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Author Details

Julia Zeitlinger
Stowers Institute for Medical Research, University of Kansas School of Medicine
1996
57
35
Nevan J Krogan (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36462664Off the deep end: What can deep learning do for the gene expression field?J Biol Chem2023
37863045The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5.Stem Cell Reports2023
37557175Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation.Dev Cell2023
37735176Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development.Nat Commun2023
37214836<i>De novo</i> distillation of thermodynamic affinity from deep learning regulatory sequence models of <i>in vivo</i> protein-DNA binding.bioRxiv2023
37080160Emerging questions in transcriptional regulation.Cell Syst2023
34807910The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters.PLoS Genet2021
33602648Evaluation of facial aesthetics by laypersons in patients undergoing intraoral quadrangular Le Fort II osteotomy compared with conventional Le Fort I osteotomy.Int J Oral Maxillofac Surg2021
33543829TATA and paused promoters active in differentiated tissues have distinct expression characteristics.Mol Syst Biol2021
33603233Base-resolution models of transcription-factor binding reveal soft motif syntax.Nat Genet2021
32822591β-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells.Stem Cell Reports2020
33134611Seven myths of how transcription factors read the cis-regulatory code.Curr Opin Syst Biol2020
31021316Reporter-ChIP-nexus reveals strong contribution of the <i>Drosophila</i> initiator sequence to RNA polymerase pausing.Elife2019
31242411A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing.Cell Rep2019
31619460An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of <i>Drosophila melanogaster</i>.G3 (Bethesda)2019
29432195Capicua controls Toll/IL-1 signaling targets independently of RTK regulation.Proc Natl Acad Sci U S A2018
30150672Author Correction: Suppression of m<sup>6</sup>A reader Ythdf2 promotes hematopoietic stem cell expansion.Cell Res2018
30065315Suppression of m<sup>6</sup>A reader Ythdf2 promotes hematopoietic stem cell expansion.Cell Res2018
30087105Highly Contiguous Genome Assemblies of 15 <i>Drosophila</i> Species Generated Using Nanopore Sequencing.G3 (Bethesda)2018
27979994Drosophila poised enhancers are generated during tissue patterning with the help of repression.Genome Res2017
28982536Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis.Dev Biol2017
28950103Hippo Reprograms the Transcriptional Response to Ras Signaling.Dev Cell2017
28784834HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets.Genome Res2017
28504701Paused RNA polymerase II inhibits new transcriptional initiation.Nat Genet2017
27678375Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis.Genome Biol2016
25751057ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.Nat Biotechnol2015
26354485Cori meets Dobzhansky: Evolution and Gene Expression in St. Louis: A report on the "Evolution and Core Processes in Gene Regulation" meeting in St. Louis, June 25-28, 2015.Bioessays2015
26335633Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation.Genome Res2015
24595285RNA polymerase II pausing during development.Development2014
24958592TRF2, but not TBP, mediates the transcription of ribosomal protein genes.Genes Dev2014
24509725Molecular evolution of the Yap/Yorkie proto-oncogene and elucidation of its core transcriptional program.Mol Biol Evol2014
23706736Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.Cell2013
23980024Identification of transcription factor binding sites from ChIP-seq data at high resolution.Bioinformatics2013
23951546A global change in RNA polymerase II pausing during the Drosophila midblastula transition.Elife2013
23260668Poised RNA polymerase II changes over developmental time and prepares genes for future expression.Cell Rep2012
21478888High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.Nat Genet2011
22179591A computational pipeline for comparative ChIP-seq analyses.Nat Protoc2011
20045679Developmental gene regulation in the era of genomics.Dev Biol2010
18505835Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.Proc Natl Acad Sci U S A2008
17322397Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.Genes Dev2007
17994021RNA polymerase is poised for activation across the genome.Nat Genet2007
17994019RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.Nat Genet2007
16625203Polycomb complexes repress developmental regulators in murine embryonic stem cells.Nature2006
16873666Activated signal transduction kinases frequently occupy target genes.Science2006
16900145High-resolution computational models of genome binding events.Nat Biotechnol2006
16122420Genome-wide map of nucleosome acetylation and methylation in yeast.Cell2005
15343339Transcriptional regulatory code of a eukaryotic genome.Nature2004
12732146Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.Cell2003
12399584Transcriptional regulatory networks in Saccharomyces cerevisiae.Science2002
11572776Serial regulation of transcriptional regulators in the yeast cell cycle.Cell2001
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Collaborators

Manolis Kellis
Massachusetts Institute of Technology
Co-authored papers 3
P Alexander Rolfe
Co-authored papers 3
Bony De Kumar
University of North Dakota School of Medicine
Co-authored papers 3
Ernest Fraenkel
Co-authored papers 3
Jay R Unruh
Stowers Institute for Medical Research
Co-authored papers 3
Anshul Kundaje
Stanford University.
Co-authored papers 3
Brian D Slaughter
Stowers Institute for Medical Research
Co-authored papers 2
Amr M Alexandari
Stanford University
Co-authored papers 2
Avanti Shrikumar
Stanford University
Co-authored papers 2
Bing Ren
Center for Epigenomics, University of California San Diego
Co-authored papers 2
Fran??ois Robert
Institut de recherches cliniques de Montreal
Co-authored papers 2
Richard Alexander
Stowers Institute for Medical Research
Co-authored papers 2
Tommi S Jaakkola
Massachusetts Institute of Technology
Co-authored papers 2
David Benjamin Gordon
Co-authored papers 2
Zulin Yu
Stowers Institute for Medical Research
Co-authored papers 2
Chuan He
Institute of Hematology, West China Hospital of Sichuan University
Co-authored papers 2
Michael McGregor
Co-authored papers 1
Tomohiro Nishino
Gladstone Institutes, USA Roddenberry Center for Stem Cell Biology at Gladstone
Co-authored papers 1
Christopher J Wilson
Co-authored papers 1
Ruth H??ttenhain
Quantitative Biosciences Institute (QBI), University of California san francisco
Co-authored papers 1
Mauro W Costa
Gladstone Institutes, USA Roddenberry Center for Stem Cell Biology at Gladstone
Co-authored papers 1
George A Kassavetis
Co-authored papers 1
Norbert Perrimon
Co-authored papers 1
Kathryn N Ivey
Gladstone Institutes, USA Roddenberry Center for Stem Cell Biology at Gladstone
Co-authored papers 1
David Gordon
Co-authored papers 1
Sascha H Duttke
College of Veterinary Medicine, Washington State University
Co-authored papers 1
Marco Blanchette
Stowers Institute for Medical Research
Co-authored papers 1
Fran Lewitter
Whitehead Institute for Biomedical Research
Co-authored papers 1
B??rbara Gonz??lez-Ter??n
Gladstone Institutes, USA Roddenberry Center for Stem Cell Biology at Gladstone
Co-authored papers 1
Žiga Avsec
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Release 1.2