William Rowell

Staff Bioinformatics 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

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
  • collaborated with Genome in a Bottle consortium to improve human small variant benchmarks

Scientific Programmer, Bioinformatics Data Services

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

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

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

  • Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Wenger AM, Rowell WJ, Xiao C, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, Schatz M, Zhou X, Sidow A, Bansal V, Barrio AM, Fiddes IT, Fungtammasan A, Chin C-S, Sedlazeck FJ, Carroll A, Salit M, Zook JM. 2020. Benchmarking challenging small variants with linked and long reads. (preprint). bioRxiv. https://doi.org/10.1101/2020.07.24.212712
  • 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