Education
George Mason University, Fairfax, VA
Thesis Research ( available here ):
Genomic Profiling of Blood For Stroke Diagnosis
Elective Research:
Effects of Anthrax on Lung, Liver, and Kidney Gene
Expression
Johns Hopkins University, Baltimore, MD
University of Maryland, College Park, MD
Specialized Skills
Software Skills
Ingenuity, Genespring, Partek, Spotfire, Lasergene,
MacVector, Genomatix, CLC Workbench, miRBase,
TargetScan, Mobyle, Galaxy, SWISS-PROT, WHAT IF,
BLAST
R, Splus, SAS, MatLab, SPSS
Perl, C, HTML, BASIC, Fortran
Access, SQL, Paradox
Expressions, FrontPage
Windows, Macontish, UNIX
General Skills
- Probability
- Hypothesis Testing
- Analysis of Variance
- Binary and Count Testing
- Correlation
- Covariance
- Dimension Reduction
- Regression Analysis
- Discriminant Analysis
- Distance-based Analysis
Work Experience
Senior Bioinformatics Scientist,
KELLY Government Solutions, Inc.
Description/Responsibilities:
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. Specifically:
- Provide omics-based research support
- Provide intern mentoring
- Manage bioinformatics software for Institute
- Represent Institute in cross-disciplined project
teams and at conferences.
Senior Member of the Professional Staff,
SRA International, Inc.
Senior Research Biostatistician,
Genomics Division,
Gene Logic, Inc.
Provide genomics-based analysis services for Clients;
including: Gene Expression Analysis, Patient
Stratification, Clinical Genomics, Biological Systems
Analysis, BioMarker Discovery, and Predictive
Toxicology.
Represent Division in cross-disciplined project teams,
Client interfacing, and provide statistical
input/guidance to toxicogenomic, pharmacogenomic,
product development, business development, and
marketing staff as needed.
Research Biostatistician,
Develop genomics-based solutions for commercial
licensing.
Associate Research Biostatistician,
Research and develop methods for predicting human
toxicity using rat gene expression (e.g., Principal
Component Regression, Forward Selection,
Discriminant Analysis, Partial Least Squares
Regression).
Perform gene expression analysis on 200+ human
toxin rat studies; totaling more than 10,000+ samples.
Bioinformatics Research Analyst,
Genomics Division Division,
Perform EST sequence analysis (i.e., mask, trim,
cluster, BLAST) in the goal to identify novel markers
of toxicity.
Research Scientist,
Research & Development Division,
Research and develop high-throughput compound
screening methods and emerging technologies (e.g.,
bDNA, multiplexed Q-RT-PCR, ACLARA, and micro-
sample amplification).
Research Group Leader,
Gene Discovery Group,
Co-Founder,
Lead research group responsible for RNA extraction,
RNA isolation, cDNA synthesis, RFLP (radioisotope,
infrared, fluorescent), Band Recovery, Band
Amplification, Band Purification, and DNA Sequencing
(fluorescent).
Recruit, train, and manage group personnel.
Develop and adhere to operations budget.
Supervise activities related to group; including: LIMS
development, reagent manufacturing, quality control,
protocol development, protocol optimization,
equipment use, equipment maintenance,
programming of robotics, and lab safety.
Research Associate,
Human Genome Sciences, Inc.
Performhigh-throughput DNA Cloning, PCR, and DNA
Sequencing in the goal to discover novel expressed
genes in Human, Rat, Mouse, Fly, Plant, and select
bacteria.
Clinical Data Supervisor,
National Cancer Institute (NCI),
Battelle, Inc.
Supervise data management staff and related
activities; including: clinical data collection, data
curation, data entry, data validation, data certification,
and code book compilation.
Teaching Experience (Part-time, Evening)
Position: Adjunct Assistant Professor
Level: Graduate
Courses: Microarray Methodology ( BINF636 )
Gene Expression Analysis ( BINF733 )
Courses: Molecular Biology ( BIOT601 )
Introduction to Bioinformatics ( BIOT630 )
Mentor Experience
- Program: NINDS Summer Research Internship
( click here to learn more )
- Duration: 3 months per year
- Number of Interns mentored per Duration: 1-2
Published Work
Oskvig DB, Elkahloun AG, Johnson KR, Phillips TM,
Herkenham M. "Maternal immune activation by LPS
selectively alters specific gene expression profiles of
interneuron migration and oxidative stress in the fetus
without triggering a fetal immune response. Brain,
Behavior, and Immunity. 2012;26(1). Epub Jan 30.
[ PMID: TBA ]
Li X, Johnson KR, Bryant M, Elkahloun AG, Amar M,
Remaley AT, De Silva R, Hallenbeck JM, Quandt JA.
"Intranasal Delivery of E-Selectin Reduces
Atherosclerosis in ApoE-/- Mice". PLoS One.
2011;6(6):e20620. Epub 2011 Jun 20.
[ PMID: 21701687 ]
Lovas G, Nielsen JA, Johnson KR, Hudson LD.
"Alterations in neuronal gene expression profiles in
response to experimental demyelination and axonal
transection". Multiple Sclerosis. 2010 Mar;16(3):303-
16. Epub 2010 Jan 19.
[ PMID: 20086029 ]
Friedman JS, Ray JW, Waseem N, Johnson KR,
Brooks MJ, Hugosson T, Breuer D, Branham KE,
Krauth DS, Bowne SJ, Sullivan LS, Ponjavic V,
Gränse L, Khanna R, Trager EH, Gieser LM,
Hughbanks-Wheaton D, Cojocaru RI, Ghiasvand NM,
Chakarova CF, Abrahamson M, Göring HH,
Webster AR, Birch DG, Abecasis GR, Fann Y,
Bhattacharya SS, Daiger SP, Heckenlively JR,
Andréasson S, Swaroop A. "Mutations in a BTB-
Kelch protein, KLHL7, cause autosomal-dominant
retinitis pigmentosa". Am J Hum Genet., Jun 2009,
84(6):792-800.
[ PMID: 19520207 ]
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 ]
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 ]
Presented Work
DYNAMICS OF AN INNATE MYELOID CELL
RESPONSE TO ACUTE CNS VIRAL INFECTION
NIH 2011 Fall Research Festival
D. Nayak, S. Heydari, B. Zinselmeyer, K. Johnson,
D. McGavern
GENOME-WIDE TRANSCRIPTOME
SEQUENCING REVEALS THE RELATIONSHIP
BETWEEN GENE EXPRESSION, SNP AND
MIRNA IN BRAIN
NINDS 2011 Summer Research Symposium
M. Chang, C. Sun, S. Wang, W. Chang, Y. Lee,
K. Johnson, Y. Fann
NINDS STEM CELL DATA MANAGEMENT
SYSTEM: GROUP COMPARISON ANALYSIS
B. Carpenter, A. Yavatkar, K. Johnson, Y. Fann
AN OBJECTIVE CRITERIA TO CORRECT NOISE
OF DIGITAL GENE EXPRESSION
BIT2011
W. Chuang, K. Johnson, Y. Fann, U. Yang
QUANTITATIVE DIFFERENCES IN ANTIBODY
RESPONSES BETWEEN NORMAL DONORS,
HAM/TSP PATIENTS, ASYMPTOMATIC CARRIERS
AND ATL PATIENTS FROM JAMAICA: ESTIMATION
OF DISEASE RISK
HTLV1 2011
Y. Akahata, A. Abrams, K. Johnson , J. Goedert,
E. Maloney, S. Jacobson
SIGNALING THOUGH HIGH-VERSUS
INTERMEDIATE-AFFINITY INTERLEUKIN-2 (IL-2)
RECEPTOR PROVIDES QUALITATIVELY
DIFFERENT SIGNALS TO T CELLS
NINDS 2011 Spring Research Retreat
P. Han, J. Perry, K. Johnson , B. Bielekova
GOPHER: A WEB-BASED TOOL FOR BIOLOGICAL
NETWORK ANALYSIS USING GENE EXPRESSION
ISMB 2010
K. Johnson , T. Reed, A. Yavatkar, Y. Fann
PASSER: POWER ANALYSIS AND SAMPLE SIZE
ESTIMATION RESOURCE
NIH 2009 Summer Research Symposium
P. Grant, K. Johnson , A. Yavatkar, Y. Fann.
IDENTIFICATION OF miRNA REGULATORY
NETWORKS IN NEURONAL AND
OLIGODENDROCYTE PROGENITORS
SON 2008
P. Lau, J. Nielsen, D. Maric, K. Johnson , J. Barker,
L. Hudson.
GENOMIC PROFILING OF BLOOD FOR STROKE
DIAGNOSIS
NIH 2008 Fall Research Festival
K. Johnson , A. Baird, Y. Fann.
EPOCH MODELING FOR MIND PREDICTION
NIH 2008 Summer Research Symposium
M. Pfifer, C. Bonin, K. Johnson , M. Hallet.
PATHFINDER: A WEB-BASED RESOURCE FOR
THE INVESTIGATION OF SIGNAL
TRANSDUCTION
J. Parker, A. Yavatkar, B. Sumal, Y. Fann,
K. Johnson , L. Eiden.
GOPHER-DB: A REFERENCE DATABASE OF
GENE ONTOLOGY AND PATHWAY ENCODED
HIERARCHIES
C. Hansen, K. Johnson , A. Yavatkar, Y. Fann.
ISMB 2008
K. Johnson, A. Baird, Y. Fann.
HLA ASSOCIATION ANALYSIS AND MODELING
FOR MULTIPLE SCLEROSIS
NIH 2007 Summer Research Symposium
B. Bennett, K. Johnson , A. Yavatkar, N. Jeffries,
S. Adams, Y. Fann.
GOPHER: GENE ONTOLOGY AND PATHWAY
HIERARCHY ENCODER
C. Merris, K. Johnson , A. Yavatkar, Y. Lin, Y. Fann.
IDENTIFICATION OF CANDIDATE TISSUE
BIOMARKERS ASSOCIATED WITH
HISTOPATHOLOGIC GRADE IN
PROSTATIC ADENOCARCINOMA
AACR 2006
K. Johnson , L. Mertz.
RAPID IDENTIFICATION OF BIOLOGICAL
PATHWAY REGULATION USING GENE
EXPRESSION DATA AND A NOVEL ALGORITHM
BASED ON MAHALANOBIS DISTANCE
ISMB 2005
K. Johnson , M. Elashoff, A. Castle, L. Mertz.
LEPTIN ACTION IN ADIPOSE TISSUE: THE
IDENTIFICATION OF BIOMARKERS USING GENE
Q. Lu, K. Johnson , P. Kulkarni, L. Mertz.
A COMPARISON BETWEEN AN ONCOLOGY
GENE EXPRESSION DATABASE FROM MULTIPLE
SOURCES (ONCOMINE) AND A DATABASE FROM
A SINGLE LABORATORY
AACR 2005
C. Morehouse, J. Zeugin, K. Johnson , M. Kuziora,
J. Cossman, E. Kaldjian.
GENE EXPRESSION PROFILING FOR
PREDICTION OF TREATMENT RESPONSE
ASCO 2004
K. Johnson , J. Gotleib, M. Elashoff, D. Schwartz,
L. Mertz, J. Cossman.
CONCORDANCE OF TOXICOGENOMIC
PREDICTIONS AND MECHANISTIC ANALYSIS
FOR COMPOUNDS TESTED IN BOTH RAT LIVER
AND PRIMARY RAT HEPATOCYTES
SOT 2003
M. Orr, B. Higgs, K. Johnson , A. Castle, D. Mendrick.
USING GENE MARKERS IDENTIFIED FROM A
LARGE DATABASE BUILT WITH PRIMARY RAT
HEPATOCYTES FOR PREDICTION OF HUMAN
HEPATOTOXICITY
D. Mendrick, B. Higgs, K. Johnson , M. Porter, A.
Castle, M. Orr.
LIVER TOXICITY PREDICTION AND
CLASSIFICATION USING MICROARRAY DATA:
APPLICATION OF REFERENCE DATA-TRAINED
MODELS TO CUSTOMER DATA SETS
A. Castle, K. Johnson , B. Higgs, M. Porter,
M. Elashoff, C. Chang, D. Mendrick.
IDENTIFICATION OF LIVER TOXICITY USING
CLINICAL CHEMISTRY VERSUS GENE
EXPRESSION MICROARRAY FACTORS
M. Elashoff, W. Zeng, A. Castle, K. Johnson ,
B. Higgs, M. Porter, C. Chang, D. Mendrick.
COMPARISON OF MICROARRAY DATA
GENERATED FROM THE SAME RNA FROM 19
DIFFERENT PROCESSING SITES
M. Porter, A. Castle, K. Johnson , B. Higgs,
PREDICTIVE MODELING OF HEPATOTOXICANTS
USING MICROARRAYS AND A LINEAR
DISCRIMINANT MODELING APPROACH
ISMB 2002
K. Johnson , A. Castle, B. Higgs, M. Porter,
M. Elashoff, D. Mendrick.
CROSS COMPOUND PREDICTIONS USING GENE
EXPRESSION PROFILES FROM
ACETAMINOPHEN OR CARBON TERACHLORIDE,
TWO STRUCTURALLY DISTINCT LIVER
TOXICANTS
SOT 2002
D. Menderick, M. Elashoff, A. Castle, K. Johnson ,
M. Porter, H. Sun, C. Chang, M. Orr.
PREDICTING TOXICITY IN TWO DISTINCT
SECTIONS OF THE KIDNEY VIA MICROARRAY
ANALYSIS
M. Orr, M. Elashoff, A. Castle, K. Johnson , M. Porter,
H. Sun, C. Chang, D. Menderick.
IDENTIFICATION THROUGH GENE EXPRESSION
OF A TOXIC RESPONSE IN THE RAT FOR A
COMPOUND THAT EXHIBITS OVERT TOXICITY
IN HUMANS, BUT NOT IN RATS
M. Porter, M. Elashoff, K. Johnson, A. Castle, M. Orr,
USING MICROARRAYS
A. Castle, M. Porter, M. Elashoff, K. Johnson, H. Sun,
M. Orr, C. Chang, D. Mendrick.
Protected Work
A. Baird, D. Moore, K. Johnson
Describes the working embodiment of genes that
are predictive for Hemorrhagic Stroke.
D. Mendrick, M. Porter, K. Johnson, B. Higgs,
A. Castle, M. Elashoff
are predictive for General Cardiotoxicity,
Cardiotoxicity-associated Pathologies, and known
Cardiotoxins.
A. Castle, M. Orr, M. Elashoff
are predictive for General Primary Rat Hepatocyte
Toxicity, Primary Rat Hepatocyte Toxicity-
associated Pathologies, and known Primary Rat
Hepatocyte Toxins.
are predictive for General Hepatotoxicity,
Hepatotoxicity-associated Pathologies, and known
Hepatotoxins.
Describes the working embodiment of genes that are
predictive for General Nephrotoxicity, Nephrotoxicity-
associated Pathologies, and known Nephrotoxins.
Acknowledged Work
Ryschkewitsch CF, Jensen PN, Monaco MC, Major
EO. "JC virus persistence following progressive
multifocal leukoencephalopathy in multiple sclerosis
patients treated with natalizumab". Ann Neurol. 2010
Sep;68(3):384-91.
( PMID: 20818792 )
Famakin B, Weiss P, Hertzberg V, McClellan W,
Presley R, Krompf K, Karp H, Frankel MR.
"Hypoalbuminemia Predicts Acute Stroke Mortality:
Paul Coverdell Georgia Stroke Registry." J Stroke
Cerebrovasc Dis. 2010 Jan;19(1):17-22.
( PMID: 20123222 )
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 )
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 )
Reviewer History
Awards & Nominations
Memberships
Federal Clearance
Bioinformatics Scientist
Mentor
Advisor
Consultant
Entrepreneur
Professor
Researcher
Reviewer