BIO5 Institute

Vlad Kalinichenko, MD, PhD is a senior investigator with a long-standing interest in transcriptional regulation of lung development and lung injury/repair. His research interests include perinatal and adult pulmonary disorders, such as Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV), Bronchopulmonary Dysplasia (BPD), Acute Lung Injury (ALI), Chronic Obstructive Pulmonary Disease (COPD) and Non-Small Cell Lung Cancer (NSCLC). Throughout his research career, Dr. Kalinichenko was interested in transcriptional regulation of lung diseases by various Forkhead Box (FOX) transcription factors. His lab generated mouse models with loss-of-function and gain-of-function of FOXM1, FOXF1 and FOXF2 and pioneered research on the role of these proteins in the lung. These unique mouse models enabled the lab to discover novel signaling, immune and transcriptional mechanisms critical for pulmonary inflammation, cellular proliferation, apoptosis and endothelial barrier function. His laboratory was involved in discovery and characterization of multiple FOXF1 mutations in ACDMPV patients and generated clinically relevant mouse models of ACDMPV by placing human FOXF1 mutations into the endogenous mouse Foxf1 gene locus. Dr. Kalinichenko has been very active in generation and distribution of >30 transgenic and knockout mice to investigators in scientific research community. His lab has also developed several nanoparticle delivery systems for the in vivo targeting of pulmonary endothelial cells with high efficiency and precision and discovered RCM-1 and TanFe small molecule compounds that specifically target FOX transcription factors in lung diseases. Recently, his lab used embryonic stem cells (ESCs) to generate bioengineered lung tissue which contains airways, alveoli and vasculature for potential applications in lung regenerative medicine. These innovative technologies are currently at different stages of preclinical testing and regulatory approvals for clinical use. The main areas of research include: - Generation of lung tissue from ESCs and iPSCs using interspecies chimeras. - Directed differentiation of ESCs/iPSCs into endothelial cell lineages. - Embryonic and postnatal development of pulmonary vasculature. - Lung regeneration in perinatal and adult pulmonary diseases. - Pulmonary inflammation and molecular mechanisms critical for innate immune responses. - Development of nanoparticle delivery systems to target endothelial cells for gene therapy. The long-term goal of the laboratory is to develop new therapies for BPD, ACDMPV and other perinatal lung diseases.

My lab employs computational as well as molecular biology approaches in our studies. This involves novel computational methods for detection and analysis of RNA from sequencing data, with a specific focus on empowering researchers using our software by making it user-friendly and accessible. We also establish new molecular assays that will help to shed light on functions of specific RNA molecules. We are especially focused on cardiovascular disease since it is the leading cause of death globally and early diagnosis and treatment are of utmost importance for public health. My current research utilizes computational and biological approaches to examine roles for different RNA species in cardiovascular diseases such as pathological cardiac hypertrophy, a condition that is characterized by the thickening of the heart muscle, a decrease in the size of the chambers of the heart, and a reduced capacity of the heart to pump blood around the body. My lab is working to generate a deeper understanding of the role of RNA molecules in disease by characterizing candidate molecules that in the future might be used to identify diseases during routine checkups, thus helping patients to receive treatment as early as possible.

The Computational Zoonosis lab takes an integrative and multidisciplinary One Health approach to develop computational and data-driven models for the study of bacterial pathogens. In doing so, the lab identifies the epidemiological, ecological, and evolutionary drivers involved in bacterial spillover events, amplification, and spread. Such approaches are essential for prioritizing surveillance strategies and predicting future disease emergence risk. At the core of the lab’s program is the curiosity to understand how interactions among individual organism’s scale to population-level dynamics. Current projects and collaborations focus on 1) studying the evolutionary processes and cross-species transmission patterns of zoonotic diseases; 2) connecting the evolutionary dynamics of infectious diseases with ecological processes through the characterization of underlying spatial and genetic patterns; 3) unraveling genomic signatures of host-pathogen interactions; and 4) developing computational tools to integrate genomic, epidemiological, and ecological data.

Dr. Salvador earned a B.Sc and a M.Sc in Computer Science from the University of Porto, and a Ph.D in Biology from the University of Lisbon, under the PhD Program in Computational Biology (collaboration between the Gulbenkian Institute of Science and Princeton University). Dr. Salvador did postdoctoral work in veterinary epidemiology and data science at the Universities of Glasgow and Edinburgh, and she was an Assistant Professor at the University of Georgia jointly appointed in the Department of Infectious Diseases in the College of Veterinary Medicine and in the Institute of Bioinformatics.