Alexandra Simas Email & Phone Number

Boston, Massachusetts, United States

I lead engineering, development, and scaling of bioinformatics pipeline development for Ginkgo Bioworks Biosecurity. We monitor known biosecurity threats and identify novel threats using agnostic and targeted metagenomic methods

Boston, Massachusetts, United States

Developing NGS sequencing and analysis pipelines.

Boston, Ma

Mentor: Caroline A. Genco, Ph.D.Dissertation work involves examining the role of periodontal disease and the oral and gut microbiomes in the development of non-alcoholic fatty liver disease and cardiovascular disease via a joint collaboration between the Tufts School Immunology Department and the Tufts Friedman School of Nutrition.- Developed, implemented large-scale mouse studies and performed multi-omics analyses involving 16S sequencing, RNA-seq, and histology.- Employed supervised learning methods and pathway-level analyses to identify host disease characteristics and microbiome & host feature sets, guiding in vitro investigation of host-microbe interactions.- Developed pipelines to streamline cross-functional analysis and data visualization using technologies including R and Amazon Web Services.- Designed collection, sequencing, and data analysis and visualization pipelines for projects involving the gut and vaginal microbiomes in mice and humans, resulting in four manuscripts currently in preparation.- Spearheaded and manages interdepartmental research investigating the microbiota of periodontal patients with collaborators from Tufts Dental School.- Contributed microbiome expertise to outside laboratories. Designed and performed collection, sequencing, and analyses of gut and vaginal microbiomes in mice and humans, resulting in manuscripts currently in preparation.

Greater Boston Area

Mentor: Andrew S. Greenberg, M.D.Elucidated diet-host-microbiome interactions that mediate the inflammatory mechanisms underlying chronic metabolic disease and related disorders in the Obesity and Metabolism Laboratory of the Tufts Human Nutrition Research Center on Aging.- Initiated, designed, and managed a research study focusing on the effects of a high-fructose diet on the gut microbiota and evaluated the role of TLR4 signaling in this model using genetically resistant mouse strain.

Greater Boston Area

- Spearheaded and implemented a semi-automated electronic workflow system for the MGH Neurogenetics DNA Diagnostic laboratory with >150 customizable reports. Reduced results reporting from days to hours.- Developed databases to accurately track breeding, genotyping, and experimental use of over 3,000 mice for diverse laboratories and tracked experimental use of frozen cell lines.- Developed and led instructional seminars. Incorporated feedback from various user types to customize database functions. Consulted with diverse front-end users to design and customize databases for a wide range of uses.

Boston, Massachusetts, United States

Mentor: Susan L. Cotman, Ph.D.- Managed budget, spending, and equipment upkeep. Trained users in microscopy and histology.- Solicited funds from and reported progress to private and public funding sources.

Greater Boston Area

Mentors: Susan L. Cotman, Ph.D. and Katherine B. Sims, M.D.Led a cross-functional investigation of atypical forms of Neuronal Ceroid Lipofuscinosis.- Derived and differentiated induced pluripotent stem cells from patient samples to characterize autophagic defects via immunofluorescence and western blotting. Performed viral and drug rescue investigations of therapeutic targets.- Evaluated the effects of diverse mutations on neurodegeneration in patients and mouse models. - Identified novel disease-causing genes and mutations by whole exome sequencing.- Designed and developed a relational database of over 2,000 patients, incorporating longitudinal clinical histories and genetic testing, linked to a biorepository containing patient-derived tissues and cell lines available for research.Communicated current research to patient families, collected patient samples, and acquired clinical histories at patient-oriented conferences. Mentored undergraduate students, guiding laboratory and clinical projects.

Wellesley, Ma

Mentor: Marc J. Tetel, Ph.D.

Greater Boston Area

Mentor: Katherine B. Sims, M.D.

Doctor Of Philosophy - Phd, Biochemical And Molecular Nutrition

Master'S Degree, Biochemical And Molecular Nutrition

Bachelor Of Arts - Ba, Neuroscience

Activities and Societies: Wellesley College Swim Team, Wellesley College Water Polo Team, Slow Food Convivium, Student Health Advisory.