Bioinformatics | Research Interests

Name	Email	PhD Program
Haendel, Melissa WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Bioinformatics & Computational Biology, Genetics & Molecular Biology RESEARCH INTEREST Bioinformatics, Developmental Biology, Developmental Disorders, Genetic Basis of Disease, Genetics, Human Subjects Research, Molecular Mechanisms of Disease, Translational Medicine	The Translational and Integrative Sciences Laboratory (TISLab) aims to weave together healthcare systems, basic science research, and patient generated data through development of data integration technologies and innovative data capture strategies. Our research focuses on the development of semantic technologies for data harmonization and analytics, such as ontologies, knowledge graphs, and data models. We leverage these semantic resources to standardize phenotypic information coming from clinical encounters, model and veterinary species, and directly from patients. As part of a longstanding international consortium called the Monarch Initiative, we utilize structured phenotype data to integrate of genotype-phenotype data across species to improve rare disease diagnosis, mechanism discovery, and to identify treatments. We work with a number of rare disease communities around the world with the goal of making our data standards available for everyone and translated into different languages so that everyone can have access to the same knowledge and have the same chance for a diagnosis. We are passionate about environmental health and understanding new ways of making environmental and nutrition data computable alongside clinical data. For example, we have integrated patient nutrition survey data together with basic research knowledge to reveal dietary risk factors of women’s reproductive disorders. We recently obtained funding to create an atlas for toxicological experiments and phenotypic outcomes in the zebrafish. TISLab has also recently created a veterinary One Health program, which focuses on understanding health influences affecting veterinary species together with their pet parents. During Covid, we led a national initiative to harmonize Electronic Health Record data to aid discovery analytics, called the National Covid Cohort Collaborative (N3C). The N3C is now the largest publicly available HIPAA-limited dataset in US history, and has ~5,000 users. We have studied long-Covid, advised the White House and governor’s offices, and have won the NIH/FASEB DataWorks! Grand prize for our work on N3C. We also lead the Center for Linkage and Aquisition of Data (CLAD) for the All of Us Research Program. The CLAD aims to link passive data streams such as insurance claims, mortality, and environmental data to program participants to provide a more comprehensive picture of their health trajectories. We have produced several global standards, such as the Human Phenotype Ontology, Phenopackets (Global Alliance for Genomics and Health and ISO certified), Mondo, and LinkML. We regularly attend the American Medical Informatics Association, the American Association of Human Genetics, the International Biocuration Society, and the Bioinformatics Open Source at ISMB conferences. TISLab members come from a wide variety of of scientific backgrounds and interests, making us effective partners in translational science and collaborative analytics.
Carmichael, Iain WEBSITE EMAIL PUBLICATIONS	PHD PROGRAM Bioinformatics & Computational Biology, Pathobiology & Translational Science RESEARCH INTEREST Bioinformatics, Cancer Biology, Cancer Genomics, Computational Biology, Medical Imaging, Pathology, Quantitative Biology, Translational Medicine	My lab builds data driven, computational systems to analyze high-resolution histology images of diseased tissue as well as other clinical data sources to improve clinical decision making and advance basic scientific investigation of disease processes. Keywords: Artificial intelligence, computer vision/medical image analysis, natural language processing, deep-learning, open-source software, multi-omic analysis, digital pathology, multiplex immunofluorescence, spatial transcriptomics, cancer
Yin, Maya EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Computational Biology	“I am interested in designing statistical analysis methods for microbiome-metabolome and/or single-cell data. I am interested in applying the methods to studying neurological disorders or marine microorganisms. I am looking forward to doing mostly computational work but with some wet lab experiments or fieldwork components.”
Taylor, Colin EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Computational Biology, Systems Biology	“I’ve really enjoyed working with imaging data in the past, and I’d love a chance to return to something involving optics (although I have a weak physics background- I would mainly be focused on the processing of images, not the acquisition of them). I’m also interested in synthetic biology, although I don’t think my particular skillset suits it very well.”
Sofian, Christina EMAIL	PHD PROGRAM RESEARCH INTEREST Bacteriology, Bioinformatics, Immunology	“My background and previous work are in bacteriology and immunology. While I would like to further my understanding on these topics, I am also interested in learning more about bioinformatics and its application related to my interests.”
Martin, Carmen EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Computational Biology, Gene Therapy, Genetic Basis of Disease, Genomics	“Research the relationship between genetic variation and genetic disease with different computational tools. Understanding the genetic basis of the disease and how the variations can be manipulated to find areas for gene therapy and increase human health.”
Liu, Amy EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Biophysics, Computational Biology	“I am interested in computational protein design and developing new tools for the task. Whether it’s for developing new therapeutics, breaking down toxins in the environment, or perhaps as detectors that can be used as a research tool, the problems protein design can address is limited only by our imagination.”
Huizar, Kaitlyn EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Computational Biology, Developmental Biology, Neurobiology	“I am broadly interested in developmental neurobiology in the context of psychiatric illnesses and learning disabilities. Within this scope, I am interested in studying time periods ranging from perinatal through adolescence and am flexible with techniques and model systems. Some topics of interest within include: alcohol and drug abuse, pharmacology, sleep, nutrition, stress exposure, cognition, genetics/epigenetics, biochemistry/cell/molecular biology, bioinformatics/computational biology. To list some techniques of interest: wet lab/biochemical assays, imaging (both tissue staining and fMRI), animal/human behavioral assays, and computational algorithms.”
Deal, Milena EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Genetics, Genomics	“I am interested in examining the heritability of complex disease using genomics. I want to use both bioinformatics and experimental techniques to work toward this goal. I have interest in other subject areas as well, such as microbiology, but do want to focus on labs that have computational PhD students.”
Campillo Minano, Beatriz EMAIL	PHD PROGRAM RESEARCH INTEREST Bioinformatics, Computational Biology, Genetics	“I am interested in developing computational methods and algorithms for solving biological questions. I would like to focus on machine-learning approaches for genetics or structural biology. I am also interested in the development of this approaches as software tools or pipelines to ensure their generalizable usage”

Research Interest: Bioinformatics