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.
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 and the Institute for Regenerative Medicine. Click here to view the schedule.
We are pleased to announce that this year's Tom Kadesch Prize in Genetic Research is being awarded to Maria Elena De Obaldia at the 2013 Genetics Symposium. Read more about Ms. De Obaldia, the Kadesch Prize, and the Symposium... Congratulations also to GGR student, Ian Silverman, who was the winner of the Symposium Poster Prize.
Becca Mueller, Abby Huntington, Ellen De Obaldia, Stephen Liebhaber
Congratulations to John Murray and his postoc Amanda Zacharais, winners of The Federation of American Societies for Experimental Biology (FASEB) 2013 BioArt Competition for their worm embryo video. See the video here...
Congratulations to Meera Sundaram, the 2013 recipient of the Jane Glick Graduate Student Teaching Award. Please join us in congratulating Meera on this well deserved recognition of her outstanding dedication to graduate student teaching. Read More...
Meera Sundaram, Stephen Liebhaber
Recent Faculty Additions
We are pleased to announce the recruitment of Christopher (Casey) Brown, Ph.D. Casey received his Ph.D. in Genetics from Stanford in 2007 in the laboratory of Arend Sidow, where he used a combination of whole embryo expression data and statistical modeling to explore the role of evolutionary processes in defining constraints over a compendium of over 70 expression-defining determinants in the tunicate, Ciona intestinalis, genome. His postdoctoral studies in the lab of Kevin White at the Institute for Genomics and Systems Biology, University of Chicago, focused on the analysis of cis-regulatory variation in human primary tissue using novel adaptations of quantitative trait locus (eQTL) mapping. Casey will join the Department as a tenure track Assistant Professor on January 1, 2013. His arrival is expected to further strengthen and expand the Department's capacities in the field of biomedical informatics and to extend our mechanistic studies of gene regulation by noncoding determinants.
Recent Genetics Faculty Publications
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.
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.
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.
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]
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.
Cytoplasmic Poly(A) Binding Protein C4 Serves a Critical Role in Erythroid Differentiation
Kini H, Kong J, and Liebhaber SA.
Mol. Cell. Biol. April 2014 vol. 34 no. 7 1300-1309.
The Poly-C Binding Proteins, αCPs, Act as Global Regulators of Alternative Polyadenylation.
Ji X, Wan J, Vishnu M, Xing Y, Liebhaber SA
Mol. Cell. Biol. July 2013 vol. 33 no. 13 2560-2573.
Distinct chromatin configurations regulate the initiation and the maintenance phases of hGH gene expression.
Ho Y., Shewchuk, B., Liebhaber SA, Cooke NE.
In press. Mol Cell Biol. 2013.
Canonical RTK-Ras-ERK signaling and related alternative pathways.
Sundaram, M. V.
Wormbook, edited by the Community of C. elegans Researchers. 2013. In press.
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
Loss of MeCP2 function is associated with distinct gene expression changes in the striatum.
Zhao Y, Goffin D, Johnson B and Zhou Z. Neurobiology of Disease. 59C:257-266, 2013.
Neuronal morphology in MeCP2 mouse models is intrinsically variable and depends on age, cell type, and Mecp2 mutation.
Wang IT, Reyes AR and Zhou Z Neurobiology of Disease. 58C:3-12, 2013.
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
Joe Zhou has been awarded an R01 from the NINDS.
Title: Understanding the Pathogenic Mechanisms of Rett Syndrome
Donna George has been awarded a P01 from the NCI.
Title: Targeted Therapies in Melanoma
John Murray has been awarded an R01 from the NIH.
Title: Mechanisms integrating lineage history with fate specification in C. elegans
Casey Brown has been awarded an R01 from the NIMH.
Title: Identification and validation of cell specific eQTLs by Bayesian modeling