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...
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Daniel J. Rader, M.D. |
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 and the Institute for Regenerative Medicine. Click here to view the schedule.
Department Highlights
Congratulations to Dr. Janine Lamonica from the Zhou lab for receiving a two-year postdoctoral fellowship from the International Rett Syndrome Foundation!
We are pleased to announce that this year's Tom Kadesch Prize in Genetic Research has been awarded to Judy I-Ting Wang. Read more about Ms. Wang, the Kadesch Prize, and the Symposium...
Zhaolan Zhou, Dan Rader, Judy Wang, Alex Kadesch, Becca Mueller
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. |
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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 MPLoS 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. In Press.
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 ZNature Neuroscience. 17(6): 804-806, 2014.
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