Stanford Career Development Program in Omics of Lung Diseases (K12). We propose a Career Development Program (CDP) in Omics of lung diseases with a major focus on pulmonary arterial hypertension (PAH). This is a logical extension of our current K12 CDP on the Genetics and Genomics of Lung Diseases that focuses on PAH. The new CDP proposal allows us to equip the next cadre of MD and PhD scientists with interdisciplinary and bioinformatic skills to integrate new high throughput genomic, proteomic and metabolomic platforms to gain a better understanding of disease pathophysiology. This proposed CDP in Omics will fuel the major cross-departmental collaborations we have built through NIH- NHLBI Interdisciplinary grants focusing on PAH. One of our NIH sponsored projects applies novel cutting-edge high-throughput proteomic methodologies to investigate inflammatory cells in autoimmune and idiopathic PAH. Another utilizes genomics and bioinformatics and induced pluripotent stem cell methodology to relate gene variants, methylation changes and RNA expression differences across the genome, to the functional behavior of native and iPSC-derived endothelial cells from PAH patients. Our role in the Pulmonary Hypertension Breakthrough Initiative Network permits access to these valuable samples, and our major clinical programs in Adult and Pediatric PAH assure that we are well-positioned to train a new generation of young scientists in this important area of research. Our Scholars will have MD or PhD backgrounds and our CDP offers extensive didactic cross training in the omics (genomics, proteomics, and metabolomics) and in computational biology, particularly for the MD with little background preparation in these areas. As well, we offer training in lung vascular anatomy, physiology and pathology for the PhD Scholar with little exposure to medicine. Each Scholar will undertake a mentored research project beginning in the first year of training, with a primary Mentor who has expertise in PAH, in the Omics fields, or in Bioinformatics, and two Co-Mentors with the complementary skills. Mentors and Co-Mentors will help the Scholar attain those skills that facilitate interpreting the large data sets resulting fro high throughput research to uncover the biological and clinical relevance of the findings. Our CDP focuses on one disease but, at the same time, provides the Scholar with the necessary tools to take on the challenges of future high throughput scientific discovery, to improve diagnosis and treatment of many other lung diseases.
Stanford Career Development Program in ?Omics? of Lung Diseases (K12) Narrative: We propose a career development program (CDP) for MD and PhD postodoctoral Scholars in the ?Omics? of lung disease that focuses on the pathobiology of pulmonary arterial hypertension (PAH). In our CDP we provide Scholars with a team of Mentor and two Co-Mentors that have complementary expertise in PAH, Bioinformatics and ?Omics? to guide the research project. We cross train the Scholars in genetics, epigenetics, proteomics, metabolism and bioinformatics as well as in lung physiology and pathology, through advanced courses, seminars and workshops.
|Vallania, Francesco; Tam, Andrew; Lofgren, Shane et al. (2018) Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases. Nat Commun 9:4735|
|Bongen, Erika; Vallania, Francesco; Utz, Paul J et al. (2018) KLRD1-expressing natural killer cells predict influenza susceptibility. Genome Med 10:45|
|Tamosiuniene, Rasa; Manouvakhova, Olga; Mesange, Paul et al. (2018) Dominant Role for Regulatory T Cells in Protecting Females Against Pulmonary Hypertension. Circ Res 122:1689-1702|
|Scott, Madeleine; Vallania, Francesco; Khatri, Purvesh (2017) META-ANALYSIS OF CONTINUOUS PHENOTYPES IDENTIFIES A GENE SIGNATURE THAT CORRELATES WITH COPD DISEASE STATUS. Pac Symp Biocomput 22:266-275|
|Sa, Silin; Gu, Mingxia; Chappell, James et al. (2017) Induced Pluripotent Stem Cell Model of Pulmonary Arterial Hypertension Reveals Novel Gene Expression and Patient Specificity. Am J Respir Crit Care Med 195:930-941|
|Lin, Y-C; Sung, Y K; Jiang, X et al. (2017) Simultaneously Targeting Myofibroblast Contractility and Extracellular Matrix Cross-Linking as a Therapeutic Concept in Airway Fibrosis. Am J Transplant 17:1229-1241|
|Gu, Mingxia; Shao, Ning-Yi; Sa, Silin et al. (2017) Patient-Specific iPSC-Derived Endothelial Cells Uncover Pathways that Protect against Pulmonary Hypertension in BMPR2 Mutation Carriers. Cell Stem Cell 20:490-504.e5|
|Sweeney, Timothy E; Haynes, Winston A; Vallania, Francesco et al. (2017) Methods to increase reproducibility in differential gene expression via meta-analysis. Nucleic Acids Res 45:e1|
|Haynes, Winston A; Vallania, Francesco; Liu, Charles et al. (2017) EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY. Pac Symp Biocomput 22:144-153|
|Nicolls, Mark R; Hsu, Joe L; Jiang, Xinguo (2016) Microvascular injury after lung transplantation. Curr Opin Organ Transplant 21:279-84|
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