M
Marijke J. van Baren
Researcher at University of California, Santa Cruz
Publications - 12
Citations - 19461
Marijke J. van Baren is an academic researcher from University of California, Santa Cruz. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 11, co-authored 12 publications receiving 17211 citations. Previous affiliations of Marijke J. van Baren include Monterey Bay Aquarium Research Institute & Washington University in St. Louis.
Papers
More filters
Journal ArticleDOI
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell,Cole Trapnell,Brian A. Williams,Geo Pertea,Ali Mortazavi,Gordon Kwan,Marijke J. van Baren,Steven L. Salzberg,Barbara J. Wold,Lior Pachter +9 more
TL;DR: The results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.
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
The developmental transcriptome of Drosophila melanogaster
Brenton R. Graveley,Angela N. Brooks,Joseph W. Carlson,Michael O. Duff,Jane M. Landolin,Li Yang,Carlo G. Artieri,Marijke J. van Baren,Nathan Boley,Benjamin W. Booth,James B. Brown,Lucy Cherbas,Carrie A. Davis,Alexander Dobin,Renhua Li,Wei Lin,John H. Malone,Nicolas R. Mattiuzzo,David Scott Miller,David Sturgill,Brian B. Tuch,Brian B. Tuch,Chris Zaleski,Dayu Zhang,Marco Blanchette,Marco Blanchette,Sandrine Dudoit,Brian D. Eads,Richard E. Green,Ann S. Hammonds,Lichun Jiang,Phil Kapranov,Laura Langton,Norbert Perrimon,Jeremy E. Sandler,Kenneth H. Wan,Aarron T. Willingham,Yu Zhang,Yi Zou,Justen Andrews,Peter J. Bickel,Steven E. Brenner,Michael R. Brent,Peter Cherbas,Thomas R. Gingeras,Thomas R. Gingeras,Roger A. Hoskins,Thomas C. Kaufman,Brian Oliver,Susan E. Celniker +49 more
TL;DR: 111,195 new elements are identified, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches.
Journal ArticleDOI
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Sushmita Roy,Jason Ernst,Peter V. Kharchenko,Pouya Kheradpour,Nicolas Nègre,Matthew L. Eaton,Jane M. Landolin,Christopher A. Bristow,Lijia Ma,Michael F. Lin,Stefan Washietl,Bradley I. Arshinoff,Ferhat Ay,Patrick E. Meyer,Nicolas Robine,Nicole L. Washington,Luisa Di Stefano,Eugene Berezikov,Christopher D. Brown,Rogerio Candeias,Joseph W. Carlson,Adrian Carr,Irwin Jungreis,Daniel Marbach,Rachel Sealfon,Michael Y. Tolstorukov,Sebastian Will,Artyom A. Alekseyenko,Carlo G. Artieri,Benjamin W. Booth,Angela N. Brooks,Qi Dai,Carrie A. Davis,Michael O. Duff,X. Feng,Andrey A. Gorchakov,Tingting Gu,Jorja G. Henikoff,Philipp Kapranov,Renhua Li,Heather K. MacAlpine,John H. Malone,Aki Minoda,Jared T. Nordman,Katsutomo Okamura,Marc D. Perry,Sara K. Powell,Nicole C. Riddle,Akiko Sakai,Anastasia Samsonova,Jeremy E. Sandler,Yuri B. Schwartz,Noa Sher,Rebecca Spokony,David Sturgill,Marijke J. van Baren,Kenneth H. Wan,Li Yang,Charles Yu,Elise A. Feingold,Peter J. Good,Mark S. Guyer,Rebecca F. Lowdon,Kami Ahmad,Justen Andrews,Bonnie Berger,Steven E. Brenner,Michael R. Brent,Lucy Cherbas,Sarah C. R. Elgin,Thomas R. Gingeras,Robert L. Grossman,Roger A. Hoskins,Thomas C. Kaufman,W. J. Kent,Mitzi I. Kuroda,Terry L. Orr-Weaver,Norbert Perrimon,Vincenzo Pirrotta,James W. Posakony,Bing Ren,Steven Russell,Peter Cherbas,Brenton R. Graveley,Suzanna E. Lewis,Gos Micklem,Brian Oliver,Peter J. Park,Susan E. Celniker,Steven Henikoff,Gary H. Karpen,Eric C. Lai,David M. MacAlpine,Lincoln Stein,Kevin P. White,Manolis Kellis +95 more
TL;DR: The Drosophila Encyclopedia of DNA Elements (modENCODE) project as mentioned in this paper has been used to map transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines.
Journal ArticleDOI
The transcriptional diversity of 25 Drosophila cell lines
Lucy Cherbas,Aarron T. Willingham,Aarron T. Willingham,Dayu Zhang,Li Yang,Yi Zou,Brian D. Eads,Joseph W. Carlson,Jane M. Landolin,Philipp Kapranov,Philipp Kapranov,Jacqueline Dumais,Anastasia Samsonova,Jeong Hyeon Choi,Johnny Roberts,Carrie A. Davis,Haixu Tang,Marijke J. van Baren,Marijke J. van Baren,Srinka Ghosh,Srinka Ghosh,Alexander Dobin,Kim Bell,Wei Lin,Laura Langton,Michael O. Duff,Aaron Tenney,Chris Zaleski,Michael R. Brent,Roger A. Hoskins,Thomas C. Kaufman,Justen Andrews,Brenton R. Graveley,Norbert Perrimon,Norbert Perrimon,Susan E. Celniker,Thomas R. Gingeras,Thomas R. Gingeras,Peter Cherbas +38 more
TL;DR: Drosophila melanogaster cell lines are cataloged to conclude that each line has retained features of an individual founder cell superimposed on a common "cell line" gene expression pattern, revealing unexpected stability of even fine-grained spatial determination.