Price, C. and Russell, J.A., 2023. AMAnD: an Automated Metagenome Anomaly Detection methodology utilizing DeepSVDD neural networks. Frontiers in Public Health, 11, p.1181911.
Keenum, I., Player, R., Kralj, J., Servetas, S., Sussman, M.D., Russell, J., Stone, J., Chandrapati, S. and Sozhamannan, S., 2023. Amplicon Sequencing Minimal Information (AsqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications. Journal of AOAC International, p.qsad047.
Parker, K., Wood, H., Russell, J.A., Yarmosh, D., Shteyman, A., Bagnoli, J., Knight, B., Aspinwall, J.R., Jacobs, J., Werking, K. and Winegar, R., 2023. Development and Optimization of an Unbiased, Metagenomics-Based Pathogen Detection Workflow for Infectious Disease and Biosurveillance Applications. Tropical Medicine and Infectious Disease, 8(2), p.121.
Davis, P. and Russell, J.A., 2021. A Genotype-to-Phenotype Modeling Framework to Predict Human Pathogenicity of Novel Coronaviruses. bioRxiv. doi: https://doi.org/10.1101/2021.09.18.460926
Li, Po-E., Russell, J.A., Yarmosh, D., Shteyman, A.G., Parker, K., Wood, H., Aspinwall, J.R., Winegar, R., Davenport, K.W., Lo, C., Bagnoli, J., Davis, P.E., Jacobs, J.L., and Chain, P.S.G. 2020. PanGIA: A Metagenomics Analytical Framework for Routine Biosurveillance and Clinical Pathogen Detection. bioRxiv. doi: https://doi.org/10.1101/2020.04.20.051813
Davis, P., Bagnoli, J, Yarmosh, D, Shteyman, A, Presser, L, Altmann, S., Bradrick, S., Russell, J.A. 2020. Vorpal: A novel RNA virus feature-extraction algorithm demonstrated through interpretable genotype-to-phenotype linear models. bioRxiv. doi: https://doi.org/10.1101/2020.02.28.969782
Yeh, K.B., Wood, H., Scullion, M., Russell, J.A., Parker, K., Gnade, B.T., Jones, A.R., Whittier, C. and Mereish, K., 2019. Molecular Detection of Biological Agents in the Field: Then & Now. mSphere, 4(6).
Russell, J.A., Campos, B., Stone, J., Blosser, E.M., Burkett-Cadena, N. and Jacobs, J.L., 2018. Unbiased strain-typing of arbovirus directly from mosquitoes using nanopore sequencing: a field-forward biosurveillance protocol. Scientific reports, 8(1), p.5417.
Russell, J.A., León-Zayas, R., Wrighton, K., and Biddle, J.F. “Deep subsurface life from North Pond: enrichment, isolation, characterization and genomes of heterotrophic bacteria,” Frontiers in Microbiology, 7, doi:10.3389/fmicb.2016.00678 (2016).
Doctoral Dissertation - University of Delaware (2015).
Russell, J.A., Brady, A.L., Cardman, Z., Slater, G.F., Lim, D.S.S., and Biddle, J.F. “Prokaryote populations of extant microbialites along a depth gradient in Pavilion Lake, British Columbia, Canada,” Geobiology, 12(3), doi:10.1111/gbi.12082: pp.250-264 (2014).
Jacobs, J.L., Russell, J.A., and Aspinwall, J.R., MRIGlobal, 2019. Modular mobile field-deployable laboratory for rapid, on-site detection and analysis of biological targets. U.S. Patent No. 11,400,454 B2
Research / Professional Experience
Principal Scientist / Group Manager -- Applied Biology & Bioinformatics
MRIGlobal, Gaithersburg, Maryland
I lead the Applied Biology & Bioinformatics Group, within the Life Sciences Division, at MRIGlobal. Our team is focused on the development of novel computational approaches, platform systems, and workflow improvement for applied microbial ecology, biosurveillance, microbial forensics, genomic epidemiology, and public health.
Streamlined metagenomics & interpretive analytics for environmental & clinical contexts
Genotype-to-phenotype predictive modeling
Single-person portable/automated/ruggedized molecular biosurveillance platforms
Applied synthetic biology
December 2017-December 2020
MRIGlobal, Gaithersburg, Maryland
Worked towards enabling genomics-based solutions in clinical diagnostics, biosurveillance, and forensics applications. Used emerging hand-held molecular hardware and development of integrated mobile platforms to push genomics and metagenomics further afield, to the point-of-need. Co-invented & led development of a novel, ultra-mobile molecular diagnostics & biosurveillance laboratory product, Mercury Lab
Post-Doctoral Research Associate
December 2015-December 2017
MRIGlobal, Gaithersburg, Maryland
Research and development of new bioinformatics solutions for the use of metagenomics in the clinical, epidemiological, biosurveillance, forensics, and public health space. Development of ultra-mobile laboratory platforms for use of portable sequencing technologies in the field.
Graduate Research Assistant
August 2010-December 2015
Use of microbial cultivations, molecular technologies and associated bioinformatics
pipelines to characterize microbial ecology in geological environments. Study sites
include microbialites from Pavilion Lake and Kelly Lake in British Columbia, the
sediment and underlying basalt crust of 'North Pond' on the Mid-Atlantic Ridge, and
the sediment of the Iberian continental margin.
Laboratory Technician II
May 2009-August 2010
Correlagen Diagnostics, Inc., Waltham, Massachusetts
Performed wet lab duties in a clinical molecular diagnostics laboratory. Duties
included DNA extraction and purification, PCR set-up and product purification,
sequencing reactions and product purification, and operation of an ABI 3730 DNA
sequence analyzer. Also assisted in development of novel assays for comprehensive
detection of genetically-linked cardiovascular diseases. Assays were developed for
use on the Heliscope, a next-generation DNA sequencing platform.
September 2008 – December 2008
Helicos BioSciences Inc., Cambridge, Massachusetts
Assisted a team of scientists in improving a novel genomic sequencing technology. Designed and performed experiments meant to improve uniformity of oligonucleotides binding to epoxide coated glass test suites.
Undergraduate Research Assistant
March 2006 – August 2008
Human Origins Genotyping Laboratory
Arizona Research Laboratories – Tucson, AZ
Maintained a DNA inventory system for a bank of over 300,000 samples using a custom LIMS. Conducted robotic liquid handling workstations for DNA manipulations and performed multiplex PCR, gel electrophoresis, and data analysis of microsatellite loci.
Undergraduate Research Assistant
December 2005 – May 2007
Astronomy Department, University of Arizona – Tucson, AZ
Compared known infrared profiles of organic molecular species deduced from high resolution molecular spectroscopy in the laboratory with infrared data of stellar region Sagittarius B2N. Data was collected from telescopes on Mt. Graham, AZ.
Selected Honors, Awards, & Funding
IARPA Principal Investigator. B24IC (Biointelligence & Biosecurity for the Intelligence Community)
MRIGlobal "Rosalind Franklin Award" for Patented Scientific Innovations -- 2023
(FRBAA14-6-1007) "Sequencing of tick-borne viral disease agents in Kazakhstan: identifying unique genomes in tick-borne encephalitis (TBE) and Crimean-Congo hemorrhagic (CCHF) viruses" -- 2020-2023: Co-Investigator.
MRIGlobal Leadership Council "Innovation Award" -- 2019
MRIGlobal Director's Award: Global Health Surveillance and Diagnostics Division -- 2018
Center for Dark Energy Biosphere Investigations (C-DEBI) Graduate Fellow: 2012 -2014
Total Award Amount: $64,000
NASA-Ames Honor Award (Group) - Pavilion Lake Research Project: 2014
Schlanger Ocean Drilling Graduate Fellowship: 2012 - 2013
Total Award Amount: $30,000
IODP Post-Expedition Award (United States Science Support Program): 2012
Total Award Amount: $15,000
Delaware Space Grant Consortium (NASA) Graduate Assistantship: 2011 - 2012
Marian R. Okie Graduate Fellowship (University of Delaware): 2010 - 2011
Kazakhstan (September 2023) -- National Biotechnology Center, Almaty
Training Event Co-Lead: molecular biosurveillance for tick-borne virus detection. DTRA/BTRP
EBTI, Ethiopia Translational Health Initiative Training Event (2019)
(served as instructor, 1 week -- Addis Ababa, Ethiopia)
CBOA 2019 (Chemical Biological Operational Assessment) -- Camp Dawson, Joint-Base West Virginia. "Field-Forward Sequencing System", DTRA/JPEO. Kingwood, WV.
NAMRU-6, U.S. DoD-funded Metagenomics Biosurveillance Training Event (2018)
(served as instructor, 2 weeks -- Lima, Peru)
Sierra Leone, U.S. DoD-funded Ebola Virus Diagnostics Training Event (2017)
(served as instructor, 6 weeks -- Freetown, Sierra Leone)
Florida Everglades (3 days): Mosquito-born Arbovirus Surveillance with FMEL (2016)
R/V JOIDES Resolution (9 weeks): IODP Expedition 336 - Mid-Atlantic Ridge Microbiology (2011)
Pavilion Lake Research Project (2 weeks): British Columbia, Canada (2011)
R/V Hugh R. Sharp (2 days): Delaware Bay (2010)
R/V Knorr (6 weeks): Cruise KN195-03 - Equatorial Pacific Ocean (2009)
Workshops and Short Courses
American Society for Microbiology: "Turning Your Science into a Company" (2016)
Primer-E Short Course on Biological Statistics: Plymouth, England (2012)
EU/US Short Course on Marine Bioinformatics: Bremen, Germany (2012)
Select Invited Oral Presentations:
"Applications of genomic feature-engineering for emerging infectious disease biosurveillance". June 2023. Sequencing, Finishing, & Analysis in the Future (SFAF) Meeting. Santa Fe, NM.
"Field-forward threat sensing through raw nanopore electrical signal: a case study in arthropod-borne pathogen detection on Saint Catherines Island”. October 2022. ASM Conference on Rapid Applied Microbial Next Generation Sequencing and Bioinformatics Pipelines.
"Field-Forward Biosurveillance on an Ultra-Portable Molecular Biology Laboratory Platform". June 2021.
28th International Biodetection Technologies Conference. Bethesda, MD.
“PanGIA Bioinformatics – A Metagenomics Analytical Framework for Routine Biosurveillance”. May 2019. Sequencing, Finishing, & Analysis in the Future (SFAF) Meeting. Santa Fe, NM
“Mercury Lab – Bring the Laboratory to the Sample”. December 2018. NIAID, Bethesda, MD
“Mercury Lab – Bring the Laboratory to the Sample”. November 2018. USDA, Ames, IA
“PanGIA Bioinformatics Pipeline – Bioinformatics for the Busy Astronaut”. July 2018. NASA Johnson Space Center, Houston, TX
“Mercury Lab – An Integrated, Ultra-Mobile Laboratory Workbench for Field-Forward Molecular Testing”. June 2018. Diagnostics of Endemic & Emerging Diseases Meeting, Kansas State University, Manhattan, KS
“Unbiased Biosurveillance with Nanopore Sequencing – Reducing Turnaround Times and Operational Footprints”. May 2018. Sequencing, Finishing, & Analysis in the Future (SFAF) Meeting. Santa Fe, NM
“Unbiased Biosurveillance with Nanopore Sequencing – Reducing Turnaround Times and Operational Footprints”. March 2018. Nanopore Day Meeting, College Park, MD
“Unbiased Strain-typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol”. October 2017. ASM – Next Generation Sequencing Meeting, Washington D.C.
“Bringing Sequencing Far Afield — The Promise & Challenge of ‘Omics in the Nanopore Age”. 2017 Next-Gen Sequencing Workshop. May 2017. Los Alamos National Laboratory, NM
“Metatranscriptome-based Detection and Phylogeny of Alphavirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-Forward Biosurveillance Protocol”. May 2017. Sequencing, Finishing, and Analysis in the Future (SFAF) Meeting, Santa Fe, NM
"Furthering the Discussion on Aerobic Heterotrophy in Deep Sediments". December 2014. American Geophysical Union Fall Meeting, San Francisco, California
"The QIIME Workflow: Making Sense of Your 16S Amplicon Data". October 2013. Bioinformatics Seminar, Banyuls-Sur-Mer, France
"Who is Active in the Iberian Margin Deep Biosphere?" October 2013, Center for Dark Energy Biosphere Investigations (CDEBI) Fall Meeting, Marina, California
"Microbial Communities of Pavilion Lake Microbialites". May 2013, University of Delaware Graduate Research Symposium, Lewes, DE
"Microbial Communities of Pavilion Lake Microbialites". January 2013, Gordon Geobiology Research Seminar and Conference, Ventura, CA
"Cyanobacteria of Pavilion Lake Microbialites". April 2011, Delaware Space Grant Spring Research Symposium, Newark, DE
Select Invited Poster Presentations:
Russell, J.A., Blosser, E., Burkett-Cadena, N., Parker, K., Campos, B., Stone, J., Jacobs, J. "Ultra-Portable Technologies for On-Site Arbovirus Surveillance of Mosquitoes: Bringing the Lab to the Sample". February 2017, ASM Biothreats Meeting, Washington D.C.
Russell, J.A., Jacobs, J.J., Winegar, R., Zimmerman, C., Aspinwall, J.R., Bagnoli, J.S., Parker, K., Stone, J., Campos B., Slezak, T., Chain, P.S., Davenport, K.W., Li. P., Anderson, J.J., Bishop-Lilly, K.A., Frey, K.G., Postlethwaite, T., Spain, T., Jakobsen, J., Boysen, C., Werking, K., Cassler, M. "Development and Validation of Metagenomics Sequencing Pipelines for Biosurveillance and Diagnostics". June 2016. Sequencing and Finishing in the Future Meeting (SFAF), Santa Fe, New Mexico
Russell, J.A., Orsi, W., Edgcomb, V., Biddle, J.F. "Molecular Insights into Microbial Ecology of the Iberian Margin Deep Biosphere". May 2015, Deep Carbon Observatory (DCO) International Science Meeting, Lisbon, Portugal
Russell, J.A., Orsi, W., Edgcomb, V., Biddle, J.F. "Molecular Insights into Microbial Ecology of the Iberian Margin Deep Biosphere". January 2015, CDEBI NSF Site Visit, Los Angeles, CA
Russell, J.A., Gartman, A., Luther, G.W., Biddle, J.F. "Microbial Cultivations from Mid- Atlantic Ridge Hydrothermal Vent Plumes". February 2014, Ocean Sciences Meeting, Honolulu, HI
Russell, J.A., Orsi. W., Edgcomb, V., Biddle, J.F. "Archaeal Populations and their Associations with Geochemical Conditions on the Iberian Margin". December 2013, American Geophysical Union Fall Meeting, San Francisco, CA
Russell, J.A., and Biddle, J.F. "Microbial Cultivations of Heterotrophic Bacteria and Marine Fungi in North Pond Sediments and Underlying Basalt Crust". January 2013, Gordon Geobiology Research Seminar and Conference, Ventura, CA
Russell, J.A., and Biddle, J.F. "Microbial Cultivations of Heterotrophic Bacteria and Marine Fungi in North Pond Sediments and Underlying Basalt Crust". June 2012, CDEBI RCN Meeting, Bremen, Germany
Russell, J.A. and Biddle, J.F. "Microbial Communities of Pavilion Lake Microbialites". December 2011, American Geophysical Union Fall Meeting, San Francisco, CA
Russell, J.A. and Biddle, J.F. "Cyanobacterial Communities of Pavilion Lake Microbialites". November 2010, DENIN External Advisory Board Poster Session, Newark, DE
Russell, J.A. and Biddle, J.F. "Cyanobacterial Communities of Pavilion Lake Microbialites". October 2010, Penn State Astrobiology Research Conference, State College, PA