Jaroslaw Meller

Jaroslaw Meller

Graduate Program Director and Associate Professor

Kettering Lab Complex

316

COM EH Bio Meller Lab - 0056

Kettering Laboratory Complex
Room 316
Cincinnati, Ohio 45267

Professional Summary

Building upon broad interdisciplinary training in molecular modeling, computational chemistry, and bioinformatics, Dr. Meller has been pursuing research at the intersection of computational genomics and biomedicine. Dr. Meller has a primary appointment in the Department of Environmental Health, University of Cincinnati College of Medicine, and joint/secondary appointments in the Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, and the School of Electrical Engineering and Computing Systems, University of Cincinnati College of Engineering and Applied Sciences. Dr. Meller has published over 70 original research articles with over 2,500 citations and ISI Web of Science H-index of 30. See professional profiles at http://scholar.google.com/citations?user=vQguoK4AAAAJ&hl=en and http://www.researcherid.com/rid/A-1971-2011 .

Dr. Meller and his group have developed a number of successful methods for the prediction of protein structure, protein-protein interactions and functional hot spots in proteins (Adamczak et al., 2004, 2005; Wagner et al., 2005; Porollo and Meller, 2007, 2010; Adamczak et al., 2011; Phatak et al., 2011). Several web servers developed by the group, including Sable, Sppider, Minnou and Polyview have widely been used, with a total of over 900,000 submissions from more than 30,000 users in many countries. For the development of successful prediction, modeling and visualization tools for structural bioinformatics and functional genomics, Dr. Meller received Ohio Cyber-infrastructure Experimental & Application Research Award. Dr. Meller has also been active in the development and applications of methods for knowledge extraction from high dimensional genomic data (Sinha and Meller, 2008; Shinde et al., 2010; Huang et al., 2012).

Benefiting from a strong emphasis on team science at the University of Cincinnati and Cincinnati Children’s Hospital Medical Center, Dr. Meller and his group have also been involved in many collaborative projects with direct medical relevance. Examples of such interdisciplinary efforts include sequencing and annotation of human pathogens, identification of markers associated with disease subtypes in cancer and autoimmunity, modeling of signal transduction pathways in differentiation and development, developing inhibitors of critical protein-protein interactions in autophagy, bone marrow transplants, and pathogen-host interactions.

Dr. Meller has been broadly involved in quantitative and computational training efforts within UC College of Medicine and College of Engineering and Applied Sciences, leading several inter-departmental and inter-collegiate initiatives in this regard. Dr. Meller serves as the Director of the newly created PhD program in Biomedical Informatics at UC, co-director of the Biomedical Informatics Graduate Certificate Program, and has been involved in several informatics and quantitative training efforts at UC College of Medicine, including T32 Advanced Multidisciplinary Training Program for Systems Biology and T32 Gene-Environment Interactions Training Grant. In addition, Dr. Meller is the co-director of the Bioinformatics Core for the Center of Environmental Genetics at the University of Cincinnati. He also serves as the director of Protein Informatics Core at Cincinnati Children’s Hospital Medical Center.

Education

Doctoral Degree, Nicholas Copernicus University 1996 (Computational Chemistry)

Doctoral Degree, Polish Academy of Sciences 2004 (Biomedical Engineering)

Research Support

Grant: #CHMC 100139 / R01 AR050688 Investigators:Meller, Jaroslaw 09-01-2006 -08-31-2008 National Institute of Arthritis, Musculoskeletal and Skin Disease Genomic Landscapes in Large Scale Integrated JRA Studies Role:PI $66,191.00 Closed Level:Federal

Grant: #CHMC 102680 / R01 AI055649 Investigators:Meller, Jaroslaw 09-01-2006 -01-01-2010 National Institute of Allergy and Infectious Diseases Norwalk-Like Viruses and their Receptors Role:PI $119,894.00 Closed Level:Federal

Grant: #P30 ES006096-16A1 Investigators:Caruso, Joseph; Deka, Ranjan; Embi, Peter; Greis, Kenneth; Ho, Shuk Mei; Lemasters, Grace; Medvedovic, Mario; Meller, Jaroslaw; Nebert, Daniel; Pinney, Susan; Puga, Alvaro; Rohs, Amy; Woo, Daniel 04-01-2008 -03-31-2013 National Institute of Environmental Health Sciences Environmental Genetics Role:Collaborator $8,028,782.00 Active Level:Federal

Grant: #08-S587-027-01-C1 Investigators:Meller, Jaroslaw 06-30-2008 -05-29-2009 Department of the Air Force Computational Modeling of Resilin and Related Polypeptides Role:PI $48,000.00 Active Level:Federal

Grant: #UTA08-479 / R01 GM067823 Investigators:Meller, Jaroslaw 08-01-2008 -08-31-2011 National Institute of General Medical Sciences Optimizing of Folding and Threading Potentials Role:PI $95,259.00 Closed Level:Federal

Grant: #CMMI 0825710 Investigators:Huang, Hongdao Samuel; Meller, Jaroslaw 09-01-2008 -08-31-2012 National Science Foundation Robust and Efficient Knowledge Discovery with Application in Cancer Foundation Role:Collaborator $374,998.00 Closed Level:Federal

Grant: #106338 / 2 P01 HD013021-31A1 Investigators:Meller, Jaroslaw 08-01-2009 -07-31-2014 National Institute of Child Health and Human Development The Role of Human Milk in Infant Nutrition and Health Role:PI $51,362.00 Active Level:Federal

Grant: #1006619 / 3 U01 AI067150-05S1 Investigators:Meller, Jaroslaw 09-01-2009 -03-31-2011 National Institute of Allergy and Infectious Diseases HLA/KIR Region Genetics in Pediatric Arthritis Role:PI $26,395.00 Closed Level:Federal

Grant: #107121 / R56AI055649 Investigators:Meller, Jaroslaw 09-07-2010 -08-31-2011 National Institute of Allergy and Infectious Diseases Norovirus and Their Receptors Role:PI $29,599.00 Closed Level:Federal

Grant: #SRS 007647 Investigators:Czyzyk-Krzeska, Maria; Meller, Jaroslaw 07-01-2011 -04-30-2015 Department of Veterans Affairs Intergovernmental Personnel Act Agreement for Jaroslow Meller Role:Collaborator $34,172.00 Active Level:Federal

Grant: #R01 CA122346 Investigators:Czyzyk-Krzeska, Maria; Meller, Jaroslaw 04-01-2013 -03-31-2018 National Cancer Institute Molecular Mechanisms in Renal Cancer Role:Collaborator $291,425.00 Active Level:Federal

Grant: #P30ES006096 Investigators:Caruso, Joseph; Chen, Aimin; Deka, Ranjan; Greis, Kenneth; Haynes, Erin; Ho, Shuk Mei; Lemasters, Grace; Leung, Yuet Kin; Medvedovic, Mario; Meller, Jaroslaw; Meloncon, Lisa; Pinney, Susan; Porollo, Alexey; Puga, Alvaro; Thomas, Michael; Woo, Daniel; Yadav, Jagjit; Yancey, Elissa 04-01-2013 -03-31-2018 National Institute of Environmental Health Sciences Environmental Genetics Role:Collaborator $1,743,768.00 Active Level:Federal

Grant: #T32 GM105526 Investigators:Meller, Jaroslaw; Montrose, Marshall 07-01-2013 -06-30-2016 National Institute of General Medical Sciences Advanced Multidisciplinary Training Program for Systems Biology Role:Collaborator $86,681.00 Active Level:Federal

Grant: #R21AI097936 Investigators:Meller, Jaroslaw; Porollo, Alexey 08-06-2013 -07-31-2015 National Institute of Allergy and Infectious Diseases Norovirus Capsid: A Novel Drug Target Role:PI $197,749.00 Awarded Level:Federal

Grant: #W81XWH-14-1-0347 / CA130028 Investigators:Czyzyk-Krzeska, Maria; Medvedovic, Mario; Meller, Jaroslaw 09-30-2014 -09-29-2016 Department of the Army Medical Research Acquisition Activity CA130028-Effects of Tobacco Smoke (TS) on growth of clear cell renal cell carcinoma (ccRCC) Role:Collaborator $474,562.00 Awarded Level:Federal

Grant: #0255-7855-4609 / U54 HL127624 Investigators:Medvedovic, Mario; Meller, Jaroslaw; Sivaganesan, Siva 09-29-2014 -04-30-2019 National Heart, Lung and Blood Institute Data Coordination and Integration Center for LINCS-BD2K Role:Collaborator $609,822.00 Active Level:Federal

Grant: #R21ES024807 Investigators:Bernstein, David; Grinshpun, Sergey; Meller, Jaroslaw; Reponen, Tiina 09-30-2015 -09-29-2017 National Institute of Environmental Health Sciences Traffic-related air pollutants and respiratory tract microbiome in children Role:Collaborator $217,917.00 Awarded Level:Federal

Grant: #R21MH107916 Investigators:Funk, Adam; Greis, Kenneth; McCullumsmith, Robert; Meller, Jaroslaw 05-13-2016 -04-30-2018 National Institute of Mental Health Proteomic analysis of the postsynaptic density-95 interactome in schizophrenia Role:Collaborator $237,000.00 Awarded Level:Federal

Grant: #R01MH107487 Investigators:McCullumsmith, Robert; Meller, Jaroslaw 07-15-2016 -04-30-2021 National Institute of Mental Health Cell-specific analysis of sub-kinomes in schizophrenia Role:Collaborator $395,000.00 Active Level:Federal

Grant: #137687 / R01HD089458 Investigators:Meller, Jaroslaw 01-01-2017 -08-31-2017 National Institute of Child Health and Human Development Pharmacogenetics of Opioids, Reducing Persistent Postoperative Pain and Opioid Dependence Role:PI $12,008.00 Awarded Level:Federal

Grant: #IN4682013UC / R01HD089458 Investigators:Meller, Jaroslaw 09-01-2017 -08-31-2018 National Institute of Child Health and Human Development Pharmacogenetics of Oxycodone, Personalized Care and Persistent Surgical Pain Role:PI $9,474.00 Active Level:Federal

Grant: #2003-UC-15 BRTT-01-A0-S0-E0 Investigators:Brackenbury, Robert; Meller, Jaroslaw 07-01-2002 -06-30-2019 Ohio Department of Higher Education Functional Genomics in Biomedical Research Role:PI $175,000.00 Active Level:State of Ohio

Grant: #F-2019-39 / R01MH107487 Investigators:Meller, Jaroslaw 01-01-2019 -04-30-2021 National Institutes of Health Cell-specific analysis of sub-kinomes in schizophrenia Role:PI $36,701.00 Awarded Level:Federal

Grant: #306131 / R01DK091566 Investigators:Meller, Jaroslaw 01-01-2019 -12-31-2022 National Inst of Diabetes and Digestive and Kidney Disease Genetic basis of virus induced Biliary Atresia Role:PI $8,526.00 Awarded Level:Federal

Grant: #0255-C015-4609 / U54HL127624 Investigators:Medvedovic, Mario; Meller, Jaroslaw; Sivaganesan, Siva 07-01-2019 -06-30-2020 National Institute of Allergy and Infectious Diseases Data Coordination and Integration Center for LINCS-BD2K Role:Collaborator $551,515.00 Active Level:Federal

Publications

Peer Reviewed Publications

Adamczak R, Porollo A, Meller J. (09-2004. )Accurate prediction of solvent accessibility using neural networks-based regression. Proteins., ,56 (4 ),753

Adamczak R, Porollo A, Meller J. (05-2005. )Combining prediction of secondary structure and solvent accessibility in proteins. Proteins., ,59 (3 ),467

Porollo A, Meller J. (02-2007. )Prediction-based fingerprints of protein-protein interactions .Proteins., ,66 (3 ),630

Sinha AU, Meller J. (03-2007. )Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics., ,8 (82 ),

Cao 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 ),303

Chen X.; Chidambaran V.; Geisler K.; Ji H.; Meller J.; Stubbeman B.; Weirauch M.; Zhang X. (07-01-2019. )Enrichment of Genomic Pathways Based on Differential DNA Methylation Associated With Chronic Postsur.Journal of Pain, ,20 (7 ),771-785

Alganem K.; Bentea E.; DePasquale E.; Funk A.; Haroutunian V.; Katsel P.; McCullumsmith R.; Meller J.; Mielnik C.; O’Donovan S.; Ramsey A.; Sullivan C.; Wen Z. (06-01-2019. )Connectivity Analyses of Bioenergetic Changes in Schizophrenia: Identification of Novel Treatments.Molecular Neurobiology, ,56 (6 ),4492-4517

A. Ryan M.; Du W.; Evelyn C.; Florian M.; Geiger H.; Guo F.; Liu W.; Meller J.; Nassar N.; Pang Q.; Rayes A.; Setchell K.; Shang X.; Wang L.; Zhao X.; Zheng Y. (03-01-2019. )Rational identification of a Cdc42 inhibitor presents a new regimen for long-term hematopoietic stem.Leukemia, ,33 (3 ),749-761

Chen Y.; Jiang X.; Li X.; Meller J.; Qian Y.; Rao Z.; Song M.; Tan M.; Xia M. (01-01-2019. )Structural adaptations of norovirus GII.17/13/21 lineage through two distinct evolutionary paths.Journal of Virology, ,93 (1 ),

Bai B.; Bentea E.; Depasquale E.; McCullumsmith R.; Meador-Woodruff J.; Meller J.; Ming G.; O'Donovan S.; Peng J.; Simmons M.; Song H.; Sullivan C.; Wen Z.; Xu C.; Zhou Y. (01-01-2019. )Kinase network dysregulation in a human induced pluripotent stem cell model of DISC1 schizophrenia.Molecular Omics, ,15 (3 ),173-188

Beutner K.; Biesiada J.; Gourraud P.; Hollenbach J.; Leslie S.; Lizee A.; Mack S.; Maiers M.; Meller J.; Motyer A.; Pappas D.; Paunic V.; Taylor K.; Vukcevic D.; Zhao L.; Zheng X. (05-22-2018. )Significant variation between SNP-based HLA imputations in diverse populations: The last mile is the.Pharmacogenomics Journal, ,18 (3 ),367-376

Adam M.; Azeloglu E.; Banuelos M.; Birtwistle M.; Bucher E.; Casale M.; Chung C.; Clark N.; Cooper D.; Coye A.; Daigle G.; Dane M.; Dardov V.; Dohlman A.; Erickson S.; Escalante-Chong R.; Fallahi-Sichani M.; Fazel M.; Feiler H.; Finkbiener S.; Forlin M.; Fraenkel E.; Golub T.; Gray J.; Gray N.; Gross S.; Hafner M.; Haston K.; He E.; Heiser L.; Ho R.; Hussain U.; Iyengar R.; Jaffe J.; Jagodnik K.; Jenkins S.; Kalra J.; Kaye J.; Keenan A.; Koch R.; Koleti A.; Koplev S.; Korkola J.; Kouril M.; Kuleshov M.; LaBarge M.; Lachmann A.; Lenail A.; Li J.; Lim R.; Lin J.; Ma'ayan A.; Mahi N.; Mandefro B.; Matlock A.; Medvedovic M.; Meller J.; Milani P.; Mills C.; Mills G.; Muhlich J.; Nederlof M.; Niepel M.; Niu W.; Ornelas L.; Osterloh J.; Papanastasiou M.; Pilarczyk M.; Ramamoorthy D.; Reichard J.; Ren Y.; Rothstein J.; Sachs K.; Sareen D.; Schürer S.; Shamsaei B.; Shamu C.; Silverstein M.; Sivaganesan S.; Sobie E.; Sorger P.; Stathias V.; Stocksdale J.; Subramanian A.; Sudar D.; Svendsen C.; Terryn R.; Thompson L.; Thompson T.; Torre D.; Van Eyk J.; Vasiliauskas J.; Venkatraman V.; Vidovic D.; Wang Z.; White S.; Williams E.; Wrobel D.; Wu J.; Zhang L. (01-24-2018. )The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of .Cell Systems, ,6 (1 ),13-24

Chew G.; Coombs K.; Green B.; Indugula R.; Meller J.; Reponen T.; Shamsaei B.; Taft D.; Ward D. (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 ,212-218

Allen B.; Chung C.; Clark N.; Cooper D.; D'Urso A.; Fazel M.; Forlin M.; Jagodnik K.; Jenkins S.; Kelley T.; Koleti A.; Ma'Ayan A.; Mader C.; Mahi N.; Medvedovic M.; Meller J.; Niu W.; Pilarczyk M.; Pillai A.; Reichard J.; Schürer S.; Shamsaei B.; Stathias V.; Terryn R.; Torre D.; Turner J.; Vasiliauskas J.; VidoviÄ ‡ D.; Wang L. (01-01-2018. )Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: Integra.Nucleic Acids Research, ,46 (D1 ),D558-D566

Depasquale E.; Funk A.; Hammond J.; Hartounian V.; Hasselfeld K.; Marwaha S.; McCullumsmith R.; McGuire J.; Meador-Woodruff J.; Meller J.; O'Donnovan S. (12-01-2017. )Abnormalities of signal transduction networks in chronic schizophrenia.npj Schizophrenia, ,3 (1 ),

Donnelly B.; Dupree P.; Lobeck I.; McNeal M.; Meller J.; Mohanty S.; Mowery S.; 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 ),

Coots A.; Donnelly B.; Dupree P.; Lobeck I.; McNeal M.; Meller J.; Mohanty S.; Sestak K.; Tiao G.; Walther A. (04-01-2017. )The SRL peptide of rhesus rotavirus VP4 protein governs cholangiocyte infection and the murine model.Hepatology, ,65 (4 ),1278-1292

Chidambaran V.; Fukuda T.; Martin L.; Meller J.; Mizuno T.; Niu J.; Sadhasivam S.; Venkatasubramanian R.; Vinks A.; Zhang X. (03-01-2017. )ABCC3 genetic variants are associated with postoperative morphine-induced respiratory depression and.Pharmacogenomics Journal, ,17 (2 ),162-169

Depasquale E.; Dorsett C.; Floyd C.; McCullumsmith R.; McGuire J.; Meller J.; Niedzielko T. (01-01-2017. )Traumatic brain injury induces alterations in cortical glutamate uptake without a reduction in gluta.Journal of Neurotrauma, ,34 (1 ),220-234

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 ),

Chen S.; Elber R.; Meller J. (01-01-2016. )Comprehensive analysis of sequences of a protein switch.Protein Science, ,25 (1 ),135-146

Azam M.; Biesiada J.; Evelyn C.; Huber E.; Kesarwani M.; Kincaid Z.; Meller J.; Rance M.; Shah N.; Thapa M.; Zheng Y. (09-30-2015. )Targeting substrate-site in Jak2 kinase prevents emergence of genetic resistance.Scientific Reports, ,5 ,

Biesiada J.; Duan X.; Evelyn C.; Meller J.; Nelson S.; Papoian R.; Seibel W.; Shang X.; Tang H.; Zheng Y. (05-15-2015. )Combined rational design and a high throughput screening platform for identifying chemical inhibitor.Journal of Biological Chemistry, ,290 (20 ),12879-12898

Chidambaran V.; Esslinger H.; Martin L.; McAuliffe J.; Meller J.; Sadhasivam S.; Zhang K.; Zhang X. (04-25-2015. )Opioid-induced respiratory depression: ABCB1 transporter pharmacogenetics.Pharmacogenomics Journal, ,15 (2 ),119-126

Adragna N.; Alqahtani T.; Flues K.; Lauf P.; Meller J. (01-01-2015. )Interaction between Na-K-ATPase and Bcl-2 proteins BclXL and Bak.American Journal of Physiology - Cell Physiology, ,308 (1 ),C51-C60

Ho S.; Levin L.; Meller J.; Song D.; Tam N.; Xiao H.; Zhang X. (01-01-2015. )Increased susceptibility of estrogen-induced bladder outlet obstruction in a novel mouse model.Laboratory Investigation, ,95 (5 ),546-560

Chidambaran V.; Kaufman K.; Martin L.; Mavi J.; McAuliffe J.; Meller J.; Mersha T.; Pilipenko V.; Sadhasivam S.; Zhang X. (01-01-2015. )Novel associations between FAAH genetic variants and postoperative central opioid-related adverse ef.Pharmacogenomics Journal, ,15 (5 ),436-442

Coots A.; Donnelly B.; Dupree P.; Lages C.; Lobeck I.; McNeal M.; Meller J.; Mohanty S.; Sestak K.; Tiao G.; Walther A. (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-G474

Biesiada J.; Duan X.; Evelyn C.; Meller J.; Seibel W.; Zheng Y. (12-18-2014. )Rational Design of Small Molecule Inhibitors Targeting the Ras GEF, SOS1.Chemistry and Biology, ,21 (12 ),1618-1628

Johansson E.; Meller J.; Reponen T.; 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 ),8773-8783

Biesiada J.; Chidambaran V.; Martin L.; Meller J.; Sadhasivam S.; Wagner M.; Zhang X. (01-01-2014. )Genetic risk signatures of opioid-induced respiratory depression following pediatric tonsillectomy.Pharmacogenomics, ,15 (14 ),1749-1762

Dong Z.; Lu S.; Meller J.; Starnes S.; Succop P.; Wang J.; Wikenheiser-Brokamp K. (01-01-2014. )Secretory phospholipase A2-IIa upregulates HER/HER2-elicited signaling in lung cancer cells.International Journal of Oncology, ,45 (3 ),978-984

Abplanalp W.; Biesiada J.; Cost N.; Czyzyk-Krzeska M.; Ehmer B.; Hall D.; Harteneck C.; Hegde S.; Kellner E.; Meller J.; Mikhaylova O.; Pandey R.; Plas D.; Stratton Y. (01-01-2014. )TRPM3 and miR-204 Establish a Regulatory Circuit that Controls Oncogenic Autophagy in Clear Cell Ren.Cancer Cell, ,26 (5 ),738-753

Bastola P.; Biesiada J.; Czyzyk-Krzeska M.; Kellner E.; Medvedovic M.; Meller J.; Mikhaylova O.; Sartor M.; Stratton Y.; Yi Y. (07-29-2013. )Folliculin Contributes to VHL Tumor Suppressing Activity in Renal Cancer through Regulation of Autop.PLoS ONE, ,8 (7 ),

Chhabra M.; Dai Y.; Jiang X.; Meller J.; Tan M.; Zhang X. (07-19-2013. )Inhibition of Histo-blood Group Antigen Binding as a Novel Strategy to Block Norovirus Infections.PLoS ONE, ,8 (7 ),

Jiang X.; Meller J.; Wei C. (02-05-2013. )Substrate specificity of Tulane virus protease.Virology, ,436 (1 ),24-32

Adragna N.; Alter G.; Brown T.; Heiny J.; Koikov L.; Lauf P.; Lepera M.; Meller J. (01-01-2013. )Canonical Bcl-2 motifs of the Na + /K + pump revealed .Cellular Physiology and Biochemistry, ,31 (2-3 ),257-276

Cushion M.; Jaiswal V.; Joshi Y.; Meller J.; Porollo A.; Smulian A. (12-03-2012. )Analysis of current antifungal agents and their targets within the pneumocystis carinii genome.Current Drug Targets, ,13 (12 ),1575-1585

Biesiada J.; Meller J.; Porollo A. (11-12-2012. )On setting up and assessing docking simulations for virtual screening.Methods in Molecular Biology, ,928 ,1-16

Biesiada J.; Castello A.; Huang P.; Jiang B.; Jiang X.; Liu Y.; Meller J.; Tan M. (09-01-2012. )Rotavirus VP8*: Phylogeny, host range, and interaction with histo-blood group antigens.Journal of Virology, ,86 (18 ),9899-9910

Huang S.; Meller J.; Mo D.; Wagner M. (05-01-2012. )Identifying a small set of marker genes using minimum expected cost of misclassification.Artificial Intelligence in Medicine, ,55 (1 ),51-59

Biesiada J.; Czyzyk-Krzeska M.; Drew A.; Ehmer B.; Gallo C.; Hall D.; Kellner E.; Meller J.; Mikhaylova O.; Plas D.; Stratton Y. (04-17-2012. )VHL-Regulated MiR-204 Suppresses Tumor Growth through Inhibition of LC3B-Mediated Autophagy in Renal.Cancer Cell, ,21 (4 ),532-546

Biesiada J.; Bosco E.; Filippi M.; Kordos M.; Kumar S.; Marchioni F.; Meller J.; Mizrahi A.; Pick E.; Seibel W.; Szczur K.; Zheng Y. (02-24-2012. )Rational design of small molecule inhibitors targeting the Rac GTPase-p67 phox.Chemistry and Biology, ,19 (2 ),228-242

Czyzyk-Krzeska M.; Meller J.; Plas D. (01-01-2012. )Not all autophagy is equal.Autophagy, ,8 (7 ),1155-1156

Adamczak R.; Meller J.; Pillardy J.; Vallat B. (12-01-2011. )Fast geometric consensus approach for protein model quality assessment.Journal of Computational Biology, ,18 (12 ),1807-1818

Filipovich A.; Johnson J.; Jordan M.; Kissell D.; Klein P.; Marsh R.; Meller J.; Risma K.; Villanueva J.; Wei Q.; Zhang K. (11-24-2011. )Hypomorphic mutations in PRF1, MUNC13-4, and STXBP2 are associated with adult-onset familial HLH.Blood, ,118 (22 ),5794-5798

Anderson M.; Ferguson D.; Jänicke R.; Johansson E.; Meller J.; Miller M.; Plas D.; Zhang Y. (09-30-2011. )Identification of a conserved anti-apoptotic protein that modulates the mitochondrial apoptosis path.PLoS ONE, ,6 (9 ),

Biesiada J.; Kouril M.; Meller J.; Porollo A.; Velayutham P. (01-01-2011. )Survey of public domain software for docking simulations and virtual screening.Human Genomics, ,5 (5 ),497-505

Adamczak R.; Cao B.; Meller J.; Phatak M.; Wagner M. (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 ),563-573

Meller J.; Phatak M. (12-01-2010. )Model quality assessment in membrane proteins using predicted lipid accessibility profiles .11th International Symposium on Artificial Intelligence and Mathematics, ISAIM 2010, ,

Adamczak R.; Meller J.; Porollo A.; Swaminathan K. (12-01-2010. )Enhanced prediction of conformational flexibility and phosphorylation in proteins.Advances in Experimental Medicine and Biology, ,680 ,307-319

Guo P.; Meller J.; Petrenko R.; Shu D.; Zhang H. (11-23-2010. )Dual-channel single-molecule fluorescence resonance energy transfer to establish distance parameters.ACS Nano, ,4 (11 ),6843-6853

Alshaikh E.; Bastola P.; Biesiada J.; Czyzyk-Krzeska M.; Levin L.; Mamedova A.; Meller J.; Mikhaylova O.; Sheridan R.; Yi Y. (11-01-2010. )Von Hippel-Lindau-dependent patterns of RNA polymerase II hydroxylation in human renal clear cell ca.Clinical Cancer Research, ,16 (21 ),5142-5152

Agata K.; Maki N.; Martinson J.; Meller J.; Nishimura O.; Tarui H.; Tsonis P. (08-20-2010. )Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequenc .Molecular Vision, ,16 ,72-78

Meller J.; Porollo A. (05-26-2010. )POLYVIEW-MM: Web-based platform for animation and analysis of molecular simulations.Nucleic Acids Research, ,38 (SUPPL. 2 ),

Babu C.; Ho S.; Isaac J.; Lam Y.; Meller J.; Yuan Y. (02-05-2010. )Comprehensive identification and modified-site mapping of S-nitrosylated targets in prostate epithel.PLoS ONE, ,5 (2 ),

Chen J.; Ghosh K.; Hu Z.; Johannes F.; Li Q.; Medvedovic M.; Meller J.; Phatak M.; Shinde K.; Vineet J. (01-13-2010. )Genomics Portals: Integrative web-platform for mining genomics data.BMC Genomics, ,11 (1 ),

Huang P.; Jiang X.; Lee B.; Meller J.; Pang X.; Tan M.; Wang T.; Xia M.; Yang Y.; Zhong W. (01-01-2010. )Genetic and phenotypic characterization of GII-4 noroviruses that circulated during 1987 to 2008.Journal of Virology, ,84 (18 ),9595-9607

Blom T.; Cao B.; Elber R.; Májek P.; Meller J.; Pillardy J.; Vallat B. (09-01-2009. )Building and assessing atomic models of proteins from structural templates: Learning and benchmarks.Proteins: Structure, Function and Bioinformatics, ,76 (4 ),930-945

Czyzyk-Krzeska M.; Greis K.; Haffey W.; Meller J.; Mikhaylova O.; Yi Y. (06-10-2009. )iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylas.Advances in Enzyme Regulation, ,49 (1 ),121-132

Bu W.; Chen Y.; Hedge R.; Jiang X.; Li X.; Meller J.; Tan M.; Xia M. (04-01-2009. )Conservation of carbohydrate binding interfaces - Evidence of human HBGA selection in norovirus evol.PLoS ONE, ,4 (4 ),

Meller J.; Sinha A. (12-01-2008. )Sensitivity analysis for reversal distance and breakpoint reuse in genome rearrangements .Pacific Symposium on Biocomputing 2008, PSB 2008, ,37-48

Cao S.; Farkas T.; Hegde R.; Huang P.; Jiang X.; Li X.; Meller J.; Rao Z.; Tan M.; Xia M. (09-30-2008. )Elucidation of strain-specific interaction of a GII-4 norovirus with HBGA receptors by site-directed.Virology, ,379 (2 ),324-334

Burd C.; Comstock C.; Groh E.; Knudsen K.; Meller J.; Morey L.; Olshavsky N.; Revelo M.; Wang Y. (05-15-2008. )Cyclin D3 action in androgen receptor regulation and prostate cancer.Oncogene, ,27 (22 ),3111-3121

Barankiewicz T.; Carmeliet P.; Czyzyk-Krzeska M.; Greis K.; Harbaugh S.; Ignacak M.; Maxwell P.; Meller J.; Mikhaylova O.; Revelo M.; Schneider M.; Van Geyte K.; Wyder M.; Yi Y. (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 ),2701-2717

Chen L.; Geh E.; Meller J.; Takatori A.; Xia Y.; Zhang L. (01-01-2008. )Differential transmission of MEKK1 morphogenetic signals by JNK1 and JNK2.Development, ,135 (1 ),23-32

Howarth J.; Meller J.; Rosevear P.; Solaro R.; Trewhella J. (10-26-2007. )Phosphorylation-dependent Conformational Transition of the Cardiac Specific N-Extension of Troponin .Journal of Molecular Biology, ,373 (3 ),706-722

Meller J.; Porollo A. (08-29-2007. )Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D.BMC Bioinformatics, ,8 ,

Adamczak R.; Arnold J.; Cushion M.; Meller J.; Porollo A.; Sesterhenn T.; Slaven B.; Smulian A.; Staben C. (05-09-2007. )Transcriptome of Pneumocystis carinii during fulminate infection: Carbohydrate metabolism and the co.PLoS ONE, ,2 (5 ),

Duch W.; Meller J.; Swaminathan K. (05-01-2007. )Artificial intelligence approaches for rational drug design and discovery.Current Pharmaceutical Design, ,13 (14 ),1497-1508

Meller J.; Sinha A. (03-26-2007. )Cinteny: Flexible analysis and visualization of synteny and genome rearrangements in multiple organi.BMC Bioinformatics, ,8 ,

Meller J.; Porollo A. (02-15-2007. )Prediction-based fingerprints of protein-protein interactions.Proteins: Structure, Function and Genetics, ,66 (3 ),630-645

Meller J.; Wagner M. (01-01-2007. )Machine learning techniques for bioinformatics: Fundamentals and applications .Computational Methods in Biomedical Research, ,46-71

Cushion M.; Meller J.; Porollo A.; Sesterhenn T.; Slaven B.; Smulian A. (11-01-2006. )Large-scale characterization of introns in the Pneumocystis carinii genome.Journal of Eukaryotic Microbiology, ,53 (SUPPL. 1 ),

Cushion M.; Meller J.; Porollo A.; Sesterhenn T.; Slaven B.; Smulian A. (11-01-2006. )Draft assembly and annotation of the Pneumocystis carinii genome.Journal of Eukaryotic Microbiology, ,53 (SUPPL. 1 ),

Jiang X.; Meller J.; Tan M. (08-01-2006. )C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein.Journal of Virology, ,80 (15 ),7322-7331

Adamczak R.; Cao B.; Jarrell M.; Meller J.; Porollo A. (02-01-2006. )Enhanced recognition of protein transmembrane domains with prediction-based structural profiles.Bioinformatics, ,22 (3 ),303-309

Ivanenkov V.; Kirley T.; Meller J. (06-28-2005. )Characterization of disulfide bonds in human nucleoside triphosphate diphosphohydrolase 3 (NTPDase3).Biochemistry, ,44 (25 ),8998-9012

Adamczak R.; Meller J.; Porollo A. (05-15-2005. )Combining prediction of secondary structure and solvent accessibility in proteins.Proteins: Structure, Function and Genetics, ,59 (3 ),467-475

Adamczak R.; Meller J.; Porollo A.; Wagner M. (05-10-2005. )Linear regression models for solvent accessibility prediction in proteins.Journal of Computational Biology, ,12 (3 ),355-369

Burd C.; Diehl J.; Gladden A.; Knudsen K.; Meller J.; Moghadam H.; Petre-Draviam C.; Williams E. (01-13-2005. )A central domain of cyclin D1 mediates nuclear receptor corepressor activity.Oncogene, ,24 (3 ),431-444

Adamczak R.; Meller J.; Porollo A. (10-12-2004. )POLYVIEW: A flexible visualization tool for structural and functional annotations of proteins.Bioinformatics, ,20 (15 ),2460-2462

Adamczak R.; Meller J.; Porollo A. (09-01-2004. )Accurate prediction of solvent accessibility using neural networks-based regression.Proteins: Structure, Function and Genetics, ,56 (4 ),753-767

Filippi M.; Gu Y.; Harris C.; Meller J.; Williams D.; Zheng Y. (07-01-2004. )Localization of Rac2 via the C terminus and aspartic acid 150 specifies superoxide generation, actin.Nature Immunology, ,5 (7 ),744-751

Adamczak 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. ),1291-1305

Czyzyk-Krzeska M.; Meller J. (04-01-2004. )Von Hippel-Lindau tumor suppressor: Not only HIF's executioner.Trends in Molecular Medicine, ,10 (4 ),146-149

Farkas T.; Huang P.; Jiang X.; Meller J.; Tan M.; Zhong W. (03-01-2004. )Erratum: Mutations within the P2 Domain of Norovirus Capsid Affect Binding to Human Histo-Blood Grou.Journal of Virology, ,78 (6 ),3201

Farkas T.; Huang P.; Jiang X.; Meller J.; Tan M.; Zhong W. (12-01-2003. )Mutations within the P2 Domain of Norovirus Capsid Affect Binding to Human Histo-Blood Group Antigen.Journal of Virology, ,77 (23 ),12562-12571

Hosoya K.; Ikegami T.; Kimata K.; Meller J.; Tanaka N.; Thornton E.; Turowski M.; Yamakawa N. (11-12-2003. )Deuterium Isotope Effects on Hydrophobic Interactions: The Importance of Dispersion Interactions in .Journal of the American Chemical Society, ,125 (45 ),13836-13849

Conaway J.; Conaway R.; Czyzyk-Krzeska M.; Ignacak M.; Kuznetsova A.; Meller J.; Nash J.; Sanchez Y.; Schnell P. (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 ),2706-2711

Heully J.; Malrieu J.; Meller J. (01-01-2003. )Size-consistent multireference configuration interaction method through the dressing of the norm of .Molecular Physics, ,101 (13 ),2029-2041

Elber R.; Meller J. (12-01-2002. )Protein recognition by sequence-tostructure fitness: Bridging efficiency and capacity of threading m .Advances in Chemical Physics, ,120 ,77-130

Elber R.; Meller J.; Wagner M. (01-15-2002. )Maximum feasibility guideline in the design and analysis of protein folding potentials.Journal of Computational Chemistry, ,23 (1 ),111-118

Elber R.; Meller J. (11-15-2001. )Linear programming optimization and a double statistical filter for protein threading protocols.Proteins: Structure, Function and Genetics, ,45 (3 ),241-261

Ehara M.; Hada M.; Meller J.; Nakatsuji H.; Wan J. (11-08-2000. )Electronic excitation spectra of furan and pyrrole: Revisited by the symmetry adapted cluster-config.Journal of Chemical Physics, ,113 (18 ),7853-7866

Alpert K.; Cong B.; Elber R.; Frary A.; Grandillo S.; Liu J.; Meller J.; Nesbitt T.; Tanksley S.; Van Der Knaap E. (07-07-2000. )fw2.2: A quantitative trait locus key to the evolution of tomato fruit size.Science, ,289 (5476 ),85-88

Elber 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 ),909-911

Duch W.; Meller J. (01-01-1999. )SGA derivation of matrix elements between spin-adapted perturbative wave functions.International Journal of Quantum Chemistry, ,74 (2 ),123-133

Elber R.; Meller J. (01-01-1998. )Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of.Biophysical Journal, ,74 (2 I ),789-802

Adamowicz 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 ),619-626

Caballol R.; Malrieu J.; Meller J. (01-01-1996. )State-specific coupled cluster-type dressing of multireference singles and doubles configuration int.Journal of Chemical Physics, ,104 (11 ),4068-4076

Heully J.; Malrieu J.; Meller J. (10-13-1995. )Multireference self-consistent size-consistent configuration interaction method. A few applications .Chemical Physics Letters, ,244 (5-6 ),440-447

Ingarden R.; Meller J. (06-01-1994. )Temperatures in linguistics as a model of thermodynamics.Open Systems & Information Dynamics, ,2 (2 ),211-230

Heully J.; Malrieu J.; Meller J. (02-11-1994. )Size-consistent self-consistent combination of selected CI and perturbation theory.Chemical Physics Letters, ,218 (3 ),276-282

Duch W.; Meller J. (01-01-1994. )On multireference superdirect configuration interaction in third order.International Journal of Quantum Chemistry, ,50 (4 ),243-271

Meller J.; Wybourne B. (12-01-1992. )Enumeration of the order-14 invariants formed from the Riemann tensor.Journal of Physics A: Mathematical and General, ,25 (22 ),5999-6003

Positions and Work Experience

2001 -2005 Assistant Professor, Cincinnati Children's Hospital Medical Center,

2005 -2006 Associate Professor, Cincinnati Children's Hospital Medical Center,

2007 -2012 Associate Professor, University of Cincinnati,

Post Graduate Training and Education

1996-1997 postdoctoral fellow, Hebrew University, ,Israel

1997-1998 JSPS fellow, Kyoto University, ,Japan

1999-2001 postdoctoral fellow, Cornell University, ,USA

Keywords

bioinformatics, biomedical informatics, computational biology, prediction methods, predictive fingerprints of disease states, protein structure and function, membrane proteins, gene finding and annotation, bioinformatics and computational biology courses

Research and Practice Interests

My research is focused on computational methods in molecular biology and genomics. In short, what we are doing may be classified either as computational biology or bioinformatics, with significant component of pattern recognition and machine learning. We are pursuing research on fundamental problems, such as protein folding process and protein-protein interactions. On a more practical side, we are also interested in developing bioinformatics tools, e.g. for protein structure and function recognition or gene annotation. We are also developing methods for identification of predictive fingerprints of disease states that aim at finding correlation between multiple genomic and clinical attributes with disease states, progression and treatment response. In collaboration with biologists, biochemists and physicians, we are applying standard and our own methods to particular problems at hands.

Contact Information

Academic - Kettering Laboratory Complex
Room 316
Cincinnati  Ohio, 45267
Phone: 513-558-1958
jaroslaw.meller@uc.edu