Jarek Meller

Jarek Meller , PhD


Kettering Laboratory Complex
Room 316
160 Panzeca Way
Cincinnati, Ohio 45267
Phone 513-558-1958
Email jaroslaw.meller@uc.edu

Professional Summary

Building upon broad interdisciplinary training, I have been pursuing research at the intersection of data science, informatics and biomedicine. My primary expertise lies in the fields of computational genomics, molecular modeling, and structural bioinformatics.

On the methodological side, with a team of collaborators, we have developed a number of successful prediction methods for structural and functional studies of proteins and their complexes (Adamczak et al., 2004, 2005, 2011, 2016; Porollo and Meller, 2007, 2010; Phatak et al., 2011). I have 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, Pappas et al., 2017). As of January of 2020, these methods and web servers developed by our group, including Sppider, Cinteny and Polyview, have been used by over 100,000 users from many countries.

I have also been involved in multiple high impact collaborative projects in the areas of basic and translational biomedical research. Examples of such interdisciplinary efforts include: sequencing, annotation and functional studies of human pathogens (Cushion et al, 2007; Liu et al., 2012, Walther et al., 2015, Mohanty et al., 2017), identification of markers associated with disease subtypes and clinical outcomes (Zhang et al., 2011; Biesiada et al., 2014, 2015, Chidambaran et al., 2017), modeling of signal transduction pathways in cancer, autoimmunity and brain disorders (Mikhaylova et al., 2012; Stratton et al., 2014, Dorsett et al., 2017), and developing inhibitors of critical protein-protein interactions or signaling events (Bosco et al., 2012; Evelyn et al., 2014, 2015, Liu et al., 2018).

To date, I have published over 100 peer-reviewed contributions, with the ISI Web of Science h-index of >35. I served as PI, co-PI or co-Investigator on multiple NIH-funded and other grants, and I have a considerable experience in coordinating large-scale multidisciplinary projects. See professional profiles at http://scholar.google.com/citations?user=vQguoK4AAAAJ&hl=en and http://www.researcherid.com/rid/A-1971-2011 .

In addition to research related activities, I have been broadly involved in quantitative and computational training efforts within the University of Cincinnati Colleges of Medicine and Engineering and Applied Sciences. I currently serve as the Director of the Division of Biostatistics and Bioinformatics, Director of the PhD Program in Biomedical Informatics, and co-director of the Biomedical Informatics Graduate Certificate Program.


Doctoral Degree: Nicolaus Copernicus University Poland, 1996 (Computational Chemistry)

Postdoctorla Fellowship: Hebrew University Jerusalem, Israel, 1997

Fellowship: Kyoto University Kyoto , Japan, 1998

Postdoctoral Fellowship : Cornell University Ithaca, NY, 2001

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

Research and Practice Interests

My research is focused on computational methods in molecular biology, genomics and biomedicine. 

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,

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

Grant: #R01GM128216 Investigators:Czyzyk-Krzeska, Maria; Greis, Kenneth; Guan, Jun-lin; Meller, Jaroslaw 09-12-2019 -08-31-2023 National Institute of General Medical Sciences Mechanisms of selective autophagy Role:Collaborator $314,708.00 Awarded Level:Federal

Grant: #R01HD109915 Investigators:DeFranco, Emily; Greis, Kenneth; Meller, Jaroslaw; Morrow, Ardythe; Newburg, David; Rivers, Laurie 08-23-2022 -05-31-2027 National Institute of Child Health and Human Development Defining the systems biology of human milk and lactation and the impact of maternal health and environmental exposures Role:Collaborator 789533.00 Awarded Level:Federal

Grant: #R01CA287260 Investigators:Cunningham, John; Czyzyk-Krzeska, Maria; Meller, Jaroslaw; Vest, Katherine 09-20-2023 -08-31-2028 National Cancer Institute Metabolic effects of cooper in renal cancer Role:Collaborator 693769.38 Hold Level:Federal


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

Chidambaran 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 ) ,771-785 More Information

Sullivan 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 ) ,4492-4517 More Information

Liu 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 ) ,749-761 More Information

Qian 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 ) , More Information

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 ) ,173-188 More Information

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 ) ,367-376 More Information

Keenan 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 ) ,13-24 More Information

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 ,212-218 More Information

Koleti 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-D566 More Information

McGuire 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 ) , More Information

Mohanty 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 ) , More Information

Mohanty 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 ) ,1278-1292 More Information

Chidambaran 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 ) ,162-169 More Information

Dorsett 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 ) ,220-234 More Information

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 ) , More Information

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

Kesarwani 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 , More Information

Evelyn 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 ) ,12879-12898 More Information

Sadhasivam 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 ) ,119-126 More Information

Lauf 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-C60 More Information

Tam 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 ) ,546-560 More Information

Sadhasivam 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 ) ,436-442 More Information

Walther 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-G474 More Information

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 ) ,1618-1628 More Information

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 ) ,8773-8783 More Information

Biesiada 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 ) ,1749-1762 More Information

Dong 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 ) ,978-984 More Information

Hall 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 ) ,738-753 More Information

Bastola 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 ) , More Information

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 ) , More Information

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

Lauf 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 + /K + pump revealed .Cellular Physiology and Biochemistry, , 31 (2-3 ) ,257-276 More Information

Porollo 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 ) ,1575-1585 More Information

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

Liu 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 ) ,9899-9910 More Information

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 ) ,51-59 More Information

Mikhaylova 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 ) ,532-546 More Information

Bosco 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 phox.Chemistry and Biology, , 19 (2 ) ,228-242 More Information

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

Adamczak 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 ) ,1807-1818 More Information

Zhang 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 ) ,5794-5798 More Information

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 ) , More Information

Biesiada 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 ) ,497-505 More Information

Phatak 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 ) ,563-573 More Information

Phatak 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 ,307-319 More Information

Shu 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 ) ,6843-6853 More Information

Yi 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 ) ,5142-5152 More Information

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 ,72-78

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

Lam 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 ) , More Information

Shinde 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 ) , More Information

Yang 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 ) ,9595-9607 More Information

Vallat 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 ) ,930-945 More Information

Haffey 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 ) ,121-132 More Information

Tan 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 ) , More Information

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

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 ) ,324-334 More Information

Olshavsky 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 ) ,3111-3121 More Information

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 ) ,2701-2717 More Information

Takatori 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 ) ,23-32 More Information

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 ) ,706-722 More Information

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

Cushion 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 ) , More Information

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

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

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

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

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 ) , More Information

Slaven 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 ) , More Information

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 ) ,7322-7331 More Information

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 ) ,303-309 More Information

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

Adamczak 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 ) ,467-475 More Information

Wagner 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 ) ,355-369 More Information

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 More Information

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

Adamczak 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 ) ,753-767 More Information

Filippi 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 ) ,744-751 More Information

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 More Information

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 More Information

Tan 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 ) ,3201 More Information

Tan 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 ) ,12562-12571 More Information

Turowski 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 ) ,13836-13849 More Information

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 ) ,2706-2711 More Information

Meller 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 ) ,2029-2041 More Information

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

Meller 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 ) ,111-118 More Information

Meller 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 ) ,241-261 More Information

Wan 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 ) ,7853-7866 More Information

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 More Information

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

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

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

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 More Information

Meller 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 ) ,4068-4076 More Information

Meller 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 ) ,440-447 More Information

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

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

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

Wybourne 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 ) ,5999-6003 More Information

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 ) , More Information

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 More Information

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-W93 More Information

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, , More Information


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

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Phone: 513-558-1958