adam rivers

I analyzed microbial effects of grease in sewers and wastewater treatment plants, ran production bacterial fermenters and freeze dryers, and designed portable fermenters for field use.

I investigated iron stress and the role of iron binding molecules called siderophores in marine Synechococcus and other cyanobacteria. My graduare advisors were Dr. Eric Webb at WHOI (now at USC) and Prof. Penny Chisholm at MIT.

I was the research scientist for the Metagenome Program and the Microbial Systems Group at JGI. I supported JGI users with metagenome, metatranscriptome and amplicon projects being sequenced and analyzed by JGI. Also conducted research to make improvements to the existing production sequencing and analyses products. I developed new research projects in RNA viral metagenomics, initiating a Directors Discretion proposal for the first deep metagenomic sequencing of soil viruses and phage and collaborating on a CSP proposal to sequence a time series of RNA viruses from temperate lakes. I wrote GeneLearn, python software to apply machine learning to classify deeply divergent viral sequences. The software uses novel feature extraction methods, SVM, and logistic regression using a range of solvers including those in the libraries Spark/MLib, Dato, and ScikitLearn. The software is under active development by a postdoc in our group.

I am a computational biologist in the Genomics and Bioinformatics Unit of the USDA Agricultural Research Service (ARS). My primary role is to develop Microbiome workflows, establish collaborations with ARS researchers on microbiome research and train scientists in microbiome research. I continue to lead research projects in viral metagenomics and machine learning applications in metagenomics.