James Cuff

James Cuff

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James Cuff

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The medical science DMZ: a network design pattern for data-intensive medical science.

J Am Med Inform Assoc 2017 Oct 6. Epub 2017 Oct 6.

ESnet, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/jamia/ocx104DOI Listing
October 2017

The Medical Science DMZ.

J Am Med Inform Assoc 2016 11 2;23(6):1199-1201. Epub 2016 May 2.

ESnet, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/jamia/ocw032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5070525PMC
November 2016

Systematic approach to conformational sampling for assigning absolute configuration using vibrational circular dichroism.

J Med Chem 2014 Jan 2;57(2):477-94. Epub 2014 Jan 2.

Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, New Jersey 07065, United States.

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http://dx.doi.org/10.1021/jm401600uDOI Listing
January 2014

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

A cascade approach to cyclic aminonitrones: reaction discovery, mechanism, and scope.

Org Lett 2009 Aug;11(15):3194-7

Department of Process Research, Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, USA.

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http://dx.doi.org/10.1021/ol9010147DOI Listing
August 2009

Distinguishing protein-coding and noncoding genes in the human genome.

Proc Natl Acad Sci U S A 2007 Dec 26;104(49):19428-33. Epub 2007 Nov 26.

Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0709013104
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http://dx.doi.org/10.1073/pnas.0709013104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2148306PMC
December 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
Publisher Site
http://dx.doi.org/10.1101/gr.6034307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

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

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

Authors:
Kerstin Lindblad-Toh Claire M Wade Tarjei S Mikkelsen Elinor K Karlsson David B Jaffe Michael Kamal Michele Clamp Jean L Chang Edward J Kulbokas Michael C Zody Evan Mauceli Xiaohui Xie Matthew Breen Robert K Wayne Elaine A Ostrander Chris P Ponting Francis Galibert Douglas R Smith Pieter J DeJong Ewen Kirkness Pablo Alvarez Tara Biagi William Brockman Jonathan Butler Chee-Wye Chin April Cook James Cuff Mark J Daly David DeCaprio Sante Gnerre Manfred Grabherr Manolis Kellis Michael Kleber Carolyne Bardeleben Leo Goodstadt Andreas Heger Christophe Hitte Lisa Kim Klaus-Peter Koepfli Heidi G Parker John P Pollinger Stephen M J Searle Nathan B Sutter Rachael Thomas Caleb Webber Jennifer Baldwin Adal Abebe Amr Abouelleil Lynne Aftuck Mostafa Ait-Zahra Tyler Aldredge Nicole Allen Peter An Scott Anderson Claudel Antoine Harindra Arachchi Ali Aslam Laura Ayotte Pasang Bachantsang Andrew Barry Tashi Bayul Mostafa Benamara Aaron Berlin Daniel Bessette Berta Blitshteyn Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Adam Brown Patrick Cahill Nadia Calixte Jody Camarata Yama Cheshatsang Jeffrey Chu Mieke Citroen Alville Collymore Patrick Cooke Tenzin Dawoe Riza Daza Karin Decktor Stuart DeGray Norbu Dhargay Kimberly Dooley Kathleen Dooley Passang Dorje Kunsang Dorjee Lester Dorris Noah Duffey Alan Dupes Osebhajajeme Egbiremolen Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Patricia Ferreira Sheila Fisher Mike FitzGerald Karen Foley Chelsea Foley Alicia Franke Dennis Friedrich Diane Gage Manuel Garber Gary Gearin Georgia Giannoukos Tina Goode Audra Goyette Joseph Graham Edward Grandbois Kunsang Gyaltsen Nabil Hafez Daniel Hagopian Birhane Hagos Jennifer Hall Claire Healy Ryan Hegarty Tracey Honan Andrea Horn Nathan Houde Leanne Hughes Leigh Hunnicutt M Husby Benjamin Jester Charlien Jones Asha Kamat Ben Kanga Cristyn Kells Dmitry Khazanovich Alix Chinh Kieu Peter Kisner Mayank Kumar Krista Lance Thomas Landers Marcia Lara William Lee Jean-Pierre Leger Niall Lennon Lisa Leuper Sarah LeVine Jinlei Liu Xiaohong Liu Yeshi Lokyitsang Tashi Lokyitsang Annie Lui Jan Macdonald John Major Richard Marabella Kebede Maru Charles Matthews Susan McDonough Teena Mehta James Meldrim Alexandre Melnikov Louis Meneus Atanas Mihalev Tanya Mihova Karen Miller Rachel Mittelman Valentine Mlenga Leonidas Mulrain Glen Munson Adam Navidi Jerome Naylor Tuyen Nguyen Nga Nguyen Cindy Nguyen Thu Nguyen Robert Nicol Nyima Norbu Choe Norbu Nathaniel Novod Tenchoe Nyima Peter Olandt Barry O'Neill Keith O'Neill Sahal Osman Lucien Oyono Christopher Patti Danielle Perrin Pema Phunkhang Fritz Pierre Margaret Priest Anthony Rachupka Sujaa Raghuraman Rayale Rameau Verneda Ray Christina Raymond Filip Rege Cecil Rise Julie Rogers Peter Rogov Julie Sahalie Sampath Settipalli Theodore Sharpe Terrance Shea Mechele Sheehan Ngawang Sherpa Jianying Shi Diana Shih Jessie Sloan Cherylyn Smith Todd Sparrow John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Sabrina Stone Sean Sykes Pierre Tchuinga Pema Tenzing Senait Tesfaye Dawa Thoulutsang Yama Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Vijay Venkataraman Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Shuli Yang Xiaoping Yang Geneva Young Qing Yu Joanne Zainoun Lisa Zembek Andrew Zimmer Eric S Lander

Nature 2005 Dec;438(7069):803-19

Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA.

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http://www.nature.com/articles/nature04338
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http://dx.doi.org/10.1038/nature04338DOI Listing
December 2005

The Ensembl computing architecture.

Genome Res 2004 May;14(5):971-5

The Broad Institute, Cambridge, Massachusetts 02141, USA.

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http://dx.doi.org/10.1101/gr.1866304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479128PMC
May 2004

The Jalview Java alignment editor.

Bioinformatics 2004 Feb 22;20(3):426-7. Epub 2004 Jan 22.

The Wellcome Trust Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1093/bioinformatics/btg430DOI Listing
February 2004

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