Kory R Johnson, MS, PhD*

  Curriculum Vitae (CV) ...

   Education

  • PhD*, Bioinformatics, 2008 Candidate
    • George Mason University
      • Thesis Research: 
        • Genomic Profiling of Blood For Stroke Diagnosis
      • Elective Research:
        • Effects of Anthrax on Lung, Liver, and Kidney Gene Expression
  • MS, Biotechnology, 2001
    •  Johns Hopkins University
  • BS, Cell and Molecular Biology and Genetics, 1995
    • University of Maryland

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   Specialized Skills 

  • Biological Systems Analysis
  • BioMarker Discovery
  • Candidate Gene Association
  • ChIP::chip Analysis
  • ChIP::seq Analysis
  • Class Discovery
  • Classification Modeling
  • Clinical Genomics
  • Comparative Genomics
  • Copy Number Variation (CNV) Analysis
  • Exon Analysis
  • Gene Prediction
  • Gene Expression Analysis
  • Mass Spectrometry Analysis (M/Z)
  • Mechanism of Action Analysis
  • Mechanism of Disease Analysis
  • Patient Stratification
  • Predictive Toxicology
  • Promoter Modeling
  • Protein Bioinformatics
  • Sample Size Estimation & Power Analysis
  • Theranostic Modeling
  • Whole Genome Association

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   Software Skills

  • Statistics
    • R, Splus, SAS, MatLab, SPSS
  • Programming
    • Perl, C, HTML, BASIC, Fortran
  • Database
    • Access, SQL, Paradox
  • Web
    • Expressions, FrontPage
  • OS
    • Windows, Macontish, UNIX

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   General Skills

  • Univariate Statistics
    • Probability
    • Hypothesis Testing
    • Analysis of Variance
    • Binary and Count Testing
  • Multivariate Statistics
    • Correlation
    • Covariance
    • Dimension Reduction
    • Regression Analysis
    • Discriminant Analysis
    • Distance-based Analysis

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   Work Experience (14 years)

  • Sep 2006 - Present
    • Senior Bioinformatics Scientist
    • Global Health Sector
    • SRA International, Inc.
      • Currently serve the National Institute of Neurological Disorders and Stroke (NINDS) at the National Institutes of Health (NIH) as the intramural resident Bioinformatics Subject Matter Expert.             
        • Provide omics-based research support (i.e., experiment design, analysis, interpretation, planning) for:
          • Laboratory of Molecular Biology, Stem Cell Differentiation and Re-Programming, PI: Dr. Ron McKay
          • Developmental and Metabolic Neurology Branch, Gauchers Disease Research, Dr. Roscoe Brady
          • Human Motor Control Section, Epoch Modeling for Mind Prediction, PI: Dr. Mark Hallett
          • Surgical and Molecular Neuro-Oncology Unit, Glioblastoma Research, PI: Dr. John Park
          • Viral Immunology Section, Multiple Sclerosis Research, PI: Dr. Steve Jacobson
          • Cellular Immunology Section, Multiple Sclerosis Research, PI: Dr. Bibi Bielekova
          • Clinical Diseases Section, Multiple Sclerosis Research, PI: Dr. Henry McFarland
          • Cellular and Developmental Neurobiology Section, Neuron Development and Migration Control, PI: Dr. Susan Wray
          • Developmental Genetics Section, Oligodendrocyte Differentiation and Fate, PI: Dr. Lynn Hudson
          • Stroke Neuroscience Unit, Stroke Research, PI: Dr. Alison Baird
          • Clinical Investigations Section, Stroke Research, Dr. John Hallenbeck
          • Surgical Neurology Branch, Von Hippel-Lindau Disease Research,PI: Russell Lonser
      • Provide intern mentoring (2/year)
      • Offer/Teach annual course in bioinformatics and statistics
      • Manage/Maintain bioinformatics related software applications for institute
      • Represent institute in cross-disciplined project teams and at conferences.

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  • Jan 2006 - Sep 2006
    • Senior Research Biostatistician
    • Genomics Division
    • Gene Logic, Inc.
      • Provided genomics based analysis services; including: Gene Expression Analysis, Patient Stratification, Clinical Genomics, Biological Systems Analysis, BioMarker Discovery, and Predictive Toxicology.  
      • Represented Division in cross-disciplined project teams, performed client interfacing, and provided statistical input/guidance to toxicogenomic, pharmacogenomic, product development, business development, and marketing staff as needed.

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  • Jan 2003 - Jan 2006
    • Research Biostatistician
    • Genomics Division
    • Gene Logic, Inc.
      • Provided genomics based analysis services; including:  Gene Expression Analysis, Patient Stratification, Clinical Genomics, Biological Systems Analysis, BioMarker Discovery, and Predictive Toxicology.  
      • Developed statistical methodology for various genomics based software solutions; including:                                                
        • Pathway PrioritizerTM, a biological systems analysis solution that        accepts gene expression data and rank prioritizes biological pathways using Mahalanobis Distance in conjunction with the Chi-square probability distribuition.
        • Marker/XTM, a biomarker discovery solution that uses the one sample t-test in conjunction with reference gene expression to identify markers for a specified target class.
        • ToxShieldTM, a drug safety solution that uses Partial Least Squares Regression based models to predict liver toxicity or heart toxicity.

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  • Jan 2000 - Jan 2003
    • Associate Research Biostatistician
    • Genomics Division
    • Gene Logic, Inc.
      • Researched and developed methods for predicting human toxicity using rat gene expression.  Methods included: Principal Component Regression (PC-R), Forward Selection, Discriminant Analysis (DA), and Partial Least Squares Regression (PLSR). 
      • Performed gene expression analysis for 200+ animal dose studies; totaling more than 10,000+ samples.

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  • Jan 1999 – Jan 2000
    • Bioinformatics Research Analyst
    • Gene Discovery Group
    • Gene Logic, Inc.                                    
      • Performed EST sequence analysis in the goal to identify novel markers of toxicity. 
      • Responsibilities included: EST sequence scoring, trimming, masking, clustering, and BLAST analysis.  

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  • Jan 1998 – Jan 1999
    • Research Scientist
    • Gene Discovery Group
    • Gene Logic, Inc.
      • Researched and developed high-throughput compound screening methods and gene discovery technologies; including:  bDNA, multiplexed Q-RT-PCR, ACLARA, and micro-sample amplification. 

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  • May 1996 – Jan 1998
    • Research Group Leader
    • Co-Founder
    • Gene Discovery Group
    • Gene Logic, Inc.
      • Founded and led genomics based service group responsible for RNA extraction, RNA isolation, cDNA synthesis, RFLP (radioisotope, infrared, fluorescent), Band Recovery, Band Amplification, Band Purification, and DNA Sequencing (fluorescent). 
      • Related responsibilities included: LIMS development, reagent manufacturing, quality control, protocol development, protocol optimization, personnel management, personnel recruitment, personnel training, development of and adherence to an operations budget, equipment management, equipment maintenance, equipment evaluation, programming of robotics (Biomek, Hamilton, Multimek), and lab safety.

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  • May 1995 – May 1996
    • Research Associate
    • Gene Discovery Group
    • Human Genome Sciences, Inc.
      • Performed high-throughput DNA Cloning, PCR, and DNA Sequencing in the goal to discover novel expressed genes in Human, Rat, Mouse, Fly, Plant, and select bacteria.

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  • May 1994 – May 1995
    • Clinical Data Supervisor
    • Battelle, Inc.
      • Served at the National Cancer Institute (NCI)
      • Supervised data management staff and related activities; including: clinical data collection, data curation, data entry, data validation, data certification, and code book compilation.

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   Teaching Experience

  • 2006 - Present
    • Course:       Applied Bioinformatics & Statistics
    • Offered:       Annually
    • At:              National Institutes of Health (NIH)
    • Duration:     12 weeks, 1 session/week
    • Audience:    Clinical Professionals

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  • 2008
    • Course:       Gene Expression Analysis
    • Offered:       Annually
    • At:              George Mason University
    • Duration:     1 class (invited)
    • Audience:    Graduate-level Students

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   Mentoring Experience

  • 2006 - Present
    • NIH Summer Research Internship Program
    • 2 Interns/Summer (3 mos)
      • Responsibilities include: project definition, project planning, training, direction, and supervision.

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   Published Work

  • Lau P, Verrier J, Nielsen J, Johnson K, Notterpek L, Hudson L. "Identification of dynamically regulated microRNA and mRNA networks in developing oligodendrocytes." Journal of Neuroscience, Nov 2008, 28(45):11720-30.  [PMID: 18987208]

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  • Jarboe J, Johnson K, Choi Y, Lonser R, Park J. "Expression of interleukin-13 receptor alpha2 in glioblastoma multiforme: implications for targeted therapies". Cancer Research, Sep 2007, 1;67(17):7983-6.  [PMID: 17804706]

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   Presented Work

  • IDENTIFICATION OF miRNA REGULATORY NETWORKS IN NEURONAL AND OLIGODENDROCYTE PROGENITORS
    Society of Neuroscience, Annual Meeting, November 2008
    P. Lau, J. Nielsen, D. Maric, K. Johnson, J. Barker, L. Hudson.

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  • GENOMIC PROFILING OF BLOOD FOR STROKE DIAGNOSIS
    NIH Fall Research Festival, Genomics Session,     October 2008
    K. Johnson, A. Baird, Y. Fann.

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  • EPOCH MODELING FOR MIND PREDICTION
    The National Institutes of Health (NIH) Summer Research Symposium, Neuroscience Session, August 2008
    M. Pfifer, C. Bonin, K. Johnson, M. Hallet.

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  • pathFINDER: A WEB-BASED RESOURCE FOR THE INVESTIGATION OF SIGNAL TRANSDUCTION
    The National Institutes of Health (NIH) Summer Research Symposium, Neuroscience Session, August 2008
    J. Parker, A. Yavatkar, B. Sumal, Y. Fann, K. Johnson, W. Odenwald.

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  • GOPHER-DB: A REFERENCE DATABASE OF GENE ONTOLOGY AND PATHWAY ENCODED HIERARCHIES
    The National Institutes of Health (NIH) Summer Research Symposium, Neuroscience Session, August 2008
    C. Hansen, K. Johnson, A. Yavatkar, Y. Fann.

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  • GENOMIC PROFILING OF BLOOD FOR STROKE DIAGNOSIS
    Intelligent Systems for Molecular Biology Conference (ISMB), Functional Genomics Session, July 2008
    K. Johnson, A. Baird, Y. Fann.

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  • HLA ASSOCIATION ANALYSIS AND MODELING FOR MULTIPLE SCLEROSIS
    The National Institutes of Health (NIH) Summer Research Symposium, Neuroscience Session, August 2007
    B. Bennett, K. Johnson, A. Yavatkar, N. Jeffries, S. Adams, Y. Fann.

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  • GOPHER: GENE ONTOLOGY AND PATHWAY HIERARCHY ENCODER
    The National Institutes of Health (NIH) Research Symposium, Neuroscience Session, August 2007,
    C. Merris, K. Johnson, A. Yavatkar, Y. Lin, Y. Fann.

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  • IDENTIFICATION OF CANDIDATE TISSUE BIOMARKERS ASSOCIATED WITH HISTOPATHOLOGIC GRADE IN PROSTATIC ADENOCARCINOMA
    The American Association for Cancer Research (AACR), BioMarker Session, April 2006
    K. Johnson, L. Mertz.

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  • RAPID IDENTIFICATION OF BIOLOGICAL PATHWAY REGULATION USING GENE EXPRESSION DATA AND A NOVEL ALGORITHM BASED ON MAHALANOBIS DISTANCE
    Intelligent Systems for Molecular Biology Conference (ISMB), Pathway Network Session, June 2005
    K. Johnson, M. Elashoff, A. Castle, L. Mertz.

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  • LEPTIN ACTION IN ADIPOSE TISSUE: THE IDENTIFICATION OF BIOMARKERS USING GENE EXPRESSION DATA AND A NOVEL ALGORITHM BASED ON MAHALANOBIS DISTANCE
    Intelligent Systems for Molecular Biology Conference (ISMB), Pathway Network Session, June 2005
    Q. Lu, K. Johnson, P. Kulkarni, L. Mertz.

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  • A COMPARISON BETWEEN AN ONCOLOGY GENE EXPRESSION DATABASE FROM MULTIPLE SOURCES (ONCOMINE) AND A DATABASE FROM A SINGLE LABORATORY
    The American Association for Cancer Research (AACR), Database Session, April 2005
    C. Morehouse, J. Zeugin, K. Johnson, M. Kuziora, J. Cossman, E. Kaldjian.

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  • GENE EXPRESSION PROFILING FOR PREDICTION OF TREATMENT RESPONSE
    American Society of Clinical Oncology (ASCO), Tumor Biology Session, June 2004
    K. Johnson, J. Gotleib, M. Elashoff, D. Schwartz, L. Mertz, J. Cossman.

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  • CONCORDANCE OF TOXICOGENOMIC PREDICTIONS AND MECHANISTIC ANALYSIS FOR COMPOUNDS TESTED IN BOTH RAT LIVER AND PRIMARY RAT HEPATOCYTES
    Society of Toxicology (SOT), Gene Expression Session, March 2003
    M. Orr, B. Higgs, K. Johnson, A. Castle, and D. Mendrick.

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  • USING GENE MARKERS IDENTIFIED FROM A LARGE DATABASE BUILT WITH PRIMARY RAT HEPATOCYTES FOR PREDICTION OF HUMAN HEPATOTOXICITY
    Society of Toxicology (SOT), Biomarkers of Exposure and Effects Session, March 2003
    D. Mendrick, B. Higgs, K. Johnson, M. Porter, A. Castle, M. Orr.

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  • LIVER TOXICITY PREDICTION AND CLASSIFICATION USING MICROARRAY DATA: APPLICATION OF REFERENCE DATA-TRAINED MODELS TO CUSTOMER DATA SETS
    Society of Toxicology (SOT), Biomarkers of Exposure and Effects Session, March 2003
    A. Castle, K. Johnson, B. Higgs, M. Porter, M. Elashoff, C. Chang, D. Mendrick.

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  • IDENTIFICATION OF LIVER TOXICITY USING CLINICAL CHEMISTRY VERSUS GENE EXPRESSION MICROARRAY FACTORS
    Society of Toxicology (SOT), Evaluation of Hepatotoxicity Mechanism Session, March 2003
    M. Elashoff, W. Zeng, A. Castle, K. Johnson, B. Higgs, M. Porter, C. Chang, D. Mendrick.

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  • COMPARISON OF MICROARRAY DATA GENERATED FROM THE SAME RNA FROM 19 DIFFERENT PROCESSING SITES
    Society of Toxicology (SOT), Evaluation of Hepatotoxicity Mechanism Session, March 2003
    M. Porter, A. Castle, K. Johnson, B. Higgs, M. Elashoff, C. Chang, D. Mendrick.

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  • PREDICTIVE MODELING OF HEPATOTOXICANTS USING MICROARRAYS AND A LINEAR DISCRIMINANT MODELING APPROACH
    Intelligent Systems for Molecular Biology Conference (ISMB), Gene Expression Session, August 2002
    K. Johnson, A. Castle, B. Higgs, M. Porter, M. Elashoff, D. Mendrick.

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  • CROSS COMPOUND PREDICTIONS USING GENE EXPRESSION PROFILES FROM ACETAMINOPHEN OR CARBON TERACHLORIDE, TWO STRUCTURALLY DISTINCT LIVER TOXICANTS
    Society of Toxicology (SOT), Comparative and Predictive Toxicogenomics Session, March 2002
    D. Menderick, M. Elashoff, A. Castle, K. Johnson, M. Porter, H. Sun, C. Chang, M. Orr.

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  • PREDICTING TOXICITY IN TWO DISTINCT SECTIONS OF THE KIDNEY VIA MICROARRAY ANALYSIS
    Society of Toxicology (SOT), Comparative and Predictive Toxicogenomics Session, March 2002
    M. Orr, M. Elashoff, A. Castle, K. Johnson, M. Porter, H. Sun, C. Chang, D. Menderick.

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  • IDENTIFICATION THROUGH GENE EXPRESSION OF A TOXIC RESPONSE IN THE RAT FOR A COMPOUND THAT EXHIBITS OVERT TOXICITY IN HUMANS, BUT NOT IN RATS
    Society of Toxicology (SOT), Comparative and Predictive Toxicogenomics Session, March 2002
    M. Porter, M. Elashoff, K. Johnson, A. Castle, M. Orr, H. Sun, C. Chang, D. Menderick.

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  • PREDICTIVE MODELING OF HEPATOTOXICANTS USING MICROARRAYS
    Society of Toxicology (SOT), Predictive Toxicogenomics Session, March 2002
    A. Castle, M. Porter, M. Elashoff, K. Johnson, H. Sun, M. Orr, C. Chang, D. Mendrick.

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   Protected Work

  • MOLECULAR TOXICOLOGY MODELING – RAT HEART (WO 03068908)
    D. Mendrick, M. Porter, K. Johnson, B. Higgs, A. Castle, M. Elashoff, Gene Logic, Inc.
    Describes the working embodiment of genes that are predictive for General Cardiotoxicity, Cardiotoxicity-associated Pathologies, and known Cardiotoxins.

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  • MOLECULAR TOXICOLOGY MODELING – RAT PRIMARY HEPATOTOCYTES (WO 03065993)
    D. Mendrick, M. Porter, K. Johnson, B. Higgs, A. Castle, M. Orr, M. Elashoff, Gene Logic, Inc.
    Describes the working embodiment of genes that are predictive for General Primary Rat Hepatocyte Toxicity, Primary Rat Hepatocyte Toxicity-associated Pathologies, and known Primary Rat Hepatocyte Toxins.

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  • MOLECULAR TOXICOLOGY MODELING – RAT LIVER (WO 03064624)
    D. Mendrick, M. Porter, K. Johnson, B. Higgs, A. Castle, M. Elashoff, Gene Logic, Inc.
    Describes the working embodiment of genes that are predictive for General Hepatotoxicity, Hepatotoxicity-associated Pathologies, and known Hepatotoxins.

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  • MOLECULAR TOXICOLOGY MODELING – RAT KIDNEY (WO 02095000)
    D. Mendrick, M. Porter, K. Johnson, B. Higgs, A. Castle, M. Elashoff, Gene Logic, Inc.
    Describes the working embodiment of genes that are predictive for General Nephrotoxicity, Nephrotoxicity-associated Pathologies, and known Nephrotoxins.

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   Acknowledged Work

  • Yavatkar AS, Lin Y, Ross J, Fann Y, Brody T, Odenwald WF: Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis. BMC Genomics. 2008, 9:106. [PMID: 18307801]

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  • Katz S, Irizarry R, Lin X, Tripputi M, Porter M: A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. BMC Bioinformatics. 2006, 7:464.  [PMID: 17059591]

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   Awards

  • 2008
    • Merit Award for Excellence, NINDS, NIH

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   Memberships

  • 2006 - Present
    • American Statistical Association
    • Virginia Academy of Sciences
    • Washington Statistical Society

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  • 2002 - Present
    • International Society for Computational Biology

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   Federal Clearance

  • 2006 - Present
    • Public Trust

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