M
Matthew Slattery
Researcher at University of Minnesota
Publications - 55
Citations - 5572
Matthew Slattery is an academic researcher from University of Minnesota. The author has contributed to research in topics: Transcription factor & Chromatin. The author has an hindex of 30, co-authored 51 publications receiving 4902 citations. Previous affiliations of Matthew Slattery include Columbia University & University of Chicago.
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Journal ArticleDOI
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Stephen G. Landt,Georgi K. Marinov,Anshul Kundaje,Pouya Kheradpour,Florencia Pauli,Serafim Batzoglou,Bradley E. Bernstein,Peter J. Bickel,James B. Brown,Philip Cayting,Yiwen Chen,Gilberto DeSalvo,Charles B. Epstein,Katherine I. Fisher-Aylor,Ghia Euskirchen,Mark Gerstein,Jason Gertz,Alexander J. Hartemink,Michael M. Hoffman,Vishwanath R. Iyer,Youngsook L. Jung,Subhradip Karmakar,Manolis Kellis,Peter V. Kharchenko,Qiang Li,Tao Liu,X. Shirley Liu,Lijia Ma,Aleksandar Milosavljevic,Richard M. Myers,Peter J. Park,Michael J. Pazin,Marc D. Perry,Debasish Raha,Timothy E. Reddy,Joel Rozowsky,Noam Shoresh,Arend Sidow,Matthew Slattery,John A. Stamatoyannopoulos,Michael Y. Tolstorukov,Kevin P. White,Simon Xi,Peggy J. Farnham,Jason D. Lieb,Barbara J. Wold,Michael Snyder +46 more
TL;DR: This work discusses how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data and develops a set of working standards and guidelines for ChIP experiments that are updated routinely.
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Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins
Matthew Slattery,Todd Riley,Peng Liu,Peng Liu,Namiko Abe,Pilar Gomez-Alcala,Iris Dror,Tianyin Zhou,Remo Rohs,Barry Honig,Barry Honig,Harmen J. Bussemaker,Richard S. Mann +12 more
TL;DR: An experimental and computational platform that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex is developed, and it is shown that Drosophila Hox proteins obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax.
Journal ArticleDOI
Absence of a simple code: how transcription factors read the genome
TL;DR: Structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA-binding preferences of many TFs to expand the understanding of TF-DNA interactions.
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Disentangling the Many Layers of Eukaryotic Transcriptional Regulation
TL;DR: This review places CRM assembly in the context of nucleosomes and condensed chromatin, and discusses how DNA accessibility and histone modifications contribute to TF function.
Journal ArticleDOI
Transcription factor choice in the Hippo signaling pathway: homothorax and yorkie regulation of the microRNA bantam in the progenitor domain of the Drosophila eye imaginal disc
TL;DR: Evidence is provided that Yki can also regulate target genes in conjunction with Homothorax (Hth) and Teashirt (Tsh), two DNA-binding transcription factors expressed in the uncommitted progenitor cells of the Drosophila eye imaginal disc.