History of the Department

On the following page is a brief history of the department, along with a video entitled “The First 48 Years of the Department of Genetics at the University of Pennsylvania”. On the subsequent page there are four additional videos: “The Billingham Chairmanship and Transplantation Immunology” (Clyde Barker and David Gasser), “The Mellman Chairmanship and Cytogenetics” (Beverly Emanuel and David Gasser), “The Mellman Chairmanship and Maternal/Fetal Medicine” (Michael Mennuti and David Gasser), and “The Kazazian Chairmanship” (Haig Kazazian and David Gasser). Read and view more about the department...

Daniel J. Rader, M.D. Professor and Chair 215-898-8586 rader@mail.med.upenn.edu

 

Seminar Series

The Department of Genetics hosts a different speaker every Monday of the academic year, with invitees ranging from postdoctoral researchers to prominent scientists presenting a broad array of current, genetics-related research. Our series is cosponsored with the Department of Cell and Developmental Biology, the Epigenetics Program, and the Institute for Regenerative Medicine. Click here to view the schedule.

Department Highlights

We are pleased to announce that this year's Tom Kadesch Prize in Genetic Research has been awarded to Derek Oldridge.

Dan Rader, Rebecca Mueller, Derek Oldridge, Abby Huntington, Hannah Kadesch, John Maris

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Recent Faculty Additions

We are pleased to announce the recruitment of Hao Wu, Ph.D. Hao joined the department as an Assistant Professor on January 1, 2016. He received his Ph.D. in Molecular and Medical Pharmacology from University of California Los Angeles in 2009, where he studied epigenetic regulation of neural stem cell differentiation. Hao then moved to Harvard as a post-doctoral fellow co-mentored by Dr. Kenneth Chien in the MGH Cardiovascular Research Center and Department of Stem Cell & Regenerative Biology and Dr. Yi Zhang, an HHMI Investigator in the Department of Genetics. His work on the TET family of 5-methylcytosine (5mC) oxidases has been nothing short of spectacular, and has led to six first-author papers in high profile journals. He was co-recruited with the Epigenetics Program, a key partner in his recruitment. Dr. Wu is highly creative in his development of new methods for interrogating oxidized 5mC DNA modifications and their biological roles. His arrival is expected to further strengthen the connection between the Genetics Department and the Epigenetics Program. He also has a strong interest in the epigenetic regulatory programs of stem cell differentiation into cardiac and neural lineages, thus bridging him to the cardiovascular and neuroscience research communities at Penn.

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Recent Genetics Faculty Publications

Yoseph Barash
In silico to in vivo splicing analysis using splicing code models.
Gazzara MR, Vaquero-Garcia J, Lynch KW, Barash Y.
Methods. S1046-2023(13)00444-1, 2013.

AVISPA: a web tool for the prediction and analysis of alternative splicing.
Barash Y, Vaquero-Garcia J, González-Vallinas J, Xiong HY, Gao W, Lee LJ, Frey BJ.
Genome Biol. 14(10):R114, 2013.

Maja Bucan
From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes.
Georgi B, Voight BF, Bucan M
PLoS Genet. 2013. 9(5): e1003484.

Genomic View of Bipolar Disorder Revealed by Whole Genome Sequencing in a Genetic Isolate
Georgi B, Craig D, Kember RL, Liu W, Lindquist I, Nasser S, Brown C, Egeland JA, Paul SM, Bucan M
PLoS Genet 10(3): e1004229. doi:10.1371/journal.pgen.1004229, 2014.

Doug Epstein
Divergent roles for Wnt/β-catenin signaling in epithelial maintenance and breakdown during semicircular canal formation.
Rakowiecki S, Epstein DJ.
Development 140(8):1730-9, 2013.

Inhibition of Sox2-dependent activation of Shh in the ventral diencephalon by Tbx3 is required for formation of the neurohypophysis.
Trowe MO, Zhao L, Weiss AC, Christoffels V, Epstein DJ, Kispert A.
Development 140(11):2299-309, 2013.

Arupa Ganguly
Parental nutrient intake and risk of retinoblastoma resulting from new germline RB1 mutation.
Bunin GR, Li Y, Ganguly A, Meadows AT, Tseng M.
Cancer Causes Control. 2013 Feb;24(2):343-55. doi: 10.1007/s10552-012-0120-x. Epub 2012 Dec 8.

A case-control study of paternal occupational exposures and the risk of childhood sporadic bilateral retinoblastoma.
Abdolahi A, van Wijngaarden E, McClean MD, Herrick RF, Allen JG, Ganguly A, Bunin GR.
Occup Environ Med. 2013 Jun;70(6):372-9. doi: 10.1136/oemed-2012-101062. Epub 2013 Mar 16.

Genomic profile of 320 uveal melanoma cases: chromosome 8p-loss and metastatic outcome.
Ewens KG, Kanetsky PA, Richards-Yutz J, Al-Dahmash S, De Luca MC, Bianciotto CG, Shields CL, Ganguly A.
Invest Ophthalmol Vis Sci. 2013 Aug 23;54(8):5721-9. doi: 10.1167/iovs.13-12195.

Dominant form of congenital hyperinsulinism maps to HK1 region on 10q.
Pinney SE, Ganapathy K, Bradfield J, Stokes D, Sasson A, Mackiewicz K, Boodhansingh K, Hughes N, Becker S, Givler S, Macmullen C, Monos D, Ganguly A, Hakonarson H, Stanley CA.
Horm Res Paediatr. 2013;80(1):18-27. doi: 10.1159/000351943. Epub 2013 Jul 13.

Enhanced Sensitivity for Detection of Low-Level Germline Mosaic RB1 Mutations in Sporadic Retinoblastoma Cases Using Deep Semiconductor Sequencing.
Chen Z, Moran K, Richards-Yutz J, Toorens E, Gerhart D, Ganguly T, Shields CL, Ganguly A.
Hum Mutat. 2013 Nov 26. doi: 10.1002/humu.22488. [Epub ahead of print]

David Gasser
Focal segmental glomerulosclerosis is associated with a PDSS2 haplotype and, independently, with a decreased content of coenzyme Q10.
Gasser DL, Winkler CA, Peng M, An P, McKenzie LM, Kirk GD, Shi Y, Xie LX, Marbois BN, Clarke CF and Kopp JB.
Am J Physiol Renal Physiol 305(8): F1228-F1238, 2013.

Yugong Ho
An -regulatory pathway establishes the definitive chromatin conformation at the Pit-1 locus
Ho Y, Cooke NE, Liebhaber SA.
Mol Cell Biol. 2015 May;35(9):1523-32. doi: 10.1128/MCB.01283-14

Thomas J. Jongens
Insulin signaling misregulation underlies circadian and cognitive deficits in a Drosophila fragile X model
Monyak RE, Emerson D, Schoenfeld BP, Zheng X, Chambers DB, Rosenfelt C, Langer S, Hinchey P, Choi CH, McDonald TV, Bolduc FV, Sehgal A, McBride SM, Jongens TA.
Mol Psychiatry. 2016 Apr 19. doi: 10.1038/mp.2016.51

Deciphering discord: How Drosophila research has enhanced our understanding of the importance of FMRP in different spatial and temporal contexts.
Weisz ED, Monyak RE, Jongens TA.
Exp Neurol. 2015 Dec;274(Pt A):14-24. Review.

PDE-4 inhibition rescues aberrant synaptic plasticity in Drosophila and mouse models of fragile X syndrome.
Choi CH, Schoenfeld BP, Weisz ED, Bell AJ, Chambers DB, Hinchey J, Choi RJ, Hinchey P, Kollaros M, Gertner MJ, Ferrick NJ, Terlizzi AM, Yohn N, Koenigsberg E, Liebelt DA, Zukin RS, Woo NH, Tranfaglia MR, Louneva N, Arnold SE, Siegel SJ, Bolduc FV, McDonald TV, McBride SM, Jongens TA.
J Neurosci. 2015 Jan 7;35(1):396-408.

Klaus Kaestner
Integration of ATAC-seq and RNA-seq Identifies Human Alpha Cell and Beta Cell Signature Genes.
Amanda M Ackermann, Zhiping Wang, Jonathan Schug, Ali Naji, Klaus H Kaestner.
Molecular Metabolism. 2016.

Foxl1-expressing mesenchymal cells constitute the intestinal stem cell niche.
Reina Aoki, Michal Shoshkes-Carmel, Nan Gao, Soona Shin, Catherine L May, Maria L Golson, Adam M Zahm, Michael Ray, Caroline L Wiser, Christopher VE Wright, Klaus H Kaestner.
CMGH Cellular and Molecular Gastroenterology and Hepatology. 2015.

The 'de novo' DNA methyltransferase Dnmt3b compensates the Dnmt1-deficient intestinal epithelium.
Elliott EN, Sheaffer KL, Kaestner KH.
Elife. 2016 Jan 25;5.

Stephen Liebhaber
An -regulatory pathway establishes the definitive chromatin conformation at the Pit-1 locus
Ho Y, Cooke NE, Liebhaber SA.
Mol Cell Biol. In Press.

Tissue Specific CTCF Occupancy and Boundary Function at the Human Growth Hormone Locus
Tsai, Y-C, Cooke, NE, and Liebhaber, SA
Nucleic Acids Research. 42: 4906-21., 2014.

Specific enrichment of the RNA-binding proteins PCBP1 and PCBP2 in chief cells of the murine gastric mucosa
Ghanem, LR, Chatterji, P, and Liebhaber, SA
Gene Expression Patterns. 14:78-87, 2014.

Autonomous Actions of the Human Growth Hormone Long-Range Enhancer
Yoo, EJ, Brown, CD., Tsai, Y-C, Cooke, NE, and Liebhaber, SA
Nucleic Acids Research. 2015.

Julia I-Ju Leu
Structural basis for the inhibition of HSP70 and DnaK chaperones by small-molecule targeting of a C-terminal allosteric pocket.
Leu JI, Zhang P, Murphy ME, Marmorstein R, George DL
ACS Chem Biol. 9(11): 2508-16, 2014.

Crystal structure of the stress-inducible human heat shock protein 70 substrate-binding domain in complex with peptide substrate.
Zhang P, Leu JI, Murphy ME, George DL, Marmorstein R
PLoS One. 9(7): e103518, 2014.

Meera Sundaram
A cell non-autonomous role for Ras signaling in C. elegans neuroblast delamination
Parry, J. M. and Sundaram, M. V.
Development 141: 4279-4284, 2014.

Sarah Tishkoff
Higher frequency of genetic variants conferring increased risk for ADRs for commonly used drugs treating cancer, AIDS and tuberculosis in persons of African descent.
Aminkeng F,  Ross CJ,  Rassekh SR,  Brunham LR,  Sistonen J,  Dube MP,  Ibrahim M,  Nyambo TB, Omar SA,  Froment A,  Bodo JM,  Tishkoff S,  Carleton BC,  Hayden MR.
The Pharmacogenomics Journal J. doi: 10.1038/tpj. 2013.

Comparison Between Southern Blots and qPCR Analysis of Leukocyte Telomere Length in the Health ABC Study.
Elbers CC,  Garcia ME,  Kimura M,  Cummings SR,  Nalls MA, Newman AB, Park V,  Sanders JL,  Tranah GJ,  Tishkoff SA, Harris TB, Aviv A.
The journals of gerontology. Series A, Biological sciences and medical sciences, published online ahead of print, 2013.

Patterns of nucleotide and haplotype diversity at ICAM-1 across global human populations with varying levels of malaria exposure.
Gomez F,  Tomas G,  Ko WY,  Ranciaro A, Froment A, Ibrahim M, Lema G, Nyambo TB, Omar SA, Wambebe C, Hirbo JB, Rocha J, Tishkoff SA.
Human Genetics 132(9): 987-99, 2013.

Identifying Darwinian selection acting on different human APOL1 variants among diverse African populations.
Ko WY, Rajan P, Gomez F, Scheinfeldt L, An P, Winkler CA, Froment A, Nyambo TB, Omar SA, Wambebe C, Ranciaro A, Hirbo JB, Tishkoff SA.
American Journal of Human Genetics 93(1): 54-66, 2013.

Great ape genetic diversity and population history.
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T.
Nature. 499(7459):471-5. 2013.

Origin and differential selection of allelic variation at TAS2R16 associated with salicin bitter taste sensitivity in Africa.
Campbell MC, Ranciaro A, Zinshteyn D, Rawlings-Goss R, Hirbo JB, Thompson SI, Woldemeskel D, Froment A, Rucker JB, Omar SA, Bodo J-M, Nyambo T, Belay G, Drayna D, Breslin PAS, Tishkoff SA.
Molecular Biology and Evolution, Advanced online publication. 2013.

Zhaolan (Joe) Zhou
Cellular origins of auditory event-related potential deficits in Rett syndrome
Goffin D, Brodkin ES, Blendy JA, Siegel SJ and Zhou Z
Nature Neuroscience. 17(6): 804-806, 2014.

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Recent Genetics Faculty Grants and Funding

Yoseph Barash has been awarded an R01 from the National Institute on Aging.
Title: Modeling Splicing in normal tissues and neurodegenerative disease
R01 AG046544-01A1

Joe Zhou has been awarded an R01 from the NINDS.
Title: Understanding the Pathogenic Mechanisms of Rett Syndrome
R01-NS081054

Donna George has been awarded a P01 from the NCI.
Title: Targeted Therapies in Melanoma
2P01 CA114046-06

John Murray has been awarded an R01 from the NIH.
Title: Mechanisms integrating lineage history with fate specification in C. elegans
1R01GM105676-01A1

Casey Brown has been awarded an R01 from the NIMH.
Title: Identification and validation of cell specific eQTLs by Bayesian modeling
1-R01-MH101822-01