Updated: 8 January 2024

Direct ionic stress sensing and mitigation by the transcription factor NFAT5.
Khandwala CB, Parjiat S, Schmidt HB, Ma M, Kinnebrew M, Ganesh VP, Patel BB, Tillo D, Lebensohn L, Rohatgi R.,

Decoding complexity in biomolecular recognition of DNA i-Motifs with microarrays.
Yazdani K, Seshadri S, Tillo D, Vinson C, Schneekloth JS.,
Nucleic Acids Research, Volume 51, Issue 22, 11 December 2023, Pages 12020-12030,

A novel GATA2 distal enhancer mutation results in the MonoMAC syndrome phenotype in two second cousins.
West RR, Bauer TR, Tuschong LM, Embree LJ,Calvo KR, Tillo D, Holland SM, Hickstein DD.,
Blood Adv 2023 Oct 24;7(20):6351-6363. doi: 10.1182/bloodadvances.2023010458.

The homeobox transcription factor DUXBL controls exit from totipotency.
Vega-Sendino M, Olbrich T, Stein P, Tillo D, Carey GI, Savy V, Saykali B, Domingo CN, Maity TK, Jenkins LM, Williams CJ, Ruiz S.
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A Knock-in Mouse Model of Thymoma With the GTF2i L424H Mutation.
He Y, Kim I-K, Bian J, Zhang Y, Luo J, Hernandez MO, Kedei N, Cam M, Borczuk AC, Apostolour E, Lee T, Han Y, Conner EA, Wong MMF, Tillo D, Umemura S, Chen V, Ruan L, White J, Altorki N, Elemento O, Divakar P, Thomas B, Giaccone G.,
JThorac Oncol. 2022, S1556-0864(22)01550-7. doi: 10.1016/j.jtho.2022.08.008.

ASXL1 and STAG2 are Common Accompanying Mutations in GATA2 Deficiency Patients with Bone Marrow Disease and Myelodysplastic Syndrome.
West RR, Calvo KR, Embree LJ, Wang W, Tuschong LM, Bauer TR, Tillo D, Lack J, Droll S, Hsu AP, Holland SM, Hickstein DD.
Blood Advances 2022, 6(3):793-807 doi: 10.1182/bloodadvances.2021005065.

Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182.
Ray S, Tillo D, Assad N, Ufot A, Porollo A, Durell SR, Vinson C.,
ACS Omega 2022, 7(1):129-139. doi: 10.1021/acsomega.1c04148.

Spatial meta-transcriptomics reveal associations of intratumor bacteria burden with lung cancer cells showing a distinct oncogenic signature.
Wong-Rolle A, Dong Q, Zhu Y, Divakar P, Hor JL, Kedei N, Wong M, Tillo D, Conner E, Rajan A, Schrump D, Jin C, Germain R, Zhao C.,
J Immunother Cancer 2022, 10(7):e004698. doi: 10.1136/jitc-2022-004698.

CTCF is a Barrier for Totipotent-like Reprogramming.
Olbrich T, Vega-Sendino M, Tillo D, Wu W, Zolnerowich N, Tran AD, Domingo CN, Franco M, Markiewicz-Potoczny M, Pegoraro G, FitzGerald PC, Kruhlak MJ, Lazzerini-Denchi E, Nora EP, Nussenzweig A, Ruiz S.
Nature Communications 2021, 12(4856).

Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria.
Sun Z, Yakhnin A, FitzGerald PC, McIntosh CE, Kashlev M.
Nature Communications 2021, 12(1):906. doi: 10.1038/s41467-021-21150-2.

REL Domain of NFATc2 Binding to Five Types of DNA Using Protein Binding Microarrays.
Ray S, Tillo D, Durell SR, Khund-Sayeed S, Vinson C.
ACS Omega 2021, 6(6):4147-4154.

Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element.
Liu X, Rye E, Tillo D, Vinson C, Ortlund E.
Nucleic Acids Research 2021, 49(15): 8923-8933.

The ETS Transcription Factor ERF controls the exit from the naïve pluripotent state in a MAPK-dependent manner.
Vega-Sendino M, Olbrich T, Tillo D, Tran AD, Domingo CM, Franco M, FitzGerald PC, Kruhlak MJ and Ruiz S,
Science Advances 2021, 7(40):eabg8306. doi: 10.1126/sciadv.abg8306.

Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes.
Ray S*, Tillo D*, Boer RE, Assad N, Barshai M, Orenstein Y, Yang D, Schneekloth JS, Vinson C.
ACS Chem Biol 2020, 15(4):925-935. *Equal contributions

Custom G4 microarrays reveal selective G-quadruplex recognition of small molecule BMVC: a large-scale assessment of ligand binding selectivity.
Wu G*, Tillo D*, Ray S*, Chang T, Schneekloth JS, Vinson C, Yang D
Molecules 2020, 25(15), 3465. *Equal contributions.

NusG controls transcription pausing and RNA polymerase translocation throughout the Bacillus subtilis genome.
Yakhnin AV, FitzGerald PC, McIntosh CE, Yakhnin H, Kireeva M, Turek-Herman J, Mandell ZF, Kashlev M, Babitzke P.
PNAS 2020, 117(35):21628-21636. doi: 10.1073/pnas.2006873117.

bZIP Dimers CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun Prefer to Bind to Some Double-Stranded DNA Sequences Containing 5-Formylcytosine and 5-Carboxylcytosine.
Ray S, Tillo D, Ufot A, Assad N, Durell S, Vinson C.
Biochemistry 2020, 59(38):3529-3540.

GABPα and CREB1 Binding to Double Nucleotide Polymorphisms of Their Consensus Motifs and Cooperative Binding to the Composite ETS ⇔ CRE Motif (ACCGGAAGTGACGTCA).
Assad N, Tillo D, Ray S, Dzienny A, FitzGerald PC, Vinson C.
ACS Omega 2019, 4(6):9904-9910.

An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific. T Cell Receptors.
Lu, YC., Zheng, ZL., Robbins, PF., Tran, E., Prickett, TD., Gartner, JJ., Li, YF., Ray, S., Franco, Z., Bliskovsky, V., FitzGerald, PC., Rosenberg, SA.,
MOLECULAR THERAPY 2018 Feb 7;26(2):379-389.

Characterization of BK Polyomaviruses from Kidney Transplant Recipients Suggests a Role for APOBEC3 in Driving In-Host Virus Evolution.
Peretti, A., Geoghegan, EM., Pastrana, DV., Smola, S., Feld, P., Sauter, M., Lohse, S., Ramesh, M., Lim, ES., Wang, D., Borgogna, C., FitzGerald, PC., Bliskovsky, V., Starrett, GJ., Law, EK., Harris, RS., Killian, JK., Zhu, J., Pineda, M., Meltzer, PS., Boldorini, R., Gariglio, M., Buck, CB.,
CELL HOST & MICROBE 2018 May 9;23(5):628-635.e7. doi: 10.1016/j.chom.2018.04.005.

Metagenomic Discovery of 83 New Human Papillomavirus Types in Patients with Immunodeficiency.
Pastrana, DV., Peretti, A., Welch, NL., Borgogna, C., Olivero, C., Badolato, R., Notarangelo, LD., Gariglio, M., FitzGerald, PC., McIntosh, CE., Reeves, J., Starrett, GJ., Bliskovsky, V., Velez, D., Brownell, I., Yarchoan, R., Wyvill, KM., Uldrick, TS., Maldarelli, F., Lisco, A., Sereti, I., Gonzalez, CM., Androphy, EJ., McBride, AA., Van Doorslaer, K., Garcia, F., Dvoretzky, I., Liu, JS., Han, J., Murphy, PM., McDermott, DH., Buck, CB,
MSPHERE 2018 Dec 12;3(6):e00645-18. doi: 10.1128/mSphereDirect.00645-18.

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

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.
. Proceedings of the National Academy of Sciences of the United States of America 2017, 114 (21)

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

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

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

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)

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

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

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

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

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

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

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

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

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

Evidence for Two Different Regulatory Mechanismsing 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)

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

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)

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 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)

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

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

CpG methylation of half-CRE sequences creates C/EBPα 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.

Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I
Sezgin E, Drosdak A, McIntosh C, Kessing B, Lautenberger J, Goedert JJ, Phair JP, Troyer JL, Smith MW, and O’Brien SJ.
Journal of human genetics 2010, 55 (9) 613-20

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

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

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

Evolution of Microsatellite Loci in the Adaptive Radiation of Hawaiian Honeycreepers
Eggert, L. S., Beadell, J. S., McClung, A, McIntosh, C. E., and Fleischer, R. C.
Journal of Heredity 2009, 102(1)1 – 11.

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

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

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

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

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

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

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

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

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

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

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

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

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)

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)