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Publications

Supporting the scientific spirit of transparency, the Stowers Institute for Medical Research makes the data underlying its scientific publications freely accessible to the scientific community. Access to original, unprocessed data allows other scientists to validate and extend findings made by Stowers researchers.

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The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters

Soffers JHM, Alcantara SG, Li X, Shao W, Seidel CW, Li H, Zeitlinger J, Abmayr SM, Workman JL. PLoS Genet. 2021;17:e1009668. doi: 10.1371/journal.pgen.1009668.

Base-resolution models of transcription-factor binding reveal soft motif syntax

Avsec Z, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Nat Genet. 2021;53:354-366.

TATA and paused promoters active in differentiated tissues have distinct expression characteristics

Ramalingam V, Natarajan M, Johnston J, Zeitlinger J. Mol Syst Biol. 2021;17:e9866. doi: 10.15252/msb.20209866.

b-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells

Tao F, Soffers J, Hu D, Chen S, Gao X, Zhang Y, Zhao C, Smith SE, Unruh JR, Zhang D, Tsuchiya D, Venkatraman A, Zhao M, Li Z, Qian P, Parmely T, He XC, Washburn M, Florens L, Perry JM, Zeitlinger J, Workman J, Li L. Stem Cell Rep. 2020;15:662-676.

An atlas of transcription factors expressed in male pupal terminalia of Drosophila melanogaster

Vincent BJ, Rice GR, Wong GM, Glassford WJ, Downs KI, Shastay JL, Charles-Obi K, Natarajan M, Gogol M, Zeitlinger J, Rebeiz M. G3 (Bethesda). 2019. doi: 10.1534/g3.119.400788.

A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing

Tettey TT, Gao X, Shao W, Story BA, Chitsazan AD, Glaser RL, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. Cell Rep. 2019;27:3770-3779 e7.

Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA Polymerase pausing

Shao W, Alcantara SG, Zeitlinger J. eLife. 2019;8:e41461. doi: 41410.47554/eLife.41461.

Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing

Miller DE, Staber C, Zeitlinger J, Hawley RS. G3 (Bethesda). 2018;8:3131-3141.

Suppression of m(6)A reader Ythdf2 promotes hematopoietic stem cell expansion

Li Z, Qian P, Shao W, Shi H, He XC, Gogol M, Yu Z, Wang Y, Qi M, Zhu Y, Perry JM, Zhang K, Tao F, Zhou K, Hu D, Han Y, Zhao C, Alexander R, Xu H, Chen S, Peak A, Hall K, Peterson M, Perera A, Haug JS, Parmely T, Li H, Shen B, Zeitlinger J, He C, Li L. Cell Res. 2018. Author Correction: Cell Res 2018:1-14. doi.org/10.1038/s41422-018-0072-0. Published online July 2018.;28:904-917.

Capicua controls Toll/IL-1 signaling targets independently of RTK regulation

Papagianni A, Fores M, Shao W, He S, Koenecke N, Andreu MJ, Samper N, Paroush Z, Gonzalez-Crespo S, Zeitlinger J, Jimenez G.  Proc Natl Acad Sci U S A.2018;115:1807-1812.

Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis

De Kumar B, Parker HJ, Paulson A, Parrish ME, Zeitlinger J, Krumlauf R. Dev Biol.2017;432:151-164.

H19 promotes cholestatic liver fibrosis by preventing ZEB1-mediated inhibition of epithelial cell adhesion molecule

Song Y, Liu C, Liu X, Trottier J, Beaudoin M, Zhang L, Pope C, Peng G, Barbier O, Zhong X, Li L, Wang L. Hepatology.2017;66:1183-1196.

HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets

De Kumar B, Parker HJ, Paulson A, Parrish ME, Pushel I, Singh NP, Zhang Y, Slaughter BD, Unruh JR, Florens L, Zeitlinger J, Krumlauf R. Genome Res.2017;27:1501-1512.

Hippo Reprograms the Transcriptional Response to Ras Signaling

Pascual J, Jacobs J, Sansores-Garcia L, Natarajan M, Zeitlinger J, Aerts S, Halder G, Hamaratoglu F. Dev Cell.2017;42:667-680.e4.

Paused RNA polymerase II inhibits new transcriptional initiation

Shao W, Zeitlinger J. Nat Genet.2017;49:1045-1051.

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Drosophila poised enhancers are generated during tissue patterning with the help of repression

Koenecke N, Johnston J, He Q, Meier S, Zeitlinger J. Genome Res. 2017;27:64-74.

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

Koenecke N, Johnston J, Gaertner B, Natarajan M, Zeitlinger J. Genome Biol. 2016;17:196.

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation.

Sun Y, Nien CY, Chen K, Liu HY, Johnston J, Zeitlinger J, Rushlow C. Genome Res. 2015;25:1703-14.

Pharmacologically blocking p53-dependent apoptosis protects intestinal stem cells and mice from radiation.

Wang X, Wei L, Cramer JM, Leibowitz BJ, Judge C, Epperly M, Greenberger J, Wang F, Li L, Stelzner MG, Dunn JC, Martin MG, Lagasse E, Zhang L, Yu J. Sci Rep. 2015;5:8566. doi: 8510.1038/srep08566.

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.

He Q, Johnston J, Zeitlinger J. Nat Biotechnol. 2015;33:395-401.

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Off the deep end: What can deep learning do for the gene expression field?

Raicu AM, Fay JC, Rohner N, Zeitlinger J, Arnosti DN. J Biol Chem. 2022:102760.

Seven myths of how transcription factors read the cis-regulatory code

Zeitlinger J. Curr Opin Syst Biol. 2020;23:22-31.

Cori meets Dobzhansky: Evolution and Gene Expression in St. Louis.

Arnosti DN, Fay JC, Zeitlinger J. A report on the "Evolution and Core Processes in Gene Regulation" meeting in St. Louis, June 25-28, 2015. BioEssays. 2015;37:1042-1044.

Osteoblast ablation burns out functional stem cells.

Zhao M, Li L. Blood. 2015;125:2590-2591.

A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis.

Gracz AD, Williamson IA, Roche KC, Johnston MJ, Wang F, Wang Y, Attayek PJ, Balowski J, Liu XF, Laurenza RJ, Gaynor LT, Sims CE, Galanko JA, Li L, Allbritton NL, Magness ST. Nat Cell Biol. 2015;17:340-349.

Homing and migration assays of hematopoietic stem/progenitor cells.

He XC, Li Z, Sugimura R, Ross J, Zhao M, Li L. Methods Mol Biol. 2014;1185:279-284.

RNA polymerase II pausing during development.

Gaertner B, Zeitlinger J. Development. 2014;141:1179-1183.

Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.

Lagha M, Bothma JP, Esposito E, Ng S, Stefanik L, Tsui C, Johnston J, Chen K, Gilmour DS, Zeitlinger J, Levine MS. Cell. 2013;153:976-987.

MAPing the role of Kras mutations in hyperplastic polyps.

Barrett T, Li L. Gastroenterology. 2011;141:799-801.

Bone Metastasis Targets The Endosteal Hematopoietic Stem Cell Niche.

Sugimura R, Li L. IBMS BoneKEy. 2011;8:381-384.

Noncanonical Wnt signaling in vertebrate development, stem cells, and diseases.

Sugimura R, Li L. Birth Defects Res C Embryo Today. 2010;90:243-256.

Functional assays for hematopoietic stem cell self-renewal.

Perry JM, Li L. Methods Mol Biol. 2010;636:45-54.

Developmental gene regulation in the era of genomics.

Zeitlinger J, Stark A. Dev Biol. 2010;339:230-239.

HSC mobilization: new incites and insights.

Ross J, Li L. Blood. 2009;114:1283-1284.

Visualize eHPCs in different zones.

Yin T, Xie Y, Li L. Blood. 2009;114:230-231.

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