The Lung Genomics Research Program integrates researchers that use genomic scale information and technologies in their research. The program is based on the Lung Translational Genomics Center (LTGC), a resource center that serves pulmonary clinicians, toxicologists and basic scientists. With the creation of Lung Translational Genomics Center (LTGC) the division of Pulmonary, Allergy and Critical Care created a knowledge and technology center that is highly accessible to scientists and to trainees. The center provides access to equipment for genomics and proteomics experiments to respiratory scientists. The center also provides expertise and support in implementation of genomic high-throughput technologies, bioinformatic approaches and preliminary proteomics to respiratory scientists as well educational activities for trainees. Faculty of the Lung Genomics Research Program, as well as other scientists at the University of Pittsburgh have used the center to analyze of lung diseases such as Interstitial Pulmonary Fibrosis (IPF), Chronic Obstructive Pulmonary Disease (COPD), Asthma, Acute Respiratory Distress Syndrome (ARDS), and Lung Transplantation as well as environmental lung diseases such as silicosis and asbestosis.
The program faculty includes Drs. Naftali Kaminski, Kevin Gibson, Anurhada Ray, Prabir Ray, Yingze Zhang, Wei Wu, Thomas Richards, and Mandal Singh. External faculty include Drs George LeiKauf (EOH) Takis Benos from the Department of Computational Biology at the University of Pittsburgh, Drs Ziv Bar-Joseph and Eric Xing from department of Computer Science in Carnegie Mellon University and Dr Friedman from the Hebrew University in Jerusalem.
Dr. Kaminski is the Director of the Simmons Center for Interstitial Lung Disease and the Lung Translational Genomics Center Dr. Kaminski received his medical degree from the Hebrew University - Hadassah Medical School in Jerusalem, Israel and completed an internship and residency in Internal Medicine at Hadassah Mount-Scopus University Hospital in Jerusalem, and a pulmonary fellowship in pulmonary medicine at Sheba Medical Center in Tel-Hashomer, Israel. Dr. Kaminski completed also completed a postdoctoral fellowship at the Cardiovascular Research Institute (CVRI) in the University of California, San Francisco (UCSF). During this period, Dr. Kaminski also trained in functional genomics and micro-array technology at the Functional Genomics laboratory at Roche Bioscience, Palo-Alto, CA. Dr. Kaminski was the head of Functional Genomics at Sheba Medical Center before being recruited to the University of Pittsburgh.
Dr. Kaminski has a long time commitment to studying the basic molecular networks that underlie pulmonary fibrosis. He has pioneered the application of micro-array technology to lung fibrosis and has applied this technology in a variety of models and disease states. Dr. Kaminski has also been actively involved in developing bioinformatic approaches to analysis of micro-array data and in educating biologists in bioinformatics, genomics and systems biology. Dr. Kaminski has authored more than 70 publications and was the editor of "Gene Express" a column on genomics at the American Thoracic Society website, as well as the chair of the Respiratory Cell and Molecular biology Assembly program Committee of the American Thoracic Society International Conference. To see some of Dr Kaminski’s publications click here
Dr. Yingze Zhang is a Research Associate Professor who received her Ph.D. from the University of Pittsburgh School of Medicine in 1997. She then completed her post-doctoral training in Human Genetics, and Rheumatology & Cellular Immunology at the Allegheny University of Health Systems and University of Pittsburgh School of Medicine, respectively. Dr. Zhang is a former faculty member at the Center for Craniofacial and Dental Genetics at the University of Pittsburgh School of Dental Medicine. Dr. Zhang has conducted research on genetic and molecular basis of a number of human diseases. Her current research interests include molecular and genetic basis of idiopathic pulmonary fibrosis, chronic obstructive pulmonary disease (COPD), and interstitial lung diseases associated with connective tissue. She is also interested in biomarker discovery for the diagnosis, prognosis, and treatment response of pulmonary diseases, and functional significance of genetic polymorphisms associated with pulmonary and other diseases. (See table)
Table: Archived Clinical Samples in the Translational Core Laboratory (Dr Zhang) |
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| Study | Subjects | Plasma | Serum | PBMC/WBC | RNA | DNA |
| COPD | 338 | 325 | 311 | 92 | 317 | 288 |
| ALI | 207 | 182 | 30 | 112 | 150 | 205 |
| ILD | 362 | 303 | 235 | 150 | 262 | 262 |
| Sleep | 33 | 99 | 12 | 101 | 167 | 30 |
| PAP | 20 | 20 | ||||
| Lung Transplant | 273 | 328 | 144 | 100 | 273 | |
| Asthma | 102 | 100 | 101 | 99 | 102 | |
| Lung Cancer | 146 | 100 | 98 | |||
| Control | 120 | 111 | 77 | 90 | 101 | 120 |
Dr. Wei Wu is a Research Assistant Professor who received her doctoral degree in computational molecular biology from Rutgers University in 2000. She then obtained a master’s degree in computer science from the University of California at Santa Cruz. She completed a bioinformatics postdoctoral fellowship in Lawrence Berkeley National Lab. Dr Wu is an expert bioinformatician; she has participated in the construction of the world-renowned UCSC Genome Browser (http://genome.ucsc.edu), and has substantial experience in handling and analyzing large-scale genomic data. She is deeply interested in sequence and genomic information analysis, microarray data normalization and analysis. Her research interests focus on developing computational algorithms, software and tools i) to help identify genetic and regulatory mechanisms underlying lung diseases; ii) to identify biomarkers, and classify and diagnose various lung diseases using meta data; and iii) to predict outcomes of patients with lung diseases using meta data.
Program Facilities, resources and datasets are listed within the Lung Translational Genomics Center. Briefly, they include all of the equipment required to run gene expression microarrays, high throughput methylation assays, microRNA profiling assays, high-throughput promoter binding assays (ChIP on chip), laser capture microdissecting microscope, exploratory proteomics (DIGE) and tarageted proteomics as well resources for computational data anaysis and systems biology.