Walter Jessen

Summary

I have several years of academic and industrial experience in the areas of bioinformatics and computational biology, with a focus on the integration of disparate sets of data to provide a broader understanding of the signals and mechanisms regulating disease development and progression. I am particularly interested in the etiology, prevention, diagnosis and treatment of neurological and oncological disease. I frequently present biological and statistical data to scientists, physicians and non-scientists, and am very comfortable communicating research and technology to others. I excel at translating research results into understandable language and formats. My Ph.D. research was completed as a wet bench scientist and focused on the molecular mechanisms of nucleosome remodeling at the Saccharomyces cerevisiae PHO5 promoter, extending the use of bacterial DNA methyltransferases as in vivo probes of chromatin structure. I am very interested in the use of internet technologies to enhance scientific collaboration, the development of a networked science culture, and the advancement of open source science.

Specialties

biomarkers, personalized medicine, functional genomics, comparative genomics, cancer neurobiology, molecular biology, statistical and computational methods, biological interpretation, medicine 2.0, health 2.0, science 2.0

Experience

Knowledge Curator

Biomarker Commons, http://biomarkercommons.org

Privately Held; Biotechnology industry
June 2010 – Present

Continually identifies, aggregates, filters, organizes, contextualizes and shares the most relevant news and research content on biomarkers. Builds custom data feeds to manipulate data from external sources. Manages various types of user communications tools (email subscriptions, RSS, Mendeley, Twitter). Built and administrates the site using the Drupal content management system.

Computational Biologist

Covance: Discovery and Translational Services, Biomarker Center of Excellence

Public Company; CVD; Pharmaceuticals industry
April 2010 – Present

Designs, implements and applies cutting edge computational methods to analyze and integrate data from a wide variety of sources including clinical data, literature and high-throughput genomic or proteomic platforms. Works closely with scientists, clinicians, statisticians, and software engineers to support the discovery and application of biomarkers in the clinical setting.

• Routinely interacts with colleagues to mine, analyze and interpret complex biological data
• Develops computational infrastructure to support Biomarker Center of Excellence
• Develops computational tools and interfaces to support biomarker data mining
• Performs data analysis on complex scientific problems
• Develops computational methods and algorithms for the analysis of complex biological data

Founder and Executive Editor

Highlight HEALTH, http://www.highlighthealth.net

Privately Held; Online Media industry
December 2006 – Present

Highlight HEALTH is a new media news organization that promotes advances in biomedical research and new ideas in health and medicine. The Highlight HEALTH Network is made up of three websites:

• Highlight HEALTH – http://www.highlighthealth.com

  Highlight HEALTH promotes advances in biomedical research and advocates for health literacy to improve self-management in health. Highlight HEALTH focuses on reporting biomedical research news for both the public and medical professionals, providing background & analysis and explaining how the results affect you, the healthcare consumer.

• Highlight HEALTH 2.0 – http://www.highlighthealth.org

  Highlight HEALTH 2.0 focuses on new ideas in health and medicine, emphasizing new concepts, ideas and innovations in the healthcare space.

• The Highlight HEALTH Web Directory – http://www.highlighthealth.info

  The Highlight HEALTH Web Directory is an online reference guide for reliable health and medical information. All links in the directory are manually reviewed by an editorial staff and must meet established guidelines prior to acceptance.

Walter Jessen, founder of Highlight HEALTH, oversees all operations and additionally focuses on brand development, marketing, website design and advertiser engagement.

Research Associate in Experimental Hematology and Cancer Biology

Cincinnati Childrens Hospital Medical Center

Non-Profit; Hospital & Health Care industry
January 2008 – April 2010

Responsible for developing data resources that will allow the use of a variety of statistical and biological analysis approaches to evaluate microarray data, as well as additional data related to variations in disease severity, histological patterns and proteomic data being collected from both mouse animal models of neurofibromatosis type 1 (NF1), individual human neurofibromas and malignant peripheral nerve sheath tumors. Collaborates with other Principle Investigators of the Neurofibromatosis Microarray and Systems Biology Consortium (http://nf1.cchmc.org/) to develop bioinformatics analyses to understand the molecular mechanisms by which tumors form and progress with the ultimate goal of developing treatment strategies.

Research Fellow in Biomedical Informatics

Cincinnati Children’s Hospital Medical Center

Non-Profit; Hospital & Health Care industry
September 2004 – December 2007

Utilized transcriptional regulatory and gene interaction networks, cancer biology and embryonic and postnatal development in human and mouse models to inform and characterize biological states, disease processes and developmental disorders. Used functional and comparative genomics approaches, as well as the incorporation of histologic patterns and clinical information, to develop an integrative biology approach that could be applied to a range of genetic diseases.

• Recipient, National Institutes of Health Pediatric Research Loan Repayment Program (2005 – 2007).
• NIH NRSA Postdoctoral Fellowship, Institute of Molecular Pharmacology and Biophysics, University of Cincinnati College of Medicine (2004 – 2007).

Skills

• Gene Expression Profiling (Expert, 7 years experience)
• Pathway Analysis (Advanced, 5 years experience)
• Functional and Comparative Genomics (Advanced, 5 years experience)
• Data/text Mining (Intermediate, 2 years experience)
• Statistical Analysis (Advanced, 7 years experience)
• Matlab (Beginner, <1 year experience)
• R/Bioconductor (Intermediate, 4 years experience)
• Perl (Beginner, <1 year experience)
• MySQL (Intermediate, 2 years experience)
• PHP (Intermediate, 4 years experience)

Recent Biomarker Publications

Gene expression analysis identifies potential biomarkers of neurofibromatosis type 1 including adrenomedullin

Clinical Cancer Research, October 15, 2010

PURPOSE: Plexiform neurofibromas (pNF) are Schwann cell tumors found in a third of individuals with neurofibromatosis type 1 (NF1). pNF can undergo transformation to malignant peripheral nerve sheath tumors (MPNST). There are no identified serum biomarkers of pNF tumor burden or transformation to MPNST. Serum biomarkers would be useful to verify NF1 diagnosis, monitor tumor burden, and/or detect transformation.

EXPERIMENTAL DESIGN: We used microarray gene expression analysis to define 92 genes that encode putative secreted proteins in neurofibroma Schwann cells, neurofibromas, and MPNST. We validated differential expression by quantitative reverse transcription-PCR, Western blotting, and ELISA assays in cell conditioned medium and control and NF1 patient sera.

RESULTS: Of 13 candidate genes evaluated, only adrenomedullin (ADM) was confirmed as differentially expressed and elevated in serum of NF1 patients. ADM protein concentrati on was further elevated in serum of a small sampling of NF1 patients with MPNST. MPNST cell conditioned medium, containing ADM and hepatocyte growth factor, stimulated MPNST migration and endothelial cell proliferation.

CONCLUSIONS: Thus, microarray analysis identifies potential serum biomarkers for disease, and ADM is a serum biomarker of NF1. ADM serum levels do not seem to correlate with the presence of pNFs but may be a biomarker of transformation to MPNST.

Integrative genomic analyses of neurofibromatosis tumours identify SOX9 as a biomarker and survival gene

EMBO Molecular Medicine, July 2009

Understanding the biological pathways critical for common neurofibromatosis type 1 (NF1) peripheral nerve tumours is essential, as there is a lack of tumour biomarkers, prognostic factors and therapeutics. We used gene expression profiling to define transcriptional changes between primary normal Schwann cells (n = 10), NF1-derived primary benign neurofibroma Schwann cells (NFSCs) (n = 22), malignant peripheral nerve sheath tumour (MPNST) cell lines (n = 13), benign neurofibromas (NF) (n = 26) and MPNST (n = 6). Dermal and plexiform NFs were indistinguishable. A prominent theme in the analysis was aberrant differentiation. NFs repressed gene programs normally active in Schwann cell precursors and immature Schwann cells. MPNST signatures strongly differed; genes up-regulated in sarcomas were significantly enriched for genes activated in neural crest cells. We validated the differential expression of 82 genes including the neural crest transcription factor SOX9 and SOX9 predicted targets. SOX9 immunoreactivity was robust in NF and MPSNT tissue sections and targeting SOX9 – strongly expressed in NF1-related tumours – caused MPNST cell death. SOX9 is a biomarker of NF and MPNST, and possibly a therapeutic target in NF1.

Additional publications with PDFs

Education

Texas A&M University

Ph.D., Molecular Biology and Biochemistry, 1998 – 2004

Developed a kinetic approach for analysis of chromatin remodeling in vivo, demonstrating that nucleosomes proximal to the transactivator binding site are remodeled earlier than those more distal. Developed an in vivo single molecule assay that identifies multiple promoter classes and supports a probabilistic model in which chromatin remodeling at PHO5 spreads from sites of transactivator binding and attenuates with distance. Bioengineered inducible DNA methyltransferase systems for the in vivo detection of chromatin structural changes, targeted methylation and factor footprints.

• Directed research projects for several rotating graduate students (1998 – 2004)
• Responsible for the primary training of a number of undergraduate students (1998 – 2004)
• Teaching Assistant, Texas A&M University, Experimental Biochemistry Lab (2003)
• Teaching Assistant, Texas A&M University, Biochemistry Laboratory I and II (1998 – 1999)

Purdue University Calumet

B.S., Physics, 1992 – 1998

Research project involved the design, construction and use of a nitrogen laser for the study of dielectric breakdown and spark generation. Presented “Dielectric Breakdown and Spark Generation” at the Eighth Annual Argonne Undergraduate Research Symposium, Argonne National Lab (1997).

• Teaching Assistant, Purdue University Calumet, Introductory Physics (1998)
• Physics and Math Tutor, Purdue University Calumet (1998)
• I was employed full-time while attending classes and maintained a GPA of 3.4 (1992-1998)

Activities and Societies: Society of Physics Students (President, 1998), “Best and Brightest” award (Department of Chemistry and Physics, 1998), Nominated to Sigma Xi (1998)