Mark Jensen Email & Phone Number

Rockville, Md, Us

Frederick, Maryland, Us

Frederick, Maryland, Us

I provide program leadership in data architecture and software development, supporting the Cancer Research Data Commons, an initiative of the National Cancer Institute's (NCI's) Center for Biomedical Informatics and Information Technology (CBIIT), as well as the Cancer Moonshot(sm) Biobank for the NCI's Biorepositories and Biospecimen Research Branch (BBRB). I manage 8 PhD-level direct reports.[ The FNLCR is operated by Leidos Biomedical Research, Inc. on behalf of the NCI. ]

Frederick, Maryland, Us

I was part of the senior leadership team managing the design, maintenance, and ongoing development of a major cancer genomic data resource, the Genomic Data Commons (GDC).[ The FNLCR is operated by Leidos Biomedical Research, Inc. on behalf of the NCI. ]Highlights:Developed ongoing close working relationships with cancer genomics experts nationally and internationally, gaining diverse thought leadership contributions and buy-in for the GDC, establishing and leading the GDC Steering Committee, GDC Data Advisory Group, and Genomic Data Publication Policy Group, among others; Developed trusted advisor relationships with NCI Center for Cancer Genomics (CCG) personnel, and have presented the GDC project in outward-facing contexts, such as the NIH Data Science Policy Council, on behalf of the CCG;Established, developed and led collaborations between GDC and the NCI Center for Biomedical Informatics and Information Technology (CBIIT), in work involving Enterprise Vocabulary Services (clinical data standards) and the NCI Cancer Cloud Resources program;Designed and managed the implementation of sophisticated and flexible metadata models and storage systems, involving graph database concepts, ontology and semantics;Provided scientific content and tools for GDC and other CCG projects, including a machine-learning-based tool for determining the tumor or normal status of a tissue sample based on raw whole exome sequence data.

Us

Fortinbras Research provides its clients custom bioinformatics code and applications.Highlights:Developed and continue to maintain http://spatyper.fortinbras.us, the only freely available web-based Staphylococcus aureus spa typing (molecular epidemiology) application;Developed and maintain Perl object bindings to the Neo4j graph database REST interface (REST::Neo4p), currently available through CPAN (http://metacpan.org/module/REST::Neo4p) and on the Neo4j site (at https://neo4j.com/developer/perl/);Developed and maintain a system for expressing Neo4j graph queries in Perl, Neo4j::Cypher::Abstract (https://metacpan.org/pod/Neo4j::Cypher::Abstract);Designed, developed, and integrated several BioPerl core modules, including Bio::DB::HIV for query-based access of the Los Alamos National Laboratory HIV Sequence Database, and Bio::Search::Tiling::MapTiling for the calculation of global sequence identity and similarity statistics based on BLAST or FASTA search reports. I continue to maintain these modules as necessary, as a BioPerl Core Developer (see Volunteer Positions).

Falls Church, Va, Us

I was the project manager of The Cancer Genome Atlas Data Coordinating Center (TCGA DCC), National Cancer Institute, National Institutes of Health.Highlights:Provided project and personnel management for a 12-member team of PhD/MS bioinformatics scientists, software engineers and software and process quality personnel for this high-visibility, high-usage program;Managed the software development life cycle for maintenance and improvement of DCC Data Portal data management and applications, in collaboration with the prime contractor Leidos BioMed and the TCGA Program Office at NCI;Developed and maintained open and collaborative communication with the TCGA Biospecimen Core Resource, CGHub, Genomic Characterization Centers, Genomic Sequencing Centers, Genomic Data Analysis Centers, and Analysis Working Groups in support of mutual goals and objectives;Provided writing, proposal development and thought leadership in business development activities within the SRA Health and Civil Group. Part of writing team that won the TCGA DCC recompete, and a major CDC bioinformatics recompete.

Falls Church, Va, Us

Lead bioinformatics scientist in support of the Data Coordinating Center of the The Cancer Genome Atlas, National Cancer Institute, National Institutes of Health.Duties:Day-to-day management of 7-member PhD/MS level bioinformatics team;Management of custom, enterprise-level software and data format specification, development and implementation;Participation in project management, corporate and client reporting, and corporate business development;Facilitation of communication and collaboration among TCGA stakeholders, including participating universities, federal agencies, and federal contractors as well as the TCGA user community;Supervision of TCGA data and metadata submissions from consortium participants and assistance with submission and database quality assurance for multiple high-throughput datatypes.

Falls Church, Va, Us

Senior-level bioinformatics scientist in support of the Data Coordinating Center of the The Cancer Genome Atlas, National Cancer Institute, National Institutes of Health.Duties:Supervision of TCGA data and metadata submissions from consortium participants and assisting in submission and database quality assurance for multiple high-throughput datatypes;Facilitation of communication and collaboration among TCGA stakeholders, including participating universities, federal agencies, and federal contractors as well as the TCGA user community;Participation in and leadership of software and data format specification and development;Participation in group management, corporate and client reporting, and corporate business development.

Falls Church, Va, Us

I organized and facilitated high-quality scientific review of research proposals for the Breast Cancer Research Program of the Congressionally Directed Medical Research Program, a process involving reviewer recruitment, proposal assignment, meeting organization, and post-review documentation.

Vancouver, British Columbia, Ca

I worked with Dr Richard Harrigan and the CFE Clinical Laboratories, doing bioinformatics research and software development for the analysis of ultra-deep HIV sequencing.

Athens, Ga, Us

Assistant Professor of Genetics and Epidemiology

Atlanta, Ga, Us

As a postdoctoral fellow at Emory University in the lab of Bruce Levin, I developed and analyzed a mathematical model of cholera epidemics that involved the interactions between the cholera bacteria, the human population, and bacterial viruses to which the cholera bacterium is susceptible. (see the paper; PubMed ID:16537404)I also developed and implemented a large database of antibiotic use and resistance information, integrating commercial anti-infective sales data with CDC antibiotic resistance data, for an ongoing project involving S. pneumoniae led by Keith Klugman at Emory and Cynthia Whitney, Chief of Respiratory Diseases, NCIRD, Centers for Disease Control and Prevention.

Seattle, Wa, Us

While studying the pathogenesis and evolution of HIV at the University of Washington, I:* designed and performed computational biological research on within-patient HIV-1 molecular evolution and its relationship to HIV disease progression and prognosis. This work included aspects of HIV pathogenesis and rational vaccine design;* designed, coded and implemented a widely used, web-based HIV sequence analysis tool for the public domain based on the above research;* developed independent collaborations with the Laboratory of Immunoregulation (NIAID, NIH), Case-Western Reserve University, University of British Columbia, University of Witwatersrand (Johannesburg, ZA), and Microsoft Research, all of which yielded publications;* wrote the scientific content and managed the submission of a funded ($1.2M) NIH R01 grant;* trained and helped manage science professionals and students.

Phd, Molecular Evolution

Fulbright Scholar, Mathematics

Msc, Mathematics

B.S., Mathematics