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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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. [published ahead of print August 24 2023]. Nature. 2023.
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.
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation
Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. [published ahead of print August 8 2023]. Dev Cell 2023;58:1-19.
Nascent mitochondrial proteins initiate the localized condensation of cytosolic protein aggregates on the mitochondrial surface
Liu Q, Fong B, Yoo S, Unruh JR, Guo F, Yu Z, Chen J, Si K, Li R, Zhou C. Proc Natl Acad Sci U S A. 2023;120:e2300475120.
Gas-assisted microfluidic step-emulsification for generating micron- and submicron-sized droplets
Huang B, Ge X, Rubinstein BY, Chen X, Wang L, Xie H, Leshansky AM, Li Z. Microsyst Nanoeng. 2023;9:86.
Cavefish mount a rapid and sustained regenerative response following skeletal muscle injury.
Olsen L, Hassan H, Xia F, Keaton S, Rohner N. Zool Res. 2023;44:776-778.
Spatial transcriptomics reveals a cnidarian segment polarity program in Nematostella vectensis
He S, Shao W, Chen SC, Wang T, Gibson MC. Curr Biol 2023;33:1-12.
Excess shear force exerted on an oscillating plate due to a nearby particle
Fouxon I, Rubinstein BY, Leshansky AM. Phys Rev Fluids. 2023;8:054104 doi: 10.1103/PhysRevFluids.8.054104.
A Borrelia burgdorferi LptD homolog is required for flipping of surface lipoproteins through the spirochetal outer membrane
He H, Pramanik AS, Swanson SK, Johnson DK, Florens L, Zuckert WR. [published ahead of print April 28 2023]. Mol Microbiol. 2023.
Recombination between heterologous human acrocentric chromosomes
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Human Pangenome Reference C, Gerton JL, Phillippy AM, Colonna V, Garrison E. Nature. 2023;617:335-343.
Myc promotes polyploidy in murine trophoblast cells and suppresses senescence
Singh VP, Hassan H, Deng F, Tsuchiya D, McKinney S, Ferro K, Gerton JL. [published ahead of print June 6 2023]. Development. 2023;150.
B chromosomes reveal a female meiotic drive suppression system in Drosophila melanogaster
Hanlon SL, Hawley RS. [published ahead of print May 5 2023]. Curr Biol 2023;33:1-7.
Selection-driven trait loss in independently evolved cavefish populations
Moran RL, Richards EJ, Ornelas-Garcia CP, Gross JB, Donny A, Wiese J, Keene AC, Kowalko JE, Rohner N, McGaugh SE. Nat Commun. 2023;14:2557 doi: 10.1038/s41467-023-37909-8.
POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies
Smallwood K, Watt KEN, Ide S, Baltrunaite K, Brunswick C, Inskeep K, Capannari C, Adam MP, Begtrup A, Bertola DR, Demmer L, Demo E, Devinsky O, Gallagher ER, Guillen Sacoto MJ, Jech R, Keren B, Kussmann J, Ladda R, Lansdon LA, Lunke S, Mardy A, McWalters K, Person R, Raiti L, Saitoh N, Saunders CJ, Schnur R, Skorvanek M, Sell SL, Slavotinek A, Sullivan BR, Stark Z, Symonds JD, Wenger T, Weber S, Whalen S, White SM, Winkelmann J, Zech M, Zeidler S, Maeshima K, Stottmann RW, Trainor PA, Weaver KN. Am J Hum Genet. 2023;110:809-825.
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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.
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 J, Beresheim AB, 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 T, Oyedele O, Pascoe MA, Person D, Reidenberg JS, Robinson RE, Rogers KA, Ros MA, Ross CF, Sanders KA, Schmitt B, Schoenwolf GC, Smith TD, Smith TC, Sumner DR, Taylor AB, Taylor MJ, Teaford MF, Topp KS, Willmore KE, Wisco JJ, Yang J, Zumwalt AC. [published ahead of print April 5 2023]. Anat Sci Educ 2023.
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.
Cell culture: in vitro model system and a promising path to in vivo applications
Zhao C.. J Histotechnol. 2023;46:1-4 doi: 10.1080/01478885.2023.2170772.
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.
Chromosome-specific behaviors during early meiosis
Billmyre KK. Curr Top Dev Biol. 2023;151:127-154.
