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Andrew R. Gehrke
Researcher at University of Chicago
Publications - 23
Citations - 3803
Andrew R. Gehrke is an academic researcher from University of Chicago. The author has contributed to research in topics: Gene & Biology. The author has an hindex of 16, co-authored 19 publications receiving 3384 citations. Previous affiliations of Andrew R. Gehrke include Harvard University & Brigham and Women's Hospital.
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Journal ArticleDOI
Diversity and Complexity in DNA Recognition by Transcription Factors
Gwenael Badis,Michael F. Berger,Michael F. Berger,Anthony A. Philippakis,Anthony A. Philippakis,Anthony A. Philippakis,Shaheynoor Talukder,Andrew R. Gehrke,Savina Jaeger,Esther T. Chan,Genita Metzler,Anastasia Vedenko,Xiaoyu Chen,Hanna Kuznetsov,Chi-Fong Wang,David Coburn,Daniel E. Newburger,Quaid Morris,Timothy P. Hughes,Martha L. Bulyk +19 more
TL;DR: A broad survey of transcription factors reveals that related proteins can have multiple and differing DNA binding specificities, which may be important in gene regulation and in the evolution of transcriptional regulatory networks.
Journal ArticleDOI
Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
Michael F. Berger,Gwenael Badis,Andrew R. Gehrke,Shaheynoor Talukder,Anthony A. Philippakis,Anthony A. Philippakis,Anthony A. Philippakis,Lourdes Peña-Castillo,Trevis M. Alleyne,Sanie Mnaimneh,Olga B. Botvinnik,Olga B. Botvinnik,Esther T. Chan,Faiqua Khalid,Wen Zhang,Daniel E. Newburger,Savina Jaeger,Quaid Morris,Martha L. Bulyk,Timothy P. Hughes +19 more
TL;DR: A computational system is developed that successfully predicts binding sites for homeodomain proteins as distant from mouse as Drosophila and C. elegans, and the results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success.
Journal ArticleDOI
Genome-Wide Analysis of ETS-Family DNA-Binding In Vitro and In Vivo
Gong-Hong Wei,Gwenael Badis,Michael F. Berger,Teemu Kivioja,Teemu Kivioja,Kimmo Palin,Martin Enge,Martin Bonke,Arttu Jolma,Markku Varjosalo,Andrew R. Gehrke,Jian Yan,Shaheynoor Talukder,Mikko P. Turunen,Mikko Taipale,Hendrik G. Stunnenberg,Esko Ukkonen,Timothy P. Hughes,Martha L. Bulyk,Jussi Taipale,Jussi Taipale +20 more
TL;DR: The results indicate that even relatively small differences in in vitro binding specificity of a TF contribute to site selectivity in vivo, and this work identifies amino‐acid residues that are critical for the differences in specificity between all the classes.
Journal ArticleDOI
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
Ingo Braasch,Andrew R. Gehrke,J. Joshua Smith,Kazuhiko Kawasaki,Tereza Manousaki,Jeremy Pasquier,Angel Amores,Thomas Desvignes,Peter Batzel,Julian M. Catchen,Aaron M. Berlin,Michael S. Campbell,Daniel Barrell,Daniel Barrell,Kyle J. Martin,John F Mulley,Vydianathan Ravi,Alison P. Lee,Tetsuya Nakamura,Domitille Chalopin,Shaohua Fan,Dustin J. Wcisel,Cristian Cañestro,Jason Sydes,Felix E.G. Beaudry,Yi Sun,Jana Hertel,Michael J. Beam,Mario Fasold,Mikio Ishiyama,Jeremy Johnson,Steffi Kehr,Marcia Lara,John H. Letaw,Gary W. Litman,Ronda T. Litman,Masato Mikami,Tatsuya Ota,Nil Ratan Saha,Louise Williams,Peter F. Stadler,Han Wang,John S. Taylor,Quenton C. Fontenot,Allyse M. Ferrara,Stephen M. J. Searle,Bronwen Aken,Bronwen Aken,Mark Yandell,Igor Schneider,Jeffrey A. Yoder,Jean-Nicolas Volff,Axel Meyer,Chris T. Amemiya,Byrappa Venkatesh,Peter W. H. Holland,Yann Guiguen,Julien Bobe,Neil H. Shubin,Federica Di Palma,Jessica Alföldi,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,John H. Postlethwait +63 more
TL;DR: In this article, the authors sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD).
Journal ArticleDOI
LUX ARRHYTHMO Encodes a Nighttime Repressor of Circadian Gene Expression in the Arabidopsis Core Clock
Anne Helfer,Dmitri A. Nusinow,Brenda Y. Chow,Andrew R. Gehrke,Martha L. Bulyk,Martha L. Bulyk,Steve A. Kay +6 more
TL;DR: Novel connections between the archetypal loops of the Arabidopsis clock represent a significant advance toward defining the molecular dynamics underlying the circadian network in plants and provide the first mechanistic insight into the molecular function of the previously orphan clock factor LUX.