Billy Rowell

Bioinformatics Data Scientist Fremont, CA

Summary

Collaborative biological data scientist with over 20 years of research experience, including 9 years in genomics. Currently focused on variant calling applications and analysis workflows for long-read sequencing data. Practical experience in genomics, human and model organism genetics, and molecular biology.

Skills

Scientific

NGS/long-read sequencing and QC · WGS/WES/targeted sequencing · NGS/long-read variant calling stacks · long-read genome assembly · RNA-Seq/Iso-Seq · human and model organism genetics · rare disease research · experimental design · high-throughput logistics

Computational

reproducible analysis with WDL/Snakemake · containerization with Docker/Singularity · Python/NumPy/pandas/Matplotlib · HPC/Slurm · Bash/Git · samtools/bedtools/bcftools · image acquisition and analysis

Professional

mentor and team leader · collaborative scientist · strong problem solver · effective communication · translates between disciplines · technical trainer · extensive customer-facing experience

Experience

Bioinformatics Scientist

February 2017 - Present Pacific Biosciences, Menlo Park, CA

Senior Staff Bioinformatics Scientist, June 2022 - Present
Staff Bioinformatics Scientist, March 2020 - May 2022
Senior Bioinformatics Scientist, February 2017 - February 2020

• Lead a small team focused on developing, improving, and applying analysis workflows to characterize genomics data.
• Developed and released HPC/multi-cloud workflows for variant calling, filtering, annotation, and prioritization for rare and inherited disease studies (HiFi-human-WGS-WDL, pb-human-wgs-workflow-snakemake, HiFi-human-assembly-WDL).
• Worked alongside customers to apply long-read sequencing to rare disease research and identify candidate variation (Del Gobbo et al., 2023), (Mehinovic et al., 2022), (Cohen et al., 2022), (Laine et al., 2021), (Cook et al., 2020), (Tseng et al., 2019), (Cheung et al., 2023), (Kucuk et al., 2023), (Fabian Morales et al., 2024), (Redfield et al., 2024).
• Worked with academic collaborators and within the NIST Genome in a Bottle consortium to improve human variant calling benchmarks (Kronenberg et al., 2024), (Porubsky et al., 2024), (Wagner et al., 2022), including in MHC (Chin et al., 2020), and other challenging medically relevant regions (Wagner et al., 2022).
• Through collaborations, guided the development and improvement of tools and applications for long-read sequencing data, e.g., HiFi WGS (Wenger et al., 2019), TRGT (Dolzhenko et al., 2024), HiPhase (Holt et al., 2024), DeepConsensus (Baid et al., 2022), (Belyaeva et al., 2022), DNAscope LongRead (Freed et al., 2022), Sawfish (Saunders et al., 2024) and PGx analysis (van der Lee et al., 2022).
• Support commercial teams by leveraging pilot experiments into sales and collateral.
• Present research at conferences or in webinars (presentations, posters), and train customers and internal teams on analysis workflows.
• Provide escalated customer support for complex data analysis and interpretation.

Scientific Programmer

September 2015 - February 2017 Q2 Solutions | EA Genomics, Durham, NC

• Processed NGS data with standard WGS, WES, and RNA-seq analysis pipelines.
• Monitored data quality and determined root cause of problems.
• Delivered data for hundreds of samples per month in a timely manner to meet customer expectations.
• Guided the development of delivery/analysis pipeline enhancements and developed tools for tracking tasks and errors.
• Recognized for providing exceptional customer service.

Research Specialist

March 2010 - September 2015 HHMI, Janelia Research Campus, Ashburn, VA

Research Specialist, September 2013 - September 2015
Research Technician III, September 2011 - August 2013
Research Technician II, March 2010 - August 2011

• Supported labs and project teams by providing consultation, conducting experiments, analyzing data, and writing software.
• Acted as liaison and translator between scientists, software engineers, and electrical engineers.
• Screened D. melanogaster lines through high-throughput locomotor, optomotor, phototaxis, flight, and olfactory assays (Aso et al., 2014), (Isaacson et al., 2023), (Namiki et al., 2022).
• Curated and analyzed experimental data and metadata.
• Aided in design of novel behavioral assays, including instrument design and testing, protocol refinement, and data analysis tools in python and MATLAB.

Education

2012 University of California, Berkeley MA in Molecular and Cell Biology

2002 University of North Carolina at Chapel Hill BS Biology, Chemistry minor

Publications

Peer-reviewed

1. Holt, J. M., Saunders, C. T., Rowell, W. J., Kronenberg, Z., Wenger, A. M., & Eberle, M. (2024). HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing. Bioinformatics, btae042. 10.1093/bioinformatics/btae042

2. Dolzhenko, E., English, A., Dashnow, H., … Eberle, M. A. (2024). Characterization and visualization of tandem repeats at genome scale. Nature Biotechnology. 10.1038/s41587-023-02057-3

3. Del Gobbo, G. F., Wang, X., Couse, M., … Boycott, K. M. (2023). Long-read genome sequencing reveals a novel intronic retroelement insertion in NR5A1 associated with 46,XY differences of sexual development. American Journal of Medical Genetics Part A. 10.1002/ajmg.a.63522

4. Cheung, W. A., Johnson, A. F., Rowell, W. J., … Pastinen, T. (2023). Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort. Nature Communications, 14(1), 3090. 10.1038/s41467-023-38782-1

5. Kucuk, E., van der Sanden, B. P. G. H., O’Gorman, L., … Gilissen, C. (2023). Comprehensive de novo mutation discovery with HiFi long-read sequencing. Genome Medicine, 15(1), 34. 10.1186/s13073-023-01183-6

6. Baid, G., Cook, D. E., Shafin, K., … Carroll, A. (2022). DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Nature Biotechnology. 10.1038/s41587-022-01435-7

7. Cohen, A. S. A., Farrow, E. G., Abdelmoity, A. T., … Pastinen, T. (2022). Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genetics in Medicine, 24(6), 1336–1348. 10.1016/j.gim.2022.02.007

8. Wagner, J., Olson, N. D., Harris, L., … Sedlazeck, F. J. (2022). Curated variation benchmarks for challenging medically relevant autosomal genes. Nature Biotechnology, 40(5), 672–680. 10.1038/s41587-021-01158-1

9. Wagner, J., Olson, N. D., Harris, L., … Zook, J. M. (2022). Benchmarking challenging small variants with linked and long reads. Cell Genomics, 2(5), 100128. 10.1016/j.xgen.2022.100128

10. Mehinovic, E., Gray, T., Campbell, M., … Turner, T. N. (2022). Germline mosaicism of a missense variant in KCNC2 in a multiplex family with autism and epilepsy characterized by long-read sequencing. American Journal of Medical Genetics Part A, 188(7), 2071–2081. 10.1002/ajmg.a.62743

11. Namiki, S., Ros, I. G., Morrow, C., Rowell, W. J., Card, G. M., Korff, W., & Dickinson, M. H. (2022). A population of descending neurons that regulates the flight motor of Drosophila. Current Biology, 32(5), 1189–1196.e6. 10.1016/j.cub.2022.01.008

12. van der Lee, M., Rowell, W. J., Menafra, R., Guchelaar, H.-J., Swen, J. J., & Anvar, S. Y. (2022). Application of long-read sequencing to elucidate complex pharmacogenomic regions: a proof of principle. The Pharmacogenomics Journal, 22(1), 75–81. 10.1038/s41397-021-00259-z

13. Laine, P., Rowell, W. J., Paulin, L., … Ekholm, J. M. (2021). Alu element in the RNA binding motif protein, X-linked 2 (RBMX2) gene found to be linked to bipolar disorder. PLOS ONE, 16(12), 1–18. 10.1371/journal.pone.0261170

14. Chin, C.-S., Wagner, J., Zeng, Q., … Zook, J. M. (2020). A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nature Communications, 11(1), 4794. 10.1038/s41467-020-18564-9

15. Cook, G. W., Benton, M. G., Akerley, W., … Emerson, L. L. (2020). Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing. PLOS ONE, 15(1), 1–21. 10.1371/journal.pone.0226340

16. Wenger, A. M., Peluso, P., Rowell, W. J., … Hunkapiller, M. W. (2019). Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature Biotechnology, 37(10), 1155–1162. 10.1038/s41587-019-0217-9

17. Tseng, E., Rowell, W. J., Glenn, O.-C., Hon, T., Barrera, J., Kujawa, S., & Chiba-Falek, O. (2019). The Landscape of SNCA Transcripts Across Synucleinopathies: New Insights From Long Reads Sequencing Analysis. Frontiers in Genetics, 10. 10.3389/fgene.2019.00584

18. Aso, Y., Sitaraman, D., Ichinose, T., … Rubin, G. M. (2014). Mushroom body output neurons encode valence and guide memory-based action selection in \textitDrosophila. ELife, 3, e04580. 10.7554/eLife.04580

19. Senger, K., Armstrong, G. W., Rowell, W. J., Kwan, J. M., Markstein, M., & Levine, M. (2004). Immunity Regulatory DNAs Share Common Organizational Features in Drosophila. Molecular Cell, 13(1), 19–32. 10.1016/S1097-2765(03)00500-8

Preprints

1. Kronenberg, Z., Nolan, C., Mokveld, T., … Eberle, M. A. (2024). The Platinum Pedigree: A long-read benchmark for genetic variants. BioRxiv. 10.1101/2024.10.02.616333

2. Redfield, S. E., Shao, W., Sun, T., … Shearer, A. E. (2024). Long-Read Sequencing Increases Diagnostic Yield for Pediatric Sensorineural Hearing Loss. MedRxiv. 10.1101/2024.09.30.24314377

3. Saunders, C. T., Holt, J. M., Baker, D. N., Lake, J. A., Belyeu, J. R., Kronenberg, Z., Rowell, W. J., & Eberle, M. A. (2024). Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling. BioRxiv. 10.1101/2024.08.19.608674

4. Porubsky, D., Dashnow, H., Sasani, T. A., … Eichler, E. E. (2024). A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree. BioRxiv. 10.1101/2024.08.05.606142

5. Fabian Morales, G. E., Ordonez Labastida, V., Rowell, W. J., Lambert, C., Fanslow, C., Robertson, A., & Zenteno Ruiz, J. C. (2024). Resolving the diagnostic odyssey in inherited retinal dystrophies through long-read genome sequencing. MedRxiv. 10.1101/2024.08.28.24312668

6. Isaacson, M. D., Eliason, J. L. M., Nern, A., … Reiser, M. B. (2023). Small-field visual projection neurons detect translational optic flow and support walking control. BioRxiv. 10.1101/2023.06.21.546024

7. Belyaeva, A., Shor, J., Cook, D. E., … Chang, P.-C. (2022). Knowledge distillation for fast and accurate DNA sequence correction. ArXiv. 10.48550/ARXIV.2211.09862

8. Freed, D., Rowell, W. J., Wenger, A. M., & Li, Z. (2022). Sentieon DNAscope LongRead – A highly Accurate, Fast, and Efficient Pipeline for Germline Variant Calling from PacBio HiFi reads. BioRxiv. 10.1101/2022.06.01.494452

Presentations
(selected)

1. Bioinformatics resources to analyze PacBio HiFi human genomes. (2024, February). PacBio Webinar Series. recording

2. W09. Structural chromosomal variation in cytogenomics: HiFi sequencing identifies likely causal variants missed by short-reads. (2023, June). Annual Meeting of the European Society of Human Genetics, Glasgow, Scotland. European Society of Human Genetics. slides

3. Comprehensive detection of variants in unsolved rare disease cases with PacBio HiFi reads. (2021, August). Annual Meeting of the European Society of Human Genetics. European Society of Human Genetics. slides

4. A Bioinformatics Workflow for Comprehensive Detection and Prioritization of Variants with PacBio HiFi Reads. (2021, April). PacBio Rare Disease Week. url

5. Comprehensive Variant Detection with PacBio HiFi Reads. (2021, April). Long Read Sequencing Opportunities at the BCM Human Genome Sequencing Center.

6. Comprehensive Variant Detection with PacBio HiFi Reads. (2020, September). Virtual Seminar for UC Schools: Get to Know the HiFi Difference. slides

7. HiFi Reads for Comprehensive Variant Detection. (2020, May). SMRT Leiden Online. slides

8. Evaluation of HG002 v4 draft benchmark against GATK calls on PacBio HiFi reads. (2019, October). Reference Assembly & Reference Materials: Updates from the GRC & GIAB, Houston, Texas, United States.

9. Advantages of HiFi reads for variant discovery and genome assembly. (2019, May). SMRT Scientific Symposium, Leiden, Netherlands.

10. Comprehensive Variant Detection with Highly Accurate Long Reads. (2019, April). HUGO Human Genome Meeting, Seoul, South Korea.

Posters
(selected)

1. Belyeu, J. R., Rowell, W. J., Lake, J. A., Holt, J. M., Kronenberg, Z., Saunders, C. T., & Eberle, M. A. (2024). Visualize complex structural variants in HiFi data with SVTopo. Annual Meeting of The American Society of Human Genetics, Denver, Colorado, United States. poster

2. Saunders, C. T., Holt, J. M., Baker, D. N., Lake, J. A., Belyeu, J. R., Kronenberg, Z., Rowell, W. J., & Eberle, M. A. (2024). Sawfish: improving long-read structural variant discovery and genotyping with local haplotype modeling. Annual Meeting of The American Society of Human Genetics, Denver, Colorado, United States. poster

3. Délot, E., Monlong, J., Chen, X., … Vilain, E. (2024). P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia. In Genetics in Medicine Open (Vol. 2). Annual Meeting of the American College of Medical Genetics and Genomics, Toronto, Canada. Elsevier. 10.1016/j.gimo.2024.101732

4. Del Gobbo, G., Couse, M., Lambert, C., … Boycott, K. (2024). O36: Long-read genome sequencing in unsolved rare genetic diseases: Preliminary experiences from the Care4Rare Canada Consortium. In Genetics in Medicine Open (Vol. 2, p. 101474). Annual Meeting of the American College of Medical Genetics and Genomics, Toronto, Canada. 10.1016/j.gimo.2024.101474

5. Kronenberg, Z. N., Munson, K. M., Porubsky, D., … Eberle, M. A. (2024). Building the spectrum of ground truth genetic variation in a four-generation 28-member CEPH family. Annual Advances in Genome Biology and Technology Meeting, Orlando, Florida, United States. poster

6. Dolzhenko, E., Erwin, G. S., Wang, K., … Eberle, M. A. (2024). Resolving variation in polymorphic regions of the human genome. Annual Advances in Genome Biology and Technology Meeting, Orlando, Florida, United States. poster

7. Holt, J. M., Saunders, C. T., Rowell, W. J., Kronenberg, Z., Wenger, A. M., & Eberle, M. (2023). HiPhase: Jointly phasing small and structural variants from HiFi sequencing. Annual Meeting of The American Society of Human Genetics, Washington, D.C., United States. poster

8. Kronenberg, Z. N., Munson, K. M., Porubsky, D., … Eberle, M. A. (2023). Building the spectrum of ground truth genetic variation in a four-generation 28-member CEPH family. Annual Meeting of The American Society of Human Genetics, Washington, D.C., United States. poster

9. Rowell, W. J., Redfield, S., Nolan, C., … Eberle, M. A. (2023). P16.011.D. PacBio HiFi WGS identifies potential causal variants not found by short read sequencing. Annual Meeting of The European Society of Human Genetics, Glasgow, Scotland. poster

10. Belyaeva, A., Baid, G., Cook, D. E., … Carroll, A. (2022). PB2960. DeepConsensus v0.3: Gap-aware sequence transformers for sequence correction. Annual Meeting of The American Society of Human Genetics, Los Angeles, California, United States.

11. Pastinen, T., Cheung, W., Rowell, W. J., Portik, D., Hall, R. J., Wenger, A. M., & Grundberg, E. (2022). PB2972. Direct haplotype-resolved 5-base HiFi genome sequencing allows for linking rare disease variants to non-coding function. Annual Meeting of The American Society of Human Genetics, Los Angeles, California, United States.

12. Lake, J. A., Rowell, W. J., & Eberle, M. A. (2022). PB2954. De novo variant detection with HiFi reads. Annual Meeting of The American Society of Human Genetics, Los Angeles, California, United States. poster

13. Del Gobbo, G., Wang, X., Couse, M., … Boycott, K. M. (2022). PB2322. Long-read HiFi genome sequencing reveals a 2.7 kilobase intronic insertion in NR5A1 as a cause of 46,XY disorder of sexual development. Annual Meeting of The American Society of Human Genetics, Los Angeles, California, United States.

14. Rowell, W. J., Wenger, A. M., Hickey, L. A., & Töpfer, A. (2020). I13. Comprehensive single-nucleotide, indel, structural, and copy-number variant detection in human genomes with PacBio HiFi reads. Annual Meeting of The Association for Molecular Pathology. poster

15. Rowell, W. J., & Wenger, A. M. (2020). A workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads. Cold Spring Harbor Biological Data Science Meeting. poster

16. Rowell, W. J., Wenger, A. M., Baid, G., Nattestad, M., Carroll, A., & Chang, P.-C. (2020). 3487. Accurate, comprehensive variant calling in difficult-to-map genes using HiFi reads (Reviewers’ Choice award). Annual Meeting of The American Society of Human Genetics. poster

17. Wenger, A. M., Rowell, W. J., Töpfer, A., & Hickey, L. (2020). P15.35.C. Comprehensive variant detection in human genomes with PacBio HiFi reads. Annual Meeting of The European Society of Human Genetics.

18. Wagner, J., Carroll, A., Fiddes, I. T., … in a Bottle Consortium, G. (2019). 1540. Using long and linked reads to generate a new Genome in a Bottle small variant benchmark. Annual Meeting of The American Society of Human Genetics, Houston, Texas, United States. poster

19. Rowell, W. J., Chakraborty, S., Baybayan, P., & Hall, R. J. (2019). 1866. Detection and phasing of small variants in Genome in a Bottle samples with highly accurate long reads. Annual Meeting of The American Society of Human Genetics, Houston, Texas, United States. poster

20. Rowell, W. J., Wenger, A. M., Kolesnikov, A., Chang, P.-C., Carroll, A., Hall, R. J., & Peluso, P. (2019). P16.85A. Comprehensive variant detection in a human genome with highly accurate long reads. Annual Meeting of The European Society of Human Genetics, Gothenburg, Sweden. poster

21. Rowell, W. J., Peluso, P., Harting, J., Qian, Y., Wenger, A. M., Hall, R. J., & Rank, D. R. (2018). Comprehensive Variant Detection in a Human Genome with PacBio High-Fidelity Reads. Cold Spring Harbor Biological Data Science Meeting, Cold Spring Harbor, New York, United States. poster

Professional Training

2016 Lean Six Sigma Yellow Belt Training, Q2 Solutions | EA Genomics

2013 Software Carpentry Instructor Training, The Carpentries

2012 High Functioning Leadership Program, HHMI Janelia Research Campus

Languages

English (native); Spanish (conversational, but rusty)

References

Available upon request.