I
Isidore Rigoutsos
Researcher at Thomas Jefferson University
Publications - 222
Citations - 24642
Isidore Rigoutsos is an academic researcher from Thomas Jefferson University. The author has contributed to research in topics: Gene & microRNA. The author has an hindex of 63, co-authored 215 publications receiving 22217 citations. Previous affiliations of Isidore Rigoutsos include Brown University & New York University.
Papers
More filters
Journal ArticleDOI
A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes
Kevin Charles Miranda,Tien Huynh,Yvonne Tay,Yen-Sin Ang,Wai Leong Tam,Andrew M. Thomson,Bing Lim,Bing Lim,Isidore Rigoutsos +8 more
TL;DR: Rna22 as discussed by the authors identifies microRNA binding sites and their corresponding heteroduplexes, and then identifies the targeting microRNAs by finding putative microRN binding sites in the sequence of interest.
Journal ArticleDOI
The draft genome of Ciona intestinalis : insights into chordate and vertebrate origins
Paramvir S. Dehal,Yutaka Satou,Robert K. Campbell,Jarrod Chapman,Bernard M. Degnan,Anthony W. De Tomaso,Brad Davidson,Anna Di Gregorio,Maarten D. Sollewijn Gelpke,David Goodstein,Naoe Harafuji,Kenneth E. M. Hastings,Isaac Ho,Kohji Hotta,Wayne Huang,Takeshi Kawashima,Patrick Lemaire,Diego Martinez,Ian A. Meinertzhagen,Simona Necula,Masaru Nonaka,Nik Putnam,Sam Rash,Hidetoshi Saiga,Masanobu Satake,Astrid Terry,Lixy Yamada,Hong Gang Wang,Satoko Awazu,Kaoru Azumi,Jeffrey L. Boore,Margherita Branno,Stephen T. Chin-Bow,Rosaria DeSantis,Sharon A. Doyle,Pilar Francino,David N. Keys,David N. Keys,Shinobu Haga,Hiroko Hayashi,Kyosuke Hino,Kaoru S. Imai,Kazuo Inaba,Shungo Kano,Shungo Kano,Kenji Kobayashi,Mari Kobayashi,Byung In Lee,Kazuhiro W. Makabe,Chitra Manohar,Giorgio Matassi,Mónica Medina,Yasuaki Mochizuki,Steve Mount,Tomomi Morishita,Sachiko Miura,Akie Nakayama,Satoko Nishizaka,Hisayo Nomoto,Fumiko Ohta,Kazuko Oishi,Isidore Rigoutsos,Masako Sano,Akane Sasaki,Yasunori Sasakura,Eiichi Shoguchi,Tadasu Shin-I,Antoinetta Spagnuolo,Didier Y.R. Stainier,Miho Suzuki,Olivier Tassy,Naohito Takatori,Miki Tokuoka,Kasumi Yagi,Fumiko Yoshizaki,Shuichi Wada,Cindy Zhang,P. Douglas Hyatt,Frank W. Larimer,Chris Detter,Norman A. Doggett,Tijana Glavina,Trevor Hawkins,Paul G. Richardson,Susan Lucas,Yuji Kohara,Michael Levine,Nori Satoh,Daniel S. Rokhsar,Daniel S. Rokhsar +89 more
TL;DR: A draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis, is generated, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development.
Journal ArticleDOI
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation
TL;DR: The findings demonstrate the abundance of CDS-located miRNA targets, some of which can be species-specific, and support an augmented model whereby animal miRNAs exercise their control on mRNAs through targets that can reside beyond the 3′ untranslated region.
Journal ArticleDOI
Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma
Benjamin J. Raphael,Ralph H. Hruban,Andrew J. Aguirre,Richard A. Moffitt,Jen Jen Yeh,Chip Stewart,A. Gordon Robertson,Andrew D. Cherniack,Manaswi Gupta,Gad Getz,Stacey Gabriel,Matthew Meyerson,Carrie Cibulskis,Suzanne S. Fei,Toshinori Hinoue,Hui Shen,Peter W. Laird,Shiyun Ling,Yiling Lu,Gordon B. Mills,Rehan Akbani,Phillipe Loher,Eric Londin,Isidore Rigoutsos,Aristeidis G. Telonis,Ewan A. Gibb,Anna Goldenberg,Aziz M. Mezlini,Katherine A. Hoadley,Eric A. Collisson,Eric S. Lander,Bradley A. Murray,Julian M. Hess,Mara Rosenberg,Louis Bergelson,Hailei Zhang,Juok Cho,Grace Tiao,Jaegil Kim,Dimitri Livitz,Ignaty Leshchiner,Brendan Reardon,Eliezer M. Van Allen,Atanas Kamburov,Rameen Beroukhim,Gordon Saksena,Steven E. Schumacher,Michael S. Noble,David I. Heiman,Nils Gehlenborg,Michael S. Lawrence,Volkan Adsay,Gloria M. Petersen,David S. Klimstra,Nabeel Bardeesy,Mark D.M. Leiserson,Reanne Bowlby,Katayoon Kasaian,Inanc Birol,Karen Mungall,Sara Sadeghi,John N. Weinstein,Paul T. Spellman,Yuexin Liu,Laufey T. Amundadottir,Joel E. Tepper,Aatur D. Singhi,Rajiv Dhir,Drwiega Paul,Thomas C. Smyrk,Lizhi Zhang,Paula Kim,Jay Bowen,Jessica Frick,Julie M. Gastier-Foster,Mark Gerken,Kevin Lau,Kristen M. Leraas,Tara M. Lichtenberg,Nilsa C. Ramirez,Jeremy Renkel,Mark E. Sherman,Lisa Wise,Peggy Yena,Erik Zmuda,Juliann Shih,Adrian Ally,Miruna Balasundaram,Rebecca Carlsen,Andy Chu,Eric Chuah,Amanda Clarke,Noreen Dhalla,Robert A. Holt,Steven J.M. Jones,Darlene Lee,Yussanne Ma,Marco A. Marra,Michael Mayo,Richard A. Moore,Andrew J. Mungall,Jacqueline E. Schein,Payal Sipahimalani,Angela Tam,Nina Thiessen,Kane Tse,Tina Wong,Denise Brooks,J. Todd Auman,Saianand Balu,Tom Bodenheimer,D. Neil Hayes,Alan P. Hoyle,Stuart R. Jefferys,Corbin D. Jones,Shaowu Meng,Piotr A. Mieczkowski,Lisle E. Mose,Charles M. Perou,Amy H. Perou,Jeffrey Roach,Yan Shi,Janae V. Simons,Tara Skelly,Matthew G. Soloway,Donghui Tan,Umadevi Veluvolu,Joel S. Parker,Matthew D. Wilkerson,Anil Korkut,Yasin Senbabaoglu,Patrick Burch,Robert R. McWilliams,Kari G. Chaffee,Ann L. Oberg,Wei Zhang,Marie-Claude Gingras,David A. Wheeler,Liu Xi,Monique Albert,John M. S. Bartlett,Harman Sekhon,Yeager Stephen,Zaren Howard,Miller Judy,Anne Breggia,Rachna T. Shroff,Sudha Chudamani,Jia Liu,Laxmi Lolla,Rashi Naresh,Todd Pihl,Qiang Sun,Yunhu Wan,Ye Wu,Smith Jennifer,Kevin Roggin,Karl-Friedrich Becker,Madhusmita Behera,Joseph J. Bennett,Lori Boice,Eric J. Burks,Carlos Gilberto Carlotti Junior,John Chabot,Daniela Pretti da Cunha Tirapelli,Jose Sebastião dos Santos,Michael Dubina,Jennifer M. Eschbacher,Mei Huang,Lori Huelsenbeck-Dill,Roger Jenkins,Alexey Karpov,Rafael Kemp,Vladimir Lyadov,Shishir K. Maithel,Georgy Manikhas,Eric Montgomery,Houtan Noushmehr,Adeboye O. Osunkoya,Taofeek K. Owonikoko,Oxana Paklina,Olga Potapova,Suresh S. Ramalingam,W. Kimryn Rathmell,Kimberly M. Rieger-Christ,Charles Saller,Galiya Setdikova,Alexey Shabunin,Gabriel Sica,Tao Su,Travis Sullivan,Pat Swanson,Katherine Tarvin,Michael Tavobilov,Leigh B. Thorne,Stefan Urbanski,Olga Voronina,Timothy C. Wang,Daniel Crain,Erin Curley,Johanna Gardner,David Mallery,Scott J. Morris,Joseph Paulauskis,Robert Penny,Candace Shelton,Troy Shelton,Klaus-Peter Janssen,Oliver F. Bathe,Nathan Bahary,Julia Slotta-Huspenina,Amber L. Johns,Hanina Hibshoosh,Rosa F. Hwang,Antonia R. Sepulveda,Amie Radenbaugh,Stephen B. Baylin,Mario Berrios,Moiz S. Bootwalla,Andrea Holbrook,Phillip H. Lai,Dennis T. Maglinte,Swapna Mahurkar,Timothy J. Triche,David Van Den Berg,Daniel J. Weisenberger,Lynda Chin,Raju Kucherlapati,Melanie H. Kucherlapati,Angeliki Pantazi,Peter J. Park,Doug Voet,Pei Lin,Scott Frazer,Timothy Defreitas,Sam Meier,Sun Young Kwon,Yong Hoon Kim,Sang Jae Park,Sung Sik Han,Seong Hoon Kim,Hark Kyun Kim,Emma E. Furth,Margaret A. Tempero,Chris Sander,Andrew V. Biankin,David K. Chang,Peter Bailey,Anthony J. Gill,James G. Kench,Sean M. Grimmond,Russell Postier,Rosemary E. Zuna,Hugues Sicotte,John A. Demchok,Martin L. Ferguson,Carolyn M. Hutter,Kenna R. Mills Shaw,Margi Sheth,Heidi J. Sofia,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jiashan Zhang,Ina Felau,Jean C. Zenklusen +265 more
TL;DR: An integrated multi-platform analysis of 150 pancreatic ductal adenocarcinoma specimens reveals a complex molecular landscape of PDAC and provides a roadmap for precision medicine.
Journal ArticleDOI
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.
Falk Warnecke,Peter Luginbuhl,Natalia Ivanova,Majid Ghassemian,Toby Richardson,Toby Richardson,Justin T. Stege,Michelle H. Cayouette,Alice C. McHardy,Gordana Djordjevic,Nahla Aboushadi,Rotem Sorek,Susannah G. Tringe,Mircea Podar,Hector Garcia Martin,Victor Kunin,Daniel Dalevi,Julita Madejska,Edward Kirton,Darren Platt,Ernest Szeto,Asaf Salamov,Kerrie Barry,Natalia Mikhailova,Nikos C. Kyrpides,Eric G. Matson,Elizabeth A. Ottesen,Xinning Zhang,Myriam Hernandez,Catalina Patricia Morales Murillo,Luis G. Acosta,Isidore Rigoutsos,Giselle Tamayo,Brian D. Green,Cathy Chang,Edward M. Rubin,Eric J. Mathur,Eric J. Mathur,Dan E. Robertson,Philip Hugenholtz,Jared R. Leadbetter +40 more
TL;DR: In this article, a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding Nasutitermes species (which do not contain cellulose-fermenting protozoa) was performed to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis.