Publications
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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Perspective on recent developments and challenges in regulatory and systems genomics
Zeitlinger J, Roy S, Ay F, Mathelier A, Medina-Rivera A, Mahony S, Sinha S, Ernst J. Bioinform Adv. 2025;5:vbaf106.
Emerging questions in transcriptional regulation : What are the sequence rules driving gene regulation?
Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk M, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Cell Syst. 2023;14:247-251.
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. 2023;299:102760.
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.
To be or not to be a stem cell: dissection of cellular and molecular components of haematopoietic stem cell niches.
Perry JM, Li L. EMBO J. 2012;31:1060-1061.
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.
Book review of Evolution, Development, and the Predictable Genome by David L. Stern.
Zeitlinger J. Am J Hum Biol. 2011;43:414-420.
Noncanonical Wnt signaling in vertebrate development, stem cells, and diseases.
Sugimura R, Li L. Birth Defects Res C Embryo Today. 2010;90:243-256.
Fountain of Youth: aged blood-forming stem cells could be rejuvenated by young microenvironment.
Yin T, Li L. Cell Res. 2010;20:504-505.
Shifting in balance between osteogenesis and adipogenesis substantially influences hematopoiesis.
Sugimura R, Li L. J Mol Cell Biol. 2010;2:61-62.
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.
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