Publications by authors named "Peter Bickel"

35Publications

NETWORK MODELLING OF TOPOLOGICAL DOMAINS USING HI-C DATA.

Ann Appl Stat 2019 Sep 17;13(3):1511-1536. Epub 2019 Oct 17.

University of California, Berkeley.

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http://dx.doi.org/10.1214/19-aoas1244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508461PMC
September 2019

GeneFishing to reconstruct context specific portraits of biological processes.

Proc Natl Acad Sci U S A 2019 09 4;116(38):18943-18950. Epub 2019 Sep 4.

Department of Statistics, University of California, Berkeley, CA 94720;

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http://dx.doi.org/10.1073/pnas.1820340116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754596PMC
September 2019

Metalearners for estimating heterogeneous treatment effects using machine learning.

Proc Natl Acad Sci U S A 2019 03 15;116(10):4156-4165. Epub 2019 Feb 15.

Department of Statistics, University of California, Berkeley, CA 94720;

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http://dx.doi.org/10.1073/pnas.1804597116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6410831PMC
March 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

Projection pursuit in high dimensions.

Proc Natl Acad Sci U S A 2018 09 27;115(37):9151-9156. Epub 2018 Aug 27.

Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100 Israel

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http://dx.doi.org/10.1073/pnas.1801177115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6140545PMC
September 2018

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

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

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.

Genome Res 2014 Jul;24(7):1086-101

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.170100.113
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http://dx.doi.org/10.1101/gr.170100.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079965PMC
July 2014

System wide analyses have underestimated protein abundances and the importance of transcription in mammals.

PeerJ 2014 27;2:e270. Epub 2014 Feb 27.

Genomics Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA.

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http://dx.doi.org/10.7717/peerj.270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940484PMC
April 2014

Navigating and mining modENCODE data.

Methods 2014 Jun 15;68(1):38-47. Epub 2014 Mar 15.

Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, CA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857704PMC
June 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

On robust regression with high-dimensional predictors.

Proc Natl Acad Sci U S A 2013 Sep 16;110(36):14557-62. Epub 2013 Aug 16.

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

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http://dx.doi.org/10.1073/pnas.1307842110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767561PMC
September 2013

Optimal M-estimation in high-dimensional regression.

Proc Natl Acad Sci U S A 2013 Sep 16;110(36):14563-8. Epub 2013 Aug 16.

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

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http://www.pnas.org/content/110/36/14563.full.pdf
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http://www.pnas.org/lookup/doi/10.1073/pnas.1307845110
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http://dx.doi.org/10.1073/pnas.1307845110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767535PMC
September 2013

Nonparametric variable selection and modeling for spatial and temporal regulatory networks.

Methods Cell Biol 2012 ;110:243-61

Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1016/B978-0-12-388403-9.00010-2DOI Listing
July 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

Nonparametric identification of regulatory interactions from spatial and temporal gene expression data.

BMC Bioinformatics 2010 Aug 4;11:413. Epub 2010 Aug 4.

Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1186/1471-2105-11-413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2933715PMC
August 2010

A nonparametric view of network models and Newman-Girvan and other modularities.

Proc Natl Acad Sci U S A 2009 Dec 23;106(50):21068-73. Epub 2009 Nov 23.

University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1073/pnas.0907096106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795514PMC
December 2009

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

Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study.

Proc Natl Acad Sci U S A 2006 Jun 12;103(25):9584-9. Epub 2006 Jun 12.

Department of Biochemistry and Biophysics, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1073/pnas.0603534103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480450PMC
June 2006

Estimating motifs under order restrictions.

Stat Appl Genet Mol Biol 2005 10;4:Article1. Epub 2005 Jan 10.

Mathematical Institute, Leiden University.

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http://dx.doi.org/10.2202/1544-6115.1100DOI Listing
May 2006

Detecting DNA regulatory motifs by incorporating positional trends in information content.

Genome Biol 2004 24;5(7):R50. Epub 2004 Jun 24.

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

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http://dx.doi.org/10.1186/gb-2004-5-7-r50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC463320PMC
October 2004

Finding important sites in protein sequences.

Proc Natl Acad Sci U S A 2002 Nov 4;99(23):14764-71. Epub 2002 Nov 4.

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

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http://dx.doi.org/10.1073/pnas.222508899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137493PMC
November 2002