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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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.
Notch2 regulates BMP signaling and epithelial morphogenesis in the ciliary body of the mouse eye.
Zhou Y, Tanzie C, Yan Z, Chen S, Duncan M, Gaudenz K, Li H, Seidel C, Lewis B, Moran A, Libby RT, Kiernan AE, Xie T. Proc Natl Acad Sci U S A. 2013;110:8966-8971.
Mechanisms of tentacle morphogenesis in the sea anemone, Nematostella vectensis.
Fritz AE, Ikmi A, Seidel C, Paulson A, Gibson MC. Development. 2013;140:2212-2223.
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. Nat Genet. 2013;45:415-421.
Defective FGF signaling causes coloboma formation and disrupts retinal neurogenesis.
Chen S, Li H, Gaudenz K, Paulson A, Guo F, Trimble R, Peak A, Seidel C, Deng C, Furuta Y, Xie T. Cell Res. 2013;23:254-273.
Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan-Vavilov Deep.
Smedile F, Messina E, La Cono V, Tsoy O, Monticelli LS, Borghini M, Giuliano L, Golyshin PN, Mushegian A, Yakimov MM. Environ Microbiol. 2013;15:167-182.
Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression.
Gaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss AS, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J. Cell Rep. 2012;2:1670-1683.
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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.
