Francesca Chiaromonte

Francesca Chiaromonte

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Francesca Chiaromonte

Publications by authors named "Francesca Chiaromonte"

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Evidence for sharp increase in the economic damages of extreme natural disasters.

Proc Natl Acad Sci U S A 2019 Oct 7. Epub 2019 Oct 7.

Institute of Economics and EMbeDS-Economics and Management in the Era of Data Science, Scuola Superiore Sant'Anna Pisa, 56127 Pisa, Italy;

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http://dx.doi.org/10.1073/pnas.1907826116DOI Listing
October 2019

Functional data analysis for computational biology.

Bioinformatics 2019 Sep;35(17):3211-3213

Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736445PMC
September 2019

High satellite repeat turnover in great apes studied with short- and long-read technologies.

Mol Biol Evol 2019 Jul 2. Epub 2019 Jul 2.

Center for Medical Genomics, Penn State, University Park, PA USA.

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http://dx.doi.org/10.1093/molbev/msz156DOI Listing
July 2019

Structured Ordinary Least Squares: A Sufficient Dimension Reduction approach for regressions with partitioned predictors and heterogeneous units.

Biometrics 2017 06 20;73(2):529-539. Epub 2016 Sep 20.

Department of Statistics, Pennsylvania State University, University Park, Pennsylvania 16802, U.S.A.

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http://dx.doi.org/10.1111/biom.12579DOI Listing
June 2017

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis.

PLoS Comput Biol 2016 06 16;12(6):e1004956. Epub 2016 Jun 16.

Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911145PMC
June 2016

An attraction-repulsion point process model for respiratory syncytial virus infections.

Biometrics 2015 Jun 6;71(2):376-85. Epub 2015 Feb 6.

Department of Statistics, The Pennsylvania State University, State College, Pennsylvania, U.S.A.

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http://dx.doi.org/10.1111/biom.12267DOI Listing
June 2015

Genomic landscape of human, bat, and ex vivo DNA transposon integrations.

Mol Biol Evol 2014 Jul 22;31(7):1816-32. Epub 2014 Apr 22.

Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, PADepartment of Biology, Penn State University, University Park, PA

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http://dx.doi.org/10.1093/molbev/msu138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069622PMC
July 2014

Segmenting the human genome based on states of neutral genetic divergence.

Proc Natl Acad Sci U S A 2013 Sep 19;110(36):14699-704. Epub 2013 Aug 19.

Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1073/pnas.1221792110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767554PMC
September 2013

Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion.

PLoS Genet 2012 9;8(8):e1002842. Epub 2012 Aug 9.

Tulane Cancer Center, Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1002842
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http://dx.doi.org/10.1371/journal.pgen.1002842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415434PMC
December 2012

A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome?

Genome Res 2012 Jun 28;22(6):993-1005. Epub 2012 Mar 28.

The Integrative Biosciences Graduate Program, Bioinformatics and Genomics Option, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1101/gr.134395.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371707PMC
June 2012

A genome-wide view of mutation rate co-variation using multivariate analyses.

Genome Biol 2011 22;12(3):R27. Epub 2011 Mar 22.

Center for Medical Genomics, Penn State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/gb-2011-12-3-r27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129677PMC
January 2012

A matter of life or death: how microsatellites emerge in and vanish from the human genome.

Genome Res 2011 Dec 12;21(12):2038-48. Epub 2011 Oct 12.

Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.122937.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227094PMC
December 2011

Exploratory Spatial Analysis of in vitro Respiratory Syncytial Virus Co-infections.

Viruses 2010 12 22;2(12):2782-802. Epub 2010 Dec 22.

Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.3390/v2122782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185596PMC
December 2010

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1.

Nucleic Acids Res 2009 Nov;37(21):7024-38

Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences.

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http://dx.doi.org/10.1093/nar/gkp747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790884PMC
November 2009

Multivariate statistical analyses demonstrate unique host immune responses to single and dual lentiviral infection.

PLoS One 2009 Oct 6;4(10):e7359. Epub 2009 Oct 6.

Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007359PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752991PMC
October 2009

Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions.

Genome Res 2009 Jul 5;19(7):1153-64. Epub 2009 Jun 5.

Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.088922.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704434PMC
July 2009

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif.

Genome Res 2008 Dec 25;18(12):1896-905. Epub 2008 Sep 25.

Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.083089.108
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http://dx.doi.org/10.1101/gr.083089.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593580PMC
December 2008

Human-macaque comparisons illuminate variation in neutral substitution rates.

Genome Biol 2008 Apr 30;9(4):R76. Epub 2008 Apr 30.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/gb-2008-9-4-r76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643947PMC
April 2008

The genome-wide determinants of human and chimpanzee microsatellite evolution.

Genome Res 2008 Jan 21;18(1):30-8. Epub 2007 Nov 21.

Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.7113408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134767PMC
January 2008

Support vector machines categorize the scaling of human grip configurations.

Behav Res Methods 2007 Nov;39(4):1001-7

University of Verona, Verona, Italy.

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November 2007

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

PLoS Comput Biol 2007 Sep 27;3(9):1772-82. Epub 2007 Jul 27.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0030176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976337PMC
September 2007

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.

Genome Res 2007 Jun;17(6):775-86

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.5592107
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http://dx.doi.org/10.1101/gr.5592107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891337PMC
June 2007

Experimental validation of predicted mammalian erythroid cis-regulatory modules.

Genome Res 2006 Dec 12;16(12):1480-92. Epub 2006 Oct 12.

Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.5353806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665632PMC
December 2006

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

Genome Res 2006 Dec 19;16(12):1596-604. Epub 2006 Oct 19.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.4537706
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http://dx.doi.org/10.1101/gr.4537706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665643PMC
December 2006

Genomic environment predicts expression patterns on the human inactive X chromosome.

PLoS Genet 2006 Sep 3;2(9):e151. Epub 2006 Aug 3.

Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1584270PMC
September 2006

Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison.

Mol Biol Evol 2006 Mar 9;23(3):565-73. Epub 2005 Nov 9.

Department of Computer Science and Engineering, Penn State University, USA.

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http://academic.oup.com/mbe/article/23/3/565/1110290/Strong-
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http://dx.doi.org/10.1093/molbev/msj060DOI Listing
March 2006

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences.

Genome Res 2005 Aug 15;15(8):1051-60. Epub 2005 Jul 15.

Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.3642605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182217PMC
August 2005

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.

Genome Res 2004 Apr;14(4):517-27

Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.1984404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383295PMC
April 2004

Insertions and deletions are male biased too: a whole-genome analysis in rodents.

Genome Res 2004 Apr;14(4):567-73

Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.1971104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383300PMC
April 2004

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.

Genome Res 2004 Apr;14(4):700-7

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.1976004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383316PMC
April 2004

Gene length and proximity to neighbors affect genome-wide expression levels.

Genome Res 2003 Dec 12;13(12):2602-8. Epub 2003 Nov 12.

Department of Statistics and Department of Health Evaluation Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.1169203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403802PMC
December 2003

Distinguishing regulatory DNA from neutral sites.

Genome Res 2003 Jan;13(1):64-72

Departments of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.817703
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http://dx.doi.org/10.1101/gr.817703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430974PMC
January 2003

Initial sequencing and comparative analysis of the mouse genome.

Authors:
Robert H Waterston Kerstin Lindblad-Toh Ewan Birney Jane Rogers Josep F Abril Pankaj Agarwal Richa Agarwala Rachel Ainscough Marina Alexandersson Peter An Stylianos E Antonarakis John Attwood Robert Baertsch Jonathon Bailey Karen Barlow Stephan Beck Eric Berry Bruce Birren Toby Bloom Peer Bork Marc Botcherby Nicolas Bray Michael R Brent Daniel G Brown Stephen D Brown Carol Bult John Burton Jonathan Butler Robert D Campbell Piero Carninci Simon Cawley Francesca Chiaromonte Asif T Chinwalla Deanna M Church Michele Clamp Christopher Clee Francis S Collins Lisa L Cook Richard R Copley Alan Coulson Olivier Couronne James Cuff Val Curwen Tim Cutts Mark Daly Robert David Joy Davies Kimberly D Delehaunty Justin Deri Emmanouil T Dermitzakis Colin Dewey Nicholas J Dickens Mark Diekhans Sheila Dodge Inna Dubchak Diane M Dunn Sean R Eddy Laura Elnitski Richard D Emes Pallavi Eswara Eduardo Eyras Adam Felsenfeld Ginger A Fewell Paul Flicek Karen Foley Wayne N Frankel Lucinda A Fulton Robert S Fulton Terrence S Furey Diane Gage Richard A Gibbs Gustavo Glusman Sante Gnerre Nick Goldman Leo Goodstadt Darren Grafham Tina A Graves Eric D Green Simon Gregory Roderic Guigó Mark Guyer Ross C Hardison David Haussler Yoshihide Hayashizaki LaDeana W Hillier Angela Hinrichs Wratko Hlavina Timothy Holzer Fan Hsu Axin Hua Tim Hubbard Adrienne Hunt Ian Jackson David B Jaffe L Steven Johnson Matthew Jones Thomas A Jones Ann Joy Michael Kamal Elinor K Karlsson Donna Karolchik Arkadiusz Kasprzyk Jun Kawai Evan Keibler Cristyn Kells W James Kent Andrew Kirby Diana L Kolbe Ian Korf Raju S Kucherlapati Edward J Kulbokas David Kulp Tom Landers J P Leger Steven Leonard Ivica Letunic Rosie Levine Jia Li Ming Li Christine Lloyd Susan Lucas Bin Ma Donna R Maglott Elaine R Mardis Lucy Matthews Evan Mauceli John H Mayer Megan McCarthy W Richard McCombie Stuart McLaren Kirsten McLay John D McPherson Jim Meldrim Beverley Meredith Jill P Mesirov Webb Miller Tracie L Miner Emmanuel Mongin Kate T Montgomery Michael Morgan Richard Mott James C Mullikin Donna M Muzny William E Nash Joanne O Nelson Michael N Nhan Robert Nicol Zemin Ning Chad Nusbaum Michael J O'Connor Yasushi Okazaki Karen Oliver Emma Overton-Larty Lior Pachter Genís Parra Kymberlie H Pepin Jane Peterson Pavel Pevzner Robert Plumb Craig S Pohl Alex Poliakov Tracy C Ponce Chris P Ponting Simon Potter Michael Quail Alexandre Reymond Bruce A Roe Krishna M Roskin Edward M Rubin Alistair G Rust Ralph Santos Victor Sapojnikov Brian Schultz Jörg Schultz Matthias S Schwartz Scott Schwartz Carol Scott Steven Seaman Steve Searle Ted Sharpe Andrew Sheridan Ratna Shownkeen Sarah Sims Jonathan B Singer Guy Slater Arian Smit Douglas R Smith Brian Spencer Arne Stabenau Nicole Stange-Thomann Charles Sugnet Mikita Suyama Glenn Tesler Johanna Thompson David Torrents Evanne Trevaskis John Tromp Catherine Ucla Abel Ureta-Vidal Jade P Vinson Andrew C Von Niederhausern Claire M Wade Melanie Wall Ryan J Weber Robert B Weiss Michael C Wendl Anthony P West Kris Wetterstrand Raymond Wheeler Simon Whelan Jamey Wierzbowski David Willey Sophie Williams Richard K Wilson Eitan Winter Kim C Worley Dudley Wyman Shan Yang Shiaw-Pyng Yang Evgeny M Zdobnov Michael C Zody Eric S Lander

Nature 2002 Dec;420(6915):520-62

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature01262DOI Listing
December 2002

Dimension reduction strategies for analyzing global gene expression data with a response.

Math Biosci 2002 Mar;176(1):123-44

Department of Statistics, Penn State University, University Park, PA 16802, USA.

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March 2002