T
Tanja M. Davidsen
Researcher at J. Craig Venter Institute
Publications - 38
Citations - 18321
Tanja M. Davidsen is an academic researcher from J. Craig Venter Institute. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 26, co-authored 38 publications receiving 15196 citations. Previous affiliations of Tanja M. Davidsen include TigerLogic.
Papers
More filters
Journal ArticleDOI
Comprehensive molecular characterization of gastric adenocarcinoma
Adam J. Bass,Vesteinn Thorsson,Ilya Shmulevich,Sheila Reynolds,Michael Miller,Brady Bernard,Toshinori Hinoue,Peter W. Laird,Christina Curtis,Hui Shen,Daniel J. Weisenberger,Nikolaus Schultz,Ronglai Shen,Nils Weinhold,David P. Kelsen,Reanne Bowlby,Andy Chu,Katayoon Kasaian,Andrew J. Mungall,A. Gordon Robertson,Payal Sipahimalani,Andrew D. Cherniack,Gad Getz,Yingchun Liu,Michael S. Noble,Chandra Pedamallu,Carrie Sougnez,Amaro Taylor-Weiner,Rehan Akbani,Ju Seog Lee,Wenbin Liu,GB Mills,Da Yang,Wei Zhang,Angeliki Pantazi,Michael Parfenov,Margaret L. Gulley,M. Blanca Piazuelo,Barbara G. Schneider,Jihun Kim,Alex Boussioutas,Margi Sheth,John A. Demchok,Charles S. Rabkin,Joseph Willis,Sam Ng,Katherine S. Garman,David G. Beer,Arjun Pennathur,Benjamin J. Raphael,Hsin-Ta Wu,Robert D. Odze,Hark Kyun Kim,Jay Bowen,Kristen M. Leraas,Tara M. Lichtenberg,Stephanie Weaver,Michael D. McLellan,Maciej Wiznerowicz,Ryo Sakai,Michael S. Lawrence,Kristian Cibulskis,Lee Lichtenstein,Sheila Fisher,Stacey Gabriel,Eric S. Lander,Li Ding,Beifang Niu,Adrian Ally,Miruna Balasundaram,Inanc Birol,Denise Brooks,Yaron S.N. Butterfield,Rebecca Carlsen,Justin Chu,Eric Chuah,Hye Jung E. Chun,Amanda Clarke,Noreen Dhalla,Ranabir Guin,Robert A. Holt,Steven J.M. Jones,Darlene Lee,Haiyan A. Li,Emilia L. Lim,Yussanne Ma,Marco A. Marra,Michael Mayo,Richard A. Moore,Karen Mungall,Ka Ming Nip,Jacqueline E. Schein,Angela Tam,Nina Thiessen,Rameen Beroukhim,Scott L. Carter,Andrew D. Cherniack,Juok Cho,Daniel DiCara,Scott Frazer,Nils Gehlenborg,David I. Heiman,Joonil Jung,Jaegil Kim,Pei Lin,Matthew Meyerson,Akinyemi I. Ojesina,Chandra Sekhar Pedamallu,Gordon Saksena,Steven E. Schumacher,Petar Stojanov,Barbara Tabak,Doug Voet,Mara Rosenberg,Travis I. Zack,Hailei Zhang,Lihua Zou,Alexei Protopopov,Netty Santoso,Semin Lee,Jianhua Zhang,Harshad S. Mahadeshwar,Jiabin Tang,Xiaojia Ren,Sahil Seth,Lixing Yang,Andrew Wei Xu,Xingzhi Song,Ruibin Xi,Christopher A. Bristow,Angela Hadjipanayis,Jonathan G. Seidman,Lynda Chin,Peter J. Park,Raju Kucherlapati,Shiyun Ling,Arvind Rao,John N. Weinstein,Sang Bae Kim,Yiling Lu,Gordon B. Mills,Moiz S. Bootwalla,Phillip H. Lai,Timothy J. Triche,David Van Den Berg,Stephen B. Baylin,James G. Herman,Bradley A. Murray,B. Arman Askoy,Giovanni Ciriello,Gideon Dresdner,Jianjiong Gao,Benjamin Gross,Anders Jacobsen,William Lee,Ricardo Ramirez,Chris Sander,Yasin Senbabaoglu,Rileen Sinha,S. Onur Sumer,Yichao Sun,Lisa Iype,Roger Kramer,Richard Kreisberg,Hector Rovira,Natalie Tasman,Santa Cruz Sam Ng,David Haussler,Josh Stuart,Roeland Verhaak,Mark D.M. Leiserson,Barry S. Taylor,Aaron D. Black,Julie Ann Carney,Julie M. Gastier-Foster,Carmen Helsel,Cynthia McAllister,Nilsa C. Ramirez,Teresa R. Tabler,Lisa Wise,Erik Zmuda,Robert Penny,Daniel Crain,Johanna Gardner,Kevin Lau,Erin Curely,David Mallery,Scott Morris,Joseph Paulauskis,Troy Shelton,Candace Shelton,Mark E. Sherman,Christopher C. Benz,Jae Hyuk Lee,Konstantin V. Fedosenko,Georgy Manikhas,Olga Potapova,Olga Voronina,Smitry Belyaev,Oleg Dolzhansky,W. Kimryn Rathmell,Jakub Brzezinski,Matthew Ibbs,Konstanty Korski,Witold Kycler,Radoslaw ŁaŸniak,Ewa Leporowska,Andrzej Mackiewicz,Dawid Murawa,Pawel Murawa,Arkadiusz Spychała,Wiktoria Maria Suchorska,Honorata Tatka,M. Teresiak,Raafat Abdel-Misih,Joseph J. Bennett,Jennifer Brown,Mary Iacocca,Brenda Rabeno,Sun Young Kwon,Ariane Kemkes,Erin Curley,Iakovina Alexopoulou,Jay Engel,John M. S. Bartlett,Monique Albert,Do-Youn Park,Rajiv Dhir,James D. Luketich,Rodney J. Landreneau,Yelena Y. Janjigian,Eunjung Cho,Marc Ladanyi,Laura H. Tang,Shannon J. McCall,Young Soo Park,Jae Ho Cheong,Jaffer A. Ajani,M. Constanza Camargo,Shelley Alonso,Brenda Ayala,Mark A. Jensen,Todd Pihl,Rohini Raman,Jessica Walton,Yunhu Wan,Greg Eley,Kenna R. Mills Shaw,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jean C. Zenklusen,Tanja M. Davidsen,Carolyn M. Hutter,Heidi J. Sofia,Robert Burton,Sudha Chudamani,Jia Liu +257 more
TL;DR: A comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project is described and a molecular classification dividing gastric cancer into four subtypes is proposed.
Journal ArticleDOI
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.
Daniel J. Brat,Roel G.W. Verhaak,Kenneth Aldape,W. K. Alfred Yung,Sofie R. Salama,Lee Cooper,Esther Rheinbay,C. Ryan Miller,Mark Vitucci,Olena Morozova,A. Gordon Robertson,Houtan Noushmehr,Peter W. Laird,Andrew D. Cherniack,Rehan Akbani,Jason T. Huse,Giovanni Ciriello,Laila M. Poisson,Jill S. Barnholtz-Sloan,Mitchel S. Berger,Cameron Brennan,Rivka R. Colen,Howard Colman,Adam E. Flanders,Caterina Giannini,Mia Grifford,Antonio Iavarone,Rajan Jain,Isaac Joseph,Jaegil Kim,Katayoon Kasaian,Tom Mikkelsen,Bradley A. Murray,Brian P. O'Neill,Lior Pachter,Donald W. Parsons,Carrie Sougnez,Erik P. Sulman,Scott R. VandenBerg,Erwin G. Van Meir,Andreas von Deimling,Hailei Zhang,Daniel Crain,Kevin Lau,David Mallery,Scott Morris,Joseph Paulauskis,Robert Penny,Troy Shelton,Mark E. Sherman,Peggy Yena,Aaron D. Black,Jay Bowen,Katie Dicostanzo,Julie M. Gastier-Foster,Kristen M. Leraas,Tara M. Lichtenberg,Christopher R. Pierson,Nilsa C. Ramirez,Cynthia Taylor,Stephanie Weaver,Lisa Wise,Erik Zmuda,Tanja M. Davidsen,John A. Demchok,Greg Eley,Martin L. Ferguson,Carolyn M. Hutter,Kenna R. Mills Shaw,Bradley A. Ozenberger,Margi Sheth,Heidi J. Sofia,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jean C. Zenklusen,Brenda Ayala,Julien Baboud,Sudha Chudamani,Mark A. Jensen,Jia Liu,Todd Pihl,Rohini Raman,Yunhu Wan,Ye Wu,Adrian Ally,J. Todd Auman,Miruna Balasundaram,Saianand Balu,Stephen B. Baylin,Rameen Beroukhim,Moiz S. Bootwalla,Reanne Bowlby,Christopher A. Bristow,Denise Brooks,Yaron S.N. Butterfield,Rebecca Carlsen,Scott L. Carter,Lynda Chin,Andy Chu,Eric Chuah,Kristian Cibulskis,Amanda Clarke,Simon G. Coetzee,Noreen Dhalla,Timothy R. Fennell,Sheila A. Fisher,Stacey Gabriel,Gad Getz,Richard A. Gibbs,Ranabir Guin,Angela Hadjipanayis,D. Neil Hayes,Toshinori Hinoue,Katherine A. Hoadley,Robert A. Holt,Alan P. Hoyle,Stuart R. Jefferys,Steven J.M. Jones,Corbin D. Jones,Raju Kucherlapati,Phillip H. Lai,Eric S. Lander,Semin Lee,Lee Lichtenstein,Yussanne Ma,Dennis T. Maglinte,Harshad S. Mahadeshwar,Marco A. Marra,Michael Mayo,Shaowu Meng,Matthew Meyerson,Piotr A. Mieczkowski,Richard A. Moore,Lisle E. Mose,Andrew J. Mungall,Angeliki Pantazi,Michael Parfenov,Peter J. Park,Joel S. Parker,Charles M. Perou,Alexei Protopopov,Xiaojia Ren,Jeffrey Roach,Thais S. Sabedot,Jacqueline E. Schein,Steven E. Schumacher,Jonathan G. Seidman,Sahil Seth,Hui Shen,Janae V. Simons,Payal Sipahimalani,Matthew G. Soloway,Xingzhi Song,Huandong Sun,Barbara Tabak,Angela Tam,Donghui Tan,Jiabin Tang,Nina Thiessen,Timothy J. Triche,David Van Den Berg,Umadevi Veluvolu,Scot Waring,Daniel J. Weisenberger,Matthew D. Wilkerson,Tina Wong,Junyuan Wu,Liu Xi,Andrew Wei Xu,Lixing Yang,Travis I. Zack,Jianhua Zhang,B. Arman Aksoy,Harindra Arachchi,Chris Benz,Brady Bernard,Daniel E. Carlin,Juok Cho,Daniel DiCara,Scott Frazer,Gregory N. Fuller,Jianjiong Gao,Nils Gehlenborg,David Haussler,David I. Heiman,Lisa Iype,Anders Jacobsen,Zhenlin Ju,Sol Katzman,Hoon Kim,Theo A. Knijnenburg,Richard Kreisberg,Michael S. Lawrence,William M. Lee,Kalle Leinonen,Pei Lin,Shiyun Ling,Wen-Bin Liu,Yingchun Liu,Yuexin Liu,Yiling Lu,Gordon B. Mills,Sam Ng,Michael S. Noble,Evan O. Paull,Arvind Rao,Sheila Reynolds,Gordon Saksena,Zack Sanborn,Chris Sander,Nikolaus Schultz,Yasin Senbabaoglu,Ronglai Shen,Ilya Shmulevich,Rileen Sinha,Josh Stuart,S. Onur Sumer,Yichao Sun,Natalie Tasman,Barry S. Taylor,Doug Voet,Nils Weinhold,John N. Weinstein,Da Yang,Kosuke Yoshihara,Siyuan Zheng,Wei Zhang,Lihua Zou,Ty Abel,Sara Sadeghi,Mark L. Cohen,Jenny Eschbacher,Eyas M. Hattab,Aditya Raghunathan,Matthew Schniederjan,Dina Aziz,Gene Barnett,Wendi Barrett,Darell D. Bigner,Lori Boice,Cathy Brewer,Chiara Calatozzolo,Benito Campos,Carlos Gilberto Carlotti,Timothy A. Chan,Lucia Cuppini,Erin Curley,Stefania Cuzzubbo,Karen Devine,Francesco DiMeco,Rebecca Duell,J. Bradley Elder,Ashley Fehrenbach,Gaetano Finocchiaro,William A. Friedman,Jordonna Fulop,Johanna Gardner,Beth Hermes,Christel Herold-Mende,Christine Jungk,Ady Kendler,Norman L. Lehman,Eric S. Lipp,Ouida Liu,Randy Mandt,Mary McGraw,Roger E. McLendon,Christopher M. McPherson,Luciano Neder,Phuong L. Nguyen,Ardene Noss,Raffaele Nunziata,Quinn T. Ostrom,Cheryl A. Palmer,Alessandro Perin,Bianca Pollo,Alexander Potapov,Olga Potapova,W. Kimryn Rathmell,D L Rotin,Lisa Scarpace,Cathy Schilero,Kelly Senecal,Kristen Shimmel,Vsevolod Shurkhay,Suzanne Sifri,Rosy Singh,Andrew E. Sloan,Kathy Smolenski,Susan M. Staugaitis,Ruth Steele,Leigh B. Thorne,Daniela Pretti da Cunha Tirapelli,Andreas Unterberg,Mahitha Vallurupalli,Yun Wang,Ronald E. Warnick,Felicia Williams,Yingli Wolinsky,Sue E. Bell,Mara Rosenberg,Chip Stewart,Franklin W. Huang,Jonna Grimsby,Amie Radenbaugh,Jianan Zhang +306 more
TL;DR: The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class.
Journal ArticleDOI
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”
Hervé Tettelin,Vega Masignani,Michael J. Cieslewicz,Claudio Donati,Duccio Medini,Naomi L. Ward,Samuel V. Angiuoli,Jonathan Crabtree,Amanda L. Jones,A. Scott Durkin,Robert T. DeBoy,Tanja M. Davidsen,Marirosa Mora,Maria Scarselli,Immaculada Margarit Y Ros,Jeremy Peterson,Christopher R. Hauser,Jaideep P. Sundaram,William C. Nelson,Ramana Madupu,Lauren M. Brinkac,Robert J. Dodson,M. J. Rosovitz,Steven A. Sullivan,Sean C. Daugherty,Daniel H. Haft,Jeremy D. Selengut,Michelle L. Gwinn,Liwei Zhou,Nikhat Zafar,Hoda Khouri,Diana Radune,George Dimitrov,Kisha Watkins,Kevin J. B. O'Connor,Shannon Smith,Teresa Utterback,Owen White,Craig E. Rubens,Guido Grandi,Lawrence C. Madoff,Dennis L. Kasper,John L. Telford,Michael R. Wessels,Rino Rappuoli,Claire M. Fraser +45 more
TL;DR: The genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans, was generated and Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactic pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.
Journal ArticleDOI
Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer.
Giovanni Ciriello,Giovanni Ciriello,Michael L. Gatza,Michael L. Gatza,Andrew H. Beck,Matthew D. Wilkerson,Suhn K. Rhie,Alessandro Pastore,Hailei Zhang,Michael D. McLellan,Christina Yau,Cyriac Kandoth,Reanne Bowlby,Hui Shen,Sikander Hayat,Robert J. Fieldhouse,Susan C. Lester,Gary M. Tse,Rachel E. Factor,Laura C. Collins,Kimberly H. Allison,Yunn Yi Chen,Kristin C. Jensen,Kristin C. Jensen,Nicole B. Johnson,Steffi Oesterreich,Gordon B. Mills,Andrew D. Cherniack,Gordon Robertson,Christopher C. Benz,Chris Sander,Peter W. Laird,Katherine A. Hoadley,Tari A. King,Rehan Akbani,J. Todd Auman,Miruna Balasundaram,Saianand Balu,Thomas Barr,Stephen C. Benz,Mario Berrios,Rameen Beroukhim,Tom Bodenheimer,Lori Boice,Moiz S. Bootwalla,Jay Bowen,Denise Brooks,Lynda Chin,Juok Cho,Sudha Chudamani,Tanja M. Davidsen,John A. Demchok,Jennifer B. Dennison,Li Ding,Ina Felau,Martin L. Ferguson,Scott Frazer,Stacey Gabriel,Jianjiong Gao,Julie M. Gastier-Foster,Nils Gehlenborg,Mark Gerken,Gad Getz,William J. Gibson,D. Neil Hayes,David I. Heiman,Andrea Holbrook,Robert A. Holt,Alan P. Hoyle,Hai Hu,Mei Huang,Carolyn M. Hutter,E. Shelley Hwang,Stuart R. Jefferys,Steven J.M. Jones,Zhenlin Ju,Jaegil Kim,Phillip H. Lai,Michael S. Lawrence,Kristen M. Leraas,Tara M. Lichtenberg,Pei Lin,Shiyun Ling,Jia Liu,Wen-Bin Liu,Laxmi Lolla,Yiling Lu,Yussanne Ma,Dennis T. Maglinte,Elaine R. Mardis,Jeffrey R. Marks,Marco A. Marra,Cynthia McAllister,Shaowu Meng,Matthew Meyerson,Richard A. Moore,Lisle E. Mose,Andrew J. Mungall,Bradley A. Murray,Rashi Naresh,Michael S. Noble,Olufunmilayo I. Olopade,Joel S. Parker,Todd Pihl,Gordon Saksena,Steven E. Schumacher,Kenna R. Mills Shaw,Nilsa C. Ramirez,W. Kimryn Rathmell,Jeffrey Roach,A. Gordon Robertson,Jacqueline E. Schein,Nikolaus Schultz,Margi Sheth,Yan Shi,Juliann Shih,Carl Simon Shelley,Craig D. Shriver,Janae V. Simons,Heidi J. Sofia,Matthew G. Soloway,Carrie Sougnez,Charlie Sun,Roy Tarnuzzer,Daniel Guimarães Tiezzi,David Van Den Berg,Doug Voet,Yunhu Wan,Zhining Wang,John N. Weinstein,Daniel J. Weisenberger,Rick K. Wilson,Lisa Wise,Maciej Wiznerowicz,Junyuan Wu,Ye Wu,Liming Yang,Travis I. Zack,Jean C. Zenklusen,Jiashan Zhang,Erik Zmuda,Charles M. Perou +141 more
TL;DR: This multidimensional molecular atlas sheds new light on the genetic bases of ILC and provides potential clinical options, suggesting differential modulation of ER activity in I LC and IDC.
Journal ArticleDOI
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
C. Robin Buell,Vinita Joardar,Magdalen Lindeberg,Jeremy D. Selengut,Ian T. Paulsen,Michelle L. Gwinn,Robert J. Dodson,Robert T. DeBoy,A. Scott Durkin,James F. Kolonay,Ramana Madupu,Sean C. Daugherty,Lauren M. Brinkac,Maureen J. Beanan,Daniel H. Haft,William C. Nelson,Tanja M. Davidsen,Nikhat Zafar,Liwei Zhou,Jia Liu,Qiaoping Yuan,Hoda Khouri,Nadia Fedorova,Bao Tran,Daniel A. Russell,Kristi Berry,Teresa Utterback,Susan Van Aken,Tamara Feldblyum,Mark D'Ascenzo,Wen Ling Deng,Adela R. Ramos,James R. Alfano,Samuel W. Cartinhour,Arun K. Chatterjee,Terrence P. Delaney,Sondra G. Lazarowitz,Gregory B. Martin,David J. Schneider,Xiaoyan Tang,Carol L. Bender,Owen White,Claire M. Fraser,Alan Collmer +43 more
TL;DR: The complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana, is reported and 1,159 genes unique to DC3000 are revealed, of which 811 lack a known function.