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)sas.upenn.edu) for inclusion on this page.

2011, 2010, 2009 papers

2013

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.

2012

Abe, M. and N. M. Bonini (2012). "MicroRNAs and neurodegeneration: role and impact." Trends in Cell Biology(Epub 9-28-12): 10.1016/j.tcb.2012.08.013.
   
Beltran, W. A., A. V. Cideciyan, A. S. Lewin, S. Iwabe, H. Khanna, A. Sumaroka, V. A. Chiodo, D. S. Fajardo, A. J. Roman, W. T. Deng, M. Swider, T. S. Aleman, S. L. Boye, S. Genini, A. Swaroop, W. W. Hauswirth, S. G. Jacobson and G. D. Aguirre (2012). "Gene therapy rescues photoreceptor blindness in dogs and paves the way for treating human X-linked retinitis pigmentosa." Proc Natl Acad Sci U S A 109(6): 2132-7.

Bennett, J., M. Ashtari, J. Wellman, K. A. Marshall, L. L. Cyckowski, D. C. Chung, S. McCague, E. A. Pierce, Y. Chen, J. L. Bennicelli, X. Zhu, G. S. Ying, J. Sun, J. F. Wright, A. Auricchio, F. Simonelli, K. S. Shindler, F. Mingozzi, K. A. High and A. M. Maguire (2012). "AAV2 gene therapy readministration in three adults with congenital blindness." Sci Transl Med 4(120): 120ra15.
   
Brisson, D., D. Drecktrah, C. H. Eggers and D. S. Samuels (2012). "Genetics of Borrelia burgdorferi." Annual Review of Genetics 46(1): 515-536.

Bucan, M., J. Eppig and S. Brown (2012). "Mouse genomics programs and resources." Mammalian Genome 23(9-10): 479-489.
   
Chen, J., K. Bittinger, E. S. Charlson, C. Hoffmann, J. Lewis, G. D. Wu, R. G. Collman, F. D. Bushman and H. Li (2012). "Associating microbiome composition with environmental covariates using generalized UniFrac distances." Bioinformatics 28(16): 2106-13.

Chen, J., F. D. Bushman, J. D. Lewis, G. D. Wu and H. Li (2012). "Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis." Biostatistics(EPub 10-15-12): 10.1093/biostatistics/kxs038.

Domchek, S. M., J.-B. Tang, J. Stopfer, D. R. Lilli, N. Hamel, M. Tischkowitz, A. N. A. Monteiro, T. E. Messick, J. Powers, A. Yonker, F. J. Couch, D. E. Goldgar, H. R. Davidson, K. L. Nathanson, W. Foulkes and R. A. Greenberg (2012). "Biallelic Deleterious BRCA1 Mutations in a Woman with Early-Onset Ovarian Cancer." Cancer Discovery.

Gardner, S. E., S. L. Hillis, K. Heilmann, J. A. Segre and E. A. Grice (2012). "The Neuropathic Diabetic Foot Ulcer Microbiome Is Associated With Clinical Factors." Diabetes: Epub (11/8/12), doi:10.2337/db12-0771.

Hawk, J. D., A. L. Bookout, S. G. Poplawski, M. Bridi, A. J. Rao, M. E. Sulewski, B. T. Kroener, D. J. Manglesdorf and T. Abel (2012). "NR4A nuclear receptors support memory enhancement by histone deacetylase inhibitors." The Journal of Clinical Investigation 122(10): 3593-3602.
   
Healy, K., V. Ray, L. J. Willis, N. Peterman, J. Bartel and M. Drndić (2012). "Fabrication and characterization of nanopores with insulated transverse nanoelectrodes for DNA sensing in salt solution." Electrophoresis 33(23): 3488-3496.

Jarvis, J. P., L. B. Scheinfeldt, S. Soi, C. Lambert, L. Omberg, B. Ferwerda, A. Froment, J. M. Bodo, W. Beggs, G. Hoffman, J. Mezey and S. A. Tishkoff (2012). "Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies." PLoS Genet 8(4): e1002641.

Kingsley, P. D., E. Greenfest-Allen, J. M. Frame, T. P. Bushnell, J. Malik, K. E. McGrath, C. J. Stoeckert and J. Palis (2012). "Ontogeny of erythroid gene expression." Blood(Epub 12-12-12): 10.1182/blood-2012-04-422394.

Kuznetsova, T., S. Iwabe, K. Boesze-Battaglia, S. Pearce-Kelling, Y. Chang-Min, K. McDaid, K. Miyadera, A. Komaromy and G. D. Aguirre (2012). "Exclusion of RPGRIP1 ins44 from Primary Causal Association with Early-Onset Cone-Rod Dystrophy in Dogs." Investigative Ophthalmology & Visual Science 53(9): 5486-5501.
   
Lachance, J., B. Vernot, C. C. Elbers, B. Ferwerda, A. Froment, J.-M. Bodo, G. Lema, W. Fu, T. B. Nyambo, T. R. Rebbeck, K. Zhang, J. M. Akey and S. A. Tishkoff (2012). "Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers." Cell 150(3): 457-469.
   
Li, M. L. and R. A. Greenberg (2012). "Links between genome integrity and BRCA1 tumor suppression." Trends in Biochemical Sciences 37(10): 418-424.

Li, Z., P. Gadue, K. Chen, Y. Jiao, G. Tuteja, J. Schug, W. Li and K. H. Kaestner (2012). "Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation." Cell: 10.1016/j.cell.2012.11.018.
   
Li, Z., G. Tuteja, J. Schug and K. H. Kaestner (2012). "Foxa1 and Foxa2 are essential for sexual dimorphism in liver cancer." Cell 148(1-2): 72-83.
   
Libby, E. A., M. Roggiani and M. Goulian (2012). "Membrane protein expression triggers chromosomal locus repositioning in bacteria." Proc Natl Acad Sci U S A 109(19): 7445-50.
   
Mijušković, M., S. M. Brown, Z. Tang, C. R. Lindsay, E. Efstathiadis, L. Deriano and D. B. Roth (2012). "A Streamlined Method for Detecting Structural Variants in Cancer Genomes by Short Read Paired-End Sequencing." PLoS One 7(10): e48314.

Morlon, H., B. D. Kemps, J. B. Plotkin and D. Brisson (2012). "Explosive radiation of a bacterial species group." Evolution 66(8): 2577-86.

Murray, J. I., T. J. Boyle, E. Preston, D. Vafeados, B. Mericle, P. Weisdepp, Z. Zhao, Z. Bao, M. Boeck and R. H. Waterston (2012). "Multidimensional regulation of gene expression in the C. elegans embryo." Genome Research 22(7): 1282-1294.

Ocwieja, K. E., S. Sherrill-Mix, R. Mukherjee, R. Custers-Allen, P. David, M. Brown, S. Wang, D. R. Link, J. Olson, K. Travers, E. Schadt and F. D. Bushman (2012). "Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing." Nucleic Acids Research 40(20): 10345-10355.
   
Parente, M. K., R. Rozen, C. N. Cearley and J. H. Wolfe (2012). "Dysregulation of Gene Expression in a Lysosomal Storage Disease Varies between Brain Regions Implicating Unexpected Mechanisms of Neuropathology." PLoS One 7(3): e32419.
   
Pickrell, J. K., N. Patterson, C. Barbieri, F. Berthold, L. Gerlach, T. Guldemann, B. Kure, S. W. Mpoloka, H. Nakagawa, C. Naumann, M. Lipson, P.-R. Loh, J. Lachance, J. Mountain, C. D. Bustamante, B. Berger, S. A. Tishkoff, B. M. Henn, M. Stoneking, D. Reich and B. Pakendorf (2012). "The genetic prehistory of southern Africa." Nat Commun 3: 1143.
   
Pizarro, A., K. Hayer, N. F. Lahens and J. B. Hogenesch (2012). "CircaDB: a database of mammalian circadian gene expression profiles." Nucleic Acids Research(Epub 11/24/12): 10.1093/nar/gks1161.

Qing, G., B. Li, A. Vu, N. Skuli, Z. E. Walton, X. Liu, P. A. Mayes, D. R. Wise, C. B. Thompson, J. M. Maris, M. D. Hogarty and M. C. Simon (2012). "ATF4 Regulates MYC-Mediated Neuroblastoma Cell Death upon Glutamine Deprivation." Cancer Cell 22(5): 631-644.
   
Sarov, M., J. I. Murray, K. Schanze, A. Pozniakovski, W. Niu, K. Angermann, S. Hasse, M. Rupprecht, E. Vinis, M. Tinney, E. Preston, A. Zinke, S. Enst, T. Teichgraber, J. Janette, K. Reis, S. Janosch, S. Schloissnig, R. K. Ejsmont, C. Slightam, X. Xu, S. K. Kim, V. Reinke, A. F. Stewart, M. Snyder, R.H. Waterston and A. A. Hyman (2012). "A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans." Cell 150(4): 855-866.

Shin, J., A. Padmanabhan, E. D. de Groh, J. S. Lee, S. Haidar, S. Dahlberg, F. Guo, S. He, M. A. Wolman, M. Granato, N. D. Lawson, S. A. Wolfe, S. H. Kim, L. Solnica-Krezel, J. P. Kanki, K. L. Ligon, J. A. Epstein and A. T. Look (2012). "Zebrafish neurofibromatosis type 1 genes have redundant functions in tumorigenesis and embryonic development." Dis Model Mech.

Solyom, S., B. Aressy, K. Pylkas, J. Patterson-Fortin, J. M. Hartikainen, A. Kallioniemi, S. Kauppila, J. Nikkila, V. M. Kosma, A. Mannermaa, R. A. Greenberg and R. Winqvist (2012). "Breast cancer-associated Abraxas mutation disrupts nuclear localization and DNA damage response functions." Sci Transl Med 4(122): 122ra23.

Sonnenberg, G. F., L. A. Monticelli, T. Alenghat, T. C. Fung, N. A. Hutnick, J. Kunisawa, N. Shibata, S. Grunberg, R. Sinha, A. M. Zahm, M. R. Tardif, T. Sathaliyawala, M. Kubota, D. L. Farber, R. G. Collman, A. Shaked, L. A. Fouser, D. B. Weiner, P. A. Tessier, J. R. Friedman, H. Kiyono, F. D. Bushman, K.-M. Chang and D. Artis (2012). "Innate Lymphoid Cells Promote Anatomical Containment of Lymphoid-Resident Commensal Bacteria." Science 336(6086): 1321-1325.

Soufi, A., G. Donahue and K. S. Zaret (2012). "Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome." Cell 151(5): 994-1004.

Sun, H., G. Zhuang, L. Chai, Z. Wang, D. Johnson, Y. Ma and Y. H. Chen (2012). "TIPE2 Controls Innate Immunity to RNA by Targeting the Phosphatidylinositol 3-Kinase-Rac Pathway." The Journal of Immunology 189(6): 2768-2773.

Wozniak, M. A., C. Q. Cheng, C. J. Shen, L. Gao, A, O. Olarerin-George, K.-J. Won, J. B. Hogenesch and C. S. Chen (2012). "Adhesion Regulates MAP Kinase/Ternary Complex Factor Exchange to Control a Proliferative Transcriptional Switch." Current Biology 22(21): 2017-2026.

Yan, Q., R. J. Carmody, Z. Qu, Q. Ruan, J. Jager, S. E. Mullican, M. A. Lazar and Y. H. Chen (2012). "Nuclear factor-kappaB binding motifs specify Toll-like receptor-induced gene repression through an inducible repressosome." Proc Natl Acad Sci U S A.

Yang, L., G. Wu and R. S. Poethig (2012). "Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis." Proc Natl Acad Sci U S A 109(1): 315-20.

Yehya, N., A. Yerrapureddy, J. Tobias and S. S. Margulies (2012). "MicroRNA modulate alveolar epithelial response to cyclic stretch." BMC Genomics 13(1): 154.

Yusuf, D., S. Butland, M. Swanson, E. Bolotin, A. Ticoll, …, J. B. Hogenesch, R. F. Hevner, C. Héligon, X. M. Luo, M. C. Blank, K. J. Millen, D. S. Sharlin, D. Forrest, K. Dahlman-Wright, C. Zhao, Y. Mishima, S. Sinha, R. Chakrabarti, E. Portales-Casamar, F. M. Sladek, P. H. Bradley and W. W. Wasserman (2012). "The Transcription Factor Encyclopedia." Genome Biology 13(3): R24.

Zhao, H., T. R. Rebbeck and N. Mitra (2012). "Analyzing genetic association studies with an extended propensity score approach." Stat Appl Genet Mol Biol 11(5).

Zheng, K. and P. J. Wang (2012). "Blockade of Pachytene piRNA Biogenesis Reveals a Novel Requirement for Maintaining Post-Meiotic Germline Genome Integrity." PLoS Genet 8(11): e1003038.