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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Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis.
Liang K, Woodfin AR, Slaughter BD, Unruh JR, Box AC, Rickels RA, Gao X, Haug JS, Jaspersen SL, Shilatifard A. Mol Cell. 2015;60:435-445.
Serine and SAM Responsive Complex SESAME Regulates Histone Modification Crosstalk by Sensing Cellular Metabolism.
Li S, Swanson SK, Gogol M, Florens L, Washburn MP, Workman JL, Suganuma T. Mol Cell. 2015;60:408-421.
Wnt signaling-mediated redox regulation maintains the germ line stem cell differentiation niche.
Wang S, Gao Y, Song X, Ma X, Zhu X, Mao Y, Yang Z, Ni J, Li H, Malanowski KE, Anoja P, Park J, Haug J, Xie T. eLife. 2015;4:e08174. doi: 08110.07554/eLife.08174.
VEGF Signals induce trailblazer cell identity that Drives Neural Crest Migration.
McLennan R, Schumacher LJ, Morrison JA, Teddy JM, Ridenour DA, Box AC, Semerad CL, Li H, McDowell W, Kay D, Maini PK, Baker RE, Kulesa PM. Dev Biol. 2015;407:12-25
Regeneration of Sensory Hair Cells Requires Localized Interactions between the Notch and Wnt Pathways.
Romero-Carvajal A, Navajas Acedo J, Jiang L, Kozlovskaja-Gumbriene A, Alexander R, Li H, Piotrowski T. Dev Cell. 2015;34:267-282.
Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells.
De Kumar B, Parrish ME, Slaughter BD, Unruh JR, Gogol M, Seidel C, Paulson A, Li H, Gaudenz K, Peak A, McDowell W, Fleharty B, Ahn Y, Lin C, Smith E, Shilatifard A, Krumlauf R. Genome Res. 2015;25:1229-1243.
Neural crest migration is driven by a few trailblazer cells with a unique molecular signature narrowly confined to the invasive front.
McLennan R, Schumacher LJ, Morrison JA, Teddy JM, Ridenour DA, Box AC, Semerad CL, Li H, McDowell W, Kay D, Maini PK, Baker RE, Kulesa PM. Development. 2015;142:2014-2025.
Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA.
Shanker S, Paulson A, Edenberg HJ, Peak A, Perera A, Alekseyev YO, Beckloff N, Bivens NJ, Donnelly R, Gillaspy AF, Grove D, Gu W, Jafari N, Kerley-Hamilton JS, Lyons RH, Tepper C, Nicolet CM. J Biomol Tech. 2015;26:4-18.
Zic2 is an enhancer-binding factor required for embryonic stem cell specification.
Luo Z, Gao X, Lin C, Smith ER, Marshall SA, Swanson SK, Florens L, Washburn MP, Shilatifard A. Mol Cell. 2015;57:685-694.
SR proteins control a complex network of RNA-processing events.
Bradley T, Cook ME, Blanchette M. RNA. 2015;21:75-92.
Histone acetyltransferase Enok regulates oocyte polarization by promoting expression of the actin nucleation factor spire.
Huang F, Paulson A, Dutta A, Venkatesh S, Smolle M, Abmayr SM, Workman JL. Genes & Dev. 2014;28:2750-2763.
Developmental Programming of Long Non-Coding RNAs during Postnatal Liver Maturation in Mice
Peng L, Paulson A, Li H, Piekos S, He X, Li L. PLoS One. 2014;9:e114917.
Swi/Snf dynamics on stress-responsive genes is governed by competitive bromodomain interactions.
Dutta A, Gogol M, Kim JH, Smolle M, Venkatesh S, Gilmore J, Florens L, Washburn MP, Workman JL. Genes Dev. 2014;29:2314-2330.
Piwi is required in multiple cell types to control germline stem cell lineage development in the Drosophila ovary.
Ma X, Wang S, Do T, Song X, Inaba M, Nishimoto Y, Liu LP, Gao Y, Mao Y, Li H, McDowell W, Park J, Malanowski K, Peak A, Perera A, Li H, Gaudenz K, Haug J, Yamashita Y, Lin H, Ni JQ, Xie T. PLoS One. 2014;9:e90267.
The DEAD Box Helicase RDE-12 Promotes Amplification of RNAi in Cytoplasmic Foci in C. elegans.
Yang H, Vallandingham J, Shiu P, Li H, Hunter CP, Mak HY. Curr Biol. 2014;24:832-838.
Context dependency of Set1/COMPASS-mediated histone H3 Lys4 trimethylation.
Thornton JL, Westfield GH, Takahashi YH, Cook M, Gao X, Woodfin AR, Lee JS, Morgan MA, Jackson J, Smith ER, Couture JF, Skiniotis G, Shilatifard A. Genes Dev. 2014;28:115-120.
The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers.
Hu D, Gao X, Morgan MA, Herz HM, Smith ER, Shilatifard A. Mol Cell Biol. 2013;33:4745-4754.
A global change in RNA polymerase II pausing during the Drosophila midblastula transition.
Chen K, Johnston J, Shao W, Meier S, Staber C, Zeitlinger J. eLife. 2013;2:e00861. doi: 00810.07554/eLife.00861.
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The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells.
Hu D, Garruss AS, Gao X, Morgan MA, Cook M, Smith ER, Shilatifard A. Nat Struct Mol Biol. 2013;20:1092-1097.
Maternal imprinting at the H19-Igf2 locus maintains adult haematopoietic stem cell quiescence.
Venkatraman A, He XC, Thorvaldsen JL, Sugimura R, Perry JM, Tao F, Zhao M, Christenson MK, Sanchez R, Yu JY, Peng L, Haug JS, Paulson A, Li H, Zhong XB, Clemens TL, Bartolomei MS, Li L. Nature. 2013;500:345-349.
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Identification and Localization of Cell Types in the Mouse Olfactory Bulb Using Slide-SeqV2
Fang A, Petentler K, Price A, Malloy S, Maddera C, Russell J, Treese M, Li H, Wang Y, McKinney S, Perera A, Yu CR. Methods Mol Biol. 2023;2710:171-183. Published Erratum Methods Mol Biol. 2023;2710:C1. doi: 10.1007/978-1-0716-3425-7_17.
Manipulation of Gene Activity in the Regenerative Model Sea Anemone, Nematostella vectensis
Hill EM, Chen CY, Del Viso F, Ellington LR, He S, Karabulut A, Paulson A, Gibson MC. Methods Mol Biol. 2022;2450:437-465.
Using fluorescent reporters in conjunction with cytometry and statistics to assess nuclear accumulation of ribosomal proteins
Kim DH, Box AC, Li H, Gerton JL. Methods Mol Biol.2017;1515:217-226.
Sec66-Dependent Regulation of Yeast Spindle-Pole Body Duplication Through Pom152.
Katta SS, Chen J, Gardner JM, Friederichs JM, Smith SE, Gogol M, Unruh JR, Slaughter BD, Jaspersen SL. Genetics. 2015;201:1479-1495
The Origin and Evolution of G Protein-Coupled Receptor Kinases.
Mushegian A, Gurevich VV, Gurevich EV. PLoS One. 2012;7:e33806.
Grand challenges in bioinformatics and computational biology.
Mushegian A. Front Genet. 2011;2:60.
Computational methods for Gene Orthology inference.
Kristensen DM, Wolf YI, Mushegian AR, Koonin EV. Brief Bioinform. 2011;12:379-391.
Thematic minireview series on computational systems biology.
Mushegian A, Conaway JW. J Biol Chem. 2011;286:23621-23622.
