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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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Semi-automated assembly of high-quality diploid human reference genomes

Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton RS, Fulton LL, Garg S, Gerton JL, Ghurye J, Granat A, Green RE, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger EB, Jain M, Kirsche M, Kolmogorov M, Korbel JO, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell MW, McDaniel J, Nie F, Olsen HE, Olson ND, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg SL, Sanders AD, Schatz MC, Schmitt A, Schneider VA, Selvaraj S, Shafin K, Shumate A, Stitziel NO, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin AV, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook JM, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH, Human Pangenome Reference C. Nature. 2022;611:519-531.

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.

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O'Neill RJ. [published ahead of print April 1 2022]. Science. 2022;376:eabk3112.

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.

PCR amplicons to determine human centromeric array copy number reveal wide-spread size variation and instability in cancer

de Lima LG, Howe E, Singh VP, Potapova T, Li H, Xu B, Castle J, Crozier S, Harrison CJ, Clifford SC, Miga KH, Ryan SL, Gerton JL. Cell Genom. 2022;1:

100064.

 doi: 10.1016/j.xgen.2021.100064.

Maternal Smc3 protects the integrity of the zygotic genome through DNA replication and mitosis

Yueh WT, Singh VP, Gerton JL. Development. 2022;148:dev199800. doi: 199810.191242/dev.199800.

Immature Follicular Origins and Disrupted Oocyte Growth Pathways Contribute to Decreased Gamete Quality During Reproductive Juvenescence in Mice

Kusuhara A, Babayev E, Zhou LT, Singh VP, Gerton JL, Duncan FE. Frontiers. 2021;9:Article 693742. doi: 693710.693389/fcell.692021.693742.

The structure, function and evolution of a complete human chromosome 8

Logsdon GA, Vollger MR, Hsieh P, Mao Y, Liskovykh MA, Koren S, Nurk S, Mercuri L, Dishuck PC, Rhie A, de Lima LG, Dvorkina T, Porubsky D, Harvey WT, Mikheenko A, Bzikadze AV, Kremitzki M, Graves-Lindsay TA, Jain C, Hoekzema K, Murali SC, Munson KM, Baker C, Sorensen M, Lewis AM, Surti U, Gerton JL, Larionov V, Ventura M, Miga KH, Phillippy AM, Eichler EE. T [published ahead of print April 9 2021]. Nature. 2021.

DNA replication, transcription, and H3K56 acetylation regulate copy number and stability at tandem repeats

Salim D, Bradford WD, Rubinstein B, Gerton JL. G3 (Bethesda). 2021:jkab082. doi:010.1093/g1093journal/jkab1082.

Protocol for mouse trophoblast stem cell isolation, differentiation and cytokine detection

Singh VP, Gerton JL. STAR Protoc. 2021;2:100242. doi: 10.1016/ j.xpro.2020.100242.

Origins and evolutionary patterns of the 1.688 satellite DNA family in Drosophila phylogeny

de Lima LG, Hanlon SL, Gerton JL. G3 (Bethesda). 2020;10:4129-4146.

Telomere-to-telomere assembly of a complete human X chromosome

Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM. Nature. 2020;585:79-84.

Persistent DNA damage and senescense in the placenta impacts developmental outcomes of embryos

Singh VP, McKinney S, Gerton JL. Dev Cell. 2020;54:333-347 e337.

Super-resolution microscopy reveals linkages between ribosomal DNA on heterologous chromosomes

Potapova TA, Unruh JR, Yu Z, Rancati G, Li H, Stampfer MR, Gerton JL. J Cell Biol. 2019;218:2492-2513.

The stoichiometry of the outer kinetochore is modulated by microtubule-proximal regulatory factors

Dhatchinamoorthy K, Unruh JR, Lange JJ, Levy M, Slaughter BD, Gerton JL. J Cell Biol. 2019;218:2124-2135.

Oocyte-specific deletion of Hdac8 in mice reveals stage-specific effects on fertility

Singh VP, Yueh WT, Gerton JL, Duncan FE. Reproduction. 2019;157:305-316.

Chromatin assembly factor-1 (CAF-1) chaperone regulates Cse4 deposition into chromatin in budding yeast​

Hewawasam GS, Dhatchinamoorthy K, Mattingly M, Seidel C, Gerton JL. Chromatin assembly factor-1 (CAF-1) chaperone regulates Cse4 deposition into chromatin in budding yeast. [published ahead of print May 8 2018]. Nucleic Acids Res.2018.

Integrative structure and functional anatomy of a nuclear pore complex

Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP. Nature.2018;555:475-482.

Cohesin facilitates zygotic genome activation in zebrafish

Meier M, Grant J, Dowdle A, Thomas A, Gerton J, Collas P, O'Sullivan JM, Horsfield JA. Development.2018;145:dev156521. 156510.151242/dev.156521.

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Nucleolar Organizer Regions as transcription-based scaffolds of nucleolar structure and function

Cockrell AJ, Gerton JL. In: M Kloc, and JZ Kubiak, eds. Nuclear, Chromosomal, and Genomic Architecture in Biology and Medicine. Results and Problems in Cell Differentiation. 2022/11/09 ed; 2022;70:551-580.

Faulty ribosome biogenesis underlies the ANE syndrome ribosomopathy

Gerton JL. Proc Natl Acad Sci U S A. 2021;118:e2107030118. doi: 2107030110.2107031073/pnas.2107030118.

Cornelia de Lange syndrome, related disorders, and the Cohesin complex: Abstracts from the 8th biennial scientific and educational symposium 2018

Kline AD, Krantz ID, Bando M, Shirahige K, Chea S, Sakata T, Rao S, Dorsett D, Singh VP, Gerton JL, Horsfield JA, Calof AL, Katz O, Grados M, Raible S, Baranano K, Lyon G, Musio A, Carrico CS, Clemens DK, Caudill P, Massa V, McGill BE, Dommestrup A, O'Connor J, Haaland RE. Am J Med Genet A. 2019;179:1030-1090.

Ribosomal DNA and the nucleolus in the context of genome organization

Potapova TA, Gerton JL. Chromosome Res. 2019;27:109-127.

Ribosomal DNA instability and genome adaptability

Salim D, Gerton JL. Chromosome Res. 2019;27:73-87.

Ribosomal DNA-connecting ribosome biogenesis and chromosome biology

Porokhovnik L, Gerton JL. Chromosome Res. 2019;27:1-3.

A transcription factor primes the condensin pump

Gerton JL. J Cell Biol.2018;217:2233-2234.

Regulation of kinetochore configuration during mitosis

Dhatchinamoorthy K, Mattingly M, Gerton JL. Curr Genet. 2018;64:1197-1203.

Mammalian oogenesis and female reproductive aging

Duncan FE, Gerton JL. Aging (Albany NY).2018;10:162-163.

Taking cohesin and condensin in context

Yuen KC, Gerton JL. PLoS Genet.2018;14:e1007118. doi: 10.1371/journal.pgen.1007118.

Cohesin and human disease: lessons from mouse models.

Singh VP, Gerton JL. Curr Opin Cell Biol. 2015;37:9-17.

Etiology and pathogenesis of the cohesinopathies.

Zakari M, Yuen K, Gerton JL. Wiley Interdiscip Rev Dev Biol. 2015;4:489-504.

The SMC loader Scc2 regulates gene expression.

Zakari M, Gerton JL. Cell Cycle. 2015;14:943.

The dynamics of the Cse4 chaperone Scm3.

Shivaraju M, Gerton JL. Cell Cycle. 2011;10:3823.

Spc25 - How the kinetochore protein plays during oocyte meiosis.

Xiong B. Spc25: Cell Cycle. 2011;10:1031-1030.

Cse4 gets a kiss-of-death from Psh1.

Hewawasam GS, Gerton JL. Cell Cycle. 2011;10:566-567.

Cohesinopathies, gene expression, and chromatin organization.

Bose T, Gerton JL. J Cell Biol. 2010;189:201-210.

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