William Rowell

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

Work Experience

Senior Staff Scientist, Bioinformatics Applications

Pacific Biosciences | 2017 - Present

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.

  • 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
  • guided the development and improvement of small variant detection and phasing workflows for PacBio HiFi WGS
  • developed the pb-human-wgs-snakemake workflow for human rare variant analysis from PacBio HiFi WGS
  • collaborated with Genome in a Bottle consortium to improve human small variant benchmarks

Scientific Programmer, Bioinformatics Data Services

Q2 Solutions | EA Genomics | 2015 - 2017

I was 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, Project Technical Resources and The Fly Olympiad

HHMI, Janelia Research Campus | 2010 - 2015

I supported the research of the project teams and labs at Janelia by providing consultation, conducting experiments, analyzing data, and writing software. I investigated the role of individual neurons or groups of neurons in altering behavior by screening Drosophila melanogaster lines through high-throughput behavioral assays.

  • acted as liaison and translator between scientists, software engineers, and engineers
  • screened D. melanogaster lines through high-throughput locomotor, optomotor, phototaxis, and olfactory assays
  • wrote custom tools in python for analysis of D. melanogaster activity/sleep data
  • wrote automated pipeline for fluorescence imagery analysis
  • aided in establishing guidelines for storing data and metadata
  • 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

Projects

Genome in a Bottle Consortium

hosted by NIST and JIMB

I have contributed small variant analysis for PacBio HiFi reads to the GIAB Consortium towards the refinement of small variant benchmarks. I have curated differences between call sets and the benchmarks to characterize the residual errors in both the call sets and the benchmarks.

Instructor

The Carpentries

I am a trained instructor for Software Carpentry and Data Carpentry at The Carpentries. I have taught for Software Carpentry at workshops at George Washington University and Howard Hughes Medical Institute, Janelia Research Campus.

Information

Publications

  • Cheung WA, Rowell WJ, Farrow EG, Johnson AF, Hall RJ, Cohen ASA, Means J, Zion TN, Portik DM, Saunders CT, Koseva B, Bi C, Schwendinger-Schreck C, Yoo B, Johnston JJ, Gibson M, Thiffault I, Younger ST, Curran T, Wenger AM, Grundberg E, Pastinen T. 2022. Direct haplotype-resolved 5-base HiFi genome sequencing reveals non-coding function of rare disease variants. medRxiv (2022). https://www.medrxiv.org/content/10.1101/2022.09.12.22279739v1 [preprint]
  • Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert J-P, Vaswani A, McLean CY, Nattestad M, Chang P-C, Carroll A. 2022. DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-022-01435-7
  • Freed D, Rowell WJ, Wenger AM, Li Z. 2022. Sentieon DNAscope LongRead - A highly Accurate, Fast, and Efficient Pipeline for Germline Variant Calling from PacBio HiFi reads. bioRxiv. https://doi.org/10.1101/2022.06.01.494452 [preprint]
  • Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, Schatz MC, Narzisi G, Byrska-Bishop M, Clarke W, Evani US, Markello C, Shafin K, Zhou X, Sidow A, Bansal V, Ebert P, Marschall T, Lansdorp P, Hanlon V, Mattsson CA, Barrio AM, Fiddes IT, Xiao C, Fungtammasan A, Chin CS, Wenger AM, Rowell WJ, Sedlazeck FJ, Carroll A, Salit M, Zook JM. 2022. Benchmarking challenging small variants with linked and long reads. Cell Genomics. https://doi.org/10.1016/j.xgen.2022.100128
  • Mehinovic E, Gray T, Campbell M, Ekholm J, Wenger AM, Rowell WJ, Grudo A, Grimwood J, Korlach J, Gurnett C, Constantino JN, Turner TN. 2022. Germline mosaicism of a missense variant in KCNC2 in a multiplex family with autism and epilepsy characterized by long-read sequencing. Am. J. Med. Genet. A. http://doi.org/10.1002/ajmg.a.62743
  • Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B, Berrios CD, Biswell RL, Buczkowicz P, Buske O, Chakraborty S, Cheung WA, Coffman KA, Cooper AM, Cross LA, Curran T, Dang TTT, Elfrink MM, Engleman KL, Fecske ED, Fieser C, Fitzgerald K, Fleming EA, Gadea RN, Gannon JL, Gelineau-Morel RN, Gibson M, Goldstein J, Grundberg E, Halpin K, Harvey BS, Heese BA, Hein W, Herd SM, Hughes SS, Ilyas M, Jacobson J, Jenkins JL, Jiang S, Johnston JJ, Keeler K, Korlach J, Kussmann J, Lambert C, Lawson C, Le Pichon J-B, Leeder JS, Little VC, Louiselle DA, Lypka M, McDonald BD, Miller N, Modrcin A, Nair A, Neal SH, Oermann CM, Pacicca DM, Pawar K, Posey NL, Price N, Puckett LMB, Quezada JF, Raje N, Rowell WJ, Rush ET, Sampath V, Saunders CJ, Schwager C, Schwend RM, Shaffer E, Smail C, Soden S, Strenk ME, Sullivan BR, Sweeney BR, Tam-Williams JB, Walter AM, Welsh H, Wenger AM, Willig LK, Yan Y, Younger ST, Zhou D, Zion TN, Thiffault I, Pastinen T. Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genet in Med (2022). https://doi.org/10.1016/j.gim.2022.02.007
  • Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, Fungtammasan A, Hwang Y-C, Gupta R, Wenger AM, Rowell WJ, Khan ZM, Farek J, Zhu Y, Pisupati A, Mahmoud M, Xiao C, Yoo B, Sahraeian SME, Miller DE, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Narzisi G, Evani US, Clarke WE, Lee J, Mason CE, Lincoln SE, Miga KH, Ebbert MTW, Shumate A, Li H, Chin C-S, Zook JM, Sedlazeck FJ. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-021-01158-1
  • Namiki S, Ros IG, Morrow C, Rowell WJ, Card GM, Korff W, Dickinson MH. 2022. A population of descending neurons that regulates the flight motor of Drosophila. Curr Biology. https://doi.org/10.1016/j.cub.2022.01.008
  • Laine P, Rowell WJ, Paulin L, Kujawa S, Raterman D, Mayhew G, Wendt J, Burgess DL, Partonen T, Paunio T, Auvinen P, Ekholm JM. 2021. Alu element in the RNA binding motif protein, X-linked 2 (RBMX2) gene found to be linked to bipolar disorder. PLoS ONE. https://doi.org/10.1371/journal.pone.0261170
  • van der Lee M, Rowell WJ, Menafra R, Guchelaar H-J, Swen JJ, Anvar SY. 2021. Application of long-read sequencing to elucidate complex pharmacogenomic regions: a proof of principle. Pharmacogenomics J. https://doi.org/10.1038/s41397-021-00259-z
  • Chin C-S, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautianinen M, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, Sedlazek FJ, Bansal V, Yoo B, Miller N, Zhou X, Carroll A, Barrio AM, Salit M, Marschall T, Dilthey AT, Zook JM. 2020. A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nat Comm (11). https://doi.org/10.1038/s41467-020-18564-9
  • Cook GW, Benton MG, Akerly W, Mayhew GF, Moehlenkamp C, Raterman D, Burgess DL, Rowell WJ, Lambert C, Eng K, Gu J, Baybayan P, Fussell JT, Herbold HD, O’Shea JM, Varghese TK, Emerson LL. 2020. Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing. PLoS ONE. https://doi.org/10.1371/journal.pone.0226340
  • Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin C-S, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW. 2019. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol (74). https://doi.org/10.1038/s41587-019-0217-9
  • Tseng E, Rowell WJ, 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. Front Genet (10). https://doi.org/10.3389/fgene.2019.00584
  • Aso Y, Sitaraman D, Ichinose T, Kaun KR, Vogt K, Belliart-Guérin G, Plaçais P-Y, Robie AA, Yamagata N, Schnaitmann C, Rowell WJ, Johnston RM, Ngo, T-TB, Chen N, Korff W, Nitabach MN, Heberlein U, Preat T, Branson KM, Tanimoto H, Rubin GM. 2014. Mushroom body output neurons encode valence and guide memory-based action selection in Drosophila. eLife (2014). https://doi.org/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). https://doi.org/10.1016/S1097-2765%2803%2900500-8

Presentations

Posters