Single Cell Analysis Symposium

March 12, 2014 @ the University of Pennsylvania

Hold the date for this all-day symposium. Speakers include Nancy Allbritton, Helen Blau, Chi Dang, Jim Eberwine, Junhyong Kim, Christopher Murray, Garry Nolan, Arjun Raj and Sherman Weissman.

More details and registration here for this free event.


The next frontier in the genome sciences will be developing technology that captures novel quantitative biological measurements ... more about genomics

PGFI Members' Papers

A sampling of PGFI members' recent papers

(bold=PGFI member)

Papers that were partially funded by PGFI are listed under PGFI-enabled papers

Members with new publications of interest to the PGFI community should send them to K. Field (kfield(at) for inclusion on this page.

2012, 2011, 2010, 2009 papers


Aurrecoechea, C., A. Barreto, J. Brestelli, B. P. Brunk, S. Cade, R. Doherty, S. Fischer, B. Gajria, X. Gao, A. Gingle, G. Grant, O. S. Harb, M. Heiges, S. Hu, J. Iodice, J. C. Kissinger, E. T. Kraemer, W. Li, D. F. Pinney, B. Pitts, D. S. Roos, G. Srinivasamoorthy, C. J. Stoeckert, H. Wang and S. Warrenfeltz (2013). "EuPathDB: The Eukaryotic Pathogen database." Nucleic Acids Research 41(D1): D684-D691.

Bartok, O., C. P. Kyriacou, J. Levine, A. Sehgal and S. Kadener (2013). "Adaptation of molecular circadian clockwork to environmental changes: a role for alternative splicing and miRNAs." Proceedings of the Royal Society B: Biological Sciences 280(1765).

Biesecker, L. G. and N. B. Spinner (2013). "A genomic view of mosaicism and human disease." Nat Rev Genet 14(5): 307-320.

Bramswig, N. C., L. J. Everett, J. Schug, C. Dorrell, C. Liu, Y. Luo, P. R. Streeter, A. Naji, M. Grompe and K. H. Kaestner (2013). "Epigenomic plasticity enables human pancreatic α to β cell reprogramming." The Journal of Clinical Investigation 123(3): 1275-1284.

Bray, P., S. McKenzie, L. Edelstein, S. Nagalla, K. Delgrosso, A. Ertel, J. Kupper, Y. Jing, E. Londin, P. Loher, H.-W. Chen, P. Fortina and I. Rigoutsos (2013). "The complex transcriptional landscape of the anucleate human platelet." BMC Genomics 14(1): 1.

Chiang, T. and M. A. Lampson (2013). Counting chromosomes in intact eggs. Mammalian Oocyte Regulation: Methods and Protocols, Humana Press. 957: 249-253.

Cideciyan, A. V., S. G. Jacobson, W. A. Beltran, A. Sumaroka, M. Swider, S. Iwabe, A. J. Roman, M. B. Olivares, S. B. Schwartz, A. M. Komáromy, W. W. Hauswirth and G. D. Aguirre (2013). "Human retinal gene therapy for Leber congenital amaurosis shows advancing retinal degeneration despite enduring visual improvement." Proceedings of the National Academy of Sciences 110(6): E517-E525.

Cruchaga, C., John S. K. Kauwe, O. Harari,…, V. M. Van Deerlin, V. M. Y. Lee,…, J. Q. Trojanowski,…, G. D. Schellenberg, et al. (2013). "GWAS of Cerebrospinal Fluid Tau Levels Identifies Risk Variants for Alzheimer’s Disease." Neuron 78(2): 256-268.

Foulkes, A. S., G. J. Matthews, U. Das, J. F. Ferguson, R. Lin and M. P. Reilly (2013). "Mixed Modeling of Meta-Analysis P-Values (MixMAP) Suggests Multiple Novel Gene Loci for Low Density Lipoprotein Cholesterol." PLoS One 8(2): e54812.

Gardner, S. E., S. L. Hillis, K. Heilmann, J. A. Segre and E. A. Grice (2013). "The Neuropathic Diabetic Foot Ulcer Microbiome Is Associated With Clinical Factors." Diabetes 62(3): 923-930.

Georgi, B., B. F. Voight and M. Bućan (2013). "From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes." PLoS Genet 9(5): e1003484.

Hasson, D., T. Panchenko, K. J. Salimian, M. U. Salman, N. Sekulic, A. Alonso, P. E. Warburton and B. E. Black (2013). "The octamer is the major form of CENP-A nucleosomes at human centromeres." Nat Struct Mol Biol 20(6): 687-695.

Kim, J., J. P. Hoffman, R. K. Alpaugh, A. D. Rhim, M. Reichert, B. Z. Stanger, E. E. Furth, A. R. Sepulveda, C.-X. Yuan, K.-J. Won, G. Donahue, J. Sands, A. A. Gumbs and K. S. Zaret (2013). "An iPSC Line from Human Pancreatic Ductal Adenocarcinoma Undergoes Early to Invasive Stages of Pancreatic Cancer Progression." Cell Reports 3(6): 2088-2099.

Ko, W.-Y., P. Rajan, F. Gomez, L. Scheinfeldt, P. An, C. A. Winkler, A. Froment, T. B. Nyambo, S. A. Omar, C. Wambebe, A. Ranciaro, J. B. Hirbo and S. A. Tishkoff (2013). "Identifying Darwinian Selection Acting on Different Human APOL1 Variants among Diverse African Populations." The American Journal of Human Genetics 93(1): 54-66.

Levesque, M. J., P. Ginart, Y. Wei and A. Raj (2013). "Visualizing SNVs to quantify allele-specific expression in single cells." Nat Meth 10(9): 865-867.

Mainland, J., J. Willer, H. Matsunami and N. Katsanis (2013). Next-Generation Sequencing of the Human Olfactory Receptors. Olfactory Receptors. C. J. Crasto, Humana Press. 1003: 133-147.

McDonald, M. K., K. E. Capasso and S. K. Ajit (2013). "Purification and microRNA Profiling of Exosomes Derived from Blood and Culture Media." J. Vis. Exp. (76), e50294, doi:10.3791/50294.

Moeller, A. H., M. Shilts, Y. Li, R. S. Rudicell, E. V. Lonsdorf, A. E. Pusey, M. L. Wilson, B. H. Hahn and H. Ochman (2013). "SIV-Induced Instability of the Chimpanzee Gut Microbiome." Cell Host & Microbe 14(3): 340-345.

Nathanson, K. L., A.-M. Martin, B. Wubbenhorst, et al. (2013). "Tumor Genetic Analyses of Patients with Metastatic Melanoma Treated with the BRAF Inhibitor Dabrafenib (GSK2118436)." Clinical Cancer Research 19(17): 4868-4878.

Olarerin-George, A., L. Anton, Y.-C. Hwang, M. Elovitz and J. Hogenesch (2013). "A functional genomics screen for microRNA regulators of NF-kappaB signaling." BMC Biology 11(1): 19.

Reitz, C., G. Jun, A. Naj…L-S. WangG. D. Schellenberg, et al. (2013). "VAriants in the atp-binding cassette transporter (abca7), apolipoprotein e ϵ4, and the risk of late-onset alzheimer disease in african americans." JAMA 309(14): 1483-1492.

Schadt, E. E., O. Banerjee, G. Fang, Z. Feng, W. H. Wong, X. Zhang, A. Kislyuk, T. A. Clark, K. Luong, A. Keren-Paz, A. Chess, V. Kumar, A. Chen-Plotkin, N. Sondheimer, J. Korlach and A. Kasarskis (2013). "Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases." Genome Research 23(1): 129-141.

Shah, P., Y. Ding, M. Niemczyk, G. Kudla and J. B. Plotkin (2013). "Rate-Limiting Steps in Yeast Protein Translation." Cell 153(7): 1589-1601.

Simonato, M., J. Bennett, N. M. Boulis, M. G. Castro, D. J. Fink, W. F. Goins, S. J. Gray, P. R. Lowenstein, L. H. Vandenberghe, T. J. Wilson, J. H. Wolfe and J. C. Glorioso (2013). "Progress in gene therapy for neurological disorders." Nat Rev Neurol 9(5): 277-291.

Venta, K., G. Shemer, M. Puster, J. A. Rodríguez-Manzo, A. Balan, J. K. Rosenstein, K. Shepard and M. Drndić (2013). "Differentiation of Short, Single-Stranded DNA Homopolymers in Solid-State Nanopores." ACS Nano 7(5): 4629-4636.

Yamaguchi, N., M.-F. Wu, C. M. Winter, M. C. Berns, S. Nole-Wilson, A. Yamaguchi, G. Coupland, B. A. Krizek and D. Wagner (2013). "A Molecular Framework for Auxin-Mediated Initiation of Flower Primordia." Developmental Cell 24(3): 271-282.

Yang, L., M. Xu, Y. Koo, J. He and R. S. Poethig (2013). "Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of MIR156A and MIR156C." eLife 2.

Younis, I., K. Dittmar, W. Wang, S. W. Foley, M. G. Berg, K. Y. Hu, Z. Wei, L. Wan and G. Dreyfuss (2013). "Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA." eLife 2.

Zhao, Y.-T., D. Goffin, B. S. Johnson and Z. Zhou (2013). "Loss of MeCP2 function is associated with distinct gene expression changes in the striatum." Neurobiology of Disease 59(0): 257-266.

Zheng, Y., T. O. Ogundiran, A. G. Falusi, K. L. Nathanson, E. M. John, A. J. M. Hennis, S. Ambs, S. M. Domchek, T. R. Rebbeck, et al. (2013). "Fine mapping of breast cancer genome-wide association studies loci in women of African ancestry identifies novel susceptibility markers." Carcinogenesis 34(7): 1520-1528.





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Based at the University of Pennsylvania, Penn Genome Frontiers Institute (PGFI) is a university-wide institute dedicated to the advancement of the interdisciplinary field of genomics research. PGFI fosters collaborations and scientific exchange across biology, veterinary medicine, pharmacology, medicine, genetics, microbiology, engineering, physics, chemistry and psychology. Our mission...