William J. Rowell

Senior Scientist, Bioinformatics

Pacific Biosciences

Biography

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.

Interests

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

Education

MA in Molecular and Cell Biology, 2010

University of California, Berkeley
BS Biology with Chemistry minor, 2002

University of North Carolina, Chapel Hill

Skills

Computational

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

Technical

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

Professional

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

Experience

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 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

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

Previously:
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

Projects

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.

Nov 14, 2019 00:00 AM Barceló Milan

PDF Project Slides

Evaluation of HG002 v4 draft benchmark against GATK calls on PacBio HiFi reads

Oct 15, 2019 00:00 AM Marriott Marquis Houston

PDF Project Project

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 …

May 8, 2019 00:00 AM Leiden University Medical Center, Buruma Hall

PDF Project

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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 …

Justin Wagner, Andrew Carroll, Ian T. Fiddes, Aaron M. Wenger, William J. Rowell, Nathan Olson, L. Harris, J. McDaniel, C. Xiao, Marc Salit, Justin Zook, Genome in a Bottle Consortium

Last updated on Oct 21, 2019

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. …

William J. Rowell, Shreyasee Chakraborty, Primo Baybayan, Richard J. Hall

Last updated on Oct 21, 2019

PgmNr 2221/T: Structural variant in the RNA binding motif protein, X-linked 2 (RBMX2) gene found to be linked to bipolar disorder.

Bipolar disorder (BD) is a phenotypically and genetically complex neurological disorder that affects 1% of the worldwide population. …

Jenny M. Ekholm, William J. Rowell, Lars Paulin, Steve Kujawa, Denise Raterman, George Mayhew, Jennifer Wendt, Daniel L. Burgess, Timo Partonen, Tiina Paunio, Pia Laine, Petri Auvinen

Last updated on Oct 12, 2019

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Featured Publications

Aaron M. Wenger, Paul Peluso, William J. Rowell, Pi-Chuan Chang, Richard J. Hall, Gregory T. Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D. Olson, Armin Töpfer, Michael Alonge, Medhat Mahmoud, Yufeng Qian, Chen-Shan Chin, Adam M. Phillippy, Michael C. Schatz, Gene Myers, Mark A. DePristo, Jue Ruan, Tobias Marschall, Fritz J. Sedlazeck, Justin M. Zook, Heng Li, Sergey Koren, Andrew Carroll, David R. Rank, Michael W. Hunkapiller

Aug 2019 Nat Biotechnol (74)

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the ‘genome in a bottle’ (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15 megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.

Project DOI