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M. Thomas P. Gilbert
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.
Displaying results 1-10 of
14
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Research
:
Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
Diana Lobo
,
Hernán E. Morales
,
Cock Van Oosterhout
,
José Vicente López-Bao
,
Pedro Silva
,
Luis Llaneza
,
Carolina Pacheco
,
Diana Castro
,
Germán Hernández-Alonso
,
George Pacheco
,
John Archer
,
M. Thomas P. Gilbert
,
Nuno Ferrand
,
and
Raquel Godinho
Genome Res.
March 2025
35
:
432
-
445
;
Published in Advance
February 14, 2025
,
doi:
10.1101/gr.279093.124
Abstract
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Research
:
Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
Juan Carlos Rivera-Mulia
,
Sebo Kim
,
Haitham Gabr
,
Abhijit Chakraborty
,
Ferhat Ay
,
Tamer Kahveci
,
and
David M. Gilbert
Genome Res.
September 2019
29
:
1415
-
1428
;
Published in Advance
August 21, 2019
,
doi:
10.1101/gr.247049.118
Abstract
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Research
:
Allele-specific control of replication timing and genome organization during development
Juan Carlos Rivera-Mulia
,
Andrew Dimond
,
Daniel Vera
,
Claudia Trevilla-Garcia
,
Takayo Sasaki
,
Jared Zimmerman
,
Catherine Dupont
,
Joost Gribnau
,
Peter Fraser
,
and
David M. Gilbert
Genome Res.
June 2018
28
:
800
-
811
;
Published in Advance
May 7, 2018
,
doi:
10.1101/gr.232561.117
Abstract
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Research
:
Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program
Vishnu Dileep
,
Ferhat Ay
,
Jiao Sima
,
Daniel L. Vera
,
William S. Noble
,
and
David M. Gilbert
Genome Res.
August 2015
25
:
1104
-
1113
;
Published in Advance
May 20, 2015
,
doi:
10.1101/gr.183699.114
Abstract
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Research
:
Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells
Juan Carlos Rivera-Mulia
,
Quinton Buckley
,
Takayo Sasaki
,
Jared Zimmerman
,
Ruth A. Didier
,
Kristopher Nazor
,
Jeanne F. Loring
,
Zheng Lian
,
Sherman Weissman
,
Allan J. Robins
,
Thomas C. Schulz
,
Laura Menendez
,
Michael J. Kulik
,
Stephen Dalton
,
Haitham Gabr
,
Tamer Kahveci
,
and
David M. Gilbert
Genome Res.
August 2015
25
:
1091
-
1103
;
Published in Advance
June 8, 2015
,
doi:
10.1101/gr.187989.114
Abstract
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Method
:
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression
Maxwell W. Libbrecht
,
Ferhat Ay
,
Michael M. Hoffman
,
David M. Gilbert
,
Jeffrey A. Bilmes
,
and
William Stafford Noble
Genome Res.
April 2015
25
:
544
-
557
;
Published in Advance
February 12, 2015
,
doi:
10.1101/gr.184341.114
Abstract
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Method
:
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
Jakob Skou Pedersen
,
Eivind Valen
,
Amhed M. Vargas Velazquez
,
Brian J. Parker
,
Morten Rasmussen
,
Stinus Lindgreen
,
Berit Lilje
,
Desmond J. Tobin
,
Theresa K. Kelly
,
Søren Vang
,
Robin Andersson
,
Peter A. Jones
,
Cindi A. Hoover
,
Alexei Tikhonov
,
Egor Prokhortchouk
,
Edward M. Rubin
,
Albin Sandelin
,
M. Thomas P. Gilbert
,
Anders Krogh
,
Eske Willerslev
,
and
Ludovic Orlando
Genome Res.
March 2014
24
:
454
-
466
;
Published in Advance
December 3, 2013
,
doi:
10.1101/gr.163592.113
Abstract
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Research
:
Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia
Tyrone Ryba
,
Dana Battaglia
,
Bill H. Chang
,
James W. Shirley
,
Quinton Buckley
,
Benjamin D. Pope
,
Meenakshi Devidas
,
Brian J. Druker
,
and
David M. Gilbert
Genome Res.
October 2012
22
:
1833
-
1844
;
Published in Advance
May 24, 2012
,
doi:
10.1101/gr.138511.112
Abstract
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Method
:
True single-molecule DNA sequencing of a pleistocene horse bone
Ludovic Orlando
,
Aurelien Ginolhac
,
Maanasa Raghavan
,
Julia Vilstrup
,
Morten Rasmussen
,
Kim Magnussen
,
Kathleen E. Steinmann
,
Philipp Kapranov
,
John F. Thompson
,
Grant Zazula
,
Duane Froese
,
Ida Moltke
,
Beth Shapiro
,
Michael Hofreiter
,
Khaled A.S. Al-Rasheid
,
M. Thomas P. Gilbert
,
and
Eske Willerslev
Genome Res.
October 2011
21
:
1705
-
1719
;
Published in Advance
July 29, 2011
,
doi:
10.1101/gr.122747.111
Abstract
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Research
:
Complete mitochondrial genome phylogeographic analysis of killer whales (
Orcinus orca
) indicates multiple species
Phillip A. Morin
,
Frederick I. Archer
,
Andrew D. Foote
,
Julia Vilstrup
,
Eric E. Allen
,
Paul Wade
,
John Durban
,
Kim Parsons
,
Robert Pitman
,
Lewyn Li
,
Pascal Bouffard
,
Sandra C. Abel Nielsen
,
Morten Rasmussen
,
Eske Willerslev
,
M. Thomas P. Gilbert
,
and
Timothy Harkins
Genome Res.
July 2010
20
:
908
-
916
;
Published in Advance
April 22, 2010
,
doi:
10.1101/gr.102954.109
Abstract
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Single-cell gene signature scoring
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Short tandem repeat genotyping using long reads
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