Ricky “Shaun” Adkins
Education
- Elon University - 2008
- BS - Biology
- BA - International Studies (Asian/Pacific concentration)
- Virginia Commmonwealth University - 2011
- MS - Bioinformatics (Professional Science Masters option)
Employment
- Institute for Genome Sciences - University of Maryland - Baltimore
- Bioinformatics Software Engineer I - Aug 2011 - July 2016
- Bioinformatics Software Engineer II - July 2016 - Present
- Current roles:
- Developer for the gene Expression Analysis Resource (gEAR) portal for analysis and visualization of multi-omic data related to hearing
- Past roles:
- Development of the Neuroscience Multi-Omic (NeMO) Data Archive for processing and storing neurological bioinformatics data
- Developed for and maintained various analyses pipelines
- Prokaryotic Genome Annotation Pipeline (lead developer)
- Transcriptomics Pipeline
- LGTSeek Lateral Gene Transfer Pipeline (lead developer)
- Pangenome Pipeline (lead developer)
- Provided assistance for the VIROME annotation pipeline in collaboration with University of Delaware researchers
Research
Papers
- BOTUX: bayesian-like operational taxonomic unit examiner. Koparde VN, Adkins RS, Fettweis JM, Serrano MG, Buck GA, Reimers MA, Sheth NU. Int J Comput Biol Drug Des. 2014;7(2-3):130-45. doi: 10.1504/IJCBDD.2014.061652. Epub 2014 May 28.
- CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline. Agrawal S, Arze C, Adkins RS, Crabtree J, Riley D, Vangala M, Galens K, Fraser CM, Tettelin H, White O, Angiuoli SV, Mahurkar A, Fricke WF. BMC Genomics. 2017 Apr 27;18(1):332. doi: 10.1186/s12864-017-3717-3.
- Aligner optimization increases accuracy and decreases compute times in multi-species sequence data. Robinson KM, Hawkins AS, Santana-Cruz I, Adkins RS, Shetty AC, Nagaraj S, Sadzewicz L, Tallon LJ, Rasko DA, Fraser CM, Mahurkar A, Silva JC, Dunning Hotopp JC. Microb Genom. 2017 Jul 8;3(9):e000122. doi: 10.1099/mgen.0.000122. eCollection 2017 Sep.
- FADU: A Feature Counting Tool for Prokaryotic RNA-Seq Analysis. Chung M, Adkins RS, Shetty AC, Sadzewicz L, Tallon LJ, Fraser CM, Rasko DA, Mahurkar A, Dunning Hotopp J. Biorxiv 337600 [Preprint]; Available from: https://doi.org/10.1101/337600
- An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types. Z Yao, H Liu, F Xie, S Fischer, RS Adkins, AI Aldrige et al. Biorxiv 2020.02.29.970558 [Preprint]; Available from: https://doi.org/10.1101/2020.02.29.970558
Presentations
- LGTSeek - A Robust, Distributable Lateral Gene Transfer Pipeline. Ricky S. Adkins, John Mattick, Robin Bromley, Matthew Chung, David Riley, Karsten Sieber, Kelly Robinson, Anup Mahurkar, and Julie C. Dunning Hotopp. Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Presented at Genome Informatics 2017 - Cold Spring Harbor Laboratory.
- Leveraging Published Multi-Omic Data for Discovery and Catalysis of Inner Ear Research via projectR - No Coding Needed. Ricky Adkins, Joshua Orvis, Beatrice Milon, Anup Mahurkar, Carlo Colantuoni, Ronna Hertzano
- Presented at the 46th Annual ARO MidWinter Meeting - Orlando, FL.
Skills
- High Proficiency
- Bash
- Docker
- Git
- Google Cloud Platform
- Compute Engine
- Cloud Functions
- Cloud Run
- Cloud Storage
- HTML
- Neo4j
- Perl
- Python
- UNIX
- Medium Proficiency
- Amazon EC2
- CSS
- Flask
- Javascript
- Julia
- SQL
- SVN
- Low Proficiency
- Awk
- Java
- Javascript
- Kubernetes
- Sed
- Typescript