Publications

Original Research Papers
Origins and evolutionary patterns of the 1.688 satellite DNA family in Drosophila phylogeny
de Lima LG, Hanlon SL, Gerton JL. [published ahead of print SeptemberG3 (Bethesda). 2020.
Original Data
Identification of Stem Cells from Large Cell Populations with Topological Scoring
Sardiu ME, Box AC, Haug JS, Washburn MP. [published ahead of print September 15 2020]. Mol Omics. 2020.
Matrix metalloprotease-mediated cleavage of neural glial-related cell adhesion molecules activates quiescent olfactory stem cells via EGFR
Chen ZH, Luo XC, Yu CR, Huang L. Mol Cell Neurosci. 2020:103552.
Feeding-dependent tentacle development in the sea anemone Nematostella vectensis
Ikmi A, Steenbergen PJ, Anzo M, McMullen MR, Stokkermans A, Ellington LR, Gibson MC. Nat Commun. 2020;11:4399. doi: 4310.1038/s41467-41020-18133-41460.
Original Data
Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates
Wang W, Hu CK, Zeng A, Alegre D, Hu D, Gotting K, Ortega Granillo A, Wang Y, Robb S, Schnittker R, Zhang S, Alegre D, Li H, Ross E, Zhang N, Brunet A, Sanchez Alvarado A. Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates. Science. 2020;369: eaaz3090. doi: 10.1126/science.aaz3090.
Original Data
Pak1ip1 loss-of-function leads to cell cycle arrest, loss of neural crest cells, and craniofacial abnormalities
Panoutsopoulos AA, De Crescenzo A, Lee A, Lu AM, Ross AP, Yarov-Yarovoy V, Borodinsky L, Marcucio R, Trainor P, Zarbalis K. Front Cell Dev Biol. 2020;8:510063. doi: 510010.513389/fcell.512020.510063.
Orderly assembly underpinning built-in asymmetry in the yeast centrosome duplication cycle requires cyclin-dependent kinase
Geymonat M, Peng Q, Guo Z, Yu Z, Unruh JRJ, S. L., Segal M. eLife. 2020;9:e5922. doi: 10.7554/eLife.59222.
Original Data
Evaluating the Effects of Cell Sorting on Gene Expression
Box A, DeLay M, Tighe S, Chittur SV, Bergeron A, Cochran M, Lopez P, Meyer EM, Saluk A, Thornton S, Brundage K. J Biomol Tech: JBT. 2020.
Original Data
b-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells
Tao F, Soffers J, Hu D, Chen S, Gao X, Zhang Y, Zhao C, Smith SE, Unruh JR, Zhang D, Tsuchiya D, Venkatraman A, Zhao M, Li Z, Qian P, Parmely T, He XC, Washburn M, Florens L, Perry JM, Zeitlinger J, Workman J, Li L. Stem Cell Rep. 2020. https://www.ncbi.nlm.nih.gov/pubmed/32822591.
Original Data
Atypical meiosis can be adaptive in outcrossed S. pombe due to wtf meiotic drivers
Bravo Nunez MA, Sabbarini IM, Eide LE, Unckless RL, Zanders SE. eLife. 2020;9:e57936. doi: 57910.57554/eLife.57936.
Original Data
CRISPR-Cas13d induces efficient mRNA knockdown in animal embryos
Kushawah G, Hernandez-Huertas L, Abugattas-Nunez Del Prado J, Martinez-Morales JR, DeVore ML, Hassan H, Moreno-Sanchez I, Tomas-Gallardo L, Diaz-Moscoso A, Monges DE, Guelfo JR, Theune WC, Brannan EO, Wang W, Corbin TJ, Moran AM, Sanchez Alvarado A, Malaga-Trillo E, Takacs CM, Bazzini AA, Moreno-Mateos MA. [published ahead of print August 10 2020]. Dev Cell. 2020.
Original Data
Retinoic acid synthesis and autoregulation mediate zonal patterning of vestibular organs and inner ear morphogenesis
Ono K, Sandell LL, Trainor PA, Wu DK. [published ahead of print August 7 2020]. Development. 2020;147.
Translation of small downstream ORFs enhances translation of canonical main open reading frames
Wu Q, Wright M, Gogol MM, Bradford WD, Zhang N, Bazzini AA. Embo J. 2020:e104763. doi:10.15252/embj.2020104763
Original Data
Adaptation to low parasite abundance affects immune investment and immunopathological responses of cavefish
Peuß R, Box AC, Chen S, et al. [published online ahead of print, 2020 Jul 20]. Nat Ecol Evol. 2020;10.1038/s41559-020-1234-2. doi:10.1038/s41559-020-1234-2.
Original Data
FAM20B-catalyzed glycosaminoglycans control murine tooth number by restricting FGFR2b signaling
Wu J, Tian Y, Han L, Liu C, Sun T, Li L, Yu Y, Lamichhane B, D'Souza RN, Millar SE, Krumlauf R, Ornitz DM, Feng JQ, Klein O, Zhao H, Zhang F, Linhardt RJ, Wang X. BMC Biol. 2020;18:87. https://doi.org/10.1186/s12915-12020-00813-12914.
Wampa is a dynein subunit required for axonemal assembly and male fertility in Drosophila
Bauerly E, Yi K, Gibson MC. Dev Biol. 2020;463:158-168.
Original Data
Telomere-to-telomere assembly of a complete human X chromosome
Miga KH, Koren S, Rhie A, et al. [published online ahead of print, 2020 Jul 14]. Nature. 2020;10.1038/s41586-020-2547-7. doi:10.1038/s41586-020-2547-7.
Original Data
37/67-laminin receptor facilitates neural crest cell migration during enteric nervous system development
Fu M, Barlow-Anacker AJ, Kuruvilla KP, Bowlin GL, Seidel CW, Trainor PA, FASEB J. 2020;34:10931–10947.
Original Data
Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping
Sas-Chen, A., Thomas, J.M., Matzov, D. et. Nature. 2020;583:638–643. https://doi.org/10.1038/s41586-020-2418-2.
Original Data
Persistent DNA damage and senescense in the placenta impacts developmental outcomes of embryos
Vijay Pratap Singh, Sean McKinney, Jennifer L. Gerton. [published ahead of print June 16 2020]. Dev Cell. 2020. doi: 10.1016/j.devcel.2020.05.025.
Original Data
Overcoming Wnt-beta-catenin dependent anticancer therapy resistance in leukaemia stem cells
Perry JM, Tao F, Roy A, Lin T, He XC, Chen S, Lu X, Nemechek J, Ruan L, Yu X, Dukes D, Moran A, Pace J, Schroeder K, Zhao M, Venkatraman A, Qian P, Li Z, Hembree M, Paulson A, He Z, Xu D, Tran TH, Deshmukh P, Nguyen CT, Kasi RM, Ryan R, Broward M, Ding S, Guest E, August K, Gamis AS, Godwin A, Sittampalam GS, Weir SJ, Li L. Nat Cell Biol. 2020;22:689-700
Original Data
Differential complex formation via paralogs in the human Sin3 protein interaction network
Adams MK, Banks CAS, Thornton JL, Kempf C, Zhang Y, Miah S, Hao Y, Sardiu ME, Killer M, Hattem G, Murray A, Katt M, Florens LA, Washburn MP. [published ahead of print May 30 2020] Mol Cell Proteomics. 2020.
Original Data
Visualizing mesoderm and neural crest cell dynamics during chick head morphogenesis
McKinney MC, McLennan R, Giniunaite R, Baker RE, Maini PK, Othmer HG, Kulesa PM. Dev Biol. 2020;461:184-196.
Original Data
Merkel cell polyomavirus activates LSD1-mediated blockade of non-canonical BAF to regulate transformation and tumorigenesis
Park DE, Cheng J, McGrath JP, Lim MY, Cushman C, Swanson SK, Tillgren ML, Paulo JA, Gokhale PC, Florens L, Washburn MP, Trojer P, DeCaprio JA. Nat Cell Biol. 2020;22:603-615. Author Correction: Nat Cell Biol. 2020;22:752.
Original Data
Dlp-mediated Hh and Wnt signaling interdependence is critical in the niche for germline stem cell progeny differentiation
Tu R, Duan B, Song X, Xie T. Sci Adv 2020;6:eaaz0480.
Original Data
Integrative Modeling of a Sin3/HDAC Complex Sub-structure
Banks, C.A.S., Zheng,Y., Miah, S., Hoa, Y., Adams, M. K., Wen, Z., Thornton, J. L., Florens, L., Washburn, M. P. Cell Rep. 2020:31;107516. doi: 10.1016/j.celrep.
Original Data
Factors promoting nuclear envelope assembly independent of the canonical ESCRT pathway
Lee IJ, Stokasimov E, Dempsey N, Varberg JM, Jacob E, Jaspersen SL, Pellman D. [published ahead of print April 4 2020] J Cell Biol. 2020:219;e201908232.
Original Data
A Systems Chemoproteomic Analysis of Acyl-CoA/Protein Interaction Networks
Levy MJ, Montgomery DC, Sardiu ME, Montano JL, Bergholtz SE, Nance KD, Thorpe AL, Fox SD, Lin Q, Andresson T, Florens L, Washburn MP, Meier JL. Cell Chem Biol. 2020;27:322-333.e5.
Original Data
Regulation of the RNAPII Pool Is Integral to the DNA Damage Response
Vidakovic AT, Mitter R, Kelly GP, Neumann M, Harreman M, Martinez MR, Herlihy A, Weems J, Boeing S, Encheva V, Gaul L, Milligan L, Tollervey D, Conaway R, Conaway J, Snijders AP, Stewart A, Svejstrup JQ. Cell. 2020;180:1245-1261.
Original Data
Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila.
Hervas R, Rau MJ, Park Y, Zhang W, Murzin AG, Fitzpatrick JAJ, Scheres SHW, Si K. Science. 2020;367:1230-1234.
Original Data
NRBP1-Containing Cul2/Cul4A regulates amyloid beta production by targeting BRI2 and BRI3 for degradation
Yasukawa T, Tsutsui A, Tomomori-Sato C, Soto S, Saraf A, Washburn MP, Florens L, Terada T, Shimizu K, Conaway RC, Conaway JW, Aso T. Cell Rep. 2020;30:3478-3491.e6. doi: 10.1016/j.celrep.2020.02.059.
Original Data
Inter-rhombomeric interactions reveal roles for fibroblast growth factors signaling in segmental regulation of EphA4 expression
Cambronero F, Ariza-McNaughton L, Wiedemann LM, Krumlauf R. Dev Dyn. 2020;249:354-368.
Original Data
The role of Mediator and Little Elongation Complex in transcription termination
Takahashi H, Ranjan A, Chen S, Suzuki H, Shibata M, Hirose T, Hirose H, Sasaki K, Abe R, Chen K, He Y, Zhang Y, Takigawa I, Tsukiyama T, Watanabe M, Fujii S, Iida M, Yamamoto J, Yamaguchi Y, Suzuki Y, Matsumoto M, Nakayama KI, Washburn MP, Saraf A, Florens L, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Hatakeyama S. Nat Commun. 2020;11:1063. doi: 10.1038/s41467-020-14849-1.
Original Data
Regulation of Polo Kinase by Matrimony Is Required for Cohesin Maintenance during Drosophila melanogaster Female Meiosis
Bonner AM, Hughes SE, Hawley RS. Curr Biol. 2020;30:715-722e713.
Original Data
Super-resolution Microscopy-based Bimolecular Fluorescence Complementation to Study Protein Complex Assembly and Co-localization
Chen J, Yu Z, Unruh JR, Slaughter BD, Jaspersen SL. Bio-Protocol. 2020;10:e3524. doi: 3510.21769/BioProtoc.23524.
Vertebrate diapause preserves organisms long term through Polycomb complex members
Hu CK, Wang W, Brind'Amour J, Singh PP, Reeves GA, Lorincz MC, Sánchez Alvarado A, Brunet A. Science. 2020;367:870-874.
Original Data
Drosophila YBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs
Zou F, Tu R, Duan B, Yang Z, Ping Z, Song X, Chen S, Price A, Li H, Scott A, Perera A, Li S, Xie T. Proc Natl Acad Sci U S A. 2020;117:3603-3609.
Original Data
Dramatically diverse Schizosaccharomyces pombe wtf meiotic drivers all display high gamete-killing efficiency
Bravo Nunez MA, Sabbarini IM, Eickbush MT, Liang Y, Lange JJ, Kent AM, Zanders SE. PLoS Genet. 2020;16:e1008350. doi: 1008310.1001371/journal.pgen.1008350.
Original Data
Synaptonemal Complex-Deficient Drosophila melanogaster Females Exhibit Rare DSB Repair Events, Recurrent Copy-Number Variation, and an Increased Rate of de Novo Transposable Element Movement
Miller DE. G3 (Bethesda). 2020;10:525-537.
Original Data
Comparative transcriptome analysis of wild and lab populations of Astyanax mexicanus uncovers differential effects of environment and morphotype on gene expression
Krishnan J, Persons JL, Peuss R, Hassan H, Kenzior A, Xiong S, Olsen L, Maldonado E, Kowalko JE, Rohner N. [published ahead of print February 6 2020]. J Exp Zool B Mol Dev Evol. 2020.
Original Data
The Chromatin Bound Proteome of the Human Malaria Parasite
Batugedara G, Lu XM, Saraf A, Sardiu ME, Cort A, Abel S, Prudhomme J, Washburn MP, Florens L, Bunnik EM, Le Roch KG. [published ahead of print February 6 2020]. Microb Genom. 2020.
Original Data
STRIPAK directs PP2A activity toward MAP4K4 to promote oncogenic transformation
Kim JW, Berrios C, Kim M, Schade AE, Adelmant G, Yeerna H, Damato E, Iniguez AB, Florens L, Washburn MP, Stegmaier K, Gray NS, Tamayo P, Gjoerup O, Marto JA, DeCaprio J, Hahn WC. eLife. 2020;9. doi: 10.7554/eLife.53003.
Original Data
Multisite Evaluation of Next-Generation Methods for Small RNA Quantification
Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. [published ahead of print January 23 2020]. J Biomol Tech. 2020.
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Rocca MD, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Kohler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. Nucleic Acids Res. 2020;48:D704-D715.
Reviews, Commentaries, Chapters or Books
Continuing the advancement of Journal of Histotechnology - one issue at a time
Wang Y. J Histotechnol. 2019;42:165-166.
Exogenous pyruvate represses histone gene expression and inhibits cancer cell proliferation via the NAMPT-NAD+-SIRT1 pathway
Ma R, Wu Y, Zhai Y, Hu B, Ma W, Yang W, Yu Q, Chen Z, Workman JL, Yu X, Li S. Nucleic Acids Res. 2019;47:11132-11150.
Export and Transportation of Zebrafish
Barton CL, Baumann DP, Cox JD. In: SC Cartner, JS Eisen, SC Farmer, KJ Guillemin, ML Kent, and GE Sanders, eds. The Zebrafish in Biomedical Research : Biology, Husbandry, Diseases, and Research Applications. Academic Press; 2020:443-450.
The Joy of Balancers
Miller DE, Cook KR, Hawley RS. PLoS Genet. 2019;15:e1008421. doi: 1008410.1001371/journal.pgen.1008421.
Rebooting the Epigenome: Erasure of Parental Histone Marks for Establishing the Regulatory Landscape in Zygotes
Bhattacharya S, Workman JL. [published ahead of print October 23 2019]. Biochemistry. 2019.
Beyond Basic at the Stowers Institute for Medical Research
Bland K, Orr AA. Mo Med. 2019;116:457-460.
Purification and enzymatic assay of class I histone deacetylase enzymes
Adams MK, Banks CAS, Miah S, Killer M, Washburn MP. Methods Enzymol. 2019;626:23-40.
Original Data
Comparing Sensory Organs to Define the Path for Hair Cell Regeneration
Denans N, Baek S, Piotrowski T. Annu Rev Cell Dev Biol. 2019;35:568-589.
NSL complex acetylates Lamin A/C
Popova VV, Workman JL. Nat Cell Biol. 2019;21:1177-1178.
Patrolling the nucleus: inner nuclear membrane-associated degradation
Smoyer CJ, Jaspersen SL. Curr Genet. 2019;65:1099-1106.
The hunt for RNA polymerase II elongation factors: a historical perspective
Conaway RC, Conaway JW. Nat Struct Mol Biol. 2019;26:771-776.
Regulation of Genomic Output and (Pluri)potency in Regeneration
Duncan EM, Sánchez Alvarado A. Annu Rev Genet. 2019;53:16.1–16.20.
Cnidofest 2018: The future is bright for cnidarian research
He S, Grasis JA, Nicotra ML, Juliano CE, Schnitzler CE. EvoDevo. 2019;10:20. doi: 10.1186/s13227-13019-10134-13225.
Histone lysine de-beta-hydroxybutyrylation by SIRT3
Abmayr SM, Workman JL. Cell Res. 2019;29:694-695.
Gene conversion generates evolutionary novelty that fuels genetic conflicts
Daugherty MD, Zanders SE. v.Curr Opin Genet De 2019;58:49-54.
A family of killers
De Carvalho M, Zanders SE. eLife. 2019;8:e46454. doi: 46410.47554/eLife.46454.
When mothers leave their mark​
Barajas-Azpeleta R, Si K. eLife. 2019;8:e48899. doi: 48810.47554/eLife.48899.
Hematopoietic Stem Cells: Self-renewal and Expansion
Li Z, He XC, Li L. Curr Opin Hematol. 2019;26:258-265.
Fertility costs of Meiotic Drivers
Zanders SE, Unckless RL. Curr Biol. 2019;29:R512-R520.
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.
Hox genes: Downstream "effectors" of retinoic acid signaling in vertebrate embryogenesis
Nolte C, De Kumar B, Krumlauf R. Genesis. 2019:e23306. doi: 10.1002/dvg.23306.
Niche cells rewired to maintain HSCs ex vivo
Venkatraman A, Li L. Nat Cell Biol. 2019;21:540-541.
Commentary on "Regeneration, duplication and transdetermination in fragments of the leg disc of Drosophila melanogaster": Schubiger, G. (1971). Dev Biol. 2019;449:63-82.
Gibson MC. Dev Biol. 2019;449:63-82.
In ovo electroporation of plasmid DNA and morpholinos into specific tissues during early embryogenesis
McLennan R, Kulesa PM. Methods Mol Biol. 2019;1976:71-82.
Original Data
Mouse embryo culture for the study of neural crest cells
Munoz WA, Trainor PA. Methods Mol Biol: Meiosis. 2019;1976:107-119.
Observation of two separate bipolar spindles in the human zygote
Xu, X., Li L, Zhang C, Meng L. J Assist Reprod Genet. 2019;36:601-602. Correction: J Assist Reprod Genet. 2019 Jul 31. pii: 10.1007/s10815-019-01539-1. doi: 10.1007/s10815-019-01539-1.
Sweet fish: Fish models for the study of hyperglycemia and diabetes
Krishnan J, Rohner N. J Diabetes. 2019;11:193-203.
Ribosomal DNA instability and genome adaptability
Salim D, Gerton JL. Chromosome Res. 2019;27:73-87.
Ribosomal DNA and the nucleolus in the context of genome organization
Potapova TA, Gerton JL. Chromosome Res. 2019;27:109-127.
The Society for Craniofacial Genetics and Developmental Biology 41st Annual Meeting
Taneyhill LA, Moody SA, Cox T, Klein OD, Marcucio R, Schneider RA, Trainor PA. Am J Med Genet A. 2019;179:864-869.
Manipulation of developmental function in turtles with notes on alligators
Moustakas-Verho JE, McLennan R, Spengler J, Kulesa PM, Cebra-Thomas JA. Methods Mol Biol. 2019;1920:247-263. Author's Correction: Methods Mol Biol. 2019;1920:C1.
Original Data
An integrative view of Lepidosaur cranial anatomy, development and diversification
Diaz Jr. RE, Trainor PA. In: Ziermann, D Jr., and Diogo, eds. Heads, Jaws and Muscles Anatomical, Functional and Developmental Diversity in Chordate Evolution, Springer; 2019:207-227.
Ribosomal DNA-connecting ribosome biogenesis and chromosome biology
Porokhovnik L, Gerton JL. Chromosome Res. 2019;27:1-3.
Recent advances in understanding intestinal stem cell regulation
Hu D, Yan H, He XC, Li L.  F1000Res. 2019;8:F1000 Faculty Rev-72. Published 2019 Jan 18. doi:10.12688/f1000research.16793.1