Jaroslaw Meller - Publications

Affiliations: 
University of Cincinnati, Cincinnati, OH 
Area:
bioinformatics, computational genomics, protein structure
Website:
http://folding.cchmc.org

82 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Chidambaran V, Venkatasubramanian R, Zhang X, Martin LJ, Niu J, Mizuno T, Fukuda T, Meller J, Vinks AA, Sadhasivam S. ABCC3 genetic variants are associated with postoperative morphine-induced respiratory depression and morphine pharmacokinetics in children. The Pharmacogenomics Journal. PMID 26810133 DOI: 10.1038/tpj.2015.98  1
2015 Kesarwani M, Huber E, Kincaid Z, Evelyn CR, Biesiada J, Rance M, Thapa MB, Shah NP, Meller J, Zheng Y, Azam M. Targeting substrate-site in Jak2 kinase prevents emergence of genetic resistance. Scientific Reports. 5: 14538. PMID 26419724 DOI: 10.1038/srep14538  1
2015 Chen SH, Meller J, Elber R. Comprehensive analysis of sequences of a protein switch. Protein Science : a Publication of the Protein Society. PMID 26073558 DOI: 10.1002/pro.2723  1
2015 Evelyn CR, Biesiada J, Duan X, Tang H, Shang X, Papoian R, Seibel WL, Nelson S, Meller J, Zheng Y. Combined rational design and a high throughput screening platform for identifying chemical inhibitors of a Ras-activating enzyme. The Journal of Biological Chemistry. 290: 12879-98. PMID 25825487 DOI: 10.1074/jbc.M114.634493  1
2015 Tam NN, Zhang X, Xiao H, Song D, Levin L, Meller J, Ho SM. Increased susceptibility of estrogen-induced bladder outlet obstruction in a novel mouse model. Laboratory Investigation; a Journal of Technical Methods and Pathology. 95: 546-60. PMID 25706094 DOI: 10.1038/labinvest.2015.30  1
2015 Sadhasivam S, Zhang X, Chidambaran V, Mavi J, Pilipenko V, Mersha TB, Meller J, Kaufman KM, Martin LJ, McAuliffe J. Novel associations between FAAH genetic variants and postoperative central opioid-related adverse effects. The Pharmacogenomics Journal. PMID 25558980 DOI: 10.1038/tpj.2014.79  1
2015 Lauf PK, Alqahtani T, Flues K, Meller J, Adragna NC. Interaction between Na-K-ATPase and Bcl-2 proteins BclXL and Bak. American Journal of Physiology. Cell Physiology. 308: C51-60. PMID 25318106 DOI: 10.1152/ajpcell.00287.2014  1
2015 Sadhasivam S, Chidambaran V, Zhang X, Meller J, Esslinger H, Zhang K, Martin LJ, McAuliffe J. Opioid-induced respiratory depression: ABCB1 transporter pharmacogenetics. The Pharmacogenomics Journal. 15: 119-26. PMID 25311385 DOI: 10.1038/tpj.2014.56  1
2014 Hall DP, Cost NG, Hegde S, Kellner E, Mikhaylova O, Stratton Y, Ehmer B, Abplanalp WA, Pandey R, Biesiada J, Harteneck C, Plas DR, Meller J, Czyzyk-Krzeska MF. TRPM3 and miR-204 establish a regulatory circuit that controls oncogenic autophagy in clear cell renal cell carcinoma. Cancer Cell. 26: 738-53. PMID 25517751 DOI: 10.1016/j.ccell.2014.09.015  1
2014 Biesiada J, Chidambaran V, Wagner M, Zhang X, Martin LJ, Meller J, Sadhasivam S. Genetic risk signatures of opioid-induced respiratory depression following pediatric tonsillectomy. Pharmacogenomics. 15: 1749-1762. PMID 25493568 DOI: 10.2217/pgs.14.137  1
2014 Evelyn CR, Duan X, Biesiada J, Seibel WL, Meller J, Zheng Y. Rational design of small molecule inhibitors targeting the Ras GEF, SOS1. Chemistry & Biology. 21: 1618-28. PMID 25455859 DOI: 10.1016/j.chembiol.2014.09.018  1
2014 Johansson E, Reponen T, Meller J, Vesper S, Yadav J. Association of Streptomyces community composition determined by PCR-denaturing gradient gel electrophoresis with indoor mold status. Environmental Monitoring and Assessment. 186: 8773-83. PMID 25331035 DOI: 10.1007/s10661-014-4071-4  1
2014 Dong Z, Meller J, Succop P, Wang J, Wikenheiser-Brokamp K, Starnes S, Lu S. Secretory phospholipase A2-IIa upregulates HER/HER2-elicited signaling in lung cancer cells. International Journal of Oncology. 45: 978-84. PMID 24913497 DOI: 10.3892/ijo.2014.2486  1
2013 Bastola P, Stratton Y, Kellner E, Mikhaylova O, Yi Y, Sartor MA, Medvedovic M, Biesiada J, Meller J, Czyzyk-Krzeska MF. Folliculin contributes to VHL tumor suppressing activity in renal cancer through regulation of autophagy. Plos One. 8: e70030. PMID 23922894 DOI: 10.1371/journal.pone.0070030  1
2013 Zhang XF, Tan M, Chhabra M, Dai YC, Meller J, Jiang X. Inhibition of histo-blood group antigen binding as a novel strategy to block norovirus infections. Plos One. 8: e69379. PMID 23894462 DOI: 10.1371/journal.pone.0069379  1
2013 Lauf PK, Heiny J, Meller J, Lepera MA, Koikov L, Alter GM, Brown TL, Adragna NC. Canonical Bcl-2 motifs of the Na+/K+ pump revealed by the BH3 mimetic chelerythrine: early signal transducers of apoptosis? Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology. 31: 257-76. PMID 23466888 DOI: 10.1159/000343366  1
2013 Wei C, Meller J, Jiang X. Substrate specificity of Tulane virus protease. Virology. 436: 24-32. PMID 23141588 DOI: 10.1016/j.virol.2012.10.010  1
2012 Biesiada J, Porollo A, Meller J. On setting up and assessing docking simulations for virtual screening. Methods in Molecular Biology (Clifton, N.J.). 928: 1-16. PMID 22956129 DOI: 10.1007/978-1-62703-008-3_1  1
2012 Porollo A, Meller J, Joshi Y, Jaiswal V, Smulian AG, Cushion MT. Analysis of current antifungal agents and their targets within the Pneumocystis carinii genome. Current Drug Targets. 13: 1575-85. PMID 22934582 DOI: 10.2174/138945012803530107  1
2012 Liu Y, Huang P, Tan M, Liu Y, Biesiada J, Meller J, Castello AA, Jiang B, Jiang X. Rotavirus VP8*: phylogeny, host range, and interaction with histo-blood group antigens. Journal of Virology. 86: 9899-910. PMID 22761376 DOI: 10.1128/JVI.00979-12  1
2012 Czyzyk-Krzeska MF, Meller J, Plas DR. Not all autophagy is equal. Autophagy. 8: 1155-6. PMID 22647376 DOI: 10.4161/auto.20650  1
2012 Mikhaylova O, Stratton Y, Hall D, Kellner E, Ehmer B, Drew AF, Gallo CA, Plas DR, Biesiada J, Meller J, Czyzyk-Krzeska MF. VHL-regulated MiR-204 suppresses tumor growth through inhibition of LC3B-mediated autophagy in renal clear cell carcinoma. Cancer Cell. 21: 532-46. PMID 22516261 DOI: 10.1016/j.ccr.2012.02.019  1
2012 Huang SH, Mo D, Meller J, Wagner M. Identifying a small set of marker genes using minimum expected cost of misclassification. Artificial Intelligence in Medicine. 55: 51-9. PMID 22387186 DOI: 10.1016/j.artmed.2012.01.004  1
2012 Bosco EE, Kumar S, Marchioni F, Biesiada J, Kordos M, Szczur K, Meller J, Seibel W, Mizrahi A, Pick E, Filippi MD, Zheng Y. Rational design of small molecule inhibitors targeting the Rac GTPase-p67(phox) signaling axis in inflammation. Chemistry & Biology. 19: 228-42. PMID 22365606 DOI: 10.1016/j.chembiol.2011.12.017  1
2011 Zhang Y, Johansson E, Miller ML, Jänicke RU, Ferguson DJ, Plas D, Meller J, Anderson MW. Identification of a conserved anti-apoptotic protein that modulates the mitochondrial apoptosis pathway. Plos One. 6: e25284. PMID 21980415 DOI: 10.1371/journal.pone.0025284  1
2011 Zhang K, Jordan MB, Marsh RA, Johnson JA, Kissell D, Meller J, Villanueva J, Risma KA, Wei Q, Klein PS, Filipovich AH. Hypomorphic mutations in PRF1, MUNC13-4, and STXBP2 are associated with adult-onset familial HLH. Blood. 118: 5794-8. PMID 21881043 DOI: 10.1182/blood-2011-07-370148  1
2011 Biesiada J, Porollo A, Velayutham P, Kouril M, Meller J. Survey of public domain software for docking simulations and virtual screening. Human Genomics. 5: 497-505. PMID 21807604 DOI: 10.1186/1479-7364-5-5-497  1
2011 Phatak M, Adamczak R, Cao B, Wagner M, Meller J. Solvent and lipid accessibility prediction as a basis for model quality assessment in soluble and membrane proteins. Current Protein & Peptide Science. 12: 563-73. PMID 21787302 DOI: 10.2174/138920311796957603  1
2011 Adamczak R, Pillardy J, Vallat BK, Meller J. Fast geometric consensus approach for protein model quality assessment. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1807-18. PMID 21244273 DOI: 10.1089/cmb.2010.0170  1
2010 Yi Y, Mikhaylova O, Mamedova A, Bastola P, Biesiada J, Alshaikh E, Levin L, Sheridan RM, Meller J, Czyzyk-Krzeska MF. von Hippel-Lindau-dependent patterns of RNA polymerase II hydroxylation in human renal clear cell carcinomas. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 16: 5142-52. PMID 20978146 DOI: 10.1158/1078-0432.CCR-09-3416  1
2010 Shu D, Zhang H, Petrenko R, Meller J, Guo P. Dual-channel single-molecule fluorescence resonance energy transfer to establish distance parameters for RNA nanoparticles. Acs Nano. 4: 6843-53. PMID 20954698 DOI: 10.1021/nn1014853  1
2010 Swaminathan K, Adamczak R, Porollo A, Meller J. Enhanced prediction of conformational flexibility and phosphorylation in proteins. Advances in Experimental Medicine and Biology. 680: 307-19. PMID 20865514 DOI: 10.1007/978-1-4419-5913-3_35  1
2010 Yang Y, Xia M, Tan M, Huang P, Zhong W, Pang XL, Lee BE, Meller J, Wang T, Jiang X. Genetic and phenotypic characterization of GII-4 noroviruses that circulated during 1987 to 2008. Journal of Virology. 84: 9595-607. PMID 20592096 DOI: 10.1128/JVI.02614-09  1
2010 Porollo A, Meller J. POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations. Nucleic Acids Research. 38: W662-6. PMID 20504857 DOI: 10.1093/nar/gkq445  1
2010 Lam YW, Yuan Y, Isaac J, Babu CV, Meller J, Ho SM. Comprehensive identification and modified-site mapping of S-nitrosylated targets in prostate epithelial cells. Plos One. 5: e9075. PMID 20140087 DOI: 10.1371/journal.pone.0009075  1
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: 72-8. PMID 20090923  1
2010 Shinde K, Phatak M, Johannes FM, Chen J, Li Q, Vineet JK, Hu Z, Ghosh K, Meller J, Medvedovic M. Genomics Portals: integrative web-platform for mining genomics data. Bmc Genomics. 11: 27. PMID 20070909 DOI: 10.1186/1471-2164-11-27  1
2010 Phatak M, Meller J. Model quality assessment in membrane proteins using predicted lipid accessibility profiles 11th International Symposium On Artificial Intelligence and Mathematics, Isaim 2010 1
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: e5058. PMID 19337380 DOI: 10.1371/journal.pone.0005058  1
2009 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: 930-45. PMID 19326457 DOI: 10.1002/prot.22401  1
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. Advances in Enzyme Regulation. 49: 121-32. PMID 19159641 DOI: 10.1016/j.advenzreg.2008.12.004  1
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: 324-34. PMID 18692213 DOI: 10.1016/j.virol.2008.06.041  1
2008 Mikhaylova O, Ignacak ML, Barankiewicz TJ, Harbaugh SV, Yi Y, Maxwell PH, Schneider M, Van Geyte K, Carmeliet P, Revelo MP, Wyder M, Greis KD, 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: 2701-17. PMID 18285459 DOI: 10.1128/MCB.01231-07  1
2008 Sinha AU, Meller J. Sensitivity analysis for reversal distance and breakpoint reuse in genome rearrangements. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 37-48. PMID 18229675  1
2008 Olshavsky NA, Groh EM, Comstock CE, Morey LM, Wang Y, Revelo MP, Burd C, Meller J, Knudsen KE. Cyclin D3 action in androgen receptor regulation and prostate cancer. Oncogene. 27: 3111-21. PMID 18084330 DOI: 10.1038/sj.onc.1210981  1
2008 Takatori A, Geh E, Chen L, Zhang L, Meller J, Xia Y. Differential transmission of MEKK1 morphogenetic signals by JNK1 and JNK2. Development (Cambridge, England). 135: 23-32. PMID 18032450 DOI: 10.1242/dev.007120  1
2007 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: 706-22. PMID 17854829 DOI: 10.1016/j.jmb.2007.08.035  1
2007 Duch W, Swaminathan K, Meller J. Artificial intelligence approaches for rational drug design and discovery. Current Pharmaceutical Design. 13: 1497-508. PMID 17504169 DOI: 10.2174/138161207780765954  1
2007 Cushion MT, Smulian AG, Slaven BE, Sesterhenn T, Arnold J, 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. PMID 17487271 DOI: 10.1371/journal.pone.0000423  1
2007 Sinha AU, Meller J. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. Bmc Bioinformatics. 8: 82. PMID 17343765 DOI: 10.1186/1471-2105-8-82  1
2007 Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins. 66: 630-45. PMID 17152079 DOI: 10.1002/prot.21248  1
2006 Slaven BE, Meller J, Porollo A, Sesterhenn T, Smulian AG, Cushion MT. Draft assembly and annotation of the Pneumocystis carinii genome. The Journal of Eukaryotic Microbiology. 53: S89-91. PMID 17169080 DOI: 10.1111/j.1550-7408.2006.00184.x  1
2006 Slaven BE, Porollo A, Sesterhenn T, Smulian AG, Cushion MT, Meller J. Large-scale characterization of introns in the Pneumocystis carinii genome. The Journal of Eukaryotic Microbiology. 53: S151-3. PMID 17169040 DOI: 10.1111/j.1550-7408.2006.00211.x  1
2006 Tan M, Meller J, Jiang X. C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein. Journal of Virology. 80: 7322-31. PMID 16840313 DOI: 10.1128/JVI.00233-06  1
2006 Cao B, Porollo A, Adamczak R, Jarrell M, Meller J. Enhanced recognition of protein transmembrane domains with prediction-based structural profiles. Bioinformatics (Oxford, England). 22: 303-9. PMID 16293670 DOI: 10.1093/bioinformatics/bti784  1
2005 Ivanenkov VV, Meller J, Kirley TL. Characterization of disulfide bonds in human nucleoside triphosphate diphosphohydrolase 3 (NTPDase3): implications for NTPDase structural modeling. Biochemistry. 44: 8998-9012. PMID 15966724 DOI: 10.1021/bi047487z  1
2005 Wagner M, Adamczak R, Porollo A, Meller J. Linear regression models for solvent accessibility prediction in proteins. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 355-69. PMID 15857247 DOI: 10.1089/cmb.2005.12.355  1
2005 Adamczak R, Porollo A, Meller J. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins. 59: 467-75. PMID 15768403 DOI: 10.1002/prot.20441  1
2005 Petre-Draviam CE, Williams EB, Burd CJ, Gladden A, Moghadam H, Meller J, Diehl JA, Knudsen KE. A central domain of cyclin D1 mediates nuclear receptor corepressor activity. Oncogene. 24: 431-44. PMID 15558026 DOI: 10.1038/sj.onc.1208200  1
2004 Adamczak R, Porollo A, Meller J. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins. 56: 753-67. PMID 15281128 DOI: 10.1002/prot.20176  1
2004 Filippi MD, Harris CE, Meller J, Gu Y, Zheng Y, Williams DA. Localization of Rac2 via the C terminus and aspartic acid 150 specifies superoxide generation, actin polarity and chemotaxis in neutrophils. Nature Immunology. 5: 744-51. PMID 15170212 DOI: 10.1038/ni1081  1
2004 Czyzyk-Krzeska MF, Meller J. von Hippel-Lindau tumor suppressor: not only HIF's executioner. Trends in Molecular Medicine. 10: 146-9. PMID 15162797 DOI: 10.1016/j.molmed.2004.02.004  1
2004 Porollo AA, Adamczak R, Meller J. POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins. Bioinformatics (Oxford, England). 20: 2460-2. PMID 15073023 DOI: 10.1093/bioinformatics/bth248  1
2004 Adamczak R, Meller J. On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations Molecular Physics. 102: 1291-1305. DOI: 10.1080/00268970410001728636  1
2003 Tan M, Huang P, Meller J, Zhong W, Farkas T, Jiang X. Mutations within the P2 domain of norovirus capsid affect binding to human histo-blood group antigens: evidence for a binding pocket. Journal of Virology. 77: 12562-71. PMID 14610179 DOI: 10.1128/JVI.77.23.12562-12571.2003  1
2003 Turowski M, Yamakawa N, Meller J, Kimata K, Ikegami T, Hosoya K, Tanaka N, Thornton ER. Deuterium isotope effects on hydrophobic interactions: the importance of dispersion interactions in the hydrophobic phase. Journal of the American Chemical Society. 125: 13836-49. PMID 14599224 DOI: 10.1021/ja036006g  1
2003 Kuznetsova AV, Meller J, Schnell PO, Nash JA, Ignacak ML, Sanchez Y, Conaway JW, Conaway RC, Czyzyk-Krzeska MF. von Hippel-Lindau protein binds hyperphosphorylated large subunit of RNA polymerase II through a proline hydroxylation motif and targets it for ubiquitination. Proceedings of the National Academy of Sciences of the United States of America. 100: 2706-11. PMID 12604794 DOI: 10.1073/pnas.0436037100  1
2003 Meller J, Malrieu JP, Heully JL. Size-consistent multireference configuration interaction method through the dressing of the norm of determinants Molecular Physics. 101: 2029-2041.  1
2002 Meller J, Wagner M, Elber R. Maximum feasibility guideline in the design and analysis of protein folding potentials. Journal of Computational Chemistry. 23: 111-8. PMID 11913376 DOI: 10.1002/jcc.10014  1
2002 Meller J, Elber R. Protein recognition by sequence-tostructure fitness: Bridging efficiency and capacity of threading models Advances in Chemical Physics. 120: 77-130.  1
2001 Meller J, Elber R. Linear programming optimization and a double statistical filter for protein threading protocols. Proteins. 45: 241-61. PMID 11599028 DOI: 10.1002/prot.1145  1
2000 Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD. fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science (New York, N.Y.). 289: 85-8. PMID 10884229 DOI: 10.1126/science.289.5476.85  1
2000 Wan J, Meller J, Hada M, Ehara M, Nakatsuji H. Electronic excitation spectra of furan and pyrrole: Revisited by the symmetry adapted cluster-configuration interaction method Journal of Chemical Physics. 113: 7853-7866. DOI: 10.1063/1.1316034  1
1999 Meller J, Duch W. SGA derivation of matrix elements between spin-adapted perturbative wave functions International Journal of Quantum Chemistry. 74: 123-133.  1
1999 Elber R, Meller J, Olender R. Stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide Journal of Physical Chemistry B. 103: 909-911.  1
1998 Meller J, Elber R. Computer simulations of carbon monoxide photodissociation in myoglobin: structural interpretation of the B states. Biophysical Journal. 74: 789-802. PMID 9533692 DOI: 10.1016/S0006-3495(98)74004-4  1
1996 Meller J, Malrieu JP, Caballol R. State-specific coupled cluster-type dressing of multireference singles and doubles configuration interaction matrix Journal of Chemical Physics. 104: 4068-4076.  1
1996 Adamowicz L, Caballol R, Malrieu JP, Meller J. A general bridge between configuration interaction and coupled-cluster methods: A multistate solution Chemical Physics Letters. 259: 619-626.  1
1995 Meller J, Malrieu JP, Heully JL. Multireference self-consistent size-consistent configuration interaction method. A few applications to ground and excited states Chemical Physics Letters. 244: 440-447. DOI: 10.1016/0009-2614(95)00959-8  1
1994 Meller J, Heully JL, Malrieu JP. Size-consistent self-consistent combination of selected CI and perturbation theory Chemical Physics Letters. 218: 276-282. DOI: 10.1016/0009-2614(93)E1475-V  1
1994 Ingarden RS, Meller J. Temperatures in linguistics as a model of thermodynamics Open Systems & Information Dynamics. 2: 211-230. DOI: 10.1007/BF02228965  1
1992 Wybourne BG, Meller J. Enumeration of the order-14 invariants formed from the Riemann tensor Journal of Physics a: Mathematical and General. 25: 5999-6003. DOI: 10.1088/0305-4470/25/22/024  1
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