Research Interest: Bioinformatics

PHD PROGRAM

RESEARCH INTEREST
Bioinformatics, Computational Biology, Evolutionary Biology

“My main research interest is in evolutionary and computational biology. I am interested in comprehending the evolutionary forces acting upon individuals that impact genetic diversity. The current scientific scenario is prolific due to the availability of large and complex genetic databases. The growing computational methods using statistics and machine learning allow the extraction of relevant information to have a deeper understanding of evolution. I am finalizing my master’s degree in evolutionary biology using computational methods to understand the dynamics of gene duplications.”

PHD PROGRAM

RESEARCH INTEREST
Bioinformatics, Genomics, Systems Biology

“I am most interested in what drives variation in human complex traits and diseases. For me, this broadly includes statistical genetics approaches to uncover the environmental, genetic, and gene x environment interactions that contribute to the variability in a disease or trait. I am interested in genomics, statistical, and multi-omics methodologies to both identify the source of this variation as well as how it functions. “

PHD PROGRAM

RESEARCH INTEREST
Bioinformatics, Computational Biology, Genomics

“I would like to study any topics related to genetic diversity, genetic population structure, drug resistance mechanisms, evolutionary changes mechanisms, host-pathogen immunological interactions, detection of evolutionary pathway in the emergence of drug resistant variants, detection of new biomarkers for infectious diseases, statistic modelling, computational software building for bioinformatics. “

PHD PROGRAM

RESEARCH INTEREST
Bioinformatics, Drug Discovery, Genomics

“I’m very interested in pursuing computer aided drug discovery. I would like to work on a project that has to do with prediction of molecular targets or drug interactions using computational tools. Or I would also like to use genomics to get a better understanding of diseases to eventually to apply to drug discovery.”

PHD PROGRAM
Bioinformatics & Computational Biology

RESEARCH INTEREST
Bioinformatics, Computational Biology, Immunology, Medical Imaging, Vaccine Development

We are a computational biology lab jointly located between the department of computer science and the computational medicine program. We develop new methods for automated, efficient, and unbiased analysis of immune profiling data, such as, flow cytometry, mass cytometry, and imaging mass cytometry. Our work specifically seeks to link particular immune cell-types and their functional responses to clinical or experimental phenotypes. Application areas of interest include, vaccine development, T-cell differentiation and designing more effective immunotherapies, neurodegenerative diseases, sexually transmitted diseases, and pregnancy. To design scalable and automated tools for these data, we develop and apply new methods using machine learning and graph signal processing.

PHD PROGRAM
Bioinformatics & Computational Biology

RESEARCH INTEREST
Bioinformatics, Cancer Genomics, Computational Biology, Genomics, Microbiome

Our research focuses on long-read (single-molecule) sequencing and informatics. We develop novel methods to enable more efficient *omic analysis and apply carefully architected high-performance computing approaches to improve the utility of genomics in studies of human diseases, including infectious disease, cancer, and GI. Ongoing work includes genomic epidemiology of SARS-CoV-2, MPXV, and antibiotic resistance; classification of pediatric leukemias and solid tumors in low-resource settings using nanopore transcriptome sequencing; and metagenomics/metataxonomics of mucosa-associated microbiota in inflammatory bowel diseases.

PHD PROGRAM
Bioinformatics & Computational Biology, Chemistry, Pharmacology

RESEARCH INTEREST
Biochemistry, Bioinformatics, Biophysics, Cancer Biology, Computational Biology, Genomics, Pharmacology, Structural Biology, Systems Biology, Translational Medicine

A growing body of work in the biomedical sciences generates and analyzes omics data; our lab’s work contributes to these efforts by focusing on the integration of different omics data types to bring mechanistic insights to the multi-scale nature of cellular processes. The focus of our research is on developing systems genomics approaches to study the impact of genomic variation on genome function. We have used this focus to study genetic and molecular variation in both natural and engineered cellular systems and approach these topics through the lens of computational biology, machine learning and advanced omics data integration. More specifically, we create methods to reveal functional relationships across genomics, transcriptomics, ribosome profiling, proteomics, structural genomics, metabolomics and phenotype variability data. Our integrative omics methods improve understanding of how cells achieve regulation at multiple scales of complexity and link to genetic and molecular variants that influence these processes. Ultimately, the goal of our research is advancing the analysis of high-throughput omics technologies to empower patient care and clinical trial selections. To this end, we are developing integrative methods to improve mutation panels by selecting more informative genetic and molecular biomarkers that match disease relevance.

PHD PROGRAM
Pathobiology & Translational Science

RESEARCH INTEREST
Bioinformatics, Cancer Biology, Genomics, Pharmacology, Translational Medicine

Our laboratory is focused on translating novel molecular biomarkers into clinical oncology practice, with the overarching goal of improving the care and survival of patients with cancer. Our group is highly collaborative and applies genomic, genetic, bioinformatic, informatic, statistical, and molecular approaches. Current projects in the laboratory include:

1. Correlative genomic testing to support clinical trials
2. Expanded clinical applications of RNA sequencing
3. Development and application of cell-free circulating tumor nucleic acid assays

PHD PROGRAM
Biochemistry & Biophysics

RESEARCH INTEREST
Biochemistry, Bioinformatics, Molecular Biology, Pathology, Translational Medicine

Our research is focused on RNA-binding proteins and their physiopathological roles. An understudied aspect of human disease is gene regulation by modulation of mRNA function. In our research lab we investigate functional connections between the RNA-binding protein Zinc Finger Protein 36 Like-2 (ZFP36L2 or L2) and human diseases. L2 is a member of the Tris-Tetra-Proline or Zinc Finger Protein 36 (TTP/ZFP36) family of RNA-binding proteins that bind Adenine-uridine-Rich Elements (AREs) in the 3’ untranslated regions of target mRNAs. Upon binding, L2 accelerates mRNA target degradation and/or inhibits mRNA translation, ultimately decreasing the protein encoded by the L2-target mRNA.

We have three particular goals:

• Determine new specific L2-mRNA targets involved in human diseases.
• Determine the mechanism(s) by which L2 modulates these novel RNA targets.
• Determine the physiological consequences of L2 ablation in specific cells types using mouse models and CRISPR/Cas9-mediated knockout system.

PHD PROGRAM
Bioinformatics & Computational Biology, Genetics & Molecular Biology

RESEARCH INTEREST
Bioinformatics, Computational Biology, Genetics, Genomics, Immunology, Pathogenesis & Infection, Systems Biology, Virology

In the Ferris lab, we use genetically diverse mouse strains to better understand the role of genetic variation in immune responses to a variety of insults. We then study these variants mechanistically. We also develop genetic and genomic datasets and resources to better identify genetic features associated with these immunological differences.