Student Publications

Graduate Students in bold; Mentors in italics.


  • Sun, M., Bloom, A. B., & Zaman, M. H. (2015). Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity. Plos One, 10(7), e0131814.
  • Conforto TL, Steinhardt GF 4th, Waxman DJ. Crosstalk between Growth Hormone-regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver. Mol Endocrinol. 2015 Jul 28:me20151028. [Epub ahead of print] PubMed PMID: 26218442.
  • Cotter KA, Nacci D, Champlin D, Chuprin J, Callard GV (2015). Cloning of multiple ERα mRNA variants in killifish (Fundulus heteroclitus), and differential expression by tissue type, stage of reproduction, and in fish from polluted and unpolluted environments. Aquatic Toxicology. 159:184-197.
  • Doloff JC, Waxman DJ (2015). Transcriptional profiling provides insights into metronomic cyclophosphamide-activated, innate immune-dependent regression of
    brain tumor xenografts. BMC Cancer.15:375. doi: 10.1186/s12885-015-1358-y. PubMed PMID: 25952672.
  • Haery L, Thompson RC, Gilmore TD (2015). Histone acetyltransferases and histone deacetylases in B- and T-cell development, physiology and malignancy. Genes Cancer. 2015 May;6(5-6):184-213.
  • Huo Y, Khatri N, Q Hou, Gilbert J, Wang G,  Man HY (2015) The deubiquitinating enzyme USP46 regulates AMPA receptor ubiquitination and trafficking Journal of Neurochemistry 134 (6), 1067-1080
  • Levin, BD, Walsh, KA, Sullivan, KK, Bren, KL, Elliott, SJ (2015). Methionine Ligand Lability of Homologous Monoheme Cytochromes c. Inorg. Chem., 2015, 54 (1), pp 38–46. DOI: 10.1021/ic501186h
  • Oppelt SA, Sennott EM, Tolan DR. (2015) Aldolase-B knockout in mice phenocopies hereditary fructose intolerance in humans. 2015 Mar;114(3):445-50.
  • Peterson, J.S., Timmons, A.K. , Mondragon, A.A., and McCall, K. (2015) The end of the beginning:  cell death in the germline, Current Topics in Developmental Biology, 114: 93-119.
  • Piacentino ML, Ramachandran J, and Bradham CA (2015). Late LvAlk4/5/7 activity is required for anterior skeletal patterning in the sea urchin embryo. Development 142 (5): 943.
  • Sholder, G. and Loechler, E.L. (2015) A Method to Accurately Quantitate Intensities of 32P-DNA Bands When Multiple Bands Appear in a Single Lane of a Gel Is Used to Study dNTP Insertion Opposite a Benzo[a]pyrene-dG Adduct by Sulfolobus DNA Polymerases Dpo4 and Dbh.”DNA Repair. 25, 97 – 103.
  • Sholder, G., Creech A. and Loechler, E.L. (2015) How Y-Family DNA Polymerase IV Is More Accurate Than Dpo4 at dCTP Insertion Opposite an N2-dG Adduct of Benzo[a]pyrene. DNA Repair. 35, 144 – 153.
  • Frato, KE, Walsh, KA and Elliott, SJ. Functionally distinct bacterial cytochrome c peroxidases proceed through a common (electro)catalytic intermediate Biochemistry,
  • Rajasekaran D, Siddiq A, ​​Willoughby JLS, Biagi JM, Christadore LM, ​​Yunes SA, Gredler R, Jariwala N, Robertson CL, Akiel MA, Shen X-N, Subler MA, Windle JJ, Schaus SE, Fisher PB, Hansen U, Sarkar D. (2015) Small molecule inhibitors Late SV40 Factor (LSF) abrogate hepatocellular carcinoma (HCC): Evaluation using an endogenous HCC model.  Oncotarget, in press



  • Bak DW, Elliott SJ. Alternative FeS cluster ligands: tuning redox potentials and chemistry. Curr Opin Chem Biol. 2014;19:50-8.
  • Bloom, A. B. & Zaman, M. H. Influence of the microenvironment on cell fate determination and migration. Physiol. Genomics 46, 309–314 (2014)
  • Bestul AJ, Christensen JR, Grzegorzewska AP, Burke TA, Sees JA, Carroll RT, Sirotkin V, Keenan RJ, Kovar DR. Fission yeast profilin is tailored to facilitate actin assembly by the cytokinesis formin Cdc12.
    Mol Biol Cell. 2014 Nov 12. pii: mbc.E13-05-0281.
  • Hubbard B, Buczek-Thomas JA, Nugent MA, Smith ML. Heparin-dependent regulation of fibronectin matrix conformation. Matrix Biol. 2014; 34:124-31.
  • Judd, E. T., Stein, N., Pacheco, A. A., & Elliott, S. J. (2014). Hydrogen-bonding networks tune proton- coupled redox steps during the enzymatic six-electron conversion of nitrite to ammonia Biochemistry. 53 (35), 5638–5646
  • Funk, M. A., Judd, E. T., Marsh, N. G., Elliott, S. J., Drennan, C.L. (2014) Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity. Proceedings of the National Academy of Sciences. 111 (28), 10161-10166.
  • Keung, A.J, Bashor, C.J., Kiriakov, S., Collins, J., Khalil, A.S. (2014) Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell 158: in Press, 2014.
  • Toran P, Smolina I, Driscoll H, Ding F, Sun Y, Cantor CR, Broude NE. Labeling native bacterial RNA in live cells. Cell Res. 2014 Apr 15.
  • Isenberg BC, Dimilla PA, Walker M, Kim S, Wong JY. Vascular smooth muscle cell durotaxis depends on substrate stiffness gradient strength. Biophys J. 2009;97:1313-22.



  • Bak DW, Elliott SJ. Conserved hydrogen bonding networks of MitoNEET tune Fe-S cluster binding and structural stability. Biochemistry. 2013 52:4687-96.
  • Cotter KA, Yershov A, Novillo A, Callard GV (2013). Multiple structurallydistinct ERα mRNA variants in zebrafish are
    differentially expressed by tissue type, stage of development and estrogen exposure.  General and Comparative Endocrinology. 194:217-229
  • Griffin, L.B, January, K. E., Ho, K.W., Cotter, K. A., Callard, G.V. (2013) Morpholino-Mediated Knockdown of ER, ERa, and
    ERb mRNAs in Zebrafish (Danio rerio) Embryos Reveals Differential Regulation of Estrogen-Inducible Genes. Endocrinology 154: 4158–4169, 2013.
  • Judd, E. T., Youngblut, M., Pacheco, A. A., & Elliott, S. J. (2012). Direct Electrochemistry of Shewanella oneidensis Cytochrome c Nitrite Reductase: Evidence of Interactions across the Dimeric Interface. Biochemistry, 51(51), 10175-10185
  • Cote, S. M., Gilmore, T. D., Shaffer, R., Weber, U., Bollam, R., Golden, M. S., Glover, K., Herscovitch, M., Ennis, T., Allen, K. N., and Whitty, A. (2013) Mutation of Nonessential Cysteines Shows That the NF-κB Essential Modulator Forms a Constitutive Noncovalent Dimer That Binds IκB Kinase-β with High Affinity. Biochemistry 9141-9154
  • Yilmaz M, Gangopadhyay SS, Leavis P, Grabarek Z, Morgan KG. Phosphorylation at Ser²⁶ in the ATP-binding site of Ca²⁺/calmodulin-dependent kinase II as a mechanism for switching off the kinase activity. Biosci Rep. 2013; 33(2).
  • Vetterkind S, Poythress RH, Lin QQ, Morgan KG. Hierarchical scaffolding of an ERK1/2 activation pathway. Cell Commun Signal. 2013; 11:65.
    Poythress RH,
    Gallant C, Vetterkind S, Morgan KG. Vasoconstrictor-induced endocytic recycling regulates focal adhesion protein localization and function in vascular smooth muscle. Am J Physiol Cell Physiol. 2013; 305:C215-27.
  • Thompson RC, Vardinogiannis I, Gilmore TD. (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
  • Toomey ME, Panaram K, Fast EM, Beatty C, & Frydman H (2013) Evolutionarily conserved Wolbachia-intrinsic factors control differential stem cell niche tropism in the Drosophila ovary and enhance vertical transmission. Proc Natl Acad Sci U S A,  110(26): 10788-10793.
  • Thompson RC, Vardinogiannis I, Gilmore TD. Identification of an NF-κB p50/p65-responsive site in the human MIR155HG promoter. BMC Mol Biol. 2013; 14:24.
  • Vega NM, Allison KR, Samuels AN, Klempner MS, Collins JJ. Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance. Proc Natl Acad Sci U S A. 2013; 110:14420-5.
  • Vega NM, Allison KR, Samuels AN, Klempner MS, Collins JJ. Reply to Blair et al.: Dose-dependent effects and oxidative stress responses in antibiotic tolerance in Salmonella typhimurium. Proc Natl Acad Sci U S A. 2013; 110:E4570.


  • Blom J, Giove T, Deshpande M, Eldred WD. (2012)  Characterization of the nitric oxide signaling pathways in the mouse retina.  The Journal of Comparative Neurology, in press.
  • Blom J, Giove TJ, Pong WW, Blute TA, Eldred WD. (2012) Evidence for a functional adrenomedullin signaling pathway in the mouse retina. Molecular Vision 18:1339-53.
  • 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.
  • Conforto TL, Waxman DJ. (2012) Sex-specific mouse liver gene expression: genome-wide analysis of developmental changes from pre-pubertal period to young adulthood. Biology of Sex Differences 3:9.
  • Conforto TL, Zhang Y, Sherman J, Waxman DJ. (2012) Impact of CUX2 on the female mouse liver transcriptome: activation of female-biased genes and repression of male-biased genes. Mol Cell Biol. 2012 Nov;32(22):4611-27. doi: 10.1128/MCB.00886-12.
  • Daughtry KD, Xiao Y, Stoner-Ma D, Cho E, Orville AM, Liu P, Allen KN. Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase. J Am Chem Soc. 2012; 134:2823-34.
  • Doloff JC, Waxman DJ. (2012) VEGF receptor inhibitors block the ability of metronomically dosed cyclophosphamide to activate innate immunity-induced tumor regression. Cancer Research 72:1103-15.
  • Youngblut, M., Judd, E. T., Srajer, V., Sayyed, B., Goelzer, T., Elliott, S. J., Schmidt, M., and Pacheco, A. A. (2012) Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system, J Biol Inorg Chem 17, 647-662.
  • Min J, Reznichenko M, Poythress RH, Gallant CM, Vetterkind S, Li Y, Morgan KG. (2012) Src modulates contractile vascular smooth muscle function via regulation of focal adhesions. Journal of Cellular Physiology, in press.
  • Russell MK, Longoni M, Wells J, Maalouf FI, Tracy AA, Loscertales M, Ackerman KG, Pober BR, Lage K, Bult CJ, Donahoe PK. Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2978-83. Epub 2012 Feb 6. PubMed PMID: 22315423; PubMed Central PMCID: PMC328694
  • Vega, N. M., K. R. Allison, A. S. Khalil. J. J. Collins. (2012). “Signaling-mediated bacterial persister formation.” Nat Chem Biol 8(5): 431-433.
  • Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR; DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G. Wisdom of crowds for robust gene network inference. Nat Methods. 2012; 9:796-804.
  • Foti JJ, Devadoss B, Winkler JA, Collins JJ, Walker GC. Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science. 2012 Apr 20; 336(6079):315-9.


  • Wang H, Guan S, Quimby A, Cohen-Karni D, Pradhan S, Wilson G, Roberts RJ, Zhu Z, Zheng Y. Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine. Nucleic Acids Res. 2011 Nov;39(21):9294-305.
  • Cohen-Karni D, Xu D, Apone L, Fomenkov A, Sun Z, Davis PJ, Kinney SR, Yamada-Mabuchi M, Xu SY, Davis T, Pradhan S, Roberts RJ, Zheng Y. The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11040-5.
  • Callard GV, Tarrant AM, Novillo A, Yacci P, Ciaccia L, Vajda S, Chuang GY, Kozakov D, Greytak SR, Sawyer  S, Hoover C, Cotter KA. 2011. Evolutionary origins of the estrogen signaling system: Insights from amphioxus. J Steroid Biochem Mol Biol. [Epub ahead of print].
  • Doloff JC, Jounaidi Y, and Waxman DJ. 2011. Dual E1A oncolytic adenovirus: Targeting tumor heterogeneity with two independent cancer-specific promoter elements, DF3/MUC1 and hTERT. Cancer Gene Therapy, Mar; 18(3): 153-66
  • Doloff JC, Jounaidi Y, Waxman DJ. Dual E1A oncolytic adenovirus: targeting tumor heterogeneity with two independent cancer-specific promoter elements, DF3/MUC1 and hTERT. Cancer Gene Ther. 2011 Mar;18(3):153-66. Epub 2010 Sep 24. Erratum in: Cancer Gene Ther. 2011 Mar;18(3):228. Jounaidi, Y [added]. PubMed PMID: 20865021; PubMed Central PMCID: PMC3010505.
  • Ma J, Chen CS, Blute T, Waxman DJ. Antiangiogenesis enhances intratumoral drug retention. Cancer Res. 2011 Apr 1;71(7):2675-85. Epub 2011 Mar 29. PubMed PMID: 21447737; PubMed Central PMCID: PMC3070759.
  • Terragni J, Nayak G, Banerjee S, Medrano JL, Graham JR, Brennan JF, Sepulveda S, Cooper GM. The E-box binding factors Max/Mnt, MITF, and USF1 act coordinately with FoxO to regulate expression of proapoptotic and cell cycle control genes by phosphatidylinositol 3-kinase/Akt/glycogen synthase kinase 3 signaling. J Biol Chem. 2011 Oct 21;286(42):36215-27.
  • Tullai, J.W., Tacheva, S., Owens, L.J., Graham, J.R. and Cooper, G.M. 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. 2011 Mar 22. [Epub ahead of print].
  • Santos G., Giuliani, M.,  Pizza, M., Rappuoli, R.,  Donnelly, J.   Determination of serum bactericidal titers against group B meningococcus by flow cytometry using fluorescent viability dyes. 11th Meeting of the European Monitoring Group on Meningococci, p. 159, 2011
  • Tanner, E.A., Blute, T.A. Brachmann, C.B. and McCall, K.  (2011)  Bcl-2 proteins and autophagy regulate mitochondrial dynamics during programmed cell death in the Drosophila ovary. Development 138: 327-338.  *Highlighted article “In This Issue.”
  • Tanner, E.A. and McCall, K.  (2011) Mitochondrial regulation of cell death in the Drosophila ovary. Autophagy, in press.
  • Garbati MR, Thompson RC, Haery L, Gilmore TD. 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 Lett. 2011 Mar 1;302(1):76-83. Epub 2011 Jan 12.
  • Thompson RC, Herscovitch M, Zhao I, Ford TJ, Gilmore TD.NF-kappaB down-regulates expression of the B-lymphoma marker CD10 through a miR-155/PU.1 pathway.
    J Biol Chem. 2011 Jan 21;286(3):1675-82. Epub 2010 Oct 14.
  • Fast EM, Toomey ME, Panaram K, Desjardins D, Kolaczyk ED, Frydman HM. (2011) Wolbachia enhance Drosophila stem cell proliferation and target the germline stem cell niche. Science 334:990-2.
  • Yiu H-W, Demidov VV, Toran P, Cantor CR, Broude NE. (2011) RNA detection in live bacterial cells using fluorescent protein complementation triggered by interaction of two RNA aptamers with two RNA-binding peptides. Pharmaceuticals 4:494-508.