Faculty Profile: Alper Uzun, PhD

Alper Uzun
Alper Uzun, PhD
Instructor in Pediatrics (Research)
Department of Pediatrics
Work: +1 401-274-1122
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.


Dr. Alper Uzun received his BS in biology from Istanbul University and MS degree in medical biochemistry from Kocaeli University in Turkey. He entered graduate school at Northeastern University where he received a Masters Degree in bioinformatics followed by a PhD in computational biology and bioinformatics. He joined Prof. James Padbury's group in the early fall of 2009 on a project merging bioinformatics with genetics and structural biology. Dr. Uzun also works with Prof. Sorin Istrail from Computer Science department and affiliated with the Center for Computational Molecular Biology (CCMB). Since joining Alpert Medical School and Women and Infants Hospital in the Department of Pediatrics, he has been working on developing bioinformatics approaches to complex diseases. Dr. Uzun is particularly focused on the genetic architecture of preterm birth and preeclampsia.

Research Description

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.

Funded Research

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

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

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) 06/01/2013-03/31/2014
Targeted sequencing for preterm birth associated genes.
Role: PI

Teaching Experience

Teaching Assistant, Biochemistry Lab
Teaching Assistant, Organic Chemistry Lab
Teaching Assistant, Human Anatomy and Physiology Lab
Biology Lab Instructor, Human Anatomy and Physiology Lab
Teaching Assistant, Bioinformatics and Computational Biology Lab
Part-time Lecturer, Bioinformatics Seminar

Selected Publications

  • Uzun A, Dewan AT, Istrail S, Padbury JF.(2013). Pathway-based genetic analysis of preterm birth.Genomics.(PMID=23298525). (2013)
  • 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). (2012)
  • Uzun A, Sharma S, Padbury J. (2012). A Bioinformatics Approach to Preterm Birth. Am J Reprod Immunol.(PMID: 22385126). (2012)
  • 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). (2012)
  • 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). (2011)
  • 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). (2009)
  • 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). (2008)
  • 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). (2007)