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Genome Analysis Unit

Publications

Updated: 02/22/2018


Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres.
Xiao, Hua, Wang, Feng, Wisniewski, Jan, Shaytan, Alexey K., Ghirlando, Rodolfo, FitzGerald, Peter C., Huang, Yingzi, Wei, Debbie, Li, Shipeng, Landsman, David, Panchenko, Anna R., Wu, Carl
Genes and Development 2017, 31 (19) 1958-1972 PMID


An efficient single-cell RNA-seq approach to identify neoantigen-specific T-cell receptors.
Lu, Yong-chen, Zheng, Zhili, Robbins, Paul F, Tran, Eric, Prickett, Todd D, Gartner, Jared J, Li, Yong F, Ray, Satyajit, Franco, Zulmarie, Bliskovsky, Valery, FitzGerald, Peter C, Rosenberg, Steven A
Molecular Therapy 2017, 26 (2) 1-11 , Link


Reciprocal modifications of CLIC4 in tumor epithelium and stroma mark malignant progression of multiple human cancers.
Suh, Kwang S., Crutchley, John M., Koochek, Arash, Ryscavage, Andrew, Bhat, Kiran, Tanaka, Takemi, Oshima, Akira, FitzGerald, Peter, Yuspa, Stuart H.
Clinical Cancer Research 2007, 13 (1) 121-131 PMID , Link


Clustering of DNA sequences in human promoters.
FitzGerald, Peter C., Shlyakhtenko, Andrey, Mir, Alain A., Vinson, Charles
Genome Research 2004, 14 (8) 1562-1574 PMID , Link


Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement.
Ranjan, Anand, Mizuguchi, Gaku, FitzGerald, Peter C., Wei, Debbie, Wang, Feng, Huang, Yingzi, Luk, Ed, Woodcock, Christopher L., Wu, Carl
Cell 2013, 154 (6) PMID , Link


Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins..
Chatterjee, R., Zhao, J., He, X., Shlyakhtenko, A., Mann, I., Waterfall, J.J., Meltzer, P., Sathyanarayana, B.K., FitzGerald, P.C., Vinson, C.
G3 (Bethesda, Md.) 2012, 2 (10)


The conserved tyrosine residues 401 and 1044 in ATP sites of human P-glycoprotein are critical for ATP binding and hydrolysis: Evidence for a conserved subdomain, the A-loop in the ATP-binding cassette.
Kim, In-Wha, Peng, Xiang Hong, Sauna, Zuben E., FitzGerald, Peter C., Xia, Di, Müller, Marianna, Nandigama, Krishnamachary, Ambudkar, Suresh V.
Biochemistry 2006, 45 (24) 7605-7616 PMID , Link


Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABP and CREB Proteins.
Chatterjee, R., Zhao, J., He, X., Shlyakhtenko, A., Mann, I., Waterfall, J. J., Meltzer, P., Sathyanarayana, B. K., FitzGerald, P. C., Vinson, C.
G3 Genes|Genomes|Genetics 2012, 2 (10) 1243-1256 PMID , Link


High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes.
Chatterjee, Raghunath, He, Ximiao, Huang, Di, FitzGerald, Peter, Smith, Andrew, Vinson, Charles
Epigenetics & Chromatin 2014, 7 (1) 35 PMID , Link


Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways.
Yu, Weishi, McIntosh, Carl, Lister, Ryan, Zhu, Iris, Han, Yixing, Ren, Jianke, Landsman, David, Lee, Eunice, Briones, Victorino, Terashima, Minoru, Leighty, Robert, Ecker, Joseph R., Muegge, Kathrin
Genome Research 2014, 24 (10) 1613-1623 PMID


Cellular stress created by intermediary metabolite imbalances.
Lee, S. J., Trostel, A., Le, P., Harinarayanan, R., FitzGerald, P. C., Adhya, S.
Proceedings of the National Academy of Sciences of the United States of America 2009, 106 (46) 19515-19520 PMID , Link


Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection..
Chinn, Leslie W, Tang, Minzhong, Kessing, Bailey D, Lautenberger, James a, Troyer, Jennifer L, Malasky, Michael J, McIntosh, Carl, Kirk, Gregory D, Wolinsky, Steven M, Buchbinder, Susan P, Gomperts, Edward D, Goedert, James J, O’Brien, Stephen J
The Journal of infectious diseases 2010, 202 (12) 1836-45 PMID , Link


Comparative genomics of Drosophila and human core promoters..
FitzGerald, Peter C, Sturgill, David, Shyakhtenko, Andrey, Oliver, Brian, Vinson, Charles
Genome biology 2006, 7 (7) R53 PMID , Link


Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo.
Imashimizu, Masahiko, Takahashi, Hiroki, Oshima, Taku, McIntosh, Carl, Bubunenko, Mikhail, Court, Donald L., Kashlev, Mikhail
Genome Biology 2015, 16 (1) 98 PMID , Link


Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe.
Mizuguchi, T., Fudenberg, G., Mehta, S., Belton, J.-M., Taneja, N., Folco, H.D., FitzGerald, P., Dekker, J., Mirny, L., Barrowman, J., Grewal, S.I.S.
Nature 2014, 516 (7531)


Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I..
Sezgin, Efe, Drosdak, Alyssa, McIntosh, Carl, Kessing, Bailey, Lautenberger, James A, Goedert, James J, Phair, John P, Troyer, Jennifer L, Smith, Michael W, O’Brien, Stephen J
Journal of human genetics 2010, 55 (9) 613-20 PMID , Link


The Principal Genetic Determinants for Nasopharyngeal Carcinoma in China Involve the HLA Class I Antigen Recognition Groove.
Tang, Minzhong, Lautenberger, James A., Gao, Xiaojiang, Sezgin, Efe, Hendrickson, Sher L., Troyer, Jennifer L., David, Victor A., Guan, Li, McIntosh, Carl E., Guo, Xiuchan, Zheng, Yuming, Liao, Jian, Deng, Hong, Malasky, Michael, Kessing, Bailey, Winkler, Cheryl A., Carrington, Mary, dé The, Guy, Zeng, Yi, O’Brien, Stephen J.
PLoS Genetics 2012, 8 (11) PMID


Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding..
He, Ximiao, Chatterjee, Raghunath, John, Sam, Bravo, Hector, Sathyanarayana, B K, Biddie, Simon C, FitzGerald, Peter C, Stamatoyannopoulos, John a, Hager, Gordon L, Vinson, Charles
BMC Genomics 2013, 14 (1) 428 PMID , Link


Stepwise histone replacement by SWR1 requires dual activation with histone H2A.Z and canonical nucleosome.
Luk, Ed, Ranjan, Anand, FitzGerald, Peter C., Mizuguchi, Gaku, Huang, Yingzi, Wei, Debbie, Wu, Carl
Cell 2010, 143 (5) 725-736 PMID , Link


High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes.
Chatterjee, R., He, X., Huang, D., FitzGerald, P., Smith, A., Vinson, C.
Epigenetics and Chromatin 2014, 7 (1)


Genome-wide association study implicates PARD3B-based AIDS restriction.
Troyer, Jennifer L., Nelson, George W., Lautenberger, James A., Chinn, Leslie, McIntosh, Carl, Johnson, Randall C., Sezgin, Efe, Kessing, Bailey, Malasky, Michael, Hendrickson, Sher L., Li, Guan, Pontius, Joan, Tang, Minzhong, An, Ping, Winkler, Cheryl A., Limou, Sophie, Le Clerc, Sigrid, Delaneau, Olivier, Zagury, Jean Francxois, Schuitemaker, Hanneke, Van Manen, Daniëlle, Bream, Jay H., Gomperts, Edward D., Buchbinder, Susan, Goedert, James J., Kirk, Gregory D., O’Brien, Stephen J.
Journal of Infectious Diseases 2011, 203 (10) 1491-1502 PMID


Hamburger polyomaviruses.
Peretti, Alberto, FitzGerald, Peter C., Bliskovsky, Valery, Buck, Christopher B., Pastrana, Diana V.
Journal of General Virology 2015, 96 (4) 833-839 PMID , Link


Comparative validation of the D. melanogaster modENCODE transcriptome annotation.
Chen, Zhen Xia Z.-X., et. al.
Genome Research 2014, 24 (7) 1209-1223 PMID , Link


CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity..
Yu, Weishi, Briones, Victorino, Lister, Ryan, McIntosh, Carl, Han, Yixing, Lee, Eunice Y, Ren, Jianke, Terashima, Minoru, Leighty, Robert M, Ecker, Joseph R, Muegge, Kathrin
Proceedings of the National Academy of Sciences of the United States of America 2014, 111 (16) 5890-5 PMID , Link


Genome-wide association study implicates PARD3B-based AIDS restriction.
Troyer, Jennifer L., Nelson, George W., Lautenberger, James A., Chinn, Leslie, McIntosh, Carl, Johnson, Randall C., Sezgin, Efe, Kessing, Bailey, Malasky, Michael, Hendrickson, Sher L., Li, Guan, Pontius, Joan, Tang, Minzhong, An, Ping, Winkler, Cheryl A., Limou, Sophie, Le Clerc, Sigrid, Delaneau, Olivier, Zagury, Jean Francxois, Schuitemaker, Hanneke, Van Manen, Daniëlle, Bream, Jay H., Gomperts, Edward D., Buchbinder, Susan, Goedert, James J., Kirk, Gregory D., O’Brien, Stephen J.
Journal of Infectious Diseases 2011, 203 (10) 1491-1502 PMID , Link


Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways.
Yu, Weishi, McIntosh, Carl, Lister, Ryan, Zhu, Iris, Han, Yixing, Ren, Jianke, Landsman, David, Lee, Eunice, Briones, Victorino, Terashima, Minoru, Leighty, Robert, Ecker, Joseph R., Muegge, Kathrin
Genome Research 2014, 24 (10) 1613-1623 PMID , Link


Genome Sequence of a Fish-Associated Polyomavirus, Black Sea Bass (Centropristis striata) Polyomavirus 1..
Peretti, Alberto, FitzGerald, P.C. Peter C, Bliskovsky, Valery, Pastrana, Diana V D.V., Buck, C.B. Christopher B
Genome announcements 2015, 3 (1) e01476-14 PMID , Link


Comparative gene analysis of Biomphalaria glabrata hemocytes pre- and post-exposure to miracidia of Schistosoma mansoni.
Raghavan, N., Miller, A.N., Gardner, M., FitzGerald, P.C., Kerlavage, A.R., Johnston, D.A., Lewis, F.A., Knight, M.
Molecular and Biochemical Parasitology 2003, 126 (2)


CpG methylation of half-CRE sequences creates C/EBPα binding sites that activate some tissue-specific genes.
Rishi, V., Bhattacharya, P., Chatterjee, R., Rozenberg, J., Zhao, J., Glass, K., FitzGerald, P., Vinson, C.
Proceedings of the National Academy of Sciences of the United States of America 2010, 107 (47)


Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection..
Nicolas, Estelle, Yamada, Takatomi, Cam, Hugh P H.P., FitzGerald, P.C. Peter C, Kobayashi, Ryuji, Grewal, S.I.S. Shiv I S
Nature structural & molecular biology 2007, 14 (5) 372-380 PMID , Link


Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo.
Imashimizu, Masahiko, Takahashi, Hiroki, Oshima, Taku, McIntosh, Carl, Bubunenko, Mikhail, Court, Donald L., Kashlev, Mikhail
Genome Biology 2015, 16 (1) 98 PMID , Link


Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome.
Cam, H.P., Sugiyama, T., Chen, E.S., Chen, X., FitzGerald, P.C., Grewal, S.I.S.
Nature Genetics 2005, 37 (8) 809-19 PMID , Link


Whole genome analysis of a schistosomiasis-transmitting freshwater snail.
Adema, C.M., et. al.
Nature Communications 2017, 8


Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis.
Wilderman, Paula J, Sowa, Nathaniel A, FitzGerald, David J, FitzGerald, Peter C, Gottesman, Susan, Ochsner, Urs A, Vasil, Michael L
Proceedings of the National Academy of Sciences of the United States of America 2004, 101 (26) 9792-9797 PMID , Link


FIV cross-species transmission: An evolutionary prospective.
Troyer, Jennifer L., VandeWoude, Sue, Pecon-Slattery, Jill, McIntosh, Carl, Franklin, Sam, Antunes, Agostinho, Johnson, Warren, O’Brien, Stephen J.
Veterinary Immunology and Immunopathology 2008, 123 (1-2) 159-166 PMID


CpG methylation of half-CRE sequences creates C/EBPalpha binding sites that activate some tissue-specific genes..
Rishi, Vikas, Bhattacharya, Paramita, Chatterjee, Raghunath, Rozenberg, Julian, Zhao, Jianfei, Glass, Kimberly, FitzGerald, Peter, Vinson, Charles
Proceedings of the National Academy of Sciences of the United States of America 2010, 107 (47) 20311-6. PMID , Link


All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues..
Rozenberg, Julian M, Shlyakhtenko, Andrey, Glass, Kimberly, Rishi, Vikas, Myakishev, Maxim V, FitzGerald, Peter C, Vinson, Charles
BMC genomics 2008, 9 (67) 1-13 PMID , Link


Overlapping ETS and CRE motifs (G/C CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins.
Chatterjee, R., Zhao, J., He, X., Shlyakhtenko, A., Mann, I., Waterfall, J.J., Meltzer, P., Sathyanarayana, B.K., FitzGerald, P.C., Vinson, C.
G3: Genes, Genomes, Genetics 2012, 2 (10)


Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection..
Chinn, Leslie W, Tang, Minzhong, Kessing, Bailey D, Lautenberger, James a, Troyer, Jennifer L, Malasky, Michael J, McIntosh, Carl, Kirk, Gregory D, Wolinsky, Steven M, Buchbinder, Susan P, Gomperts, Edward D, Goedert, James J, O’Brien, Stephen J
The Journal of infectious diseases 2010, 202 (12) 1836-45 PMID , Link


FIV cross-species transmission: An evolutionary prospective.
Troyer, Jennifer L., VandeWoude, Sue, Pecon-Slattery, Jill, McIntosh, Carl, Franklin, Sam, Antunes, Agostinho, Johnson, Warren, O’Brien, Stephen J.
Veterinary Immunology and Immunopathology 2008, 123 (1-2) 159-166 PMID , Link


Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution.
He, X., Tillo, D., Vierstra, J., Syed, K.-S., Deng, C., Ray, G.J., Stamatoyannopoulos, J., FitzGerald, P.C., Vinson, C.
Genome Biology and Evolution 2015, 7 (11)


Transcription factor binding sites and other features in human and Drosophila proximal promoters..
Vinson, Charles, Chatterjee, Raghunath, FitzGerald, Peter
Sub-cellular biochemistry 2011, PMID , Link


Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes..
He, Ximiao, Chatterjee, Raghunath, Tillo, Desiree, Smith, Andrew, FitzGerald, Peter, Vinson, Charles
Epigenetics & chromatin 2014, 7 (1) 34 PMID , Link


Differential gene expression in haemocytes of the snail Biomphalaria glabrata: Effects of Schistosoma mansoni infection.
Miller, A.N., Raghavan, N., FitzGerald, P.C., Lewis, F.A., Knight, M.
International Journal for Parasitology 2001, 31 (7)


Integration profiling of gene function with dense maps of transposon integration.
Guo, Yabin, Park, Jung Min, Cui, Bowen, Humes, Elizabeth, Gangadharan, Sunil, Hung, Stevephen, FitzGerald, Peter C., Hoe, Kwang Lae, Grewal, Shiv I S, Craig, Nancy L., Levin, Henry L.
Genetics 2013, 195 (2) 599-609 PMID , Link


A Divergent Variant of the Eleventh Human Polyomavirus Species , Saint Louis Polyomavirus.
Pastrana, DV, FitzGerald, PC, Phan, GQ, Raiji, MT, Murphy, PM, McDermott, DH, Velez, D, Bliskovsky, V, McBride, AA, Buck, CB
Genome Announcements 2013, 1 (5) 2-3 PMID , Link


Reactivity of human sera in a sensitive, high-throughput pseudovirus-based papillomavirus neutralization assay for HPV16 and HPV18.
Pastrana, Diana V. D.V., Buck, Christopher B. C.B., Pang, Y.-Y.S. Yuk Ying S, Thompson, C.D. Cynthia D., Castle, Philip E. P.E., FitzGerald, P.C. Peter C., Kjaer, Susanne Krüger S.K., Lowy, D.R. Douglas R., Schiller, J.T. John T.
Virology 2004, 321 (2) 205-216 PMID , Link


Shelterin components mediate genome reorganization in response to replication stress.
Mizuguchi, T., Taneja, N., Matsuda, E., Belton, J.-M., FitzGerald, P., Dekker, J., Grewal, S.I.S.
Proceedings of the National Academy of Sciences of the United States of America 2017, 114 (21)


Evidence for Two Different Regulatory Mechanisms Linking Replication and Segregation of Vibrio cholerae Chromosome II.
Venkova-Canova, Tatiana, Baek, J.H. Jong Hwan, FitzGerald, P.C. Peter C., Blokesch, Melanie, Chattoraj, Dhruba K. D.K.
PLoS Genetics 2013, 9 (6) PMID , Link


Small RNA regulators and the bacterial response to stress.
Gottesman, S., McCullen, C. A., Guillier, M., Vanderpool, C. K., Majdalani, N., Benhammou, J., Thompson, K. M., FitzGerald, P. C., Sowa, N. A., FitzGerald, D. J.
Cold Spring Harbor Symposia on Quantitative Biology 2006, 71 1-11 PMID , Link


The mouse S100A15 ortholog parallels genomic organization, structure, gene expression, and protein-processing pattern of the human S100A7/A15 subfamily during epidermal maturation..
Wolf, Ronald, Voscopoulos, Christopher J, FitzGerald, Peter C, Goldsmith, Paul, Cataisson, Christophe, Gunsior, Michele, Walz, Markus, Ruzicka, Thomas, Yuspa, Stuart H
Journal of Investigative Dermatology 2006, 126 (7) 1600-8 PMID , Link


CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity..
Yu, Weishi, Briones, Victorino, Lister, Ryan, McIntosh, Carl, Han, Yixing, Lee, Eunice Y, Ren, Jianke, Terashima, Minoru, Leighty, Robert M, Ecker, Joseph R, Muegge, Kathrin
Proceedings of the National Academy of Sciences of the United States of America 2014, 111 (16) 5890-5 PMID , Link


Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe..
Mizuguchi, Takeshi, Fudenberg, Geoffrey, Mehta, Sameet, Belton, Jon-Matthew, Taneja, Nitika, Folco, Hernan Diego, FitzGerald, Peter, Dekker, Job, Mirny, Leonid, Barrowman, Jemima, Grewal, Shiv I S
Nature 2014, 516 (7531) 432-5 PMID , Link


The Principal Genetic Determinants for Nasopharyngeal Carcinoma in China Involve the HLA Class I Antigen Recognition Groove.
Tang, Minzhong, Lautenberger, James A., Gao, Xiaojiang, Sezgin, Efe, Hendrickson, Sher L., Troyer, Jennifer L., David, Victor A., Guan, Li, McIntosh, Carl E., Guo, Xiuchan, Zheng, Yuming, Liao, Jian, Deng, Hong, Malasky, Michael, Kessing, Bailey, Winkler, Cheryl A., Carrington, Mary, dé The, Guy, Zeng, Yi, O’Brien, Stephen J.
PLoS Genetics 2012, 8 (11) PMID , Link


Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I..
Sezgin, Efe, Drosdak, Alyssa, McIntosh, Carl, Kessing, Bailey, Lautenberger, James A, Goedert, James J, Phair, John P, Troyer, Jennifer L, Smith, Michael W, O’Brien, Stephen J
Journal of human genetics 2010, 55 (9) 613-20 PMID , Link