Career Profile
I apply bioinformatics principles to public health and would like to continue in this avenue. This has led to exciting applications such as genomic epidemiology for bacterial pathogens.
Experiences
Genomics of Food Safety group (Gen-FS)
- Facilitating interagency whole genome sequencing standards and analysis working group.
- This is a working group under the Genomics Food Safety collaboration (Gen-FS) between CDC, FDA, USDA, and NCBI.
- Determination of fact-based thresholds for whole genome sequencing to aid in the missions of CDC, FDA, USDA, and NCBI.
- Creation of whole genome sequencing benchmark datasets.
- Creation of a data download script.
- Datasets and script published in Timme et al 2017; I am senior author.
- I have also reached out to other labs at CDC including the Legionella lab to help contribute datasets.
- We meet once a month, and I facilitate the calls and record notes for the group.
Global Microbial Identifier (GMI).
- Facilitating international workgroup under the Global Microbial Identifier (GMI). My workgroup (workgroup 3) focuses on data analytics. Benchmark datasets from Gen-FS have been donated to this group and we have collected datasets from international partners.
- Advisor for GIGte, the monthly division-wide workshop in bioinformatics
- Member of MCT-DART
- Member of MCT SIAG
- Detail to Waterborne branch (WDPB), CDC - October 2019 - February 2020
Senior bioinformatician for the Enteric Diseases Laboratory Branch
- Supervisor Dr. Heather Carleton
- acting team leads 2020-present - Drs. A. Jo Williams and Andrew Huang
- Comparing cgMLST methods on the command line (ChewBBACA, etc)
- Creating an ONT assembly workflow with Curtis Kapsak
- Creating a new metagenomics profiler with Henk Den Bakker called Sepia (He is the main developer)
- Developing custom metagenomics database for the Kraken suite
- Helped advise CFU bioinformatics when it was being created
- Developing rapid WGS tree-making pipeline called Mashtree. Provide assistance to users at CDC, nationally, and worldwide.
- Developing a genome sketches repository for rapid cluster detection using Mash, the HPC, and crontab
- Continued development of SneakerNet for other platforms and workflows, e.g., Ion Torrent, metagenomics
- Developing high-quality SNP pipeline called Lyve-SET at https://github.com/lskatz/Lyve-SET (Published in Frontiers). Seeking feedback from bioinformaticians, PulseNet, epidemiologists across my division at CDC.
- Maintaining hardware for EDLB
- Supervising technical working group, for teaching ourselves bioinformatics techniques. This group is called the Genome Interest Group, Technical (GIGte, “giggity”).
- Founding member of the CDC-wide bioinformatics group BITCOP
- Experience with data from Illumina, 454, Ion Torrent, Oxford Nanopore, Pacific Biosciences (PacBio), Sanger
DFWED/NWSS/tiger team (Oct 2021 - Dec 2021)
- NWSS created a tiger team with members across the division
- NWSS objective is to create a set of standards for wastewater SARS-CoV-2 metagenomics sequencing and analysis
- Supporting the team with bioinformatics insights
- Guiding the bioinformatics activities
Team lead, Technical Outreach and Assistances to States Team (TOAST) - Jan 2021-April 2021
- Team Lead for 10 members, plus me
- Under OAMD; my supervisors were Greg Armstrong and Duncan MacCannell
- Provided technical assistance to state/local labs
- Gave two SPHERES talks of 15 minutes each
- Created “menu” of protocols on protocols.io
- Benchmark datasets - paper is being planned. 5 datasets of 1 outbreak, 2 coronahit datasets, 1 of various lineages, 1 of bad data.
- Data viz recommendations
- One-off help
- Created system to triage questions
- Created and led TOAST office hours, similar to 50 state calls 1/wk
- Led BRR calls 1/wk
- Gap analysis/needs assessment with fishbone diagram
QA/QC for WGS in the SneakerNet SARS-CoV-2 workflow
- Created QA/QC pipeline for primary data QA/QC for SARS-CoV-2 from Illumina
- SneakerNet framework - github.com/lskatz/sneakernet
- Created additional workflow for transferring CLIA reads to the correct place for the EDLB/CLIA team to analyze further under CLIA framework
Clinical Team, supervisors Drs. Karen Wong and James Lee; August - October 2020
- Reinfections project
- Gave 101 presentation to clinical people on genomics
- Published reinfections paper - James Lee et al 2021
bioinformatician for Vibrio and Listeria
- Analyzing genomes of L. monocytogenes from clinical and food samples across the United States and the world.
- Providing phylogenies of whole genomes for the purposes of molecular epidemiology
- Helped investigate outbreak cases in Crave Brothers Cheese, Roos Foods, and many unsolved cases
- Creation of SneakerNet. This bioinformatics workflow is how we quality-control all raw reads from an Illumina instrument (read counts, quality scores, contamination detection), transfer data to the data repository, and email a report. I also created a job aid under QMS for following the SneakerNet protocol. Concurrently, I also helped in other QMS documents for data transfer and QC such as the Access database protocol.
- Creation of a data repository. With colleagues, administered a 40TB machine to hold all raw data and a data recovery plan. Also created network folders accessible to Windows machines with read only access. Created the file structure needed for long term organization.
- Uploading data to SRA immediately after sequencing. I developed and followed a protocol for sending sequences to SRA. I also developed a job aid under QMS for uploading sequences to SRA.
- Contracting company IHRC until 2012; converted in 2012 to title 42 (GS-13, 601 job series). Began using CDC administrative tools such as PMAS.
- Studying virulence factors in whole genomes of Vibrio spp.
- Studying Haiti cholera outbreak through comparative genomics. Studying in vivo evolution of V. cholerae. Helped choose isolates to sequence based on PFGE patterns. Katz et al 2013.
- Predicting PCR assay targets for serogroups O75 and O141 (from recent US outbreaks) Characterizing an Iraqi genome with an odd phage arrangement
- Continuing as lead developer for CG-Pipeline and MGIP, but also transferring duties for MGIP development back to the Meningitis and Jordan Labs
Real time genomic epidemiology of Listeria
- Analyzing genomes of L. monocytogenes from clinical and food samples across the United States and the world.
- Providing phylogenies of whole genomes for the purposes of molecular epidemiology
- Helped investigate outbreak cases in Crave Brothers Cheese, Roos Foods, and many unsolved cases
- Creation of SneakerNet. This bioinformatics workflow is how we quality-control all raw reads from an Illumina instrument (read counts, quality scores, contamination detection), transfer data to the data repository, and email a report. I also created a job aid under QMS for following the SneakerNet protocol. Concurrently, I also helped in other QMS documents for data transfer and QC such as the Access database protocol.
- Creation of a data repository. With colleagues, administered a 40TB machine to hold all raw data and a data recovery plan. Also created network folders accessible to Windows machines with read only access. Created the file structure needed for long term organization.
- Uploading data to SRA immediately after sequencing. I developed and followed a protocol for sending sequences to SRA. I also developed a job aid under QMS for uploading sequences to SRA.
Computational genomics of Vibrio
- Studying virulence factors in whole genomes of Vibrio spp.
- Studying Haiti cholera outbreak through comparative genomics. Studying in vivo evolution of V. cholerae. Helped choose isolates to sequence based on PFGE patterns. Katz et al 2013.
- Predicting PCR assay targets for serogroups O75 and O141 (from recent US outbreaks)
- Characterizing an Iraqi genome with an odd phage arrangement
Computational genomics of STEC
- Acting as a bioinformatics liaison between Expression Analysis who generated PacBio and Illumina data for 250 STEC genomes, my branch at CDC, and the SRA contracting group who is analyzing the data.
- Also working as a bioinformatics liaison with DNAStar for additional analysis of the sequencing data.
- Searching for a core genome, for making a whole genome MLST scheme Several additional analyses
- Creating a standardized pipeline for analyzing PacBio data, for use in CG-Pipeline
Metagenomics of stool
- Planning a metagenomics project where DNA in stool is sequenced.
- Pathogen discovery
- Source attribution
Bioinformatician in Meningitis Lab
- Supervisor Dr. L. W. Mayer, Contracting company Logistics Health Incorporated
- Collaborating with the Jordan Lab, Georgia Institute of Technology
- Lead developer of CG-Pipeline (see publications and nbase.biology.gatech.edu)
- Lead developer of NBase (see publications and nbase.biology.gatech.edu)
- Working on species molecular typing between Haemophilus influenzae and H. haemolyticus; molecular typing on Neisseria meningitidis and Bordetella spp.
- Studying antimicrobial resistance mutations for rifampin, penicillin, and ciprofloxacin
- Some overlap with finishing my dissertation between September and November
collaboration with Meningitis and Vaccine Preventable Diseases Branch at CDC
- Collaborating with the Meningitis and Vaccine Preventable Diseases Branch (MVPDB) of Centers for Disease Control and Prevention (CDC) and with the Core Facility of CDC
- Developed a database of genomes called Neisseria Base at http://nbase.biology.gatech.edu
- Assembled and annotated new genomes using 454 pyrosequencing data.
- Supervised a team of bioinformatics M.S. and Ph.D. students
- Compared genomes to discover SNPs and to ascertain their biological relevance to pathogenesis
- Collaboration with Influenza Sequencing Lab at CDC (PoC: John Barnes)
- Creating a platform InGen
- Created a typing platform similar to MLST for influenza called Sequence Typing and Reassortant Screen (STaRS)
- Being used around the world including the US, Egypt, and Bangladesh
Meningococcus Genome Informatics Platform developer
- Created MGIP as a website at http://mgip.biology.gatech.edu
- The code lives at https://sourceforge.net/projects/mgip/
- MGIP has become a standard for multilocus sequence typing (MLST) data analysis, and has also been expanded to encompass other molecular typing data
- World-renown labs such as the MVPDB Lab at CDC and Martin Maiden’s lab are in support of * MGIP as the world-wide standard MLST software
- MGIP is being expanded to aid in the typing of influenza, in collaboration with the CDC Flu Lab
cichlid evolution research
- First research project in PhD, one semester rotation
- PI was Todd Streelman
- Topic was cichlid evolution; resulted in publication in Loh et al
Graduate student with courses
- Took core classes for bioinformatics including bioinformatics, statistics, molecular structures
Studied microRNA
- Soojin Yi’s lab
Chairing and awards
These are a list of activities that I host or help host, and awards/grants that I have earned
ASM NGS Hackathon, organizer and chair
(2020)
- Objective: to create continuous integration on bioinformatics software.
- Organized about 20 participants around the ASM NGS conference.
- Invited and hosted a keynote speaker.
- Created an environment on Zoom and Discord.
- The hackathon is resulting in a publication for recommendations in bioinformatics software testing. This is in preparation: Putten et al, MBio.
Microbinfie virtual lab conference co-facilitator and co-chair
- Created a conference to absorb bioinformatics talks that were canceled due to the pandemic
- Equal partners in facilitating, organizing, etc, with Dr. Nabil-Fareed Alikhan
- Facilitated 12 talks over four weeks
- Facilitated a happy hour with a trivia night
Microbinfie virtual lab talks co-facilitator and co-chair
(2019 - 2020)
Hosted a virtual lab talk once a month and recorded the talks. Each talk is 15 or 20 minutes plus Q&A, for a total of 1-hour sessions.
Microbinfie podcast host
(2019 -)
- Podcast discusses topics in the intersection of bioinformatics and public health
- Co-host with Drs. Andrew Page and Nabil-Fareed Alikhan
- Record podcast on Zoom
- Edit audio on Audacity and/or Descript
- Release an episode of 20-40 minutes every two weeks
- Always a relevant bioinformatics topic
- Some episodes have guests; some are panel discussions at conferences
- About 30k cumulative listens as of 2021-10-13
- Most played episode is at 1.1k
- About 460 “listens” per episode
- Least listened episode is at 330
- Reaches at least 50 countries of at least 10 listens each
Microbial bioinformatics forum administrator
(September 2016 -)
- This workspace represents a new generation of international microbial bioinformaticians, with direct links to peers in all international major public health services, public health institutions, and affiliated universities.
- I developed a code of conduct for the forum, which describes actions not permitted, and actions that the administrators can take when there is a violation.
- The purpose is strictly not a help desk but is a place to get help directly from the source, e.g., understanding undocumented workflows or putting forth ideas directly with the author of a software package.
Spaceball1 computer for DFWED/MCT-DART
(2020)
Received an FIA (Fund If Available) for a 192-thread computer lovingly named Spaceball1. $80k
- hosted in scicomp
- 1.5 TB RAM, 192 threads, 6T fast scratch space
- I am the point of contact
- Saves the division money by obviating any local scientific workstations
- More powerful than virtually all other computers at CDC
Seed grant, Center for Food Safety, University of GA
(2019)
To develop the Mashpit genomic epidemiology platform. Collaborators are Xiangyu Deng and Henk Den Bakker. ($30k)
Seed grant, Center for Food Safety, University of GA
(2018)
To develop the Kalamari metagenomics database. Collaborators are Xiangyu Deng and Henk Den Bakker. ($30k)
Emerging Leadership Certificate Program
(June 2018 - Oct 2018)
- Learning skills for leadership including interpersonal, leadership, and communication skills.
- Several classes June 2018 - Oct 2018
- The next level: powering your potential
- Decision mojo
- Strategic thinking
- Think like a leader and collaborate between groups
- The art of communication
- Build a powerful professional brand
- 360 review - 6 colleagues gave feedback on how I am in the workplace
- Major project, completed Oct 2018. Created a plan along with four others in my cohort to create a career counselor professional at CDC, career days, and improvements on the trainings intranet site.
Nakano Citation, NCEZID/CDC
(2017)
For one of the best laboratory papers of 2017 in the NCEZID center in CDC (Lyve-SET paper)
Shepard award nomination, CDC
(2017)
For best laboratory manuscript
CDC award
(2015)
For the Listeria whole genome sequencing project
NCEZID award
(2015)
For the Listeria whole genome sequencing project
HHS Innovates Secretary's Pick award
(2014)
For a project in The Department of Health and Human Services which shows innovation to solve important challenges in the workplace. The Secretary of HHS chose the project herself. This award was given for the Listeria project Whole Genome Sequencing Future of Food Safety.
Nakano Citation
(2014)
For one of the best papers of 2013 in the NCEZID center in CDC. The paper was the Haiti cholera paper.
Shepard Award 2014 nomination
(2013)
For best paper at CDC under the laboratory science category, namely the Haiti cholera work
Breakfast with the Director
(2012)
A select few from CDC are chosen to have breakfast with the director of CDC to discuss ideas. I was able to introduce the idea of a bioinformatics internship program with the director. Since then, several higher-level committees have been discussing how best to implement an internship program with several universities such as GA Tech. This eventually culminated, driven by higher-ups at CDC and not driven by me, into a bioinformatics fellowship under APHL.
Certificate of Appreciation
(2011)
Given to the MenAfriVac Development and Implementation Group. This is a major group for the virtual elimination of meningococcal A disease in Africa.
Partners in Public Health Improvement Award
(2009)
Given by CDC to a team of collaborators who improve upon a public health initiative. I was a graduate student in the Jordan lab, collaborating with the Meningitis Laboratory at CDC.
Grant for Research Dissertation, CDC
(2008)
A grant to fund my dissertation. Microbial Genome Informatics Platform. a Computational Resource for Computational Genomics. (1R36GD000075-01) ($37,386).
Publications
These are my selected publications