Publications

Original Research Papers
An axial Hox code controls axial patterning and tissue segmentation in Nematostella vectensis
He S, Del Viso F, Chen CY, Ikmi A, Kroesen AE, Gibson MC. Science. 2018;361:1377-1380.
Original Data
Probing the Sensitivity of the Orbitrap Lumos Mass Spectrometer using a Standard Reference Protein in a Complex Background
Levy MJ, Washburn MP, Florens L. J Proteome Res. 2018;17:3586-3592.
Original Data
The role of gene flow in rapid and repeated evolution of cave related traits in Mexican tetra, Astyanax mexicanus
Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandzija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-Garcia CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE. [published ahead of print September 27 2018]. Mol Ecol. 2018.
Origin, Composition, and Structure of the Supernumerary B Chromosome of Drosophila melanogaster
Hanlon SL, Miller DE, Eche S, Hawley RS. Origin, Composition, and Structure of the Supernumerary B Chromosome of Drosophila melanogaster. [published ahead of print September 27 2018]. Genetics. 2018.
Original Data
Local Inversion Heterozygosity Alters Recombination throughout the Genome
Crown KN, Miller DE, Sekelsky J, Hawley RS. Curr Biol. 2018;28:2984-2990.e2983.
Original Data
PTPN14 regulates Roquin2 stability by tyrosine dephosphorylation
Choi J, Saraf A, Florens L, Washburn MP, Busino L. [published ahead of print September 14 2018]. Cell Cycle. 2018:12.
Original Data
Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly
Banks CAS, Miah S, Adams MK, Eubanks CG, Thornton JL, Florens L, Washburn MP. Sci Rep. 2018;9:18712.
Original Data
CTD-dependent and -independent mechanisms govern co-transcriptional capping of Pol II transcripts
Noe Gonzalez M, Sato S, Tomomori-Sato C, Conaway JW, Conaway RC. Nat Commun. 2018;9:3392. doi: 3310.1038/s41467-41018-05923-w.
Original Data
DYRK1A interacts with histone acetyl transferase p300 and CBP and localizes to enhancers
Li S, Xu C, Fu Y, Lei PJ, Yao Y, Yang W, Zhang Y, Washburn MP, Florens L, Jaiswal M, Wu M, Mohan M. [published ahead of print August 22 2018]. Nucleic Acids Res. 2018.
Original Data
A chemotactic model of trunk neural crest cell migration
Dyson L, Holmes A, Li A, Kulesa PM. Genesis. 2018:e23239. doi: 23210.21002/dvg.23239.
Original Data
GENOME REPORT: Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
Miller DE, Staber C, Zeitlinger J, Hawley RS. [published ahead of print August 7 2018]. G3 (Bethesda). 2018.
Original Data
Schizosaccharomyces pombe Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex
Gopalan S, Gibbon DM, Banks CAS, Zhang Y, Florens LA, Washburn MP, Dabas P, Sharma N, Seidel CW, Conaway RC, Conaway JW. Nucleic Acids Res. 2018;1:gky173. doi: 110.1093/nar/gky1713.
Original Data
MPTAC Determines APP Fragmentation via Sensing Sulfur Amino Acid Catabolism
Suganuma T, Swanson SK, Gogol M, Garrett TJ, Conkright-Fincham J, Florens L, Washburn MP, Workman JL. Cell Rep. 2018;24:1585-1596.
Original Data
Combined expansion microscopy with structured illumination microscopy for analyzing protein complexes
Wang Y, Yu Z, Cahoon CK, Parmely T, Thomas N, Unruh JR, Slaughter BD, Hawley RS. Nat Protoc. 2018;13:1869-1895.
Original Data
Suppression of m(6)A reader Ythdf2 promotes hematopoietic stem cell expansion
Li Z, Qian P, Shao W, Shi H, He XC, Gogol M, Yu Z, Wang Y, Qi M, Zhu Y, Perry JM, Zhang K, Tao F, Zhou K, Hu D, Han Y, Zhao C, Alexander R, Xu H, Chen S, Peak A, Hall K, Peterson M, Perera A, Haug JS, Parmely T, Li H, Shen B, Zeitlinger J, He C, Li L. [published ahead of print August 2 2018]. Cell Res. 2018. Author Correction: Cell Res 2018:1-14. https://doi.org/10.1038/s41422-018-0072-0. [Published online July 2018].
Original Data
The half-bridge component Kar1 promotes centrosome separation and duplication during budding yeast meiosis
Agarwal M, Jin H, McClain M, Fan J, Koch BA, Jaspersen SL, Yu HG.  Mol Biol Cell. 2018;29:1798-1810.
Original Data
Key phosphorylation events in Spc29 and Spc42 guide multiple steps of yeast centrosome duplication
Jones MH, O'Toole ET, Fabritius AS, Muller EG, Meehl JB, Jaspersen SL, Winey M. Mol Biol Cell. 2018:mbcE18050296.
FGF-2 Antiproliferative Stimulation Induces Proteomic Dynamic Changes and High Expression of fosB and junB in K-Ras-Driven Mouse Tumor Cells
Vitorino FNL, Montoni F, Moreno JN, de Souza BF, Lopes MC, Cordeiro B, Fonseca CS, Gilmore JM, Sardiu MI, Reis MS, Florens LA, Washburn MP, Armelin HA, da Cunha JPC. FGF-2 Antiproliferative Stimulation Induces Proteomic Dynamic Changes and High Expression of fosB and junB in K-Ras-Driven Mouse Tumor Cells. Proteomics. 2018:e1800203.
Original Data
Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing
Solares EA, Chakraborty M, Miller DE, Kalsow S, Hall K, Perera AG, Emerson JJ, Hawley RS. G3 (Bethesda). 2018.
Original Data
Quantifying nucleation in vivo reveals the physical basis of prion-like phase behavior
Khan T, Kandola TS, Wu J, Venkatesan S, Ketter E, Lange JJ, Rodriguez Gama A, Box A, Unruh JR, Cook M, Halfmann R. Mol Cell. 2018;71:155-168.e157.
Original Data
Early adipogenesis contributes to excess fat accumulation in cave populations of Astyanax mexicanus
Xiong S, Krishnan J, Peuss R, Rohner N. [published ahead of print June 6 2018]. Dev Biol. 2018.
Original Data
The budding yeast RSC complex maintains policy by promoting spindle pole body insertion
Sing TL, Hung MP, Ohnuki S, Suzuki G, San Luis BJ, McClain M, Unruh JR, Yu Z, Ou J, Marshall-Sheppard J, Huh WK, Costanzo M, Boone C, Ohya Y, Jaspersen SL, Brown GW. The budding yeast RSC complex maintains ploidy by promoting spindle pole body insertion. J Cell Biol. 2018;217:2445-2462.
Original Data
Retinoic acid signaling promotes the cytoskeletal rearrangement of embryonic epicardial cells
Wang S, Yu J, Jones JW, Pierzchalski K, Kane MA, Trainor PA, Xavier-Neto J, Moise AR. FASEB J. 2018;32:3765-3781.
Histone H3 threonine 11 phosphorylation by Sch9 and CK2 regulates chronological lifespan by controlling the nutritional stress response.
Oh S, Suganuma T, Gogol MM, Workman JL. eLife. 2018;7:e36157. doi: 36110.37554/eLife.36157.
Original Data
Wave2 scaffold Hem-1 is required for transition of fetal liver hematopoiesis to bone marrow
Shao L, Chang J, Feng W, Wang X, Williamson EA, Li Y, Schajnovitz A, Scadden D, Mortensen LJ, Lin CP, Li L, Paulson A, Downing J, Zhou D, Hromas RA.  Nat Commun. 2018;9:2377. doi: 2310.1038/s41467-41018-04716-41465.
Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins.
Capitanchik C, Dixon C, Swanson SK, Florens L, Kerr ARW, Schirmer EC. [published ahead of print June 19 2018]. Nucleus. 2018.
Original Data
Prospectively Isolated Tetraspanin(+) Neoblasts Are Adult Pluripotent Stem Cells Underlying Planaria Regeneration
Zeng A, Li H, Guo L, Gao X, McKinney S, Wang Y, Yu Z, Park J, Semerad C, Ross E, Cheng LC, Davies E, Lei K, Wang W, Perera A, Hall K, Peak A, Box A, Sánchez Alvarado A. Cell. 2018;173:1593-1608.e20.
Original Data
Robustness and evolvability of heterogeneous cell populations
Kucharavy A, Rubinstein B, Zhu J, Li R. Mol Biol Cell. 2018;29:1400-1409.
Alterations in RA Signaling Affect the Development of the Mouse Coronary Vasculature
Wang S, Huang W, Castillo HA, Kane MA, Xavier-Neto J, Trainor PA, Moise AR. [published ahead of print May 29 2018]. Dev Dyn. 2018.
tp53-dependent and independent signaling underlies the pathogenesis and possible prevention of Acrofacial Dysostosis - Cincinnati type
Watt KEN, Neben CL, Hall S, Merrill AE, Trainor PA. [published ahead of print May 12 2018] Hum Mol Genet. 2018.
Original Data
Somatic clones heterozygous for recessive disease alleles of BMPR1A exhibit unexpected phenotypes in Drosophila
Akiyama T, User SD, Gibson MC. eLife. 2018;7:e35258. doi: 35210.37554/eLife.35258.
Original Data
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.​
Original Data
Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis
Qian P, De Kumar B, He XC, Nolte C, Gogol M, Ahn Y, Chen S, Li Z, Xu H, Perry JM, Hu D, Tao F, Zhao M, Han Y, Hall K, Peak A, Paulson A, Zhao C, Venkatraman A, Box A, Perera A, Haug JS, Parmely T, Li H, Krumlauf R, Li L. Cell Stem Cell. 2018;22:740-754 e747.
Original Data
Loss of KLHL6 promotes diffuse large B-cell lymphoma growth and survival by stabilizing the mRNA decay factor roquin2
Choi J, Lee K, Ingvarsdottir K, Bonasio R, Saraf A, Florens L, Washburn MP, Tadros S, Green MR, Busino L. Nat Cell Biol. 2018;20:586-596.
Original Data
First-principles X-ray absorption dose calculation for time-dependent mass and optical density
Berejnov V, Rubinstein B, Melo LGA, Hitchcock AP.  J Synchrotron Radiat. 2018;25:833-847.
Predicting neuroblastoma using developmental signals and a logic-based model
Kasemeier-Kulesa JC, Schnell S, Woolley T, Spengler JA, Morrison JA, McKinney MC, Pushel I, Wolfe LA, Kulesa PM. Biophys Chem. 2018;238:30-38.
Original Data
Temperature preference of cave and surface populations of Astyanax mexicanus
Tabin JA, Aspiras A, Martineau B, Riddle M, Kowalko J, Borowsky R, Rohner N, Tabin CJ. [published ahead of print April 29 2018]. Dev Biol. 2018.
Dynamic sex chromosomes in Old World chameleons (Squamata: Chamaeleonidae)
Nielsen SV, Banks JL, Diaz RE, Jr., Trainor PA, Gamble T.  J Evol Biol. 2018;31:484-490.
A structured workflow for mapping human Sin3 histone deacetylase complex interactions using Halo-MudPIT AP-MS
Banks CAS, Thornton JL, Eubanks CG, Adams MK, Miah S, Boanca G, Liu X, Katt ML, Parmely TJ, Florens L, Washburn MP. Mol Cell Proteomics. 2018;17:1432-1447.
Original Data
The Molecular and Genetic Characterization of Second Chromosome Balancers in Drosophila melanogaster
Miller DE, Cook KR, Hemenway EA, Fang V, Miller AL, Hales KG, Hawley RS. G3 (Bethesda). 2018;8:1161-1171.
Original Data
Insulin resistance in cavefish as an adaptation to a nutrient-limited environment
Riddle MR, Aspiras AC, Gaudenz K, Peuss R, Sung JY, Martineau B, Peavey M, Box AC, Tabin JA, McGaugh S, Borowsky R, Tabin CJ, Rohner N. Nature. 2018;555:647-651.
Original Data
CRISPR mutagenesis reveals the role of oca2 in melanin pigmentation in Astyanax mexicanus
Klaassen H, Wang Y, Adamski K, Rohner N, Kowalko JE. [published ahead of print March 2018]. Dev Biol. 2018.
Original Data
dCas9-targeted locus-specific protein isolation method identifies histone gene regulators
Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R. Proc Natl Acad Sci U S A. 2018;115:E2734-E2741.
Original Data
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.
Original Data
An adaptable chromosome preparation methodology for use in invertebrate research organisms
Guo L, Accorsi A, He S, Guerrero-Hernandez C, Sivagnanam S, McKinney S, Gibson M, Sanchez Alvarado A. BMC Biol.  2018;16:25. doi: 10.1186/s12915-12018-10497-12914.
Original Data
The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT. Nat Genet. 2018;50:270-277.  Publisher Correction: Nat Genet. 2018;50:768. 
Original Data
Capicua controls Toll/IL-1 signaling targets independently of RTK regulation
Papagianni A, Fores M, Shao W, He S, Koenecke N, Andreu MJ, Samper N, Paroush Z, Gonzalez-Crespo S, Zeitlinger J, Jimenez G.  Proc Natl Acad Sci U S A. 2018;115:1807-1812.
Original Data
Pof8 is a La-related protein and a constitutive component of telomerase in fission yeast
Paez-Moscoso DJ, Pan L, Sigauke RF, Schroeder MR, Tang W, Baumann P. Nat Commun. 2018;9:587.​
Original Data
Ventral neural patterning in the absence of a Shh activity gradient from the floorplate
Iulianella A, Sakai D, Kurosaka H, Trainor PA. Dev Dyn. 2018;247:170-184.
NGF reprograms metastatic melanoma to a bipotent glial-melanocyte neural crest-like precursor
Kasemeier-Kulesa JC, Romine MH, Morrison JA, Bailey CM, Welch DR, Kulesa PM. Biol Open. 2018;7:bio030817. doi: 030810.031242/bio.030817.
Original Data
NECAPs are negative regulators of the AP2 clathrin adaptor complex.
Beacham GM, Partlow EA, Lange JJ, Hollopeter G. eLife. 2018;7:e32242. doi: 32210.37554/eLife.32242.
Original Data
Cellular, ultrastructural and molecular analysis of epidermal cell development in the planarian Scmidtea mediterranea
Cheng LC, Tu KC, Seidel CW, Robb SMC, Guo F, Sánchez Alvarado A. Dev Biol. 2018;433:357-373.
Original Data
Beta-catenin cleavage enhances transcriptional activation
Goretsky T, Bradford EM, Ye Q, Lamping OF, Vanagunas T, Moyer MP, Keller PC, Sinh P, Llovet JM, Gao T, She QB, Li L, Barrett TA. Sci Rep. 2018;8:671. doi: 10.1038/s41598-017-18421-8.
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.
Reviews, Commentaries, Chapters or Books
Sweet Fish. Fish Models for the Study of Hyperglycemia and Diabetes
Krishnan J, Rohner N. [published ahead of print September 29 2018]. J Diabetes. 2018.
Seeing the future of Histotechnology through its history
Wang Y. [published ahead of print October 12 2018]. J Histotechnol. 2018.
B chromosomes in the Drosophila genus
Hanlon SL, Hawley RS. B Chromosomes in the Drosophila Genus. [published ahead of print September 29 2018]. Genes (Basel). 2018;9.
Original Data
Seeing a bright future for a blind fish
Gore AV, Rohner N, Retaux S, Jeffery WR. Dev Biol. 2018;441:207-208.
Functional Analysis of the Yeast LINC Complex Using Fluctuation Spectroscopy and Super-Resolution Imaging
Unruh JR, Slaughter BD, Jaspersen SL. Functional Analysis of the Yeast LINC Complex Using Fluctuation Spectroscopy and Super-Resolution Imaging. Methods Mol Biol: Meiosis. 2018;1840:137-161.
The anatomy of a nucleus: As revealed by chromosome painting
Slaughter BD, Hawley RS. PLoS Genet. 2018;14:e1007445. doi: 10.1371/journal.pgen.1007445.
A transcription factor primes the condensin pump
Gerton JL. J Cell Biol. 2018;217:2233-2234.
Veni, vidi, vici: the success of wtf meiotic drivers in fission yeast
Lopez Hernandez JF, Zanders SE. Yeast. 2018;35:447-453.
Planarians and the History of Animal Regeneration: Paradigm Shifts and Key Concepts in Biology
Elliott SA, Sánchez Alvarado A. Methods Mol Biol. 2018;1774:207-239.
Chromatin and Metabolism
Suganuma T, Workman JL. Annu Rev Biochem. 2018;87:27-49.
Metabolic Regulation of Transcription and Chromatin
Conaway RC. Annu Rev Biochem. 2018;87:23-25.
Translational Control by Prion-like Proteins
Li L, McGinnis JP, Si K. Trends Cell Biol. 2018;28:494-505.
Planarian High Molecular Weight DNA Isolation by Spooling
Zhang S, Sánchez Alvarado A. Methods Mol Biol. 2018;1774:277-284.
Whole-Mount BrdU Staining with Fluorescence In Situ Hybridization in Planarians
Cheng LC, Sánchez Alvarado A. Methods Mol Biol. 2018;1774:423-434.
Systemic RNA Interference in Planarians by Feeding of dsRNA Containing Bacteria.
Adler CE, Sánchez Alvarado A. Methods Mol Biol. 2018;1774:445-454.
Culturing planarians in the laboratory
Merryman MS, Sánchez Alvarado A, Jenkin JC. Methods Mol Biol: Meiosis. 2018;1774:241-258.
Neural crest cells and their application in regenerative medicine
Trainor PA. In: N Antonio, and AR Ten Cate, eds. Ten Cate's Oral Histology - Development, Structure and Function. 9th ed. St. Louis: Elsevier; 2018:21-22.
The Society for Craniofacial Genetics and Developmental Biology 40th Annual Meeting
Gammill L, Cox T, Moody S, Taneyhill L, Trainor P, Marcucio R. Am J Med Genet A. 2018;176:1270-1273.
Regulation of kinetochore configuration during mitosis
Dhatchinamoorthy K, Mattingly M, Gerton JL. [published ahead of print April 29 2018]. Curr Genet. 2018.
To Make a Long Spindle Short: Nuclear Envelope Breakdown during Meiosis
Varberg JM, Jaspersen SL. Cell Rep. 2018;23:931-932.
Cavefish as an evolutionary mutant model system for human disease
Rohner N. [published ahead of print April 24 2018]. Dev Biol. 2018.
The convergent roles of CD271/p75 in neural crest-derived melanoma plasticity
Kasemeier-Kulesa JC, Kulesa PM. [published ahead of print April 17 2018]. Dev Biol. 2018.
New insights and changing paradigms in the regulation of vitamin A metabolism in development.
Shannon SR, Moise AR, Trainor PA. WIREs Dev Biol 2017;6:e264. doi: 210.1002/wdev.1264.
Coupling the roles of Hox genes to regulatory networks patterning cranial neural crest
Parker HJ, Pushel I, Krumlauf R. [published ahead of print March 25 2018]. Dev Biol. 2018.
Female meiosis: synapsis, recombination, and segregation in Drosophila melanogaster
Hughes SE, Miller DE, Miller AL, Hawley RS. Genetics. 2018;208:875-908.
Genetic Villains: Killer Meiotic Drivers
Bravo Nunez MA, Nuckolls NL, Zanders SE. [published ahead of print February 27 2018]. Trends Genet. 2018.
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.
Mechanical plasticity during oligodendrocyte differentiation and myelination
Domingues HS, Cruz A, Chan JR, Relvas JB, Rubinstein B, Pinto IM. Glia. 2018;66:5-14.
Developmental biology - more dynamic than ever!
Trainor PA. Dev Dyn. 2018;247:8-9.
To solve old problems, study new research organisms.
Sánchez Alvarado A. Dev Biol. 2018;433:111-114.
Therapeutic potential of Mediator complex subunits in metabolic diseases
Ranjan A, Ansari SA. Therapeutic potential of Mediator complex subunits in metabolic diseases. Biochimie. 2018;144:41-49.​