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2014 Published Papers

Gaurav Pandey, Sonali Arora, Sahil Manocha and Sean Whalen (2014). "Enhancing the Functional Content of Eukaryotic Protein Interaction Networks." PLoS ONE 9(10): e109130. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109130

Altman DR*, Sebra R*, Hand J, Attie O, Deikus G, Carpini KWD, Patel G, Rana M, Arvelakis A, Grewal P, Dutta J, Rose H, Shopsin B, Daefler S, Schadt E, Kasarskis A, van Bakel H*, Bashir A*, Huprikar S*. Transmission of Methicillin-Resistant Staphylococcus aureus via Deceased Donor Liver Transplantation Confirmed by Whole Genome Sequencing. Am J Transplant. 2014 Sep 22. doi: 10.1111/ajt.12897. http://www.ncbi.nlm.nih.gov/pubmed/25250641

*De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, et al: "Synaptic, transcriptional and chromatin genes disrupted in autism." Nature, Nov. 2014. http://dx.doi.org/10.1038/nature13772

*Gaugler T, Klei L, Sanders SJ, Bodea CA, Goldberg AP, Lee AB, Mahajan M, Manaa D, Pawitan Y, Reichert J, et al: "Most genetic risk for autism resides with common variation." Nat Genet 2014, 46:881-885. http://dx.doi.org/10.1038/ng.3039
*The aforementioned (2) papers were both recently cited as a "Simons Foundation Autism Research Initiative (SFARI) notable paper for 2014”.

Reed S. Shabman, Omar J. Jabado, Chad E. Mire, Timothy B. Stockwell, Megan Edwards, Milind Mahajan, Thomas W. Geisbert, and Christopher F. Basler, "Deep Sequencing Identifies Noncanonical Editing of Ebola and Marburg Virus RNAs in Infected Cells." 5:6 e02011-14; Published 4 November 2014, doi:10.1128/mBio.02011-14. Link: http://mbio.asm.org/content/5/6/e02011-14.full

Yoo, S., Huang, T., Campbell, J., Lee, E., Tu, Z., Geraci, M., Powell, C., Schadt, E., Spira, A., Zhu, J., "MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis." PLOS Computational Biology (2014) Aug 14. http://www.ncbi.nlm.nih.gov/pubmed/25122495

Li, J., Vootukuri, S., Shang, Y., Negri, A., Jiang, J.-K., Nedelman, M., Diacovo, T.G., Filizola, M., Thomas, C.J., Coller, B.S. “RUC-4: A Novel αIIbβ3 Antagonist for Pre-hospital Therapy of Myocardial Infarction.” Arteriosclerosis, Thrombosis, and Vascular Biology (2014) Aug 21. [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/25147334

Hoffman GE, Mezey JG2, Schadt EE. "lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R." Bioinformatics (advanced access published July 14, 2014). http://bioinformatics.oxfordjournals.org/content/early/2014/07/25/bioinf...

M. Rejwan Ali, Rauf Latif, Terry F. Davies & Mihaly Mezei. "Monte Carlo loop refinement and virtual screening of the thyroid-stimulating hormone receptor transmembrane domain." Journal of Biomolecular Structure and Dynamics, published online July 11, 2014. http://www.tandfonline.com/doi/abs/10.1080/07391102.2014.932310#.U-TffqM...

Shang, Y., LeRouzic, V., Schneider, S., Bisignano, P., Pasternak, G.W., and Filizola, M. “Mechanistic Insights into the Allosteric Modulation of Opioid Receptors by Sodium Ions” Biochemistry (2014) Jul 29. [Epub ahead of print] http://pubs.acs.org/doi/abs/10.1021/bi5006915

Pinto D, Delaby E, Merico D, Barbosa M, Merikangas A, Klei L, Thiruvahindrapuram B, Xu X, Ziman R, Wang Z, et al. "Convergence of genes and cellular pathways dysregulated in autism spectrum disorders." Am J Hum Genet. 2014 May 1;94(5):677-94.
http://www.cell.com/ajhg/fulltext/S0002-9297%2814%2900150-5

Zhang XY, Birtwistle M.R., Gallo J.M.. "A general network pharmacodynamic model-based design pipeline for customized cancer therapy applied to the VEGFR pathway." CPT Pharmacometrics Syst Pharmacol. 2014 Jan 15;3:e92 http://www.ncbi.nlm.nih.gov/pubmed/24429593

Johnston, J.M. & Filizola, M. “Differential stability of the crystallographic interfaces of mu- and kappa-opioid receptors” PLOS One (2014) DOI: 10.1371/journal.pone.0090694. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0090694

Provasi, D., Negri, A., Coller, B.S., Filizola, M. “Talin-driven inside-out activation mechanism of platelet αIIbβ3 integrin probed by multi-microsecond, all-atom molecular dynamics simulations” PROTEINS: Structure, Function, and Bioinformatics (2014) DOI: 10.1002/prot.24540. http://onlinelibrary.wiley.com/doi/10.1002/prot.24540/abstract

Gerold Bongers, Michelle E. Pacer, Thais H. Geraldino, Lili Chen, Zhengxiang He, Daigo Hashimoto, Glaucia C. Furtado, Jordi Ochando, Kevin A. Kelley, Jose C. Clemente, Miriam Merad, Harm van Bakel, and Sergio A. Lira, Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice. Published March 3, 2014 // JEM vol. 211 no. 3 457-472, The Rockefeller University Press, doi: 10.1084/jem.20131587, http://jem.rupress.org/content/211/3/457

Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, Gormley P, Georgieva L, Rees E, Palta P, Ruderfer DM, Carrera N, Humphreys I, JJ, Roussos P, Barker DD, Banks E, Milanova V, Grant SGN, Hannon E, Rose SA, Chambert K, Mahajan M, Scolnick EM, Moran JL, Kirov G, Palotie A, McCarroll SA, Holmans P, Sklar P, Owen MJ, Purcell SM, O’Donovan MD. De novo mutations in schizophrenia implicate synaptic networks. Nature Published online 22 January 2014.
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12929.html

Purcell SM, Moran JL, Fromer M, Ruderfer DM, Solovieff N, Roussos P, O’Dushlaine C, Chambert K, Bergen SE, Kähler A, Duncan L, Stahl E, Genovese G, Fernández E, Collins MO, Komiyama NH, Choudhary JS, Magnusson PKE, Banks E, Shakir K, Garimella K, Fennell T, de Pristo M, Grant SGN, Haggarty S, Gabriel S, Scolnick EM, Lander ES, Hultman C, Sullivan PF, McCarroll SA, Sklar P. A polygenic burden of rare disruptive mutations in schizophrenia. Nature Published online 22 January 2014. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12975.html

Scarabelli, G., Provasi, D., Negri, A., and Filizola, M., Bioactive Conformations of Two Seminal Delta Opioid Receptor Penta-peptides Inferred from Free-Energy Profiles, Biopolymers (2014) 101(1):21-27. http://www.ncbi.nlm.nih.gov/pubmed/23564013.

Jiang, J.-K. McCoy, J.G., Shen, M., LeClair, C., Huang, W., Negri, A., Li, J., Blue, R., Harrington, A., Naini, S., David, G. III, Choi, W.-S., Volpi, E., Fernandez, J., Babayeva, M., Nedelman, M.A., Filizola, M., Coller, B.S., Thomas, C.G. A novel class of ion displacement ligands as antagonists of the αIIbβ3 receptor that limit conformational reorganization of the receptor, Bioorganic & Medicinal Chemistry Letters (2014), accepted.

Johnston, J.M. & Filizola, M. Differential stability of the crystallographic interfaces of mu- and kappa-opioid receptors, PLOS One (2014), accepted.

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