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J. Zeitlinger · SciRah

Researcher profile · Semantic Scholar

J. Zeitlinger

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J. Zeitlinger — researcher profile on SciRah

h-index: 42
Works: 90
Citations: 18K

Most-cited papers

Polycomb complexes repress developmental regulators in murine embryonic stem cells
L. Boyer, K. Plath, J. Zeitlinger, T. Brambrink +12 more
2006Nature2,706 citations
Semantic Scholar
Transcriptional regulatory code of a eukaryotic genome
Christopher T. Harbison, D. B. Gordon, T. Lee, Nicola J. Rinaldi +16 more
2004Nature2,390 citations Open access
Semantic Scholar
Supporting online material for : Transcriptional Regulatory Networks in Saccharomyces cerevisiae
T. Lee, Nicola J. Rinaldi, François Robert, D. Odom +17 more
20021,763 citations
Semantic Scholar
Genome-wide map of nucleosome acetylation and methylation in yeast.
Dmitry K. Pokholok, Christopher T. Harbison, S. Levine, Megan F. Cole +10 more
2005Cell1,598 citations Open access
Semantic Scholar
Genome-wide location and function of DNA binding proteins.
Bing Ren, François Robert, John J. Wyrick, O. Aparicio +10 more
2000Science1,549 citations
Semantic Scholar
RNA polymerase is poised for activation across the genome
Ginger W Muse, Daniel A. Gilchrist, S. Nechaev, Ruchir R. Shah +4 more
2007Nature Genetics823 citations Open access
Semantic Scholar
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
J. Zeitlinger, A. Stark, Manolis Kellis, Joung-Woo Hong +4 more
2007Nature Genetics816 citations Open access
Semantic Scholar
Serial regulation of transcriptional regulators in the yeast cell cycle.
I. Simon, J. Barnett, N. Hannett, Christopher T. Harbison +7 more
2001Cell714 citations Open access
Semantic Scholar
Base-resolution models of transcription factor binding reveal soft motif syntax
Žiga Avsec, Melanie Weilert, A. Shrikumar, S. Krueger +7 more
2021Nature Genetics599 citations Open access
Semantic Scholar
Transcriptional Regulatory Networks in Saccharomyces cerevisiae
T. Lee, Nicola J. Rinaldi, François Robert, D. Odom +17 more
2002Science448 citations
Semantic Scholar
Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.
J. Zeitlinger, R. Zinzen, A. Stark, Manolis Kellis +3 more
2007Genes & Development330 citations Open access
Semantic Scholar
Activated Signal Transduction Kinases Frequently Occupy Target Genes
Dmitry K. Pokholok, J. Zeitlinger, N. Hannett, David B. Reynolds +1 more
2006Science258 citations
Semantic Scholar
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.
J. Zeitlinger, I. Simon, Christopher T. Harbison, N. Hannett +3 more
2003Cell244 citations Open access
Semantic Scholar
Paused RNA polymerase II inhibits new transcriptional initiation
Wan-Qing Shao, J. Zeitlinger
2017Nature Genetics238 citations
Semantic Scholar
Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion
Zhenrui Li, Pengxu Qian, Wan-Qing Shao, Hailing Shi +27 more
2018Cell Research215 citations Open access
Semantic Scholar
Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo
Mounia Lagha, Jacques P. Bothma, E. Esposito, Samuel Ng +7 more
2013Cell190 citations Open access
Semantic Scholar
Short tandem repeats bind transcription factors to tune eukaryotic gene expression
Connor A. Horton, Amr M. Alexandari, Michael G. B. Hayes, E. Marklund +11 more
2022bioRxiv187 citations
Semantic Scholar
Promoter elements associated with RNA Pol II stalling in the Drosophila embryo
D. Hendrix, Joung-Woo Hong, J. Zeitlinger, D. Rokhsar +1 more
2008Proceedings of the National Academy of Sciences of the United States of America187 citations Open access
Semantic Scholar
Thorax closure in Drosophila: involvement of Fos and the JNK pathway.
J. Zeitlinger, Dirk Bohmann
1999Development181 citations
Semantic Scholar
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
Yu-Jia Sun, C. Nien, Kai Chen, Hsiao-yun Liu +3 more
2015Genome Research169 citations Open access
Semantic Scholar
Jun in Drosophila development: redundant and nonredundant functions and regulation by two MAPK signal transduction pathways.
L. Kockel, J. Zeitlinger, L. Staszewski, M. Mlodzik +1 more
1997Genes & Development158 citations Open access
Semantic Scholar
A global change in RNA polymerase II pausing during the Drosophila midblastula transition
Kai Chen, Jeff Johnston, Wan-Qing Shao, Samuel R. Meier +2 more
2013eLife157 citations Open access
Semantic Scholar
ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints
Qi-Ye He, Jeff Johnston, J. Zeitlinger
2015Nature Biotechnology142 citations Open access
Semantic Scholar
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
Qi-Ye He, A. Bardet, Brianne E. Patton, J. Purvis +5 more
2011Nature Genetics138 citations
Semantic Scholar
Defective dorsal closure and loss of epidermal decapentaplegic expression in Drosophila fos mutants
J. Zeitlinger, L. Kockel, F. Peverali, D. B. Jackson +2 more
1997EMBO Journal132 citations Open access
Semantic Scholar
RNA polymerase II pausing during development
B. Gaertner, J. Zeitlinger
2014Development127 citations Open access
Semantic Scholar
Endogenous retinoids in the zebrafish embryo and adult
P. Costaridis, C. Horton, J. Zeitlinger, Nigel Holder +1 more
1996Developmental Dynamics118 citations Open access
Semantic Scholar
A computational pipeline for comparative ChIP-seq analyses
A. Bardet, Qi-Ye He, J. Zeitlinger, A. Stark
2011Nature Protocols113 citations
Semantic Scholar
Poised RNA Polymerase II changes over developmental time and prepares genes for future expression
B. Gaertner, Jeff Johnston, Kai Chen, Nina Wallaschek +6 more
2012Cell Reports108 citations Open access
Semantic Scholar
High-resolution computational models of genome binding events
Yuan Qi, A. Rolfe, K. Macisaac, G. Gerber +8 more
2006Nature Biotechnology96 citations
Semantic Scholar
Seven myths of how transcription factors read the cis-regulatory code
J. Zeitlinger
2020Current Opinion in Systems Biology91 citations Open access
Semantic Scholar
TRF2, but not TBP, mediates the transcription of ribosomal protein genes
Yuan-Liang Wang, Sascha H. Duttke, Kai Chen, Jeff Johnston +3 more
2014Genes & Development86 citations Open access
Semantic Scholar
Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
Danny E. Miller, C. Staber, J. Zeitlinger, R. S. Hawley
2018G3: Genes, Genomes, Genetics71 citations Open access
Semantic Scholar
GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing
Danny E. Miller, C. Staber, J. Zeitlinger, R. S. Hawley
2018bioRxiv69 citations Open access
Semantic Scholar
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation
Kaelan J. Brennan, Melanie Weilert, S. Krueger, Anusri Pampari +7 more
2023Developmental Cell68 citations Open access
Semantic Scholar
Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis
Nina Koenecke, Jeff Johnston, B. Gaertner, Malini Natarajan +1 more
2016Genome Biology63 citations Open access
Semantic Scholar
Identification of transcription factor binding sites from ChIP-seq data at high resolution
A. Bardet, Jonas Steinmann, S. Bafna, Juergen A. Knoblich +2 more
2013Bioinform.61 citations Open access
Semantic Scholar
Drosophila poised enhancers are generated during tissue patterning with the help of repression
Nina Koenecke, Jeff Johnston, Qi-Ye He, Samuel R. Meier +1 more
2016bioRxiv57 citations Open access
Semantic Scholar
Molecular Evolution of the Yap/Yorkie Proto-Oncogene and Elucidation of Its Core Transcriptional Program
A. Ikmi, B. Gaertner, C. Seidel, M. Srivastava +2 more
2014Molecular biology and evolution55 citations Open access
Semantic Scholar
A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing.
T. Tettey, Xin Gao, Wan-Qing Shao, Hua Li +9 more
2019Cell Reports52 citations Open access
Semantic Scholar
Developmental gene regulation in the era of genomics.
J. Zeitlinger, A. Stark
2010Developmental Biology46 citations Open access
Semantic Scholar
Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis.
Bony De Kumar, H. Parker, A. Paulson, M. Parrish +2 more
2017Developmental Biology44 citations Open access
Semantic Scholar
Hippo Reprograms the Transcriptional Response to Ras Signaling.
J. Pascual, J. Jacobs, L. Sansores-García, Malini Natarajan +4 more
2017Developmental Cell43 citations Open access
Semantic Scholar
embryoDrosophila suggests integration of diverse patterning processes in the Whole-genome ChIP – chip analysis of Dorsal , Twist , and Snail data
J. Zeitlinger, R. Zinzen, Alexander Stark, M. Kellis +3 more
200743 citations
Semantic Scholar
HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets
Bony De Kumar, H. Parker, A. Paulson, M. Parrish +8 more
2016bioRxiv39 citations Open access
Semantic Scholar
Capicua controls Toll/IL-1 signaling targets independently of RTK regulation
A. Papagianni, M. Forés, Wan-Qing Shao, Shuo-Nan He +7 more
2018Proceedings of the National Academy of Sciences of the United States of America37 citations Open access
Semantic Scholar
Deep learning at base-resolution reveals motif syntax of the cis-regulatory code
Žiga Avsec, Melanie Weilert, A. Shrikumar, Amr M. Alexandari +7 more
2019bioRxiv36 citations Open access
Semantic Scholar
TATA and paused promoters active in differentiated tissues have distinct expression characteristics
Vivekanandan Ramalingam, Malini Natarajan, Jeff Johnston, J. Zeitlinger
2020bioRxiv25 citations Open access
Semantic Scholar
Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing
Wan-Qing Shao, Sergio G.-M. Alcantara, J. Zeitlinger
2019eLife24 citations Open access
Semantic Scholar
An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster
Ben J. Vincent, Gavin R. Rice, Gabriella Wong, William J. Glassford +7 more
2019G3: Genes, Genomes, Genetics22 citations Open access
Semantic Scholar

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