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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Environmental and molecular regulation of asexual reproduction in the cnidarian Nematostella vectensis
Al-Shaer L, Leach W, Baban N, Yagodich M, Gibson MC, Layden MJ. R Soc Open Sci. 2023;10:230152.
Ac/Ds transposition for CRISPR/dCas9-SID4x epigenome modulation in zebrafish
Chong-Morrison V, Mayes S, Simoes FC, Senanayake U, Carroll DS, Riley PR, Wilson SW, Sauka-Spengler T. Biol Open. 2023;12.
Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility
Olsen L, Levy M, Medley JK, Hassan H, Miller B, Alexander R, Wilcock E, Yi K, Florens L, Weaver K, McKinney SA, Peuss R, Persons J, Kenzior A, Maldonado E, Delventhal K, Gluesenkamp A, Mager E, Coughlin D, Rohner N. Proc Natl Acad Sci U S A. 2023;120:e2204427120.
FGF2 antiproliferative effect in K-ras-driven tumor cells involves modulation of rRNA and nucleolus
de Luna Vitorino FN, Levy MJ, Mansano Wailemann RA, Lopes M, Silva ML, Sardiu ME, Garcia BA, Motta MCM, Oliveira CC, Armelin HA, Florens LA, Washburn MP, da Cunha JPC. [published ahead of print Novermber 3 2023]. J Cell Sci. 2023.
Reproductive seasonality of Astyanax mexicanus
Espinasa L, Rohner N, Retaux S. Zool Res. 2023;44:698-700.
The multi-lineage transcription factor ISLI controls cardiomyocyte cell fate through interaction with NKX2.5
Maven BEJ, Gifford CA, Weilert M, Gonzalez-Teran B, Huttenhain R, Pelonero A, Ivey KN, Samse-Knapp K, Kwong W, Gordon D, McGregor M, Nishino T, Okorie E, Rossman S, Costa MW, Krogan NJ, Zeitlinger J, Srivastava D. Stem Cell Rep. [published ahead of print October 21 2023]. 2023.
Short tandem repeats bind transcription factorsto tune eukaryotic gene expression
Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordan R, Zeitlinger J, Kundaje A, Fordyce PM. Science. 2023;381:eadd1250.
Phylogeographic relationships and morphological evolution between cave and surface Astyanax mexicanus populations (De Filippi 1853) (Actinopterygii, Characidae)
Garduno-Sanchez M, Hernandez-Lozano J, Moran RL, Miranda-Gamboa R, Gross JB, Rohner N, Elliott WR, Miller J, Lozano-Vilano L, McGaugh SE, Ornelas-Garcia CP. Mol Ecol. 2023;32:5626-5644.
Understanding and Overcoming Immunosuppression Shaped by Cancer Stem Cells
Li L, Jensen RA. Cancer Res. 2023;83:2096-2104.
The Swi-Snf chromatin remodeling complex mediates gene repression through metabolic control
Church MC, Price A, Li H, Workman JL. Nucleic Acids Res. 2023;51:10278-10291.
Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal
Kandola T, Venkatesan S, Zhang J, Lerbakken B, Schulze AV, Blanck JF, Wu J, Unruh J, Berry P, Lange JJ, Box A, Cook M, Sagui C, Halfmann R. eLife 2023;12:RP86939. doi: 10.7554/eLife.86939.
SYCP1 head-to-head assembly is required for chromosome synapsis in mouse meiosis
Billmyre KK, Kesler EA, Tsuchiya D, Corbin TJ, Weaver K, Moran A, Yu Z, Adams L, Delventhal K, Durnin M, Davies OR, Hawley RS. Sci Adv. 2023;9:eadi1562.
Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development.
Ramalingam V, Yu X, Slaughter BD, Unruh JR, Brennan KJ, Onyshchenko A, Lange JJ, Natarajan M, Buck M, Zeitlinger J. Nat Commun. 2023;14:5862 doi: 10.1038/s41467-023-41408-1.
Phase plane dynamics of ERK phosphorylation
Shvartsman SY, McFann S, Wuhr M, Rubinstein BY. [published ahead of print September 11 2023]. J Biol Chem. 2023:105234.
Hypomyelination, hypodontia and craniofacial abnormalities in a Polr3b mouse model of leukodystrophy
Michell-Robinson MA, Watt KEN, Grouza V, Macintosh J, Pinard M, Tuznik M, Chen X, Darbelli L, Wu CL, Perrier S, Chitsaz D, Uccelli NA, Liu H, Cox TC, Muller CW, Kennedy TE, Coulombe B, Rudko DA, Trainor PA, Bernard G. [published ahead of print August 28 2023]. Brain. 2023:1-16.
rRNA transcription is integral to phase separation and maintenance of nucleolar structure
Dash S, Lamb MC, Lange JJ, McKinney MC, Tsuchiya D, Guo F, Zhao X, Corbin TJ, Kirkman M, Delventhal K, Moore EL, McKinney S, Shiang R, Trainor PA. PLoS Genet. 2023;19:e1010854.
Cell-type profiling of the sympathetic nervous system using spatial transcriptomics and spatial mapping of mRNA..
Kasemeier-Kulesa JC, Morrison JA, McKinney S, Li H, Gogol M, Hall K, Chen S, Wang Y, Perera A, McLennan R, Kulesa PM. Dev Dyn. 2023;252:1130-1142.
The complete sequence of a human Y chromosome
Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. Nature. 2023;621:344-354.
Gap Junction-transported cAMP from the Niche Controls Stem Cell Progeny Differentiation
Tu R, Tang XA, Xu R, Ping Z, Yu Z, Xie T. [published ahead of print August 21 2023]. PNAS. 2023;120:e2304168120.
Extravillous trophoblast cell lineage development is associated with active remodeling of the chromatin landscape
Varberg KM, Dominguez EM, Koseva B, Varberg JM, McNally RP, Moreno-Irusta A, Wesley ER, Iqbal K, Cheung WA, Schwendinger-Schreck C, Smail C, Okae H, Arima T, Lydic M, Holoch K, Marsh C, Soares MJ, Grundberg E. Nat Commun. 2023;14:4826 doi: 10.1038/s41467-023-40424-5.
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Chromatin balances cell redox and energy homeostasis
Sugamuna T, Workman J. Epigenet Chromatin. 2023;16:46. https://doi.org/10.1186/s13072-13023-00520-13078.
A Generalist's Guide to Quantifying Swimming Behavior Within Traditional and Nontraditional Teleost Models
Olsen L, Alexander R, Krishnan J, Rohner N. In: W Wang, Y Wang, and N Rohner, eds. Emerging Model Organisms. New York, NY: Humana, New York, NY; 2023;194:263-272.
The SWI/SNF Complex in Neural Crest Cell Development and Disease
Fountain DM, Sauka-Spengler T. Annu Rev Genomics Hum Genet. 2023;24:203-223.
Unraveling the Molecular Arms Race: Grapevine Fanleaf Virus Proteins as Suppressors of Plant Antiviral Silencing Pathways
Sankari S, Lovelace AH. Mol Plant Microbe Interact. 2023;36:534-535.
Second Special Issue on Methods for Omics Research: Proteome Research and Beyond
Florens L, Dong MQ, LaBaer J. J Proteome Res. 2023;22:1381-1384.
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.
Serial block-face scanning electron microscopy of Schmidtea mediterranea.
McClain ML, Nowotarski SH. Methods Cell Biol. 2023;177:213-240.
The cavefish Astyanax mexicanus
Rohner N. Nat Methods. 2023;20:948-950.
(mis)‑Targeting of SWI/SNF complex(es) in cancer
Reddy D, Bhattacharya S, Workman JL. Cancer Metastasis Rev. 2023.
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.
Establishment, long-term maintenance, and Characterization of Primary Liver Cells from Astyanax mexicanus
Rajendran N, Deng F, Wang Y, Kenzior O, Krishnan J, Biswas T, Parmely T, Rohner N, Zhao C. Curr Protoc. 2023;3:e736.
Personal autonomy and self-determination are crucial for professionalism in healthcare
Organ JM, Smith HF, Trainor PA, Allen K, Balta JY, Beresheim AC, Brewer-Deluce D, Brown KM, Burrows AM, Byers KT, Byram JN, Cale AS, Carroll MA, Champney T, Cornwall J, Dayal MR, DeLeon VB, Dunnwald M, Ferrigno C, Finn GM, Fox GM, Geller PL, Guttmann GD, Harper N, Harrell KM, Hartstone-Rose A, Hildebrandt S, Hortsch M, Jackson J, Johnson LE, Lohman Bonfiglio CM, McCumber TL, Menegaz RA, Mussell JC, O'Loughlin VD, Otobo TM, Oyedele O, Pascoe MA, Person D, Reidenberg JS, Robinson RE, Rogers KA, Ros MA, Ross CF, Sanders KA, Schmitt B, Schoenwolf GC, Smith TC, Smith TD, Sumner DR, Taylor AB, Taylor MJ, Teaford MF, Topp KS, Willmore KE, Wisco JJ, Yang J, Zumwalt AC. Anat Sci Educ. 2023;16:571-573.
Translation and mRNA Stability Control
Wu Q, Bazzini AA. [published ahead of print April 1 2023]. Annu Rev Biochem 2023.
Epithelial to mesenchymal transition during mammalian neural crest cell delamination
Zhao R, Trainor PA. Semin Cell Dev Biol. 2023;138:54-67.
RNA Polymerases I and III in development and disease
Watt KE, Macintosh J, Bernard G, Trainor PA. Semin Cell Dev Biol. 2023;136:49-63.
Gene-environment interactions in the pathogenesis of common craniofacial anomalies
Fitriasari S, Trainor PA. Curr Top Dev Biol. 2023;152:139-168.
ISSCR Education Committee Syllabus and Learning Guide for Enhancing Stem Cell Literacy
Perlin JR, Anderson WJ, Bartfeld S, Couturier A, de Soysa Y, Hawley RS, Hu P, Loh YH, Mandal L, Master Z, Muotri AR, Piddini E, Polo JM, Mazzoni EO. Stem Cell Rep. 2023;18:417-419
Emerging Model Organisms
Wang W, Rohner N, Wang Y, eds. Neuromethods, Springer Protocols: Humana Press. 2023.
Multiplexed Quantitative Proteomics Analysis of Developing Human Brain Organoids
Florens L, Saraf A, Hao Y, Zhang Y, Wang Y, Parmely TJ, Zhao C, Washburn MP. In: W Wang, Y Wang, and N Rohner, eds. Emerging Model Organisms; 2023;194:325-355.
Generation of mini-brains from hiPSCs
Wang Y, Tsuchiya D, Zhao C. In: W Wang, Y Wang, and N Rohner, eds. Emerging model organism. New York, New York: Humana, New Yor, NY; 2023;194:291-306.
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