Praveen Sethupathy, Ph.D. - Publications

Affiliations: 
2008 University of Pennsylvania, Philadelphia, PA, United States 
Area:
Bioinformatics Biology, Genetics, Computer Science

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

Year Citation  Score
2016 Irani S, Pan X, Peck BC, Iqbal J, Sethupathy P, Hussain MM. MicroRNA-30c Mimic Mitigates Hypercholesterolemia and Atherosclerosis in Mice. The Journal of Biological Chemistry. PMID 27365390 DOI: 10.1074/jbc.M116.728451  0.48
2016 Sollome J, Martin E, Sethupathy P, Fry RC. Environmental Contaminants and microRNA Regulation: Transcription Factors as Regulators of Toxicant-Altered microRNA Expression. Toxicology and Applied Pharmacology. PMID 27292125 DOI: 10.1016/j.taap.2016.06.009  0.48
2016 Peck BC, Sincavage J, Feinstein S, Mah AT, Simmons JG, Lund PK, Sethupathy P. miR-30 family controls proliferation and differentiation of intestinal epithelial cell models by directing a broad gene expression program that includes SOX9 and the ubiquitin ligase pathway. The Journal of Biological Chemistry. PMID 27261459 DOI: 10.1074/jbc.M116.733733  0.48
2016 Sethupathy P. The Promise and Challenge of Therapeutic MicroRNA Silencing in Diabetes and Metabolic Diseases. Current Diabetes Reports. 16: 52. PMID 27112956 DOI: 10.1007/s11892-016-0745-3  0.48
2015 Swahari V, Nakamura A, Baran-Gale J, Garcia I, Crowther AJ, Sons R, Gershon TR, Hammond S, Sethupathy P, Deshmukh M. Essential Function of Dicer in Resolving DNA Damage in the Rapidly Dividing Cells of the Developing and Malignant Cerebellum. Cell Reports. PMID 26748703 DOI: 10.1016/j.celrep.2015.12.037  0.48
2015 Baran-Gale J, Kurtz CL, Erdos MR, Sison C, Young A, Fannin EE, Chines PS, Sethupathy P. Addressing Bias in Small RNA Library Preparation for Sequencing: A New Protocol Recovers MicroRNAs that Evade Capture by Current Methods. Frontiers in Genetics. 6: 352. PMID 26734062 DOI: 10.3389/fgene.2015.00352  0.48
2015 Selitsky SR, Dinh TA, Toth CL, Kurtz CL, Honda M, Struck BR, Kaneko S, Vickers KC, Lemon SM, Sethupathy P. Transcriptomic Analysis of Chronic Hepatitis B and C and Liver Cancer Reveals MicroRNA-Mediated Control of Cholesterol Synthesis Programs. Mbio. 6. PMID 26646011 DOI: 10.1128/mBio.01500-15  0.48
2015 Roman TS, Marvelle AF, Fogarty MP, Vadlamudi S, Gonzalez AJ, Buchkovich ML, Huyghe JR, Fuchsberger C, Jackson AU, Wu Y, Civelek M, Lusis AJ, Gaulton KJ, Sethupathy P, Kangas AJ, et al. Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol. American Journal of Human Genetics. 97: 801-15. PMID 26637976 DOI: 10.1016/j.ajhg.2015.10.016  0.48
2015 Selitsky SR, Sethupathy P. tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data. Bmc Bioinformatics. 16: 354. PMID 26530785 DOI: 10.1186/s12859-015-0800-0  0.48
2015 Reid LM, Sethupathy P. The DNAJB1-PRKACA chimera: Candidate biomarker and therapeutic target for fibrolamellar carcinomas. Hepatology (Baltimore, Md.). PMID 26505878 DOI: 10.1002/hep.28307  0.48
2015 Oikawa T, Wauthier E, Dinh TA, Selitsky SR, Reyna-Neyra A, Carpino G, Levine R, Cardinale V, Klimstra D, Gaudio E, Alvaro D, Carrasco N, Sethupathy P, Reid LM. Model of fibrolamellar hepatocellular carcinomas reveals striking enrichment in cancer stem cells. Nature Communications. 6: 8070. PMID 26437858 DOI: 10.1038/ncomms9070  0.48
2015 Rutledge H, Baran-Gale J, de Villena FP, Chesler EJ, Churchill GA, Sethupathy P, Kelada SN. Identification of microRNAs associated with allergic airway disease using a genetically diverse mouse population. Bmc Genomics. 16: 633. PMID 26303911 DOI: 10.1186/s12864-015-1732-9  0.48
2015 Kurtz CL, Fannin EE, Toth CL, Pearson DS, Vickers KC, Sethupathy P. Inhibition of miR-29 has a significant lipid-lowering benefit through suppression of lipogenic programs in liver. Scientific Reports. 5: 12911. PMID 26246194 DOI: 10.1038/srep12911  0.48
2015 Peck BC, Weiser M, Lee SE, Gipson GR, Iyer VB, Sartor RB, Herfarth HH, Long MD, Hansen JJ, Isaacs KL, Trembath DG, Rahbar R, Sadiq TS, Furey TS, Sethupathy P, et al. MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility. Inflammatory Bowel Diseases. PMID 26164662 DOI: 10.1097/MIB.0000000000000478  0.48
2015 Welch JD, Baran-Gale J, Perou CM, Sethupathy P, Prins JF. Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential. Bmc Genomics. 16: 113. PMID 25765044 DOI: 10.1186/s12864-015-1227-8  0.48
2015 Selitsky SR, Baran-Gale J, Honda M, Yamane D, Masaki T, Fannin EE, Guerra B, Shirasaki T, Shimakami T, Kaneko S, Lanford RE, Lemon SM, Sethupathy P. Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C. Scientific Reports. 5: 7675. PMID 25567797 DOI: 10.1038/srep07675  0.48
2014 Franceschini N, Hu Y, Reiner AP, Buyske S, Nalls M, Yanek LR, Li Y, Hindorff LA, Cole SA, Howard BV, Stafford JM, Carty CL, Sethupathy P, Martin LW, Lin DY, et al. Prospective associations of coronary heart disease loci in African Americans using the MetaboChip: the PAGE study. Plos One. 9: e113203. PMID 25542012 DOI: 10.1371/journal.pone.0113203  0.48
2014 Vickers KC, Landstreet SR, Levin MG, Shoucri BM, Toth CL, Taylor RC, Palmisano BT, Tabet F, Cui HL, Rye KA, Sethupathy P, Remaley AT. MicroRNA-223 coordinates cholesterol homeostasis. Proceedings of the National Academy of Sciences of the United States of America. 111: 14518-23. PMID 25246565 DOI: 10.1073/pnas.1215767111  0.48
2014 Vencken SF, Sethupathy P, Blackshields G, Spillane C, Elbaruni S, Sheils O, Gallagher MF, O'Leary JJ. An integrated analysis of the SOX2 microRNA response program in human pluripotent and nullipotent stem cell lines. Bmc Genomics. 15: 711. PMID 25156079 DOI: 10.1186/1471-2164-15-711  0.48
2014 Collins AL, Kim Y, Bloom RJ, Kelada SN, Sethupathy P, Sullivan PF. Transcriptional targets of the schizophrenia risk gene MIR137. Translational Psychiatry. 4: e404. PMID 24984191 DOI: 10.1038/tp.2014.42  0.48
2014 Kurtz CL, Peck BC, Fannin EE, Beysen C, Miao J, Landstreet SR, Ding S, Turaga V, Lund PK, Turner S, Biddinger SB, Vickers KC, Sethupathy P. MicroRNA-29 fine-tunes the expression of key FOXA2-activated lipid metabolism genes and is dysregulated in animal models of insulin resistance and diabetes. Diabetes. 63: 3141-8. PMID 24722248 DOI: 10.2337/db13-1015  0.48
2014 Tabet F, Vickers KC, Cuesta Torres LF, Wiese CB, Shoucri BM, Lambert G, Catherinet C, Prado-Lourenco L, Levin MG, Thacker S, Sethupathy P, Barter PJ, Remaley AT, Rye KA. HDL-transferred microRNA-223 regulates ICAM-1 expression in endothelial cells. Nature Communications. 5: 3292. PMID 24576947 DOI: 10.1038/ncomms4292  0.48
2013 Furey TS, Sethupathy P. Genetics. Genetics driving epigenetics. Science (New York, N.Y.). 342: 705-6. PMID 24202168 DOI: 10.1126/science.1246755  0.48
2013 Baran-Gale J, Fannin EE, Kurtz CL, Sethupathy P. Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes. Plos One. 8: e73240. PMID 24039891 DOI: 10.1371/journal.pone.0073240  0.48
2013 Sethupathy P. Illuminating microRNA Transcription from the Epigenome. Current Genomics. 14: 68-77. PMID 23997652 DOI: 10.2174/138920213804999183  0.48
2013 Kelada S, Sethupathy P, Okoye IS, Kistasis E, Czieso S, White SD, Chou D, Martens C, Ricklefs SM, Virtaneva K, Sturdevant DE, Porcella SF, Belkaid Y, Wynn TA, Wilson MS. miR-182 and miR-10a are key regulators of Treg specialisation and stability during Schistosome and Leishmania-associated inflammation. Plos Pathogens. 9: e1003451. PMID 23825948 DOI: 10.1371/journal.ppat.1003451  0.48
2013 Bulik-Sullivan B, Selitsky S, Sethupathy P. Prioritization of genetic variants in the microRNA regulome as functional candidates in genome-wide association studies. Human Mutation. 34: 1049-56. PMID 23595788 DOI: 10.1002/humu.22337  0.48
2013 Vickers KC, Sethupathy P, Baran-Gale J, Remaley AT. Complexity of microRNA function and the role of isomiRs in lipid homeostasis. Journal of Lipid Research. 54: 1182-91. PMID 23505317 DOI: 10.1194/jlr.R034801  0.48
2013 Sethupathy P. Needles in the genetic haystack of lipid disorders: single nucleotide polymorphisms in the microRNA regulome. Journal of Lipid Research. 54: 1168-73. PMID 23505316 DOI: 10.1194/jlr.R035766  0.48
2013 Peters U, North KE, Sethupathy P, Buyske S, Haessler J, Jiao S, Fesinmeyer MD, Jackson RD, Kuller LH, Rajkovic A, Lim U, Cheng I, Schumacher F, Wilkens L, Li R, et al. A systematic mapping approach of 16q12.2/FTO and BMI in more than 20,000 African Americans narrows in on the underlying functional variation: results from the Population Architecture using Genomics and Epidemiology (PAGE) study. Plos Genetics. 9: e1003171. PMID 23341774 DOI: 10.1371/journal.pgen.1003171  0.48
2013 Paredes SH, Melgar MF, Sethupathy P. Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index. Bioinformatics (Oxford, England). 29: 1485-7. PMID 23047559 DOI: 10.1093/bioinformatics/bts596  0.48
2013 Vickers KC, Shoucri BM, Levin MG, Wu H, Pearson DS, Osei-Hwedieh D, Collins FS, Remaley AT, Sethupathy P. MicroRNA-27b is a regulatory hub in lipid metabolism and is altered in dyslipidemia. Hepatology (Baltimore, Md.). 57: 533-42. PMID 22777896 DOI: 10.1002/hep.25846  0.48
2012 Avery CL, Sethupathy P, Buyske S, He Q, Lin DY, Arking DE, Carty CL, Duggan D, Fesinmeyer MD, Hindorff LA, Jeff JM, Klein L, Patton KK, Peters U, Shohet RV, et al. Fine-mapping and initial characterization of QT interval loci in African Americans. Plos Genetics. 8: e1002870. PMID 22912591 DOI: 10.1371/journal.pgen.1002870  0.48
2012 Bonner SM, Pietropaolo SL, Fan Y, Chang Y, Sethupathy P, Morran MP, Beems M, Giannoukakis N, Trucco G, Palumbo MO, Solimena M, Pugliese A, Polychronakos C, Trucco M, Pietropaolo M. Sequence variation in promoter of Ica1 gene, which encodes protein implicated in type 1 diabetes, causes transcription factor autoimmune regulator (AIRE) to increase its binding and down-regulate expression. The Journal of Biological Chemistry. 287: 17882-93. PMID 22447927 DOI: 10.1074/jbc.M111.319020  0.48
2012 Valdmanis PN, Gu S, Schüermann N, Sethupathy P, Grimm D, Kay MA. Expression determinants of mammalian argonaute proteins in mediating gene silencing. Nucleic Acids Research. 40: 3704-13. PMID 22210886 DOI: 10.1093/nar/gkr1274  0.48
2011 Melgar MF, Collins FS, Sethupathy P. Discovery of active enhancers through bidirectional expression of short transcripts. Genome Biology. 12: R113. PMID 22082242 DOI: 10.1186/gb-2011-12-11-r113  0.48
2011 Stone N, Pangilinan F, Molloy AM, Shane B, Scott JM, Ueland PM, Mills JL, Kirke PN, Sethupathy P, Brody LC. Bioinformatic and genetic association analysis of microRNA target sites in one-carbon metabolism genes. Plos One. 6: e21851. PMID 21765920 DOI: 10.1371/journal.pone.0021851  0.48
2011 Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S. Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Molecular Biology and Evolution. 28: 2615-27. PMID 21478372 DOI: 10.1093/molbev/msr085  0.48
2010 Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ, Margulies EH, Boehnke M, Furey TS, Crawford GE, et al. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metabolism. 12: 443-55. PMID 21035756 DOI: 10.1016/j.cmet.2010.09.012  0.48
2010 Dupuis J, Langenberg C, Prokopenko I, Saxena R, Soranzo N, Jackson AU, Wheeler E, Glazer NL, Bouatia-Naji N, Gloyn AL, Lindgren CM, Mägi R, Morris AP, Randall J, Johnson T, ... ... Sethupathy P, et al. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nature Genetics. 42: 105-16. PMID 20081858 DOI: 10.1038/ng.520  0.48
2010 Megraw M, Sethupathy P, Gumireddy K, Jensen ST, Huang Q, Hatzigeorgiou AG. Isoform specific gene auto-regulation via miRNAs: A case study on miR-128b and ARPP-21 Theoretical Chemistry Accounts. 125: 593-598. DOI: 10.1007/s00214-009-0647-4  0.48
2009 Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, ... ... Sethupathy P, et al. The completion of the Mammalian Gene Collection (MGC). Genome Research. 19: 2324-33. PMID 19767417 DOI: 10.1101/gr.095976.109  0.48
2009 Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, et al. Accurate microRNA target prediction correlates with protein repression levels. Bmc Bioinformatics. 10: 295. PMID 19765283 DOI: 10.1186/1471-2105-10-295  0.48
2009 Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences of the United States of America. 106: 9362-7. PMID 19474294 DOI: 10.1073/pnas.0903103106  0.48
2009 Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG. The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Research. 37: D155-8. PMID 18957447 DOI: 10.1093/nar/gkn809  0.48
2008 Sethupathy P, Hannenhalli S. A tutorial of the poisson random field model in population genetics. Advances in Bioinformatics. 257864. PMID 19920987 DOI: 10.1155/2008/257864  1
2008 Sethupathy P, Giang H, Plotkin JB, Hannenhalli S. Genome-wide analysis of natural selection on human cis-elements. Plos One. 3: e3137. PMID 18781197 DOI: 10.1371/journal.pone.0003137  0.48
2008 Sethupathy P, Collins FS. MicroRNA target site polymorphisms and human disease. Trends in Genetics : Tig. 24: 489-97. PMID 18778868 DOI: 10.1016/j.tig.2008.07.004  0.48
2008 Zhang L, Volinia S, Bonome T, Calin GA, Greshock J, Yang N, Liu CG, Giannakakis A, Alexiou P, Hasegawa K, Johnstone CN, Megraw MS, Adams S, Lassus H, Huang J, ... ... Sethupathy P, et al. Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer. Proceedings of the National Academy of Sciences of the United States of America. 105: 7004-9. PMID 18458333 DOI: 10.1073/pnas.0801615105  0.48
2008 Gartner JJ, Sethupathy P, Hatzigeorgiou AG, Fraser NW. Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature. 451: 600. PMID 18235505 DOI: 10.1038/nature06621  0.48
2007 Sethupathy P, Borel C, Gagnebin M, Grant GR, Deutsch S, Elton TS, Hatzigeorgiou AG, Antonarakis SE. Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes. American Journal of Human Genetics. 81: 405-13. PMID 17668390 DOI: 10.1086/519979  0.48
2007 Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K. Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science (New York, N.Y.). 315: 1137-40. PMID 17322061 DOI: 10.1126/science.1138050  0.48
2007 Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG. miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Research. 35: D149-55. PMID 17108354 DOI: 10.1093/nar/gkl904  0.48
2007 Sethupathy P, Megraw M, Hatzigeorgiou AG. Computational approaches to elucidate miRNA biology Micrornas: From Basic Science to Disease Biology. 187-198. DOI: 10.1017/CBO9780511541766.016  0.48
2006 Sethupathy P, Megraw M, Hatzigeorgiou AG. A guide through present computational approaches for the identification of mammalian microRNA targets. Nature Methods. 3: 881-6. PMID 17060911 DOI: 10.1038/nmeth954  0.48
2006 Gupta A, Gartner JJ, Sethupathy P, Hatzigeorgiou AG, Fraser NW. Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature. 442: 82-5. PMID 16738545 DOI: 10.1038/nature04836  0.48
2006 Cleland TA, Sethupathy P. Non-topographical contrast enhancement in the olfactory bulb. Bmc Neuroscience. 7: 7. PMID 16433921 DOI: 10.1186/1471-2202-7-7  0.48
2006 Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets. Rna (New York, N.Y.). 12: 192-7. PMID 16373484 DOI: 10.1261/rna.2239606  0.48
2005 Sethupathy P, Megraw M, Barrasa MI, Hatzigeorgiou AG. Computational identification of regulatory factors involved in MicroRNA transcription Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3746: 457-468. DOI: 10.1007/11573036_43  0.48
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