Graduate Student Publications

Graduate Students in bold; Mentors in italics.

Cell and Molecular Biology

2014

  • Haery L, JG Lugo-Picó, RA Henry, AW Andrews & TD Gilmore. 2014. Histone acetyltransferase-deficient p300 mutants in diffuse large B-cell lymphoma have altered transcriptional regulatory activities and are required for optimal cell growth. Molecular Cancer 13: 29

  • Siggers T, TD Gilmore, B Barron & A Penvose. 2014. Characterizing the DNA binding site specificity of NF-κB with protein binding microarrays. Methods in Molecular Biology, in press

2013

  • Cotter KA, Yershov A, Novillo A, Callard GV (2013). Multiple structurally distinct ERa mRNA variants in zebrafish are differentially expressed by tissue type, stage of development and estrogen exposure. Gen Comp Endocrinol 194: 217-229 (http://dx.doi.org/10.1016/j.ygcen.2013.09.014)

  • Estrella, N.L. and Naya, F.J. Transcriptional networks regulating the costamere, sarcomere, and other cytoskeletal structures in striated muscle. Cell Mol Life Sci. 2013 Nov 12. [Epub ahead of print]

  • Griffin LB, January K, Ho K, Cotter K, Callard GV (2013). Morpholino-mediated knockdown of genes encoding estrogen receptor-a, -ba and –bb in zebrafish embryos reveals differential regulation of estrogen responsive target genes. Endocrinology 154:4158-4169 (doi10.1210/en2013-1446).


  • Cote S, TD Gilmore, R Schaffer, U Weber, R Bollom, MS Golden, K Glover, M Herscovitch, T Ennis, KN Allen & A Whitty. 2013. Mutation of nonessential cysteines shows that the NF-κB essential modulator (NEMO) forms a constitutive noncovalent dimer that binds IκB kinase-β (IKKβ)with high affinity. Biochemistry 52: 9141-9154 *Co-corresponding authors

  • Jenkins, V.J., Timmons, A. K. and McCall, K. (2013) Diversity of cell death pathways: insight from the Drosophila ovary, Trends in Cell Biology 23: 567-574.

  • Layden MJ, E Rottinger, FS Wolenski, TD Gilmore & MQ Martindale. 2013. Microinjection techniques for reverse genetic analysis in the starlet sea anemone, Nematostella vectensis. Nature Protocols 8: 924-934. (Abstract Link)

  • Stanley Yip K, Suvorov A, Connerney J, Lodato NJ, Waxman DJ. Changes in Mouse Uterine Transcriptome in Estrus and Proestrus. Biol Reprod. 2013 Jun 5. [Epub ahead of print]

  • Snyder CM, Rice AL, Estrella NL, Held A, Kandarian SC, Naya FJ (2013). MEF2A regulates the Gtl2-Dio3 microRNA mega-cluster to modulate Wnt signaling in skeletal muscle regeneration. Development. 140(1):31-42.

  • Stefanik, D. J., Friedman, L. E., & Finnerty, J. R. (2013). Collecting, rearing, spawning and inducing regeneration of the starlet sea anemone, Nematostella vectensis. Nature protocols, 8(5), 916–923.

  • Stefanik, D. J., Wolenski, F. S., Friedman, L. E., Gilmore, T. D., & Finnerty, J. R. (2013). Isolation of DNA, RNA and protein from the starlet sea anemone Nematostella vectensis. Nature protocols, 8(5), 892–899.

  • Thompson RC, I Vardinogiannis & TD Gilmore. 2013. The sensitivity of diffuse large B-cell lymphoma cell lines to histone deacetylase inhibitor-induced apoptosis is modulated by BCL-2 family protein activity. PLoS ONE 8: e62822 (Abstract Link)

  • Thompson RC, I Vardinogiannis & TD Gilmore. 2013. Identification of an NF-κB p50-p65-responsive site in the human MIR155HG promoter. BMC Molecular Biology 14: 24

  • Thompson RC, I Vardinogiannis & TD Gilmore. 2013. The sensitivity of diffuse large B-cell lymphoma cell lines to histone deacetylase inhibitor-induced apoptosis is modulated by BCL-2 family protein activity. PLoS ONE 8: e62822

  • Timmons, A.K., Meehan, T.L., Gartmond, T.D. and McCall, K. (2013) Use of Necrosis Markers in the Drosophila ovary, in Necrosis Methods and Protocols, Methods in Molecular Biology series, Humana Press, McCall, K. and Klein, C., eds., in press.

  • Toomey ME*, Panaram K*, Fast EM, Beatty C, & Frydman H (2013) Evolutionarily conserved Wolbachia-intrinsicfactors control differential stem cell niche tropism in the Drosophila ovary and enhance vertical transmission. Proc Natl Acad Sci U S A, in press.

  • Wolenski, FS, Bradham, CA, FInnerty, JR, Gilmore, TD. NF-κB is required for cnidocyte development in the sea anemone Nematostella vectensis. Developmental Biology Volume 373, Issue 1, 1 January 2013

  • Wolenski FS, MJ Layden MQ Martindale, TD Gilmore & JR Finnerty. 2013. Characterizing the spatiotemporal expression of RNAs and proteins in the starlet sea anemone, Nematostella vectensis. Nature Protocols 8: 900-915. (Abstract Link)

  • Layden MJ, E Röttinger, FS Wolenski, TD Gilmore & MQ Martindale. 2013. Microinjection techniques for reverse genetic analysis in the starlet sea anemone, Nematostella vectensis. Nature Protocols 8: 924-934

2012

  • Grant TJ, Bishop JA, Christadore LM, Barot G, Chin HG, Woodson S, Kavouris J, Siddiq A, Gredler R, Shen XN, Sherman J, Meehan T, Fitzgerald K, Pradhan S, Briggs LA, Andrews WH, Sarkar D, Schaus SE, Hansen U. (2012). Antiproliferative small molecule inhibitors of the transcription factor LSF reveal oncogene addiction in hepatocellular carcinoma. Proceedings of the National Academy of Sciences, U.S.A., 109:4503-4508.

  • Pritchett, T.L. and McCall, K. (2012). Role of the insulin/Tor signaling network in starvation-induced programmed cell death in Drosophila oogenesis. Cell Death and Differentiation, 19: 1069-79.
  • Gilmore TD, Wolenski FS (2012). Evolution of NF-kB: where did it come from and why? Immunological Reviews, 246: 14-35.
  • Callard GV, Greytak SR, Novillo A, Cotter KA, Meyer R (2012). Brain Aromatase in Fishes. In: Balthazart J, Ball G (eds), Brain Aromatase, Estrogens and Behavior, Oxford Univ Press, pp. 2-42.

  • Chaufty, J*, Sullivan, SE*, and Ho, A. “Intracellular APP Sorting and Aβ Secretion are Regulated by Src-mediated Phosphorylation of Mint2.” J Neurosci. (2012 Jul 11;32(28):9613-25; * equal contribution).

  • Grant TJ, Bishop JA, Christadore LM, Barot G, Chin HG, Woodson S, Kavouris J, Siddiq A, Gredler R, Shen XN, Sherman J, Meehan T, Fitzgerald K, Pradhan S, Briggs LA, Andrews WH, Sarkar D, Schaus SE, Hansen U. (2012). Antiproliferative small molecule inhibitors of the transcription factor LSF reveal oncogene addiction in hepatocellular carcinoma. Proceedings of the National Academy of Sciences, U.S.A., 109:4503-4508.

  • Wolenski FS & TD Gilmore. 2012. Evolution of NF-κB: where did it come from and why? Immunological Reviews 246: 14-35

  • Wolenski F, J Finnerty & T Gilmore. 2012. Preparation of antiserum and detection of proteins by Western blotting using the starlet sea anemone, Nematostella vectensis. Protocol Exchange


2011

  • Terragni J, Nayak G, Banerjee S, Medrano JL, Graham JR, Brennan JF, Sepulveda S, Cooper GM (2011). The E-Box binding factors Max/Mnt, MITF and USF1 Act coordinately with FoxO to regulate expression of Pro-apoptotic and cell cycle control genes by phosphatidylinositol 3-kinase/Akt/GSK3 signaling. J. Biol. Chem. 286: 36215-36227.
  • Doloff JC, Jounaidi Y, Waxman DJ (2011). Dual E1A oncolytic adenovirus: targeting tumor heterogeneity with two independent cancer-specific promoter elements, DF3/MUC1 and hTERT. Canc Gene Therapy in press.
  • Callard GV, Tarrant A, Novillo A, Yacci P, Ciaccia L, Vajda S, Chuang G-Y, Kozakov D, Greytak SR, Sawyer S, Hoover C, Cotter K. (2011). Evolutionary origins of the estrogen signaling system: insights from amphioxus. J Steroid Biochem Mol Biol 127: 176-188.
  • Ewen EP, Snyder CM, Wilson M, Desjardins D, and Naya FJ (2011). The Mef2A transcription factor coordinately regulates a costamere gene program in cardiac muscle. J Biol Chem. 286(34):29644-53.
  • Fast E, Toomey M, Panaram K, Desjardins D, Kolaczyk E, Frydman HM (2011). Wolbachia enhance Drosophila stem cell proliferation and target the germline stem cell niche. Science (in press).
  • Garbati MR, Thompson RC, Haery L, Gilmore TD (2011). A rearranged EP300 gene in the human B-cell lymphoma cell line RC-K8 encodes a disabled transcriptional co-activator that contributes to cell growth and oncogenicity. Cancer Letters 302: 76-83
  • Gilmore TD, Garbati MR (2011). Inhibition of NF-kB Signaling as a Strategy in Disease Therapy. Current Topics in Microbiology and Immunology 349: 245-263
  • Tullai JW, Tacheva S, Owens LJ, Graham JR, Cooper GM (2011). AP-1 is a component of the transcriptional network regulated by GSK-3 in quiescent cells. PLoS ONE 6:e20150.
  • Kielbasa OM, Reynolds JG, Wu CL, Snyder CM, Cho MY, Weiler H, Kandarian S, Naya FJ (2011). Myospryn is a calcineurin-interacting protein that negatively modulates slow-fiber-type transformation and skeletal muscle regeneration. FASEB J. 25(7):2276-86.
  • Lynes MD, Narisawa S, Millán JL, Widmaier EP (2011). Interactions between CD36 and global intestinal alkaline phosphatase in mouse small intestine and effects of high-fat diet. American Journal of Physiology: Regulatory, Integrative and Comparative Physiology, 301:R1738-47.
  • Lynes MD and Widmaier EP (2011). Involvement of CD36 and intestinal alkaline phosphatases in fatty acid transport in enterocytes, and the response to a high-fat diet. Life Sciences, 88:384-391.
  • Mullenbrock S, Shah J, Cooper GM (2011). Global expression analysis identified a preferentially nerve growth factor-induced transcriptional program regulated by sustained mitogen-activated protein kinase/extracellular signal-regulated kinase (ERK) and AP-1 activation during PC12 differentiation. J. Biol. Chem. 286:45131-45145.
  • Nonhebel HM, Al-Amier H, Pieck M, Akor, Ahamed A, Cohen JD, Celenza JL, Normanly J (2010). Redirection of Trp metabolism in tobacco by ectopic expression of an Arabidopsis indolic glucosinolate biosynthetic gene. Phytochemistry. Published online doi:10.1016/j.phytochem.2010.10.01.
  • Stopa JS, DR Tolan (2011). Stabilization of the predominant hereditary fructose intolerance causing aldolase variant (A149P) with zwitterionic osmolytes. Biochemistry, 50, 663-671.
  • Tanner EA, Blute TA, Brachmann CB, McCall K (2011). Bcl-2 proteins and autophagy regulate mitochondrial dynamics during programmed cell death in the Drosophila ovary. Development 138: 327-338.
  • Tanner EA, McCall K (2011). Mitochondrial regulation of cell death in the Drosophila ovary. Autophagy 7:793-4.
  • Thompson RC*, Herscovitch M*, Zhao I, Ford TJ, Gilmore TD (2011). NF-kB down-regulates expression of the B-lymphoma marker CD10 through a miR-155/PU.1 pathway. Journal of Biological Chemistry 286: 1675-1682 (*co-first authors)
  • Wonglapsuwan M, Chotigeat W, Timmons A, McCall K (2011). Conserved role for Rpl10A in oogenesis progression in the banana prawn Ferneropenaeus merguiensis and Drosophila melanogaster. General and Comparative Endocrinology 173: 356–363.
  • Wolenski FS, Chandani S, Stefanik DJ, Jiang N, Chu E, Finnerty JR, Gilmore TD (2011). Two polymorphic residues account for the differences in DNA binding and transcriptional activation by NF-kB proteins encoded by naturally occurring alleles in Nematostella vectensis. Journal of Molecular Evolution, 73: 325-336.
  • Wolenski FS, Garbati MR, Lubinski TJ, Traylor-Knowles N, Dresselhaus E, Stefanik DJ, Goucher H, Finnerty JR, Gilmore TD (2011). Characterization of the Core Elements of the NF-{kappa}B Signaling Pathway of the Sea Anemone Nematostella vectensis. Molecular and Cellular Biology 31, 1076-1087.

2010

  • Coffee EM, Yerkes L, Ewen EP, Zee T, Tolan DR (2010). Increased prevalence of mutant null alleles that cause hereditary fructose intolerance in the American population. Journal of Inherited Metabolic Disease, 33, 33-42.
  • Coffee EM, Tolan DR (2010). Mutations in the promoter region of the Aldolase B gene that cause Hereditary Fructose Intolerance are common among Hispanics and African-Americans. Journal of Inherited Metabolic Disease, 33, 715-725.
  • Zheng Y, Cohen-Karni D, Xu D, Chin HG, Wilson G, Pradhan S, Roberts RJ (2010). A unique family of Mrr-like modification-dependent restriction endonucleases. Nucleic Acids Res. [Epub ahead of print] PMID: 20444879
  • Wanunu M, Cohen-Karni D, Johnson RR, Fields L, Benner J, Peterman N, Zheng Y, Klein ML, Drndic M (2010). Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules.. J Am Chem Soc. Dec 14. [Epub ahead of print]
  • Funari VA, Voevodski K. Leyfer D, Yerkes L, Cramer D, Tolan DR (2010). Quantitative gene-expression profiles in real time from expressed sequence tag databases. Gene Expression, 14, 321-336.
  • Swanson HI, Njar VCO, Yu Z, Castro DJ, Gonzalez FJ, Williams DE, Huang Y, Kong AT, Doloff JC, Ma J, Waxman DJ, and Scott EE (2010). Targeting Drug-Metabolizing Enzymes for Effective Chemoprevention and Chemotherapy. Drug Metab Dispos. Apr; 38(4): 539-44.
  • Doloff JC, Waxman DJ (2010). Dual E1A Oncolytic Adenovirus: Targeting Tumor Heterogeneity With Two Independent Cancer-specific Promoter Elements, DF3/MUC1 and hTERT. Cancer Gene Ther, in press.
  • Doloff JC, Su T, Waxman DJ (2010). Adenoviral delivery of pan-caspase inhibitor p35 enhances bystander killing by P450 gene-directed prodrug therapy using cyclophosphamide. BMC Cancer 10: 487.
  • Swanson HI, Njar VCO, Yu Z, Castro DJ, Gonzalez FJ, Williams DE, Huang Y, Kong ANT, Doloff JC, Ma J, Waxman DJ, Scott EE (2010). Targeting drug-metabolizing enzymes for effective chemoprevention and chemotherapy. Drug Metab Dispos 38, 539-544.
  • McCalmon SA, Desjardins D, Ahmad S, Davidoff K, Snyder CM, Sato K, Ohashi K, Kielbasa O, Mathew M, Ewen EP, Gavras H, Walsh K, Naya FJ (2010). Modulation of angiotensin II-mediated cardiac remodeling by the MEF2A target gene Xirp2. Circ Res. 106(5):952-60.
  • Garbati MR, Alco G, Gilmore TD (2010). Histone acetyltransferase p300 is a coactivator for transcription factor REL and is C-terminally truncated in the human diffuse large B-cell lymphoma cell line RC-K8. Cancer Letters 291, 237-245.
  • Giove TJ, Sena-Esteves M, Eldred WD (2010). Transduction of the inner mouse retina using AAVrh8 and AAVrh10 via intravitreal injection. Exp. Eye Res., 91-652-659.
  • Graham JR, Tullai JR, Cooper GM (2010). GSK-3 represses growth factor-inducible genes by inhibiting NF-κB in quiescent cells. J. Biol. Chem. 285: 4472-4480.
  • Graham JR, Hendershott MC, Terragni J, Cooper GM (2010). mRNA degradation plays a significant role in the program of gene expression regulated by phosphatidylinositol 3-kinase signaling. Mol. Cell. Biol. 30: 5295-5305.
  • Greytak SR, Tarrant A, Nacci D, Hahn ME, Callard GV (2010). Estrogen responses in killifish (Fundulus heteroclitus) from polluted and unpolluted environments are site- and gene-specific. Aquatic Toxicol. 99(2): 291–299.
  • Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M, Hearn J, Emili A, Xie XS (2010). Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells. Science 329: 533-538.
  • Mazza ME, Pang K, Reitzel AM, Martindale MQ, Finnerty JR (2010). A conserved cluster of three PRD-class homeobox genes (homeobrain, rx, and orthopedia) in the Cnidaria and Protostomia. EvoDevo. 1: 3.
  • McCurley A, Callard GV (2010). Time course analysis of gene expression patterns in zebrafish eye during optic nerve regeneration. J Exptl Neurosci 4:17-33.
  • Bakhrat A, Pritchett TL, McCall K, Abdu U (2010). Drosophila Chk2 and p53 proteins induce stage-specific cell death independently during oogenesis, Apoptosis15:1425-1434.
  • Yoo BK, Emdad L, Gredler R, Fuller C, Dumur CI, Jones KH, Jackson-Cook C, Su ZZ, Chen D, Saxena UH, Hansen U, Fisher PB, Sarkar D (2010). Transcription factor Late SV40 Factor (LSF) functions as an oncogene in hepatocellular carcinoma. Proceedings of the National Academy of Sciences, U.S.A. 107:8357-8362.
  • Saxena UH, Owens L, Graham JR, Cooper GM, Hansen U (2010) Prolyl isomerase Pin1 regulates transcription factor LSF (TFCP2) by facilitating dephosphorylation at two serine-proline motifs. J. Biol. Chem. 285:31139-31147.
  • Wauthier V, Sugathan A, Meyer RD, Dombkowski AA, Waxman DJ (2010). Intrinsic sex-differences in the early growth hormone responsiveness of sex-specific genes in mouse liver. Molec Endocrinol 24, 667-678.
  • Ling G, Sugathan A, Mazor T, Fraenkel E, Waxman DJ (2010). Unabiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Molec Cell Biol 30, 5531-5544.
  • Gilmore TD, Thompson RC, Faber AC (2010). Cyclins D3 and E go hand in hand with Cdk4/6 in diffuse large B-cell lymphoma. Cell Cycle 14: 448-449
  • Zhu N, Hansen U (2010). Transcriptional regulation by HMGN proteins. Bioch. Biophys. Acta - Gene Regulatory Mechanisms 1799:74-79.

2009

  • Blom JT, Blute TA, Eldred WD (2009). Functional localization of the nitric oxide/cGMP pathway in the salamander retina. Vis. Neurosci., 26:275-286.
  • Bradham CA, Oikonomou C, Kühn A, Core AB, Modell JM, McClay DR, and AJ Poustka (2009). Chordin is required for neural but not axial development in sea urchin embryos. Developmental Biology 328:221-233.
  • Doloff JC, Khan N, Ma J, Demidenko E, Swartz HM, and Jounaidi Y (2009). Increased tumor oxygenation and drug uptake during anti-angiogenic weekly low dose cyclophosphamide enhances the anti-tumor effect of weekly tirapazamine. Curr Cancer Drug Targets. Sept.; 9(6): 777-88.
  • GioveTJ, Deshpande MM, Eldred WD (2009). Identification of alternate transcripts of neuronal nitric oxide synthase in the mouse retina. J. Neurosci. Res., 87: 3134-3142.
  • Giove TJ, Deshpande MM, Gagen CS, Eldred WD (2009). Increased neuronal nitric oxide synthase activity in retinal neurons in early diabetic retinopathy. Molecular Vis., 15:2249-2258.
  • Chin M, Herscovitch M, Zhang N, Waxman DJ, Gilmore TD (2009). Overexpression of an activated version of the REL oncoprotein enhances the oncogenie properties of the human B-lymphoma BJAB cell line and alters its gene expression prolife. Oncogene 28: 2100-2111
  • Waxman DJ, Holloway MG (2009). Centennial Perspective: Sex differences in the expression of hepatic drug metabolizing enzymes. Molec Pharmacol 76, 215-228.
  • Ma J, DJ Waxman (2009). Dominant effect of antiangiogenesis in combination therapy involving cyclophosphamide and axitinib. Clin Cancer Res. Jan 15;15(2):578-88.
  • Pong WW, Eldred WD (2009). Interactions of the gaseous neuromodulators nitric oxide, carbon monoxide, and hydrogen sulfide in the salamander retina. J. Neurosci. Res., 87:2356-2364.
  • Pritchett TL, Tanner EA, and McCall K (2009). Cracking open cell death in the Drosophila ovary, Apoptosis 14, 969-79.
  • McCall K, Pritchett TL, Peterson JS (2009). Detection of cell death in Drosophila. Methods in Molecular Biology, Apoptosis Methods and Protocols (P. Erhardt, ed.), 559:343-56.
  • Repetny KJ, Zhou X, Holodick NE, Rothstein TL, Hansen U (2009). Bioding of LBP-1a to specific immunoglobulin switch regions in vivo correlates with specific repression of class switch recombination. European Journal of Immunology, 39:1387-1394.
  • Hansen U, Owens L, Saxena UH (2009). Transcription factors LSF and E2Fs: Tandem cyclists driving G0 to S? Cell Cycle, 8:2146-2151.
  • Yoo BK, Chen D, Gredler R, Vozhilla N, Su Z-z, Chen D, Shah K, Saxena UH, Hansen U, Fisher PB, Sarkar D (2009). Identification of important genes conferring resistance to 5-fluorouracil. Proc. Natl. Acad. Sci. USA 106:12038-12043.
  • Saxena UH, Powell CMH, Fecko JK, Cacioppo R, Chou HS, Cooper GM, Hansen U (2009). Phosphorylation by cyclin C/CDK2 following mitogenic stimulation of murine fibroblasts inhibits transcriptional activity of LSF during G1 progression. Molecular and Cellular Biology, 29:2335-2345.
  • Laz EV, Sugathan A, Waxman DJ. 2009. Dynamic in vivo binding of STAT5 to growth hormone-regulated genes in intact rat liver. Sex specific binding at low but not high affinity STAT5 sites. Molec Endocrinol 23, 1242-1254
  • Sullivan JD, Wolenski FS, Reitzel AM, French CE, Traylor-Knowles N, Gilmore TD, Finnerty JR (2009). Two alleles encoding transcription factor NF-kB in the sea anemone Nematostella vectensis are widely dispersed in natural populations and encode proteins with distinct activities. PLoS ONE 4: e7311.