Education/CredentialsDoctoral Degree: Polish Academy of Sciences (Biomedical Engineering)Postdoctoral Fellowship : Cornell UniversityFellowship: Kyoto UniversityPostdoctorla Fellowship: Hebrew UniversityDoctoral Degree: Nicolaus Copernicus University (Computational Chemistry) Contact Information Medical Sciences Building 316 Office 513-558-1958 Email mellerj@ucmail.uc.edu Research InterestsMy research is focused on computational methods in molecular biology, genomics and biomedicine. Peer Reviewed Publications Adamczak R.;Meller J. 12-28-2016. UQlust: Combining profile hashing with linear-time ranking for efficient clustering and analysis of BMC Bioinformatics, 17 1, Evelyn C.;Duan X.;Biesiada J.;Seibel W.;Meller J.;Zheng Y. 12-18-2014. Rational Design of Small Molecule Inhibitors Targeting the Ras GEF, SOS1 Chemistry and Biology, 21 12, 1618-1628Porollo A.;Meller J.;Joshi Y.;Jaiswal V.;Smulian A.;Cushion M. 12-03-2012. Analysis of current antifungal agents and their targets within the pneumocystis carinii genome Current Drug Targets, 13 12, 1575-1585McGuire J.L.;Depasquale E.A.;Funk A.J.;O'Donnovan S.M.;Hasselfeld K.;Marwaha S.;Hammond J.H.;Hartounian V.;Meador-Woodruff J.H.;Meller J.;McCullumsmith R.E. 12-01-2017. Abnormalities of signal transduction networks in chronic schizophrenia npj Schizophrenia, 3 1, Johansson E.;Reponen T.;Meller J.;Vesper S.;Yadav J. 12-01-2014. Association of Streptomyces community composition determined by PCR-denaturing gradient gel electrop Environmental Monitoring and Assessment, 186 12, 8773-8783Adamczak R.;Pillardy J.;Vallat B.;Meller J. 12-01-2011. Fast geometric consensus approach for protein model quality assessment Journal of Computational Biology, 18 12, 1807-1818Phatak M.;Meller J. 12-01-2010. Model quality assessment in membrane proteins using predicted lipid accessibility profiles 11th International Symposium on Artificial Intelligence and Mathematics, ISAIM 2010, , Swaminathan K.;Adamczak R.;Porollo A.;Meller J. 12-01-2010. Enhanced prediction of conformational flexibility and phosphorylation in proteins Advances in Experimental Medicine and Biology, 680 , 307-319Sinha A.;Meller J. 12-01-2008. Sensitivity analysis for reversal distance and breakpoint reuse in genome rearrangements Pacific Symposium on Biocomputing 2008, PSB 2008, , 37-48Tan M.;Huang P.;Meller J.;Zhong W.;Farkas T.;Jiang X. 12-01-2003. Mutations within the P2 Domain of Norovirus Capsid Affect Binding to Human Histo-Blood Group Antigen Journal of Virology, 77 23, 12562-12571Meller J.;Elber R. 12-01-2002. Protein recognition by sequence-tostructure fitness: Bridging efficiency and capacity of threading m Advances in Chemical Physics, 120 , 77-130Wybourne B.;Meller J. 12-01-1992. Enumeration of the order-14 invariants formed from the Riemann tensor Journal of Physics A: Mathematical and General, 25 22, 5999-6003Zhang K.;Jordan M.;Marsh R.;Johnson J.;Kissell D.;Meller J.;Villanueva J.;Risma K.;Wei Q.;Klein P.;Filipovich A. 11-24-2011. Hypomorphic mutations in PRF1, MUNC13-4, and STXBP2 are associated with adult-onset familial HLH Blood, 118 22, 5794-5798Shu D.;Zhang H.;Petrenko R.;Meller J.;Guo P. 11-23-2010. Dual-channel single-molecule fluorescence resonance energy transfer to establish distance parameters ACS Nano, 4 11, 6843-6853Meller J.;Elber R. 11-15-2001. Linear programming optimization and a double statistical filter for protein threading protocols Proteins: Structure, Function and Genetics, 45 3, 241-261Biesiada J.;Porollo A.;Meller J. 11-12-2012. On setting up and assessing docking simulations for virtual screening Methods in Molecular Biology, 928 , 1-16Turowski M.;Yamakawa N.;Meller J.;Kimata K.;Ikegami T.;Hosoya K.;Tanaka N.;Thornton E. 11-12-2003. Deuterium Isotope Effects on Hydrophobic Interactions: The Importance of Dispersion Interactions in Journal of the American Chemical Society, 125 45, 13836-13849Wan J.;Meller J.;Hada M.;Ehara M.;Nakatsuji H. 11-08-2000. Electronic excitation spectra of furan and pyrrole: Revisited by the symmetry adapted cluster-config Journal of Chemical Physics, 113 18, 7853-7866Yi Y.;Mikhaylova O.;Mamedova A.;Bastola P.;Biesiada J.;Alshaikh E.;Levin L.;Sheridan R.;Meller J.;Czyzyk-Krzeska M. 11-01-2010. Von Hippel-Lindau-dependent patterns of RNA polymerase II hydroxylation in human renal clear cell ca Clinical Cancer Research, 16 21, 5142-5152Slaven B.;Meller J.;Porollo A.;Sesterhenn T.;Smulian A.;Cushion M. 11-01-2006. Draft assembly and annotation of the Pneumocystis carinii genome Journal of Eukaryotic Microbiology, 53 SUPPL. 1, Slaven B.;Porollo A.;Sesterhenn T.;Smulian A.;Cushion M.;Meller J. 11-01-2006. Large-scale characterization of introns in the Pneumocystis carinii genome Journal of Eukaryotic Microbiology, 53 SUPPL. 1, Howarth J.W.;Meller J.;Solaro R.J.;Trewhella J.;Rosevear P.R. 10-26-2007. Phosphorylation-dependent Conformational Transition of the Cardiac Specific N-Extension of Troponin Journal of Molecular Biology, 373 3, 706-722Meller J.;Malrieu J.;Heully J. 10-13-1995. Multireference self-consistent size-consistent configuration interaction method. A few applications Chemical Physics Letters, 244 5-6, 440-447Porollo A.;Adamczak R.;Meller J. 10-12-2004. POLYVIEW: A flexible visualization tool for structural and functional annotations of proteins Bioinformatics, 20 15, 2460-2462Kesarwani M.;Huber E.;Kincaid Z.;Evelyn C.R.;Biesiada J.;Rance M.;Thapa M.B.;Shah N.P.;Meller J.;Zheng Y.;Azam M. 09-30-2015. Targeting substrate-site in Jak2 kinase prevents emergence of genetic resistance Scientific Reports, 5 , Zhang Y.;Johansson E.;Miller M.L.;Jänicke R.U.;Ferguson D.J.;Plas D.;Meller J.;Anderson M.W. 09-30-2011. Identification of a conserved anti-apoptotic protein that modulates the mitochondrial apoptosis path PLoS ONE, 6 9, Tan M.;Xia M.;Cao S.;Huang P.;Farkas T.;Meller J.;Hegde R.;Li X.;Rao Z.;Jiang X. 09-30-2008. Elucidation of strain-specific interaction of a GII-4 norovirus with HBGA receptors by site-directed Virology, 379 2, 324-334Adamczak R, Porollo A, Meller J. 09-2004. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins., 56 4, 753Adamowicz L.;Caballol R.;Malrieu J.;Meller J. 09-13-1996. A general bridge between configuration interaction and coupled-cluster methods: A multistate solutio Chemical Physics Letters, 259 5-6, 619-626Liu Y.;Huang P.;Tan M.;Liu Y.;Biesiada J.;Meller J.;Castello A.;Jiang B.;Jiang X. 09-01-2012. Rotavirus VP8*: Phylogeny, host range, and interaction with histo-blood group antigens Journal of Virology, 86 18, 9899-9910Vallat B.K.;Pillardy J.;Májek P.;Meller J.;Blom T.;Cao B.Q.;Elber R. 09-01-2009. Building and assessing atomic models of proteins from structural templates: Learning and benchmarks Proteins: Structure, Function and Bioinformatics, 76 4, 930-945Adamczak R.;Porollo A.;Meller J. 09-01-2004. Accurate prediction of solvent accessibility using neural networks-based regression Proteins: Structure, Function and Genetics, 56 4, 753-767Porollo A.;Meller J. 08-29-2007. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D BMC Bioinformatics, 8 , Maki N.;Martinson J.;Nishimura O.;Tarui H.;Meller J.;Tsonis P.;Agata K. 08-20-2010. Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequenc Molecular Vision, 16 , 72-78Mohanty S.;Donnelly B.;Dupree P.;Lobeck I.;Mowery S.;Meller J.;McNeal M.;Tiao G. 08-01-2017. A point mutation in the rhesus rotavirus VP4 protein generated through a rotavirus reverse genetics Journal of Virology, 91 15, Tan M.;Meller J.;Jiang X. 08-01-2006. C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein Journal of Virology, 80 15, 7322-7331Bastola P.;Stratton Y.;Kellner E.;Mikhaylova O.;Yi Y.;Sartor M.;Medvedovic M.;Biesiada J.;Meller J.;Czyzyk-Krzeska M. 07-29-2013. Folliculin Contributes to VHL Tumor Suppressing Activity in Renal Cancer through Regulation of Autop PLoS ONE, 8 7, Zhang X.;Tan M.;Chhabra M.;Dai Y.;Meller J.;Jiang X. 07-19-2013. Inhibition of Histo-blood Group Antigen Binding as a Novel Strategy to Block Norovirus Infections PLoS ONE, 8 7, Frary A.;Nesbitt T.;Frary A.;Grandillo S.;Van Der Knaap E.;Cong B.;Liu J.;Meller J.;Elber R.;Alpert K.;Tanksley S. 07-07-2000. fw2.2: A quantitative trait locus key to the evolution of tomato fruit size Science, 289 5476, 85-88 Shamsaei B.; Chojnacki S.; Pilarczyk M.; Najafabadi M.; Niu W.; Chen C.; Ross K.; Matlock A.; Muhlich J.; Chutipongtanate S.; Zheng J.; Turner J.; Vidovi? D.; Jaffe J.; MacCoss M.; Wu C.; Pillai A.; Ma'ayan A.; Schürer S.; Kouril M.; Medvedovic M.; Meller J. 07-02-2020. piNET: a versatile web platform for downstream analysis and visualization of proteomics data Nucleic acids research, 48 W1, W85-W93Chidambaran V.;Zhang X.;Geisler K.;Stubbeman B.;Chen X.;Weirauch M.;Meller J.;Ji H. 07-01-2019. Enrichment of Genomic Pathways Based on Differential DNA Methylation Associated With Chronic Postsur Journal of Pain, 20 7, 771-785Filippi M.;Harris C.;Meller J.;Gu Y.;Zheng Y.;Williams D. 07-01-2004. Localization of Rac2 via the C terminus and aspartic acid 150 specifies superoxide generation, actin Nature Immunology, 5 7, 744-751Ivanenkov V.V.;Meller J.;Kirley T.L. 06-28-2005. Characterization of disulfide bonds in human nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) Biochemistry, 44 25, 8998-9012Haffey W.;Mikhaylova O.;Meller J.;Yi Y.;Greis K.;Czyzyk-Krzeska M. 06-10-2009. iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylas Advances in Enzyme Regulation, 49 1, 121-132Adamczak R.;Meller J. 06-10-2004. On the transferability of folding and threading potentials and sequence-independent filters for prot Molecular Physics, 102 11-12 SPEC. ISS., 1291-1305Sullivan C.;Mielnik C.;O’Donovan S.;Funk A.;Bentea E.;DePasquale E.;Alganem K.;Wen Z.;Haroutunian V.;Katsel P.;Ramsey A.;Meller J.;McCullumsmith R. 06-01-2019. Connectivity Analyses of Bioenergetic Changes in Schizophrenia: Identification of Novel Treatments Molecular Neurobiology, 56 6, 4492-4517Ingarden R.;Meller J. 06-01-1994. Temperatures in linguistics as a model of thermodynamics Open Systems & Information Dynamics, 2 2, 211-230Porollo A.;Meller J. 05-26-2010. POLYVIEW-MM: Web-based platform for animation and analysis of molecular simulations Nucleic Acids Research, 38 SUPPL. 2, Pappas D.J.;Lizee A.;Paunic V.;Beutner K.R.;Motyer A.;Vukcevic D.;Leslie S.;Biesiada J.;Meller J.;Taylor K.D.;Zheng X.;Zhao L.P.;Gourraud P.A.;Hollenbach J.A.;Mack S.J.;Maiers M. 05-22-2018. Significant variation between SNP-based HLA imputations in diverse populations: The last mile is the Pharmacogenomics Journal, 18 3, 367-376Adamczak R, Porollo A, Meller J. 05-2005. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins., 59 3, 467Evelyn C.;Biesiada J.;Duan X.;Tang H.;Shang X.;Papoian R.;Seibel W.;Nelson S.;Meller J.;Zheng Y. 05-15-2015. Combined rational design and a high throughput screening platform for identifying chemical inhibitor Journal of Biological Chemistry, 290 20, 12879-12898Olshavsky N.;Groh E.;Comstock C.;Morey L.;Wang Y.;Revelo M.;Burd C.;Meller J.;Knudsen K. 05-15-2008. Cyclin D3 action in androgen receptor regulation and prostate cancer Oncogene, 27 22, 3111-3121Adamczak R.;Porollo A.;Meller J. 05-15-2005. Combining prediction of secondary structure and solvent accessibility in proteins Proteins: Structure, Function and Genetics, 59 3, 467-475Wagner M.;Adamczak R.;Porollo A.;Meller J. 05-10-2005. Linear regression models for solvent accessibility prediction in proteins Journal of Computational Biology, 12 3, 355-369Cushion M.;Smulian A.;Slaven B.;Sesterhenn T.;Arnold J.;Staben C.;Porollo A.;Adamczak R.;Meller J. 05-09-2007. Transcriptome of Pneumocystis carinii during fulminate infection: Carbohydrate metabolism and the co PLoS ONE, 2 5, Huang S.;Mo D.;Meller J.;Wagner M. 05-01-2012. Identifying a small set of marker genes using minimum expected cost of misclassification Artificial Intelligence in Medicine, 55 1, 51-59Duch W.;Swaminathan K.;Meller J. 05-01-2007. Artificial intelligence approaches for rational drug design and discovery Current Pharmaceutical Design, 13 14, 1497-1508Sadhasivam S.;Chidambaran V.;Zhang X.;Meller J.;Esslinger H.;Zhang K.;Martin L.;McAuliffe J. 04-25-2015. Opioid-induced respiratory depression: ABCB1 transporter pharmacogenetics Pharmacogenomics Journal, 15 2, 119-126Mikhaylova O.;Stratton Y.;Hall D.;Kellner E.;Ehmer B.;Drew A.F.;Gallo C.A.;Plas D.R.;Biesiada J.;Meller J.;Czyzyk-Krzeska M.F. 04-17-2012. VHL-Regulated MiR-204 Suppresses Tumor Growth through Inhibition of LC3B-Mediated Autophagy in Renal Cancer Cell, 21 4, 532-546Mohanty S.;Donnelly B.;Lobeck I.;Walther A.;Dupree P.;Coots A.;Meller J.;McNeal M.;Sestak K.;Tiao G. 04-01-2017. The SRL peptide of rhesus rotavirus VP4 protein governs cholangiocyte infection and the murine model Hepatology, 65 4, 1278-1292Tan M.;Xia M.;Chen Y.;Bu W.;Hedge R.;Meller J.;Li X.;Jiang X. 04-01-2009. Conservation of carbohydrate binding interfaces - Evidence of human HBGA selection in norovirus evol PLoS ONE, 4 4, Mikhaylova O.;Ignacak M.;Barankiewicz T.;Harbaugh S.;Yi Y.;Maxwell P.;Schneider M.;Van Geyte K.;Carmeliet P.;Revelo M.;Wyder M.;Greis K.;Meller J.;Czyzyk-Krzeska M. 04-01-2008. The von Hippel-Lindau tumor suppressor protein and Egl-9-type proline hydroxylases regulate the larg Molecular and Cellular Biology, 28 8, 2701-2717Czyzyk-Krzeska M.;Meller J. 04-01-2004. Von Hippel-Lindau tumor suppressor: Not only HIF's executioner Trends in Molecular Medicine, 10 4, 146-149Sinha A.;Meller J. 03-26-2007. Cinteny: Flexible analysis and visualization of synteny and genome rearrangements in multiple organi BMC Bioinformatics, 8 , Sinha AU, Meller J. 03-2007. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics., 8 82, Kuznetsova A.;Meller J.;Schnell P.;Nash J.;Ignacak M.;Sanchez Y.;Conaway J.;Conaway R.;Czyzyk-Krzeska M. 03-04-2003. Von Hippel-Lindau protein binds hyperphosphorylated large subunit of RNA polymerase II through a pro Proceedings of the National Academy of Sciences of the United States of America, 100 5, 2706-2711Liu W.;Du W.;Shang X.;Wang L.;Evelyn C.;Florian M.C.;A. Ryan M.;Rayes A.;Zhao X.;Setchell K.;Meller J.;Guo F.;Nassar N.;Geiger H.;Pang Q.;Zheng Y. 03-01-2019. Rational identification of a Cdc42 inhibitor presents a new regimen for long-term hematopoietic stem Leukemia, 33 3, 749-761Chidambaran V.;Venkatasubramanian R.;Zhang X.;Martin L.;Niu J.;Mizuno T.;Fukuda T.;Meller J.;Vinks A.;Sadhasivam S. 03-01-2017. ABCC3 genetic variants are associated with postoperative morphine-induced respiratory depression and Pharmacogenomics Journal, 17 2, 162-169Tan M.;Huang P.;Meller J.;Zhong W.;Farkas T.;Jiang X. 03-01-2004. Erratum: Mutations within the P2 Domain of Norovirus Capsid Affect Binding to Human Histo-Blood Grou Journal of Virology, 78 6, 3201Bosco E.;Kumar S.;Marchioni F.;Biesiada J.;Kordos M.;Szczur K.;Meller J.;Seibel W.;Mizrahi A.;Pick E.;Filippi M.;Zheng Y. 02-24-2012. Rational design of small molecule inhibitors targeting the Rac GTPase-p67 <sup>phox</sup> Chemistry and Biology, 19 2, 228-242Porollo A, Meller J. 02-2007. Prediction-based fingerprints of protein-protein interactions Proteins., 66 3, 630Cao B, Porollo A, Adamczak R, Jarrell M, Meller J. 02-2006. Enhanced recognition of protein transmembrane domains with prediction-based structural profiles. Bioinformatics., 22 3, 303Porollo A.;Meller J. 02-15-2007. Prediction-based fingerprints of protein-protein interactions Proteins: Structure, Function and Genetics, 66 3, 630-645Elber R.;Meller J.;Olender R. 02-11-1999. Stochastic path approach to compute atomically detailed trajectories: Application to the folding of Journal of Physical Chemistry B, 103 6, 909-911Meller J.;Heully J.;Malrieu J. 02-11-1994. Size-consistent self-consistent combination of selected CI and perturbation theory Chemical Physics Letters, 218 3, 276-282Wei C.;Meller J.;Jiang X. 02-05-2013. Substrate specificity of Tulane virus protease Virology, 436 1, 24-32Lam Y.W.;Yuan Y.;Isaac J.;Babu C.V.S.;Meller J.;Ho S.M. 02-05-2010. Comprehensive identification and modified-site mapping of S-nitrosylated targets in prostate epithel PLoS ONE, 5 2, Cao B.;Porollo A.;Adamczak R.;Jarrell M.;Meller J. 02-01-2006. Enhanced recognition of protein transmembrane domains with prediction-based structural profiles Bioinformatics, 22 3, 303-309Keenan A.B.;Jenkins S.L.;Jagodnik K.M.;Koplev S.;He E.;Torre D.;Wang Z.;Dohlman A.B.;Silverstein M.C.;Lachmann A.;Kuleshov M.V.;Ma'ayan A.;Stathias V.;Terryn R.;Cooper D.;Forlin M.;Koleti A.;Vidovic D.;Chung C.;Schürer S.C.;Vasiliauskas J.;Pilarczyk M.;Shamsaei B.;Fazel M.;Ren Y.;Niu W.;Clark N.A.;White S.;Mahi N.;Zhang L.;Kouril M.;Reichard J.F.;Sivaganesan S.;Medvedovic M.;Meller J.;Koch R.J.;Birtwistle M.R.;Iyengar R.;Sobie E.A.;Azeloglu E.U.;Kaye J.;Osterloh J.;Haston K.;Kalra J.;Finkbiener S.;Li J.;Milani P.;Adam M.;Escalante-Chong R.;Sachs K.;Lenail A.;Ramamoorthy D.;Fraenkel E.;Daigle G.;Hussain U.;Coye A.;Rothstein J.;Sareen D.;Ornelas L.;Banuelos M.;Mandefro B.;Ho R.;Svendsen C.N.;Lim R.G.;Stocksdale J.;Casale M.S.;Thompson T.G.;Wu J.;Thompson L.M.;Dardov V.;Venkatraman V.;Matlock A.;Van Eyk J.E.;Jaffe J.D.;Papanastasiou M.;Subramanian A.;Golub T.R.;Erickson S.D.;Fallahi-Sichani M.;Hafner M.;Gray N.S.;Lin J.R.;Mills C.E.;Muhlich J.L.;Niepel M.;Shamu C.E.;Williams E.H.;Wrobel D.;Sorger P.K.;Heiser L.M.;Gray J.W.;Korkola J.E.;Mills G.B.;LaBarge M.;Feiler H.S.;Dane M.A.;Bucher E.;Nederlof M.;Sudar D.;Gross S. 01-24-2018. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Cell Systems, 6 1, 13-24Meller J.;Wagner M.;Elber R. 01-15-2002. Maximum feasibility guideline in the design and analysis of protein folding potentials Journal of Computational Chemistry, 23 1, 111-118Shinde K.;Phatak M.;Johannes F.;Chen J.;Li Q.;Vineet J.;Hu Z.;Ghosh K.;Meller J.;Medvedovic M. 01-13-2010. Genomics Portals: Integrative web-platform for mining genomics data BMC Genomics, 11 1, Petre-Draviam C.E.;Williams E.B.;Burd C.J.;Gladden A.;Moghadam H.;Meller J.;Diehl J.A.;Knudsen K.E. 01-13-2005. A central domain of cyclin D1 mediates nuclear receptor corepressor activity Oncogene, 24 3, 431-444 Shukla R.; Henkel N.D.; Alganem K.; Hamoud A.r.; Reigle J.; Alnafisah R.S.; Eby H.M.; Imami A.S.; Creeden J.F.; Miruzzi S.A.; Meller J.; Mccullumsmith R.E. 01-01-2021. Signature-based approaches for informed drug repurposing: targeting CNS disorders Neuropsychopharmacology, 46 1, 116-130 Gasilina A.; Premnauth G.; Gurjar P.; Biesiada J.; Hegde S.; Milewski D.; Ma G.; Kalin T.V.; Merino E.; Meller J.; Seibel W.; Cancelas J.A.; Vinnedge L.P.; Nassar N.N. 01-01-2020. IODVA1, a guanidinobenzimidazole derivative, targets Rac activity and Ras-driven cancer models PLoS ONE, 15 3, Niemeier-Walsh C.; Ryan P.H.; Meller J.; Ollberding N.J.; Adhikari A.; Indugula R.; Reponen T. 01-01-2020. The mycobiomes and bacteriomes of sputum, saliva, and home dust Indoor Air, , Bentea E.;Depasquale E.A.K.;O'Donovan S.M.;Sullivan C.R.;Simmons M.;Meador-Woodruff J.H.;Zhou Y.;Xu C.;Bai B.;Peng J.;Song H.;Ming G.L.;Meller J.;Wen Z.;McCullumsmith R.E. 01-01-2019. Kinase network dysregulation in a human induced pluripotent stem cell model of DISC1 schizophrenia Molecular Omics, 15 3, 173-188Qian Y.;Song M.;Jiang X.;Xia M.;Meller J.;Tan M.;Chen Y.;Li X.;Rao Z. 01-01-2019. Structural adaptations of norovirus GII.17/13/21 lineage through two distinct evolutionary paths Journal of Virology, 93 1, Coombs K.;Taft D.;Ward D.;Green B.;Chew G.;Shamsaei B.;Meller J.;Indugula R.;Reponen T. 01-01-2018. Variability of indoor fungal microbiome of green and non-green low-income homes in Cincinnati, Ohio Science of the Total Environment, 610-611 , 212-218Koleti A.;Terryn R.;Stathias V.;Chung C.;Cooper D.J.;Turner J.P.;VidoviÄ ‡ D.;Forlin M.;Kelley T.T.;D'Urso A.;Allen B.K.;Torre D.;Jagodnik K.M.;Wang L.;Jenkins S.L.;Mader C.;Niu W.;Fazel M.;Mahi N.;Pilarczyk M.;Clark N.;Shamsaei B.;Meller J.;Vasiliauskas J.;Reichard J.;Medvedovic M.;Ma'Ayan A.;Pillai A.;Schürer S.C. 01-01-2018. Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: Integra Nucleic Acids Research, 46 D1, D558-D566Dorsett C.;McGuire J.;Niedzielko T.;Depasquale E.;Meller J.;Floyd C.;McCullumsmith R. 01-01-2017. Traumatic brain injury induces alterations in cortical glutamate uptake without a reduction in gluta Journal of Neurotrauma, 34 1, 220-234Chen S.;Meller J.;Elber R. 01-01-2016. Comprehensive analysis of sequences of a protein switch Protein Science, 25 1, 135-146Lauf P.;Alqahtani T.;Flues K.;Meller J.;Adragna N. 01-01-2015. Interaction between Na-K-ATPase and Bcl-2 proteins BclXL and Bak American Journal of Physiology - Cell Physiology, 308 1, C51-C60Sadhasivam S.;Zhang X.;Chidambaran V.;Mavi J.;Pilipenko V.;Mersha T.;Meller J.;Kaufman K.;Martin L.;McAuliffe J. 01-01-2015. Novel associations between FAAH genetic variants and postoperative central opioid-related adverse ef Pharmacogenomics Journal, 15 5, 436-442Tam N.;Zhang X.;Xiao H.;Song D.;Levin L.;Meller J.;Ho S. 01-01-2015. Increased susceptibility of estrogen-induced bladder outlet obstruction in a novel mouse model Laboratory Investigation, 95 5, 546-560Walther A.;Mohanty S.;Donnelly B.;Coots A.;Lages C.;Lobeck I.;Dupree P.;Meller J.;McNeal M.;Sestak K.;Tiao G. 01-01-2015. Rhesus rotavirus VP4 sequence-specific activation of mononuclear cells is associated with cholangiop American Journal of Physiology - Gastrointestinal and Liver Physiology, 309 6, G466-G474Biesiada J.;Chidambaran V.;Wagner M.;Zhang X.;Martin L.;Meller J.;Sadhasivam S. 01-01-2014. Genetic risk signatures of opioid-induced respiratory depression following pediatric tonsillectomy Pharmacogenomics, 15 14, 1749-1762Dong Z.;Meller J.;Succop P.;Wang J.;Wikenheiser-Brokamp K.;Starnes S.;Lu S. 01-01-2014. Secretory phospholipase A2-IIa upregulates HER/HER2-elicited signaling in lung cancer cells International Journal of Oncology, 45 3, 978-984Hall D.P.;Cost N.G.;Hegde S.;Kellner E.;Mikhaylova O.;Stratton Y.;Ehmer B.;Abplanalp W.A.;Pandey R.;Biesiada J.;Harteneck C.;Plas D.R.;Meller J.;Czyzyk-Krzeska M.F. 01-01-2014. TRPM3 and miR-204 Establish a Regulatory Circuit that Controls Oncogenic Autophagy in Clear Cell Ren Cancer Cell, 26 5, 738-753Lauf P.;Heiny J.;Meller J.;Lepera M.;Koikov L.;Alter G.;Brown T.;Adragna N. 01-01-2013. Canonical Bcl-2 motifs of the Na <sup>+</sup> /K <sup>+</sup> pump revealed Cellular Physiology and Biochemistry, 31 2-3, 257-276Czyzyk-Krzeska M.;Meller J.;Plas D. 01-01-2012. Not all autophagy is equal Autophagy, 8 7, 1155-1156Biesiada J.;Porollo A.;Velayutham P.;Kouril M.;Meller J. 01-01-2011. Survey of public domain software for docking simulations and virtual screening Human Genomics, 5 5, 497-505Phatak M.;Adamczak R.;Cao B.;Wagner M.;Meller J. 01-01-2011. Solvent and lipid accessibility prediction as a basis for model quality assessment in soluble and me Current Protein and Peptide Science, 12 6, 563-573Yang Y.;Xia M.;Tan M.;Huang P.;Zhong W.;Pang X.;Lee B.;Meller J.;Wang T.;Jiang X. 01-01-2010. Genetic and phenotypic characterization of GII-4 noroviruses that circulated during 1987 to 2008 Journal of Virology, 84 18, 9595-9607Takatori A.;Geh E.;Chen L.;Zhang L.;Meller J.;Xia Y. 01-01-2008. Differential transmission of MEKK1 morphogenetic signals by JNK1 and JNK2 Development, 135 1, 23-32Meller J.;Wagner M. 01-01-2007. Machine learning techniques for bioinformatics: Fundamentals and applications Computational Methods in Biomedical Research, , 46-71Meller J.;Malrieu J.;Heully J. 01-01-2003. Size-consistent multireference configuration interaction method through the dressing of the norm of Molecular Physics, 101 13, 2029-2041Meller J.;Duch W. 01-01-1999. SGA derivation of matrix elements between spin-adapted perturbative wave functions International Journal of Quantum Chemistry, 74 2, 123-133Meller J.;Elber R. 01-01-1998. Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of Biophysical Journal, 74 2 I, 789-802Meller J.;Malrieu J.;Caballol R. 01-01-1996. State-specific coupled cluster-type dressing of multireference singles and doubles configuration int Journal of Chemical Physics, 104 11, 4068-4076Duch W.;Meller J. 01-01-1994. On multireference superdirect configuration interaction in third order International Journal of Quantum Chemistry, 50 4, 243-271
Research InterestsMy research is focused on computational methods in molecular biology, genomics and biomedicine.
Peer Reviewed Publications Adamczak R.;Meller J. 12-28-2016. UQlust: Combining profile hashing with linear-time ranking for efficient clustering and analysis of BMC Bioinformatics, 17 1, Evelyn C.;Duan X.;Biesiada J.;Seibel W.;Meller J.;Zheng Y. 12-18-2014. Rational Design of Small Molecule Inhibitors Targeting the Ras GEF, SOS1 Chemistry and Biology, 21 12, 1618-1628Porollo A.;Meller J.;Joshi Y.;Jaiswal V.;Smulian A.;Cushion M. 12-03-2012. Analysis of current antifungal agents and their targets within the pneumocystis carinii genome Current Drug Targets, 13 12, 1575-1585McGuire J.L.;Depasquale E.A.;Funk A.J.;O'Donnovan S.M.;Hasselfeld K.;Marwaha S.;Hammond J.H.;Hartounian V.;Meador-Woodruff J.H.;Meller J.;McCullumsmith R.E. 12-01-2017. Abnormalities of signal transduction networks in chronic schizophrenia npj Schizophrenia, 3 1, Johansson E.;Reponen T.;Meller J.;Vesper S.;Yadav J. 12-01-2014. Association of Streptomyces community composition determined by PCR-denaturing gradient gel electrop Environmental Monitoring and Assessment, 186 12, 8773-8783Adamczak R.;Pillardy J.;Vallat B.;Meller J. 12-01-2011. Fast geometric consensus approach for protein model quality assessment Journal of Computational Biology, 18 12, 1807-1818Phatak M.;Meller J. 12-01-2010. Model quality assessment in membrane proteins using predicted lipid accessibility profiles 11th International Symposium on Artificial Intelligence and Mathematics, ISAIM 2010, , Swaminathan K.;Adamczak R.;Porollo A.;Meller J. 12-01-2010. Enhanced prediction of conformational flexibility and phosphorylation in proteins Advances in Experimental Medicine and Biology, 680 , 307-319Sinha A.;Meller J. 12-01-2008. Sensitivity analysis for reversal distance and breakpoint reuse in genome rearrangements Pacific Symposium on Biocomputing 2008, PSB 2008, , 37-48Tan M.;Huang P.;Meller J.;Zhong W.;Farkas T.;Jiang X. 12-01-2003. Mutations within the P2 Domain of Norovirus Capsid Affect Binding to Human Histo-Blood Group Antigen Journal of Virology, 77 23, 12562-12571Meller J.;Elber R. 12-01-2002. Protein recognition by sequence-tostructure fitness: Bridging efficiency and capacity of threading m Advances in Chemical Physics, 120 , 77-130Wybourne B.;Meller J. 12-01-1992. Enumeration of the order-14 invariants formed from the Riemann tensor Journal of Physics A: Mathematical and General, 25 22, 5999-6003Zhang K.;Jordan M.;Marsh R.;Johnson J.;Kissell D.;Meller J.;Villanueva J.;Risma K.;Wei Q.;Klein P.;Filipovich A. 11-24-2011. Hypomorphic mutations in PRF1, MUNC13-4, and STXBP2 are associated with adult-onset familial HLH Blood, 118 22, 5794-5798Shu D.;Zhang H.;Petrenko R.;Meller J.;Guo P. 11-23-2010. Dual-channel single-molecule fluorescence resonance energy transfer to establish distance parameters ACS Nano, 4 11, 6843-6853Meller J.;Elber R. 11-15-2001. Linear programming optimization and a double statistical filter for protein threading protocols Proteins: Structure, Function and Genetics, 45 3, 241-261Biesiada J.;Porollo A.;Meller J. 11-12-2012. On setting up and assessing docking simulations for virtual screening Methods in Molecular Biology, 928 , 1-16Turowski M.;Yamakawa N.;Meller J.;Kimata K.;Ikegami T.;Hosoya K.;Tanaka N.;Thornton E. 11-12-2003. Deuterium Isotope Effects on Hydrophobic Interactions: The Importance of Dispersion Interactions in Journal of the American Chemical Society, 125 45, 13836-13849Wan J.;Meller J.;Hada M.;Ehara M.;Nakatsuji H. 11-08-2000. Electronic excitation spectra of furan and pyrrole: Revisited by the symmetry adapted cluster-config Journal of Chemical Physics, 113 18, 7853-7866Yi Y.;Mikhaylova O.;Mamedova A.;Bastola P.;Biesiada J.;Alshaikh E.;Levin L.;Sheridan R.;Meller J.;Czyzyk-Krzeska M. 11-01-2010. Von Hippel-Lindau-dependent patterns of RNA polymerase II hydroxylation in human renal clear cell ca Clinical Cancer Research, 16 21, 5142-5152Slaven B.;Meller J.;Porollo A.;Sesterhenn T.;Smulian A.;Cushion M. 11-01-2006. Draft assembly and annotation of the Pneumocystis carinii genome Journal of Eukaryotic Microbiology, 53 SUPPL. 1, Slaven B.;Porollo A.;Sesterhenn T.;Smulian A.;Cushion M.;Meller J. 11-01-2006. Large-scale characterization of introns in the Pneumocystis carinii genome Journal of Eukaryotic Microbiology, 53 SUPPL. 1, Howarth J.W.;Meller J.;Solaro R.J.;Trewhella J.;Rosevear P.R. 10-26-2007. Phosphorylation-dependent Conformational Transition of the Cardiac Specific N-Extension of Troponin Journal of Molecular Biology, 373 3, 706-722Meller J.;Malrieu J.;Heully J. 10-13-1995. Multireference self-consistent size-consistent configuration interaction method. A few applications Chemical Physics Letters, 244 5-6, 440-447Porollo A.;Adamczak R.;Meller J. 10-12-2004. POLYVIEW: A flexible visualization tool for structural and functional annotations of proteins Bioinformatics, 20 15, 2460-2462Kesarwani M.;Huber E.;Kincaid Z.;Evelyn C.R.;Biesiada J.;Rance M.;Thapa M.B.;Shah N.P.;Meller J.;Zheng Y.;Azam M. 09-30-2015. Targeting substrate-site in Jak2 kinase prevents emergence of genetic resistance Scientific Reports, 5 , Zhang Y.;Johansson E.;Miller M.L.;Jänicke R.U.;Ferguson D.J.;Plas D.;Meller J.;Anderson M.W. 09-30-2011. Identification of a conserved anti-apoptotic protein that modulates the mitochondrial apoptosis path PLoS ONE, 6 9, Tan M.;Xia M.;Cao S.;Huang P.;Farkas T.;Meller J.;Hegde R.;Li X.;Rao Z.;Jiang X. 09-30-2008. Elucidation of strain-specific interaction of a GII-4 norovirus with HBGA receptors by site-directed Virology, 379 2, 324-334Adamczak R, Porollo A, Meller J. 09-2004. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins., 56 4, 753Adamowicz L.;Caballol R.;Malrieu J.;Meller J. 09-13-1996. A general bridge between configuration interaction and coupled-cluster methods: A multistate solutio Chemical Physics Letters, 259 5-6, 619-626Liu Y.;Huang P.;Tan M.;Liu Y.;Biesiada J.;Meller J.;Castello A.;Jiang B.;Jiang X. 09-01-2012. Rotavirus VP8*: Phylogeny, host range, and interaction with histo-blood group antigens Journal of Virology, 86 18, 9899-9910Vallat B.K.;Pillardy J.;Májek P.;Meller J.;Blom T.;Cao B.Q.;Elber R. 09-01-2009. Building and assessing atomic models of proteins from structural templates: Learning and benchmarks Proteins: Structure, Function and Bioinformatics, 76 4, 930-945Adamczak R.;Porollo A.;Meller J. 09-01-2004. Accurate prediction of solvent accessibility using neural networks-based regression Proteins: Structure, Function and Genetics, 56 4, 753-767Porollo A.;Meller J. 08-29-2007. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D BMC Bioinformatics, 8 , Maki N.;Martinson J.;Nishimura O.;Tarui H.;Meller J.;Tsonis P.;Agata K. 08-20-2010. Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequenc Molecular Vision, 16 , 72-78Mohanty S.;Donnelly B.;Dupree P.;Lobeck I.;Mowery S.;Meller J.;McNeal M.;Tiao G. 08-01-2017. A point mutation in the rhesus rotavirus VP4 protein generated through a rotavirus reverse genetics Journal of Virology, 91 15, Tan M.;Meller J.;Jiang X. 08-01-2006. C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein Journal of Virology, 80 15, 7322-7331Bastola P.;Stratton Y.;Kellner E.;Mikhaylova O.;Yi Y.;Sartor M.;Medvedovic M.;Biesiada J.;Meller J.;Czyzyk-Krzeska M. 07-29-2013. Folliculin Contributes to VHL Tumor Suppressing Activity in Renal Cancer through Regulation of Autop PLoS ONE, 8 7, Zhang X.;Tan M.;Chhabra M.;Dai Y.;Meller J.;Jiang X. 07-19-2013. Inhibition of Histo-blood Group Antigen Binding as a Novel Strategy to Block Norovirus Infections PLoS ONE, 8 7, Frary A.;Nesbitt T.;Frary A.;Grandillo S.;Van Der Knaap E.;Cong B.;Liu J.;Meller J.;Elber R.;Alpert K.;Tanksley S. 07-07-2000. fw2.2: A quantitative trait locus key to the evolution of tomato fruit size Science, 289 5476, 85-88 Shamsaei B.; Chojnacki S.; Pilarczyk M.; Najafabadi M.; Niu W.; Chen C.; Ross K.; Matlock A.; Muhlich J.; Chutipongtanate S.; Zheng J.; Turner J.; Vidovi? D.; Jaffe J.; MacCoss M.; Wu C.; Pillai A.; Ma'ayan A.; Schürer S.; Kouril M.; Medvedovic M.; Meller J. 07-02-2020. piNET: a versatile web platform for downstream analysis and visualization of proteomics data Nucleic acids research, 48 W1, W85-W93Chidambaran V.;Zhang X.;Geisler K.;Stubbeman B.;Chen X.;Weirauch M.;Meller J.;Ji H. 07-01-2019. Enrichment of Genomic Pathways Based on Differential DNA Methylation Associated With Chronic Postsur Journal of Pain, 20 7, 771-785Filippi M.;Harris C.;Meller J.;Gu Y.;Zheng Y.;Williams D. 07-01-2004. Localization of Rac2 via the C terminus and aspartic acid 150 specifies superoxide generation, actin Nature Immunology, 5 7, 744-751Ivanenkov V.V.;Meller J.;Kirley T.L. 06-28-2005. Characterization of disulfide bonds in human nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) Biochemistry, 44 25, 8998-9012Haffey W.;Mikhaylova O.;Meller J.;Yi Y.;Greis K.;Czyzyk-Krzeska M. 06-10-2009. iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylas Advances in Enzyme Regulation, 49 1, 121-132Adamczak R.;Meller J. 06-10-2004. On the transferability of folding and threading potentials and sequence-independent filters for prot Molecular Physics, 102 11-12 SPEC. ISS., 1291-1305Sullivan C.;Mielnik C.;O’Donovan S.;Funk A.;Bentea E.;DePasquale E.;Alganem K.;Wen Z.;Haroutunian V.;Katsel P.;Ramsey A.;Meller J.;McCullumsmith R. 06-01-2019. Connectivity Analyses of Bioenergetic Changes in Schizophrenia: Identification of Novel Treatments Molecular Neurobiology, 56 6, 4492-4517Ingarden R.;Meller J. 06-01-1994. Temperatures in linguistics as a model of thermodynamics Open Systems & Information Dynamics, 2 2, 211-230Porollo A.;Meller J. 05-26-2010. POLYVIEW-MM: Web-based platform for animation and analysis of molecular simulations Nucleic Acids Research, 38 SUPPL. 2, Pappas D.J.;Lizee A.;Paunic V.;Beutner K.R.;Motyer A.;Vukcevic D.;Leslie S.;Biesiada J.;Meller J.;Taylor K.D.;Zheng X.;Zhao L.P.;Gourraud P.A.;Hollenbach J.A.;Mack S.J.;Maiers M. 05-22-2018. Significant variation between SNP-based HLA imputations in diverse populations: The last mile is the Pharmacogenomics Journal, 18 3, 367-376Adamczak R, Porollo A, Meller J. 05-2005. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins., 59 3, 467Evelyn C.;Biesiada J.;Duan X.;Tang H.;Shang X.;Papoian R.;Seibel W.;Nelson S.;Meller J.;Zheng Y. 05-15-2015. Combined rational design and a high throughput screening platform for identifying chemical inhibitor Journal of Biological Chemistry, 290 20, 12879-12898Olshavsky N.;Groh E.;Comstock C.;Morey L.;Wang Y.;Revelo M.;Burd C.;Meller J.;Knudsen K. 05-15-2008. Cyclin D3 action in androgen receptor regulation and prostate cancer Oncogene, 27 22, 3111-3121Adamczak R.;Porollo A.;Meller J. 05-15-2005. Combining prediction of secondary structure and solvent accessibility in proteins Proteins: Structure, Function and Genetics, 59 3, 467-475Wagner M.;Adamczak R.;Porollo A.;Meller J. 05-10-2005. Linear regression models for solvent accessibility prediction in proteins Journal of Computational Biology, 12 3, 355-369Cushion M.;Smulian A.;Slaven B.;Sesterhenn T.;Arnold J.;Staben C.;Porollo A.;Adamczak R.;Meller J. 05-09-2007. Transcriptome of Pneumocystis carinii during fulminate infection: Carbohydrate metabolism and the co PLoS ONE, 2 5, Huang S.;Mo D.;Meller J.;Wagner M. 05-01-2012. Identifying a small set of marker genes using minimum expected cost of misclassification Artificial Intelligence in Medicine, 55 1, 51-59Duch W.;Swaminathan K.;Meller J. 05-01-2007. Artificial intelligence approaches for rational drug design and discovery Current Pharmaceutical Design, 13 14, 1497-1508Sadhasivam S.;Chidambaran V.;Zhang X.;Meller J.;Esslinger H.;Zhang K.;Martin L.;McAuliffe J. 04-25-2015. Opioid-induced respiratory depression: ABCB1 transporter pharmacogenetics Pharmacogenomics Journal, 15 2, 119-126Mikhaylova O.;Stratton Y.;Hall D.;Kellner E.;Ehmer B.;Drew A.F.;Gallo C.A.;Plas D.R.;Biesiada J.;Meller J.;Czyzyk-Krzeska M.F. 04-17-2012. VHL-Regulated MiR-204 Suppresses Tumor Growth through Inhibition of LC3B-Mediated Autophagy in Renal Cancer Cell, 21 4, 532-546Mohanty S.;Donnelly B.;Lobeck I.;Walther A.;Dupree P.;Coots A.;Meller J.;McNeal M.;Sestak K.;Tiao G. 04-01-2017. The SRL peptide of rhesus rotavirus VP4 protein governs cholangiocyte infection and the murine model Hepatology, 65 4, 1278-1292Tan M.;Xia M.;Chen Y.;Bu W.;Hedge R.;Meller J.;Li X.;Jiang X. 04-01-2009. Conservation of carbohydrate binding interfaces - Evidence of human HBGA selection in norovirus evol PLoS ONE, 4 4, Mikhaylova O.;Ignacak M.;Barankiewicz T.;Harbaugh S.;Yi Y.;Maxwell P.;Schneider M.;Van Geyte K.;Carmeliet P.;Revelo M.;Wyder M.;Greis K.;Meller J.;Czyzyk-Krzeska M. 04-01-2008. The von Hippel-Lindau tumor suppressor protein and Egl-9-type proline hydroxylases regulate the larg Molecular and Cellular Biology, 28 8, 2701-2717Czyzyk-Krzeska M.;Meller J. 04-01-2004. Von Hippel-Lindau tumor suppressor: Not only HIF's executioner Trends in Molecular Medicine, 10 4, 146-149Sinha A.;Meller J. 03-26-2007. Cinteny: Flexible analysis and visualization of synteny and genome rearrangements in multiple organi BMC Bioinformatics, 8 , Sinha AU, Meller J. 03-2007. Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics., 8 82, Kuznetsova A.;Meller J.;Schnell P.;Nash J.;Ignacak M.;Sanchez Y.;Conaway J.;Conaway R.;Czyzyk-Krzeska M. 03-04-2003. Von Hippel-Lindau protein binds hyperphosphorylated large subunit of RNA polymerase II through a pro Proceedings of the National Academy of Sciences of the United States of America, 100 5, 2706-2711Liu W.;Du W.;Shang X.;Wang L.;Evelyn C.;Florian M.C.;A. Ryan M.;Rayes A.;Zhao X.;Setchell K.;Meller J.;Guo F.;Nassar N.;Geiger H.;Pang Q.;Zheng Y. 03-01-2019. Rational identification of a Cdc42 inhibitor presents a new regimen for long-term hematopoietic stem Leukemia, 33 3, 749-761Chidambaran V.;Venkatasubramanian R.;Zhang X.;Martin L.;Niu J.;Mizuno T.;Fukuda T.;Meller J.;Vinks A.;Sadhasivam S. 03-01-2017. ABCC3 genetic variants are associated with postoperative morphine-induced respiratory depression and Pharmacogenomics Journal, 17 2, 162-169Tan M.;Huang P.;Meller J.;Zhong W.;Farkas T.;Jiang X. 03-01-2004. Erratum: Mutations within the P2 Domain of Norovirus Capsid Affect Binding to Human Histo-Blood Grou Journal of Virology, 78 6, 3201Bosco E.;Kumar S.;Marchioni F.;Biesiada J.;Kordos M.;Szczur K.;Meller J.;Seibel W.;Mizrahi A.;Pick E.;Filippi M.;Zheng Y. 02-24-2012. Rational design of small molecule inhibitors targeting the Rac GTPase-p67 <sup>phox</sup> Chemistry and Biology, 19 2, 228-242Porollo A, Meller J. 02-2007. Prediction-based fingerprints of protein-protein interactions Proteins., 66 3, 630Cao B, Porollo A, Adamczak R, Jarrell M, Meller J. 02-2006. Enhanced recognition of protein transmembrane domains with prediction-based structural profiles. Bioinformatics., 22 3, 303Porollo A.;Meller J. 02-15-2007. Prediction-based fingerprints of protein-protein interactions Proteins: Structure, Function and Genetics, 66 3, 630-645Elber R.;Meller J.;Olender R. 02-11-1999. Stochastic path approach to compute atomically detailed trajectories: Application to the folding of Journal of Physical Chemistry B, 103 6, 909-911Meller J.;Heully J.;Malrieu J. 02-11-1994. Size-consistent self-consistent combination of selected CI and perturbation theory Chemical Physics Letters, 218 3, 276-282Wei C.;Meller J.;Jiang X. 02-05-2013. Substrate specificity of Tulane virus protease Virology, 436 1, 24-32Lam Y.W.;Yuan Y.;Isaac J.;Babu C.V.S.;Meller J.;Ho S.M. 02-05-2010. Comprehensive identification and modified-site mapping of S-nitrosylated targets in prostate epithel PLoS ONE, 5 2, Cao B.;Porollo A.;Adamczak R.;Jarrell M.;Meller J. 02-01-2006. Enhanced recognition of protein transmembrane domains with prediction-based structural profiles Bioinformatics, 22 3, 303-309Keenan A.B.;Jenkins S.L.;Jagodnik K.M.;Koplev S.;He E.;Torre D.;Wang Z.;Dohlman A.B.;Silverstein M.C.;Lachmann A.;Kuleshov M.V.;Ma'ayan A.;Stathias V.;Terryn R.;Cooper D.;Forlin M.;Koleti A.;Vidovic D.;Chung C.;Schürer S.C.;Vasiliauskas J.;Pilarczyk M.;Shamsaei B.;Fazel M.;Ren Y.;Niu W.;Clark N.A.;White S.;Mahi N.;Zhang L.;Kouril M.;Reichard J.F.;Sivaganesan S.;Medvedovic M.;Meller J.;Koch R.J.;Birtwistle M.R.;Iyengar R.;Sobie E.A.;Azeloglu E.U.;Kaye J.;Osterloh J.;Haston K.;Kalra J.;Finkbiener S.;Li J.;Milani P.;Adam M.;Escalante-Chong R.;Sachs K.;Lenail A.;Ramamoorthy D.;Fraenkel E.;Daigle G.;Hussain U.;Coye A.;Rothstein J.;Sareen D.;Ornelas L.;Banuelos M.;Mandefro B.;Ho R.;Svendsen C.N.;Lim R.G.;Stocksdale J.;Casale M.S.;Thompson T.G.;Wu J.;Thompson L.M.;Dardov V.;Venkatraman V.;Matlock A.;Van Eyk J.E.;Jaffe J.D.;Papanastasiou M.;Subramanian A.;Golub T.R.;Erickson S.D.;Fallahi-Sichani M.;Hafner M.;Gray N.S.;Lin J.R.;Mills C.E.;Muhlich J.L.;Niepel M.;Shamu C.E.;Williams E.H.;Wrobel D.;Sorger P.K.;Heiser L.M.;Gray J.W.;Korkola J.E.;Mills G.B.;LaBarge M.;Feiler H.S.;Dane M.A.;Bucher E.;Nederlof M.;Sudar D.;Gross S. 01-24-2018. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Cell Systems, 6 1, 13-24Meller J.;Wagner M.;Elber R. 01-15-2002. Maximum feasibility guideline in the design and analysis of protein folding potentials Journal of Computational Chemistry, 23 1, 111-118Shinde K.;Phatak M.;Johannes F.;Chen J.;Li Q.;Vineet J.;Hu Z.;Ghosh K.;Meller J.;Medvedovic M. 01-13-2010. Genomics Portals: Integrative web-platform for mining genomics data BMC Genomics, 11 1, Petre-Draviam C.E.;Williams E.B.;Burd C.J.;Gladden A.;Moghadam H.;Meller J.;Diehl J.A.;Knudsen K.E. 01-13-2005. A central domain of cyclin D1 mediates nuclear receptor corepressor activity Oncogene, 24 3, 431-444 Shukla R.; Henkel N.D.; Alganem K.; Hamoud A.r.; Reigle J.; Alnafisah R.S.; Eby H.M.; Imami A.S.; Creeden J.F.; Miruzzi S.A.; Meller J.; Mccullumsmith R.E. 01-01-2021. Signature-based approaches for informed drug repurposing: targeting CNS disorders Neuropsychopharmacology, 46 1, 116-130 Gasilina A.; Premnauth G.; Gurjar P.; Biesiada J.; Hegde S.; Milewski D.; Ma G.; Kalin T.V.; Merino E.; Meller J.; Seibel W.; Cancelas J.A.; Vinnedge L.P.; Nassar N.N. 01-01-2020. IODVA1, a guanidinobenzimidazole derivative, targets Rac activity and Ras-driven cancer models PLoS ONE, 15 3, Niemeier-Walsh C.; Ryan P.H.; Meller J.; Ollberding N.J.; Adhikari A.; Indugula R.; Reponen T. 01-01-2020. The mycobiomes and bacteriomes of sputum, saliva, and home dust Indoor Air, , Bentea E.;Depasquale E.A.K.;O'Donovan S.M.;Sullivan C.R.;Simmons M.;Meador-Woodruff J.H.;Zhou Y.;Xu C.;Bai B.;Peng J.;Song H.;Ming G.L.;Meller J.;Wen Z.;McCullumsmith R.E. 01-01-2019. Kinase network dysregulation in a human induced pluripotent stem cell model of DISC1 schizophrenia Molecular Omics, 15 3, 173-188Qian Y.;Song M.;Jiang X.;Xia M.;Meller J.;Tan M.;Chen Y.;Li X.;Rao Z. 01-01-2019. Structural adaptations of norovirus GII.17/13/21 lineage through two distinct evolutionary paths Journal of Virology, 93 1, Coombs K.;Taft D.;Ward D.;Green B.;Chew G.;Shamsaei B.;Meller J.;Indugula R.;Reponen T. 01-01-2018. Variability of indoor fungal microbiome of green and non-green low-income homes in Cincinnati, Ohio Science of the Total Environment, 610-611 , 212-218Koleti A.;Terryn R.;Stathias V.;Chung C.;Cooper D.J.;Turner J.P.;VidoviÄ ‡ D.;Forlin M.;Kelley T.T.;D'Urso A.;Allen B.K.;Torre D.;Jagodnik K.M.;Wang L.;Jenkins S.L.;Mader C.;Niu W.;Fazel M.;Mahi N.;Pilarczyk M.;Clark N.;Shamsaei B.;Meller J.;Vasiliauskas J.;Reichard J.;Medvedovic M.;Ma'Ayan A.;Pillai A.;Schürer S.C. 01-01-2018. Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: Integra Nucleic Acids Research, 46 D1, D558-D566Dorsett C.;McGuire J.;Niedzielko T.;Depasquale E.;Meller J.;Floyd C.;McCullumsmith R. 01-01-2017. Traumatic brain injury induces alterations in cortical glutamate uptake without a reduction in gluta Journal of Neurotrauma, 34 1, 220-234Chen S.;Meller J.;Elber R. 01-01-2016. Comprehensive analysis of sequences of a protein switch Protein Science, 25 1, 135-146Lauf P.;Alqahtani T.;Flues K.;Meller J.;Adragna N. 01-01-2015. Interaction between Na-K-ATPase and Bcl-2 proteins BclXL and Bak American Journal of Physiology - Cell Physiology, 308 1, C51-C60Sadhasivam S.;Zhang X.;Chidambaran V.;Mavi J.;Pilipenko V.;Mersha T.;Meller J.;Kaufman K.;Martin L.;McAuliffe J. 01-01-2015. Novel associations between FAAH genetic variants and postoperative central opioid-related adverse ef Pharmacogenomics Journal, 15 5, 436-442Tam N.;Zhang X.;Xiao H.;Song D.;Levin L.;Meller J.;Ho S. 01-01-2015. Increased susceptibility of estrogen-induced bladder outlet obstruction in a novel mouse model Laboratory Investigation, 95 5, 546-560Walther A.;Mohanty S.;Donnelly B.;Coots A.;Lages C.;Lobeck I.;Dupree P.;Meller J.;McNeal M.;Sestak K.;Tiao G. 01-01-2015. Rhesus rotavirus VP4 sequence-specific activation of mononuclear cells is associated with cholangiop American Journal of Physiology - Gastrointestinal and Liver Physiology, 309 6, G466-G474Biesiada J.;Chidambaran V.;Wagner M.;Zhang X.;Martin L.;Meller J.;Sadhasivam S. 01-01-2014. Genetic risk signatures of opioid-induced respiratory depression following pediatric tonsillectomy Pharmacogenomics, 15 14, 1749-1762Dong Z.;Meller J.;Succop P.;Wang J.;Wikenheiser-Brokamp K.;Starnes S.;Lu S. 01-01-2014. Secretory phospholipase A2-IIa upregulates HER/HER2-elicited signaling in lung cancer cells International Journal of Oncology, 45 3, 978-984Hall D.P.;Cost N.G.;Hegde S.;Kellner E.;Mikhaylova O.;Stratton Y.;Ehmer B.;Abplanalp W.A.;Pandey R.;Biesiada J.;Harteneck C.;Plas D.R.;Meller J.;Czyzyk-Krzeska M.F. 01-01-2014. TRPM3 and miR-204 Establish a Regulatory Circuit that Controls Oncogenic Autophagy in Clear Cell Ren Cancer Cell, 26 5, 738-753Lauf P.;Heiny J.;Meller J.;Lepera M.;Koikov L.;Alter G.;Brown T.;Adragna N. 01-01-2013. Canonical Bcl-2 motifs of the Na <sup>+</sup> /K <sup>+</sup> pump revealed Cellular Physiology and Biochemistry, 31 2-3, 257-276Czyzyk-Krzeska M.;Meller J.;Plas D. 01-01-2012. Not all autophagy is equal Autophagy, 8 7, 1155-1156Biesiada J.;Porollo A.;Velayutham P.;Kouril M.;Meller J. 01-01-2011. Survey of public domain software for docking simulations and virtual screening Human Genomics, 5 5, 497-505Phatak M.;Adamczak R.;Cao B.;Wagner M.;Meller J. 01-01-2011. Solvent and lipid accessibility prediction as a basis for model quality assessment in soluble and me Current Protein and Peptide Science, 12 6, 563-573Yang Y.;Xia M.;Tan M.;Huang P.;Zhong W.;Pang X.;Lee B.;Meller J.;Wang T.;Jiang X. 01-01-2010. Genetic and phenotypic characterization of GII-4 noroviruses that circulated during 1987 to 2008 Journal of Virology, 84 18, 9595-9607Takatori A.;Geh E.;Chen L.;Zhang L.;Meller J.;Xia Y. 01-01-2008. Differential transmission of MEKK1 morphogenetic signals by JNK1 and JNK2 Development, 135 1, 23-32Meller J.;Wagner M. 01-01-2007. Machine learning techniques for bioinformatics: Fundamentals and applications Computational Methods in Biomedical Research, , 46-71Meller J.;Malrieu J.;Heully J. 01-01-2003. Size-consistent multireference configuration interaction method through the dressing of the norm of Molecular Physics, 101 13, 2029-2041Meller J.;Duch W. 01-01-1999. SGA derivation of matrix elements between spin-adapted perturbative wave functions International Journal of Quantum Chemistry, 74 2, 123-133Meller J.;Elber R. 01-01-1998. Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of Biophysical Journal, 74 2 I, 789-802Meller J.;Malrieu J.;Caballol R. 01-01-1996. State-specific coupled cluster-type dressing of multireference singles and doubles configuration int Journal of Chemical Physics, 104 11, 4068-4076Duch W.;Meller J. 01-01-1994. On multireference superdirect configuration interaction in third order International Journal of Quantum Chemistry, 50 4, 243-271
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Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D BMC Bioinformatics, 8 , Maki N.;Martinson J.;Nishimura O.;Tarui H.;Meller J.;Tsonis P.;Agata K. 08-20-2010. Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequenc Molecular Vision, 16 , 72-78Mohanty S.;Donnelly B.;Dupree P.;Lobeck I.;Mowery S.;Meller J.;McNeal M.;Tiao G. 08-01-2017. A point mutation in the rhesus rotavirus VP4 protein generated through a rotavirus reverse genetics Journal of Virology, 91 15, Tan M.;Meller J.;Jiang X. 08-01-2006. C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein Journal of Virology, 80 15, 7322-7331Bastola P.;Stratton Y.;Kellner E.;Mikhaylova O.;Yi Y.;Sartor M.;Medvedovic M.;Biesiada J.;Meller J.;Czyzyk-Krzeska M. 07-29-2013. Folliculin Contributes to VHL Tumor Suppressing Activity in Renal Cancer through Regulation of Autop PLoS ONE, 8 7, Zhang X.;Tan M.;Chhabra M.;Dai Y.;Meller J.;Jiang X. 07-19-2013. Inhibition of Histo-blood Group Antigen Binding as a Novel Strategy to Block Norovirus Infections PLoS ONE, 8 7, Frary A.;Nesbitt T.;Frary A.;Grandillo S.;Van Der Knaap E.;Cong B.;Liu J.;Meller J.;Elber R.;Alpert K.;Tanksley S. 07-07-2000. fw2.2: A quantitative trait locus key to the evolution of tomato fruit size Science, 289 5476, 85-88 Shamsaei B.; Chojnacki S.; Pilarczyk M.; Najafabadi M.; Niu W.; Chen C.; Ross K.; Matlock A.; Muhlich J.; Chutipongtanate S.; Zheng J.; Turner J.; Vidovi? 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Characterization of disulfide bonds in human nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) Biochemistry, 44 25, 8998-9012Haffey W.;Mikhaylova O.;Meller J.;Yi Y.;Greis K.;Czyzyk-Krzeska M. 06-10-2009. iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylas Advances in Enzyme Regulation, 49 1, 121-132Adamczak R.;Meller J. 06-10-2004. On the transferability of folding and threading potentials and sequence-independent filters for prot Molecular Physics, 102 11-12 SPEC. ISS., 1291-1305Sullivan C.;Mielnik C.;O’Donovan S.;Funk A.;Bentea E.;DePasquale E.;Alganem K.;Wen Z.;Haroutunian V.;Katsel P.;Ramsey A.;Meller J.;McCullumsmith R. 06-01-2019. Connectivity Analyses of Bioenergetic Changes in Schizophrenia: Identification of Novel Treatments Molecular Neurobiology, 56 6, 4492-4517Ingarden R.;Meller J. 06-01-1994. 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Identifying a small set of marker genes using minimum expected cost of misclassification Artificial Intelligence in Medicine, 55 1, 51-59Duch W.;Swaminathan K.;Meller J. 05-01-2007. Artificial intelligence approaches for rational drug design and discovery Current Pharmaceutical Design, 13 14, 1497-1508Sadhasivam S.;Chidambaran V.;Zhang X.;Meller J.;Esslinger H.;Zhang K.;Martin L.;McAuliffe J. 04-25-2015. Opioid-induced respiratory depression: ABCB1 transporter pharmacogenetics Pharmacogenomics Journal, 15 2, 119-126Mikhaylova O.;Stratton Y.;Hall D.;Kellner E.;Ehmer B.;Drew A.F.;Gallo C.A.;Plas D.R.;Biesiada J.;Meller J.;Czyzyk-Krzeska M.F. 04-17-2012. VHL-Regulated MiR-204 Suppresses Tumor Growth through Inhibition of LC3B-Mediated Autophagy in Renal Cancer Cell, 21 4, 532-546Mohanty S.;Donnelly B.;Lobeck I.;Walther A.;Dupree P.;Coots A.;Meller J.;McNeal M.;Sestak K.;Tiao G. 04-01-2017. The SRL peptide of rhesus rotavirus VP4 protein governs cholangiocyte infection and the murine model Hepatology, 65 4, 1278-1292Tan M.;Xia M.;Chen Y.;Bu W.;Hedge R.;Meller J.;Li X.;Jiang X. 04-01-2009. Conservation of carbohydrate binding interfaces - Evidence of human HBGA selection in norovirus evol PLoS ONE, 4 4, Mikhaylova O.;Ignacak M.;Barankiewicz T.;Harbaugh S.;Yi Y.;Maxwell P.;Schneider M.;Van Geyte K.;Carmeliet P.;Revelo M.;Wyder M.;Greis K.;Meller J.;Czyzyk-Krzeska M. 04-01-2008. The von Hippel-Lindau tumor suppressor protein and Egl-9-type proline hydroxylases regulate the larg Molecular and Cellular Biology, 28 8, 2701-2717Czyzyk-Krzeska M.;Meller J. 04-01-2004. Von Hippel-Lindau tumor suppressor: Not only HIF's executioner Trends in Molecular Medicine, 10 4, 146-149Sinha A.;Meller J. 03-26-2007. Cinteny: Flexible analysis and visualization of synteny and genome rearrangements in multiple organi BMC Bioinformatics, 8 , Sinha AU, Meller J. 03-2007. 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Traumatic brain injury induces alterations in cortical glutamate uptake without a reduction in gluta Journal of Neurotrauma, 34 1, 220-234Chen S.;Meller J.;Elber R. 01-01-2016. Comprehensive analysis of sequences of a protein switch Protein Science, 25 1, 135-146Lauf P.;Alqahtani T.;Flues K.;Meller J.;Adragna N. 01-01-2015. Interaction between Na-K-ATPase and Bcl-2 proteins BclXL and Bak American Journal of Physiology - Cell Physiology, 308 1, C51-C60Sadhasivam S.;Zhang X.;Chidambaran V.;Mavi J.;Pilipenko V.;Mersha T.;Meller J.;Kaufman K.;Martin L.;McAuliffe J. 01-01-2015. Novel associations between FAAH genetic variants and postoperative central opioid-related adverse ef Pharmacogenomics Journal, 15 5, 436-442Tam N.;Zhang X.;Xiao H.;Song D.;Levin L.;Meller J.;Ho S. 01-01-2015. Increased susceptibility of estrogen-induced bladder outlet obstruction in a novel mouse model Laboratory Investigation, 95 5, 546-560Walther A.;Mohanty S.;Donnelly B.;Coots A.;Lages C.;Lobeck I.;Dupree P.;Meller J.;McNeal M.;Sestak K.;Tiao G. 01-01-2015. Rhesus rotavirus VP4 sequence-specific activation of mononuclear cells is associated with cholangiop American Journal of Physiology - Gastrointestinal and Liver Physiology, 309 6, G466-G474Biesiada J.;Chidambaran V.;Wagner M.;Zhang X.;Martin L.;Meller J.;Sadhasivam S. 01-01-2014. Genetic risk signatures of opioid-induced respiratory depression following pediatric tonsillectomy Pharmacogenomics, 15 14, 1749-1762Dong Z.;Meller J.;Succop P.;Wang J.;Wikenheiser-Brokamp K.;Starnes S.;Lu S. 01-01-2014. 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