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Our lab develops and applies computational approaches for data mining, analysis and knowledge extraction from biomedical data. We are particularly active in the fields of structural bioinformatics, computational genomics and systems biology.
Our lab recently developed a number of novel methods for analysis and prediction of protein interactions, including those for membrane proteins, and for model quality assessment. We are also pursuing development of improved data mining methods that combine docking simulations, chemical similarity and toxicogenomics to predict activity of environmental factors and other small molecules.
We apply the methods we develop in the context of collaborative projects, and develop bioinformatics tools for functional and structural annotation of proteins and their complexes. Several of these tools, including SABLE, SPPIDER and POLYVIEW-3D, are available to the community as web servers and are being widely used by researchers from many countries.
Porollo A, Meller J. POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations. Nucleic Acid Res. 38:W662. 2010.
Lam YW, Yuan Y, Babu S, Isaac J, Meller J, Ho SM. Comprehensive Identification and Modified-site Mapping of S-Nitrosylated Targets in Prostate Epithelial Cells. PLoS One. 5(2): e9075. 2010.
Maki N, Martinson J, Nishimura O, Tarui H, Meller J, Tsonis PA, Agata K. Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequence tags. Molecular Vision. 16:72-78. 2010.
Vallat BK, Pillardy J, Májek P, Meller J, Blom T, Cao B, Elber R. Building and assessing atomic models of proteins from structural templates: learning and benchmarks. Proteins. 76(4):930-45. 2009.
Haffey WD, Mikhaylova O, Meller J, Yi Y, Greis,KD, Czyzyk-Krzeska MF. iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylase knockdown in renal carcinoma cells. Adv Enzyme Regul. 49(1):121-32. 2009.
Tan M, Xia M, Chen Y, Bu W, Hegde RS, Meller J, Li X, Jiang X. Conservation of carbohydrate binding interfaces: evidence of human HBGA selection in norovirus evolution. PLoS ONE. 4(4):e5058. 2009.
Mikhaylova, O, Ignacak, ML, Barankiewicz, TJ, Harbaugh, SV, Yi, Y, Meller, J, Czyzyk-Krzeska, MF. The von Hippel-Lindau tumor suppressor protein and Egl-9-Type proline hydroxylases regulate the large subunit of RNA polymerase II in response to oxidative stress. Molecular and Cellular Biology. 28(8):2701-17. 2008.
Sinha A, Meller J. Sensitivity analysis for reversal distance and breakpoint reuse in genome rearrangements. Pac Symp Biocomput. 37-48. 2008.
Tan M, Xia M, Cao S, Huang P, Farkas T, Meller J, Hegde RS, Li X, Rao Z, Jiang X. Elucidation of strain-specific interaction of a GII-4 norovirus with HBGA receptors by site-directed mutagenesis study. Virology. 379(2):324-34. 2008.
Olshavsky N, Groh EM, Comstock CES, Morey LM, Wang Y, Revelo MP, Moghadam H, Burd CJ, Meller J, Knudsen KE. Cyclin D3 action in androgen receptor regulation and prostate cancer. Oncogene. 27(22):3111-21. 2008.
Takatori A, Geh E, Chen L, Zhang L, Meller J, Xia Y. Differential transmission of MEKK1 morphogenetic signals by JNK1 and JNK2. Development. 135(1):23-32. 2008.
Howarth JW, Meller J, Solaro RJ, Trewhella J, Rosevear PR. Phosphorylation-Dependent Conformational Transition of the Cardiac Specific N-Extension of Troponin I in Cardiac Troponin. Journal of Molecular Biology. 373(3):706-22. 2007.
Porollo A, Meller J. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. BMC Bioinformatics. 8:316. 2007.
Duch W, Swaminathan K, Meller J. Artificial intelligence approaches for rational drug design and discovery. Pharmaceutical Design. 13(14): 1497-1508. 2007.
Cushion MT, Smulian AG, Slaven BE, Sesterhenn T, Arnold J, Weiss M, Staben C, Porollo A, Adamczak R, Meller J. Transcriptome of Pneumocystis carinii During Fulminate Infection: Carbohydrate Metabolism and the Concept of a Compatible Parasite. PLoS One. 2:e423. 2007.
Sinha A, Meller J. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics. 8:82. 2007.
Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins. 66(3), 630-645. 2007.
Jarek Meller, PhDDivision of Biomedical Informatics3333 Burnet Ave.Cincinnati, OH 45229Phone: 513-636-0270Email: email@example.com
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