Brian T. Luke, Ph.D.

List of Publications

   
  1. Jemmis ED, Chandrasekhar J, Wurthwein EU, Schleyer PvR, Chinn JW, Landro FJ, Laglow RJ, Luke BT, Pople JA. Lithiated Carbocations. The Generation, Structure, and Stability of CLi5+. J. Am. Chem. Soc. 1982:104:4275-4276.
  2. Schleyer PvR, Tidor B, Jemmis ED, Chandrasekhar J, Wurthwein EU, Kos AJ, Luke BT, Pople JA, Lithium-Stabilized Methanonium Ions, CLin-5Hn+. J. Am. Chem. Soc. 1983:105:484-488.
  3. Schleyer PvR, Apeloig Y, Arad D, Luke BT, Pople JA. The Structure and Energy of SiH5+. Comparisons with CH5+ and BH5. Chem. Phys. Lett. 1983:95:477-482.
  4. Luke BT, Pople JA, Schleyer PvR. A Theoretical Comparison of the Lowest-lying Singlet and Triplet States of H2CBe and HCBeH. Chem. Phys. Lett. 1983:97:265-269.
  5. Del Bene JE, Mette HD, Frisch MJ, Luke BT, Pople JA. Ab Initio Computation of the Enthalpies of Some Gas-Phase Hydration Reactions. J. Phys. Chem. 1983:87:3279-3282.
  6. Pople JA, Frisch MJ, Luke BT, Binkley JS. A Moller-Plesset Study of the Energies of AHn Molecules (A=Li to F). Int. J. Quant. Chem. Symp. 1983:17:307-320.
  7. Luke BT, Pople JA, Schleyer PvR. Theoretical Study of the Carbeniod CH2FLi: Structures and Energies of the Stable Configurations and the Transition States. Chem. Phys. Lett. 1983:102:148-154.
  8. Luke BT, Gupta AG, Loew GH, Lawless JG, White DH. Theoretical Investigation of the Role of Clay Edges in Prebiotic Peptide Bond Formation. I. Structures of Acetic Acid, Glycine, H2SO4, H3PO4, Si(OH)4 and Al(OH)4-. Int. J. Quant. Chem. QBS 1984:11:117-135.
  9. Pople JA, Luke BT, Frisch MJ, Binkley JS. Theoretical Thermochemistry 1. Heats of Formation of Neutral AHn Molecules (A = Li to Cl). J. Phys. Chem. 1985:89:2198-2203.
  10. Luke BT, Loew GH. A Theoretical Investigation of the First Step in the Metabolic Reduction of Halogenated Methanes by Cytochrome P450. Int. J. Quant. Chem. QBS 1985:12:99-112.
  11. Luke BT, McLean AD. A Theoretical Investigation of Atmospheric Sulfur Chemistry. I. The HSO/HOS Energy Separation and the Heat of Formation of HSO, HOS, and HS2. J. Phys. Chem. 1985:89:4592-4596.
  12. Luke BT, Pople JA, Schleyer PvR. A Theoretical Comparison of the Lowest-lying Singlet and Triplet States of HCB and HBC. Chem. Phys. Lett. 1985:122:19-22.
  13. Luke BT, Pople JA, Krogh-Jespersen MB, Apeloig Y, Chandrasekhar J, and Schleyer PvR. A Theoretical Survey of Singly Bonded Silicon Compounds. Comparison of Silyl and Methyl Derivatives. J. Am. Chem. Soc. 1986:108:260-269.
  14. Luke BT, Pople JA, Krogh-Jespersen MB, Apeloig Y, Karni M, Schleyer PvR, Chandrasekhar J. A Theoretical Survey of Multiply Bonded Silicon Compounds. Comparison of Silyl and Methyl Derivatives. J. Am. Chem. Soc. 108, 270-284 (1986).
  15. Luke BT, Loew GH, and McLean AD. A Theoretical Examination of Substituent Effects on the Detoxification Reaction between Glutathione and Halogenated Methanes. Int. J. Quant. Chem. 1986:29:883-896.
  16. Loew G, Keys C, Luke B, Polgar W, Toll L. Structure Affinity Studies of Morphiceptin Analogs: Receptor Binding and Molecular Determinants of mu-Affinity and Selectivity., Mol. Pharm. 1986:29:546-553.
  17. Collins JR, Luke BT, and Loew GH. Quantum Mechanical Study of Putative Intermediates in Adduct Formation by the Suicude Substrate Ethylene with Cytochrome P450., Int. J. Quant. Chem. QBS 1986:13:143-154.
  18. Loew GH, Collins J, Luke B, Waleh A, Pudzianowski A. Theoretical Studies of Cytochrome P450: Characterization of Stable and Transient Active States, Reaction Mechanisms and Substrate-Enzyme Interactions. Enzyme 1986:36:54-78.
  19. Luke BT, Loew GH, McLean AD. A Theoretical Study of Anaerobic Reduction of Halogenated Alkanes by Cytochrome P450. 1. Structures, Inversion Barriers and Heats of Formation of Halogenated Methyl Radicals. J. Am. Chem. Soc. 1987:109:1307-1317.
  20. Schleyer PvR, Luke BT, Pople JA. On the Existence of Methylborlene. An Ab Initio Investigation of the CBH3 Poetntial Energy Surface. Organometallics 1987:6:1997-2000.
  21. Koch W, Frenking G, Luke BT. Theoretical Investigations of the Low-lying Electronic States of the HeC2+ Dication. Chem. Phys. Lett. 1987:139:149-154.
  22. Collins JR, Loew GH, Luke BT, White DH. Theoretical Investigation of the Role of Clay Edges in Prebiotic Peptide Bond Formation. II. Structures and thermodynamics of the activated complex species. Origins of Life 1988:18:107-119.
  23. Luke BT, Loew GH, McLean AD. Theoretical Investigation of the Anaerobic Reduction of Halogenated Alkanes by Cytochrome P-450. 2. Vertical Electron Affinities of Chlorofluoromethanes as a Measure of Their Activity. J. American Chemical Society 1988:110:3396-3400.
  24. Luke BT, Collins JR, Loew GH, McLean AD. Theoretical Investigations of Terminal Alkenes as Putative Suicide Substrates of Cytochrome P-450. J. American Chemical Society 1990:112:8686-8691.
  25. Luke BT. Displaying the Structure of Molecules by Multidimensional Plots of Their Torsion Angles. J. Chem. Inf. Comput. Sci. 1993:33:135-142.
  26. Luke BT. An ab Initio Investigation of the Lowest Potential Energy Surface of Disiloxane. J. Phys. Chem. 1993:97:7505-7510.
  27. Luke BT, A Quantum Mechanical Conformational Search of Captopril, A Potent Inhibitor of the Angiotensin-Converting Enzyme. J. Mol. Struct. (THEOCHEM) 1994:309:1-11.
  28. Luke BT. Stable Conformations of CH3CH2OCH2CH2OH: A Comparison of Theoretical Methods. J. Comput. Chem. 1994:15:1176-1185.
  29. Luke BT. Evolutionary Programming Applied to the Development of Quantitative Structure-Activity Relationships and Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. 1994:34:1279-1287.
  30. Luke BT, A Quantum Mechanical Conformational Search of 1-(3-Mercaptipropionyl)-L-proline; the Demethylated Analogue of the Potent Angiotensin-Converting Enzyme Inhibitor Captopril., J. Mol. Struct. (THEOCHEM) 1995::332:25-37.
  31. Luke BT A Theoretical Investigation of Chlorine-Oxygen Compounds. I. G2 and G2(MP2) Energies of ClO, Cl2O, ClO2 and Cl2O2. J. Mol. Struct. (THEOCHEM) 1995:332:283-289.
  32. Luke BT. An Overview of Genetic Methods. In PRINCIPLES IN QSAR AND DRUG DESIGN, VOLUME 1: Genetic Algorithms in Molecular Modelling, J. Devillers (ed), Academic Press Ltd, London (1996) pp. 35-66.
  33. Luke BT. Applications of Distributed Computing to Conformational Searches. In RATIONAL DRUG DESIGN, The IMA Volumes in Mathematics and its Applications, Vol. 108, D.G. Truhlar, W.J. Howe, A.J. Hopfinger, J. Blaney and R.A. Dammkoehler (eds.), Springer-Verlag, New York (1999), 191-206.
  34. Luke BT. Comparison of three different QSAR/QSPR generation techniques. J. Mol. Struct. (Theochem) 1999:468:13-20.
  35. Luke BT. Comparison of Different Data Set Screening Methods for Use in QSAR/QSPR Generation Studies. J. Mol. Struct. (Theochem) 2000:507:229-238.
  36. Laco GS, Collins JR, Luke BT, Kroth H, Sayer JM, Jerina DM, Pommier Y. Human Topoisomerase I Inhibition: Docking Camptothecin and Derivatives into a Structure-Based Active Site Model. Biochem. 2002:41:1428-1435.
  37. Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KHJ, Ward VK. The Palm Subdomain-based Active Site is Internally Permuted in Viral RNS-dependent RNA Polymerase of an Ancient Lineage. J. Mol. Biol. 2002:324:47-62.
  38. Luke BT. Fuzzy Structure-Activity Relationships. SAR QSAR Environ. Res. 2003:14:41-57.
  39. Medjahed D, Tontesh TS, Smythers GW, Luke BT, Lemkin PF, Monroe DJ. TMAP (Tissue Molecular Anatomy Project). In 2002 Congress of Applied Proteomics, P.M. Palagi et al. (Eds.), 3-5 December 2002, Lausanne, Switzerland (FontisMedia SA, Switzerland) pp. 71-72.
  40. Medjahed D, Luke BT, Tontesh TS, Smythers GW, Monroe DJ, Lemkin PF. TMAP (Tissue Molecular Anatomy Project), an Expression Database for Comparitive Cancer Proteomics. Proteomics, 2003:3:1445-1453.
  41. Luke BT. Genetic Algorithms and Beyond. In Nature-Inspired Methods in Chemometrics: Genetic Algorithms and Neural Networks, R. Leardi (Ed.), (Elsevier, The Netherlands, 2003) Chapter 1.
  42. Luke BT. Applying Genetic Algorithms and Neural Networks to Chemometric Problems. In Nature-Inspired Methods in Chemometrics: Genetic Algorithms and Neural Networks, R. Leardi (Ed.), (Elsevier, The Netherlands, 2003) Chapter 12.
  43. Lucas DA, Luke B, Collins J, Van QN, Klose J, Chmurny GN, Prieto DA, Conrads TP, Burt SK, Keay SK, Veenstra TD. The Analysis Of Urine Proteomic and Metabonomic Patterns for the Diagnosis of Cystitis. Abstracts of the 51st Conference on Mass Spectrometry and Applied Topics, Montreal, June 2003, pg. 1313.
  44. Xiao Z, Luke BT, Izmirlian G, Umar A, Lynch P, Phillips R, Patterson S, Conrads TP, Veenstra TD, Greenwald P, Hawk ET, Ali IU. Serum Proteomic Profiles Suggest Celecoxib-Modulated Targets and Response Predictors. Cancer Res. 2004:64(8):2904-2909.
  45. Van QN, Klose JR, Lucas DA, Prieto DA, Luke B, Collins J, Burt SK, Chmurny GN, Issaq HJ, Conrads TP, Veenstra TD, Keay SK. The use of urine proteomic and metabonomic patterns for the diagnosis of interstitial cystitis and bacterial cystitis. Dis. Markers 2003-2004:19(4-5):169-183.
  46. Luke BT. A Survey of Techniques for Extracting Information from Large Proteomic Datasets. In Informatics in Proteomics, S. Srivasta (Ed.), (CRC Press, New York, 2005), Chapter 19.
  47. Tsang S, Sun Z, Luke B, Stewart C, Lum N, Gregory M, Wu X, Subleski M, Jenkins NA, Copeland NG, Munroe DJ. A comprehensive SNP-based genetic analysis of inbred mouse strains. Mamm. Genome 2005:16(7):476-480.
  48. Luke BT. Are Proteomic-Based Classifiers Useful as Diagnostic Tools? Proceedings of the 8th International Symposium on Protein Structure Function Relationship in Karachi, Pakistan, January 2005.
  49. Ali IU, Luke BT, Dean M, Greenwald P. Allelic Variants in regulatory regions of cyclooxygenase-2: association with advanced colorectal adenoma. British J. Cancer 2005:93(8):953-959.
  50. Goodman JE, Mechanic LE, Luke BT, Ambs S, Chanock S, Harris CC. Exploring SNP-SNP interactions and colon cancer risk using Polymorphism Interaction Analysis. Intl. J. Cancer 2006:118:1790-1797.
  51. Wu X, Luke BT, Burgess SM. Redefining the common insertion sites. Virology 2006:344:292-295.
  52. Ali IU, Xiao Z, Malone W, Smith M, Conrads TP, Veenstra TD, Greenwald P, Luke BT, McLarty JW. Plasma proteomic profiling: search for lung cancer diagnostic and early detection markers. Oncol. Rep. 2006:15(5):1367-1372.
  53. Habermann JK, Roblick UJ, Luke BT, Prieto DA, Finlay WJ, Podust VN, Roman JM, Oevermann E, Schiedeck T, Homann N, Conrads TP, Veenstra TD, Burt SK, Bruch HP, Auer G, Ried T. Increased serum levels of complement C3a anaphylatoxin indicate the presence of colorectal tumors. Gastroenterology 2006:131:1020-1029; Habermann JK, Luke BT, T. Ried T. Reply, 2007:132:824.
  54. Boersma BJ, Reimers M, Yi M, Ludwig JA, Luke BT, Stephens RM, Yfantis HG, Lee DH, Weinstein JN, Ambs S. A stromal gene signature associated with inflammatory breast cancer. Int. J. Cancer 2008:122(6):1324-32.
  55. Luke BT. Cambridge Healthtech Institute's 2007 Biomarker Discovery Summit. Expert Rev. Mol. Diagn. 2007:7(6):755-7.
  56. Mechanic LE, Luke BT, Goodman JE, Chanock SJ, Harris CC. Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions. BMC Bioinformatics 2008:9:146.
  57. Issaq HJ, Nativ O, Waybright T, Luke B, Veenstra TD, Issaq EJ, Kravstov A, Mullerad M. Detection of bladder cancer in human urine by metabolomic profiling using high performance liquid chromatography/mass spectrometry. J. Urol. 2008:179(6):2422-6.
  58. Ashktorab H, Tsang S, Luke B, Sun Z, Adam-Campbell L, Kwagyan J, Poirier R, Akter S, Akhgar A, Smoot D, Munroe DJ, Ali IU. Protective effect of Cox-2 allelic variants on risk of colorectal adenoma development in African Americans. Anticancer Res. 2008:28(5B):3119-23.
  59. Luke BT, Collins JR. Examining the significance of fingerprint-based classifiers. BMC Bioinformatics 2008:9(1):545.
  60. Fatima N, Chelius D, Luke BT, Yi M, Zhang T, Stauffer S, Stephens R, Lynch P, Miller K, Guszczynski T, Boring D, Greenwald P, Ali IU. Label-free Global Serum Proteomic Profiling Reveals Novel Celecoxib-modulated Proteins in Familial Adenomatous Polyposis Patients. Cancer Genomics & Proteomics 2009:6:41-50.
  61. Ye X, Luke B, Andresson T, Blonder J. 18O Stable Isotopic Labeling in MS-based Proteomics. Briefings in Functional Genomics and Proteomics 2009:2:136-144.
  62. Zeddam JL, Gordon KHJ, Lauber C, Alves CAF, Luke BT, Hanzlik TN, Ward VK, Gorbalenya AE. Euprosterna elaeasa virus genome sequence and evolution of the Tetraviridae family: emergence of bipartite genomes and conservation of the VPg signal with the ds RNA Birnaviridae family Virology 2010:397:145-54.
  63. Ye X, Luke BT, Johann DJ Jr, Ono A, Prieto DA, Chan KC, Issaq HJ, Veenstra TD, Blonder J. Optimized method for computing (18)O/(16)O ratios of differentially stable-isotope labeled peptides in the context of postdigestion (18)O exchange/labeling. Anal. Chem. 2010:82(13):5878-86.
  64. Cer RZ, Bruce KH, Mudunuri US, Yi M, Volfovsky N, Luke BT, Bacolla A, Collins JR, Stephens RM. Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes. Nucleic Acids Res. 2011:39(Database issue):D383-91.
  65. Temiz NA, Donohue DE, Bacolla A, Luke BT, Collins JR (2012) The Role of Methylation in the Intrinsic Dynamics of B- and Z-DNA. PLoS ONE 2012:7(4):e35558. doi:10.1371/journal.pone.0035558.
  66. Luke BT, Collins JR. A Comparison of Biomarker and Fingerprint-Based Classifiers of Disease. Biomarker. Khan TK (Ed.), InTech (2012) Chapter 9. ISBN 978-953-51-0577-0.
  67. Ye X, Luke BT, Johann Jr DJ, Chan KC, Prieto DA, Ono A, Veenstra TD, Blonder J. Post-digestion 18O Exchange/Labeling for Quantitative Shotgun Proteomics of Membrane Proteins. in Quantitative Methods in Proteomics: Methods in Molecular Biology, 2012, Volume 893, Part 3, 223-240, DOI: 10.1007/978-1-61779-885-6_15.
  68. Cer RZ, Bruce KH, Donohue DE, Temiz NA, Mudunuri US, Yi M, Volfovsky N, Bacolla A, Luke BT, Collins JR, and Stephens RM. Searching for Non-B DNA-Forming Motifs Using nBMST (Non-B DNA Motif Search Tool). Current Protocols in Human Genetics 2012:18.7.1-18.7.22. DOI: 10.1002/0471142905.hg1807s73.
  69. Wei BR, Simpson RM, Johann DJ, Jr., Dwyer JE, Prieto DA, Kumar M, Ye X, Luke B, Shive HR, Webster JD, Hoover SB, Veenstra TD, Blonder J. Proteomic Profiling of H-Ras-G12V Induced Hypertrophic Cardiomyopathy in Transgenic Mice Using Comparative LC-MS Analysis of Thin Fresh-Frozen Tissue Sections. J. Proteome Res. 2012:11(3):1561-1570.
  70. Ivanic J, Schmidt MW, Luke B. High-level theoretical study of the NO dimer and tetramer: Has the tetramer been observed? J. Chem. Phys. 2012:137:214316.
  71. Callahan R, Mudunuri U, Bargo S, Raafat A, McCurdy D, Boulanger C, Lowther W, Stephens R, Luke BT, Stewart C, Wu X, Munroe D, Smith GH. Genes affected by mouse mammary tumor virus (MMTV) proviral insertions in mouse mammary tumors are deregulated or mutated in primary human mammary tumors. Oncotarget 2012:3(11):1320-34.
  72. Cer RZ, Donohue DE, Mudunuri US, Temiz NA, Loss MA, Starner NJ, Halusa GN, Volfovsky N, Yi M, Luke BT, Bacolla A, Collins LR, Stephens RM. Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools. Nucl. Acids Res. 2013:41(D1):D94-D100. doi: 10.1093/nar/gks955.
  73. Ye X, Chan KC, Prieto DA, Luke BT, Johann DJ, Stockwin LH, Newton DL, Blonder J. Trypsin-mediated (18)o/ (16)o labeling for biomarker discovery. Methods in Molecular biology 2013:1002:133-49. DOI:10.1007/978-1-62703-360-2_12.
  74. Bacolla A, Temiz NA, Yi M, Ivanic J, Cer RZ, Donohue DE, Ball EV, Mudunuri US, Wang G, Jain A, Volfovsky N, Luke BT, Stephens RM, Cooper DN, Collins JR, Vasquez KM. Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease. PLoS Genet 9(9): e1003816. doi:10.1371/journal.pgen.1003816.
  75. Mudunuri US, Khouja M, Repetski S, Venkataraman G, Che A, Luke BT, Girard FP, Stephens RM. Knowledge and Theme Discovery Across Very Large Biological Data Sets Using Distributed Queries: A Prototype Combining Unstructured and Structured Data. PLoS ONE 2013; 8(12):e80503. doi:10.1371/journal.pone.0080503
  76. Yan Z, Luke BT, Tsang SX, Xing R, Pan Y, Liu Y, Wang J, Geng T, Li J, Lu Y. Identification of Gene Signatures Used to Recognize Biological Characteristics of Gastric Cancer Upon Gene Expression Data. Biomarker Insights 2014:9 67-76

  77. Ravichandran S, Singh N, Donnelly D, Migliore M, Johnson P, Fishwick C, Luke BT, Martin B, Maudsley S, Fugmann SD, Moaddel R. Pharmacophore model of the quercetin binding site of the SIRT6 protein Journal of Molecular Graphics and Modelling, 49, 2014, 38–46.

  78. Gautam A, D’Arpa P, Donohue DE, Muhie S, Chakraborty N, Luke BT, Grapov D, Carroll EE, Meyerhoff JL, Hammamieh R, Jett M. (2015) Acute and Chronic Plasma Metabolomic and Liver Transcriptomic Stress Effects in a Mouse Model with Features of Post-Traumatic Stress Disorder. PLoS ONE 10(1): e0117092. doi:10.1371/journal.pone.0117092

  79. Ravichandran S, Luke BT, Collins JR. Can structural features of kinase receptors provide clues on selectivity and inhibition? A molecular modeling study. Journal of Molecular Graphics and Modelling, 57, 2015, 36–48.