Microbial profiling studies generate large volumes of information-rich data. Transitioning this mass of data to meaningful microbiome research findings requires significant expertise and understanding of both microbial ecology and bioinformatic analyses. Drawing from leading academic centers, industry, government, and laboratories, Second Genome has built an expert team of microbial bioinformaticians that will work side by side with you to prevent bottlenecks and distill down to key findings within the promised turnaround time.
Meet Our Team
Todd DeSantis is Second Genome Co-founder and Senior Director of Bioinformatics. Todd has 17 years of experience designing and implementing bioinformatics solutions for analyzing microbial community dynamics. At Lawrence Berkeley National Laboratory he led the development of novel microbiome assays and analysis pipelines as a Molecular Microbial Ecology Software Developer. He is the chief architect of Greengenes™, an international effort to catalog global microbial diversity that provides microbial ecologists with reference databases for DNA quality assessment, alignment and classification. Todd also served as an analyst for the NIH Human Microbiome Project and has published over 60 scientific papers. At Second Genome, he manages all informatics work including identifying and recruiting microbiome scientist leaders, integration of multi-omics pipelines, cloud deployment for big-data analytics, and therapeutic pathway discovery.
Shoko Iwai is a bioinformatics scientist at Second Genome. Shoko's chief responsibilities include developing novel bioinformatics software to uncover causative mechanisms of microbiome-related disease. She manages cloud-enabled work-flow designs to ensure cost-effective big-data processing. She analyzes multi-omics data sets produced from internal R&D experiments as well as public data and then integrate to reveal microbial cross-cohort continuity. Shoko's academic degrees and training are in environmental engineering, environmental microbiology and human microbiome.
Sunit is a Meta’omics Scientist at Second Genome. Prior to joining the Second Genome R&D team, he was the Bioinformatics Specialist at the University of Michigan Geomicrobiology Lab for 6 years. During this time Sunit spearheaded efforts to explore the interplay between microbial communities and their environments using various Meta'omic techniques. His expertise in the field have led him to work with data from environments such as deep sea hydrothermal vents, the Great Lakes (US), Sinkholes and Wastewater management systems among others.
One of the highlights of his career has been using Meta'omic techniques to discover novel organisms and explore the pathways used to produce natural products of clinical importance, like ET-734 aka YolendisTM (Schofield and Jain et. al. Environmental Microbiology 2015). Sunit is also a co-inventor for a patent on “Nonribosomal Peptide Synthases” (US Patent Application No: US 20150361470 A1, Dec 17, 2015). More recently, Sunit has been involved in developing tools using NoSQL technologies to manage and explore meaningful connections in Big (Bio) Data.
Caitlin Ryan completed her PhD in Environmental Toxicology at Texas Tech University. Her work examined the effects of exogenous chemical stressors on the microbiomes of a wide variety of host species including several species of fish, amphibians, and crustaceans. As a member of the solutions team at Second Genome, she lends her expertise in microbial communities analysis in collaborative projects from researchers from academia and industry.
Cheryl-Emiliane (Cheryl) Chow is a Bioinformatics Scientist at Second Genome. Previously, she was a postdoctoral researcher at the University of British Columbia exploring marine viral dark matter. During that time, she developed wet-lab and bioinformatics approaches to investigate the diversity and ecology of known and unknown viruses. She completed her PhD in Biology at the University of Southern California. Her work there included one of the first reports on potential interactions among natural marine viruses, bacteria, and protists over time using microbial profiling assays and network analysis (Chow et al, (2014) The ISME Journal 8:816–829). She also has expertise in development and validation of new microbial profiling assays and quantitative assessments of gene targets (e.g. QPCR). Other research opportunities have led her to explore microbial roles in an array of environments, including methane seeps, coastal and open oceans, mudflats, groundwater, and aerosols. As a member of the Second Genome Solutions team, she applies her microbial ecology expertise to microbiome studies across all fields in collaboration with academic and industry partners.
Before coming to Second Genome Kathryn helped develop software tools and techniques to analyze the human gut microbiome and its role in health and disease at the University of Michigan. Her previous work was focused on developing new approaches to study the microbiome with applications in colorectal cancer, clostridium difficile infection and healthy populations. This included work as a developer for the microbial ecology software package mothur. Kathryn takes an interdisciplinary approach to microbial informatics using methods from ecology, evolutionary biology, statistics and computer science to provide insights into microbial communities and their interactions with each other and the environment. Kathryn has a masters degree in Bioinformatics from University of Michigan.