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Joaquín Navajas Acedo ’13

Thesis Mentor: Tatjana Piotrowski, PhD
Thesis: Dissecting the role of the Planar Cell Polarity (PCP) and Wnt signaling pathways during the establishment of hair cell orientation in zebrafish.
Thesis Defense Date: November 2019
First Post-Graduate Position: Postdoctoral Researcher in the Alexander F. Schier lab at the Biozentrum, University of Basel, Switzerland


PCP and Wnt pathway components act in parallel during zebrafish mechanosensory hair cell orientation
Joaquin Navajas Acedo, Matthew G Voas, Richard L Alexander, Thomas Woolley, Jay Unruh, Hua Li, Cecilia Moens, Tatjana Piotrowski. (2019) Nature Communications
Original Data

Evolutionary Origin and Nomenclature of Vertebrate Wnt11-Family Genes
Postlethwait JH, Navajas Acedo J, Piotrowski T. Zebrafish. 2019;16:469-476.

Retinoic acid is required and Fgf, Wnt, and Bmp signaling inhibit posterior lateral line placode induction in zebrafish
Nikaido M, Acedo JN, Hatta K, Piotrowski T. Dev Biol. 2017;431:215-225.
Original Data

Imaging collective cell migration and hair cell regeneration in the sensory lateral line
Venero Galanternik M, Navajas Acedo J, Romero-Carvajal A, Piotrowski T. Methods Cell Biol.2016;134:211-256.
Original Data

Regeneration of Sensory Hair Cells Requires Localized Interactions between the Notch and Wnt Pathways.
Romero-Carvajal A, Navajas Acedo J, Jiang L, Kozlovskaja-Gumbriene A, Alexander R, Li H, Piotrowski T. Dev Cell. 2015;34:267-282.
Original Data

Acrofacial Dysostosis, Cincinnati Type, a Mandibulofacial Dysostosis Syndrome with Limb Anomalies, Is Caused by POLR1A Dysfunction.
Weaver KN, Watt KE, Hufnagel RB, Navajas Acedo J, Linscott LL, Sund KL, Bender PL, Konig R, Lourenco CM, Hehr U, Hopkin RJ, Lohmann DR, Trainor PA, Wieczorek D, Saal HM. Am J Hum Genet. 2015;96:765-774.
Original Data



Raquel Barajas Azpeleta ’14

Thesis Mentor: Kausik Si, PhD
Thesis: Modulation of Nervous System Functions: A Surprising Role for Antimicrobial Peptides
Thesis Defense Date: October 2019
First Post-Graduate Position: Postdoctoral Researcher Scholar, Ribeiro Lab, Champalimaud Center for the Unknown, Lisbon, Portugal


Antimicrobial peptides modulate long-term memory
Barajas-Azpeleta R, Wu J, Gill J, Welte R, Seidel C, McKinney S, Dissel S, Si K. PLoS Genet. 2018;14:e1007440. doi: 1007410.1001371/journal.pgen.1007440.
Original Data

Reviews, Commentaries, Chapters or Books
When mothers leave their mark.
Barajas-Azpeleta R, Si K. eLife. 2019;8:e48899. doi: 48810.47554/eLife.48899..​



Amanda Bonner ’12

Thesis Mentor: R. Scott Hawley, PhD
Thesis: The Evolution and Function of Matrimony, a Meiotic Regulator of Polo Kinase
Thesis Defense Date: May 2019
First Post-Graduate Position: Postdoctoral Research Scholar, Singh Lab, University of Oregon


Narya, a RING finger domain-containing protein, is required for both meiotic DNA double-strand break formation and crossover maturation in Drosophila melanogaster
Lake CM, Nielsen RJ, Bonner AM, Eche S, White-Brown S, McKim KS, Hawley RS. PLoS Genet. 2019;15:e1007886. doi: 1007810.1001371/journal.pgen.1007886.​
Original Data

Functional consequences of the evolution of matrimony, a meiosis-specific inhibitor of Polo kinase
Bonner AM, Hawley RS. Mol Biol Evol. 2019;36:69-83.
Original Data

Binding of Drosophila Polo kinase to its regulator Matrimony is noncanonical and involves two separate functional domains.
Bonner AM, Hughes SE, Chisholm JA, Smith SK, Slaughter BD, Unruh JR, Collins KA, Friederichs JM, Florens L, Swanson SK, Pelot MC, Miller DE, Washburn MP, Jaspersen SL, Hawley RS. Proc Natl Acad Sci U S A. 2013;110:E1222-1231.
Original Data

Reviews, Commentaries, Chapters or Books
A Nucleoporin at the Meiotic Kinetochore
Bonner AM, Hawley RS. Dev Cell. 2016;38:447-448.​



Melvin Noé González ’12

Thesis Mentor: Joan Conaway, PhD, and Ron Conaway, PhD
Thesis: Through bubbles, scaffolds and cassettes: Reconstituting the link between Pol II transcription and RNA capping.
Thesis Defense Date: May 2019
First Post-Graduate Position: Postdoctoral Training Fellow, The Francis Crick Institute, London, England


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.

Frozen in transcription: Cryo-EM structures of Pol II transcribing through a nucleosome
Noe Gonzalez M, Conaway RC, Conaway JW.  Mol Cell. 2018;72:802-804.

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
Noe Gonzalez, M., Conaway, J. W., & Conaway, R. C.  Journal of Visualized Experiments. (147), e59497.



Christine Smoyer ’12

Thesis Mentor: Sue Jaspersen, PhD
Thesis: Analysis of Inner Nuclear Membrane Composition by SPLIT-GFP.
Thesis Defense Date: October 2018
First Post-Graduate Position: Postdoctoral Scholar, Dr. Kassandra Ori-McKenney, Department of Molecular and Cellular Biology, UC Davis, Davis, California


Distribution of Proteins at the Inner Nuclear Membrane Is Regulated by the Asi1 E3 Ligase in Saccharomyces cerevisiae.
Smoyer CJ, Smith SE, Gardner JM, McCroskey S, Unruh JR, Jaspersen SL. Genetics. 2019 Feb 1. pii: genetics.301911.2019. doi: 10.1534/genetics.119.301911. [Epub ahead of print]

Analysis of membrane proteins localizing to the inner nuclear envelope in living cells.
Smoyer CJ, Katta SS, Gardner JM, Stoltz L, McCroskey S, Bradford WD, McClain M, Smith SE, Slaughter BD, Unruh JR, Jaspersen SL. J Cell Biol. 2016 Nov 21;215(4):575-590. Epub 2016 Nov 9.

Breaking down the wall: the nuclear envelope during mitosis.
Smoyer CJ, Jaspersen SL. Curr Opin Cell Biol. 2014 Feb;26:1-9. doi: 10.1016/ Epub 2013 Sep 4. Review.

The SUN protein Mps3 controls Ndc1 distribution and function on the nuclear membrane.
Chen J, Smoyer CJ, Slaughter BD, Unruh JR, Jaspersen SL. J Cell Biol. 2014 Feb 17;204(4):523-39. doi: 10.1083/jcb.201307043. Epub 2014 Feb 10.

Destination: inner nuclear membrane.
Katta SS, Smoyer CJ, Jaspersen SL. Trends Cell Biol. 2014 Apr;24(4):221-9. doi: 10.1016/j.tcb.2013.10.006. Epub 2013 Nov 19. Review.

Genetic analysis of Mps3 SUN domain mutants in Saccharomyces cerevisiae reveals an interaction with the SUN-like protein Slp1.
Friederichs JM, Gardner JM, Smoyer CJ, Whetstine CR, Gogol M, Slaughter BD, Jaspersen SL. G3 (Bethesda). 2012 Dec;2(12):1703-18. doi: 10.1534/g3.112.004614. Epub 2012 Dec 1.

Acetylation of the SUN protein Mps3 by Eco1 regulates its function in nuclear organization.
Ghosh S, Gardner JM, Smoyer CJ, Friederichs JM, Unruh JR, Slaughter BD, Alexander R, Chisholm RD, Lee KK, Workman JL, Jaspersen SL. Mol Biol Cell. 2012 Jul;23(13):2546-59. doi: 10.1091/mbc.E11-07-0600. Epub 2012 May 16.

The SUN protein Mps3 is required for spindle pole body insertion into the nuclear membrane and nuclear envelope homeostasis.
Friederichs JM, Ghosh S, Smoyer CJ, McCroskey S, Miller BD, Weaver KJ, Delventhal KM, Unruh J, Slaughter BD, Jaspersen SL. PLoS Genet. 2011 Nov;7(11):e1002365. doi: 10.1371/journal.pgen.1002365. Epub 2011 Nov 17.

Targeting of the SUN protein Mps3 to the inner nuclear membrane by the histone variant H2A.Z.
Gardner JM, Smoyer CJ, Stensrud ES, Alexander R, Gogol M, Wiegraebe W, Jaspersen SL. J Cell Biol. 2011 May 2;193(3):489-507. doi: 10.1083/jcb.201011017. Epub 2011 Apr 25.



Wanqing Shao ’12

Thesis Mentor: Julia Zeitlinger, PhD
Thesis: The interplay between transcription initiation, RNA polymerase II pausing and core promoter elements: A genomics perspective.
Thesis Defense Date: July 2018
First Post-Graduate Position: Postdoctoral Research Associate, Genetics Department, Washington University, St. Louis, MO


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. 28(9):904-917.

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

Paused RNA polymerase II inhibits new transcriptional initiation
Shao W, Zeitlinger J. Nat Genet.2017;49:1045-1051..
Original Data

A global change in RNA Polymerase II pausing during the Drosophila mid bastula transition. eLife 2013 doi: 10.7554/eLife.00861
Chen, K., Johnston, J., Shao, W., Meier, S., Staber, C., and Zeitlinger, J.



Cori Cahoon ’12

Thesis Mentor: R. Scott Hawley, PhD
Thesis: Understanding the structure and function of the Drosophila synaptonemal complex in female meiosis.
Thesis Defense Date: April 2018
First Post-Graduate Position: Postdoctoral Researcher, University of Oregon, Eugene, OR


Superresolution expansion microscopy reveals the three-dimensional organization of the Drosophila synaptonemal complex.
Cahoon CK, Yu Z, Wang Y, Guo F, Unruh JR, Slaughter BD, Hawley RS. Proc Natl Acad Sci U S A.2017;114:E6857-E6866.

Regulating the construction and demolition of the synaptonemal complex
Cahoon CK, Hawley RS. Nat Struct Mol Biol. 2016;23:369-377.

Meiosis: Cohesins are not just for sisters anymore.
Cahoon CK, Hawley RS. Current Biology. 2016 Jun 11;26(13):R523-5.

Flies get a head start on meiosis.
Cahoon CK, Hawley RS. PLoS Genet. 2013;9:e1004051.

Multiple opposing constraints govern chromosome interactions during meiosis.
Liu DY, Cahoon CK, Burgess S.  PLoS Genet. 2013;9:e1003197



Kobe Yuen ’12

Thesis Mentor: Jennifer Gerton, PhD
Thesis: Structural Maintenance Proteins - Roles in Chromatin Organization and Gene Expression
Thesis Defense Date: December 2016
First Post-Graduate Position: Postdoctoral Researcher, Genentech, San Francisco CA


"The Stowers graduate program was instrumental in preparing for my position in Genentech. The well-designed modules sparked my interest in studying gene expression on a genomic scale. I then started my project to investigate how genome organization regulates gene expression. I gained skills in bioinformatics and genomics analysis, which greatly facilitates the transition into my postdoc position in which I am analyzing a large amount of genomic data to study disease mechanisms and drug responses."



Taking cohesin and condensin in context
Yuen KC, Gerton JL. PLoS Genet.2018;14:e1007118. doi: 10.1371/journal.pgen.1007118.

Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports expression of active dense gene clusters
Yuen, KC, Slaughter, BD, andGerton JL. Sci Adv. 2017;3:e1700191. doi: 1700110.1701126/sciadv.1700191. .
Original Data

NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR.
Yuen KC, Xu B, Krantz, ID, and Gerton, JL (2016) Cell Rep. Jan 5;14(1):93-102.

Etiology and pathogenesis of the cohesinopathies.
Zakari M, Yuen K, Gerton JL. (2015) Wiley Interdiscip Rev Dev Biol. Sep-Oct;4(5):489-504.

Mef2c-F10N enhancer drive β-galactosidase (LacZ) and Cre recombinase mice facilitate analyses of gene function and lineage fate in neural crest cells. 
Aoto, K, Sandell, L.L., Butler Tjaden, N.E., Yuen, K.C., Watt, K.E., Black B.L., Durnin, M., and Trainor, P.A. (2015) Dev Biol, 402(1):3-16 

From skeleton to cytoskeleton: osteocalcin transforms vascular fibroblasts to myofibroblasts via angiotensin II and Toll-like receptor 4.
Yuen CY, Wong SL, Lau CW, Tsang SY, Xu A, Zhu Z, Ng CF, Yao X, Kong SK, Lee HK, Huang Y. (2012) Circ Res. 111(3):e55-66.

Telmisartan inhibits vasoconstriction via PPARγ-dependent expression and activation of endothelial nitric oxide synthase.
Yuen, C.Y., Wong, W.T., Tian, X.Y., Wong, S.L., Lau, C. W., Yu, J., Tomlinson, B., Yao, X. and Huang, Y. Cardiovasc Res, 90(1):122-129.