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Abel Tamar Abel, Ph.D. |
Bar Harbor, ME |
Combines genetic and computational tools to better understand the pathogenesis of complex diseases at a genetic, molecular, and cellular level.
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My goal is to model the genetic, molecular, and cellular origins of Alzheimer's pathogenesis using multiomics in novel animal models of late onset disease. As part of the MODEL-AD and associated consortiums I will work to achieve these goals and to compare findings in model systems with data from human populations to increase the translational potential for research findings.
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Tamar Abel on Orcid
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Aging|Bioinformatics|Computational Biology|Genetics and Genomics |
Aging|Bioinformatics|Computational Biology|Genetics and Genomics |
The Carter Lab |
Postdoctoral Associate |
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Barakat Yehya Barakat |
Bar Harbor, ME |
I am interested in improving drug discovery for neuropsychiatric disorders using genetics and bioinformatics.
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I worked as a pharmacist following my undergraduate education. Shortly in my clinical work, I was frustrated with the progress of pharmaceuticals in the field of neuropsychiatric disorders. I was especially moved by my friend's struggles with limerence, a disorder that is still undiagnosable and with very little literature surrounding it. I was motivated to go into a research-based program in Boston; there I received my Master's degree in pharmacology and drug development. I got immersed in the field of neurogenetics by my previous mentor Dr. Leon Reijmers and I have decided that's the type of training I want to focus on. I got accepted to the Tufts-JAX collaborative Ph.D. program in neuroscience and I have never made a better choice than to join this program. Under the mentorship of Dr. Vivek Kumar, I feel I will get the training I need to ask and answer critical questions that can lead to better drug targets for neuropsychiatric disorders with unmet needs.
My project is involved in understanding the causal mechanisms involved in age dependent hyperactivity disorder and its relationship to cortical cell death.
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Behavioral Disorders|Bioinformatics|Complex Traits|Genetics and Genomics |
Behavioral Disorders|Bioinformatics|Complex Traits|Genetics and Genomics |
The Kumar Lab |
Predoc |
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Doing Georgia Doing, Ph.D. |
Farmington, CT |
I study the skin microbiome and the pathobiont Staphylococcus epidermidis, identifying patterns in large compendia of data and testing molecular mechanisms in the laboratory.
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I am driven by the stories microbes tell in order to live. My goal in research is to understand the functional diversity of the human microbiome by developing computational tools to facilitate the characterization of less studied species, strains and genes. My academic and research training allow me to probe this fundamental microbiological question using the wealth of publicly available 'omics data using computational methods. As an undergraduate at Bard College I majored in both biology and computer science and as a Ph.D. student in Dr. Deborah Hogan’s laboratory at Dartmouth College I studied microbial interactions between bacterial and fungal opportunistic pathogens. Now, as a postdoc in Dr. Julia Oh's lab, my focus is centered on deciphering molecular mechanisms of microbial and host interactions within health- and disease-promoting microbiomes, with a focus on the opportunistic pathogen Staphylococcus epidermidis. Specifically, I aim to develop and test the utility of a machine-learning model to identify virulence-associated transcriptional signals, validate the predictive utility of the model using gene knock-down experiments, and apply an investigation of gene essentiality to S. epidermidis behavior in polymicrobial co-culture.
Education:
Dartmouth College Ph.D., microbiology and immunology Adv: Deborah Hogan 2015-2021
Bard College B.A., biology and computer science 2011-2015
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Georgia Doing on Orcid
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Bioinformatics|Computational Biology|Genetics and Genomics|Infectious Disease Research |
Bioinformatics|Computational Biology|Genetics and Genomics|Infectious Disease Research |
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Postdoctoral Associate |
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Englander Ryan Englander |
Farmington, CT |
I am investigating splicing-derived neo-antigens in breast and lung cancer using long-read RNA-sequencing in collaboration with the Palucka Lab.
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Leveraging emergent techniques in genetics and immunology to identify and exploit therapeutic vulnerabilities in cancer
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Bioinformatics|Cancer|Genetics and Genomics|Immune Disorders |
Bioinformatics|Cancer|Genetics and Genomics|Immune Disorders |
The Anczukow Lab|The Palucka Lab |
Predoc |
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Ferraj Ardian Ferraj, Ph.D. |
Farmington, CT |
My research interests include the application of next generation sequencing and genomic data to answer complex biological questions.
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My doctoral research included studying the impact of large genetic variants on diverse genomes, focusing on the effects of mobile element insertions on stem cell transcription. In my current work, I employ advanced sequencing technologies to study tumor-stroma interactions of patient derived xenograft models in cancer therapy.
Ardian Ferraj on Orcid
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Bioinformatics|Computational Biology|Genetics and Genomics |
Bioinformatics|Computational Biology|Genetics and Genomics |
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Lab Staff|Predoc |
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Garretson Alexis Garretson, MS |
Bar Harbor, ME |
Leveraging genetic diversity and computational techniques to investigate the architecture of complex traits
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Genetically diverse animal models are critical to understanding complex traits. While the use of classical inbred strains has enabled significant genetic research, these strains do not adequately represent the genetic diversity amongst humans. Multiparent populations like the collaborative cross mice and outbred populations like the diversity outbred mice allow us to model human diversity and better understand the genetic architecture of complex traits. Genetic variation itself, however, can also be considered a complex trait that arises from mutation, recombination, and chromosome assortment. Using diverse mouse strains and computational tools, I am investigating how candidate genes can alter mutation rates and resulting population genetic variability.
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Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics |
Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics |
The Dumont Lab |
Predoc |
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Gong Minghao Gong, Ph.D. |
Farmington, CT |
Works in the crossroads of microbiology, immunology, and multi-omics analyses (esp. Metabolomics), focused on the metabolomic tools development and the applications of metabolomics in microbe-host interaction and immunological studies.
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I have been working across multiple disciplines including immunology, microbiology, and bioinformatics. My research efforts during my Ph. D has built towards the application of multi-omics approaches to understanding microbe-host interaction. Thrilled by the recent development of metabolomics, I committed my efforts to develop metabolomic tools and analysis pipelines to decipher metabolic phenotypes in immune-related disorders and other diseases.
My current research includes developing metabolomic tools to the reconstruction of biochemical networks. The milestone towards this will be developing tools to upgrade genome scale metabolic models by using mass spectrometry data, via a combination of computational, genetic, cellular and isotope tracing techniques.
Minghao Gong on ORCID
Minghao Gong on Google Scholar
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Bioinformatics|Computational Biology|Immune Disorders|Infectious Disease Research |
Bioinformatics|Computational Biology|Immune Disorders|Infectious Disease Research |
The Li Lab |
Postdoctoral Associate |
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Iwasaki Takeshi Iwasaki, M.D., Ph.D. |
Bar Harbor, ME |
Functional genomics of autoimmune disease associated genetic variants.
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As a rheumatologist, I have been exposed to a mysterious clinical course of patients. A person who was fine yesterday develops joint pain, which spreads to systemic arthritis. Behind this, there must be a complex and ever-changing interaction between genetic polymorphisms and the environment. At JAX, I want to disentangle the fundamental rules governing such interactions one by one, since such an accumulation of efforts will lead to the future treatment of each patient.
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Takeshi Iwasaki on Google Scholar
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Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics |
Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics |
The Tewhey Lab |
Postdoctoral Associate |
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Kang Hyeongu Kang, Ph.D. |
Farmington, CT |
Transcriptome data analysis, Aberrant RNA splicing mechanism and implications in aging and disease.
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- Spatial transcriptome analysis of young and old mice breast tissue to identify an association aging and transcriptome changes - Refinement of the Iso-seq and MAS-seq pipeline and development of RNA splicing consequence estimation approach
- Exploring transcriptome changes in longitudinal samples to elucidate PARPi resistance mechanism in ovarian cancer patients
- Large-scale isoform analysis to find cancer-specific isoform expression patterns (Long/short read RNA seq)
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Hyeongu Kang on Orcid
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Aging|Bioinformatics|Cancer |
Aging|Bioinformatics|Cancer |
The Anczukow Lab |
Postdoctoral Associate |
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Kim Kwondo Kim, Ph.D. |
Farmington, CT |
My studies focus on evolution and function implications of structural variations in human population.
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Bioinformatics|Computational Biology|Genetics and Genomics |
Bioinformatics|Computational Biology|Genetics and Genomics |
The Lee Lab |
Postdoctoral Associate |
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Kuffler Lauren Kuffler |
Bar Harbor, ME |
Studying the genomics of complex diseases.
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Lauren is a Ph.D. student in the Tufts University Mammalian Genetics program.
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Bioinformatics|Data Science at The Jackson Laboratory|Complex Traits |
Bioinformatics|Data Science at The Jackson Laboratory|Complex Traits |
The Baker Lab |
Predoc |
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Kumar Sonal Kumar |
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Studying the basis and progression of Alzheimer's disease using a multi-omics approach.
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I am a PhD student in the Tufts University Neuroscience program. I am interested in understanding the contribution of sex-based differences in gene expression in the etiology and progression of Alzheimer's disease. In the Carter lab, I aim to better dissect the heterogeneity of Alzheimer's disease in humans using different model organisms for achieving improved translational outcomes.
Sonal Kumar on ORCID
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Aging|Bioinformatics|Computational Biology|Genetics and Genomics |
Aging|Bioinformatics|Computational Biology|Genetics and Genomics |
The Carter Lab |
Predoc |
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Larson Peter Larson, BS |
Farmington, CT |
Engineering the human skin microbiome to treat diseases and prevent infections.
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I've brought my background in synthetic biology to the Oh Lab with the aspiration to leverage the human microbiome (the bacteria, fungi, viruses, and other microbes that live on us) to promote health, prevent infections, and treat diseases. Here I have been engineering Staphylococcus epidermidis, a ubiquitous skin commensal, to detect and kill pathogens, as well as secrete therapeutics. Additionally, I have been conducting a sizable clinical metagenome study investigating the relationship between aging, health, and the microbiome. This study should help us understand how we can leverage the microbiome to promote healthy aging, combat chronic illnesses, and prevent infections commonly acquired by older adults in healthcare settings. Finally, I have been exploring the use of human skin explants and stem cell derived skin “organoids” to model human skin microbiome interactions. This will allow us and others to test engineered skin microbiome therapeutics, and better identify mechanisms by which the skin microbiome modulates health and disease.
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Aging|Bioinformatics|Computational Biology|Genetics and Genomics |
Aging|Bioinformatics|Computational Biology|Genetics and Genomics |
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Predoc |
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Liew Yi Juin Liew, Ph.D. |
Farmington, CT |
Study Alzheimer's disease using omics-based approaches to better understand disease progression.
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Completed PhD work in the field of computational neuroscience. Worked on thesis project that studies the transformation of sensory representation across brain structures in the somatosensory pathway.
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Aging|Bioinformatics|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases |
Aging|Bioinformatics|Genetics and Genomics|Neurodegenerative and Neuromuscular Diseases |
The Carter Lab |
Postdoctoral Associate |
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Melo Carrillo Adrian Melo Carrillo, Ph.D. |
Farmington, CT |
Single-cell comparative multiomics
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As an evolutionary biologist, I’m interested in the molecular mechanisms that shape genetic diversity and drive adaptation. Through my work, I aim to uncover new insights into these processes and their implications for human health. Ultimately, I am driven by a vision of using this knowledge to develop innovative research projects that can lead to the improvement of human health. In the Robson lab, I’m part of the Molecular Phenotypes of Null Alleles in Cells (MorPhiC) initiative. I implement single-cell comparative transcriptomics to identify target genes that possess primate-specific features and are implicated in human disease. Before joining the Robson lab, I worked mostly on the evolution of the Major Histocompatibility Complex (MHC) in platyrrhine monkeys, with a focus on gene duplication and species hybridization. Other projects involved phylogeography and conservation genetics of primates in the Americas. More recently, I was part of a familial glioblastoma study that aimed at identifying heritable genetic variants associated with an increased risk of the disease.
Adrian Melo Carrillo on Orcid
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Bioinformatics|Computational Biology|Genetics and Genomics |
Bioinformatics|Computational Biology|Genetics and Genomics |
The Robson Lab |
Postdoctoral Associate |
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Naddaf Lamis Naddaf, Ph.D. |
Farmington, CT |
I utilize computational and machine learning methods to identify genetic and epigenetic signatures associated with aging and cancer.
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During my postdoctoral training, I transitioned my research focus to the single-cell level, specifically delving into the investigation of epigenetic patterns in Acute Myeloid Leukemia (AML) within the context of aging. Additionally, I am working on establishing correlations between somatic mutations and these epigenetic changes. This in-depth analysis, which combines multiple types of biological data, has the potential to facilitate early detection, treatment, and prevention of AML in the aging population. We are fortunate to be in an era where biological data is exponentially increasing, awaiting deciphering. The analysis of such vast datasets necessitates the development of novel computational methodologies, a realm I am actively exploring in my postdoctoral research.
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Aging|Bioinformatics|Cancer|Computational Biology |
Aging|Bioinformatics|Cancer|Computational Biology |
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Postdoctoral Associate |
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O'Neill Francis O'Neill, M.D., M.A. |
Farmington, CT |
My primary area of research is the identification of cancer specific proteins and the development of novel anti-cancer immunotherapies for solid tumors, such as osteosarcoma.
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My primary area of research is the identification of cancer specific proteins and the development of novel anti-cancer immunotherapies for solid tumors, such as osteosarcoma. Utilizing high performance computing, we combine RNA sequencing and protein analysis in a proteogenomics workflow. The Jackson Laboratory for Genomic performs both long-read sequencing (Pacific Biosciences platform) and short-read sequencing (Illumina platform) on oncology patient samples. Our hybrid sequencing approach allows for generating a highly accurate cancer transcriptome upon which we can explore multiple biological mechanisms, such as RNA splicing and chromosomal rearrangements, leading to cancer specific mRNA isoforms. Mass spectrometry identification of isoform specific peptides aids in selecting candidates for validation in the laboratory. A central goal of my research is to expand current cancer treatment options and provide novel therapeutic agents with improved tumor specificity.
Francis O'Neil on ORCID
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Bioinformatics|Cancer|Computational Biology|Diabetes and Obesity |
Bioinformatics|Cancer|Computational Biology|Diabetes and Obesity |
The Lau Lab |
Postdoctoral Associate |
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Opoku Frempong Hilda Opoku Frempong |
Bar Harbor, ME |
Exploring Genetic recombination and Meiotic dysregulation
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During meiosis, maternal and paternal chromosomes undergo exchanges by homologous recombination. This is essential for fertility and contributes to genome evolution. In many eukaryotes, sites of meiotic recombination, also called hotspots, are regions of accessible chromatin, but in many vertebrates, their location follows a distinct pattern and is specified by PR domain-containing protein 9 (PRDM9). The control of the recombination landscape by PRDM9 has many implications in terms of the molecular mechanisms underlying the interaction between homologues during meiotic prophase and genetic diversity. My project seeks to explore molecular mechanisms in genetic recombination rate and meiotic dysregulation using mouse hybrids.
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Bioinformatics|Complex Traits|Computational Biology|Developmental Disorders |
Bioinformatics|Complex Traits|Computational Biology|Developmental Disorders |
The Dumont Lab |
Predoc |
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Pan Ziwei Pan |
Farmington, CT |
I am interested in applying machine learning and advanced statistical modelling into biological questions.
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I am a graduate student in Biomedical Sciences in Uconn Health with the supervisor of Dr. Sheng Li. I am interested in applying machine learning and advanced statistical modeling into biological questions.
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Bioinformatics|Computational Biology|Genetics and Genomics|Cancer |
Bioinformatics|Computational Biology|Genetics and Genomics|Cancer |
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Predoc |
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Ravichandran Sathyabaarathi Ravichandran, Ph.D. |
Farmington, CT |
Focuses on understanding the age-associated changes in immune responses to vaccination, particularly to seasonal influenza and pneumococcal vaccines, using single-cell approaches.
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I specialize in systems immunology, with a keen interest in deciphering how the immune system reacts to infections and vaccinations. Currently, my research is centered on exploring the age-associated changes in immune responses to vaccines, particularly those for seasonal influenza and pneumococcal diseases, employing single-cell technologies. The overarching goal of my work is to identify blood-based immunological biomarkers capable of distinguishing between individuals who respond to vaccines and those who do not.
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Sathyabaarathi Ravichandranon Orcid
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Aging|Bioinformatics|Computational Biology|Infectious Disease Research |
Aging|Bioinformatics|Computational Biology|Infectious Disease Research |
The Ucar Lab |
Postdoctoral Associate |
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Taylor Aaron Taylor, Ph.D. |
Farmington, CT |
Multi-omic profiling of pediatric brain and bone cancer to discover novel prognostic biomarkers and therapeutic targets.
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The purpose of my research at the Ching Lau Lab is to examine genomic and epigenomic data from pediatric cancers in order to discover molecular phenotypes, prognostic biomarkers, and candidate therapeutic targets. My work includes method and pipeline development for integration of multi-omic data in the analysis of pediatric brain and bone tumors to develop a better molecular understanding of these often-lethal cancers. Currently, my research focuses on osteosarcoma, ependymoma, and intracranial germ cell tumors.
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Cancer|Bioinformatics|Computational Biology|Genetics and Genomics |
Cancer|Bioinformatics|Computational Biology|Genetics and Genomics |
The Lau Lab |
Postdoctoral Associate |
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Wells Ann Wells, Ph.D. |
Bar Harbor, ME |
Modeling genetic interactions to better understand neurodegenerative diseases.
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I am interested in understanding how genetics and environment interact to influence disease status. I will be using and developing computational tools to understand these complex genetic systems, particularly in the context of neurodegenerative diseases.
My previous work investigated the role of diet, genetics, and sex on the tissue metabolome. Using metabolomics and various computational and statistical techniques I aimed to understand the complex interactions between diet, genetics, and sex and how each influenced physiological parameters in mice.
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Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics |
Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics |
The Carter Lab |
Postdoctoral Associate |