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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Topological structures and syntenic conservation in sea anemone genomes
Zimmermann B, Montenegro JD, Robb SMC, Fropf WJ, Weilguny L, He S, Chen S, Lovegrove-Walsh J, Hill EM, Chen CY, Ragkousi K, Praher D, Fredman D, Schultz D, Moran Y, Simakov O, Genikhovich G, Gibson MC, Technau U. Nat Commun. 2023;14:8270.
Microglial Rac1 is essential for experience-dependent brain plasticity and cognitive performance
Socodato R, Almeida TO, Portugal CC, Santos ECS, Tedim-Moreira J, Galvao-Ferreira J, Canedo T, Baptista FI, Magalhaes A, Ambrosio AF, Brakebusch C, Rubinstein B, Moreira IS, Summavielle T, Pinto IM, Relvas JB. Cell Rep. 2023;42:113447 doi: 10.1016/j.celrep.2023.113447.
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.
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.
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.
An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes.
Timoshevskaya N, Eskut KI, Timoshevskiy VA, Robb SMC, Holt C, Hess JE, Parker HJ, Baker CF, Miller AK, Saraceno C, Yandell M, Krumlauf R, Narum SR, Lampman RT, Gemmell NJ, Mountcastle J, Haase B, Balacco JR, Formenti G, Pelan S, Sims Y, Howe K, Fedrigo O, Jarvis ED, Smith JJ. Cell Rep. 2023;42:112263.
S. pombe wtf use dual transcriptional regulation and selective protein exclusion from spores to cause meiotic drive
Nuckolls NL, Nidamangala Srinivasa A, Mok AC, Helston RM, Bravo Nunez MA, Lange JJ, Gallagher TJ, Seidel CW, Zanders SE. PLos Genet. 2022:e1009847 doi: 10.1371/journal.pgen.1009847.
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies
Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D. Database (Oxford). 2022;2022.
Lamb-type solution and properties of unsteady Stokes equation
Fouxon I, Leshansky A, Rubinstein B, Or Y. Phys Rev Fluids. 2022;7:094103 doi: 10.1103/PhysRevFluids.7.094103.
The architecture and operating mechanism of a cnidarian stinging organelle
Karabulut A, McClain M, Rubinstein B, Sabin KZ, McKinney SA, Gibson MC. Nat Commun. 2022;13:3494. doi: 10.1038/s41467-41022-31090.
Nature of the Poynting Vector Field Singularities in Resonant Light Scattering by Nanoparticles
Tribelsky MI, Rubinstein BY. Nanomaterials (Basel). 2022;12:1878. doi: 1810.3390/nano12111878.
Mediator recruits the cohesin loader Scc2 to RNA Pol II transcribed genes and promotes sister chromatid cohesion
Mattingly M, Seidel C, Munoz S, Hao Y, Zhang Y, Wen Z, Florens L, Uhlmann F, Gerton JL. [published ahead of print June 3 2022]. Curr Biol. 2022;32.
Complete genomic and epigenetic maps of human centromeres
Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. [published ahead of print April 1 2022]. Science. 2022;376:eabl4178.
The complete sequence of a human genome
Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sovic I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. Science. 2022;376:44-53.
The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters
Soffers JHM, Alcantara SG, Li X, Shao W, Seidel CW, Li H, Zeitlinger J, Abmayr SM, Workman JL. PLoS Genet. 2021;17:e1009668. doi: 10.1371/journal.pgen.1009668.
Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals
Arnold CP, Lozano AM, Mann FG, Jr., Nowotarski SH, Haug JO, Lange JJ, Seidel CW, Sánchez Alvarado A. Nat Commun. 2021;12:6706. doi: 6710.1038/s41467-41021-26986-41462.
Tumor-initiating stem cell shapes its microenvironment into an immunosuppressive barrier and pro-tumorigenic niche
He X, Smith SE, Chen S, Li H, Wu D, Meneses-Giles PI, Wang Y, Hembree M, Yi K, Zhao X, Guo F, Unruh JR, Maddera LE, Yu Z, Scott A, Perera A, Wang Y, Zhao C, Bae K, Box A, Haug JS, Tao F, Hu D, Hansen DM, Qian P, Saha S, Dixon D, Anant S, Zhang D, Lin EH, Sun W, Wiedemann LM, Li L. Cell Rep. 2021;36:109674.doi: 10.1016/j.celrep.2021.109674.
The Planarian Anatomy Ontology: A resource to connect data within and across experimental platforms
Nowotarski SH, Davies EL, Robb SMC, Ross EJ, Matentzoglu N, Doddihal V, Mir M, McClain M, Sánchez Alvarado A. Development. 2021;148:dev196097. doi: 196010.191242/dev.196097.
Biphasic co-flow through a sudden expansion or contaction of Hele-Shaw channel
Rubinstien BY, Zusmanovich D, Li Z, Leshansky AM. Phys Rev Fluids. 2021;6:074201. doi: 10.1103/PhysRevFluids.6.074201.
Repeated evolution of circadian clock dysregulation in cavefish populations
Mack KL, Jaggard JB, Persons JL, Roback EY, Passow CN, Stanhope BA, Ferrufino E, Tsuchiya D, Smith SE, Slaughter BD, Kowalko J, Rohner N, Keene AC, McGaugh SE. PLoS Genet. 2020;17:e1009642.
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Mechanical plasticity during oligodendrocyte differentiation and myelination
Domingues HS, Cruz A, Chan JR, Relvas JB, Rubinstein B, Pinto IM. Glia.2018;66:5-14.
Stability of Unduloidal and Nodoidal Menisci between two Solid Spheres
Rubinstein B, Fel L. J Geom Symmetry Phys.2015;39:77-98.
Epithelia migration: a spatiotemporal interplay between contraction and adhesion
Rubinstein B, Pinto IM. Cell Adh Migr. 2015:340-4.
SmedGD 2.0: The Schmidtea mediterranea genome database.
Robb SM, Gotting K, Ross E, Sanchez Alvarado A. Genesis. 2015;53:535-546.
Imaging methodologies for systems biology.
Smith SE, Slaughter BD, Unruh JR. Cell Adh & Migr. 2014;8:468-477.
Symmetry breaking and polarity establishment during mouse oocyte maturation.
Yi K, Rubinstein B, Li R. Philos Trans R Soc Lond B Biol Sci. 2013;368:20130002.
Force to divide: structural and mechanical requirements for actomyosin ring contraction.
Mendes Pinto I, Rubinstein B, Li R. Biophys J. 2013;105:547-554.
Whole chromosome aneuploidy: Big mutations drive adaptation by phenotypic leap.
Chen G, Rubinstein B, Li R. BioEssays. 2012;34:893-900.
Cbk1 regulation of the RNA-binding protein Ssd1 integrates cell fate with translational control.
Jansen JM, Wanless AG, Seidel CW, Weiss EL. Curr Biol. 2009;19:2114-2120.
