William J. Rowell

Senior Scientist, Bioinformatics

Pacific Biosciences


Billy Rowell is a Senior Bioinformatics Scientist on the Bioinformatics Applications Team at PacBio. His research interests include the detection and phasing of small variants in long read sequencing data. He has experience in classical genetics in model organisms, neurogenetics, and human genetics. At PacBio, he has focused on the detection and phasing of variants in targeted capture or whole genome sequencing data from human samples.


  • long read sequencing
  • variant detection (SNVs, small indels, structural variants)
  • variant phasing and haplotype generation
  • target capture and amplicon sequencing
  • workflow design


  • MA in Molecular and Cell Biology, 2010

    University of California, Berkeley

  • BS Biology with Chemistry minor, 2002

    University of North Carolina, Chapel Hill



shell scripting, HPC clusters & version control • Python, Jupyter, NumPy, pandas & Matplotlib • reproducible analysis • next generation sequencing and third generation sequencing applications, including whole genome sequencing, targeted sequencing, RNASeq, and Iso-Seq • interpreting the quality of sequencing data • bioinformatic tools including BWA, Bowtie, STAR, GATK, minimap2, samtools, bedtools, bcftools, whatshap • designing and maintaining production grade bioinformatics analysis workflows • 20 years of experience administering home Linux servers and workstations

Molecular biology and genetics

quality control, critical interpretation & troubleshooting problems with NGS data • nucleic acid isolation, manipulation, cloning & analysis • RNA in situ hybridization & visualization • bacterial genetics, fruit fly husbandry & classical eukaryotic genetics


adapting techniques, off-the-shelf products & custom hardware and software • experimental design & protocol refinement • equipment testing, calibration & maintenance • logistics for high-throughput operation • wide field microscopy & confocal fluorescence microscopy • image acquisition & analysis


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



Senior Bioinformatics, Scientist

Pacific Biosciences of California

Feb 2017 – Present Menlo Park, California
Description: 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 workflow for phasing of targeted capture long-read sequencing data • collaborated with wet lab scientists to improve targeted capture sequencing protocols • provided data analysis solutions and expertise for multiple targeted sequencing collaborations

Scientific Programmer

Q2 Solutions | EA Genomics

Sep 2015 – Feb 2017 Morrisville, North Carolina
Description: 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

Research Specialist

Howard Hughes Medical Institute, Janelia Research Campus

Mar 2010 – Sep 2015 Ashburn, Virginia

Research Specialist (2013-2015)
Research Technician (2010-2013)

Department: Project Technical Resources (Sep 2012 - Sep 2015)
Description: 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)
Description: I investigated 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

Recent Posts


PacBio HiFi Variant Detection

Calling all variants with highly accurate long reads

Genome in a Bottle Consortium

A public-private-academic consortium hosted by NIST to develop reference materials and standards for clinical sequencing

Fly Olympiad

High-throughput behavioral assays to understand the Drosophila brain

Recent & Upcoming Talks

Variant detection and de novo assembly with HiFi reads

Applications update for comprehensive variant detection and de novo assembly with HiFi reads.

Advantages of HiFi reads for variant discovery and genome assembly

The PacBio Sequel II System is capable of generating highly accurate, long reads (HiFi reads) that can be used for variant detection …

Recent & Upcoming Posters

PgmNr 1540/T: Using long and linked reads to generate a new Genome in a Bottle small variant benchmark.

The Genome in a Bottle (GIAB) consortium performs authoritative characterization of 7 human genomes. Here, we describe work towards …

PgmNr 1866/W: Detection and phasing of small variants in Genome in a Bottle samples with highly accurate long reads

Introduction: Long-read PacBio SMRT Sequencing has been applied successfully to assemble genomes and detect structural variants. …

Recent Publications

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