Publications by authors named "James B Brown"

48Publications

Multigenerational Exposures of Daphnia Magna to Pristine and Aged Silver Nanoparticles: Epigenetic Changes and Phenotypical Ageing Related Effects.

Small 2020 May 27;16(21):e2000301. Epub 2020 Apr 27.

University of Birmingham, School of Geography, Earth and Environmental Sciences, Birmingham, B15 2TT, UK.

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http://dx.doi.org/10.1002/smll.202000301DOI Listing
May 2020

*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments.

Gigascience 2020 03;9(3)

Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge SE-141 83, Sweden.

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http://dx.doi.org/10.1093/gigascience/giaa024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069921PMC
March 2020

Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals?

Curr Opin Biotechnol 2020 02 18;61:217-225. Epub 2020 Feb 18.

Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo, VT 01100, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2020.01.010DOI Listing
February 2020

Complete Genome Sequence of sp. Strain 33MFTa1.1, Isolated from Roots.

Microbiol Resour Announc 2019 Sep 12;8(37). Epub 2019 Sep 12.

BioSciences Area, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/MRA.00432-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742783PMC
September 2019

International medical graduates and general practice training: How do educational leaders facilitate the transition from new migrant to local family doctor?

Med Teach 2019 09 19;41(9):1065-1072. Epub 2019 Jun 19.

Northern Medical Program, University of British Columbia , British Columbia , Canada.

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http://dx.doi.org/10.1080/0142159X.2019.1616681DOI Listing
September 2019

Rhizobacteria Mediate the Phytotoxicity of a Range of Biorefinery-Relevant Compounds.

Environ Toxicol Chem 2019 09 26;38(9):1911-1922. Epub 2019 Jul 26.

Biological Systems and Engineering Division, Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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http://dx.doi.org/10.1002/etc.4501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711798PMC
September 2019

Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy.

Proc Natl Acad Sci U S A 2019 01 31;116(3):900-908. Epub 2018 Dec 31.

Molecular Ecosystems Biology Department, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;

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http://dx.doi.org/10.1073/pnas.1808833115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338827PMC
January 2019

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective.

Genome Biol Evol 2018 08 1;10(8):1988-2007. Epub 2018 Aug 1.

Warwick Medical School, University of Warwick, Coventry, United Kingdom.

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https://academic.oup.com/gbe/article/10/8/1988/5061321
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http://dx.doi.org/10.1093/gbe/evy155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097596PMC
August 2018

An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys.

RNA 2018 09 29;24(9):1255-1265. Epub 2018 Jun 29.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1261/rna.066951.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097662PMC
September 2018

Iterative random forests to discover predictive and stable high-order interactions.

Proc Natl Acad Sci U S A 2018 02 19;115(8):1943-1948. Epub 2018 Jan 19.

Data Driven Decisions Department, Preminon LLC, Antioch, CA 94531;

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http://dx.doi.org/10.1073/pnas.1711236115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828575PMC
February 2018

Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy.

Nat Commun 2016 08 31;7:12619. Epub 2016 Aug 31.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 977, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1038/ncomms12619DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013662PMC
August 2016

Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila.

Genome Res 2015 Nov 20;25(11):1692-702. Epub 2015 Aug 20.

Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA;

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http://dx.doi.org/10.1101/gr.182675.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617965PMC
November 2015

Lessons from modENCODE.

Annu Rev Genomics Hum Genet 2015 26;16:31-53. Epub 2015 Jun 26.

Department of Statistics, University of California, Berkeley, California 94720; email:

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http://dx.doi.org/10.1146/annurev-genom-090413-025448DOI Listing
May 2016

Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility.

Authors:
Jennifer Wessel Audrey Y Chu Sara M Willems Shuai Wang Hanieh Yaghootkar Jennifer A Brody Marco Dauriz Marie-France Hivert Sridharan Raghavan Leonard Lipovich Bertha Hidalgo Keolu Fox Jennifer E Huffman Ping An Yingchang Lu Laura J Rasmussen-Torvik Niels Grarup Margaret G Ehm Li Li Abigail S Baldridge Alena Stančáková Ravinder Abrol Céline Besse Anne Boland Jette Bork-Jensen Myriam Fornage Daniel F Freitag Melissa E Garcia Xiuqing Guo Kazuo Hara Aaron Isaacs Johanna Jakobsdottir Leslie A Lange Jill C Layton Man Li Jing Hua Zhao Karina Meidtner Alanna C Morrison Mike A Nalls Marjolein J Peters Maria Sabater-Lleal Claudia Schurmann Angela Silveira Albert V Smith Lorraine Southam Marcus H Stoiber Rona J Strawbridge Kent D Taylor Tibor V Varga Kristine H Allin Najaf Amin Jennifer L Aponte Tin Aung Caterina Barbieri Nathan A Bihlmeyer Michael Boehnke Cristina Bombieri Donald W Bowden Sean M Burns Yuning Chen Yii-DerI Chen Ching-Yu Cheng Adolfo Correa Jacek Czajkowski Abbas Dehghan Georg B Ehret Gudny Eiriksdottir Stefan A Escher Aliki-Eleni Farmaki Mattias Frånberg Giovanni Gambaro Franco Giulianini William A Goddard Anuj Goel Omri Gottesman Megan L Grove Stefan Gustafsson Yang Hai Göran Hallmans Jiyoung Heo Per Hoffmann Mohammad K Ikram Richard A Jensen Marit E Jørgensen Torben Jørgensen Maria Karaleftheri Chiea C Khor Andrea Kirkpatrick Aldi T Kraja Johanna Kuusisto Ethan M Lange I T Lee Wen-Jane Lee Aaron Leong Jiemin Liao Chunyu Liu Yongmei Liu Cecilia M Lindgren Allan Linneberg Giovanni Malerba Vasiliki Mamakou Eirini Marouli Nisa M Maruthur Angela Matchan Roberta McKean-Cowdin Olga McLeod Ginger A Metcalf Karen L Mohlke Donna M Muzny Ioanna Ntalla Nicholette D Palmer Dorota Pasko Andreas Peter Nigel W Rayner Frida Renström Ken Rice Cinzia F Sala Bengt Sennblad Ioannis Serafetinidis Jennifer A Smith Nicole Soranzo Elizabeth K Speliotes Eli A Stahl Kathleen Stirrups Nikos Tentolouris Anastasia Thanopoulou Mina Torres Michela Traglia Emmanouil Tsafantakis Sundas Javad Lisa R Yanek Eleni Zengini Diane M Becker Joshua C Bis James B Brown L Adrienne Cupples Torben Hansen Erik Ingelsson Andrew J Karter Carlos Lorenzo Rasika A Mathias Jill M Norris Gina M Peloso Wayne H-H Sheu Daniela Toniolo Dhananjay Vaidya Rohit Varma Lynne E Wagenknecht Heiner Boeing Erwin P Bottinger George Dedoussis Panos Deloukas Ele Ferrannini Oscar H Franco Paul W Franks Richard A Gibbs Vilmundur Gudnason Anders Hamsten Tamara B Harris Andrew T Hattersley Caroline Hayward Albert Hofman Jan-Håkan Jansson Claudia Langenberg Lenore J Launer Daniel Levy Ben A Oostra Christopher J O'Donnell Stephen O'Rahilly Sandosh Padmanabhan James S Pankow Ozren Polasek Michael A Province Stephen S Rich Paul M Ridker Igor Rudan Matthias B Schulze Blair H Smith André G Uitterlinden Mark Walker Hugh Watkins Tien Y Wong Eleftheria Zeggini Markku Laakso Ingrid B Borecki Daniel I Chasman Oluf Pedersen Bruce M Psaty E Shyong Tai Cornelia M van Duijn Nicholas J Wareham Dawn M Waterworth Eric Boerwinkle W H Linda Kao Jose C Florez Ruth J F Loos James G Wilson Timothy M Frayling David S Siscovick Josée Dupuis Jerome I Rotter James B Meigs Robert A Scott Mark O Goodarzi

Nat Commun 2015 Jan 29;6:5897. Epub 2015 Jan 29.

1] Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA [2] Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA.

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http://dx.doi.org/10.1038/ncomms6897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4311266PMC
January 2015

Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes.

PLoS One 2014 2;9(10):e109443. Epub 2014 Oct 2.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109443PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183604PMC
December 2015

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Genome-guided transcript assembly by integrative analysis of RNA sequence data.

Nat Biotechnol 2014 Apr 16;32(4):341-6. Epub 2014 Mar 16.

1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2] Department of Statistics, University of California at Berkeley, Berkeley, California, USA. [3].

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http://search.proquest.com/openview/5a27f43084800d7458173e64
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http://www.nature.com/doifinder/10.1038/nbt.2850
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http://dx.doi.org/10.1038/nbt.2850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4037530PMC
April 2014

Modeling gene expression using chromatin features in various cellular contexts.

Genome Biol 2012 Jun 13;13(9):R53. Epub 2012 Jun 13.

Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1186/gb-2012-13-9-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491397PMC
June 2012

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.

Proc Natl Acad Sci U S A 2011 Dec 1;108(50):19867-72. Epub 2011 Dec 1.

Department of Statistics, University of California, Berkeley, CA 94720, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1113972108
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http://dx.doi.org/10.1073/pnas.1113972108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250192PMC
December 2011

Types of ovarian activity in women and their significance: the continuum (a reinterpretation of early findings).

Authors:
James B Brown

Hum Reprod Update 2011 Mar-Apr;17(2):141-58. Epub 2010 Oct 5.

University of Melbourne, Melbourne, Victoria 3010, Australia.

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http://dx.doi.org/10.1093/humupd/dmq040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039221PMC
June 2011

An overview of recent developments in genomics and associated statistical methods.

Philos Trans A Math Phys Eng Sci 2009 Nov;367(1906):4313-37

Department of Statistics University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1098/rsta.2009.0164DOI Listing
November 2009

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Genome Res 2007 Jun;17(6):760-74

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://mendel.stanford.edu/sidowlab/pdfs/2007EncodeGR.pdf
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http://www.genome.org/cgi/doi/10.1101/gr.6034307
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http://dx.doi.org/10.1101/gr.6034307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

Hormonal monitoring of ovarian activity using the Ovarian Monitor, part I. Validation of home and laboratory results obtained during ovulatory cycles by comparison with radioimmunoassay.

Steroids 2003 May;68(5):465-76

Department of Chemistry, Institute of Fundamental Sciences, Massey University, Private Box 11222, Palmerston North, New Zealand.

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http://dx.doi.org/10.1016/s0039-128x(03)00049-7DOI Listing
May 2003