Recognition and Publications

Recent publications by current and most recently graduated SMD students. SMD students and faculty authors are in bold.

Duivenvoorden R, Tang J, Cormode DP, Mieszawska AJ, Izquierdo-Garcia D, Ozcan C, Otten MJ, Zaidi N, Lobatto ME, van Rijs SM, Priem B, Kuan EL, Martel C, Hewing B, Sager H, Nahrendorf M, Randolph GJ, Stroes ES, Fuster V, Fisher EA, Fayad ZA, Mulder WJ. A statin-loaded reconstituted high-density lipoprotein nanoparticle inhibits atherosclerotic plaque inflammation. Nature Commun. 2014 Jan 20;5:3065. PMID: 24445279

Plotnikov AN, Yang S, Zhou TJ, Rusinova E, Frasca A, Zhou MM. Structural Insights into Acetylated-Histone H4 Recognition by the Bromodomain-PHD Finger Module of Human Transcriptional Coactivator CBP. Structure. 2013 Dec 18. pii: S0969-2126(13)00437-1. doi: 10.1016/j.str.2013.10.021. [Epub ahead of print] PMID:24361270

Meslamani J, Smith SG, Sanchez R, Zhou MM. ChEpiMod: A Knowledgebase for Chemical Modulators of Epigenome Reader Domains. Bioinformatics. 2014 Jan 27. [Epub ahead of print] PMID: 24470572

Ummat A, Rechkoblit O, Jain R, Roy Choudhury J, Johnson RE, Silverstein TD, Buku A, Lone S, Prakash L, Prakash S, Aggarwal AK. Structural basis for cisplatin DNA damage tolerance by human polymerase η during cancer chemotherapy. Nat Struct Mol Biol. 2012 May 6;19(6):628-32. PMID: 22562137

Wu M, Hernandez M, Shen S, Sabo JK, Kelkar D, Wang J, O'Leary R, Phillips GR, Cate HS, Casaccia P. Differential modulation of the oligodendrocyte transcriptome by sonic hedgehog and bone morphogenetic protein 4 via opposing effects on histone acetylation. J Neurosci. 2012 May 9;32(19):6651-64. PMID: 22573687

Malu S, De Ioannes P, Kozlov M, Greene M, Francis D, Hanna M, Pena J, Escalante CR, Kurosawa A, Erdjument-Bromage H, Tempst P, Adachi N, Vezzoni P, Villa A, Aggarwal AK, Cortes P. Artemis C-terminal region facilitates V(D)J recombination through its interactions with DNA Ligase IV and DNA-PKcs. J Exp Med. 2012 May 7;209(5):955-63. PMID: 22529269

Lin Y, Yoo S, Sanchez R. SiteComp: a server for ligand binding site analysis in protein structures. Bioinformatics. 2012 Apr 15;28(8):1172-3. PMID: 22368247

Sarkar AX, Christini DJ, Sobie EA. Exploiting mathematical models to illuminate electrophysiological variability between individuals. J Physiol. 2012 Jun 1;590(Pt 11):2555-67. PMID: 22495591

Tang J, Lobatto ME, Read JC, Mieszawska AJ, Fayad ZA, Mulder WJ. Nanomedical Theranostics in Cardiovascular Disease. Curr Cardiovasc Imaging Rep. 2012 Feb;5(1):19-25. PMID: 22308199

Provasi D, Artacho MC, Negri A, Mobarec JC, Filizola M. Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques. PLoS Comput Biol. 2011 Oct;7(10):e1002193. PMID: 22022248

De Ioannes P, Escalante CR, Aggarwal AK. Structures of apo IRF-3 and IRF-7 DNA binding domains: effect of loop L1 on DNA binding. Nucleic Acids Res. 2011 Sep 1;39(16):7300-7. PMID: 21596780

Gerona-Navarro G, Yoel-Rodríguez, Mujtaba S, Frasca A, Patel J, Zeng L, Plotnikov AN, Osman R, Zhou MM. Rational design of cyclic peptide modulators of the transcriptional coactivator CBP: a new class of p53 inhibitors. J Am Chem Soc. 2011 Feb 23;133(7):2040-3. PMID: 21271695

Gianella A, Jarzyna PA, Mani V, Ramachandran S, Calcagno C, Tang J, Kann B, Dijk WJ, Thijssen VL, Griffioen AW, Storm G, Fayad ZA, Mulder WJ. Multifunctional nanoemulsion platform for imaging guided therapy evaluated in experimental cancer. ACS Nano. 2011 Jun 28;5(6):4422-33. PMID: 21557611

Ummat A, Silverstein TD, Jain R, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Human DNA polymerase η is pre-aligned for dNTP binding and catalysis. J Mol Biol. 2012 Jan 27;415(4):627-34. PMID: 22154937

Sobie EA, Sarkar AX. Regression methods for parameter sensitivity analysis: applications to cardiac arrhythmia mechanisms. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:4657-60. PMID: 22255376

Sarkar AX, Sobie EA. Quantification of repolarization reserve to understand interpatient variability in the response to proarrhythmic drugs: a computational analysis. Heart Rhythm. 2011 Nov;8(11):1749-55. PMID: 21699863

Vanamee ES, Viadiu H, Chan SH, Ummat A, Hartline AM, Xu SY, Aggarwal AK. Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI. Nucleic Acids Res. 2011 Jan;39(2):712-9. PMID: 20833632

Sarkar AX, Sobie EA. Regression analysis for constraining free parameters in electrophysiological models of cardiac cells. PLoS Comput Biol. 2010 Sep 2;6(9):e1000914. PMID: 20824123

Xiao K, Sun J, Kim J, Rajagopal S, Zhai B, Villén J, Haas W, Kovacs JJ, Shukla AK, Hara MR, Hernandez M, Lachmann A, Zhao S, Lin Y, Cheng Y, Mizuno K, Ma'ayan A, Gygi SP, Lefkowitz RJ. Global phosphorylation analysis of beta-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR). Proc Natl Acad Sci U S A. 2010 Aug 24;107(34):15299-304. PMID: 20686112

Hernandez M, Lachmann A, Zhao S, Xiao K, Ma'ayan A. Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. Proc IEEE Int Symp Bioinformatics Bioeng. 2010; 2010:180-184. PMID: 21552464