Billy Rowell

Bioinformatics Data Scientist Fremont, CA

Summary

Collaborative biological data scientist with over 20 years of research experience, including 8 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

Computational

Python/NumPy/pandas/Matplotlib · Bash/Git · HPC/Slurm/SGE · BFX workflows · WDL/Snakemake · reproducible analysis · BWA/minimap2/ngmlr · GATK/DeepVariant/WhatsHap · samtools/bedtools/bcftools · hifasm/gfatools · image acquisition and analysis

Scientific

sequence QC · NGS/long-read sequencing · WGS/WES/targeted sequencing · RNA-Seq/Iso-Seq · model organism genetics · human genetics · rare disease research · experimental design · high-throughput logistics

Professional

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

Experience

Sr. Staff Bioinformatics Scientist

2017 - Present Pacific Biosciences Menlo Park, CA

• Through internal and external collaborations, guided the development and improvement of variant detection applications
• Worked with NIST Genome in a Bottle consortium to improve human variant calling benchmarks
• Developed workflows for variant calling, filtering, annotation, and prioritization for rare and inherited disease studies
• Support customers and collaborators by applying analysis workflows to their data, resulting in publications
• Support commercial teams by leveraging pilot experiments into instrument sales and marketing collateral
• Lead a small team focused on developing, improving, and applying analysis workflows and characterizing genomics data

Scientific Programmer

2015 - 2017 Q2 Solutions | EA Genomics Durham, NC

• Responsible for analyzing and delivering NGS sequence data for hundreds of samples to customers each month
• Processed NGS data with standard WGS, WES, and RNA-seq analysis pipelines
• Monitored sequence quality and determined root cause of problems
• Delivered data in a timely manner to meet customer expectations
• Guided the development of delivery and analysis pipeline enhancements
• In a rapidly expanding team, developed tools for tracking tasks and errors
• Recognized for providing exceptional customer service

Research Specialist

2010 - 2015 HHMI, Janelia Research Campus Ashburn, VA

• Supported the research of the project teams and labs at Janelia by providing consultation, conducting experiments, analyzing data, and writing software
• Screened D. melanogaster lines through high-throughput locomotor, optomotor, phototaxis, and olfactory assays
• Acted as liaison and translator between scientists, software engineers, and electrical engineers
• Wrote custom tools for analysis of activity/sleep data and fluorescence imagery analysis
• Curated and analyzed 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

Journal Articles

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. doi

2. Dolzhenko, E., English, A., Dashnow, H., De Sena Brandine, G., Mokveld, T., Rowell, W. J., Karniski, C., Kronenberg, Z., Danzi, M. C., Cheung, W. A., Bi, C., Farrow, E., Wenger, A., Chua, K. P., Martı́nez-Cerdeño Verónica, Bartley, T. D., Jin, P., Nelson, D. L., Zuchner, S., … Eberle, M. A. (2024). Characterization and visualization of tandem repeats at genome scale. Nature Biotechnology. doi

3. Del Gobbo, G. F., Wang, X., Couse, M., Mackay, L., Goldsmith, C., Marshall, A. E., Liang, Y., Lambert, C., Zhang, S., Dhillon, H., Fanslow, C., Rowell, W. J., Consortium, C. R. C., Marshall, C. R., Kernohan, K. D., & 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. doi

4. Cheung, W. A., Johnson, A. F., Rowell, W. J., Farrow, E., Hall, R., Cohen, A. S. A., Means, J. C., Zion, T. N., Portik, D. M., Saunders, C. T., Koseva, B., Bi, C., Truong, T. K., Schwendinger-Schreck, C., Yoo, B., Johnston, J. J., Gibson, M., Evrony, G., Rizzo, W. B., … 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. doi

5. Kucuk, E., van der Sanden, B. P. G. H., O’Gorman, L., Kwint, M., Derks, R., Wenger, A. M., Lambert, C., Chakraborty, S., Baybayan, P., Rowell, W. J., Brunner, H. G., Vissers, L. E. L. M., Hoischen, A., & Gilissen, C. (2023). Comprehensive de novo mutation discovery with HiFi long-read sequencing. Genome Medicine, 15(1), 34. doi

6. Baid, G., Cook, D. E., Shafin, K., Yun, T., Llinares-López, F., Berthet, Q., Belyaeva, A., Töpfer, A., Wenger, A. M., Rowell, W. J., Yang, H., Kolesnikov, A., Ammar, W., Vert, J.-P., Vaswani, A., McLean, C. Y., Nattestad, M., Chang, P.-C., & Carroll, A. (2022). DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Nature Biotechnology. doi

7. Cohen, A. S. A., Farrow, E. G., Abdelmoity, A. T., Alaimo, J. T., Amudhavalli, S. M., Anderson, J. T., Bansal, L., Bartik, L., Baybayan, P., Belden, B., Berrios, C. D., Biswell, R. L., Buczkowicz, P., Buske, O., Chakraborty, S., Cheung, W. A., Coffman, K. A., Cooper, A. M., Cross, L. A., … Pastinen, T. (2022). Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genetics in Medicine, 24(6), 1336–1348. doi

8. Wagner, J., Olson, N. D., Harris, L., McDaniel, J., Cheng, H., Fungtammasan, A., Hwang, Y.-C., Gupta, R., Wenger, A. M., Rowell, W. J., Khan, Z. M., Farek, J., Zhu, Y., Pisupati, A., Mahmoud, M., Xiao, C., Yoo, B., Sahraeian, S. M. E., Miller, D. E., … Sedlazeck, F. J. (2022). Curated variation benchmarks for challenging medically relevant autosomal genes. Nature Biotechnology, 40(5), 672–680. doi

9. 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. doi

10. 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. doi

11. Mehinovic, E., Gray, T., Campbell, M., Ekholm, J., Wenger, A., Rowell, W., Grudo, A., Grimwood, J., Korlach, J., Gurnett, C., Constantino, J. N., & 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. doi

12. Wagner, J., Olson, N. D., Harris, L., Khan, Z., Farek, J., Mahmoud, M., Stankovic, A., Kovacevic, V., Yoo, B., Miller, N., Rosenfeld, J. A., Ni, B., Zarate, S., Kirsche, M., Aganezov, S., Schatz, M. C., Narzisi, G., Byrska-Bishop, M., Clarke, W., … Zook, J. M. (2022). Benchmarking challenging small variants with linked and long reads. Cell Genomics, 2(5), 100128. doi

13. Laine, P., Rowell, W. J., Paulin, L., Kujawa, S., Raterman, D., Mayhew, G., Wendt, J., Burgess, D. L., Partonen, T., Paunio, T., Auvinen, P., & 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. doi

14. Chin, C.-S., Wagner, J., Zeng, Q., Garrison, E., Garg, S., Fungtammasan, A., Rautiainen, M., Aganezov, S., Kirsche, M., Zarate, S., Schatz, M. C., Xiao, C., Rowell, W. J., Markello, C., Farek, J., Sedlazeck, F. J., Bansal, V., Yoo, B., Miller, N., … Zook, J. M. (2020). A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nature Communications, 11(1), 4794. doi

15. Cook, G. W., Benton, M. G., Akerley, W., Mayhew, G. F., Moehlenkamp, C., Raterman, D., Burgess, D. L., Rowell, W. J., Lambert, C., Eng, K., Gu, J., Baybayan, P., Fussell, J. T., Herbold, H. D., O’Shea, J. M., Varghese, T. K., & 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. doi

16. Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., Töpfer, A., Alonge, M., Mahmoud, M., Qian, Y., Chin, C.-S., Phillippy, A. M., Schatz, M. C., Myers, G., DePristo, M. A., … 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. doi

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. doi

18. Aso, Y., Sitaraman, D., Ichinose, T., Kaun, K. R., Vogt, K., Belliart-Guérin, G., Plaçais, P.-Y., Robie, A. A., Yamagata, N., Schnaitmann, C., Rowell, W. J., Johnston, R. M., Ngo, T.-T. B., Chen, N., Korff, W., Nitabach, M. N., Heberlein, U., Preat, T., Branson, K. M., … Rubin, G. M. (2014). Mushroom body output neurons encode valence and guide memory-based action selection in \textitDrosophila. ELife, 3, e04580. doi

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. doi

Preprints

1. Isaacson, M. D., Eliason, J. L. M., Nern, A., Rogers, E. M., Lott, G. K., Tabachnik, T., Rowell, W. J., Edwards, A. W., Korff, W. L., Rubin, G. M., Branson, K., & Reiser, M. B. (2023). Small-field visual projection neurons detect translational optic flow and support walking control. BioRxiv. doi

2. 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. BioRxiv. doi

3. Dolzhenko, E., English, A., Dashnow, H., Brandine, G. D. S., Mokveld, T., Rowell, W. J., Karniski, C., Kronenberg, Z., Danzi, M. C., Cheung, W., Bi, C., Farrow, E., Wenger, A., Martı́nez-Cerdeño Verónica, Bartley, T. D., Jin, P., Nelson, D., Zuchner, S., Pastinen, T., … Eberle, M. A. (2023). Resolving the unsolved: Comprehensive assessment of tandem repeats at scale. BioRxiv. doi

4. 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. doi

5. Belyaeva, A., Shor, J., Cook, D. E., Shafin, K., Liu, D., Töpfer, A., Wenger, A. M., Rowell, W. J., Yang, H., Kolesnikov, A., McLean, C. Y., Nattestad, M., Carroll, A., & Chang, P.-C. (2022). Knowledge distillation for fast and accurate DNA sequence correction. ArXiv. doi

6. Cheung, W. A., Rowell, W. J., Farrow, E., Johnson, A. F., Hall, R., Cohen, A. S. A., Means, J. C., Zion, T., Portik, D. M., Saunders, C. T., Koseva, B., Bi, C., Truong, T., Schwendinger-Schreck, C., Yoo, B., Johnston, J. J., Gibson, M., Evrony, G., Rizzo, W. B., … Pastinen, T. (2022). Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort. MedRxiv. doi

7. Wagner, J., Olson, N. D., Harris, L., McDaniel, J., Cheng, H., Fungtammasan, A., Hwang, Y.-C., Gupta, R., Wenger, A. M., Rowell, W. J., Khan, Z. M., Farek, J., Zhu, Y., Pisupati, A., Mahmoud, M., Xiao, C., Yoo, B., Sahraeian, S. M. E., Miller, D. E., … Sedlazeck, F. J. (2021). Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes. BioRxiv. doi

8. Cohen, A. S. A., Farrow, E. G., Abdelmoity, A. T., Alaimo, J. T., Amudhavalli, S. M., Anderson, J. T., Bansal, L., Bartik, L., Baybayan, P., Belden, B., Berrios, C. D., Biswell, R. L., Buczkowicz, P., Buske, O., Chakraborty, S., Cheung, W. A., Coffman, K. A., Cooper, A. M., Cross, L. A., … Pastinen, T. (2021). IGenomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. MedRxiv. doi

9. Wagner, J., Olson, N. D., Harris, L., McDaniel, J., Khan, Z., Farek, J., Mahmoud, M., Stankovic, A., Kovacevic, V., Yoo, B., Miller, N., Rosenfeld, J. A., Ni, B., Zarate, S., Kirsche, M., Aganezov, S., Schatz, M., Narzisi, G., Byrska-Bishop, M., … Zook, J. M. (2021). Benchmarking challenging small variants with linked and long reads. BioRxiv. doi

10. Namiki, S., Ros, I. G., Morrow, C., Rowell, W. J., Card, G. M., Korff, W., & Dickinson, M. H. (2021). A population of descending neurons that regulate the flight motor of Drosophila. BioRxiv. doi

11. Mehinovic, E., Gray, T., Campbell, M., Ekholm, J., Wenger, A., Rowell, W., Grudo, A., Grimwood, J., Korlach, J., Gurnett, C., Constantino, J. N., & Turner, T. N. (2021). Germline mosaicism of a missense variant in KCNC2 in a multiplex family with autism and epilepsy. MedRxiv. doi

12. Baid, G., Cook, D. E., Shafin, K., Yun, T., Llinares-López, F., Berthet, Q., Wenger, A. M., Rowell, W. J., Nattestad, M., Yang, H., Kolesnikov, A., Töpfer, A., Ammar, W., Vert, J.-P., Vaswani, A., McLean, C. Y., Chang, P.-C., & Carroll, A. (2021). DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction. BioRxiv. doi

13. Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., Töpfer, A., Alonge, M., Mahmoud, M., Qian, Y., Chin, C.-S., Phillippy, A. M., Schatz, M. C., Myers, G., DePristo, M. A., … Hunkapiller, M. W. (2019). Highly-accurate long-read sequencing improves variant detection and assembly of a human genome. BioRxiv. doi

14. 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. BioRxiv. doi

Presentations

1. Rowell, W. (2024). Bioinformatics resources to analyze PacBio HiFi human genomes. Presented at the PacBio Webinar Series. https://www.youtube.com/watch?v=inxVEjQhntI

2. Rowell, W. (2023). W09 Structural chromosomal variation in cytogenomics: HiFi sequencing identifies likely causal variants missed by short-reads. Presented at the Annual Meeting of the European Society of Human Genetics. European Society of Human Genetics. https://speakerdeck.com/williamrowell/hifi-sequencing-identifies-likely-causal-variants-missed-by-short-reads

3. Rowell, W. (2021). Comprehensive detection of variants in unsolved rare disease cases with PacBio HiFi reads. Presented at the Annual Meeting of the European Society of Human Genetics. European Society of Human Genetics. https://speakerdeck.com/williamrowell/comprehensive-detection-of-variants-in-rare-disease-research-with-pacbio-hifi-reads

4. Rowell, W. (2021). A Bioinformatics Workflow for Comprehensive Detection and Prioritization of Variants with PacBio HiFi Reads. Presented at the PacBio Rare Disease Week. https://events.pacb.com/rare-disease-2021/agenda

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

6. Rowell, W. (2020). Comprehensive Variant Detection with PacBio HiFi Reads. Presented at the Virtual Seminar for UC Schools: Get to Know the HiFi Difference. https://speakerdeck.com/williamrowell/comprehensive-variant-detection-with-pacbio-hifi-reads

7. Rowell, W. (2020). HiFi Reads for Comprehensive Variant Detection. Presented at the SMRT Leiden Online. https://speakerdeck.com/williamrowell/hifi-reads-for-comprehensive-variant-detection

8. Rowell, W. (2019). Variant detection and de novo assembly with HiFi reads. Presented at the PacBio User Group Meeting EMEA, Milano, Italy.

9. Rowell, W. (2019). Evaluation of HG002 v4 draft benchmark against GATK calls on PacBio HiFi reads. Presented at the Reference Assembly & Reference Materials: Updates from the GRC & GIAB, Houston, TX.

10. Rowell, W. (2019). Advantages of HiFi reads for variant discovery and genome assembly. Presented at the SMRT Scientific Symposium, Leiden, Netherlands.

11. Rowell, W. (2019). Comprehensive Variant Detection with Highly Accurate Long Reads. Presented at the PacBio User Group Meeting Korea, Seoul, South Korea.

12. Rowell, W. (2019). Comprehensive Variant Detection with Highly Accurate Long Reads. Presented at the HUGO Human Genome Meeting, Seoul, South Korea.

13. Rowell, W. (2019). Comprehensive Variant Detection with Highly Accurate Long Reads. Presented at the PacBio User Group Meeting China, Beijing, China.

14. Rowell, W. (2019). Reviewing benchmark v3.3.2 PacBio CCS discrepancies in benchmark v4alpha. Presented at the Genome in a Bottle Consortium Workshop, Stanford, CA, US.

15. Rowell, W. (2019). Detecting and Phasing Small Variants with Highly Accurate Long Reads. Presented at the SMRT Informatics Developers Conference, San Diego, CA, US.

Posters

1. Délot, E., Monlong, J., Chen, X., Barseghyan, H., Bhattacharya, S., LoTempio, J., McNulty, B., Negi, S., O’Rourke, S., Robertson, A., Rowell, W., Berger, S., Miga, K., Paten, B., Cool, J., & Vilain, E. (2024). P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia*. Presented at the Genetics in Medicine Open (Vol. 2). Elsevier. doi

2. Del Gobbo, G., Couse, M., Lambert, C., Zhang, S., Dhillon, H., Fanslow, C., Rowell, W., Dolzhenko, E., De Sena Brandine, G., Eberle, M., Marshall, C., Kernohan, K., & Boycott, K. (2024). O36: Long-read genome sequencing in unsolved rare genetic diseases: Preliminary experiences from the Care4Rare Canada Consortium. Presented at the Genetics in Medicine Open (Vol. 2, p. 101474). doi

3. Kronenberg, Z. N., Munson, K. M., Porubsky, D., Nolan, C., Rowell, W. J., Pedersen, B. S., Fanslow, C., Baybayan, P., Koundinya, N., Harvey, W., Hoekzema, K., Knuth, J., Garcia, G., Mokveld, T., Dolzhenko, E., Watkins, S., Neklason, D. W., Quinlan, A. R., Jorde, L. B., … Eberle, M. A. (2024). Building the spectrum of ground truth genetic variation in a four-generation 28-member CEPH family. Presented at the Annual Advances in Genome Biology and Technology Meeting. https://www.pacb.com/wp-content/uploads/AGBT-2024-Poster-Zev-Kronenberg.pdf

4. Dolzhenko, E., Erwin, G. S., Wang, K., Kronenberg, Z., Rowell, W. J., Ferrari, A. C., Pease, G., Schwartz, D., Gartrell, B., Aboumohamed, A., Sankin, A., Maria, P., Watts, K., Greally, J. M., Wilkinson, P., Rajpurohit, Y., Loffredo, J., Smirnov, D., Sepulveda, M. A., … Eberle, M. A. (2024). Resolving variation in polymorphic regions of the human genome. Presented at the Annual Advances in Genome Biology and Technology Meeting. https://www.pacb.com/wp-content/uploads/AGBT-2024-Poster-Egor-Dolzhenko.pdf

5. Kronenberg, Z. N., Munson, K. M., Porubsky, D., Nolan, C., Rowell, W. J., Pedersen, B. S., Fanslow, C., Baybayan, P., Koundinya, N., Harvey, W., Hoekzema, K., Knuth, J., Garcia, G., Mokveld, T., Dolzhenko, E., Watkins, S., Neklason, D. W., Quinlan, A. R., Jorde, L. B., … Eberle, M. A. (2023). Building the spectrum of ground truth genetic variation in a four-generation 28-member CEPH family. Presented at the Annual Meeting of The American Society of Human Genetics. https://www.pacb.com/wp-content/uploads/ASHG-2023-Kronenberg-poster.pdf

6. 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. Presented at the Annual Meeting of The American Society of Human Genetics. https://www.pacb.com/wp-content/uploads/ASHG-2023-Matt-Holt-HiPhase-poster.pdf

7. Rowell, W. J., Redfield, S., Nolan, C., Holt, J. M., Chen, X., Fanslow, C., Lampraki, E. M., Lambert, C., Saunders, C., Kenna, M. A., & Eberle, M. A. (2023). PacBio HiFi WGS identifies potential causal variants not found by short read sequencing. Presented at the P16.011.D. Annual Meeting of The European Society of Human Genetics. https://www.pacb.com/wp-content/uploads/PacBio-HiFi-WGS-identifies-potential-causal-variants-not-found-by-short-read-sequencing.pdf

8. Del Gobbo, G., Wang, X., Couse, M., Lambert, C., Zhang, S., Dhillon, S., Fanslow, C., Rowell, W. J., Storer, C., Marshall, C. R., Kernohan, K. D., & Boycott, K. M. (2022). Long-read HiFi genome sequencing reveals a 2.7 kilobase intronic insertion in NR5A1 as a cause of 46,XY disorder of sexual development. Presented at the PB2322. Annual Meeting of The American Society of Human Genetics.

9. Lake, J. A., Rowell, W. J., & Eberle, M. A. (2022). PB2954. De novo variant detection with HiFi reads. Presented at the Annual Meeting of The American Society of Human Genetics. https://www.pacb.com/wp-content/uploads/poster_lake.pdf

10. Belyaeva, A., Baid, G., Cook, D. E., Shafin, K., Yun, T., Llinares-López, F., Berthet, Q., Töpfer, A., Wenger, A. M., Rowell, W. J., Yang, H., Kolesnikov, A., Ammar, W., Vert, J.-P., Vaswani, A., McLean, C. Y., Nattestad, M., Chang, P.-C., & Carroll, A. (2022). PB2960. DeepConsensus v0.3: Gap-aware sequence transformers for sequence correction. Presented at the Annual Meeting of The American Society of Human Genetics.

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. Presented at the Annual Meeting of The American Society of Human Genetics.

12. Freed, D., Rowell, W. J., Wenger, A. M., & Li, Z. (2022). PB3129. Sentieon DNAscope LongRead: a highly accurate, fast, and efficient pipeline for germline variant calling from PacBio HiFi reads. Presented at the Annual Meeting of The American Society of Human Genetics.

13. 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. Presented at the Annual Meeting of The Association for Molecular Pathology. https://www.pacb.com/wp-content/uploads/Rowell-AMP-2020-Comprehensive-single-nucleotide-indel-structural-and-copy-number-variant-detection-in-human-genomes-with-PacBio-HiFi-reads.pdf

14. Rowell, W. J., & Wenger, A. M. (2020). A workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads. Presented at the Cold Spring Harbor Biological Data Science Meeting. https://www.pacb.com/wp-content/uploads/Rowell-CSH-BDS-2020-A-workflow-for-the-comprehensive-detection-and-prioritization-of-variants-in-human-genomes-with-PacBio-HiFi-reads.pdf

15. 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). Presented at the Annual Meeting of The American Society of Human Genetics. https://www.pacb.com/wp-content/uploads/Rowell-ASHG-2020-Accurate-comprehensive-variant-calling-in-difficult-to-map-genes-using-HiFi-reads.pdf

16. Mitchell, M. W., Baybayan, P., Wenger, A., Rowell, W. J., Zhu, L., Smith, G., & Requesens, D. V. (2020). 3523. High molecular weight DNA extraction and long-read next-generation sequencing of human genomic reference standard. Presented at the Annual Meeting of The American Society of Human Genetics. https://www.pacb.com/wp-content/uploads/ASHG-2020-HMW-DNA-Coriell-PacBio-Poster.pdf

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. Presented at the Annual Meeting of The European Society of Human Genetics.

18. Vogelsang, R., Rowell, W. J., Wenger, A. M., & Hall, R. J. (2019). Comprehensive variant detection in a human genome with highly accurate long reads. Presented at the Presented at Genome Science.

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. Presented at the Annual Meeting of The American Society of Human Genetics. https://www.pacb.com/wp-content/uploads/Rowell-ASHG-2019-Detection-and-phasing-of-small-variants-in-Genome-in-a-Bottle-samples-with-highly-accurate-long-reads.pdf

20. Wagner, J., Carroll, A., Fiddes, I. T., Wenger, A. M., Rowell, W. J., Olson, N., Harris, L., McDaniel, J., Xiao, C., Salit, M., Zook, J., & in a Bottle Consortium, G. (2019). 1540. Using long and linked reads to generate a new Genome in a Bottle small variant benchmark. Presented at the Annual Meeting of The American Society of Human Genetics. https://www.slideshare.net/GenomeInABottle/giab-ashg-2019-small-variant-poster

21. Ekholm, J. M., Rowell, W. J., Paulin, L., Kujawa, S., Raterman, D., Mayhew, G., Wendt, J., Burgess, D. L., Partonen, T., Paunio, T., Laine, P., & Auvinen, P. (2019). 2221. Structural variant in the RNA binding motif protein, X-linked 2 (RBMX2) gene found to be linked to bipolar disorder. Presented at the Annual Meeting of The American Society of Human Genetics. https://www.pacb.com/wp-content/uploads/Ekholm-ASHG-2019-Structural-variant-in-the-RNA-Binding-Motif-Protein-X-Linked-2-RBMX2-gene-found-to-be-linked-to-bipolar-disorder.pdf

22. 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. Presented at the Annual Meeting of The European Society of Human Genetics. https://www.pacb.com/wp-content/uploads/Rowell-ESHG-2019-Comprehensive-variant-detection-in-a-human-genome-with-highly-accurate-long-reads.pdf

23. Fijneman, R., Mekkes, N., Broek, E., Stringer, B., Glas, R., Komor, M., Rausch, C., Lieshout, S., Cuppen, E., Smith, M., Sebra, R., Rowell, W. J., Ashby, M., Carvalho, B., Meijer, G., & Abeln, S. (2019). 1738. Characterization of structural variants within MACROD2 in the pathogenesis of colorectal cancer. Presented at the Annual Meeting of The American Association for Cancer Research. doi

24. 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. Presented at the Cold Spring Harbor Biological Data Science Meeting. https://www.pacb.com/wp-content/uploads/Rowell-CSHLBioData-2018-Comprehensive-Variant-Detection-in-a-Human-Genome-with-PacBio-High-Fidelity-Reads.pdf

25. Vierra, M., Kingan, S. B., Clark, T. A., Fedrigo, O., Hon, T., Mountcastle, J., Rowell, W. J., Tseng, E., Korlach, J., & Jarvis, E. D. (2018). Full-length transcript (Iso-Seq) profiling for improved genome annotations. Presented at the Annual Advances in Genome Biology and Technology Meeting. https://www.pacb.com/wp-content/uploads/Vierra-AGBT-2018-Full-length-transcript-profiling-with-the-Iso-Seq-method-for-improved-genome-annotations.pdf

26. Ashby, M., Rowell, W. J., Bowman, B., Gu, J., Baybayan, P., Kujawa, S., & Chakraborty, S. (2018). Mitochondrial DNA Sequencing Using PacBio SMRT Technology. Presented at the Annual Advances in Genome Biology and Technology Meeting. https://www.pacb.com/wp-content/uploads/Chakraborty-AGBT-2018-Mitochondrial-DNA-Sequencing-Using-the-PacBio-Sequel-System-.pdf

27. McLaughlin, I., Baybayan, P., Hall, R. J., Harting, J., & Rowell, W. J. (2017). 1533F. Targeted Sequencing Using a Long-Read Sequencing Technology. Presented at the Annual Meeting of The American Society of Human Genetics. https://www.pacb.com/wp-content/uploads/McLaughlin-ASHG-2017-Targeted-Sequencing-Using-a-Long-Read-Sequencing-Technology.pdf

28. Reiser, M. B., Rowell, W. J., Lee, A., & Korff, W. (2012). Probing Drosophila visual behaviors in high throughput. Presented at the Tenth International Congress of Neuroethology. doi

29. Korff, W., Anderson, D. J., Branson, K. M., Card, G., Chen, N., Hayes, S., Hirokawa, J., Hoopfer, E., Kimmel, B., Kladt, N., Low, S., McKellar, C., Phillips, M., Reiser, M. B., Roberts, S., Robie, A. A., Rowell, W. J., Rubin, G., Simpson, J. H., … Triphan, T. (2012). The Fly Olympiad: A series of high-throughput, quantitative behavioral experiments in Drosophila neurobiology. Presented at the Tenth International Congress of Neuroethology. doi

Professional Training

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

2013 Software Carpentry Instructor Training, The Carpentries

2012 High Functioning Leadership Program, HHMI Janelia Research Campus, Ashburn, VA

Languages

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

References

Available upon request.