Mark Evans

Mark Evans Email and Phone Number

Director, Bioinformatics and Scientific Data Engineering @ Exact Sciences
California, United States
Mark Evans's Location
San Francisco Bay Area, United States, United States
Mark Evans's Contact Details
About Mark Evans

Beginning as a molecular biologist at the Salk Institute, most of the last twenty years have been spent working in the pharmaceutical industry providing bioinformatics solutions for biologics drug development, most recently as Associate Director. Whether it was characterizing the soluble proteome at Bayer, or developing new antibody epitope prediction methods at Monogram Biosciences, or building a software development team that created multiple LIMS and cutting-edge antibody sequence analysis programs at Xoma, significant impacts have been made at each organization by enhancing capabilities, increasing throughput and creating value.Most recently, work at Xoma was recognized by winning the BioIT World Best Practices Award in 2016. Authored ten scientific publications, twelve major scientific abstracts and seven patent applications (3 issued).Experience includes hands-on research, software and database development, bioinformatics analysis, interdisciplinary teamwork with biologists, business development and legal departments, and management of software development and bioinformatics teams. Strong experience in scientific software development in the areas of genetics, antibody and protein engineering, including next-gen sequencing (NGS) and laboratory information management systems (LIMS). Excels at analyzing complex situations and synthesizing new solutions to improve business processes and maximize use of technology. Enjoys the challenge of new scientific problems that allow leadership of a team of creative people to develop innovative solutions that deliver significant impact.Specialties: Python, R, PHP, Perl, HTML, SQL, Django, Jupyter, iPython, PostgreSQL, Oracle, MySQL, database architecture, software design, Accelrys DiscoveryStudio, SAMtools, Knime, MacOS, Linux, Windows, GitHub, protein modeling, antibody structure analysis, NGS, Next-gen sequence analysis, Javascript, UI/UX, HMMER, CLUSTALW, Biovia ELN

Mark Evans's Current Company Details
Exact Sciences

Exact Sciences

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Director, Bioinformatics and Scientific Data Engineering
California, United States
Website:
exactsciences.com
Employees:
6196
Mark Evans Work Experience Details
  • Exact Sciences
    Director, Bioinformatics And Scientific Data Engineering
    Exact Sciences
    California, United States
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  • Exact Sciences
    Director, Bioinformatics & Scientific Data Engineering
    Exact Sciences Mar 2021 - Present
    Madison, Wisconsin, Us
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  • Exact Sciences
    Associate Director, Bioinformatics & Scientific Data Engineering
    Exact Sciences Oct 2019 - Mar 2021
    Madison, Wisconsin, Us
    My team of Bioinformatics Data Engineers and I strive to provide ETL and analytical support for Commercial, Clinical and Process Engineering data pipelines for Lab Developed qPCR Tests and In vitro diagnostic devices (IVD). Currently deeply involved in software development activities to support new product development for multiple NGS-based cancer screening panels (liquid and solid tumor), as well as IVD development for various qPCR platforms. Implementing technology infrastructure utilizing AWS, Python, JupyterHub, R Shiny, Apache Zeppelin, MSSQL, Tableau, Docker and Django.
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  • Self
    Bioinformatics Consultant
    Self Feb 2017 - Present
  • Abalone Bio
    Scientific Advisor
    Abalone Bio Aug 2018 - Present
    Emeryville, Ca, Us
    https://www.abalonebio.com/Abalone is shifting the paradigm for antibody development, isolating drug candidates directly by their modulating effects on integral membrane proteins. Abalone is an early stage biotech start-up in the San Francisco Bay Area. We are partnering with leading academic labs, targeting G protein-coupled receptors (GPCRs) and ion channels. Our drug development programs address unmet needs in oncology, inflammation and pain sensation.
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  • Kotai Biotechnologies, Inc.
    Scientific Advisor
    Kotai Biotechnologies, Inc. Aug 2017 - Feb 2021
    https://www.kotai-bio.com/High-throughput structural modeling and analysis platform for immune cell sequences derived from patient blood samples, revealing the structure and function of immune cell receptors with unprecedented resolution.
  • Genomic Health
    Associate Director, Biomedical Data Computing
    Genomic Health Oct 2017 - Oct 2019
    Redwood City, Ca, Us
    Located within the Product Services R&D division of GHI, my team of Data Engineers and I strive to provide ETL and analytical support for Commercial, Clinical and Process Engineering data pipelines for Lab Developed qPCR Tests and In vitro diagnostic devices (IVD). Currently deeply involved in software development activities to support new product development for a cancer IVD on the Biocartis Idylla qPCR platform. Implementing technology infrastructure utilizing JupyterHub, R Shiny, Apache Zeppelin, MSSQL, Tableau, Docker and Django.
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  • Xoma
    Associate Director, Technology Innovation & Bioinformatics, Discovery Research
    Xoma Jan 2013 - Feb 2017
    Emeryville, California, Us
    After a 3 year hiatus, during which Xoma underwent a significant workforce restructuring, brought back to re-establish the Bioinformatics function by hiring two people.• Significantly reduced data integrity errors, while providing more workflow flexibility and an improved UI/UX interface by redesigning the integrated assay LIMS and sequence analysis software. Consequently, this software won the BioIT World Best Practices Editors Choice Award in 2016 ( http:// goo.gl/mP2m0h ).• Developed an NGS analysis pipeline for Ion Torrent™ data that was able to identify 1000x more potential antibody candidates from a single experiment.• Significantly enhanced protein modeling capabilities by licensing software from the University of Oxford and integrating it with open-source tools to create an automated antibody 3D-structure prediction pipeline.• Initiated a research program that took some existing assets with no current value and explored their utility in a new HIV indication. Succeeded in demonstrating activity and provided Business Development with a new, valuable asset for less than a $100K investment.• Developed technology innovation strategic plan for the Discovery Research department. Identified outside consulting agency to work with as a partner to map out existing processes and workflow, identify equipment utilization patterns and develop long-term proposal for improvement• Re-implemented software code lifecycle management platform on GitHub• Participate as team member on company-wide IT governance committee
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  • Monogram Biosciences
    Principal Bioinformatics Scientist
    Monogram Biosciences Aug 2010 - Jan 2013
    South San Francisco, California, Us
    Monogram is the largest and most respected HIV testing company in the world, with their genetic tests providing the gold standard. Mining their patient database for HIV mutation trends and characteristics in response to pharmaceutical company queries was always a fascinating exercise. • Developed a novel software algorithm to predict the co-receptor tropism of HIV1 based upon DNA sequence with an overall concordance rate of more than 81% when compared to existing enhanced sensitivity Trofile® phenotypic assay which was incorporated in a new diagnostic test product.• Developed an XML Rule Engine that assesses patients HCV genotype and determines drug resistance which formed the core of the new HCV GenoSure® NS3/NS4A drug resistance assay product.• Developed software to perform in silico antibody epitope mapping on HIV targets with high accuracy, resulting in a published patent, publication in BMC Bioinformatics in 2014 and a poster presentation at the AIDS Vaccine conference in 2012.
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  • Xoma (Us) Llc
    Associate Director, Research Informatics, Preclinical Research & Development
    Xoma (Us) Llc Apr 2005 - Dec 2009
    Emeryville, California, Us
    Brought to establish the Bioinformatics function initially as a Sr. Scientist. Ultimately hired 3 software engineers and together created LIMS and scientific analysis capabilities for Discovery Research that allowed for the first time, true knowledge management abilities, standardization of analysis methods and allowed the researchers to move beyond using Excel for everything.• Created web-based integrated assay LIMS / DNA analysis software that reduced analysis time per assay from weeks to minutes and allowed a 10x increase in the number of antibodies that could be screened and a 3x increase in the number of drug targets that could be evaluated per year.• Implemented the manual algorithm for antibody human engineering in software, was able to reduce the lead time to engineering start from 1 month to 1 day, increasing capacity by 30%.• Designed and wrote several LIMS systems for use by various functional groups to manage scientific data and analysis during antibody discovery, batch records for antibody production and freezer inventory management. Developed custom antibody DNA and protein sequence analysis software.• Member of Translational Medicine task force working to identify potential biomarkers for late stage antibody discovery projects. Worked closely with collaborators to design, analyze and interpret genomics and proteomics experiments to support this goal.• Worked with Legal on FTO analyses for discovery programs and for I.P. filing. Supported Legal with technology evaluations.• Assisted Business Development to close 3 Technology Collaboration deals of which internally developed software was a component with Takeda SF, Arana Therapeutics, and Kaketsukan totaling $46 Million in 2009.
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  • Biotrue Inc.
    Software Development Manager
    Biotrue Inc. Oct 2004 - Mar 2005
    Us
    Managed two programmers and created a module for their LIMS system that managed FACS data using LAMP stack
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  • Bayer Pharmaceuticals
    Sr. Research Scientist In Bioinformatics
    Bayer Pharmaceuticals Apr 2000 - Mar 2004
    Leverkusen, North Rhine-Westphalia, De
    • Supported Affymetrix microarray analysis, including designing a custom chip for use at Bayer• Developed custom LIMS system that resulted in $300K saving and a special recognition award• Created Oracle data warehouse that integrated public and private data sources with a web-based UI, resulting in a Scientific Achievement award• Developed a web interface for a commercial Oracle-based LIMS, which dramatically improved user adoption and salvaged the company’s investment of more than $400K
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  • Genomics Discovery Tools
    Software Consultant
    Genomics Discovery Tools 2003 - 2004
    • Develop custom GUI/data analysis modules for Company’s Visual Genome product. Modules, written in Perl/Tk, are rapidly developed in response to customer requests/ feedback. The product uses a MySQL database.
  • Invitrogen
    Bioinformatics Programmer
    Invitrogen Jan 1999 - Mar 2000
    Waltham, Ma, Us
    • Significantly redesigned and improved legacy clone tracking database systems for high throughput cloning team, resulting in increased efficiency and decreased product defects.• Developed software and methods for identification of full-length genes in various genomes from public databases• Generated scientific data regarding company products for use by Marketing & Technical Service departments.• Assisted in developing corporate website
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  • Invitrogen
    Applications Scientist
    Invitrogen Jan 1998 - Jan 1999
    Waltham, Ma, Us
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  • Invitrogen
    Sr. Technical Service Rep
    Invitrogen Jan 1996 - Jan 1998
    Waltham, Ma, Us
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  • Ucsd Extension
    Instructor, Introduction To Bioinformatics
    Ucsd Extension 1998 - 1999
    La Jolla, Ca, Us
    • Design and prepare course materials. Teach introductory course consisting of 2 full-day seminars. Assist students with computer lab tasks. Administer and grade exams.
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  • American Red Cross Research Laboratory
    Research Assistant
    American Red Cross Research Laboratory Aug 1993 - Jan 1996
  • The Salk Institute
    Research Assistant
    The Salk Institute Jan 1991 - Mar 1993
    La Jolla, Ca, Us
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Mark Evans Skills

Bioinformatics Biotechnology Protein Chemistry Molecular Biology Antibodies Lims Drug Discovery Biomarker Discovery Life Sciences Proteomics Computational Biology Biochemistry Python Microarray Analysis High Throughput Screening Perl Analysis Html Dna Sequencing Team Leadership Sql Homology Modeling Software Development Php Software Design Bioinformatics Analysis Biological Databases Designs Genome Analysis Laboratory Information Management System R Django Database Architecture Lims Design Antibody Structure Analysis Blast Protein Modeling Dna Sequence Analysis Algorithm Design Biological Data Analysis Agile And Waterfall Methodologies Software Development Life Cycle Management Software Project Management Database Design Data Analysis Data Engineering Data Visualization Mssql Protein Engineering

Mark Evans Education Details

  • Ucla
    Ucla
    Biochemistry
  • Uc San Diego
    Uc San Diego
    Biochemistry & Cell Biology

Frequently Asked Questions about Mark Evans

What company does Mark Evans work for?

Mark Evans works for Exact Sciences

What is Mark Evans's role at the current company?

Mark Evans's current role is Director, Bioinformatics and Scientific Data Engineering.

What is Mark Evans's email address?

Mark Evans's email address is ev****@****oma.com

What is Mark Evans's direct phone number?

Mark Evans's direct phone number is +151064*****

What schools did Mark Evans attend?

Mark Evans attended Ucla, Uc San Diego.

What are some of Mark Evans's interests?

Mark Evans has interest in New Technology, Education, Scuba Diving, Northcreek Church Job Network, Digital Photography.

What skills is Mark Evans known for?

Mark Evans has skills like Bioinformatics, Biotechnology, Protein Chemistry, Molecular Biology, Antibodies, Lims, Drug Discovery, Biomarker Discovery, Life Sciences, Proteomics, Computational Biology, Biochemistry.

Who are Mark Evans's colleagues?

Mark Evans's colleagues are Mindy Grafing-Gwin, Nelson Plapp, John Paul Samia, Michael Poplawski, Carly Stephens, Mba, Saad Aqrab, Linda Verhotz.

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