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Özgün Babur
Researcher at University of Massachusetts Boston
Publications - 59
Citations - 4800
Özgün Babur is an academic researcher from University of Massachusetts Boston. The author has contributed to research in topics: BioPAX : Biological Pathways Exchange & Visualization. The author has an hindex of 23, co-authored 59 publications receiving 3548 citations. Previous affiliations of Özgün Babur include Bilkent University & Memorial Sloan Kettering Cancer Center.
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Journal ArticleDOI
Pathway Commons, a web resource for biological pathway data
Ethan Cerami,Benjamin Gross,Emek Demir,Igor Rodchenkov,Özgün Babur,Nadia Anwar,Nikolaus Schultz,Gary D. Bader,Chris Sander +8 more
TL;DR: A web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data.
Journal ArticleDOI
The BioPAX community standard for pathway data sharing
Emek Demir,Emek Demir,Michael P. Cary,Suzanne M. Paley,Ken Fukuda,Christian Lemer,Imre Vastrik,Guanming Wu,Peter D'Eustachio,Carl F. Schaefer,Joanne S. Luciano,Frank Schacherer,Irma Martínez-Flores,Zhenjun Hu,Verónica Jiménez-Jacinto,Geeta Joshi-Tope,Kumaran Kandasamy,Alejandra López-Fuentes,Huaiyu Mi,Elgar Pichler,Igor Rodchenkov,Andrea Splendiani,Andrea Splendiani,Sasha Tkachev,Jeremy Zucker,Gopal R. Gopinath,Harsha Rajasimha,Harsha Rajasimha,Ranjani Ramakrishnan,Imran Shah,Mustafa H Syed,Nadia Anwar,Özgün Babur,Özgün Babur,Michael L. Blinov,Erik Brauner,Dan Corwin,Sylva L. Donaldson,Frank Gibbons,Robert N. Goldberg,Peter Hornbeck,Augustin Luna,Peter Murray-Rust,Eric K. Neumann,Oliver Reubenacker,Matthias Samwald,Matthias Samwald,Martijn P. van Iersel,Sarala M. Wimalaratne,Keith Allen,Burk Braun,Michelle Whirl-Carrillo,Kei-Hoi Cheung,Kam D. Dahlquist,Andrew Finney,Marc Gillespie,Elizabeth M. Glass,Li Gong,Robin Haw,Michael Honig,Olivier Hubaut,David W. Kane,Shiva Krupa,Martina Kutmon,Julie Leonard,Debbie Marks,David Merberg,Victoria Petri,Alexander R. Pico,Dean Ravenscroft,Liya Ren,Nigam H. Shah,Margot Sunshine,Rebecca Tang,Ryan Whaley,Stan Letovksy,Kenneth H. Buetow,Andrey Rzhetsky,Vincent Schächter,Bruno S. Sobral,Ugur Dogrusoz,Shannon K. McWeeney,Mirit I. Aladjem,Ewan Birney,Julio Collado-Vides,Susumu Goto,Michael Hucka,Nicolas Le Novère,Natalia Maltsev,Akhilesh Pandey,Paul Thomas,Edgar Wingender,Peter D. Karp,Chris Sander,Gary D. Bader +94 more
TL;DR: Thousands of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases, and this large amount of pathway data in a computable form will support visualization, analysis and biological discovery.
Journal ArticleDOI
Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma
A. Gordon Robertson,Juliann Shih,Juliann Shih,Christina Yau,Ewan A. Gibb,Junna Oba,Karen Mungall,Julian M. Hess,Vladislav Uzunangelov,Vonn Walter,Vonn Walter,Ludmila Danilova,Tara M. Lichtenberg,Melanie H. Kucherlapati,Patrick K. Kimes,Ming Tang,Alexander V Penson,Özgün Babur,Rehan Akbani,Christopher A. Bristow,Katherine A. Hoadley,Lisa Iype,Matthew T. Chang,Matthew T. Chang,Mohamed H. Abdel-Rahman,Adrian Ally,J. Todd Auman,Miruna Balasundaram,Saianand Balu,Christopher C. Benz,Rameen Beroukhim,Inanc Birol,Tom Bodenheimer,Jay Bowen,Reanne Bowlby,Denise Brooks,Rebecca Carlsen,Colleen M. Cebulla,Andrew D. Cherniack,Andrew D. Cherniack,Lynda Chin,Juok Cho,Eric Chuah,Sudha Chudamani,Carrie Cibulskis,Kristian Cibulskis,Leslie Cope,Sarah E. Coupland,Timothy Defreitas,John A. Demchok,Laurence Desjardins,Noreen Dhalla,Bita Esmaeli,Ina Felau,Martin L. Ferguson,Scott Frazer,Stacey Gabriel,Julie M. Gastier-Foster,Nils Gehlenborg,Mark Gerken,Jeffrey E. Gershenwald,Gad Getz,Klaus G. Griewank,Elizabeth A. Grimm,D. Neil Hayes,Apurva M. Hegde,David I. Heiman,Carmen Helsel,Shital Hobensack,Robert A. Holt,Alan P. Hoyle,Xin Hu,Carolyn M. Hutter,Martine J. Jager,Stuart R. Jefferys,Corbin D. Jones,Steven J.M. Jones,Cyriac Kandoth,Katayoon Kasaian,Jaegil Kim,Raju Kucherlapati,Eric S. Lander,Michael S. Lawrence,Alexander J. Lazar,Semin Lee,Kristen M. Leraas,Pei Lin,Jia Liu,Wen-Bin Liu,Laxmi Lolla,Yiling Lu,Yussanne Ma,Harshad S. Mahadeshwar,Odette Mariani,Marco A. Marra,Michael Mayo,Sam Meier,Shaowu Meng,Matthew Meyerson,Piotr A. Mieczkowski,Gordon B. Mills,Richard A. Moore,Lisle E. Mose,Andrew J. Mungall,Bradley A. Murray,Rashi Naresh,Michael S. Noble,Angeliki Pantazi,Michael Parfenov,Peter J. Park,Joel S. Parker,Charles M. Perou,Todd Pihl,Robert Pilarski,Alexei Protopopov,Amie Radenbaugh,Karan Rai,Nilsa C. Ramirez,Xiaojia Ren,Sheila Reynolds,Jeffrey Roach,Sergio Roman-Roman,Jason Roszik,Sara Sadeghi,Gordon Saksena,Xavier Sastre,Dirk Schadendorf,Jacqueline E. Schein,Lynn Schoenfield,Steven E. Schumacher,Jonathan G. Seidman,Sahil Seth,Geetika Sethi,Margi Sheth,Yan Shi,Carol L. Shields,Ilya Shmulevich,Janae V. Simons,Arun D. Singh,Payal Sipahimalani,Tara Skelly,Heidi J. Sofia,Matthew G. Soloway,Xingzhi Song,Marc-Henri Stern,Joshua M. Stuart,Qiang Sun,Huandong Sun,Angela Tam,Donghui Tan,Jiabin Tang,Roy Tarnuzzer,Barry S. Taylor,Nina Thiessen,Vesteinn Thorsson,Kane Tse,Umadevi Veluvolu,Roel G.W. Verhaak,Doug Voet,Yunhu Wan,Zhining Wang,John N. Weinstein,Matthew D. Wilkerson,Michelle D. Williams,Lisa Wise,Scott E. Woodman,Tina Wong,Ye Wu,Liming Yang,Lixing Yang,Jean C. Zenklusen,Jiashan Zhang,Hailei Zhang,Erik Zmuda +173 more
TL;DR: Within D3-UM, EIF1AX- and SRSF2/SF3B1-mutant tumors have distinct somatic copy number alterations and DNA methylation profiles, providing insight into the biology of these low- versus intermediate-risk clinical mutation subtypes.
Journal ArticleDOI
Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas.
Lawrence A. Donehower,Thierry Soussi,Anil Korkut,Yuexin Liu,Andre Schultz,Maria F. Cardenas,Xubin Li,Özgün Babur,Teng-Kuei Hsu,Olivier Lichtarge,John N. Weinstein,Rehan Akbani,David A. Wheeler +12 more
TL;DR: Tumors with TP53 mutations differ from their non-mutated counterparts in RNA, miRNA, and protein expression patterns, with mutant TP53 tumors displaying enhanced expression of cell cycle progression genes and proteins.
Journal ArticleDOI
The Human Tumor Atlas Network: Charting Tumor Transitions Across Space and Time at Single-Cell Resolution
Orit Rozenblatt-Rosen,Aviv Regev,Aviv Regev,Aviv Regev,Philipp Oberdoerffer,Tal Nawy,Anna Hupalowska,Jennifer Rood,Orr Ashenberg,Ethan Cerami,Robert J. Coffey,Emek Demir,Li Ding,Edward D. Esplin,James M. Ford,Jeremy Goecks,Sharmistha Ghosh,Joe W. Gray,Justin Guinney,Justin Guinney,Sean E. Hanlon,Shannon K. Hughes,E. Shelley Hwang,Christine A. Iacobuzio-Donahue,Judit Jané-Valbuena,Bruce E. Johnson,Ken S. Lau,Tracy Lively,Sarah A. Mazzilli,Dana Pe'er,Sandro Santagata,Sandro Santagata,Alex K. Shalek,Denis Schapiro,Denis Schapiro,Michael Snyder,Peter K. Sorger,Avrum E. Spira,Avrum E. Spira,Sudhir Srivastava,Kai Tan,Kai Tan,Robert West,Elizabeth H. Williams,Elizabeth H. Williams,Denise Aberle,Samuel Achilefu,Foluso O. Ademuyiwa,Andrew Adey,Rebecca Aft,Rachana Agarwal,Ruben A. Aguilar,Fatemeh Alikarami,Viola Allaj,Christopher I. Amos,Robert A. Anders,Michael R. Angelo,Kristen Anton,Jon C. Aster,Özgün Babur,Amir Bahmani,Akshay Balsubramani,David M. Barrett,Jennifer Beane,Diane Bender,Kathrin M. Bernt,Lynne D. Berry,Courtney Betts,Julie Bletz,Katie Blise,Adrienne Boire,Genevieve M. Boland,Alexander D. Borowsky,Kristopher R. Bosse,Matthew J. Bott,Edward S. Boyden,James D. Brooks,Raphael Bueno,Erik A. Burlingame,Qiuyin Cai,Joshua D. Campbell,Wagma Caravan,Hassan Chaib,Joseph M. Chan,Young Hwan Chang,Deyali Chatterjee,Ojasvi Chaudhary,Alyce A. Chen,Bob Chen,Changya Chen,Chia hui Chen,Feng Chen,Yuan Chen,Milan G. Chheda,Koei Chin,Roxanne Chiu,Shih Kai Chu,Rodrigo Chuaqui,Jaeyoung Chun,Luis Cisneros,Graham A. Colditz,Kristina A. Cole,Natalie B. Collins,Kévin Contrepois,Lisa M. Coussens,Allison L. Creason,Daniel J. Crichton,Christina Curtis,Tanja M. Davidsen,Sherri R. Davies,Ino de Bruijn,Laura DelloStritto,Angelo M. De Marzo,David G. DeNardo,Dinh Diep,Sharon J. Diskin,Xengie Doan,Julia L. Drewes,Stephen Dubinett,Michael A. Dyer,Jacklynn V. Egger,Jennifer Eng,Barbara E. Engelhardt,Graham Erwin,Laura J. Esserman,Alex Felmeister,Heidi S. Feiler,Ryan C. Fields,Stephen A. Fisher,Keith T. Flaherty,Jennifer Flournoy,Angelo Fortunato,Allison Frangieh,Jennifer L. Frye,Robert S. Fulton,Danielle Galipeau,Siting Gan,Jianjiong Gao,Long Gao,Peng Gao,Vianne R. Gao,Tim Geiger,Ajit George,Gad Getz,Marios Giannakis,David L Gibbs,William E. Gillanders,Simon P. Goedegebuure,Alanna Gould,Kate H.C. Gowers,William J. Greenleaf,Jeremy Gresham,Jennifer L. Guerriero,Tuhin Kumar Guha,Alexander R. Guimaraes,David A. Gutman,Nir Hacohen,Sean E. Hanlon,Casey R. Hansen,Olivier Harismendy,Kathleen A. Harris,Aaron N. Hata,Akimasa Hayashi,Cody N. Heiser,Karla Helvie,John M. Herndon,Gilliam Hirst,Frank Hodi,Travis J. Hollmann,Aaron M. Horning,James J. Hsieh,Shannon Hughes,Won Jae Huh,Stephen P. Hunger,Shelley Hwang,Heba Ijaz,Benjamin Izar,Connor A. Jacobson,Sam M. Janes,Reyka G Jayasinghe,Lihua Jiang,Brett Johnson,Bruce E. Johnson,Tao Ju,Humam Kadara,Klaus H. Kaestner,Jacob Kagan,Lukas Kalinke,Robert L. Keith,Aziz Khan,Warren A. Kibbe,Albert H. Kim,Erika Kim,Junhyong Kim,Annette Kolodzie,Mateusz Kopytra,Eran Kotler,Robert Krueger,Kostyantyn Krysan,Anshul Kundaje,Uri Ladabaum,Blue B. Lake,Huy Lam,Rozelle Laquindanum,Ashley M. Laughney,Hayan Lee,Marc E. Lenburg,Carina A. Leonard,Ignaty Leshchiner,Rochelle Levy,Jerry Li,Christine G. Lian,Kian-Huat Lim,Jia-Ren Lin,Yiyun Lin,Qi Liu,Ruiyang Liu,William J.R. Longabaugh,Teri A. Longacre,Cynthia X. Ma,Mary Catherine Macedonia,Tyler Madison,Christopher G. Maher,Anirban Maitra,Netta Makinen,Danika Makowski,Carlo C. Maley,Zoltan Maliga,Diego Mallo,John M. Maris,Nick Markham,Jeffrey R. Marks,Daniel Martinez,Robert J. Mashl,Ignas Masilionais,Jennifer Mason,Joan Massagué,Pierre P. Massion,Marissa Mattar,Richard Mazurchuk,Linas Mazutis,Eliot T. McKinley,Joshua F. McMichael,Daniel T. Merrick,Matthew Meyerson,Julia R. Miessner,Gordon B. Mills,Meredith A. Mills,Suman B. Mondal,Motomi Mori,Yuriko Mori,Elizabeth Moses,Yael P. Mosse,Jeremy L. Muhlich,George F. Murphy,Nicholas Navin,Michel Nederlof,Reid M. Ness,Stephanie A. Nevins,Milen Nikolov,Ajit J. Nirmal,Garry P. Nolan,Edward Novikov,Brendan O'Connell,Michael Offin,Stephen T. Oh,Anastasiya Olson,Alex Ooms,Miguel Ossandon,Kouros Owzar,Swapnil Parmar,Tasleema Patel,Gary J. Patti,Itsik Pe'er,Tao Peng,Daniel Persson,Marvin Petty,Hanspeter Pfister,Kornelia Polyak,Kamyar Esmaeili Pourfarhangi,Sidharth V. Puram,Qi Qiu,Álvaro Quintanal-Villalonga,Arjun Raj,Marisol A. Ramirez-Solano,Rumana Rashid,Ashley N. Reeb,Mary E. Reid,Adam C. Resnick,Sheila Reynolds,Jessica L. Riesterer,Scott J. Rodig,Joseph T. Roland,Sonia Rosenfield,Asaf Rotem,Sudipta Roy,Charles M. Rudin,Marc D. Ryser,Maria Santi-Vicini,Kazuhito Sato,Deborah Schrag,Nikolaus Schultz,Cynthia L. Sears,Rosalie C. Sears,Subrata Sen,Triparna Sen,Alex K. Shalek,Jeff Sheng,Quanhu Sheng,Kooresh I. Shoghi,Martha J. Shrubsole,Yu Shyr,Alexander B. Sibley,Kiara Siex,Alan J. Simmons,Dinah S. Singer,Shamilene Sivagnanam,Michal Slyper,Artem Sokolov,Sheng-Kwei Song,Austin N. Southard-Smith,Avrum Spira,Janet Stein,Phillip B. Storm,Elizabeth H. Stover,Siri H. Strand,Timothy Su,Damir Sudar,Ryan P. Sullivan,Lea F. Surrey,Mario L. Suvà,Nadezhda V. Terekhanova,Luke Ternes,Lisa Thammavong,Guillaume Thibault,George Thomas,Vesteinn Thorsson,Ellen Todres,Linh M. Tran,Madison Tyler,Yasin Uzun,Anil Vachani,Eliezer M. Van Allen,Simon N. Vandekar,Deborah J. Veis,Sébastien Vigneau,Arastoo Vossough,Angela J. Waanders,Nikhil Wagle,Liang-Bo Wang,Michael C. Wendl,Robert B. West,Chi yun Wu,Hao Wu,Hung Yi Wu,Matthew A. Wyczalkowski,Yubin Xie,Xiaolu Yang,Clarence Yapp,Wenbao Yu,Yinyin Yuan,Dadong Zhang,Kun Zhang,Mianlei Zhang,Nan Zhang,Yantian Zhang,Yanyan Zhao,Daniel Cui Zhou,Zilu Zhou,Houxiang Zhu,Qin Zhu,Xiangzhu Zhu,Yuankun Zhu,Xiaowei Zhuang +373 more
TL;DR: The Human Tumor Atlas Network (HTAN), part of the NCI Cancer Moonshot Initiative, will establish a clinical, experimental, computational, and organizational framework to generate informative and accessible three-dimensional atlases of cancer transitions for a diverse set of tumor types.