Uzun, Alper

Alper Uzun

Associate Professor of Pediatrics (Research), Associate Professor of Pathology and Laboratory Medicine (Research)

Overview

Dr. Uzun exhibits a diverse academic background, with training as a molecular biologist at Istanbul University and as a medical biochemist at Kocaeli University in Turkey. He furthered his academic journey by completing a Masters and PhD in computational biology and bioinformatics at Northeastern University. During his post-doctoral training at the Department of Pediatrics at Women and Infants Hospital under the guidance of Prof. James Padbury and at the Department of Computer Science, Brown University under Prof. Sorin Istrail, Dr. Uzun acquired invaluable expertise in his field.

Currently serving as an Associate professor of Pathology and Laboratory Medicine with a secondary appointment in Pediatrics, Dr. Uzun holds the position of Director of Cancer Bioinformatics at Legorreta Cancer Center at Brown University. His research is centered around utilizing genomics and bioinformatics to unravel the complex genetic architecture of preterm birth, preeclampsia, and cancer.

Driven by his extensive proficiency in data processing, analysis, and interpretation of genomic data derived from translational research projects, Dr. Uzun leads the development and implementation of customized bioinformatics data pipelines for the analysis of next-generation sequencing (NGS) assays.

Within his dynamic laboratory, Dr. Uzun and his team actively engage in comparative network analysis of various cancer subtypes. Their primary focus lies in designing and developing innovative computational tools related to network biology and variant visualizations.

Research Group website:

Genomics and Machine Intelligence Lab (GMI Lab)

Brown Affiliations

Research Areas

On the Web

Bioinformatics Tool- VIVA (Visualization of Variants)

Bioinformatics Tool- Proteinarium (Multi-Sample Protein-Protein Interaction Analysis and Visualization Tool)

Database for Preterm Birth

Database for Preeclampsia

Biocomicals, webcomic about medicine and biology

"Pathway-based genetic analysis of preterm birth" made the cover of Genomics

Editorial on our publication for Preeclampsia in Obstetrics and Gynecology

Medicine@Brown Research Boom

Editor’s Focus at Pediatric Research; Runs of homozygosity

Medicine@Brown "An Interview about Biocomicals"

Biocomicals cartoon made the cover of "Trends in Genetics" of November 2017 issue

Winner design of PLoS Computational Biology 2011

LabLIFE - Comic strip about biology lab tools

Publications Visualize it

Najrana T, Ahsan N, Abu-Eid R, Uzun A, Noble L, Tollefson G, Sanchez-Esteban J. "Proteomic analysis of a murine model of lung hypoplasia induced by oligohydramnios." Pediatric pulmonology, 2021.

Full Text PubMed

Bliss JM, Tollefson GA, Cuevas A, Longley SJ, Neale MN, Uzun A, Shaw SK. "Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis." mSphere, vol. 6, no. 1, 2021.

Full Text PubMed

Najrana T, Mahadeo A, Abu-Eid R, Kreienberg E, Schulte V, Uzun A, Schorl C, Goldberg L, Quesenberry P, Sanchez-Esteban J. "Mechanical stretch regulates the expression of specific miRNA in extracellular vesicles released from lung epithelial cells." Journal of cellular physiology, 2020.

Full Text PubMed

Armanious, David, Schuster, Jessica, Tollefson, George A., Agudelo, Anthony, DeWan, Andrew T., Istrail, Sorin, Padbury, James, Uzun, Alper. "Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool." Genomics, vol. 112, no. 6, 2020, pp. 4288-4296.

Full Text PubMed

Schuster, Jessica, Uzun, Alper, Stablia, Joan, Schorl, Christoph, Mori, Mari, Padbury, James F. "Effect of prematurity on genome wide methylation in the placenta." BMC Medical Genetics, vol. 20, no. 1, 2019, pp. 116.

Full Text PubMed

Schuster J, Superdock M, Agudelo A, Stey P, Padbury J, Sarkar IN, Uzun A. "Machine learning approach to literature mining for the genetics of complex diseases." Database : the journal of biological databases and curation, vol. 2019, 2019.

Full Text PubMed

Ugur MR, Kutchy NA, de Menezes EB, Ul-Husna A, Haynes BP, Uzun A, Kaya A, Topper E, Moura A, Memili E. "Retained Acetylated Histone Four in Bull Sperm Associated With Fertility." Frontiers in veterinary science, vol. 6, 2019, pp. 223.

Full Text PubMed

Tollefson GA, Schuster J, Gelin F, Agudelo A, Ragavendran A, Restrepo I, Stey P, Padbury J, Uzun A. "VIVA (VIsualization of VAriants): A VCF File Visualization Tool." Scientific reports, vol. 9, no. 1, 2019, pp. 12648.

Full Text PubMed

Xu Y, Gray A, Hardie DG, Uzun A, Shaw S, Padbury JF, Phornphutkul C, Tseng YT. "A novel, de novo mutation in the <i>PRKAG2</i> gene: infantile-onset phenotype and the signaling pathway involved." American Journal of Physiology - Heart and Circulatory Physiology, vol. 313, no. 2, 2017, pp. H283-H292.

Full Text PubMed

Uzun, Alper, Triche, Elizabeth W., Schuster, Jessica, Dewan, Andrew T., Padbury, James F. "dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes." Database : the journal of biological databases and curation, vol. 2016, 2016, pp. baw006.

Full Text PubMed

Giarraputo, James, DeLoach, Jordan, Padbury, James, Uzun, Alper, Marsit, Carmen, Hawes, Katheleen, Lester, Barry. "Medical Morbidities and DNA Methylation of NR3C1 in Preterm Infants." Pediatric Research, vol. 81, no. 1-1, 2016, pp. 68-74.

Full Text PubMed

Uzun A, Sahin Y, Schuster JS, Zheng X, Ryckman K, Feingold E, Padbury J. "Structural and Genomic Variation in Preterm Birth." Pediatric Research, vol. 80, no. 6, 2016, pp. 829-836.

Full Text PubMed

Uzun A, Schuster J, McGonnigal B, Schorl C, Dewan A, Padbury J. "Targeted Sequencing and Meta-Analysis of Preterm Birth." PLOS ONE, vol. 11, no. 5, 2016, pp. e0155021.

Full Text PubMed

Saunders AC, McGonnigal B, Uzun A, Padbury J. "The developmental expression of the CDK inhibitor p57(kip2) (Cdkn1c) in the early mouse placenta." Mol. Reprod. Dev., vol. 83, no. 5, 2016, pp. 405-12.

Full Text PubMed

Triche EW, Uzun A, DeWan AT, Kurihara I, Liu J, Occhiogrosso R, Shen B, Parker J, Padbury JF. "Bioinformatic approach to the genetics of preeclampsia." Obstetrics and gynecology, vol. 123, no. 6, 2014, pp. 1155-61.

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Uzun A, Dewan AT, Istrail S, Padbury JF. "Pathway-based genetic analysis of preterm birth." Genomics, vol. 101, no. 3, 2013, pp. 163-70.

Full Text PubMed

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. "PT19c, Another Nonhypercalcemic Vitamin D2 Derivative, Demonstrates Antitumor Efficacy in Epithelial Ovarian and Endometrial Cancer Models." Genes & Cancer, vol. 4, no. 11-12, 2013, pp. 524-34.

Full Text PubMed

Uzun A, Sharma S, Padbury J. "A bioinformatics approach to preterm birth." American Journal of Reproductive Immunology, vol. 67, no. 4, 2012, pp. 273-7.

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Uzun A, Laliberte A, Parker J, Andrew C, Winterrowd E, Sharma S, Istrail S, Padbury JF. "dbPTB: a database for preterm birth." Database : the journal of biological databases and curation, vol. 2012, 2012, pp. bar069.

Full Text PubMed

Govindaraju A, Uzun A, Robertson L, Atli MO, Kaya A, Topper E, Crate EA, Padbury J, Perkins A, Memili E. "Dynamics of microRNAs in bull spermatozoa." Reproductive biology and endocrinology : RB&E, vol. 10, 2012, pp. 82.

Full Text PubMed

Moore RG, Lange TS, Robinson K, Kim KK, Uzun A, Horan TC, Kawar N, Yano N, Chu SR, Mao Q, Brard L, DePaepe ME, Padbury JF, Arnold LA, Brodsky A, Shen TL, Singh RK. "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, vol. 7, no. 4, 2012, pp. e34443.

Full Text PubMed

DeMaso CR, Kovacevic I, Uzun A, Cram EJ. "Structural and functional evaluation of C. elegans filamins FLN-1 and FLN-2." PLoS ONE, vol. 6, no. 7, 2011, pp. e22428.

Full Text PubMed

Uzun A, Rodriguez-Osorio N, Kaya A, Wang H, Parrish JJ, Ilyin VA, Memili E. "Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis." BMC genomics, vol. 10, 2009, pp. 183.

Full Text PubMed

Abyzov A, Uzun A, Strauss PR, Ilyin VA. "An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces." PLOS Computational Biology, vol. 4, no. 4, 2008, pp. e1000066.

Full Text PubMed

Marziale F, Pucciarelli S, Ballarini P, Melki R, Uzun A, Ilyin VA, Detrich HW 3rd, Miceli C. "Different roles of two gamma-tubulin isotypes in the cytoskeleton of the Antarctic ciliate Euplotes focardii: remodelling of interaction surfaces may enhance microtubule nucleation at low temperature." The FEBS journal, vol. 275, no. 21, 2008, pp. 5367-82.

Full Text PubMed

Uzun A, Leslin CM, Abyzov A, Ilyin V. "Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways." Nucleic acids research, vol. 35, no. Web Server issue, 2007, pp. W384-92.

Full Text PubMed

Shehadi IA, Abyzov A, Uzun A, Wei Y, Murga LF, Ilyin V, Ondrechen MJ. "Active site prediction for comparative model structures with thematics." Journal of bioinformatics and computational biology, vol. 3, no. 1, 2005, pp. 127-43.

Full Text PubMed

Research

Research Overview

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.

Research Statement

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

The Legorreta Cancer Center, Brown University, Pilot Grant.
Network Analysis Approach to Discover Potential Cancer Drug Targets
March 1, 2022 – August 31, 2023
Role: Co-PI

Burroughs Wellcome Fund
July 15, 2021-April 30, 2023
Computational Approaches to the Genetics of Complex Diseases: Proteinarium – A network analysis of complex diseases.
Role: PI

Pilot Research Awards from the William and Mary Oh-William and Elsa Zopfi Professorship in Pediatrics for Perinatal Research
July 1, 2019 – June 30, 2020
Bioinformatic and glycomic approach to identifying potential virulence pathways of Candida parapsilosis

Role: Co-PI

William and Mary Oh – William and Elsa Zopfi Professorship in Pediatrics for Perinatal Research.
June 1, 2018 – May 31, 2019
Bioinformatic approach to identifying potential virulence pathways of Candida parapsilosis.

Role: Co-PI

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

Scholarly Work

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).

Background

Education and Training

Year	Degree	Institution
2009	PhD	Northeastern University
2003	MS	Northeastern University
1998	MS	Kocaeli University
1995	BS	Istanbul University

Postdoctoral/Other Training

Postdoctoral Research Fellow

Women and Infants Hospital of Rhode Island, Pediatrics

2009-2012

Providence, RI

Honors and Awards

Research assistantship, Institute for Complex Scientific Software, Northeastern University, 2003.
Teaching assistantship, Biology Department, Northeastern University, 2003-2009
Teaching assistant accreditation for expert level, Northeastern University, 2004

Affiliations Visualize it

Collaborators

Name	Title
Amin, Ali	Associate Professor of Surgery, Associate Professor of Pathology and Laboratory Medicine
Carneiro, Benedito	Associate Professor of Medicine
DeSouza, Andre	Assistant Professor of Medicine
Istrail, Sorin	James A. and Julie N. Brown Professor of Computational and Mathematical Sciences
Padbury, James	William and Mary Oh - William and Elsa Zopfi Professor of Pediatrics for Perinatal Research
Sarkar, Neil	Associate Professor of Medical Science, Associate Professor of Health Services, Policy and Practice
Schorl, Christoph	Assistant Professor of Biology (Research)
Schuster, Jessica	Assistant Professor of Pediatrics (Research)
Sharma, Surendra	Professor of Pathology and Laboratory Medicine (Research), Professor of Pediatrics (Research)
Shaw, Sunil	Associate Professor of Pediatrics (Research)
Uzun, Dilber	Assistant Professor of Pathology and Laboratory Medicine

Affiliations

Brown University, Center for Computational Molecular Biology (CCMB) - Affiliate Member

Appointments

Assistant Professor of Pediatrics (Research). 2014-2021

Researchers@Brown

Researchers@Brown

Alper Uzun

Associate Professor of Pediatrics (Research), Associate Professor of Pathology and Laboratory Medicine (Research)

Overview

Brown Affiliations

Research Areas

On the Web

Publications Visualize it

Research

Research Overview

Research Statement

Funded Research

Scholarly Work

Background

Education and Training

Postdoctoral/Other Training

Honors and Awards

Affiliations Visualize it

Collaborators

Affiliations

Appointments

Teaching

Teaching Overview