USF Genomics

Grants

John Adams, Ph.D. Functional Genomics of Malaria Parasites  

Amy Alman, Ph.D. Epidemiology of the oral-systemic connection in cardiovascular disease and diabetes  

Mya Breitbart, Ph.D. Viral Discovery using Metagenomics; DNA Barcoding of Marine Organisms from Bacterial to Vertebrates  

Feng Cheng, Ph.D. Computer Aided Drug Discovery and Development  

Liwang Cui, Ph.D. Functional genomics to understand drug resistance and sexual development of malaria parasites  

Larry Dishaw, Ph.D. Immunological mechanisms of the gut microbiome  

Maureen Groer, Ph.D., MSN Microbiome studies of very low weight infants  

Thao Ho, D.O. Anemia and intestinal health in very low birth weight infants

Rays Jiang, Ph.D. Computational and Integrative biology approach to genomics  

Nataša Jonoska, Ph.D. Mathematical models for DNA-DNA and RNA-DNA interactions  

Kami Kim, M.D. Pathogenesis of toxoplasmosis and malaria  

Stephen Liggett, M.D. Genomics approach to drug discovery and personalized medicine  

Xiaoming Liu, Ph.D. Computational Human Genomics  

Lynn Martin, Ph.D. Ecoimmunology and Disease Ecology  

Thomas McDonald, M.D. Functional Genomics in Cardiovascular Disease  

Christina Richards, Ph.D. Ecological Genomics and Epigenetics

Kathleen Scott, Ph.D. Comparative genomics of autotrophic organisms  

Lindsey Shaw, Ph.D. Genomics approach to bacterial pathogenesis and antibacterial drug discovery

Xingmin Sun, Ph.D. Allergy, Immunology & Infectious Disease  

Monica Uddin, Ph.D. Genomics of social adversity and stress-related mental disorders  

Thomas Unnasch, Ph.D. Disease control and elimination of vector-borne pathogens  

Arjan van der Vaart, Ph.D. Computational Biophysical Chemistry  

Derek Wildman, Ph.D. Evolutionary Genomics of Human Health and Disease  

Lee Woodcock, Ph.D. Computational Chemistry/Biophysical Chemistry

John Adams

Chemogenomic Profiling of Plasmodium Falciparum Drug Responses and Resistance (PI) NIH/NIAID/R01AI117017

Discovering the essential genome of Plasmodium Falciparum (PI) NIH/NIAID/R01AI130171

Accelerating discovery of an efficacious Plasmodium vivax multivalent multi-stage vaccine  (PI)  NIH/NIAID/R01AI130171 

Structural vaccinology and design of novel immunogens for malaria vaccine development (Co-investigator)NIH/NIAID/R01AI137162

Evaluation of ivermectin as an antimalarial therapy against P. falciparum liver stage (PI)  NIH/NIAID/R21AI149730

Exploiting cross-reactive, conserved epitopes in Plasmodium vivax to develop a vaccine against falciparum placental malaria (Co-investigator)  NIH/NIAID/R01AI150944 

Plasmodium ovale hypnozoite development and relapse: a coordinated in vivo in vitro study  (MPI) NIH/NIAID/R21AI152260 


Amy Alman

The Oral Microbiome in Type 1 Diabetes and Sub-Clinical Cardiovascular Disease (PI) NIDRC/NIH/R01DE026480


Mya Brietbart

Ecology and Evolution of Seagrass Viruses (PI) University of South Florida (Internal Funding)

New Interdisciplinary Approaches to Enhance Red Tide Tracking and Forecasting on the West Florida Shelf (PI) Florida Fish and Wildlife Conservation Commission

Spawning Habitat and Early-Life Linkages to Fisheries (SHELF) (PI) Florida RESTORE Act Centers of Excellence Program

Coastal SEES Collaborative Research: Integration of human behavior and perception into a risk-based microbial water quality management approach (PI) NSF/OCE/1566562 

Deciphering the ecology of aquatic single-stranded DNA phages (Microviridae/Gokushovirinae) (PI) ENSF/DEB/1555854

  

Feng Cheng

Identification of Potential Drug-drug Interactions in Alzheimer's Disease Patients (PI) NIH/NIA/1R03AG070536-01

Identification of Drug-disease interaction in AD patients from GAAIN (PI) Alzheimer's Association/GEENA-Q-19-596192

Renal hemodynamics and hypertension during pregnancy (Co-investigator) NIH/NHLBI/R01HL137987

The Oral Microbiome in Type 1 Diabetes and Sub-Clinical Cardiovascular Disease (Co-Investigator) NIDRC/NIH/R01DE026480


Liwang Cui

Southeast Asia Malaria Research Center (PI) NIAID/NIH/U19AI089672

Molecular Mechanisms of Artemisinin Resistance (PI) NIAID/NIH/R01AI128940


Larry Dishaw 

Investigations of an Invertebrate Secreted Immune Effector that Influences Microbial Communities of the Gut (PI) NSF/MCB1817308


Maureen Groer 

Chronic Toxoplasma Gondii, Pregnancy Reactivation, and Perinatal Depression (PI)NICHD/NIH/R01HD086805 

Characteristics of Stool and Skin Breakdown in Neonatal Abstinence Syndrome (PI) Procter & Gamble Pharmaceuticals, Inc.

Exploring the Gut Microbiome in SARS-CoV-2 Infection Across Pregnancy (PI) University of South Florida (Internal Funding)


Thao “Tina” Ho

Enteral Iron Supplementation and Intestinal Health in Preterm Infants (PI) NIH/NHLBI/K23HL150300-01A1                                        

A Multimodal Approach for Monitoring Prolonged Acute Pain in Neonates (Co-investigator) NIH/NINR/1R21NR018756-01A1

Preterm vitamin A intake: from maternal diet to gut microbiome and postnatal growth (PI) USF Women's Health Collaborative Foundation


Rays Jiang

Chemogenomic Profiling of Plasmodium Falciparum Drug Responses and Resistance (Co-investigator)NIH/NIAID/R01AI117017

Targeting Mutant KRas for Cancer Therapy (Co-investigator) NIH/NCI/R35CA1977313D

Targeting heme dependency in leukemia (PI)  Florida Department of Health, Bankhead – Coley Cancer Award 

Constraints of biomass on innate immunity across terrestrial mammals. USF share $517,695 from  This project reveals that innate immune defenses scale allometrically in terrestrial mammals. (Co-investigator) NSF/IOS-1656618

IMAGINE: Epigenetic potential and range expansion in the house sparrow. (Co-investigator) NSF/IOS-2027040 


Nataša Jonoska

Deciphering the cryptic language of ribose incorporation in human DNA (Co-investigator) W.M. Keck Foundation

Collaborative Research: Discrete and Topological Models for Template-Guided Genome Rearrangements (PI) NSF/DMS1800443

Collaborative Research FTE-Medium: Three Dimensional Algorithmic Assembly and Information Storage (PI) NSF/CCF-2107267

Collaborative Research: Modeling R-loop formation and topology using braids and graphs coupled with single-molecule footprinting (PI) NSF/DMS-2054321

NSF-Simons Research Center: Southeast Center for Mathematics (Co-investigator) Georgia Institute of Technology/NSF/594594 


Kami Kim

Composition and Formation of the Cyst Wall (PI) Albert Einstein College of Medicine


Stephen Liggett

Molecular Properties of B-Adrenergic Receptors in Asthma (PI) NIH/NHLBI/R01HL045967

Novel Molecular Mechanisms Promote GPCR-Induced Bronchodilation in Asthma, Project 2 Airway Smooth Muscle Bitter Taste Receptors as Targets for Novel Bronchodilators (PI)  Rutgers University/NIH/NHLBI/5P01HL114471-05

Effects of Rare Genetic Variants and Ancestry on Beta Agonist Response in Asthma and COPD (PI) Wake Forest University/NIH/NHLBI/1R01HL142992-01A1


Xiaoming Liu

Accurately inferring demographic histories of human populations using large whole genome sequence data (PI) NHGRI/NIH/R01HG009524

Extend and improve the functional annotation tools dbNSFP and WGSA (PI) NHGRI/NIH/R03HG011075


Lynn Martin

IMAGINE: Epigenetic potential and range expansion in the house sparrow. (PI) NSF/IOS-2027040 

RCN: Integrating Organismal Biology into NEON (Co-investigator) NSF/IOS-2110233

IMAGINE Collaborative Research: Linking individual variation in immunity and behavior to landscape patterns in disease risk using the National Ecological Observatory Network (NEON) (PI) NSF/IOS-2110070


Thomas McDonald

Large-scale functional phenotyping of ion channel arrhythmia genomic variants (PI) NHLBI/NIH/R33HL12078


Christina Richards

Collaborative Research: Effects of Genetic Diversity, Epigentic Change and Root-associated Fungal Colonization on Trait variation in the Foundation Plant Spartina Alterniflora (PI) NSF/1556820

Multi-Trait Plasticity in Response to a Changing Climate (PI) Australian Research Council

Genomics and epigenetics of plant invasion (PI) Make Our Planet Great Again - German Research Initiative

The tumor-host evolutionary arms race (co-investigator) Supplement to Parent Grant: Cancer as a Complex Adaptive System U54CA193489


Kathleen Scott

Enigmatic carboxysomes from the marine and hypersaline chemolithoautotrophic bacteria of genus Thiomicrospira (PI) NSF/MCB1952676


Lindsey Shaw

Dissecting the Influence of a C-Terminal Processing Protease on S. aureus Pathogenesis (PI)NIH/NIAID/R01 AI157506-01

The Role and Regulation of Extracellular Proteases in Staphylococcus aureus (PI) NIAID/NIH/R01AI14458

PepSAVI-MS for Discovery of Novel Botanical Antimicrobial Peptides (PI) NIH/R01GM125814

Natural Product Derived Inhibitors of ESKAPE Pathogens (co-Investigator) NIH/NIAID/1R56 AI154922

Evolution and inhibition of carbapenemase in beta-lactam resistance (Co-investigator) NIH/NIAID/R01 AI161762-01

Role of the Enterococcal Site 2 Protease in Biofilm Formation (Co-investigator) NIH/NIAID/R01 AI141961


Xingmin Sun

Multivalent Vaccines Against Clostridium Difficile Infection (PI) NIAID/NIH/R01AI132711

Novel polymer biomaterials combating C. difficile infection (mPI) NIH/R01AI149852

Support for Clostridium difficile infection related research (PI) Anthony Gagliardi Foundation 

Bile acid salt inhibitors and Clostridioides difficile infection (Co-investigator) NIH/R21AI59745                 


Monica Uddin

The impact of traumatic stress on the methylome: implications for PTSD (MPI) Emory University/NIMH/NIH/R01MH108826

Epigenomic Predictors of PTSD and Traumatic Stress in an African American Cohort (PI)NIMHD/NIH/R01MD011728

Transgenerational Epigenomics of Trauma and PTSD in Rwanda (MPI) University of Rwanda/NIMH/NIH/U01MH115485

Epigenetic Mechanisms of T Cell Disregulation in PTSD (Co-investigator) University of South Carolina/NIAID/NIH/R01AI129788


Thomas Unnasch

Community-Directed Vector Control to Enhance Mass Drug Administration for Onchocerciasis Elimination in Africa (PI) NIH/NIAID/R01AI123245

Southeastern Regional CoE in Vector-Borne Diseases: The Gateway Program (Co-investigator) University of Florida/CDC/U01CK000510

Development of a Tool Kit for Human Fillarial Transfection (PI) NIAID/NIH/R21AI135172

Onchocerciasis Elimination Program (PI) The Carter Center, Inc.

Laboratory strengthening through technical support and training (PI) The Task Force for Global Health/USAID/NTD-USAID


Arjan van der Vaart

Collaborative research: Role of DNA sequence and deformability on lesion recognition and excision in the base excision repair pathway (PI) NSF/MCB1919096


Derek Wildman

Epigenomic Predictors of PTSD and Traumatic Stress in an African American Cohort (MPI) NIMHD/NIH/R01MD011728

Transgenerational Epigenomics of Trauma and PTSD in Rwanda (MPI) University of Rwanda/NIMH/NIH/U01MH115485


Lee Woodcock

Design and Application of Robust and Efficient QM/MM Free Energy Simulation Methods for Biomolecular Systems NIH/NIGMSR01GM129519