbana, IL, 61801, USA.

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http://dx.doi.org/10.1111/1462-2920.12325DOI Listing
June 2014

Detection of 1α,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing.

Zebrafish 2014 Jun 20;11(3):207-18. Epub 2014 Mar 20.

1 Nephrology and Hypertension Research, Department of Internal Medicine, Mayo Clinic , Rochester, Minnesota.

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http://dx.doi.org/10.1089/zeb.2013.0899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4050706PMC
June 2014

Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures.

PLoS Comput Biol 2013 25;9(7):e1003148. Epub 2013 Jul 25.

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

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http://dx.doi.org/10.1371/journal.pcbi.1003148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3723500PMC
February 2014

Demystifying disease, democratizing health care.

Sci Transl Med 2014 Feb;6(225):225ed5

Leroy Hood is President of the Institute for Systems Biology, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1126/scitranslmed.3008665DOI Listing
February 2014

Systems pharmacology modeling: an approach to improving drug safety.

Biopharm Drug Dispos 2014 Jan 20;35(1):1-14. Epub 2013 Nov 20.

Office of Clinical Pharmacology, Office of Translational Science, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, 20993, USA.

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http://dx.doi.org/10.1002/bdd.1871DOI Listing
January 2014

ITEP: an integrated toolkit for exploration of microbial pan-genomes.

BMC Genomics 2014 Jan 3;15. Epub 2014 Jan 3.

Institute for Systems Biology, 401 Terry Ave, N,, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1186/1471-2164-15-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890548PMC
January 2014

Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii.

Appl Environ Microbiol 2013 Oct 19;79(19):5853-63. Epub 2013 Jul 19.

Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

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http://dx.doi.org/10.1128/AEM.00971-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811342PMC
October 2013

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance.

Database (Oxford) 2013 9;2013:bat059. Epub 2013 Aug 9.

Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA.

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http://dx.doi.org/10.1093/database/bat059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3739857PMC
October 2013

Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746.

Biotechnol J 2013 Sep 26;8(9):1070-9. Epub 2013 Mar 26.

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://dx.doi.org/10.1002/biot.201200266DOI Listing
September 2013

Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population.

Proc Natl Acad Sci U S A 2013 Aug 1;110(34):14006-11. Epub 2013 Aug 1.

Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1073/pnas.1222569110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3752265PMC
August 2013

A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism).

Methods Mol Biol 2013 ;985:103-12

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.

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http://dx.doi.org/10.1007/978-1-62703-299-5_6DOI Listing
July 2013

The limits of de novo DNA motif discovery.

PLoS One 2012 7;7(11):e47836. Epub 2012 Nov 7.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3492406PMC
April 2013

Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain.

Proc Natl Acad Sci U S A 2013 Feb 5;110(8):3095-100. Epub 2013 Feb 5.

Institute for Genomic Biology and Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1073/pnas.1222897110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581870PMC
February 2013

P4 medicine: how systems medicine will transform the healthcare sector and society.

Per Med 2013 ;10(6):565-576

Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA.

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http://dx.doi.org/10.2217/pme.13.57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4204402PMC
January 2013

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE.

BMC Syst Biol 2012 Dec 13;6:153. Epub 2012 Dec 13.

Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-6-153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3576361PMC
December 2012

Mechanistic modeling of aberrant energy metabolism in human disease.

Front Physiol 2012 25;3:404. Epub 2012 Oct 25.

Institute for Systems Biology Seattle, WA, USA.

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http://dx.doi.org/10.3389/fphys.2012.00404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3480659PMC
November 2012

The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules.

BMC Bioinformatics 2012 Sep 11;13:227. Epub 2012 Sep 11.

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

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http://dx.doi.org/10.1186/1471-2105-13-227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663421PMC
September 2012

Molecular signatures from omics data: from chaos to consensus.

Biotechnol J 2012 Aug 23;7(8):946-57. Epub 2012 Apr 23.

Institute for Systems Biology, Seattle, WA, USA.

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http://doi.wiley.com/10.1002/biot.201100305
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http://dx.doi.org/10.1002/biot.201100305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418428PMC
August 2012

Network biology methods integrating biological data for translational science.

Brief Bioinform 2012 Jul 5;13(4):446-59. Epub 2012 Mar 5.

Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA.

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http://dx.doi.org/10.1093/bib/bbr075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404396PMC
July 2012

Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A.

J Bacteriol 2012 Feb 2;194(4):855-65. Epub 2011 Dec 2.

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

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http://dx.doi.org/10.1128/JB.06040-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272958PMC
February 2012

Genetic co-occurrence network across sequenced microbes.

PLoS Comput Biol 2011 Dec 29;7(12):e1002340. Epub 2011 Dec 29.

Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248385PMC
December 2011