Faculty Scholarship

Peer reviewed publications 2015

  • Kim N, Zahran M, Schlick T. Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approach. Methods Enzymol. 2015;553:115-35. doi: 10.1016/bs.mie.2014.10.054. Epub 2015 Feb 7. PubMed PMID: 25726463.
  • Macrander J, Brugler MR, Daly M. A RNA-seq approach to identify putative toxins from acrorhagi in aggressive and non-aggressive Anthopleura elegantissima polyps. BMC Genomics. 2015 Mar 21;16:221. doi: 10.1186/s12864-015-1417-4. PubMed PMID: 25886045; PubMed Central PMCID: PMC4397815.
  • Ceballos-Chávez M, Subtil-Rodríguez A, Giannopoulou EG, Soronellas D, Vázquez-Chávez E, Vicent GP, Elemento O, Beato M, Reyes JC. The Chromatin Remodeler CHD8 Is Required for Activation of Progesterone Receptor-Dependent Enhancers. PLoS Genet. 2015 Apr 20;11(4):e1005174. doi:10.1371/journal.pgen.1005174. eCollection 2015 Apr. PubMed PMID: 25894978; PubMed Central PMCID: PMC4403880.
  • Shanmugam M, Li D, Gao S, Fefelova N, Shah V, Voit A, Pachon R, Yehia G, Xie LH, Babu GJ. Cardiac specific expression of threonine 5 to alanine mutant sarcolipin results in structural remodeling and diastolic dysfunction. PLoS One. 2015 Feb 11;10(2):e0115822. doi: 10.1371/journal.pone.0115822. eCollection 2015. PubMed PMID: 25671318; PubMed Central PMCID: PMC4324845.
  • Yu Y, Harris AJ, Blair C, He X. RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography. Mol Phylogenet Evol. 2015 Jun;87:46-9. doi: 10.1016/j.ympev.2015.03.008. Epub 2015 Mar 26. PubMed PMID: 25819445.
  • Blair C, Noonan BP, Brown JL, Raselimanana AP, Vences M, Yoder AD. Multilocus phylogenetic and geospatial analyses illuminate diversification patterns and the biogeographic history of Malagasy endemic plated lizards (Gerrhosauridae:Zonosaurinae). J Evol Biol. 2015 Jan 22. doi: 10.1111/jeb.12586. [Epub ahead of print] PubMed PMID: 25611210.
  • Blair C, Méndez de la Cruz FR, Law C, Murphy RW. Molecular phylogenetics andspecies delimitation of leaf-toed geckos (Phyllodactylidae: Phyllodactylus)
    throughout the Mexican tropical dry forest. Mol Phylogenet Evol. 2015 Jan
    22;84C:254-265. doi: 10.1016/j.ympev.2015.01.003. [Epub ahead of print] PubMed
    PMID: 25620603.
  • Blair C, Campbell CR, Yoder AD. Assessing the utility of whole genome amplified DNA for next-generation molecular ecology. Mol Ecol Resour. 2015 Jan 24. doi: 10.1111/1755-0998.12376. [Epub ahead of print] PubMed PMID: 25619406.

Peer reviewed publications 2014

  • Rodríguez E, Barbeitos MS, Brugler MR, Crowley LM, Grajales A, Gusmão L, Häussermann V, Reft A, Daly M. Hidden among sea anemones: the first comprehensive phylogenetic reconstruction of the order Actiniaria (Cnidaria, Anthozoa, Hexacorallia) reveals a novel group of hexacorals. PLoS One. 2014 May 7;9(5):e96998. doi: 10.1371/journal.pone.0096998. eCollection 2014. PubMed PMID: 24806477; PubMed Central PMCID: PMC4013120.
  • Blair C, Heckman KL, Russell AL, Yoder AD. Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species. BMC Evol Biol. 2014 Mar 24;14(1):57. doi: 10.1186/1471-2148-14-57. PubMed PMID: 24661555; PubMed Central PMCID: PMC3987692.
  • Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, Hennig S, Mosquera JM,
    Pauwels J, Park K, Kossai M, MacDonald TY, Fontugne J, Erho N, Vergara IA, Ghadessi M, Davicioni E, Jenkins RB, Palanisamy N, Chen Z, Nakagawa S, Hirose T, Bander NH, Beltran H, Fox AH, Elemento O, Rubin MA. The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat Commun. 2014 Nov 21;5:5383. doi: 10.1038/ncomms6383. PubMed PMID: 25415230; PubMed Central PMCID: PMC4241506.
  • González-Muñoz R, Simões N, Mascaró M, Tello-Musi JL, Brugler MR, Rodríguez E, 2014. Morphological and molecular variability of the sea anemone Phymanthus crucifer (Cnidaria, Anthozoa, Actiniaria, Actinoidea). Journal of the Marine Biological Association of the United Kingdom.
  • Park-Min KH, Lim E, Lee MJ, Park SH, Giannopoulou E, Yarilina A, van der Meulen M, Zhao B, Smithers N, Witherington J, Lee K, Tak PP, Prinjha RK, Ivashkiv LB. Inhibition of osteoclastogenesis and inflammatory bone resorption by targeting BET proteins and epigenetic regulation. Nat Commun. 2014 Nov 13;5:5418. doi: 10.1038/ncomms6418. PubMed PMID: 25391636; PubMed Central PMCID: PMC4249944.
  • Li S, Miller CH, Giannopoulou E, Hu X, Ivashkiv LB, Zhao B. RBP-J imposes a requirement for ITAM-mediated costimulation of osteoclastogenesis. J Clin Invest. 2014 Nov 3;124(11):5057-73. doi: 10.1172/JCI71882. Epub 2014 Oct 20. PubMed PMID: 25329696.
  • Popovic R, Martinez-Garcia E, Giannopoulou EG, Zhang Q, Zhang Q, Ezponda T, Shah MY, Zheng Y, Will CM, Small EC, Hua Y, Bulic M, Jiang Y, Carrara M, Calogero RA, Kath WL, Kelleher NL, Wang JP, Elemento O, Licht JD. Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation. PLoS Genet. 2014 Sep 4;10(9):e1004566.
  • Rose H, Holzman RS, Altman DR, Smyth DS, Wasserman GA, Kafer JM, Wible M, Mendes RE, Novick RP, Torres VJ, Shopsin, B. Cytotoxic virulence predicts mortality in nosocomial pneumonia due to methicillin-resistant Staphylococcus aureus. 2014. J Infect Dis. Accepted for publication.
  • Yu S, Yehia G, Wang J, Stypulkowski E, Sakamori R, Jiang P, Hernandez-Enriquez EB, Tran TS, Bonder EM, Guo W, Gao N. Global Ablation of Mouse Rab11a Impairs Early Embryogenesis and Matrix Metalloproteinase Secretion. J Biol Chem. 2014. Epub ahead of print
  • Torres-Rosas R, Yehia G, Peña G, Mishra P, del Rocio Thompson-Bonilla M, Moreno-Eutimio MA, Arriaga-Pizano LA, Isibasi A, Ulloa L. Dopamine mediates vagal modulation of the immune system by electroacupuncture. Nat Med. 2014 20(3):291-5.
  • Donlin LT, Jayatilleke A, Giannopoulou EG, Kalliolias GD, Ivashkiv LB. Modulation of TNF-Induced Macrophage Polarization by Synovial Fibroblasts. J Immunol. 2014 Sep 1;193(5):2373-83.
  • Tsenova L, O’Brien P, Holloway J, Peixoto B, Soteropoulos P, Fallows D, Kaplan G, Subbian S. Etanercept Exacerbates Inflammation and Pathology in a Rabbit Model of Active Pulmonary Tuberculosis. J Interferon Cytokine Res. 2014 Epub Ahead of Print
  • Solis AD. Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device. PLoS One. 2014 4;9(6):e94334.
  • Dutta DJ, Zameer A, Mariani JN, Zhang J, Asp L, Huynh J, Mahase S, Laitman BM, Argaw AT, Mitiku N, Urbanski M, Melendez-Vasquez CV, Casaccia P, Hayot F, Bottinger EP, Brown CW, John GR. Combinatorial actions of Tgfβ and Activin ligands promote oligodendrocyte development and CNS myelination. Development. 2014 141(12):2414-28.

Peer reviewed publications 2013

  • Vasu K, Nagamalleswari E, Zahran M, Imhof P, Xu SY, Zhu Z, Chan SH, Nagaraja V. Increasing cleavage specificity and activity of restriction endonuclease KpnI. Nucleic Acids Res. 2013. 41(21):9812-24.
  • Laing C, Jung S, Kim N, Elmetwaly S, Zahran M, Schlick T. Predicting helical topologies in RNA junctions as tree graphs. PLoS One. 2013. 26;8(8):e71947.
  • Hariharan N, Ikeda Y, Hong C, Alcendor RR , Usui S, Gao S, Maejima Y, Sadoshima J. Autophagy plays an essential role in mediating regression of hypertrophy during unloading of the heart. PLoS One. 2013;8(1):e51632.
  • Dantham V.R., Holler S., Barbre C., Keng D., Kolchenko V., Arnold S. Label-Free Detection of Single Protein Using a Nanoplasmonic-Photonic Hybrid Microcavity Taking whispering gallery-mode single virus detection and sizing to the limit. 2013. Nano Letters, 13, 3347-335.
  • Hoque M, Ji Z, Zheng D, Luo W, Li W, You B, Park JY, Yehia G, Tian B. Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing. Nat Methods. 2013 Feb;10(2):133-9.
  • Subbian S., N. Bandyopadhyay, L. Tsenova, P. O’Brien, V. Khetani, et al. Early innate immunity determines outcome of Mycobacterium tuberculosis pulmonary infection in rabbits. Cell Commun Signal. 2013 Aug 19;11(1):60.
  • Subbian S., O’Brien P., Kushner NL, Yang G., Tsenova L., Peixoto B.,F allows D. and Kaplan G. Molecular Immunologic Correlates of Spontaneous Latency in a Rabbit Model of Pulmonary Tuberculosis. Cell Commun Signal. 2013 Feb 28;11(1):16.

Peer reviewed publications 2012

  • Identification of Three Residues Essential for 5-Hydroxytryptamine 2A-Metabotropic Glutamate 2 (5-HT2A:mGlu2) Receptor Heteromerization and Its Psychoactive Behavioral Function. Moreno JL, Muguruza C, Umali A, Mortillo S, Holloway T, Pilar-Cuéllar F, Mocci G, Seto J, Callado LF, Neve RL, Milligan G, Sealfon SC, López-Giménez JF, Meana JJ, Benson DL, González-Maeso J. J Biol Chem. 2012 Dec 28;287(53):44301-19
  • Astrocyte-derived VEGF-A drives blood-brain barrier disruption in CNS inflammatory disease. Argaw AT, Asp L, Zhang J, Navrazhina K, Pham T, Mariani JN, Mahase S, Dutta DJ, Seto J, Kramer EG, Ferrara N, Sofroniew MV, John GR. J Clin Invest. 2012 Jul 2;122(7):2454-68
  • Lipson, S.M., R. S. Gordon, L. Karthikeyan, F. S. Ozen. Effect of pH on the antiviral activity of comestible juices and proanthocyanidins utilizing a cell-free assay system. 2012. Food and Environ Virol 4: 168-78.
  • Lipson, S.M., R.E. Gordon, F. S. Ozen, L. Karthikeyan, G. Stotzky. 2012. Effect of Cranberry and grape juices on tight junction function and structural integrity among rotavirus-infected money kidney epithelial cell culture monolayers. Food and Environ Virol. 3: 46-54
  • Mendes RE, Deshpande LM, Smyth DS, Shopsin B, Farrell DJ, Jones RN. Characterization of methicillin-resistant Staphylococcus aureus strains recovered from a Phase IV clinical trial for linezolid versus vancomycin for treatment of nosocomial pneumonia. 2012. J Clin Microbiol. 50(11): 3694-702.
  • Smyth DS, Kafer JM, Wasserman GA, Velickovic L, Mathema B, Holzman RS, Knipe TA, Becker K, von Eiff C, Peters G, Chen L, Kreiswirth BN, Novick RP, Shopsin B. Nasal carriage as a source of agr-defective Staphylococcus aureus bacteremia. 2012. J Infect Dis. 206(8): 1168-77.
  • Subbian S., L. Tsenova, P. O’Brien, G. Yang, N. Lynn Hart, S. Parsons, B. Peixoto, D. Fallows and G. Kaplan. Spontaneous Latency in a Rabbit Model of Pulmonary Tuberculosis. Am J Pathol. 2012 Nov;181(5):1711-24.

Book Chapters 2013

  • Gotesman, M., Williams, S.A., Garcés, J.A., and Gavin, R.H. 2013. Chromosome Walking by Inverse PCR. In: Nolan, T. (ed.), PCR Technology: Current Innovations, 3rd Edition. CRC Press, Florida.

Book Chapters 2012

  • MacDonald, S., Sodeinde, O., & Zameer, A.Theories in practice: A focus on STEM at City Tech. In R. D. Lansiquot (Ed.) Cases on interdisciplinary research trends in science, technology, engineering, and mathematics: Studies on urban classrooms. New York: IGI Global. October 2012
  • Shashidharan, P. and L. Karthikeyan 2012. Causes of Dystonia: Implications of Genetic and Environmental Factors in the Manifestation of Dystonia in G.Rajarami Reddy, Dr. Flora and Dr. Riyaz (ed), Environmental pollution, Ecology and Human Health. NAROSA Publishing Co, New Delhi, India.
  • Brown, G.C., and L. Karthikeyan. 2012. Integration of Civic Engagement Pedagogies in the STEM Disciplines in the book, titled “Cases on Interdisciplinary Research Trends in Science, Technology, Engineering, and Mathematics: Studies on Urban Classrooms”, published in 2012 by IGI Global.