M
Melissa S. Cline
Researcher at University of California, Santa Cruz
Publications - 33
Citations - 6425
Melissa S. Cline is an academic researcher from University of California, Santa Cruz. The author has contributed to research in topics: Alternative splicing & Genome. The author has an hindex of 18, co-authored 33 publications receiving 6020 citations.
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An integrated encyclopedia of DNA elements in the human genome
Ian Dunham,Anshul Kundaje,Shelley Force Aldred,Patrick J. Collins,Carrie A. Davis,Francis Doyle,Charles B. Epstein,Seth Frietze,Jennifer Harrow,Rajinder Kaul,Jainab Khatun,Bryan R. Lajoie,Stephen G. Landt,Bum Kyu Lee,Florencia Pauli,Kate R. Rosenbloom,Peter J. Sabo,Alexias Safi,Amartya Sanyal,Noam Shoresh,Jeremy M. Simon,Lingyun Song,Nathan D. Trinklein,Robert C. Altshuler,Ewan Birney,James B. Brown,Chao Cheng,Sarah Djebali,Xianjun Dong,Jason Ernst,Terrence S. Furey,Mark Gerstein,Belinda Giardine,Melissa C. Greven,Ross C. Hardison,Robert S. Harris,Javier Herrero,Michael M. Hoffman,Sowmya Iyer,Manolis Kellis,Pouya Kheradpour,Timo Lassmann,Qiang Li,Xinying Lin,Georgi K. Marinov,Angelika Merkel,Ali Mortazavi,Stephen C. J. Parker,Timothy E. Reddy,Joel Rozowsky,Felix Schlesinger,Robert E. Thurman,Jie Wang,Lucas D. Ward,Troy W. Whitfield,Steven P. Wilder,Weisheng Wu,Hualin S. Xi,Kevin Y. Yip,Jiali Zhuang,Bradley E. Bernstein,Eric D. Green,Chris Gunter,Michael Snyder,Michael J. Pazin,Rebecca F. Lowdon,Laura A.L. Dillon,Leslie B. Adams,Caroline J. Kelly,Julia Zhang,Judith R. Wexler,Peter J. Good,Elise A. Feingold,Gregory E. Crawford,Job Dekker,Laura Elnitski,Peggy J. Farnham,Morgan C. Giddings,Thomas R. Gingeras,Roderic Guigó,Tim Hubbard,W. James Kent,Jason D. Lieb,Elliott H. Margulies,Richard M. Myers,John A. Stamatoyannopoulos,Scott A. Tenenbaum,Zhiping Weng,Kevin P. White,Barbara J. Wold,Yanbao Yu,John A. Wrobel,Brian A. Risk,Harsha P. Gunawardena,Heather C. Kuiper,Christopher W. Maier,Ling Xie,Xian Chen,Tarjei S. Mikkelsen,Shawn M. Gillespie,Alon Goren,Oren Ram,Xiaolan Zhang,Li Wang,Robbyn Issner,Michael Coyne,Timothy Durham,Manching Ku,Thanh Truong,Matthew L. Eaton,Alexander Dobin,Andrea Tanzer,Julien Lagarde,Wei Lin,Chenghai Xue,Brian A. Williams,Chris Zaleski,Marion S. Röder,Felix Kokocinski,Rehab F. Abdelhamid,Tyler Alioto,Igor Antoshechkin,Michael T. Baer,Philippe Batut,Ian Bell,Kimberly Bell,Sudipto K. Chakrabortty,Jacqueline Chrast,Joao Curado,Thomas Derrien,Jorg Drenkow,Erica Dumais,Jackie Dumais,Radha Duttagupta,Megan Fastuca,Kata Fejes-Toth,Pedro G. Ferreira,Sylvain Foissac,Melissa J. Fullwood,Hui Gao,David Gonzalez,Assaf Gordon,Cédric Howald,Sonali Jha,Rory Johnson,Philipp Kapranov,Brandon King,Colin Kingswood,Guoliang Li,Oscar Junhong Luo,Eddie Park,Jonathan B. Preall,Kimberly Presaud,Paolo Ribeca,Daniel Robyr,Xiaoan Ruan,Michael Sammeth,Kuljeet Singh Sandhu,Lorain Schaeffer,Lei-Hoon See,Atif Shahab,Jørgen Skancke,Ana Maria Suzuki,Hazuki Takahashi,Hagen Tilgner,Diane Trout,Nathalie Walters,Huaien Wang,Yoshihide Hayashizaki,Alexandre Reymond,Stylianos E. Antonarakis,Gregory J. Hannon,Yijun Ruan,Piero Carninci,Cricket A. Sloan,Katrina Learned,Venkat S. Malladi,Matthew C. Wong,Galt P. Barber,Melissa S. Cline,Timothy R. Dreszer,Steven G. Heitner,Donna Karolchik,Vanessa M. Kirkup,Laurence R. Meyer,Jeffrey C. Long,Morgan Maddren,Brian J. Raney,Linda L. Grasfeder,Paul G. Giresi,Anna Battenhouse,Nathan C. Sheffield,Kimberly A. Showers,Darin London,Akshay Bhinge,Christopher Shestak,Matthew R. Schaner,Seul K.C. Kim,Zhuzhu Zhang,Piotr A. Mieczkowski,Joanna O. Mieczkowska,Zheng Liu,Ryan M. McDaniell,Yunyun Ni,Naim U. Rashid,Min Jae Kim,Sheera Adar,Zhancheng Zhang,Tianyuan Wang,Deborah R. Winter,Damian Keefe,Vishwanath R. Iyer,Meizhen Zheng,Ping Wang,Jason Gertz,Jost Vielmetter,Partridge Ec,Katherine E. Varley,Clarke Gasper,Anita Bansal,Shirley Pepke,Preti Jain,Henry Amrhein,Kevin M. Bowling,Michael Anaya,Marie K. Cross,Michael Muratet,Kimberly M. Newberry,Kenneth McCue,Amy S. Nesmith,Katherine I. Fisher-Aylor,Barbara N. Pusey,Gilberto DeSalvo,Stephanie L. Parker,Sreeram Balasubramanian,Nicholas S. Davis,Sarah Meadows,Tracy Eggleston,J. Scott Newberry,Shawn Levy,Devin Absher,Wing Hung Wong,Matthew J. Blow,Axel Visel,Len A. Pennachio,Hanna Petrykowska,Alexej Abyzov,Bronwen Aken,Daniel Barrell,Gemma Barson,Andrew Berry,Alexandra Bignell,Veronika Boychenko,Giovanni Bussotti,Claire Davidson,Gloria Despacio-Reyes,Mark Diekhans,Iakes Ezkurdia,Adam Frankish,James Gilbert,José M. González,Ed Griffiths,Rachel A. Harte,David A. Hendrix,Toby Hunt,Irwin Jungreis,M. Kay,Ekta Khurana,Jing Leng,Michael F. Lin,Jane E. Loveland,Zhi Lu,Deepa Manthravadi,Marco Mariotti,Jonathan M. Mudge,Gaurab Mukherjee,Cedric Notredame,Baikang Pei,Jose Manuel Rodriguez,Gary Saunders,Andrea Sboner,Stephen M. J. Searle,Cristina Sisu,Catherine E. Snow,Charles A. Steward,Electra Tapanari,Michael L. Tress,Marijke J. van Baren,Stefan Washietl,Laurens G. Wilming,Amonida Zadissa,Zhengdong D. Zhang,Michael R. Brent,David Haussler,Alfonso Valencia,Nicholas Addleman,Roger P. Alexander,Raymond K. Auerbach,Suganthi Balasubramanian,Keith Bettinger,Nitin Bhardwaj,Alan P. Boyle,Alina R. Cao,Philip Cayting,Alexandra Charos,Yong Cheng,Catharine L. Eastman,Ghia Euskirchen,Joseph D. Fleming,Fabian Grubert,Lukas Habegger,Manoj Hariharan,Arif Harmanci,Sushma Iyengar,Victor X. Jin,Konrad J. Karczewski,Maya Kasowski,Phil Lacroute,Hugo Y. K. Lam,Nathan Lamarre-Vincent,Jin Lian,Marianne Lindahl-Allen,Renqiang Min,Benoit Miotto,Hannah Monahan,Zarmik Moqtaderi,Xinmeng J. Mu,Henriette O'Geen,Zhengqing Ouyang,Dorrelyn Patacsil,Debasish Raha,Lucía Ramírez,Brian Reed,Minyi Shi,Teri Slifer,Heather Witt,Linfeng Wu,Xiaoqin Xu,Koon-Kiu Yan,Xinqiong Yang,Kevin Struhl,Sherman M. Weissman,Luiz O. F. Penalva,Subhradip Karmakar,Raj R. Bhanvadia,Alina Choudhury,Marc Domanus,Lijia Ma,Jennifer L. Moran,Alec Victorsen,Thomas O. Auer,Lazaro Centanin,Michael P. Eichenlaub,Franziska Gruhl,Stephan Heermann,Burkhard Hoeckendorf,Daigo Inoue,Tanja Kellner,Stephan Kirchmaier,Claudia Mueller,Robert Reinhardt,Lea Schertel,Stephanie Schneider,Rebecca Sinn,Beate Wittbrodt,Jochen Wittbrodt,E. Christopher Partridge,Gaurav Jain,Gayathri Balasundaram,Daniel Bates,Rachel Byron,Theresa K. Canfield,Morgan Diegel,Douglas Dunn,Abigail K. Ebersol,Tristan Frum,Kavita Garg,Erica Gist,R. Scott Hansen,Lisa Boatman,Eric Haugen,Richard Humbert,Audra K. Johnson,Ericka M. Johnson,Tattyana V. Kutyavin,Kristen Lee,Dimitra Lotakis,Matthew T. Maurano,Shane Neph,Fiedencio V. Neri,Eric D. Nguyen,Hongzhu Qu,Alex Reynolds,Vaughn Roach,Eric Rynes,Minerva E. Sanchez,Richard Sandstrom,Anthony Shafer,Andrew B. Stergachis,Sean Thomas,Benjamin Vernot,Jeff Vierstra,Shinny Vong,Hao Wang,Molly Weaver,Yongqi Yan,Miaohua Zhang,Joshua M. Akey,M. A. Bender,Michael O. Dorschner,Mark Groudine,Michael J. MacCoss,Patrick A. Navas,George Stamatoyannopoulos,Kathryn Beal,Alvis Brazma,Paul Flicek,Nathan R. Johnson,Margus Lukk,Nicholas M. Luscombe,Daniel Sobral,Juan M. Vaquerizas,Serafim Batzoglou,Arend Sidow,Nadine Hussami,Sofia Kyriazopoulou-Panagiotopoulou,Max Libbrecht,Marc A. Schaub,Webb Miller,Peter J. Bickel,Balazs Banfai,Nathan Boley,Haiyan Huang,Jingyi Jessica Li,William Stafford Noble,Jeff A. Bilmes,Orion J. Buske,Avinash Das Sahu,Peter V. Kharchenko,Peter J. Park,Dannon Baker,James Taylor,Lucas Lochovsky +442 more
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
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.
Journal ArticleDOI
Integrated Molecular Characterization of Uterine Carcinosarcoma
Andrew D. Cherniack,Hui Shen,Vonn Walter,Chip Stewart,Bradley A. Murray,Reanne Bowlby,Xin Hu,Shiyun Ling,Robert A. Soslow,Russell Broaddus,Rosemary E. Zuna,Gordon Robertson,Peter W. Laird,Raju Kucherlapati,Gordon B. Mills,Rehan Akbani,Adrian Ally,J. Todd Auman,Miruna Balasundaram,Saianand Balu,Stephen B. Baylin,Rameen Beroukhim,Tom Bodenheimer,Faina Bogomolniy,Lori Boice,Moiz S. Bootwalla,Jay Bowen,Russell R. Broaddus,Denise Brooks,Rebecca Carlsen,Juok Cho,Eric Chuah,Sudha Chudamani,Kristian Cibulskis,Melissa S. Cline,Fanny Dao,Mutch David,John A. Demchok,Noreen Dhalla,Sean C. Dowdy,Ina Felau,Martin L. Ferguson,Scott Frazer,Jessica Frick,Stacey Gabriel,Julie M. Gastier-Foster,Nils Gehlenborg,Mark Gerken,Gad Getz,Manaswi Gupta,David Haussler,D. Neil Hayes,David I. Heiman,Julian M. Hess,Katherine A. Hoadley,Robert Hoffmann,Robert A. Holt,Alan P. Hoyle,Mei Huang,Carolyn M. Hutter,Stuart R. Jefferys,Steven J.M. Jones,Corbin D. Jones,Rupa S. Kanchi,Cyriac Kandoth,Katayoon Kasaian,Sarah E. Kerr,Jaegil Kim,Phillip H. Lai,Eric S. Lander,Michael S. Lawrence,Darlene Lee,Kristen M. Leraas,Ignaty Leshchiner,Douglas A. Levine,Tara M. Lichtenberg,Pei Lin,Jia Liu,Wen-Bin Liu,Yuexin Liu,Laxmi Lolla,Yiling Lu,Yussanne Ma,Dennis T. Maglinte,Marco A. Marra,Michael Mayo,Shaowu Meng,Matthew Meyerson,Piotr A. Mieczkowski,Richard A. Moore,Lisle E. Mose,Andrew J. Mungall,Karen Mungall,Rashi Naresh,Michael S. Noble,Narciso Olvera,Joel S. Parker,Charles M. Perou,Amy H. Perou,Todd Pihl,Amie Radenbaugh,Nilsa C. Ramirez,W. Kimryn Rathmell,Jeffrey Roach,A. Gordon Robertson,Sara Sadeghi,Gordon Saksena,Helga B. Salvesen,Jacqueline E. Schein,Steven E. Schumacher,Margi Sheth,Yan Shi,Juliann Shih,Janae V. Simons,Payal Sipahimalani,Tara Skelly,Heidi J. Sofia,Matthew G. Soloway,Carrie Sougnez,Charlie Sun,Angela Tam,Donghui Tan,Roy Tarnuzzer,Nina Thiessen,Leigh B. Thorne,Kane Tse,Jill Tseng,David Van Den Berg,Umadevi Veluvolu,Roel G.W. Verhaak,Doug Voet,Amanda von Bismarck,Yunhu Wan,Zhining Wang,Chen Wang,John N. Weinstein,Daniel J. Weisenberger,Matthew D. Wilkerson,Boris Winterhoff,Lisa Wise,Tina Wong,Ye Wu,Liming Yang,Jean C. Zenklusen,Jiashan Zhang,Hailei Zhang,Wei Zhang,Jing chun Zhu,Erik Zmuda +148 more
TL;DR: UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features and a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases was attributable to epigenetic alterations at microRNA promoters.
Journal ArticleDOI
Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser
Melissa S. Cline,Brian Craft,Teresa Swatloski,Mary Goldman,Singer Ma,David Haussler,Jingchun Zhu +6 more
TL;DR: The UCSC Cancer Genomics Browser offers interactive visualization and exploration of TCGA genomic, phenotypic, and clinical data, as produced by the Cancer Genome Atlas Research Network.
Journal ArticleDOI
Splicing biomarkers of disease severity in myotonic dystrophy
Masayuki Nakamori,Krzysztof Sobczak,Araya Puwanant,Steve Welle,Katy Eichinger,Shree Pandya,Jeannne Dekdebrun,Chad Heatwole,Michael P. McDermott,Tian Chen,Melissa S. Cline,Rabi Tawil,Robert Osborne,Thurman M. Wheeler,Maurice S. Swanson,Richard T. Moxley,Charles A. Thornton +16 more
TL;DR: To develop RNA splicing biomarkers of disease severity and therapeutic response in myotonic dystrophy type 1 (DM1) and type 2 (DM2) and to establish a database of these biomarkers and describe their mechanisms of action.