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Manolis Kellis
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28
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:
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
Jonathan M. Mudge
,
Irwin Jungreis
,
Toby Hunt
,
Jose Manuel Gonzalez
,
James C. Wright
,
Mike Kay
,
Claire Davidson
,
Stephen Fitzgerald
,
Ruth Seal
,
Susan Tweedie
,
Liang He
,
Robert M. Waterhouse
,
Yue Li
,
Elspeth Bruford
,
Jyoti S. Choudhary
,
Adam Frankish
,
and
Manolis Kellis
Genome Res.
December 2019
29
:
2073
-
2087
;
Published in Advance
September 19, 2019
,
doi:
10.1101/gr.246462.118
Abstract
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Research
:
An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
Zhizhuo Zhang
,
Kern Rei Chng
,
Shreyas Lingadahalli
,
Zikai Chen
,
Mei Hui Liu
,
Huy Hoang Do
,
Shaojiang Cai
,
Nicola Rinaldi
,
Huay Mei Poh
,
Guoliang Li
,
Ying Ying Sung
,
Charlie L. Heng
,
Leighton J. Core
,
Si Kee Tan
,
Xiaoan Ruan
,
John T. Lis
,
Manolis Kellis
,
Yijun Ruan
,
Wing-Kin Sung
,
and
Edwin Cheung
Genome Res.
February 2019
29
:
223
-
235
;
Published in Advance
January 3, 2019
,
doi:
10.1101/gr.230243.117
Abstract
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Method
:
Co-expression networks reveal the tissue-specific regulation of transcription and splicing
Ashis Saha
,
Yungil Kim
,
Ariel D.H. Gewirtz
,
Brian Jo
,
Chuan Gao
,
Ian C. McDowell
,
The GTEx Consortium
,
Barbara E. Engelhardt
,
and
Alexis Battle
Genome Res.
November 2017
27
:
1843
-
1858
;
Published in Advance
October 11, 2017
,
doi:
10.1101/gr.216721.116
Abstract
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Method
:
Identifying
cis
-mediators for
trans
-eQTLs across many human tissues using genomic mediation analysis
Fan Yang
,
Jiebiao Wang
,
The GTEx Consortium
,
Brandon L. Pierce
,
and
Lin S. Chen
Genome Res.
November 2017
27
:
1859
-
1871
;
Published in Advance
October 11, 2017
,
doi:
10.1101/gr.216754.116
Abstract
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Resource
:
Comparative validation of the
D. melanogaster
modENCODE transcriptome annotation
Zhen-Xia Chen
,
David Sturgill
,
Jiaxin Qu
,
Huaiyang Jiang
,
Soo Park
,
Nathan Boley
,
Ana Maria Suzuki
,
Anthony R. Fletcher
,
David C. Plachetzki
,
Peter C. FitzGerald
,
Carlo G. Artieri
,
Joel Atallah
,
Olga Barmina
,
James B. Brown
,
Kerstin P. Blankenburg
,
Emily Clough
,
Abhijit Dasgupta
,
Sai Gubbala
,
Yi Han
,
Joy C. Jayaseelan
,
Divya Kalra
,
Yoo-Ah Kim
,
Christie L. Kovar
,
Sandra L. Lee
,
Mingmei Li
,
James D. Malley
,
John H. Malone
,
Tittu Mathew
,
Nicolas R. Mattiuzzo
,
Mala Munidasa
,
Donna M. Muzny
,
Fiona Ongeri
,
Lora Perales
,
Teresa M. Przytycka
,
Ling-Ling Pu
,
Garrett Robinson
,
Rebecca L. Thornton
,
Nehad Saada
,
Steven E. Scherer
,
Harold E. Smith
,
Charles Vinson
,
Crystal B. Warner
,
Kim C. Worley
,
Yuan-Qing Wu
,
Xiaoyan Zou
,
Peter Cherbas
,
Manolis Kellis
,
Michael B. Eisen
,
Fabio Piano
,
Karin Kionte
,
David H. Fitch
,
Paul W. Sternberg
,
Asher D. Cutter
,
Michael O. Duff
,
Roger A. Hoskins
,
Brenton R. Graveley
,
Richard A. Gibbs
,
Peter J. Bickel
,
Artyom Kopp
,
Piero Carninci
,
Susan E. Celniker
,
Brian Oliver
,
and
Stephen Richards
Genome Res.
July 2014
24
:
1209
-
1223
;
Published in Advance
July 1, 2014
,
doi:
10.1101/gr.159384.113
Abstract
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Resource
:
Diverse patterns of genomic targeting by transcriptional regulators in
Drosophila melanogaster
Matthew Slattery
,
Lijia Ma
,
Rebecca F. Spokony
,
Robert K. Arthur
,
Pouya Kheradpour
,
Anshul Kundaje
,
Nicolas Nègre
,
Alex Crofts
,
Ryan Ptashkin
,
Jennifer Zieba
,
Alexander Ostapenko
,
Sarah Suchy
,
Alec Victorsen
,
Nader Jameel
,
A. Jason Grundstad
,
Wenxuan Gao
,
Jennifer R. Moran
,
E. Jay Rehm
,
Robert L. Grossman
,
Manolis Kellis
,
and
Kevin P. White
Genome Res.
July 2014
24
:
1224
-
1235
;
Published in Advance
July 1, 2014
,
doi:
10.1101/gr.168807.113
Abstract
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Research
:
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
Stefan Washietl
,
Manolis Kellis
,
and
Manuel Garber
Genome Res.
April 2014
24
:
616
-
628
;
Published in Advance
January 15, 2014
,
doi:
10.1101/gr.165035.113
Abstract
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Method
:
Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
Yi-Chieh Wu
,
Matthew D. Rasmussen
,
Mukul S. Bansal
,
and
Manolis Kellis
Genome Res.
March 2014
24
:
475
-
486
;
Published in Advance
December 5, 2013
,
doi:
10.1101/gr.161968.113
Abstract
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Resource
:
Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
Ali Mortazavi
,
Shirley Pepke
,
Camden Jansen
,
Georgi K. Marinov
,
Jason Ernst
,
Manolis Kellis
,
Ross C. Hardison
,
Richard M. Myers
,
and
Barbara J. Wold
Genome Res.
December 2013
23
:
2136
-
2148
;
Published in Advance
October 29, 2013
,
doi:
10.1101/gr.158261.113
Abstract
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Research
:
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
Jason Ernst
and
Manolis Kellis
Genome Res.
July 2013
23
:
1142
-
1154
;
Published in Advance
April 17, 2013
,
doi:
10.1101/gr.144840.112
Abstract
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