Alper UzunAssistant Professor of Pediatrics (Research)
Dr. Uzun was trained as a molecular biologist at Istanbul University and a medical biochemist at Kocaeli University in Turkey before starting his Masters and PhD in computational biology and bioinformatics at Northeastern University. He did his post-doctoral training at Prof. James Padbury’s lab at Women and Infants Hospital and Prof Sorin Istrail at the department of computer science, Brown University. He was promoted to Instructor of Pediatrics at Brown University at Alpert Medical school in 2012 and promoted to Assistant Professor of Pediatrics in 2014. His research focuses on using genomics and bioinformatics to understand the genetic architecture of preterm birth and preeclampsia. He is managing large scale data (whole-genome genotyping data, RNA-Seq, targeted sequencing) and developing bioinformatics approaches towards deep sequencing to identify causal variants of both diseases.
Kawar N, Maclaughlan S, Horan TC, Uzun A, Lange TS, Kim KK, Hopson R, Singh AP, Sidhu PS, Glass KA, Shaw S, Padbury JF, Vorsa N, Arnold LA, Moore RG, Brard L, Singh RK. (2013). PT19c, Another Nonhypercalcemic Vitamin D2 Derivative, Demonstrates Antitumor Efficacy in Epithelial Ovarian and Endometrial Cancer Models. Genes Cancer. (PMID:24386512)
Uzun A, Dewan AT, Istrail S, Padbury JF.(2013). Pathway-based genetic analysis of preterm birth.Genomics.(PMID:23298525).
Uzun A, Laliberte A, Parker J, Andrew C, Winterrowd E, Sharma S, Istrail S, Padbury JF. (2012). dbPTB: a database for preterm birth. Database 2012:bar069 (PMID: 22323062).
Uzun A, Sharma S, Padbury J. (2012). A Bioinformatics Approach to Preterm Birth. Am J Reprod Immunol.(PMID: 22385126).
Richard G. Moore, Thilo S. Lange, Katina Robinson, Kyu K. Kim, Alper Uzun, Timothy C. Horan, Nada Kawar, Naohiro Yano, Sharon R. Chu, Quanfu Mao, Laurent Brard, Monique E. DePaepe, James F. Padbury, Leggy A. Arnold, Alexander Brodsky, Tun-Li Shen, Rakesh K. Singh.(2012) Efficacy of a Non-Hypercalcemic Vitamin-D2 Derived Anti-Cancer Agent (MT19c) and Inhibition of Fatty Acid Synthesis in an Ovarian Cancer Xenograft Model. PLoS ONE. (PMID:22509304).
DeMaso CR, Kovacevic I, Uzun A, Cram EJ. (2011). Structural and functional evaluation of C. elegans filamins FLN-1 and FLN-2. PLoS One 6(7):e22428 (PMID: 21799850).
Uzun A, Rodriguez-Osorio N, Kaya A, Wang H, Parrish JJ, Ilyin VA, Memili E. (2009). Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis. BMC Genomics 10:183(PMID: 19393058).
Abyzov A, Uzun A, Strauss PR, Ilyin VA. (2008). An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces. PLoS Comput Biol. 4(4):e1000066 (PMID: 18437203).
Uzun A, Leslin CM, Abyzov A, Ilyin V. (2007). Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Res.35(Web Server issue):W384-92 (PMID: 17537826).
My background in computational biology and bioinformatics directs my research towards pathways analysis, genome-wide association studies and particularly genetic architecture of preterm birth and preeclampsia.
I have been working on developing bioinformatics approach to complex diseases. I am particularly working on the genetic architecture of preterm birth and preeclampsia. I have built a web-based aggregation tool which we have used to aggregate the published medical literature, information from public databases, linkage analyses and finally pathway analysis to the genes involved in preterm birth. This computational approach allows us a much more robust evaluation of new GWAS data on preterm birth. Using this tool, we have demonstrated three logs greater statistical inferences for genes involved in preterm birth compared to the conventional genome-wide approach. This work has been presented for the last two years at the American Society of Human Genetics, and database for preterm birth (dbPTB) was published in 2012. Most recently we have created a tool to examine the genes involved in preeclampsia. I have built another web-based aggregation tool and we have begun the curation.
Since I'm studying the genetic architecture of preterm birth and preeclampsia, I focused on pathway analysis on connection with phenotype and genotype correlations of these diseases. In addition, I am managing and analyzing the large scale data (whole-genome genotyping data) of genome wide associations and developing bioinformatics approaches towards deep sequencing to identify casual variants.
COBRE: Center for Computational Biology of Human Disease #1P20GM109035-01A1 06/01/2016-2/28/2021
Computational Genomics of Preeclampsia Role:PI
Pilot Project Program of the COBRE for Perinatal Biology Uzun (PI) 09/01/2015-04/30/2016 Transcriptome Profiling of Extracellular Vesicles Defines Molecular Phenotypes of Preeclampsia Role:PI
National Foundation March of Dimes #21-FY14-154 Padbury (PI) 03/01/2014-02/28/2017 Bioinformatics and Targeted Resequencing in Preterm Birth. Role: Co-I
Rhode Island Foundation Uzun (PI) 03/01/2014-02/28/2015 Targeted Exome Sequencing of Extreme Phenotypes of Preterm Birth. Role:PI
COBRE Center for Cancer Signaling Networks Pilot Project Fund Uzun (PI) 06/01/2013-03/31/2014 Targeted sequencing for preterm birth associated genes. Role: PI
1R21HD070177-01A1 Triche And Dewan (PIs) 04/01/2012-03/31/2014 Fetal Genetic Contributions to Preeclampsia. Role: Co-I
COBRE Center for Cancer Signaling Networks Pilot Project Fund Uzun (PI) 07/01/2011-03/31/2012 Targeted Genomic Resequencing in Preterm Birth. Role: PI
National Foundation March of Dimes #21-FY08-563 Padbury (PI) 03/01/2009-02/28/2012 Preterm Birth: A Novel Bioinformatics and Genomics Approach. Role: Postdoctoral Researcher/Co-Investigator
Teaching Assistant, Biochemistry Lab, Northeastern University
Teaching Assistant, Organic Chemistry Lab, Northeastern University
Teaching Assistant, Human Anatomy and Physiology Lab, Northeastern University
Biology Lab Instructor, Human Anatomy and Physiology Lab, Northeastern University
Teaching Assistant, Bioinformatics and Computational Biology Lab, Northeastern University
Part-time Lecturer, Bioinformatics Seminar, Northeastern University