J
Jeena Rajan
Researcher at European Bioinformatics Institute
Publications - 22
Citations - 5980
Jeena Rajan is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: European Nucleotide Archive & Biology. The author has an hindex of 13, co-authored 19 publications receiving 5202 citations. Previous affiliations of Jeena Rajan include University of California, Santa Cruz & Wellcome Trust Sanger Institute.
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Journal ArticleDOI
GENCODE: The reference human genome annotation for The ENCODE Project
Jennifer Harrow,Adam Frankish,José M. González,Electra Tapanari,Mark Diekhans,Felix Kokocinski,Bronwen Aken,Daniel Barrell,Amonida Zadissa,Stephen M. J. Searle,If H. A. Barnes,Alexandra Bignell,Veronika Boychenko,Toby Hunt,M. Kay,Gaurab Mukherjee,Jeena Rajan,Gloria Despacio-Reyes,Gary Saunders,Charles A. Steward,Rachel A. Harte,Michael F. Lin,Cédric Howald,Andrea Tanzer,Thomas Derrien,Jacqueline Chrast,Nathalie Walters,Suganthi Balasubramanian,Baikang Pei,Michael L. Tress,Jose Manuel Rodriguez,Iakes Ezkurdia,Jeltje Van Baren,Michael R. Brent,David Haussler,Manolis Kellis,Alfonso Valencia,Alexandre Reymond,Mark Gerstein,Roderic Guigó,Tim Hubbard +40 more
TL;DR: This work has examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites, and over one-third of GENCODE protein-Coding genes aresupported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas.
Journal ArticleDOI
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
Kim D. Pruitt,Jennifer Harrow,Rachel A. Harte,Craig Wallin,Mark Diekhans,Donna Maglott,Steve Searle,Catherine M. Farrell,Jane E. Loveland,Barbara J. Ruef,Elizabeth M. Hart,Marie-Marthe Suner,Melissa J. Landrum,Bronwen Aken,Sarah Ayling,Robert Baertsch,Julio Fernandez-Banet,Joshua L. Cherry,Val Curwen,Michael DiCuccio,Manolis Kellis,Jennifer M. Lee,Michael F. Lin,Michael Schuster,Andrew Shkeda,Clara Amid,Garth Brown,Oksana Dukhanina,Adam Frankish,Jennifer Hart,Bonnie L. Maidak,Jonathan M. Mudge,Michael R. Murphy,Terence Murphy,Jeena Rajan,Bhanu Rajput,Lillian D. Riddick,Catherine E. Snow,Charles A. Steward,David Webb,Janet Weber,Laurens G. Wilming,Wenyu Wu,Ewan Birney,David Haussler,Tim Hubbard,James Ostell,Richard Durbin,David J. Lipman +48 more
TL;DR: The CCDS database centralizes the function of identifying well-supported, identically-annotated, protein-coding regions and indicates that the entries in the CCDS set are highly likely to represent real proteins, more so than annotations from contributing groups not included in CCDS.
Journal ArticleDOI
The DNA sequence and biological annotation of human chromosome 1
Simon G. Gregory,Simon G. Gregory,K F Barlow,Kirsten McLay,Rajinder Kaul,David Swarbreck,Andrew Dunham,Carol Scott,Kevin L. Howe,Kathryn Woodfine,Chris C. A. Spencer,Matthew Jones,Christopher J. Gillson,S. Searle,Yi Zhou,Felix Kokocinski,L McDonald,R Evans,Katharine A. Phillips,A Atkinson,R Cooper,C Jones,R. E. Hall,T D Andrews,Christine Lloyd,R Ainscough,J P Almeida,K D Ambrose,F Anderson,R. W. Andrew,R I S Ashwell,K Aubin,A K Babbage,C L Bagguley,J Bailey,Helen Beasley,Graeme Bethel,Christine P. Bird,S Bray-Allen,J Y Brown,A J Brown,D. Buckley,John Burton,Jacqueline M. Bye,C Carder,J C Chapman,S Y Clark,G Clarke,C M Clee,V. Cobley,R. E. Collier,N Corby,G. J. Coville,Jim Davies,Rebecca Deadman,Matthew Dunn,M Earthrowl,A. G. Ellington,H Errington,Adam Frankish,J Frankland,Lisa French,P Garner,J Garnett,M. R J Ghori,Richard Gibson,L M Gilby,Will Gillett,Rebecca Glithero,Darren Grafham,C Griffiths,Sam Griffiths-Jones,Russell J. Grocock,S Hammond,Elliot Harrison,E. Hart,Eric Haugen,Paul Heath,S. Holmes,Kathryn E. Holt,Philip Howden,Adrienne Hunt,Sarah E. Hunt,G Hunter,J Isherwood,R. James,Chris Johnson,D. Johnson,A Joy,M. Kay,J K Kershaw,M. Kibukawa,A M Kimberley,A. King,Andrew J Knights,Heena V. Lad,Gavin K. Laird,S Lawlor,Daniel Leongamornlert,D. M. Lloyd,Jane E. Loveland,J Lovell,Michael J. Lush,Rachel Lyne,Sancha Martin,M Mashreghi-Mohammadi,Lucy Matthews,Nicholas Matthews,Stuart McLaren,Sarah Milne,S. Mistry,M. J F Moore,T Nickerson,C. Odell,Karen Oliver,A. Palmeiri,Sophie Palmer,Anne Parker,D. Patel,A. V. Pearce,A I Peck,Sarah Pelan,Karen A. Phelps,Benjamin Phillimore,Robert W. Plumb,Jeena Rajan,Charles F. Raymond,Greg W. Rouse,Channakhone Saenphimmachak,Harminder Sehra,E Sheridan,Ratna Shownkeen,Sarah Sims,C. D. Skuce,Michelle Smith,Charles A. Steward,Sankaran Subramanian,N Sycamore,Alan Tracey,A Tromans,Z. Van Helmond,Melanie M. Wall,J. M. Wallis,Simon D. M. White,S. Whitehead,Jane E. Wilkinson,David Willey,H. Williams,Laurens G. Wilming,Paul Wray,Z. Wu,Alan Coulson,M. Vaudin,John Sulston,Richard Durbin,Tim Hubbard,Richard Wooster,Ian Dunham,Nigel P. Carter,G. McVean,Mark T. Ross,Jennifer Harrow,Maynard V. Olson,Stephan Beck,Jane Rogers,David R. Bentley +165 more
TL;DR: The finished sequence and biological annotation of human chromosome 1 is reported, which reveals patterns of sequence variation that reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident.
Journal ArticleDOI
Current status and new features of the Consensus Coding Sequence database
Catherine M. Farrell,Nuala A. O'Leary,Rachel A. Harte,Jane E. Loveland,Laurens G. Wilming,Craig Wallin,Mark Diekhans,Daniel Barrell,Stephen M. J. Searle,Bronwen Aken,Susan M. Hiatt,Adam Frankish,Marie-Marthe Suner,Bhanu Rajput,Charles A. Steward,Garth Brown,Ruth Bennett,Michael R. Murphy,Wendy Wu,M. Kay,Jennifer Hart,Jeena Rajan,Janet Weber,Catherine Snow,Lillian D. Riddick,Toby Hunt,David Webb,Mark G. Thomas,Pamela Tamez,Sanjida H. Rangwala,Kelly M. McGarvey,Shashikant Pujar,Andrei Shkeda,Jonathan M. Mudge,José M. González,James G. R. Gilbert,Stephen J. Trevanion,Robert Baertsch,Jennifer Harrow,Tim Hubbard,James Ostell,David Haussler,Kim D. Pruitt +42 more
TL;DR: The current status and recent growth in the CCDS dataset is described, as well as recent changes to the web and FTP sites, which include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and the approach to representing genes for which support evidence is incomplete.
Journal ArticleDOI
The European Nucleotide Archive in 2019.
Clara Amid,Blaise T. F. Alako,Vishnukumar Balavenkataraman Kadhirvelu,Tony Burdett,Josephine Burgin,Jun Fan,Peter W. Harrison,Sam Holt,Abdulrahman Hussein,Eugene Ivanov,Suran Jayathilaka,Simon Kay,Thomas M. Keane,Rasko Leinonen,Xin Liu,Josué Martínez-Villacorta,Annalisa Milano,Amir Pakseresht,Nadim Rahman,Jeena Rajan,Kethi Reddy,Edward Richards,Dmitriy Smirnov,Alexey Sokolov,Senthilnathan Vijayaraja,Guy Cochrane +25 more
TL;DR: Making the world’s public sequencing datasets available to the scientific community, the ENA represents a globally comprehensive nucleotide sequence resource in 2019 and provides an insight into selected key areas of development.