Bernard B. Suh
University of California, Santa Cruz
17 Papers
218 Citations
Bernard B. Suh is an academic researcher from University of California, Santa Cruz. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 16, co-authored 16 publications. Previous affiliations of Bernard B. Suh include J. Craig Venter Institute & TigerLogic.
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Papers
Genome sequence of the human malaria parasite Plasmodium falciparum
Malcolm J. Gardner,Neil Hall,Eula Fung,Owen White,Matthew Berriman,Richard W. Hyman,Jane M. Carlton,Arnab Pain,Karen E. Nelson,Sharen Bowman,Ian T. Paulsen,Keith D. James,Jonathan A. Eisen,Kim Rutherford,Steven L. Salzberg,Alister Craig,Sue Kyes,Man Suen Chan,Vishvanath Nene,Shamira J. Shallom,Bernard B. Suh,Jeremy Peterson,Samuel V. Angiuoli,Mihaela Pertea,Jonathan E. Allen,Jeremy D. Selengut,Daniel H. Haft,Michael W. Mather,Akhil B. Vaidya,David M. A. Martin,Alan H. Fairlamb,Martin Fraunholz,David S. Roos,Stuart A. Ralph,Geoffrey I. McFadden,Leda M. Cummings,G. Mani Subramanian,Christopher J. Mungall,J. Craig Venter,Daniel J. Carucci,Stephen L. Hoffman,Chris I. Newbold,Ronald W. Davis,Claire M. Fraser,Bart Barrell +44 more
TL;DR: The genome sequence of P. falciparum clone 3D7 is reported, which is the most (A + T)-rich genome sequenced to date and is being exploited in the search for new drugs and vaccines to fight malaria.
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
Richard M. Myers,John A. Stamatoyannopoulos,Michael Snyder,Ian Dunham,Ross C. Hardison,Bradley E. Bernstein,Bradley E. Bernstein,Thomas R. Gingeras,W. James Kent,Ewan Birney,Barbara J. Wold,Gregory E. Crawford,Charles B. Epstein,Noam Shoresh,Jason Ernst,Jason Ernst,Tarjei S. Mikkelsen,Pouya Kheradpour,Pouya Kheradpour,Xiaolan Zhang,Li Wang,Robbyn Issner,Michael Coyne,Timothy Durham,Manching Ku,Thanh Truong,Lucas D. Ward,Lucas D. Ward,Robert C. Altshuler,Michael F. Lin,Michael F. Lin,Manolis Kellis,Manolis Kellis,Carrie A. Davis,Philipp Kapranov,Alexander Dobin,Chris Zaleski,Felix Schlesinger,Philippe Batut,Sudipto K. Chakrabortty,Sonali Jha,Wei Lin,Jorg Drenkow,Huaien Wang,Kim Bell,Ian Bell,Hui Gao,Erica Dumais,Jacqueline Dumais,Stylianos E. Antonarakis,Catherine Ucla,Christelle Borel,Roderic Guigó,Sarah Djebali,Julien Lagarde,Colin Kingswood,Paolo Ribeca,Micha Sammeth,Tyler Alioto,Angelika Merkel,Hagen Tilgner,Piero Carninci,Yoshihide Hayashizaki,Timo Lassmann,Hazuki Takahashi,Rehab F. Abdelhamid,Gregory J. Hannon,Katalin Toth Fejes,Jonathan B. Preall,Assaf Gordon,Vihra Sotirova,Alexandre Reymond,Cédric Howald,Emilie Aït Yahya Graison,Jacqueline Chrast,Yijun Ruan,Xiaoan Ruan,Atif Shahab,Wan Ting Poh,Chia-Lin Wei,Terrence S. Furey,Alan P. Boyle,Nathan C. Sheffield,Lingyun Song,Yoichiro Shibata,Teresa Vales,Deborah R. Winter,Zhancheng Zhang,Darin London,Tianyuan Wang,Damian Keefe,Vishwanath R. Iyer,Bum Kyu Lee,Ryan M. McDaniell,Zheng Liu,Anna Battenhouse,Akshay Bhinge,Jason D. Lieb,Linda L. Grasfeder,Kimberly A. Showers,Paul G. Giresi,Seul K.C. Kim,Christopher Shestak,Florencia Pauli,Timothy E. Reddy,Jason Gertz,E. Christopher Partridge,Preti Jain,Rebekka O. Sprouse,Anita Bansal,Barbara N. Pusey,Michael Muratet,Katherine E. Varley,Kevin M. Bowling,Kimberly M. Newberry,Amy S. Nesmith,Jason A. Dilocker,Stephanie L. Parker,Lindsay L. Waite,Krista Thibeault,Kevin Roberts,Devin Absher,Ali Mortazavi,Brian Williams,Georgi K. Marinov,Diane Trout,Brandon King,Kenneth McCue,Anthony Kirilusha,Gilberto DeSalvo,Katherine Aylor Fisher,Henry Amrhein,Shirley Pepke,Jost Vielmetter,Gavin Sherlock,Arend Sidow,Serafim Batzoglou,Rami Rauch,Anshul Kundaje,Max Libbrecht,Elliott H. Margulies,Stephen C. J. Parker,Laura Elnitski,Eric D. Green,Tim Hubbard,Jennifer Harrow,Stephen M. J. Searle,Felix Kokocinski,Felix Kokocinski,Browen Aken,Adam Frankish,Toby Hunt,Gloria Despacio-Reyes,M. Kay,Gaurab Mukherjee,Alexandra Bignell,Gary Saunders,Veronika Boychenko,Michael R. Brent,M. van Baren,Randall H. Brown,Mark Gerstein,Mark Gerstein,Ekta Khurana,Suganthi Balasubramanian,Hugo Y. K. Lam,Philip Cayting,Philip Cayting,R. Robilotto,Zhi Lu,Thomas Derrien,Andrea Tanzer,David G. Knowles,Marco Mariotti,David Haussler,Rachel A. Harte,Mark Diekhans,Michael F. Lin,Michael F. Lin,Alfonso Valencia,Michael L. Tress,Stephen G. Landt,Stephen G. Landt,Debasish Raha,Minyi Shi,Ghia Euskirchen,Fabian Grubert,Maya Kasowski,Jin Lian,Phil Lacroute,Youhan Xu,Hannah Monahan,Dorrelyn Patacsil,Teri Slifer,Xinqiong Yang,Alexandra Charos,Brian Reed,Linfeng Wu,Raymond K. Auerbach,Lukas Habegger,Manoj Hariharan,Joel Rozowsky,Alexej Abyzov,Sherman M. Weissman,Kevin Struhl,Nathan Lamarre-Vincent,Marianne Lindahl-Allen,Benoit Miotto,Zarmik Moqtaderi,Joseph D. Fleming,Peter E. Newburger,Peggy J. Farnham,Peggy J. Farnham,Seth Frietze,Seth Frietze,Henriette O'Geen,Xiaoqin Xu,Kim Blahnik,Alina R. Cao,Sushma Iyengar,Rajinder Kaul,Robert E. Thurman,Hao Wang,Patrick A. Navas,Richard Sandstrom,Peter J. Sabo,Molly Weaver,Theresa K. Canfield,Kristen Lee,Shane Neph,Vaughan Roach,Alex Reynolds,Audra K. Johnson,Eric Rynes,Erika Giste,Shinny Vong,Jun Neri,Tristan Frum,Eric D. Nguyen,Abigail K. Ebersol,Minerva E. Sanchez,Hadar H. Sheffer,Dimitra Lotakis,Eric Haugen,Richard Humbert,Tanya Kutyavin,Tony Shafer,William Stafford Noble,Job Dekker,Bryan R. Lajoie,Amartya Sanyal,Kate R. Rosenbloom,Timothy R. Dreszer,Brian J. Raney,Galt P. Barber,Laurence R. Meyer,Cricket A. Sloan,Venkat S. Malladi,Melissa S. Cline,Katrina Learned,Vanessa K. Swing,Ann S. Zweig,Brooke Rhead,Pauline A. Fujita,Krishna M. Roskin,Donna Karolchik,Robert M. Kuhn,Steven P. Wilder,Daniel Sobral,Javier Herrero,Kathryn Beal,Margus Lukk,Alvis Brazma,Juan M. Vaquerizas,Nicholas M. Luscombe,Peter J. Bickel,Nathan Boley,James B. Brown,Qiang Li,Haiyan Huang,Andrea Sboner,Kevin Y. Yip,Chao Cheng,Koon-Kiu Yan,Nitin Bhardwaj,Jing Wang,Lucas Lochovsky,Justin Jee,Theodore Gibson,Jing Leng,Jiang Du,Robert S. Harris,Giltae Song,Webb Miller,Bernard B. Suh,Benedict Paten,Michael M. Hoffman,Orion J. Buske,Zhiping Weng,Xianjun Dong,Jie Wang,Hualin Xi,Scott A. Tenenbaum,Frank Doyle,Sridar V. Chittur,Luiz O. F. Penalva,Thomas D. Tullius,Kevin P. White,Subhradip Karmakar,Alec Victorsen,Nader Jameel,Nick Bild,Robert L. Grossman,Patrick J. Collins,Nathan D. Trinklein,Morgan C. Giddings,Morgan C. Giddings,Jainab Khatun,Christopher W. Maier,Ting Wang,Troy W. Whitfield,Xian Chen,Yanbao Yu,Harsha P. Gunawardena,Elise A. Feingold,Rebecca F. Lowdon,Laura A.L. Dillon,Peter J. Good,Brian A. Risk +328 more
TL;DR: An overview of the project and the resources it is generating and the application of ENCODE data to interpret the human genome are provided.
The genome of the protist parasite Entamoeba histolytica
Brendan J. Loftus,Iain J. Anderson,Robert L. Davies,U. Cecilia M. Alsmark,John Samuelson,Paolo Amedeo,Paola Roncaglia,Matthew Berriman,Robert P. Hirt,Barbara J. Mann,Tomo Nozaki,Bernard B. Suh,Mihai Pop,Michael Duchêne,John P. Ackers,Egbert Tannich,Matthias Leippe,Margit Hofer,Iris Bruchhaus,Ute Willhoeft,Alok Bhattacharya,Tracey Chillingworth,Carol Churcher,Zahra Hance,Barbara Harris,David Harris,Kay Jagels,Sharon Moule,Karen Mungall,Doug Ormond,Rob Squares,Sally Whitehead,Michael A. Quail,Ester Rabbinowitsch,Halina Norbertczak,Claire Price,Zheng Wang,Nancy Guillén,Carol A. Gilchrist,Suzanne Stroup,Sudha Bhattacharya,Anuradha Lohia,Peter G. Foster,Thomas Sicheritz-Pontén,Christian Weber,Upinder Singh,Chandrama Mukherjee,Najib M. El-Sayed,William A. Petri,C. Graham Clark,T. Martin Embley,Bart Barrell,Claire M. Fraser,Neil Hall,Neil Hall +54 more
TL;DR: The genome of E. histolytica is presented, which reveals a variety of metabolic adaptations shared with two other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis, and provides new insights into the workings and genome evolution of a major human pathogen.
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
Jane M. Carlton,Samuel V. Angiuoli,Bernard B. Suh,Taco W. A. Kooij,Mihaela Pertea,Joana C. Silva,Maria D. Ermolaeva,Jonathan E. Allen,Jeremy D. Selengut,Hean L. Koo,Jeremy Peterson,Mihai Pop,Daniel S. Kosack,Martin Shumway,Shelby L. Bidwell,Shamira J. Shallom,Susan Van Aken,Steven B. Riedmuller,Tamara Feldblyum,Jennifer Cho,John Quackenbush,Martha Sedegah,Azadeh Shoaibi,Leda M. Cummings,Laurence Florens,John R. Yates,J. Dale Raine,Robert E. Sinden,Michael Harris,Deirdre A. Cunningham,Peter R. Preiser,Lawrence W. Bergman,Akhil B. Vaidya,Leo H.M. van Lin,Chris J. Janse,Andrew P. Waters,Hamilton O. Smith,Owen White,Steven L. Salzberg,J. Craig Venter,Claire M. Fraser,Stephen L. Hoffman,Malcolm J. Gardner,Daniel J. Carucci +43 more
TL;DR: This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.
Comparative and demographic analysis of orang-utan genomes.
Devin P. Locke,LaDeana W. Hillier,Wesley C. Warren,Kim C. Worley,Lynne V. Nazareth,Donna M. Muzny,Shiaw-Pyng Yang,Zhengyuan Wang,Asif T. Chinwalla,Patrick Minx,Makedonka Mitreva,Lisa Cook,Kim D. Delehaunty,Catrina Fronick,Heather Schmidt,Lucinda Fulton,Robert S. Fulton,Joanne O. Nelson,Vincent Magrini,Craig Pohl,Tina Graves,Chris Markovic,Andy Cree,Huyen Dinh,Jennifer Hume,Christie Kovar,Gerald R. Fowler,Gerton Lunter,Gerton Lunter,Stephen Meader,Andreas Heger,Chris P. Ponting,Tomas Marques-Bonet,Tomas Marques-Bonet,Can Alkan,Lin Chen,Ze Cheng,Jeffrey M. Kidd,Evan E. Eichler,Evan E. Eichler,Simon D. M. White,Stephen M. J. Searle,Albert J. Vilella,Yuan Chen,Paul Flicek,Jian Ma,Jian Ma,Brian J. Raney,Bernard B. Suh,Richard Burhans,Javier Herrero,David Haussler,Rui Faria,Rui Faria,Olga Fernando,Olga Fernando,Fleur Darré,Domènec Farré,Elodie Gazave,Meritxell Oliva,Arcadi Navarro,Roberta Roberto,Oronzo Capozzi,Nicoletta Archidiacono,Giuliano Della Valle,Stefania Purgato,Mariano Rocchi,Miriam K. Konkel,Jerilyn A. Walker,Brygg Ullmer,Mark A. Batzer,Arian F.A. Smit,Robert Hubley,Claudio Casola,Daniel R. Schrider,Matthew W. Hahn,Víctor Quesada,Xose S. Puente,Gonzalo R. Ordóñez,Carlos López-Otín,Tomas Vinar,Brona Brejova,Aakrosh Ratan,Robert S. Harris,Webb Miller,Carolin Kosiol,Heather A. Lawson,Vikas Taliwal,André L. Martins,Adam Siepel,Arindam RoyChoudhury,Xin Ma,Jeremiah D. Degenhardt,Carlos Bustamante,Ryan N. Gutenkunst,Thomas Mailund,Julien Y. Dutheil,Asger Hobolth,Mikkel H. Schierup,Oliver A. Ryder,Yuko Yoshinaga,Pieter J. de Jong,George M. Weinstock,Jeffrey Rogers,Elaine R. Mardis,Richard A. Gibbs,Richard K. Wilson +106 more
TL;DR: The orang-utan species, Pongo abelii and Pongo pygmaeus, are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution and a primate polymorphic neocentromere, found in both Pongo species are described.