Paul Hengen

Current

Bioinformaticist at NanoString Technologies

Past

Assistant Research Scientist at City of Hope National Medical Center
Staff Scientist at USC Keck School of Medicine
R&D Scientist at Applied Biosystems

Post-Doctoral Fellow and Staff Scientist at National Cancer Institute
Technical Columnist at Trends in Biochemical Sciences

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2 more...

Education

Carleton University
University of Vermont
University of Maryland College Park

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Recommended

5 people have recommended Paul

Connections

261 connections

Industry

Biotechnology

Websites

Paul Hengen’s Summary

I have equal experience in molecular genetics and computational biology. My goal has been to combine computer science and genetics for making discoveries of medical importance. I am particularly interested in the molecular pathology of disease, personalized medicine, and medical or pharmaceutical discovery.

Keywords: Molecular Genetics, Computational Biology, Bioinformatics, Microbiology, Cancer Research.

Paul Hengen’s Specialties:

Gene Target and Biomarker Discovery.

Genetics Domain Object Model Expert, Database Design.

Genetic Data Extraction, Conversion and Analysis (10+ years of Perl programming experience), Combining genotype and gene expression data.

DNA binding-site prediction for annotation (Transcription Factors, Human Splice Junctions), DNA and RNA sequence analysis using DNA sequence Logos (NAR 18:6097-6100) and Walkers (NAR 25:4408-4415).

Paul Hengen’s Experience

Bioinformaticist

NanoString Technologies

(Privately Held; Biotechnology industry)

August 2009 — Present (4 months)

NanoString Technologies manufactures and sells the nCounter Analysis System, a research platform that utilizes a novel digital technology that is based on direct multiplexed measurement of gene expression and offers high levels of precision and sensitivity (<1 copy per cell). The technology uses molecular barcodes and single molecule imaging to detect and count hundreds of unique nucleic acids in a single reaction. Although originally designed for gene expression profiling, the nCounter system can be utilized for direct measurment of individual molecules in a single reaction without amplification for many biological applications. NanoString's technology may be used for basic research, translational medicine, and molecular diagnostics.
Assistant Research Scientist

City of Hope National Medical Center

(Biotechnology industry)

August 2007 — February 2009 (1 year 7 months)

Identified molecular markers of risk for therapy-related
myelodysplastic syndrome (t-MDS) after autologous bone
marrow transplantation with hematopoietic stem cells (HSC).
t-MDS and acute myologenous leukemia (AML) are serious bone
marrow complications following cancer therapy. We used
Affymetrix Gene Chip hybridization arrays to identify genes
misregulated within peripheral blood stem cells (PBSC) and
bone marrow stem cells in patients undergoing bone marrow
transplant (BMT). Gene Set Enrichment Analysis (GSEA)
revealed many genes within cell signaling pathways altered
in their expression levels and these genes were further
analyzed for their potential as therapeutic targets.
Follow-up studies with mathematical models of nuclear
transcription factor binding sites should elucidate the
mechanisms of gene regulation in the development of leukemia
and secondary bone marrow cancers.
Staff Scientist

USC Keck School of Medicine

(Biotechnology industry)

August 2006 — April 2007 (9 months)

As part of a team, worked in collaboration with wet bench
scientists to identify molecular markers of prostate cancer
progression and metastasis to bone. The androgen receptor
(AR) belongs to a family of ligand-activated nuclear
receptors that mediate gene expression through
transcriptional activation. The role of the AR in prostate
cancer initiation and progression is well established;
however, there is little knowledge of how AR target genes
play a role in prostate cancer initiation and progression,
typically resulting in secondary metastasis to the bone
marrow. We combined the laboratory method of ChIP-on-chip
and a bioinformatic approach utilizing a mathematical model
of AR DNA binding sites to discover and characterize novel
AR target genes in prostate cancer cells. The goal was to
investigate the possible role of these genes in formation of
bone marrow cancer.
R&D Scientist

Applied Biosystems

(Biotechnology industry)

April 2000 — August 2005 (5 years 5 months)

For this company, personally designed the genetics object
model for ABI's instrumentation and data analysis software.
This object-oriented domain model, based on fundamental
principles of Mendelian characterization, was designed to be
independent of instrumentation. The design allows for
genetic data to be gathered from phenotype, genotype, and
gene expression information sources and then combined for
the purpose of association studies, mathematical modeling,
and data-mining. The genetics object model was specifically
designed to aid the discovery of new predictors of genetic
processes (biomarkers) and for applications in molecular
medicine.
Post-Doctoral Fellow and Staff Scientist

National Cancer Institute

(Biotechnology industry)

1992 — 1998 (6 years )

As part of a team used information theory techniques
to create mathematical models of DNA binding sites. By
comparing the models to natural binding sites, made
predictions about the properties of DNA-protein
interactions concerning transcriptional regulation (gene
expression) and other molecular recognition. Showed the
feasibility of using such a method for scanning DNA
sequences to predict sites bound by the Factor for Inversion
Stimulation (Fis), a pleiotropic protein that enhances site-
specific recombination, controls DNA replication, and
regulates transcription of a number of genes in Escherichia
coli and Salmonella typhimurium.
Technical Columnist

Trends in Biochemical Sciences

(Biotechnology industry)

1993 — 1997 (4 years )

Authored over 45 articles published as a `Methods and Reagents' monthly series within Trends in Biochemical Sciences from 1993 through 1997. All manuscripts are freely available on the web from my archive site at: http://www-lecb.ncifcrf.gov/~pnh/readme.html

Paul Hengen’s Education

Carleton University

Ph.D. , Molecular Genetics , 1985 — 1991

Activities and Societies:

Tunnel Rat, Canadian Inland Telemark Surf Team, Midnight Canal Skater's Club, Prince of Wales Polar Bear Jacuzzi Runners
University of Vermont

M.S. , Microbiology , 1983 — 1985
University of Maryland College Park

B.S. , Microbiology , 1979 — 1983

Activities and Societies:

Phi Sigma National Honorary Fraternity, Kappa Kappa Psi National Honorary Fraternity, Maryland Marching Band

Additional Information

Paul Hengen’s Websites:

Paul Hengen’s Interests:

I am interested in the molecular pathology of disease, personalized medicine, and medical or pharmaceutical discovery.

Paul Hengen’s Groups:

Carleton University Alumni
Lifesciences Opportunities in US
Chessmasters
University of Vermont Alumni
Computational Biology
Bioinformatics geeks
MolecularLab (Community of Molecular Biology & Biotech companies, students, researchers)
University of Maryland, College Park Alumni Association
Lindy Hop
Personalized Medicine
American Society of Human Genetics (ASHG)
Biomarkers in Discovery & Development
Cancer Sequencing
NGS (Next Generation Sequencing)
Genomics: Next Generation DNA Sequencing (NGS) and Microarray