Curriculum Vitae – Josiah Seaman

Download A Copy Here: CV Josiah Seaman

RESEARCH INTERESTS
Comparative Genomics – Regulatory DNA – Transcription Regulatory Networks – Chromatin Folding – Gene Copy Evolution – Genome Browsers and Visualization – Machine Learning for Sequence Pattern Recognition – Phase Condensates – RNA-RNA Interactions – Acquiring New Areas of Knowledge

EDUCATION
Ph.D. in Bioinformatics
, 2021 – Queen Mary University of London. Dissertation: “Visualization Tools for Comparative Genomics Applied to Convergent Evolution in Ash Trees”
B.S. Computer Science, June 2007 – Colorado State University

PUBLICATIONS
First Author Papers
Seaman, Josiah, and Richard J. A. Buggs. 2020. “FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments.” Frontiers in Genetics 11 (April): 292.

Seaman, Josiah D., and John C. Sanford. 2009. “Skittle: A 2-Dimensional Genome Visualization Tool.” BMC Bioinformatics 10 (December): 452.

Publications
Eizenga, Jordan M., Adam M. Novak, Jonas A. Sibbesen, Simon Heumos, Ali Ghaffaari, Glenn Hickey, Xian Chang, et al. 2020. “Pangenome Graphs.” Annual Review of Genomics and Human Genetics 21. https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-120219-080406.

Crusoe, Michael R., Hussien F. Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, et al. 2015. “The Khmer Software Package: Enabling Efficient Nucleotide Sequence Analysis.” F1000Research 4 (September): 900.

Schoenbaum, Melissa, Dawit Assefa, Lindsey Holmstrom, Amy Delgado, Josiah Seaman, Fort Collins, and Colorado Colorado Springs. n.d. “Simulating Foot-and-Mouth Disease in the United States Using the Animal Disease Spread Model.” http://modsimworld.org/papers/2017/Simulating_Foot-and-Mouth_Disease_in_the_United_States_using_the_Animal_Disease_Spread_Model.pdf

Conference Papers
Seaman, Josiah, Simon Heumos, Andrea Guarracino, Artem Tarasov, Bonface Munyoki, Christine Seaman, Dmytro Trybushnyi, et al. 2020. “Pantograph: Scalable Interactive Graph Genome Visualization.” In ISMB. ISCB 2020

Yokoyama, Toshiyuki T., Simon Heumos, Josiah Seaman, Dmytro Trybushnyi, Torsten Pook, Andrea Guarracino, Erik Garrison, and Jerven T. Bolleman. 2020. “Semantic Variation Graphs: Ontologies for Pangenome Graphs.” In. ISCB.

Seaman, Josiah. 2013. “DNA.EXE: A Sequence Comparison between the Human Genome and Computer Code.” In Biological Information. https://doi.org/10.1142/9789814508728_0016.

Preprint Papers
Chester M, Papadopulos A, Seaman J, Soltis D, Soltis P. n.d. “Chromosomal Dynamics in Newly Formed Allotetraploid Plant Populations.” Kew Gardens.

PRESENTATIONS
“FluentDNA and Graph Genomes” Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany, September 2019

“FluentDNA Visualization: Scalable Graphics for Nucleotides to Populations” Earlham Institute, Norwich, Norfolk, United Kingdom, June 2019

“FluentDNA Visualization: Gene Annotated Chromosomes on One Poster” BDISeminar Series, Oxford Big Data Institute, Oxford, United Kingdom, November 2018

“Tools for Comparative Genomics” 1001 Genome Project, Max Planck Institute, Tubingen, Germany, December 2018

“Inverted Repeat Pairs Bracketing Functionally Related Sequences” Brown Bag Series, National Institute of Health, Bethesda, Maryland, USA, August 2016

“DNASkittle.com: Repeat Patterns in the Human Genome” Lightning Talk, PyCon, Montreal, Quebec, Canada April 2015

“DNASkittle Genome Browser” Technology Track, ISMB Conference, Berlin, Germany, July 2013 


POSITIONS HELD
Royal Botanic Garden Kew – Pantograph
April 2019 – February 2021
Bioinformatician, 1001 Genomes Project Graphgenome.org

Leading the team developing Pantograph, an open source browsable pangenome visualization for graph genomes. It scales to thousands of individuals while preserving all types of sequence variation. Other tools either are not scalable or discard all genome rearrangements.

In March 2020 we realized that Pantograph could make a significant contribution to the work being done by researchers and vaccine developers in the global fight against SARS-Cov-2. Presenting a paper and talk, “Pantograph – Scalable Interactive Graph Genome Visualization” at the 2020 International Society of Computational of Biologists in July.

Mission of Pantograph:
Provide a public server with an instance of Pantograph available to all genetic researchers and vaccine developers
Generate a SARS-CoV-2 pangenome from the largest dataset available of de novo genome assemblies
Phylogenetic tree with regional labels
Integrate knowledge graph of COVID-19 patient outcomes


Royal Botanic Garden Kew  
2016-2019
PhD Candidate, Queen Mary University of London

PhD thesis on the repeatability of evolution of gene copy loss after a whole genome duplication in Ash trees with 30 newly assembled genomes and a phylogenetic comparison of 900,000 genes.

  • FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments”. Seaman and Buggs, 2020, Frontiers in Genetics

Newline Technical Innovations
Co-Founder, Lead Developer
2012-2016
Contract Work including

  • USDA Animal Disease Spread Model
  • DNASkittle.com
  • PRS Magnetic Pipe Scanning
  • Autoponics:

USDA – Animal Disease Spread Model
2013-2016
Lead Developer, contracted through Newline Technical InnovationsReplaced legacy Delphi Interface with UI based on latest web technology stack: Python, Django, React.js, Redux (flux architecture), SQL, JQuery, Bootstrap

Scientific simulation of stochastic model of farms with GIS and data visualization

“Simulating Foot-and-Mouth Disease in the United States Using the Animal Disease Spread Model.” Schoenbaum, Melissa, Dawit Assefa, Lindsey Holmstrom, Amy Delgado, Josiah Seaman. MODSIM World 2017

DNASkittle.com
2012-2013
Creator and Lead Developer – Contracted through Newline

  • Founded Newline Technical Innovations, a software development company
  • Created data processing back end for data visualization entirely in Python
  • Implemented 10 scientific visualizations for a real time genome browser on the web
  • Conference presentation: ISCB Berlin 2013

PRS – Magnetic Pipe Scanning and Business Automation                                   
2015-2016
Frontend Developer – Contracted through Newline

  • Designed and implemented a system for handling a time stream from sensors in the field and extracting actionable conclusions in data visualization and summaries. 
  • Invoicing and business automation system built on React/Redux back by Django for quick navigation of a relational database. Python, Django, React.js, Redux, SQL, JQuery, Bootstrap

Autoponics  
2012-2015
Lead Developer – Contracted through Newline

  • Web interface for remote monitoring and control of aquaponics central control system. 
  • Power relays for automated control of pumps, heaters and lights based on trigger rules in the software.
  • Data visualizations to show trends over time and dispatch alert emails
  • Top to bottom: HTML, Javascript, Python Django, Raspberry Pi

FMS Foundation – Research / Development
2007-2012
Software Developer

  • Invented a 2-dimensional genome sequence visualization that uncovered as yet unnoticed genome-wide repeating patterns in the Human genome and others.
  • EXE: A Sequence Comparison between the Human Genome and Computer Code” Conference proceedings Cornell 2012
  • Skittle: A 2-Dimensional Genome Visualization Tool”. Seaman and Sanford, 2009 BMC Bioinformatics

ICR – Geosciences Research Software Developer
2007-2007
Software Developer

  • Expanded the graphical capabilities of TERRA, a Fortran simulation of plate tectonics developed at Los Alamos National Laboratory.
  • Dynamically generated triangle-mesh iso-surfaces based on temperature data.

MEMBERSHIPS / AFFILIATIONS
Graph Genome Consortium, Founder
BioVis, Website Chair
International Society of Computational Biologists, Member