2013 Publications

  1. Huang GT, Cunningham K, Benos PV, Chennubhotla C (2013) Spectral clustering strategies for heterogeneous disease expression data. Pac Symp Biocomput, 212-223.
  2. Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP (2013) Lung HIV Microbiome Project. Widespread colonization of the lung by  Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med May 15;187(10):1110-7. [JIF=11.041]
  3. Koes DR, Baumgartner MP, Camacho CJ (2013) Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise. J Chem Inf Model. [JIF=4.675]
  4. Zomot E, Bahar I (2013) Intracellular Gating in an Inward-facing State of Aspartate Transporter GltPh Is Regulated by the Movements of the Helical Hairpin HP2 J Biol Chem 288: 8231-8237. [JIF=4.651]
  5. Travers T, Shao H, Wells A, Camacho CJ (2013) Modeling the Assembly of the Multiple Domains of α-actinin-4 and Its Role in Actin Cross-linking. Biophys J104(3):705-15. [JIF= 3.668]
  6. Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC,  Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM; Lung HIV  Microbiome Project. (2013) Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Resp Crit Care May 15;187(10):1067-75. [JIF=11.041]
  7. Mao P, Joshi K, Li J, Santana-Santos L, Luthra S, Chandran UR, Benos PV, Smith L, DeWang M, Hu B, Cheng SY, Sobol RW, Nakano I (2013) Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3. Proc Natl Acad Sci USA, accepted.
  8. Melnikow E, Xu S, Liu J, Bell AJ, Ghedin E, Unnasch TR, Lustigman S. (2013) A potential role for the interaction of Wolbachia surface proteins with the Brugia  malayi glycolytic enzymes and cytoskeleton in maintenance of endosymbiosis. PLoS  Negl Trop Dis Apr 4;7(4):e2151. Print 2013. [JIF=4.569]
  9. Jain S, Kapetanaki MG, Raghavachari N, Woodhouse K, Yu G, Barge S, Coronnello C, Benos PV,  Kato GJ, Kaminski N, Gladwin MT (2013) Expression of regulatory platelet miRNAs in patients with sickle cell disease. PLoS One8:e60932.  [JIF=3.730]
  10. (Web tool) Coronnello C, Benos PV (2013) ComiR: Combinatorial microRNA target prediction tool. Nucl Acids Res, accepted. [JIF=8.278]
  11. Saira K, Lin X, Depasse JV, Halpin R, Twaddle A, Stockwell T, Angus B, Cozzi-Lepri A, Delfino M, Dugan V, Dwyer DE, Freiberg M, Horban A, Losso M, Lynfield R, Wentworth DN, Holmes EC, Davey R, Wentworth DE, Ghedin E. (2013) Sequence Analysis of In Vivo Defective Interfering-Like RNA of Influenza A H1N1 Pandemic Virus. J Virol 2013 Jul;87(14):8064-74. Epub 2013 May 15. [JIF=5.076]
  12. Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR (2013) Special section dedicated to The Sixth q-bio Conference: meeting report and preface. Phys Biol Jun;10(3):030301. [JIF=3.109]
  13. Price I, Ermentrout B, Zamora R, Wang B, Azhar N, Mi Q, Constantine G, Faeder JR, Luckhart S, Vodovotz Y (2013) In vivo, in vitro, and in silico studies suggest a conserved immune module that regulates malaria parasite transmission from mammals to mosquitoes. J Theor Biol pii: S0022-5193(13)00258-0. [JIF=2.371]
  14. Vasilakis N, Widen S, Mayer SV, Seymour R, Wood TG, Popov V, Guzman H, Travassos da Rosa AP, Ghedin E, Holmes EC, Walker PJ, Tesh RB (2013) Niakha virus: A novel member of the family Rhabdoviridae isolated from phlebotomine sandflies in  Senegal. Virology Jun 14. [Epub ahead of print] [JIF=3.367]
  15. Min JY, Santos C, Fitch A, Twaddle A, Toyoda Y, Depasse JV, Ghedin E, Subbarao K (2013) Mammalian adaptation in the PB2 gene of avian H5N1 influenza virus. J Virol Jul 17. [Epub ahead of print] [JIF=5.076]
  16. Cui L, Morris A, Ghedin E (2013) The human mycobiome in health and disease. Genome Med Jul 30;5(7):63. [Epub ahead of print] [JIF=3.397]
  17. Cheng MH, Bahar I (2013) Coupled Global and Local Changes Direct Substrate Translocation by Neurotransmitter-Sodium Symporter Ortholog LeuT Biophys J105: 630-639. [JIF=3.668]
  18. Lu TY, Lin B, Li Y, Arora A, Han L, Cui C, Coronnello C, Sheng Y, Benos PV, Yang L (2013) Overexpression of MicroRNA-1 Promotes Cardiomyocyte Commitment from Human Cardiovascular Progenitors via Suppressing WNT and FGF Signaling Pathways J Mol Cell Cardiol 2013 Oct;63C:146-154. [JIF= 5.148]
  19. Shao H, Travers T, Camacho CJ, Wells A (2013) The carboxyl tail of alpha-actinin-4 regulates its susceptibility to m-calpain and thus functions in cell migration and spreading Int J Biochem Cell B 45(6):1051-63. [JIF= 4.152]
  20. Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK (2013) Protein Conformational Populations and Functionally Relevant Substates Accounts Chem Res Aug 29 [Epub ahead of print]. [JIF=20.833]
  21. Kerr PJ, Rogers MB, Fitch A, Depasse JV, Cattadori IM, Hudson PJ, Tscharke DC, Holmes EC, Ghedin E (2013) Comparative analysis of the complete genome sequence of the Californian MSW strain of myxoma virus reveals potential host adaptations J Virol Aug 28 [Epub ahead of print]. [JIF=5.076]
  22. Kwun HJ, Shuda M, Feng H, Camacho CJ, Moore PS, Chang Y (2013) Merkel Cell Polyomavirus Small T Antigen Controls Viral Replication and Oncoprotein Expression by Targeting the Cellular Ubiquitin Ligase SCF(Fbw7.) Cell Host Microbe 14(2):125-35. [JIF=12.609]
  23. Kerr PJ, Rogers MB, Fitch A, Depasse JV, Cattadori IM, Twaddle AC, Hudson PJ, Tscharke DC, Read AF, Holmes EC, Ghedin E (2013) Genome scale evolution of myxoma virus (MYXV) reveals host-pathogen adaptation and rapid geographic spread J Virol 87(23):12900-15. [JIF=5.076]
  24. Ghedin E, Rogers MB, Widen SG, Guzman H, Travassos da Rosa AP, Wood TG, Fitch A, Popov V, Holmes EC, Walker PJ, Vasilakis N, Tesh RB (2013) Kolente virus, a rhabdovirus species isolated from ticks and bats in the Republic of Guinea J Gen Virol 94 Pt 12:2609-15. [JIF=3.127]
  25. Castro JB, Ramanathan A, Chennubhotla CS (2013) Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorizationPLoS One 8(9):e73289. [JIF=3.730]
  26. Gur M, Zomot E, Bahar I (2013) Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions J Chem Phys 139(12):121912. [JIF=3.164]
  27. Donovan RM, Sedgewick AJ, Faeder JRZuckerman DM (2013) Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories J Chem Phys 139(11):115105. [JIF=3.164]
  28. Gur M, Madura JD, Bahar I (2013) Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase Biophys J105(7):1643-1652. [JIF=3.668]
  29. Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS (2013) Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems Wiley Interdiscip Rev Syst Biol Med Sept 30 [Epub ahead of print]. [JIF=3.676]
  30. Berg JM (2013) Scientific approaches to science policy Mol Biol Cell 24(21):3273-4. [JIF=4.803]
  31. Miskov-Zivanov N, Turner MS, Kane LP, Morel PA, Faeder JR (2013) The duration of T cell stimulation is a critical determinant of cell fate and plasticity Sci Signal 6(300):ra97. [JIF=7.648]
  32. Chu CT, Ji J, Dagda RK, Jiang JF, Tyurina YY, Kapralov AA, Tyurin VA, Yanamala N, Shrivastava IH, Mohammadyani D, Qiang Wang KZ, Zhu J, Klein-Seetharaman J, Balasubramanian K, Amoscato AA, Borisenko G, Huang Z, Gusdon AM, Cheikhi A, Steer EK, Wang R, Baty C, Watkins S, Bahar I, Bayır H, Kagan VE (2013) Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells Nat Cell BiolOct;15(10):1197-205. [JIF=20.761]
  33. Cobanoglu MC, Liu C, Hu F, Oltvai ZN, Bahar I (2013) Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization J Chem Inf Model 53 (12), pp 3399–3409. [JIF=4.304]
  34. Twigg HL, Morris A, Ghedin E, Curtis JL3, Huffnagle GB, Crothers K, Campbell TB, Flores SC, Fontenot AP, Beck JM, Huang L, Lynch S, Knox KS, Weinstock G; Lung HIV Microbiome Project (2013) Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise Lancet Respir Med 1(5):354-6.
  35. Wisastra R, Kok PA, Eleftheriadis N, Baumgartner MP, Camacho CJ, Haisma HJ, Dekker FJ. “Discovery of a novel activator of 5-lipoxygenase from an anacardic acid derived compound collection.” Bioorg Med Chem. 2013 Dec 15;21(24):7763-78 67.
  36. Bhushan A, Senutovitch N, Bale SS, McCarty WJ, Hegde M, Jindal R, Golberg I, Berk Usta O, Yarmush ML, Vernetti LGough A, Bakan A, Shun T, Biasio R,Lansing Taylor D (2013) “Towards a three-dimensional microfluidic liver platform for predicting drug efficacy and toxicity in humans” Stem Cell Res Ther; Epub.
  37. Basu A, Bodycombe NE, Cheah JH, Price EV, Liu K, Schaefer GI, Ebright RY, Stewart ML, Ito D, Wang S, Bracha AL, Liefeld T, Wawer M, Gilbert JC, Wilson AJ, Stransky N, Kryukov GV, Dancik V, Barretina J, Garraway LA, Hon CS, Munoz B, Bittker JA, Stockwell BR, Khabele D, Stern AM, Clemons PA, Shamji AF, Schreiber SL. (2013). An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell 154(5): 1151-1161. PMID: 23993102
  38. Adams DJ, Boskovic ZV, Theriault JR, Wang AJ, Stern AM, Wagner BK, Shamji AF, Schreiber SL. Discovery of small-molecule enhancers of reactive oxygen species that are nontoxic or cause genotype-selective cell death.  ACS Chem Biol.  2013 May 17;8(5):923-9.  PMID: 23477340.  PMCID:  PMC365855
  39. Hartwell KA, Miller PG, Mukherjee S, Kahn AR, Stewart AL, Logan DJ, Negri JM, Duvet M, Järås M, Puram R, Dancik V, Al-Shahrour F, Kindler T, Tothova Z, Chattopadhyay S, Hasaka T, Narayan R, Dai M, Huang C, Shterental S, Chu LP, Haydu JE, Shieh JH, Steensma DP, Munoz B, Bittker JA, Shamji AF, Clemons PA, Tolliday NJ, Carpenter AE, Gilliland DG, Stern AM, Moore MAS, Scadden DT, Schreiber SL, Ebert BL, Golub TR (2013) Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nat Chem Biol. 2013;9(12):840-8. PMID: 24161946
  40. Li M, Khambu B, Zhang H, Kang JH, Chen X, Chen D, Vollmer L, Liu PQ, Vogt A, Yin XM. Suppression of lysosome function induces autophagy via a feedback down-regulation of MTOR complex 1 (MTORC1) activity. J Biol Chem. 2013;288(50):35769-80. PMID: 24174532; PMCID: PMC3861628.
  41.  Gao Y, Vogt A, Forsyth CJ, Koide K (2013) Comparison of splicing factor 3b inhibitors in human cells. Chembiochem.14(1):49-52. [JIF=3.945
  42. Lessa JA, Soares MA, Dos Santos RG, Mendes IC, Salum LB, Daghestani HN, Andricopulo AD, Day BW, Vogt A, Beraldo H (2013) Gallium(III) complexes with 2-acetylpyridine-derived thiosemicarbazones: antimicrobial and cytotoxic effects and investigation on the interactions with tubulin. Biometals. 2013;26(1):151-65.  [JIF=2.320]
  43. Salum LB, Altei WF, Chiaradia LD, Cordeiro MNS, Canevarolo RR, Melo CPS, Winter E, Mattei B, Daghestani HN, Santos-Silva MCu, Creczynski-Pasa TB, Yunes RA, Yunes JA, Andricopulo AD, Day BW, Nunes RJ, and Vogt A (2013) Cytotoxic 3,4,5-trimethoxychalcones as mitotic arresters and cell migration inhibitors.European Journal of Medicinal Chemistry.  2013;20(11):3396-40 [JIF=3.193]
  44. Sanker, S., Cirio, M.C., Vollmer, L.L., Goldberg, N.D., McDermott, L.A., Hukriede, N.A., and Vogt, A (2013)  Development of high-content assays for kidney progenitor cell expansion in transgenic zebrafish.  Journal of Biomolecular Screening (in press) [JIF=2.500]
  45. Wang Q, Chikina M, Zaslavsky E, Pincas H, Sealfon SC (2013) β-catenin regulates GnRH-induced FSHβ gene expression Mol Endocrinol 27(2):224-37.

  46. Uchida H, Chan J, Shrivastava I, Reinhart B, Grandi P, Glorioso JC, Cohen JB (2013) Novel mutations in gB and gH circumvent the requirement for known gD Receptors in herpes simplex virus 1 entry and cell-to-cell spread J Virol. 87(3):1430-42.
  47. Tarca AL, Lauria M, Unger M, Bilal E, Boue S, Kumar Dey K, Hoeng J, Koeppl H, Martin F, Meyer P, Nandy P, Norel R, Peitsch M, Rice JJ, Romero R, Stolovitzky G, Talikka M, Xiang Y, Zechner C; IMPROVER DSC Collaborators (2013) Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge Bioinformatics 29(22):2892-9.
  48. Aghaeepour N, Finak G; FlowCAP Consortium; DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH (2013) Critical assessment of automated flow cytometry data analysis techniques Nat Methods 10(3):228-38.