Digital Genomics Staff

Digital Genomics was co-founded by John Obenauer and Perdeep Mehta, who each previously managed the bioinformatics core facility at St. Jude Children's Research Hospital in Memphis, Tennessee. Both have experience analyzing next-generation sequencing data, expression and genotyping microarrays, assembly and alignment of Sanger sequences, phylogenetics, motif detection, pathway analysis, database development, and other bioinformatics methods. To request a project with Digital Genomics, contact us at info@digitalgenomics.net, or at either of these phone numbers: (901) 634-3562, or (901) 268-2494.



John C. Obenauer, Ph.D.
Chief Executive Officer
Email: obenauer@digitalgenomics.net
Phone: (901) 634-3562 Cell
CV: Obenauer CV


Perdeep K. Mehta, Ph.D.
President
Email: mehta@digitalgenomics.net
Phone: (901) 268-2494 Cell
CV: Mehta CV

Dr. John Obenauer has a Ph.D. in Biochemistry from Brandeis University, where he studied protein nuclear magnetic resonance (NMR) of iron-sulfur proteins. He followed that with a postdoctoral fellowship in bioinformatics at the Massachusetts Institute of Technology, where he developed and published Scansite 2.0, a widely used and highly cited website for predicting protein interactions based on binding sequence motifs. In 2003 he moved to St. Jude Children's Research Hospital to join their bioinformatics core facility, eventually becoming the group leader of a staff of 12 scientists and programmers from 2006-2012. He and Perdeep founded Digital Genomics in September 2013.

Publications

  1. Koçer ZA, Obenauer J, Zaraket H, Zhang J, Rehg JE, Russell CJ, Webster RG. Fecal influenza in mammals: selection of novel variants. J Virol. 2013 Aug 21. [Epub ahead of print] PubMed PMID: 23966381.
  2. Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, Loh ML, Devidas M, Wood B, Winter S, Dunsmore KP, Fulton RS, Fulton LL, Hong X, Harris CC, Dooling DJ, Ochoa K, Johnson KJ, Obenauer JC, Evans WE, Pui CH, Naeve CW, Ley TJ, Mardis ER, Wilson RK, Downing JR, Mullighan CG. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature. 2012 Jan 11;481(7380):157-63. doi: 10.1038/nature10725. PubMed PMID: 22237106; PubMed Central PMCID: PMC3267575.
  3. Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer JC, Naeve C, Mardis ER, Wilson RK, Downing JR, Zhang J. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods. 2011 Jun 12;8(8):652-4. doi: 10.1038/nmeth.1628. PubMed PMID: 21666668; PubMed Central PMCID: PMC3527068.
  4. Liu X, Nguyen P, Liu W, Cheng C, Steeves M, Obenauer JC, Ma J, Geiger TL. T cell receptor CDR3 sequence but not recognition characteristics distinguish autoreactive effector and Foxp3(+) regulatory T cells. Immunity. 2009 Dec 18;31(6):909-20. doi: 10.1016/j.immuni.2009.09.023. Epub 2009 Dec 10. PubMed PMID: 20005134; PubMed Central PMCID: PMC2878844.
  5. Galea CA, High AA, Obenauer JC, Mishra A, Park CG, Punta M, Schlessinger A, Ma J, Rost B, Slaughter CA, Kriwacki RW. Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome. J Proteome Res. 2009 Jan;8(1):211-26. doi: 10.1021/pr800308v. PubMed PMID: 19067583; PubMed Central PMCID: PMC2760310.
  6. Hargrove PW, Kepes S, Hanawa H, Obenauer JC, Pei D, Cheng C, Gray JT, Neale G, Persons DA. Globin lentiviral vector insertions can perturb the expression of endogenous genes in beta-thalassemic hematopoietic cells. Mol Ther. 2008 Mar;16(3):525-33. doi: 10.1038/sj.mt.6300394. Epub 2008 Jan 15. PubMed PMID: 18195719.
  7. Krauss S, Obert CA, Franks J, Walker D, Jones K, Seiler P, Niles L, Pryor SP, Obenauer JC, Naeve CW, Widjaja L, Webby RJ, Webster RG. Influenza in migratory birds and evidence of limited intercontinental virus exchange. PLoS Pathog. 2007 Nov;3(11):e167. PubMed PMID: 17997603; PubMed Central PMCID: PMC2065878.
  8. Finkelstein DB, Mukatira S, Mehta PK, Obenauer JC, Su X, Webster RG, Naeve CW. Persistent host markers in pandemic and H5N1 influenza viruses. J Virol. 2007 Oct;81(19):10292-9. Epub 2007 Jul 25. PubMed PMID: 17652405; PubMed Central PMCID: PMC2045501.
  9. Pottier N, Cheok MH, Yang W, Assem M, Tracey L, Obenauer JC, Panetta JC, Relling MV, Evans WE. Expression of SMARCB1 modulates steroid sensitivity in human lymphoblastoid cells: identification of a promoter SNP that alters PARP1 binding and SMARCB1 expression. Hum Mol Genet. 2007 Oct 1;16(19):2261-71. Epub 2007 Jul 5. PubMed PMID: 17616514.
  10. Galea CA, Pagala VR, Obenauer JC, Park CG, Slaughter CA, Kriwacki RW. Proteomic studies of the intrinsically unstructured mammalian proteome. J Proteome Res. 2006 Oct;5(10):2839-48. PubMed PMID: 17022655.
  11. Obenauer JC, Denson J, Mehta PK, Su X, Mukatira S, Finkelstein DB, Xu X, Wang J, Ma J, Fan Y, Rakestraw KM, Webster RG, Hoffmann E, Krauss S, Zheng J, Zhang Z, Naeve CW. Large-scale sequence analysis of avian influenza isolates. Science. 2006 Mar 17;311(5767):1576-80. Epub 2006 Jan 26. PubMed PMID: 16439620.
  12. Wadkins RM, Hyatt JL, Wei X, Yoon KJ, Wierdl M, Edwards CC, Morton CL, Obenauer JC, Damodaran K, Beroza P, Danks MK, Potter PM. Identification and characterization of novel benzil (diphenylethane-1,2-dione) analogues as inhibitors of mammalian carboxylesterases. J Med Chem. 2005 Apr 21;48(8):2906-15. PubMed PMID: 15828829.
  13. Mansfield JH, Harfe BD, Nissen R, Obenauer J, Srineel J, Chaudhuri A, Farzan-Kashani R, Zuker M, Pasquinelli AE, Ruvkun G, Sharp PA, Tabin CJ, McManus MT. MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet. 2004 Oct;36(10):1079-83. Epub 2004 Sep 12. Erratum in: Nat Genet. 2004 Nov;36(11):1238. PubMed PMID: 15361871.
  14. Obenauer JC, Yaffe MB. Computational prediction of protein-protein interactions. Methods Mol Biol. 2004;261:445-68. Review. PubMed PMID: 15064475.
  15. Obenauer JC, Cantley LC, Yaffe MB. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 2003 Jul 1;31(13):3635-41. PubMed PMID: 12824383; PubMed Central PMCID: PMC168990.
  16. Kostic M, Pochapsky SS, Obenauer J, Mo H, Pagani GM, Pejchal R, Pochapsky TC. Comparison of functional domains in vertebrate-type ferredoxins. Biochemistry. 2002 May 14;41(19):5978-89. PubMed PMID: 11993992.
Dr. Perdeep Mehta has a Ph.D. in Biochemical Engineering and Biotechnology from Indian Institute of Technology - Delhi, where he studied microbial oxidation of methane to methanol. He briefly continued the enzymatic assay work with a postdoctoral fellowship at the Dept of Biochemistry in University of Zurich, Switzerland to develop a novel method for aliphatic decarboxylases before switching to an emerging area of Bio-computing in 1990. In 1992 he obtained a postdoctoral fellowship in the European Molecular Biology Laboratory at Heidelberg, Germany to receive a formal training in Bioinformatics, where he developed and published an algorithm to predict the secondary structure of proteins from multiply aligned sequences. He continued the bioinformatics work after returning to University of Zurich, Switzerland in 1994 to develop and publish a novel Family Profile Analysis (FPA) algorithm to detect very distant evolutionary relationships and published several other articles on unknown homologies among a large family of pyridoxal phosphate-dependent enzymes. In 1999 he was recruited to St. Jude Children's Research Hospital to start a bioinformatics core facility that would eventually grow to a staff of 12, and he served as the group leader from 2001-2006. He and John founded Digital Genomics in September 2013.

Publications

  1. Zhao H, Mehta PK, Persons DA. Gene therapy for canine leukocyte adhesion deficiency with lentiviral vectors. Blood, in preparation.
  2. Greene MR, Lockey T, Mehta PK, Kim YS, Eldridge PW, Gray JT, Sorrentino BP. Transduction of human CD34+ repopulating cells with a self-inactivating lentiviral vector for SCID-X1 produced at clinical scale by a stable cell line. Hum Gene Ther Methods. 2012 Oct;23(5):297-308. doi: 10.1089/hgtb.2012.150. Epub 2012 Nov 7. PubMed PMID: 23075105.
  3. Pemble CW 4th, Mehta PK, Mehra S, Li Z, Nourse A, Lee RE, White SW. Crystal structure of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase•dihydropteroate synthase bifunctional enzyme from Francisella tularensis. PLoS One. 2010 Nov 30;5(11):e14165. doi: 10.1371/journal.pone.0014165. PubMed PMID: 21152407; PubMed Central PMCID: PMC2994781.
  4. Zhao H, Pestina TI, Nasimuzzaman M, Mehta P, Hargrove PW, Persons DA. Amelioration of murine beta-thalassemia through drug selection of hematopoietic stem cells transduced with a lentiviral vector encoding both gamma-globin and the MGMT drug-resistance gene. Blood. 2009 Jun 4;113(23):5747-56. doi: 10.1182/blood-2008-10-186684. Epub 2009 Apr 13. PubMed PMID: 19365082; PubMed Central PMCID: PMC2700315.
  5. Finkelstein DB, Mukatira S, Mehta PK, Obenauer JC, Su X, Webster RG, Naeve CW. Persistent host markers in pandemic and H5N1 influenza viruses. J Virol. 2007 Oct;81(19):10292-9. Epub 2007 Jul 25. PubMed PMID: 17652405; PubMed Central PMCID: PMC2045501.
  6. Magdaleno S, Jensen P, Brumwell CL, Seal A, Lehman K, Asbury A, Cheung T, Cornelius T, Batten DM, Eden C, Norland SM, Rice DS, Dosooye N, Shakya S, Mehta P, Curran T. BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol. 2006 Apr;4(4):e86. Epub 2006 Mar 28. PubMed PMID: 16602821; PubMed Central PMCID: PMC1413568.
  7. Obenauer JC, Denson J, Mehta PK, Su X, Mukatira S, Finkelstein DB, Xu X, Wang J, Ma J, Fan Y, Rakestraw KM, Webster RG, Hoffmann E, Krauss S, Zheng J, Zhang Z, Naeve CW. Large-scale sequence analysis of avian influenza isolates. Science. 2006 Mar 17;311(5767):1576-80. Epub 2006 Jan 26. PubMed PMID: 16439620.
  8. Christen P, Mehta PK. From cofactor to enzymes. The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes. Chem Rec. 2001;1(6):436-47. Review. PubMed PMID: 11933250.
  9. Blanco JG, Dervieux T, Edick MJ, Mehta PK, Rubnitz JE, Shurtleff S, Raimondi SC, Behm FG, Pui CH, Relling MV. Molecular emergence of acute myeloid leukemia during treatment for acute lymphoblastic leukemia. Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10338-43. PubMed PMID: 11526240; PubMed Central PMCID: PMC56962.
  10. Ma Z, Morris SW, Valentine V, Li M, Herbrick JA, Cui X, Bouman D, Li Y, Mehta PK, Nizetic D, Kaneko Y, Chan GC, Chan LC, Squire J, Scherer SW, Hitzler JK. Fusion of two novel genes, RBM15 and MKL1, in the t(1;22)(p13;q13) of acute megakaryoblastic leukemia. Nat Genet. 2001 Jul;28(3):220-1. PubMed PMID: 11431691.
  11. Salzmann D, Christen P, Mehta PK, Sandmeier E. Rates of evolution of pyridoxal-5'-phosphate-dependent enzymes. Biochem Biophys Res Commun. 2000 Apr 13;270(2):576-80. PubMed PMID: 10753666.
  12. Mehta PK, Christen P. The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes. Adv Enzymol Relat Areas Mol Biol. 2000;74:129-84. Review. PubMed PMID: 10800595.
  13. Mehta PK, Argos P, Barbour AD, Christen P. Recognizing very distant sequence relationships among proteins by family profile analysis. Proteins. 1999 Jun 1;35(4):387-400. PubMed PMID: 10382666.
  14. Tormay P, Wilting R, Lottspeich F, Mehta PK, Christen P, Böck A. Bacterial selenocysteine synthase--structural and functional properties. Eur J Biochem. 1998 Jun 15;254(3):655-61. PubMed PMID: 9688279.
  15. Mehta PK, Heringa J, Argos P. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%. Protein Sci. 1995 Dec;4(12):2517-25. PubMed PMID: 8580842; PubMed Central PMCID: PMC2143048.
  16. Alexander FW, Sandmeier E, Mehta PK, Christen P. Evolutionary relationships among pyridoxal-5'-phosphate-dependent enzymes. Regio-specific alpha, beta and gamma families. Eur J Biochem. 1994 Feb 1;219(3):953-60. PubMed PMID: 8112347.
  17. Christen P., Mehta P.K., and Sandmeier E. Molecular evolution of pyridoxal 5'-phosphate-dependent enzymes. In "Biochemistry of Vitamin B6 & PQQ", (Eds. G. Marino, G. Sannia and F. Bossa), pp 9-13, 1994.
  18. Mehta PK, Christen P. Homology of 1-aminocyclopropane-1-carboxylate synthase, 8-amino-7-oxononanoate synthase, 2-amino-6-caprolactam racemase, 2,2-dialkylglycine decarboxylase, glutamate-1-semialdehyde 2,1-aminomutase and isopenicillin-N-epimerase with aminotransferases. Biochem Biophys Res Commun. 1994 Jan 14;198(1):138-43. PubMed PMID: 8292015.
  19. Mehta PK, Christen P. A comment on: 'Homology of the NifS family of proteins to a new class of pyridoxal phosphate-dependent enzymes', by Christos Ouzounis and Chris Sander (1993) FEBS Lett. 322, 159-164. FEBS Lett. 1993 Sep 13;330(2):241-2. PubMed PMID: 8365495.
  20. Mehta PK, Hale TI, Christen P. Aminotransferases: demonstration of homology and division into evolutionary subgroups. Eur J Biochem. 1993 Jun 1;214(2):549-61. PubMed PMID: 8513804.
  21. Mehta PK, Christen P. Homology of pyridoxal-5'-phosphate-dependent aminotransferases with the cobC (cobalamin synthesis), nifS (nitrogen fixation), pabC (p-aminobenzoate synthesis) and malY (abolishing endogenous induction of the maltose system) gene products. Eur J Biochem. 1993 Jan 15;211(1-2):373-6. PubMed PMID: 8425548.
  22. Mehta PK, Ghose TK, Mishra S. Methanol biosynthesis by covalently immobilized cells of Methylosinus trichosporium: batch and continuous studies. Biotechnol Bioeng. 1991 Mar 15;37(6):551-6. PubMed PMID: 18600643.
  23. Mehta P.K., Hale T.I., and Christen P. Evolutionary relationships among pyridoxal phosphate-dependent enzymes. In "Enzymes Dependent on Pyridoxal Phosphate and other Carbonyl Compounds as Cofactors", (Eds. T. Fukui, H. Kagamiyama, K. Soda, and H. Wada), pp 35-42, 1991.
  24. Christen P, Jaussi R, Juretic N, Mehta PK, Hale TI, Ziak M. Evolutionary and biosynthetic aspects of aspartate aminotransferase isoenzymes and other aminotransferases. Ann N Y Acad Sci. 1990;585:331-8. Review. PubMed PMID: 2192617.
  25. Mehta PK, Hale TI, Christen P. Evolutionary relationships among aminotransferases. Tyrosine aminotransferase, histidinol-phosphate aminotransferase, and aspartate aminotransferase are homologous proteins. Eur J Biochem. 1989 Dec 8;186(1-2):249-53. PubMed PMID: 2574669.
  26. Kochhar S, Mehta PK, Christen P. Assay for aliphatic amino acid decarboxylases by high-performance liquid chromatography. Anal Biochem. 1989 May 15;179(1):182-5. PubMed PMID: 2667391.
  27. Mehta P.K., Mishra S., and Ghose T.K. Growth kinetics and methanol oxidation in M. trichosporium NCIB 11131. Biotechnol. Appl. Biochem. 1989;11:328-35.
  28. Mehta P.K., Mishra S., and Ghose T.K. Methanol accumulation by resting cells of M. trichosporium. J. Gen. Microb. 1987;33:221-29.