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William J Rowell

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I provide insight and practical solutions for problems in bioinformatics.

Skills

Computational

Bash, Python (NumPy/pandas/Matplotlib), Perl, MATLAB • relational database ETL with sqlite, MySQL, and PostgreSQL • SGE and slurm cluster usage • data manipulation and code maintenance using Linux and command line tools • bioinformatic analysis with published tools • MS Windows, Mac OS X, Linux • 20 years of experience administering home Linux servers and workstations

Professional

proven track record in collaborative science • determined problem solver • data-driven process improvement • training researchers in biological techniques and laboratory management skills • training researchers in introductory programming and best practices • liaising and translating between research staff and operations staff • consulting for sales, project managers, and clients • presenting data in written and oral formats

Molecular biology and genetics

quality control, critical interpretation, and troubleshooting problems with NGS data • nucleic acid isolation, manipulation, cloning, and analysis • cell culture assays of transcriptional reporter activation • RNA in situ hybridization and visualization • fruit fly husbandry • classical eukaryotic genetics • bacterial genetics

Technical

adapting techniques, off-the-shelf products, and custom hardware and software for use in high-throughput behavioral assays and data analysis workflows • experimental design and protocol refinement • equipment testing, calibration, and maintenance • logistics for high-throughput operations • image acquisition • wide field and confocal fluorescence microscopy • fluorescence imagery analysis

Experience

Sr Scientist, Bioinformatics PacBio - Feb 2017 - Present

  • Department: Bioinformatics Applications Team
    • Goal: I work with customers and internal teams to develop new or improve existing applications and analysis workflows for single molecule, long-read sequencing. I help my associates in sales and marketing turn proof of principle or pilot experiments into equipment sales or marketing collateral.
    • Accomplishments: developed and improved upon workflows for variant calling and phasing of PacBio circular consensus sequence data • collaborated with wet lab scientists to improve targeted capture sequencing protocol • provided data analysis solutions and expertise for multiple targeted sequencing collaborations

Scientific Programmer EA|Q2 Solutions - Sep 2015 - Feb 2017

  • Department: Bioinformatics Client Services
    • Goal: I delivered high-quality next-generation sequencing data to our clients in a timely manner.
    • Accomplishments: with others in my team, guided the development of delivery and analysis pipeline enhancements • developed tools for tracking tasks and errors • data-driven process improvement • recognized for providing exceptional customer service

Consultant HHMI, JRC - Sep 2015 - Present

Research Specialist I HHMI, JRC - Sep 2013 - Sep 2015

Research Technician III HHMI, JRC - May 2011 - Aug 2013

Research Technician II HHMI, JRC - Mar 2010 - May 2011

  • Department: Project Technical Resources (Sep 2012 - Sep 2015)
    • Goal: I supported the research of the project teams and labs at Janelia by providing consultation, conducting experiments, analyzing data, and writing software.
    • Accomplishments: acted as liaison and translator between different disciplines • screened over 200 Drosophila melanogaster lines through high-throughput locomotor / optomotor / phototaxis assay • screened over 300 D. mel. lines through high-throughput olfactory assay • curated and analyzed data and metadata • aided in design of novel behavioral assays, including instrument design and testing, protocol refinement, and data analysis tools • wrote suite of tools for analysis of D. mel. activity / sleep data • wrote and maintained automated pipeline for fluorescence imagery analysis
  • Department: Fly Olympiad Team Project (Mar 2010 - Sep 2012)
    • Goal: To understand the role of individual neurons or groups of neurons in altering behavior by screening Drosophila melanogaster lines through high-throughput behavioral assays.
    • Accomplishments: acted as liaison and translator between different disciplines in large-scale scientific collaboration • screened over 2000 D. mel. lines through high-throughput locomotor / optomotor / phototaxis assay • aided in establishing guidelines for storing data and metadata • aided in establishing a more flexible scheme for describing line nomenclature and relationships

Graduate Student Researcher UC Berkeley - (2002 - 2009)

  • Advisor: Dr. Tom Cline
    • Project: A genetic selection to identify regulatory elements driving the earliest zygotic transcription in Drosophila melanogaster.
    • Techniques: inverse PCR • cloning • Northern blot • bioinformatic sequence analysis • fruit fly husbandry • classical genetics • P-element mobilization • RNA fluorescence in situ hybridization • confocal microscopy
  • Advisor: Dr. Michael Levine
    • Project: Investigating the grammar and organization of regulatory elements for Drosophila melanogaster developmental and immune response genes.
    • Techniques: cloning • SELEX • bioinformatic sequence analysis • cell culture • cell culture assays of transcriptional reporter activation • RNA fluorescence in situ hybridization • fruit fly husbandry • production of transgenic flies

Graduate Student Instructor UC Berkeley - (2003, 2005, 2007)

  • Survey of General Genetics, Fall 2003
  • Heredity and Society, Spring 2005
    • Led two weekly 35-student sections in discussion, developed questions, wrote quizzes and evaluated students.
  • Introduction to Programming for Bioinformatics, Spring 2007
    • Assisted instructors with group and one-on-one instruction in Perl programming for this two-week, full-time course.

Undergraduate Research Assistant UNC Chapel Hill - (1999 - 2002)

  • Advisor: Dr. Jeff Dangl
    • Project: Using classical genetic techniques and molecular biology to dissect the genetics of the resistance of Arabidopsis thaliana to the fungal pathogen Peronospora parasitica.
    • Techniques: PCR • cloning • DNA/RNA purification • sequence analysis • Southern blot • northern blot • western blot • in vitro quantification of innate immune response • tissue fixation and staining • cultivation of Arabidopsis thaliana • cultivation of Peronospora parasitica • classical genetics
Education

University of California, Berkeley

MA Molecular and Cell Biology, Spring 2012

University of North Carolina, Chapel Hill

BS Biology with Chemistry minor, Spring 2002

Related Experience

Volunteer Instructor, Software Carpentry 2013 – Present

  • George Washington University Ashburn, VA April 2014
  • Howard Hughes Medical Institute Ashburn, VA July 2014
    • Conduct on-site workshops to train researchers in core software skills to improve their efficacy, such as use of the Unix shell and Python for data analysis.

Instructor, Introduction to Python Programming 2015

  • Howard Hughes Medical Institute Ashburn, VA March 2015
  • Howard Hughes Medical Institute Ashburn, VA July 2015
    • Organized, planned curriculum, wrote lessons, and led instruction for class tailored to the needs of JRC researchers.
Publications
  • Aso Y, Sitaraman D, Ichinose T, Kaun K, Vogt K, Belliart-Guérin G, Plaçais P, Robie A, Yamagata N, Schnaitmann C, Rowell WJ, Johnston RM, Ngo TT, Chen N, Korff W, Nitabach MN, Heberlein U, Preat T, Branson K, Tanimoto H, Rubin GM. 2014. Mushroom body output neurons encode valence and guide memory-based action selection in Drosophila. eLife 3:e04580. doi:10.7554/eLife.04580
  • Senger K, Armstrong GW, Rowell WJ, Kwan JM, Markstein M, Levine M. 2004. Immunity regulatory DNAs share common organizational features in Drosophila. Mol. Cell 13:19–32. doi:10.1016/S1097-2765(03)00500-8
Presentations
  • Rowell WJ, Lee WC, Cline TW. 2007. Pre-blastoderm Gene Expression in Drosophila melanogaster. UCB, MCB, Genetics, Genomics, and Development Annual Retreat, Lake Tahoe, CA.
Posters
  • Korff W, Namiki S, Rowell W, Dickinson M, Card G. 2016. Functional dissection and organization of descending interneurons during flight control in Drosophila. Twelfth International Congress of Neuroethology.
  • Korff W, Anderson DJ, Branson K, Card G, Chen N, Hayes S, Hirokawa J, Hoopfer E, Kimmel B, Kladt N, Low S, McKellar C, Phillips M, Reiser MB, Roberts S, Robie A, Rowell W, Rubin G, Simpson JH, Shusterman D, Strauss R and Triphan T. 2012. The Fly Olympiad: A series of high-throughput, quantitative behavioral experiments in Drosophila neurobiology. Front. Behav. Neurosci. Conference Abstract: Tenth International Congress of Neuroethology. doi:10.3389/conf.fnbeh.2012.27.00426
  • Reiser MB, Rowell W, Lee A and Korff W. 2012. Probing Drosophila visual behaviors in high throughput. Front. Behav. Neurosci. Conference Abstract: Tenth International Congress of Neuroethology. doi:10.3389/conf.fnbeh.2012.27.00420
  • Rowell WJ, Lee WC, Cline TW. 2007. A genetic selection to identify regulatory information driving the earliest zygotic transcription in Drosophila melanogaster. A. Dros. Res. Conf. 48.
  • Rowell WJ, Cline TW. 2005. A genetic selection to identify regulatory information driving the earliest zygotic transcription in Drosophila melanogaster. A. Dros. Res. Conf. 46.
  • Senger K, Armstrong GW, Rowell WJ, Kwan JM, Markstein M, Levine M. 2004. Immunity regulatory DNAs share common organizational features in Drosophila. A. Dros. Res. Conf. 45.
Professional Enrichment
  • Lean Six Sigma Yellow Belt training (2016), Q2 Solutions.
  • Nominated for and graduated from three-month internal leadership training course at Janelia Research Campus (High Functioning Leadership Program, 2012) covering many aspects of management training.
  • Negotiation Power Skills workshop (2105), Janelia Research Campus.
  • Glaser and Associates BreakThrough Conflict workshop (2014), Janelia Research Campus.
  • Persuasive Communication workshop (2014), Janelia Research Campus.
  • Fundamentals of Light Microscopy course (2013), Janelia Research Campus.
  • Supplemented formal education with open online courses, including: Rice Fundamentals of Computing Specialization (3 courses and capstone exam), JHU Data Science Specialization (9 courses), Stanford Machine Learning, Stanford Introduction to Databases
Hobbies
camping • hiking • ultimate frisbee • writing
Links
GitHub
GitLab
ORCID iD iconorcid.org/0000-0002-7422-1194
ResearcherID
Google Scholar