Richard R Rodrigues

PeerJ Author & Reviewer

Summary

I am a skilled data scientist with interdisciplinary research experience and a proven publication record. I am proficient in multiple programming languages (R, python, perl, and Java) with over 10 years of experience in biological data analyses.

Studied microbial ecology in:
- Medicine: gut of humans and mice
- Agriculture: nodules of soybean, rhizosphere of switchgrass and invasive plants
- Environment: gut of honey bees and soils of different ages (chronosequences)

Bioinformatics Computational Biology Genetics Genomics Microbiology

Past or current institution affiliations

Oregon State University

University of Rochester

Virginia Tech

Work details

Postdoctoral Scholar

Oregon State University

July 2016

Pharmaceutical Sciences

• Investigated the host-microbial interactions and identified causal microbes in cervical cancer and diabetic mouse model. • Designed experiments, developed pipelines for metagenomics and transcriptomics data and transkingdom network analyses, and interpreted results. • Managed next-generation sequencing data and high-performance computing resources. • Authored one book chapter and two peer-reviewed publications.

Bioinformatician

University of Rochester

June 2010 - February 2011

• Identified signature pathways in hepatocellular carcinoma gene expression datasets. • Authored one journal article.

Graduate Research Assistant

Virginia Polytechnic Institute and State University (Virginia Tech)

January 2012 - May 2016

Genetics, Bioinformatics, and Computational Biology

Host-microbiota: • Investigated the microbial ecology in rhizosphere of switchgrass and invasive plants. • Developed pipelines that have been used in the analysis of microbial communities in chronosequences, soybean nodules, and gut of honey bees. • Authored six journal publications. Host side: • Compared the gene expression profiles of 2D and 3D in-vitro liver models. • Collaborated to develop algorithms merging molecular interaction networks with gene expression data to identify key genes in yeast cell cycle and human diseases. • Resulted in five journal articles.

Websites

September 19, 2018

Transkingdom network reveals bacterial players associated with cervical cancer gene expression program

Khiem Chi Lam, Dariia Vyshenska, Jialu Hu, Richard Rosario Rodrigues, Anja Nilsen, Ryszard A. Zielke, Nicholas Samuel Brown, Eva-Katrine Aarnes, Aleksandra E. Sikora, Natalia Shulzhenko, Heidi Lyng, Andrey Morgun

https://doi.org/10.7717/peerj.5590 PubMed 30294508

February 15, 2018

COREMIC: a web-tool to search for a niche associated CORE MICrobiome

Richard R. Rodrigues, Nyle C. Rodgers, Xiaowei Wu, Mark A. Williams

https://doi.org/10.7717/peerj.4395 PubMed 29473009

May 24, 2018 - Version: 1

Transkingdom network reveals bacterial players associated with cervical cancer gene expression program

Khiem Chi Lam, Dariia Vyshenska, Jialu Hu, Richard Rosario Rodrigues, Anja Nilsen, Ryszard A. Zielke, Nicholas Samuel Brown, Eva-Katrine Aarnes, Aleksandra E. Sikora, Natalia Shulzhenko, Heidi Lyng, Andrey Morgun

https://doi.org/10.7287/peerj.preprints.26957v1