Works

Dr. Jason McDermott, senior research scientist at the Pacific Northwest National Laboratory, has extensive research experience in molecular and structural virology and data resource design, data integration and prediction of biological networks, bridging experimental and computational biology. Currently, his research interests include data integration of high-throughput ‘omics data for biomarker discovery, developing systems biology models in a number of systems focusing on host-pathogen interactions, characterizing phylogenetic and functional relationships in complex eukaryotic microbial communities, and using network inference and topology to characterize organism-level phenotypes.

Projects

Internal links

External links

Publications

Peer-reviewed journal articles

  1. Wang J, Ma Z, Carr SA, Mertins P, Zhang H, Zhang Z, Chan DW, Ellis MJC, Townsend RR, Smith RD, McDermott JE, Chen X, Paulovich AG, Boja ES, Mesri M, Kinsinger CR, Rodriguez H, Rodland KD, Liebler DC, Zhang B. Network analysis reveals a dominant role of protein-level regulation in coordinating gene functions. MCP
  2. Mitchell HD, Markillie M, Chrisler WB, Hu D, Szymanski CJ, Xie Y, Taylor RC, Grate EK, Cooley SK, McDermott JE, Heredia-Langner A, Orr G. Cells respond to unique nanoparticle properties with multiple strategies as revealed by single-cell RNA-Seq. ACS Nano
  3. McDermott JE, Mitchell HD, Gralinski LE, Eisfeld AJ, Bankhead A, Josset L, Tchitchek N, Chang J, Neumann G, Tilton SC, Li C, Fan S, McWeeney S, Kawaoka Y, Baric RS, Katze MG, Waters KM. The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus. BMC Systems Biology.
  4. McClure RS, Overall CS, Hill E, Markille LM, McCue LA, Nelson W, Taylor RC, Ludwig M, Bryant DA, Konopka A, McDermott JE, Beliaev AS. 2015. Global Transcriptome Analysis of Synechococcus sp. PCC 7002 From a Compendium of RNA-seq Data. NAR
  5. Bernstein H, McClure R, Hill E, Markillie L, Chrisler W, Romine M, McDermott JE, Posewitz M, Bryant D, Konoipka A, Fredrickson J, and Beliaev A. Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultra-Fast Growth. mBio 7(4)
  6. Shi T, Niepel M, McDermott JE, Chrisler WB, Markillie LM, Rodland KD, Sorger PK, Qian WJ, Wiley HS. Conserved Stoichiometry and Abundance of Proteins in the ERK Signaling Pathway Across EGF-Responsive Cell Lines. Science Signaling. 9(436):rs6
  7. Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou J, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Won Cha S, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Choi C, Monroe ME, Thomas S, Moore RJ, Yu K, Tabb DL, Fenyo D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD, and the CPTAC Investigators. 2016. Integrated proteogenomic characterization of human high grade serous ovarian cancer. Cell. 166(3): 755-65
  8. Oxford KL, Wendler JP, McDermott JE, White III RA, Powell JD, Jacobs JM, Adkins JN, Waters KM. 2016. The landscape of viral proteomics and its potential to impact human health. Expert Reviews in Proteomics. 13(6):579-91
  9. Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis M.J.C., Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Zhang B, Zhang H, Zhang Z, Zhou J, Liebler DC, and the NCI CPTAC. 2015. Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts. Journal of Proteome Research 15(3):691-706
  10. Lie J, Overall CO, Johnson RC, Jones MB, McDermott JE, Heffron F, Adkins JN, Cambronne ED. ChIP-seq analysis of the σE regulon of Salmonella enterica serovar Typhimurium reveals new genes implicated in heat shock and oxidative stress response. PLoS ONE 10(9):e0138466
  11. Webb-Robertson BJ, Wiberg HK, Matzke MM, Brown J, Wang J, McDermott JE, Smith RD, Rodland KD, Metz TO, Pounds JG, Waters KM. 2015. A Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-based Label-free Global Proteomics. Journal of Proteome Research 14(5):1993-2001
  12. McDermott JE, Bruillard P, Overall CO, Gosink L, Lindemann SR. 2015. Prediction of multi-drug resistance transporters using a novel sequence analysis method. F1000 Research 4:60
  13. Li J, Nakayasu ES, Overall CC, Johnson RC, Cambronne ED, Kidwai AS, McDermott JE, Ansong C, Heffron F, Adkins JN. Global analysis of Salmonella alternative sigma factor E on protein translation. Journal of Proteome Research 14(4):1716-26
  14. Li J, Overall CC, Nakayasu ES, Kidwai A, Jones MB, Nguyen NT, McDermott JE, Adkins JN, Heffron F. Analysis of the Salmonella σE regulatory network suggests new mechanisms of virulence regulation. Frontiers in Microbiology doi: 10.3389/fmicb.2015.00027. eCollection 2015 PMID: 25713562
  15. Bilal E, Sakellaropoulos T, Challenge Participants*, Me-las I, Messinis D, Belcastro V, Rhrissorrakrai K, Meyer P, Norel R, Iskandar A, Blaese E, Rice JJ, Peitsch MC, Hoeng J, Stolovitzky G, Alexopoulos LG, Poussin C. 2014. A crowd sourcing approach for the construction of species-specific cell signaling networks. Bioinformatics  *author inclusion
  16. Vartanian K, Mitchell H, Stevens SL, McDermott JE, and Stenzel-Poore MP. 2014. CpG preconditioning regulates miRNA expression that modulates genomic reprogramming associated with neuroprotection against ischemic injury. Journal of Cerebral Blood Flow & Metabolism (JCBFM) 35(2):257-66
  17. Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Nicora CD, Shukla,AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM. 2014. Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements. MCP 13(12):3639-46
  18. Aevermann B, Pickett B, Kumar S, Klem EB, Agnihothram S, Bankhead A III, Bolles M, Chang J, Carter V, Clauss TRW, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kelly S, Law GL, Li C, Long C, Luna ML, Matzke M, McDermott JE, Menachery V, Metz TO, Mitchell H, Monroe ME, Neumann G, Purvine SO, Schepmoes AA, Shukla AK, Sims A, Sova P, Tchitchek N, Tilton SC, Totura AT, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Katze MG, Scheuermann RH. A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection. Nature Scientific Data 1:140033
  19. Kang S, Kahan S, McDermott JE, Flann NS, Shmulevich I. 2014. Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models. Bioinformatics 30(21):3101-8
  20. Zhang B, Wang J, Wang Z, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Kinsinger CR, Rivers RC, Rodriguez HA, Townsend RR, Ellis MJC, Carr SA, Tabb DL, Coffey RJ, Slebos RJC, Liebler DC, *NCI CPTAC Network. 2014. Proteogenomic characterization of human colon and rectal cancer. Nature. (in press) *consortium author listing
  21. McDermott JE, Zhang B, Huang Y, Xu H, Zhao Z. 2014. Integrative Genomics and Computational Systems Medicine. BioMed Research International 945253 PMID: 25025078
  22. Zhao Z, Bing Z, Huang Y, Xu H, McDermott JE. 2014. Computational Methods for Biomedical Big Data. Int. J. Computational Biology and Drug Design 7(2-3):97-101 PMID: 24878722
  23. Zhang B, Huang Y, McDermott JE, Posey RH, Xu H, Zhao Z. Interdisciplinary Dialogue for Education, Collaboration, and Innovation: Intelligent Biology and Medicine In and Beyond 2013. BMC Genomics 14(Suppl 8):S1
  24. Hafen R, Gosink L, Clevland WS, McDermott JE, Rodland K, Kleese-Van Dam K. Trelliscope: A system for detailed visualization in statistical analysis of large complex data. In IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV 2013), October 13-14, Atlanta, Georgia.
  25. Wang J, Webb-Robertson BJ, Matzke MM, Varnum SM, Brown JN, Riensche RM, Adkins JN, Jacobs JM, Hoidal JR, Scholand MB, Pounds JG, Blackburn MR, Rodland KD, McDermott JE. 2013. A Semi-automated Framework for Integrating Expert Knowledge into Disease Marker Identification. Disease Markers. Disease Markers. 35:513-23
  26. McDermott, JE. Reproducibility: Two more red flags for suspect work. Nature 499:284
  27. Hovis K, Mojica S, McDermott JE, Pedersen L, Simhi C, Rank R, Ravel J, Bavoil P. Genus-optimized strategy for the identification of chlamydial type III secretion effectors. Pathogens and Disease 69:213-22
  28. Sanfilippo A., Haack J, McDermott J.E., Stevens S.L., Stenzel-Poore M.P. 2013. Modeling Emergence in Neuroprotective Regulatory Networks. Complex Sciences Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering Volume 126:291-302
  29. Mitchell HD, Eisfeld AJ, Sims AC, McDermott JE, Matzke MM, Webb-Robertson BM, Tilton SC, Tchitchek N, Josset L, Bennecke AG, Chang JH, Metz TO, Neumann G, Baric RS, Kawaoka Y, Katze MG, Waters 2013. A Network Integration Approach to Identify Highly Conserved Regulatory Targets Related to Pathogenicity for Influenza and SARS-CoV Respiratory Viruses. PLoS One 9(6):1522-34. PMID: 23559334
  30. Kim Y, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong CK, Hyduke DR, Metz TO, Adkins 2013. Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes. Mol BioSystems 9:1522-34
  31. Webb-Robertson BJ, Matzke MM, Metz TO, McDermott JE, Walker H, Rodland KD, Pounds JG, Waters KM. 2013. Sequential projection pursuit principal component analysis – dealing with missing data associated with new –omics technologies. BioTechniques 54(3):165-8
  32. Niemann GS, Brown RN, Mushamiri IT, Stufkens A, Smith RD, Adkins JN, McDermott JE, Heffron F. 2013. An RNA-encoded type III secretion signal that requires Hfq. J. Bacteriology 195(10):2119-25. PMID: 23396917
  33. Ansong C, Schrimpe-Rutledge AC, MitchellH, Chauhan S,Jones MB, Kim Y-M, McAteerK, Deatherage B, Dubois JL, Brewer HM, Frank BC, McDermottJE, Metz TO, Peterson SN, Motin VL, Adkins JN. A multi-omic systems approach to elucidating Yersinia virulence mechanisms.Molecular Biosystems 2012. In press.
  34. McDermott JE, Jarman K, Taylor R, Lancaster M, Stevens S, Vartanian K, Stenzel-Poore M, Sanfilippo A. Modeling Dynamic Regulatory Processes in Stroke. PLoS Computational Biology 2012 8(10):e1002722
  35. Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, Shukla AK, Smith RD, Waters KM, McDermott JE, Webb-Robertson BJ. 2013. A comparative analysis of computational approaches to protein quantification in label-free LC-MS proteomics experiments. Proteomics Reviews. In press.
  36. McDermott JE, Wang J, Mitchell H, Webb-Roberston BJ, Hafen R, Ramey J, Rodland K. 2012. Challenges in Biomarker Discovery:  Combining Expert Insights with Statistical Analysis of Complex Omics Data. Expert Opinion On Medical Diagnostics. In press.
  37. Acquaah-Mensah G, Malhotra D, Vulimiri M, McDermott JE, Biswal S.: Suppressed Expression of T-Box Transcription Factors is Important for Senescence in Chronic Obstructive Pulmonary Disease. PLoS Computational Biology 2012 8(7):e1002597
  38. McDermott JE, Vartanian KB, Mitchell H, Stevens SL, Sanfilippo A, Stenzel-Poore MP: Identification and validation of Ifit1 as an important innate immune bottleneck. PLoS ONE 2012, 7(6):e36465.
  39. McDermott JE, Corley C, Rasmussen AL, Diamond DL, Katze MG, Waters KM: Using network analysis to identify therapeutic targets from global proteomics data. BMC systems biology 2012, 6:28.
  40. Archuleta MN, McDermott JE, Resat H, and Edwards J. An adaptive coarse graining method for signal transduction in three-dimensions. Fundamenta Informaticae 2012 118(4): 371-384
  41. Yoon H, Ansong C, McDermott JE, Gritsenko M, Smith RD, Heffron F, Adkins JN: Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella. BMC systems biology 2011, 5:100.
  42. Taylor RC, Sanfilippo A, McDermott JE, Baddeley B, Riensche R, Jensen R, Verhagen M, Pustejovsky J: Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts. Int J Comput Biol Drug Des 2011, 4(1):56-82.
  43. Rasmussen AL, Diamond DL, McDermott JE, Gao X, Metz TO, Matzke MM, Carter VS, Belisle SE, Korth MJ, Waters KM et al: Systems virology identifies a mitochondrial Fatty Acid oxidation enzyme, dodecenoyl coenzyme a delta isomerase, required for hepatitis C virus replication and likely pathogenesis. Journal of virology 2011, 85(22):11646-11654.
  44. Niemann GS, Brown RN, Gustin JK, Stufkens A, Shaikh-Kidwai AS, Li J, McDermott JE, Brewer HM, Schepmoes A, Smith RD et al: Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants. Infect Immun 2011, 79(1):33-43.
  45. McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F: Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol 2011, 2:121.
  46. McDermott JE, Shankaran H, Eisfeld AJ, Belisle SE, Neumann G, Li C, McWeeney SK, Sabourin CL, Kawaoka Y, Katze MG et al: Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems. BMC systems biology 2011, 5(1):190.
  47. McDermott JE, Oehmen CS, McCue LA, Hill E, Choi DM, Stockel J, Liberton M, Pakrasi HB, Sherman LA: A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142. Molecular bioSystems 2011, 7(8):2407-2418.
  48. McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F: Computational prediction of type III and IV secreted effectors in gram-negative bacteria. Infect Immun 2011, 79(1):23-32.
  49. McDermott JE, Archuleta M, Thrall BD, Adkins JN, Waters KM: Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation. PLoS ONE 2011, 6(2):e14673.
  50. McDermott JE, Archuleta M, Stevens SL, Stenzel-Poore MP, Sanfilippo A: Defining the players in higher-order networks: predictive modeling for reverse engineering functional influence networks. Pac Symp Biocomput 2011:314-325.
  51. Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S, Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C et al: A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm. MBio 2011, 2(1):e00325-00310.
  52. McDermott JE, Costa M, Janszen D, Singhal M, Tilton SC: Separating the drivers from the driven: Integrative network and pathway approaches aid identification of disease biomarkers from high-throughput data. Dis Markers 2010, 28(4):253-266.
  53. Buchko GW, Niemann G, Baker ES, Belov ME, Heffron F, Adkins JN, McDermott JE (2011). A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins. Molecular Biosystems. 6(12):2448-58.
  54. Lawrence PK, Kittichotirat W, Bumgarner RE, McDermott JE, Herndon DR, Knowles DP, Srikumaran S: Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates. J Bacteriol 2010, 192(4):1167-1168
  55. Wang J, Zhang J, Li R, Zheng H, Li J, Zhang Y, Li H, Ni P, Li S, Li S, Wang J, Liu D, McDermott J, Samudrala R, Liu S, Wang J, Yang H, Yu J, Wong GK Evolutionary transients in the rice transcriptome. Genomics Proteomics Bioinformatics 2010 8(4):211-28.
  56. Diamond DL, Syder AJ, Jacobs JM, Sorensen CM, Walters KA, Proll SC, McDermott JE, Gritsenko MA, Zhang Q, Zhao R et al: Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics. PLoS Pathog 2010, 6(1):e1000719.
  57. Yoon H, McDermott JE, Porwollik S, McClelland M, Heffron F: Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium. PLoS Pathog 2009, 5(2):e1000306.
  58. Webb-Robertson BJ, McCue LA, Beagley N, McDermott JE, Wunschel DS, Varnum SM, Hu JZ, Isern NG, Buchko GW, McAteer K et al: A Bayesian integration model of high-throughput proteomics and metabolomics data for improved early detection of microbial infections. Pac Symp Biocomput 2009:451-463.
  59. Toepel J, McDermott J, Summerfield TC, Sherman LA: Transcriptional analysis of the unicellular, diazotrophic cyanobacterium Cyanothece Sp. ATCC 51142 grown under short day/night cycles. Journal of Phycology 2009, 45:610-620.
  60. Taylor RC, Singhal M, Weller J, Khoshnevis S, Shi L, McDermott J: A network inference workflow applied to virulence-related processes in Salmonella typhimurium. Annals of the New York Academy of Sciences 2009, 1158:143-158.
  61. Sanfilippo A, Baddeley B, Beagley N, McDermott J, Riensche R, Taylor R, Gopalan B: Using the gene ontology to enrich biological pathways. Int J Comput Biol Drug Des 2009, 2(3):221-235.
  62. Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TRW, Heffron F, Smith RD, and Adkins JN. Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Salmonella Infection. Infection and Immunity 2009, 77(8):3227-33.
  63. Shi L, Ansong C, Smallwood H, Rommereim L, McDermott JE, Brewer HM, Norbeck AD, Taylor RC, Gustin JK, Heffron F, Smith RD, Adkins JN. Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg/pH Medium. J Proteomics Bioinform. 2009; 2:388-397.
  64. Samudrala R, Heffron F, McDermott JE: Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS Pathog 2009, 5(4):e1000375.
  65. McDermott JE, Taylor RC, Yoon H, Heffron F: Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimurium. J Comput Biol 2009, 16(2):169-180.
  66. Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD: Proteomics Analysis of the Causative Agent of Typhoid Fever. J Proteome Res 2008.
  67. Chang AN, McDermott J, Frazier Z, Guerquin M, Samudrala R: INTEGRATOR: interactive graphical search of large protein interactomes over the Web. BMC Bioinformatics 2006, 7:146.
  68. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C et al: The Genomes of Oryza sativa: A History of Duplications. PLoS Biol 2005, 3(2):e38.
  69. Wang W, Zheng H, Yang S, Yu H, Li J, Jiang H, Su J, Yang L, Zhang J, McDermott J et al: Origin and evolution of new exons in rodents. Genome Res 2005, 15(9):1258-1264.
  70. McDermott J, Guerquin M, Frazier Z, Chang AN, Samudrala R: BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes. Nucleic Acids Res 2005, 33(Web Server issue):W324-325.
  71. McDermott J, Bumgarner R, Samudrala R: Functional annotation from predicted protein interaction networks. Bioinformatics 2005, 21(15):3217-3226.
  72. Chang AN, McDermott J, Samudrala R: An enhanced Java graph applet interface for visualizing interactomes. Bioinformatics 2005, 21(8):1741-1742.
  73. McDermott J, Samudrala R: Enhanced functional information from predicted protein networks. Trends Biotechnol 2004, 22(2):60-62.
  74. McDermott J, Samudrala R: Bioverse: functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res 2003, 31(13):3736-3737.
  75. Mayo K, Huseby D, McDermott J, Arvidson B, Finlay L, Barklis E: Retrovirus capsid protein assembly arrangements. J Mol Biol 2003, 325(1):225-237.
  76. McDermott J, Barklis E: EMXtalOrg: an EM tilt data organization and processing system. Ultramicroscopy 2002, 93(1):11-17.
  77. Mayo K, Vana ML, McDermott J, Huseby D, Leis J, Barklis E: Analysis of Rous sarcoma virus capsid protein variants assembled on lipid monolayers. J Mol Biol 2002, 316(3):667-678.
  78. Mayo K, McDermott J, Barklis E: Hexagonal organization of Moloney murine leukemia virus capsid proteins. Virology 2002, 298(1):30-38.
  79. Zuber G, McDermott J, Karanjia S, Zhao W, Schmid MF, Barklis E: Assembly of retrovirus capsid-nucleocapsid proteins in the presence of membranes or RNA. Journal of virology 2000, 74(16):7431-7441.
  80. McDermott J, Mayo K, Barklis E: Three-dimensional organization of retroviral capsid proteins on a lipid monolayer. J Mol Biol 2000, 302(1):121-133.
  81. McDermott J, Karanjia S, Love Z, Barklis E: Crosslink analysis of N-terminal, C-terminal, and N/B determining regions of the Moloney murine leukemia virus capsid protein. Virology 2000, 269(1):190-200.
  82. Barklis E, McDermott J, Wilkens S, Fuller S, Thompson D: Organization of HIV-1 capsid proteins on a lipid monolayer. J Biol Chem 1998, 273(13):7177-7180.
  83. Barklis E, McDermott J, Wilkens S, Schabtach E, Schmid MF, Fuller S, Karanjia S, Love Z, Jones R, Rui Y et al: Structural analysis of membrane-bound retrovirus capsid proteins. Embo J 1997, 16(6):1199-1213.
  84. McDermott J, Farrell L, Ross R, Barklis E: Structural analysis of human immunodeficiency virus type 1 Gag protein interactions, using cysteine-specific reagents. Journal of virology 1996, 70(8):5106-5114.
  85. Wang CT, Zhang Y, McDermott J, Barklis E: Conditional infectivity of a human immunodeficiency virus matrix domain deletion mutant. Journal of virology 1993, 67(12):7067-7076.

Books/book chapters/articles

  1. Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P,  Kim Y, Nakayasu ES, Li J, KidwaiA, NiemannG, Brown RN, Metz TO, McAteer K, HeffronF,  Peterson SN, Motin V, Palsson BO, SmithRD, Adkins, JN. 2012.Integrating Host-Pathogen Interactions using Omics and Modeling for Pathogenic Salmonellae and Yersiniae. Systems Biology. Current Topics in Microbiology and Immunology. Book Chapter (accepted)
  2. Book chapter: Heffron F, G Niemann, H Yoon, AS Kidwai, RN Brown, JE McDermott, RD Smith, and JN Adkins.  2011.  Salmonella secreted virulence factors.  In Salmonella: Genome to Function. Chapter 10.
  3. McDermott J, Samudrala R, Bumgarner R, Montgomery K, Ireton R (eds.): Computational Systems Biology. New York: Humana Press; 2009.
  4. Wichadakul D, McDermott J, Samudrala R: Prediction and integration of regulatory and protein-protein interactions. In: Computational Systems Biology. Edited by Mcdermott J, Samudrala R, Bumgarner R, Montgomery K, Ireton R, vol. 541. New York: Humana Press; 2009: 101-144.
  5. Rashid I, McDermott J, Samudrala R: Inferring molecular interactions pathws from eQTL data. In: Computational Systems Biology. Edited by Mcdermott J, Samudrala R, Bumgarner R, Montgomery K, Ireton R, vol. 541. New York: Humana Press; 2009: 211-224.
  6. Guerquin M, McDermott J, Frazier Z, Samudrala R: The Bioverse API and Web Application. In: Computational Systems Biology. Edited by Mcdermott J, Samudrala R, Bumgarner R, Montgomery K, Ireton R, vol. 541. New York: Humana Press; 2009: 511-534.
  7. Frazier Z, McDermott J, Guerquin M, Samudrala R: Computational representation of biological systems. In: Computational Systems Biology. Edited by Mcdermott J, Samudrala R, Bumgarner R, Montgomery K, Ireton R, vol. 541. New York: Humana Press; 2009: 535-550.
  8. Book chapter: McDermott JE, J Wang, J Yu, and R Samudrala. 2009.  “Prediction and Annotation of Plant Protein Interaction Networks.”  In Application of Genomics and Bioinformatics in Plant Biotechnology, Studium Press
  9. Article: Gorton I., Oehmen C. and McDermott JE. 2008. It takes glue to tango. Scientific Computing. High-performance computing special edition.

6 thoughts on “Works

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  2. Lucas your blog title and said “There are really Mad Scientists in the world? And they make candy?” So I showed him your “about” page and said “Sound familiar?” Yes… but…. so I opened the page with your photo, scrolled down, and HORROR movie screams from Lucas and Galileo. I was rolling on the floor laughing! Uncle Jason, secretly a Mad Scientist. They are very impressed!

  3. Pingback: How long is long: Time in review for scientific publications | The Mad Scientist Confectioner's Club

  4. Pingback: Time to review for scientific publications revisited | The Mad Scientist Confectioner's Club

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