Publications

Drug Discovery

  1. Discovery of substituted 4-aminoquinazolines as selective Toll-like receptor 4 ligands.
    Nour A, Hayashi T, Chan M, Yao S, Tawatao RI, Crain B, Tsigelny IF, Kouznetsova VL, Ahmadiiveli A, Messer K, Pu M, Corr M, Carson DA, Cottam HB.
    Bioorg Med Chem Lett. 2014 Sep 22.
    pii: S0960-894X(14)00981-0. doi: 10.1016/j.bmcl.2014.09.039. [Epub ahead of print]
    PMID: 25288184 [PubMed - as supplied by publisher]
  2. Neuroprotective effects of the anti-cancer drug Sunitinib in models of HIV- neurotoxicity: potential for drug repositioning for the treatment of neurodegenerative disorders.
    Wrasidlo W, Crews LA, Tsigelny IF, Stocking E, Kouznetsova VL, Price D, Paulino A, Gonzales T, Overk CR, Patrick C, Rockenstein E, Masliah E.
    Br J Pharmacol. 2014 Aug 13.
    doi: 10.1111/bph.12875. [Epub ahead of print]
    PMID: 25117211 [PubMed - as supplied by publisher]
  3. Development of a pharmacophore model for the catecholamine release-inhibitory peptide catestatin: virtual screening and functional testing identify novel small molecule therapeutics of hypertension.
    Tsigelny IF, Kouznetsova VL, Biswas N, Mahata SK, O'Connor DT.
    Bioorg Med Chem. 2013 Sep 15;21(18):5855–5869.
    doi: 10.1016/j.bmc.2013.07.008. Epub 2013 Jul 17.
    PMID: 23916146 [PubMed - indexed for MEDLINE]
     
  4. Identification of substituted pyrimido[5,4-b]indoles as selective Toll-like receptor 4 ligands.
    Chan M, Hayashi T, Mathewson RD, Nour A, Hayashi Y, Yao S, Tawatao RI, Crain B, Tsigelny IF, Kouznetsova VL, Messer K, Pu M, Corr M, Carson DA, Cottam HB.
    J Med Chem. 2013 Jun 13;56(11):4206–4223.
    doi: 10.1021/jm301694x. Epub 2013 May 24.
    PMID: 23656327 [PubMed - indexed for MEDLINE]  Free PMC Article
  5. Elucidation of common pharmacophores from analysis of targeted metabolites transported by the multispecific drug transporter-Organic anion transporter1 (Oat1).
    Kouznetsova VL, Tsigelny IF, Nagle MA, Nigam SK.
    Bioorg Med Chem. 2011 Jun 1;19(11):3320–3340.
    doi: 10.1016/j.bmc.2011.04.045. Epub 2011 Apr 28.
    PMID: 21571536 [PubMed - indexed for MEDLINE]  Free PMC Article
  6. Untargeted metabolomics identifies enterobiome metabolites and putative uremic toxins as substrates of organic anion transporter 1 (Oat1).
    Wikoff WR, Nagle MA, Kouznetsova VL, Tsigelny IF, Nigam SK.
    J Proteome Res. 2011 Jun 3;10(6):2842–2851.
    doi: 10.1021/pr200093w. Epub 2011 Apr 22.
    PMID: 21476605 [PubMed - indexed for MEDLINE]  Free PMC Article
  7. Synthesis of 5-(6-hydroxy-7H-purine-8-ylthio)- 2-(N-hydroxyformamido)pentanoic acid.
    Zhang Y, Elliot G, Saldanha A, Tsigelny I, Carson D, Wrasidlo W.
    Beilstein J Org Chem. 2010 Sep 1;6:742–747.
    doi: 10.3762/bjoc.6.93.
    PMID: 20978615 [PubMed]  Free PMC Article
  8. Disruption of angiogenesis and tumor growth with an orally active drug that stabilizes the inactive state of PDGFRbeta/B-RAF.
    Murphy EA, Shields DJ, Stoletov K, Dneprovskaia E, McElroy M, Greenberg JI, Lindquist J, Acevedo LM, Anand S, Majeti BK, Tsigelny I,, Saldanha A, Walsh B, Hoffman RM, Bouvet M, Klemke RL, Vogt PK, Arnold L, Wrasidlo W, Cheresh DA.
    Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4299–4304.
    doi: 10.1073/pnas.0909299107. Epub 2010 Feb 12.
    PMID: 20154271 [PubMed - indexed for MEDLINE]  Free PMC Article
  9. Interaction of organic cations with organic anion transporters.
    Ahn SY, Eraly SA, Tsigelny I, Nigam SK.
    J Biol Chem. 2009 Nov 6;284(45):31422–31430.
    doi: 10.1074/jbc.M109.024489. Epub 2009 Sep 8.
    PMID: 19737926 [PubMed - indexed for MEDLINE]  Free PMC Article
  10. Inactivation of an invertebrate acetylcholinesterase by sulfhydryl reagents: a reconsideration of the implications for insecticide design.
    Rowland M, Tsigelny I, Wolfe M, Pezzementi L.
    Chem Biol Interact. 2008 Sep 25;175(1-3):73–75.
    doi: 10.1016/j.cbi.2008.02.006. Epub 2008 Feb 23.
    PMID: 18384763 [PubMed - indexed for MEDLINE]  Free PMC Article
  11. Inactivation of an invertebrate acetylcholinesterase by sulfhydryl reagents: the roles of two cysteines in the catalytic gorge of the enzyme.
    Pezzementi L, Rowland M, Wolfe M, Tsigelny I.
    Invert Neurosci
    . 2006 Jun;6(2):47–55. Epub 2006 Apr 4.
    PMID: 16586114 [PubMed - indexed for MEDLINE]

Protein Structure Analysis and Prediction

  1. Structural diversity of Alzheimer's disease amyloid-β dimers and their role in oligomerization and fibril formation.
    Tsigelny IF, Sharikov Y, Kouznetsova VL, Greenberg JP, Wrasidlo W, Gonzalez T, Desplats P, Michael SE, Trejo-Morales M, Overk CR, Masliah E.
    J Alzheimers Dis. 2014;39(3):583–600.
    doi: 10.3233/JAD-131589.
    PMID: 24240640 [PubMed - indexed for MEDLINE]
  2. p75 neurotrophin receptor is a clock gene that regulates oscillatory components of circadian and metabolic networks.
    Baeza-Raja B, Eckel-Mahan K, Zhang L, Vagena E, Tsigelny IF, Sassone-Corsi P, Ptácek LJ, Akassoglou K.
    J Neurosci. 2013 Jun 19;33(25):10221–10234.
    doi: 10.1523/JNEUROSCI.2757-12.2013.
    PMID: 23785138 [PubMed - indexed for MEDLINE]
    Free PMC Article
  3. An all-atom model of the structure of human copper transporter 1.
    Tsigelny IF, Sharikov Y, Greenberg JP, Miller MA, Kouznetsova VL, Larson CA, Howell SB.
    Cell Biochem Biophys. 2012 Jul;63(3):223–234.
    doi: 10.1007/s12013-012-9358-x.
    PMID: 22569840 [PubMed - indexed for MEDLINE]  Free PMC Article
  4. Role of α-synuclein penetration into the membrane in the mechanisms of oligomer pore formation.
    Tsigelny IF, Sharikov Y, Wrasidlo W, Gonzalez T, Desplats PA, Crews L, Spencer B, Masliah E.
    FEBS J. 2012 Mar;279(6):1000–1013.
    doi: 10.1111/j.1742-4658.2012.08489.x.  Epub 2012 Feb 27.
    PMID: 22251432 [PubMed - indexed for MEDLINE]  Free PMC Article
  5. Conformational changes of the multispecific transporter organic anion transporter 1 (OAT1/SLC22A6) suggests a molecular mechanism for initial stages of drug and metabolite transport.
    Tsigelny IF, Kovalskyy D, Kouznetsova VL, Balinskyi O, Sharikov Y, Bhatnagar V, Nigam SK.
    Cell Biochem Biophys. 2011 Nov;61(2):251–259.
    doi: 10.1007/s12013-011-9191-7.
    PMID: 21499753 [PubMed - indexed for MEDLINE]
  6. Cell-to-cell transmission of non-prion protein aggregates.
    Lee SJ, Desplats P, Sigurdson C, Tsigelny I
    , Masliah E.
    Nat Rev Neurol. 2010 Dec;6(12):702-6. doi: 10.1038/nrneurol.2010.145.
    Epub 2010 Oct 12.
    Erratum in: Nat Rev Neurol. 2011 Jan;7(1):5.
    PMID: 21045796 [PubMed - indexed for MEDLINE]
  7. Tetramerization domain mutations in KCNA5 affect channel kinetics and cause abnormal trafficking patterns.
    Burg ED, Platoshyn O, Tsigelny IF, Lozano-Ruiz B, Rana BK, Yuan JX.
    Am J Physiol Cell Physiol. 2010 Mar;298(3):C496–C509.
    doi: 10.1152/ajpcell.00464.2009. Epub 2009 Dec 16.
    PMID: 20018952 [PubMed - indexed for MEDLINE]  Free PMC Article
  8. Interaction of organic cations with organic anion transporters.
    Ahn SY, Eraly SA, Tsigelny I, Nigam SK.
    J Biol Chem. 2009 Nov 6;284(45):31422–31430.
    doi: 10.1074/jbc.M109.024489. Epub 2009 Sep 8.
    PMID: 19737926 [PubMed - indexed for MEDLINE]  Free PMC Article
  9. Role of synucleins in Alzheimer's disease.
    Crews L, Tsigelny I, Hashimoto M, Masliah E.
    Neurotox Res. 2009 Oct;16(3):306–317.
    doi: 10.1007/s12640-009-9073-6. Epub 2009 Jun 24.
    PMID: 19551456 [PubMed - indexed for MEDLINE]  Free PMC Article
  10. Modeling of glycerol-3-phosphate transporter suggests a potential 'tilt' mechanism involved in its function.
    Tsigelny IF, Greenberg J, Kouznetsova V, Nigam SK.
    J Bioinform Comput Biol. 2008 Oct;6(5):885–904.
    PMID: 18942157 [PubMed - indexed for MEDLINE]  Free PMC Article
  11. Mechanisms of hybrid oligomer formation in the pathogenesis of combined Alzheimer's and Parkinson's diseases.
    Tsigelny IF, Crews L, Desplats P, Shaked GM, Sharikov Y, Mizuno H, Spencer B, Rockenstein E, Trejo M, Platoshyn O, Yuan JX, Masliah E.
    PLoS One. 2008 Sep 4;3(9):e3135.
    doi: 10.1371/journal.pone.0003135.
    PMID: 18769546 [PubMed - indexed for MEDLINE]  Free PMC Article
  12. Thermal denaturation of wild type and mutant recombinant acetylcholinesterase from amphioxus: effects of the temperature of in vitro expression and of reversible inhibitors.
    Perrin B, Rowland M, Wolfe M, Tsigelny I, Pezzementi L.
    Invert Neurosci. 2008 Sep;8(3):147–155.
    doi: 10.1007/s10158-008-0075-5. Epub 2008 Aug 2.
    PMID: 18677525 [PubMed - indexed for MEDLINE]  Free PMC Article
  13. Mechanism of alpha-synuclein oligomerization and membrane interaction: theoretical approach to unstructured proteins studies.
    Tsigelny IF, Sharikov Y, Miller MA, Masliah E.
    Nanomedicine. 2008 Dec;4(4):350–357.
    doi: 10.1016/j.nano.2008.05.005. Epub 2008 Jul 18.
    PMID: 18640077 [PubMed - indexed for MEDLINE]  Free PMC Article
     
  14. Acetylcholinesterase from the invertebrate Ciona intestinalis is capable of assembling into asymmetric forms when co-expressed with vertebrate collagenic tail peptide.
    Frederick A, Tsigelny I, Cohenour F, Spiker C, Krejci E, Chatonnet A, Bourgoin S, Richards G, Allen T, Whitlock MH, Pezzementi L.
    FEBS J. 2008 Mar;275(6):1309–1322.
    doi: 10.1111/j.1742-4658.2008.06292.x. Epub 2008 Feb 12.
    PMID: 18279391 [PubMed - indexed for MEDLINE]
  15. MAPAS: a tool for predicting membrane-contacting protein surfaces.
    Sharikov Y, Walker RC, Greenberg J, Kouznetsova V, Nigam SK, Miller MA, Masliah E, Tsigelny IF.
    Nat Methods. 2008 Feb;5(2):119.
    doi: 10.1038/nmeth0208-119. No abstract available.
    PMID: 18235431 [PubMed - indexed for MEDLINE]
  16. Fibrinogen signal transduction as a mediator and therapeutic target in inflammation: lessons from multiple sclerosis.
    Adams RA, Schachtrup C, Davalos D, Tsigelny I, Akassoglou K.
    Curr Med Chem. 2007;14(27):2925–2936. Review.
    PMID: 18045138 [PubMed - indexed for MEDLINE]
  17. p75 neurotrophin receptor regulates tissue fibrosis through inhibition of plasminogen activation via a PDE4/cAMP/PKA pathway.
    Sachs BD, Baillie GS, McCall JR, Passino MA, Schachtrup C, Wallace DA, Dunlop AJ, MacKenzie KF, Klussmann E, Lynch MJ, Sikorski SL, Nuriel T, Tsigelny I, Zhang J, Houslay MD, Chao MV, Akassoglou K.
    J Cell Biol. 2007 Jun 18;177(6):1119–1132.
    PMID: 17576803 [PubMed - indexed for MEDLINE]  Free PMC Article
  18. Synaptic arrangement of the neuroligin/beta-neurexin complex revealed by X-ray and neutron scattering.
    Comoletti D, Grishaev A, Whitten AE, Tsigelny I, Taylor P, Trewhella J.
    Structure. 2007 Jun;15(6):693–705.
    PMID: 17562316 [PubMed - indexed for MEDLINE]  Free PMC Article
  19. Cystic fibrosis transmembrane conductance regulator (CFTR) functionality is dependent on coatomer protein I (COPI).
    Yu Y, Platoshyn O, Safrina O, Tsigelny I, Yuan JX, Keller SH.
    Biol Cell. 2007 Aug;99(8):433–444.
    PMID: 17388782 [PubMed - indexed for MEDLINE]
  20. Dynamics of alpha-synuclein aggregation and inhibition of pore-like oligomer development by beta-synuclein.
    Tsigelny IF, Bar-On P, Sharikov Y, Crews L, Hashimoto M, Miller MA, Keller SH, Platoshyn O, Yuan JX, Masliah E.
    FEBS J. 2007 Apr;274(7):1862–1877.
    PMID: 17381514 [PubMed - indexed for MEDLINE]
  21. A tryptophan in the bottleneck of the catalytic gorge of an invertebrate acetylcholinesterase confers relative resistance to carbamate and organophosphate inhibitors.
    Patel R, Sanders R, Brown L, Baker S, Tsigelny I, , Pezzementi L.
    Cell Biochem Biophys. 2006;46(3):253–264.
    PMID: 17272851 [PubMed - indexed for MEDLINE]
  22. Alpha-conotoxin OmIA is a potent ligand for the acetylcholine-binding protein as well as alpha3beta2 and alpha7 nicotinic acetylcholine receptors.
    Talley TT, Olivera BM, Han KH, Christensen SB, Dowell C, Tsigelny I, Ho KY, Taylor P, McIntosh JM.
    J Biol Chem. 2006 Aug 25;281(34):24678–24686.
    Epub 2006 Jun 27.
    PMID: 16803900 [PubMed - indexed for MEDLINE]  Free Article
  23. The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state.
    Varughese KI, Tsigelny I, Zhao H.
    J Bacteriol. 2006 Jul;188(13):4970–4977. Erratum in: J Bacteriol. 2007 Apr;189(8):3328.
    PMID: 16788205 [PubMed - indexed for MEDLINE]  Free PMC Article
  24. Inactivation of an invertebrate acetylcholinesterase by sulfhydryl reagents: the roles of two cysteines in the catalytic gorge of the enzyme.
    Pezzementi L, Rowland M, Wolfe M, Tsigelny I.
    Invert Neurosci. 2006 Jun;6(2):47–55. Epub 2006 Apr 4.
    PMID: 16586114 [PubMed - indexed for MEDLINE]
  25. Dissection of synapse induction by neuroligins: effect of a neuroligin mutation associated with autism.
    Chubykin AA, Liu X, Comoletti D, Tsigelny I, Taylor P, Südhof TC.
    J Biol Chem. 2005 Jun 10;280(23):22365–22374.
    Epub 2005 Mar 29.
    PMID: 15797875 [PubMed - indexed for MEDLINE]  Free Article
  26. Identification of molecular determinants that modulate trafficking of DeltaF508 CFTR, the mutant ABC transporter associated with cystic fibrosis.
    Tsigelny I, Hotchko M, Yuan JX, Keller SH.
    Cell Biochem Biophys. 2005;42(1):41–53.
    PMID: 15673927 [PubMed - indexed for MEDLINE]
  27. The Arg451Cys-neuroligin-3 mutation associated with autism reveals a defect in protein processing.
    Comoletti D, De Jaco A, Jennings LL, Flynn RE, Gaietta G, Tsigelny I, Ellisman MH, Taylor P.
    J Neurosci. 2004 May 19;24(20):4889–4893.
    PMID: 15152050 [PubMed - indexed for MEDLINE]  Free Article
  28. SNP analysis combined with protein structure prediction defines structure-functional relationships in cancer related cytochrome P450 estrogen metabolism.
    Tsigelny IF, Kotlovyi V, Wasserman L.
    Curr Med Chem. 2004 Mar;11(5):525–538. Review.
    PMID: 15032601 [PubMed - indexed for MEDLINE]
  29. Structural characterization of recombinant soluble rat neuroligin 1: mapping of secondary structure and glycosylation by mass spectrometry.
    Hoffman RC, Jennings LL, Tsigelny I, Comoletti D, Flynn RE, Sudhof TC, Taylor P.
    Biochemistry. 2004 Feb 17;43(6):1496–1506.
    PMID: 14769026 [PubMed - indexed for MEDLINE]
  30. Conformational preferences and activities of peptides from the catecholamine release-inhibitory (catestatin) region of chromogranin A.
    Preece NE, Nguyen M, Mahata M, Mahata SK, Mahapatra NR, Tsigelny I, O'Connor DT.
    Regul Pept. 2004 Apr 15;118(1-2):75–87.
    PMID: 14759560 [PubMed - indexed for MEDLINE]
  31. Amino acids defining the acyl pocket of an invertebrate cholinesterase.
    Pezzementi L, Johnson K, Tsigelny I, Cotney J, Manning E, Barker A, Merritt S.
    Comp Biochem Physiol B Biochem Mol Biol. 2003 Dec;136(4):813–832.
    PMID: 14662305 [PubMed - indexed for MEDLINE]
  32. Identification of the protein kinase A regulatory RIalpha-catalytic subunit interface by amide H/2H exchange and protein docking.
    Anand GS, Law D, Mandell JG, Snead AN, Tsigelny I, Taylor SS, Ten Eyck LF, Komives EA.
    Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13264–13269.
    Epub 2003 Oct 28.
    PMID: 14583592 [PubMed - indexed for MEDLINE]  Free PMC Article
  33. Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information.
    Law DS, Ten Eyck LF, Katzenelson O, Tsigelny I, Taylor SS, Ten Eyck LF, Komives EA.
    Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13264–13269.
    Epub 2003 Oct 28.
    PMID: 14583592 [PubMed - indexed for MEDLINE]  Free PMC Article
  34. Tryptophan fluorescence reveals conformational changes in the acetylcholine binding protein.
    Hansen SB, Radic' Z, Talley TT, Molles BE, Deerinck T, Tsigelny I, Taylor P.
    J Biol Chem. 2002 Nov 1;277(44):41299–41302.
    Epub 2002 Sep 13.
    PMID: 12235129 [PubMed - indexed for MEDLINE]  Free PMC Article
  35. Residues in the epsilon subunit of the nicotinic acetylcholine receptor interact to confer selectivity of waglerin-1 for the alpha-epsilon subunit interface site.
    Molles BE, Tsigelny I, Nguyen PD, Gao SX, Sine SM, Taylor P.
    Biochemistry. 2002 Jun 25;41(25):7895–7906.
    PMID: 12069578 [PubMed - indexed for MEDLINE]
  36. Hidden Markov models-based system (HMMSPECTR) for detecting structural homologies on the basis of sequential information.
    Tsigelny I, Sharikov Y, Ten Eyck LF.
    Protein Eng. 2002 May;15(5):347–352.
    PMID: 12034853 [PubMed - indexed for MEDLINE]  Free Article
  37. Electrostatic environment surrounding the activation loop phosphotyrosine in the oncoprotein v-Fps.
    Leon BC, Tsigelny I, Adams JA.
    Biochemistry. 2001 Aug 28;40(34):10078–10086.
    PMID: 11513586 [PubMed - indexed for MEDLINE]
  38. Protein docking using continuum electrostatics and geometric fit.
    Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck LF.
    Protein Eng. 2001 Feb;14(2):105–113.
    PMID: 11297668 [PubMed - indexed for MEDLINE]  Free Article
  39. Catalytic assessment of the glycine-rich loop of the v-Fps oncoprotein using site-directed mutagenesis.
    Hirai TJ, Tsigelny I, Adams JA.
    Biochemistry. 2000 Oct 31;39(43):13276–13284.
    PMID: 11052681 [PubMed - indexed for MEDLINE]
  40. Subunit interface selective toxins as probes of nicotinic acetylcholine receptor structure.
    Taylor P, Malanz S, Molles BE, Osaka H, Tsigelny I.
    Pflugers Arch. 2000;440(5 Suppl):R115–R117. Review.
    PMID: 11005635 [PubMed - indexed for MEDLINE]
  41. Common EF-hand motifs in cholinesterases and neuroligins suggest a role for Ca2+ binding in cell surface associations.
    Tsigelny I, Shindyalov IN, Bourne PE, Südhof TC, Taylor P.
    Protein Sci. 2000 Jan;9(1):180–185.
    PMID: 10739260 [PubMed - indexed for MEDLINE]  Free PMC Article
  42. 600 ps molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase.
    Tsigelny I, Greenberg JP, Cox S, Nichols WL, Taylor SS, Ten Eyck LF.
    Biopolymers. 1999 Oct 15;50(5):513–524.
    PMID: 10479734 [PubMed - indexed for MEDLINE]
  43. Delineation of selective cyclic GMP-dependent protein kinase Ialpha substrate and inhibitor peptides based on combinatorial peptide libraries on paper.
    Dostmann WR, Nickl C, Thiel S, Tsigelny I, Frank R, Tegge WJ.
    Pharmacol Ther. 1999 May-Jun;82(2-3):373–387.
    PMID: 10454213 [PubMed - indexed for MEDLINE]
  44. Analysis of cholinesterase inactivation and reactivation by systematic structural modification and enantiomeric selectivity.
    Taylor P, Wong L, Radić Z, Tsigelny I, Brüggemann R, Hosea NA, Berman HA.
    Chem Biol Interact. 1999 May 14;119-120:3–15. Review.
    PMID: 10421434 [PubMed - indexed for MEDLINE]

 

BOOKS and BOOK CHAPTERS

  1. Prediction of Membrane-Contacting Protein Surfaces.
    Tsigelny IF, Sharikov Y, Walker RC, Greenberg J, Kouznetsova V, Miller MA, Masliah E.
    In: Membrane-Active Peptides: Methods and Results on Structure and Function (IUL Biotechnology, 9). M.A.R.B. Castanho, ed. 2010, Intl Univ Line, La Jolla, Calif., pp. 55–81.

     
  2. Protein Structure Prediction: Bioinfomatic Approach (IUL Biotechnology, 3).
    I.F. Tsigelny, ed. 2002, Intl Univ Line, La Jolla, Calif., 517pp.
  • Protein Structure Prediction Using Hidden Markov Model Structural Libraries. Tsigelny I, Sharikov Y, Ten Eyck LF. pp. 109–124.
  • Protein Structure Prediction on the Basis of Combinatorial Peptide Library Screening. Tsigelny I, Sharikov Y, Kotlovyi V, Kelner M, Ten Eyck LF. pp. 341–352.
  • A Flexible Method for Structural Alignment: Applications to Structure Prediction Assessments. Kotlovyi V, Tsigelny I, Ten Eyck LF. pp. 431–448.

Gene-Network Analysis

  1. bHLH Transcription factors inhibitors for cancer therapy: general features for in silico drug design.
    Tsigelny IF, Kouznetsova VL, Pingle SC, Kesari S.
    Curr Med Chem. 2014;21(28):3227–3243.
    PMID: 24735358 [PubMed - in process]
  2. A hierarchical coherent-gene-group model for brain development.
    Tsigelny IF, Kouznetsova VL, Baitaluk M, Changeux JP.
    Genes Brain Behav. 2013 Mar;12(2):147–165.
    doi: 10.1111/gbb.12005. Epub 2012 Dec 28.
    PMID: 23173912 [PubMed - indexed for MEDLINE]
  3. Analysis of metagene portraits reveals distinct transitions during kidney organogenesis.
    Tsigelny IF, Kouznetsova VL, Sweeney DE, Wu W, Bush KT, Nigam SK.
    Sci Signal. 2008 Dec 9;1(49):ra16.
    doi: 10.1126/scisignal.1163630.
    PMID: 19066399 [PubMed - indexed for MEDLINE]  Free PMC Article
  4. p75 neurotrophin receptor regulates tissue fibrosis through inhibition of plasminogen activation via a PDE4/cAMP/PKA pathway.
    Sachs BD, Baillie GS, McCall JR, Passino MA, Schachtrup C, Wallace DA, Dunlop AJ, MacKenzie KF, Klussmann E, Lynch MJ, Sikorski SL, Nuriel T, Tsigelny I,, Zhang J, Houslay MD, Chao MV, Akassoglou K.
    J Cell Biol. 2007 Jun 18;177(6):1119–1132.
    PMID: 17576803 [PubMed - indexed for MEDLINE]  Free PMC Article
  5. Coherent expression chromosome cluster analysis reveals differential regulatory functions of amino-terminal and distal parathyroid hormone-related protein domains in prostate carcinoma.
    Tsigelny I, Burton DW, Sharikov Y, Hastings RH, Deftos LJ.
    J Biomed Biotechnol. 2005;2005(4):353–363.
    PMID: 16489268 [PubMed]
    Free PMC Article
  6. Complex dynamics of chaperone-protein interactions under cellular stress.
    Tsigelny IF, Nigam SK.
    Cell Biochem Biophys. 2004;40(3):263–276.
    PMID: 15211027 [PubMed - indexed for MEDLINE]

Microarray Gene Expression Data High Level Analysis

  1. A hierarchical coherent-gene-group model for brain development.
    Tsigelny IF, Kouznetsova VL, Baitaluk M, Changeux JP.
    Genes Brain Behav. 2013 Mar;12(2):147–165.
    doi: 10.1111/gbb.12005. Epub 2012 Dec 28.
    PMID: 23173912 [PubMed - indexed for MEDLINE]
  2. Analysis of metagene portraits reveals distinct transitions during kidney organogenesis.
    Tsigelny IF, Kouznetsova VL, Sweeney DE, Wu W, Bush KT, Nigam SK.
    Sci Signal. 2008 Dec 9;1(49):ra16.
    doi: 10.1126/scisignal.1163630.
    PMID: 19066399 [PubMed - indexed for MEDLINE]  Free PMC Article

Nanomedicine

  1. Direct recognition of superparamagnetic nanocrystals by macrophage scavenger receptor SR-AI.
  2. Chao Y, Karmali PP, Mukthavaram R, Kesari S, Kouznetsova VL, Tsigelny IF, Simberg D.
    ACS Nano. 2013 May 28;7(5):4289–4298.
    doi: 10.1021/nn400769e. Epub 2013 Apr 30.
    PMID: 23614696 [PubMed - indexed for MEDLINE]
  3. Recognition of dextran-superparamagnetic iron oxide nanoparticle conjugates (Feridex) via macrophage scavenger receptor charged domains.
    Chao Y, Makale M, Karmali PP, Sharikov Y, Tsigelny I, Merkulov S, Kesari S, Wrasidlo W, Ruoslahti E, Simberg D.
    Bioconjug Chem. 2012 May 16;23(5):1003–1009.
    doi: 10.1021/bc200685a. Epub 2012 Apr 26.
    PMID: 22515422 [PubMed - indexed for MEDLINE]  Free PMC Article
  4. Has the Time for In silico Design of Nanomedicines Finally Arrived?
    Tsigelny IF, Simberg D.
    J Nanomedic Biotherapeu Discover. 2011;1(2):2. Editorial.
    doi: 10.4172/2155-983X.1000104e.

     

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P.O.Box 2525

La Jolla, CA 92038

 

Phone: 1-858-457-0595

Fax: 1-858-581-9073

E-mail: it@biana.info

 

Or use our contact form.

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