CV

Education

• Ph.D., Bioinformatics and Biostatistics, Acibadem University, Istanbul, Turkey, 2022 - Present
  • Thesis: TBD
• M.Sc., Bioengineering, Abdullah Gül University, Kayseri, Turkey, 2017 - 2020
  • Thesis: Characterization of novel ciliary gene tmem145
• B.S., Molecular Biology and Genetics, Bilkent University, Ankara, Turkey, 2010 - 2017
  • Thesis: Design of whole cell urea and uric acid sensors in E. coli

Work Experience

• Bioinformatics Scientist, Abdullah Gül University, Kaplan Lab, 2020 - 2022
  • Developed an R package to compare genomes and find matching variants between species
  • Built pipeline to generate and analyze data for ConVarT
  • Implemented ML models to improve predictive capability of CilioGenics
  • Did statistical analysis and generated figures for various projects
• Research Assistant, Abdullah Gül University, Kaplan Lab, 2017 - 2020
  • Curated, analysed and visualized the data for ConVarT, a search engine for matching human genetic variants with variants from non-human species (convart.org)
  • Developed an integrative bioinformatics tool for predicting ciliary genes (CilioGenics) and a shiny app to explore the data from this tool (ciliogenics.com)
  • Identified new ciliary genes from single cell data and functionally characterized them using C. elegans as a model organism
• Undergraduate Researcher, UNAM, Bilkent University, Seker Lab, 2015 - 2016
  • Design of whole cell urea and uric acid sensors in E. coli
• Undergraduate Researcher, Kyoto University, Japan, Laboratory of Molecular and Cellular Immunology (Fujita Lab), June 2015 - August 2015
  • Revealing biochemical properties of mouse MDA5 protein

Skills

Programming Languages:

• R (Advanced)
• Python (Intermediate)
• Bash (Intermediate)
• Matlab (Basic)
• Java (Basic)
• SQL (Basic)

Wet-lab Skills:

• CRISPR/Cas9 gene modification
• PCR, RT-PCR
• DNA and RNA isolation
• Molecular cloning
• Fluorescent microscope
• Cell culture
• Dissection from mouse and rat
• Sanger sequencing
• Working on C. elegans

Publications

WDR31 is a novel ciliopathy protein displaying functional redundancy with GTPase-activating proteins ELMOD and RP2 in recruiting BBSome to cilium

Sebiha Cevik, Xiaoyu Peng, Tina Beyer, Mustafa S Pir, Ferhan Yenisert, Franziska Woerz, Felix Hoffmann, Betul Altunkaynak, Betul Pir, Karsten Boldt, Asli Karaman, Miray Cakiroglu, S Sadik Oner, Ying Cao, Marius Ueffing, Oktay I Kaplan

Matching variants for functional characterization of genetic variants

Sebiha Cevik, Pei Zhao, Atiyye Zorluer, Mustafa S Pir, Wenyin Bian, Oktay I Kaplan

ConVarT: Search Engine for Missense Variants Between Humans and Other Organisms

Mustafa S Pir, Sebiha Cevik, Oktay I Kaplan

ConVarT: a new search engine for orthologous variants for functional inference of human genetic variants

Mustafa S Pir, Halil I Bilgin, Ahmet Sayici, Fatih Coskun, Furkan M Torun, Pei Zhao, Yahong Kang, Sebiha Cevik, Oktay I Kaplan

ConVarT: a search engine for matching human genetic variants with variants from non-human species

Mustafa S Pir, Halil I Bilgin, Ahmet Sayici, Fatih Coşkun, Furkan M Torun, Pei Zhao, Yahong Kang, Sebiha Cevik, Oktay I Kaplan

Talks & Presentations

Leveraging AlphaFold Computed Structures for Pathogenicity Classification

October 01, 2023

Poster presentation at Ankara, Turkey, 16th The International Symposium on Health Informatics and Bioinformatics (HIBIT)

Enhancing Functional Maturation of iPSC-derived Endodermal Hepatic Organoid through Modified Culture Conditions

October 01, 2023

Poster Abstract at EMBL Heidelberg, Germany, EMBL Symposium on Organoids: modelling organ development and disease in 3D culture

ConVarT: a search tool for orthologous variants and functional inference of human genetic variants

January 01, 2021

Talk at E-symposium, 20th BSCB GenSoc UK Cilia Network e-symposium

ConVarT: a new search engine for orthologous variants for functional inference of human genetic variants

January 01, 2021

E-poster presentation at E-symposium, ESHG 2021 (European Human Genetics Conference)

Functional Characterization of Joubert Syndrome Associated CEP41

January 01, 2019

Poster presentation at Istanbul, Turkey, 7th International Congress of the Molecular Biology Association of Turkey

Teaching

Genetics class

CRISPR/Cas9 workshop

Awards

• Conference Fellowship, European Human Genetic Conference (ESHG), 2021

References

• Uğur Sezerman, PhD
  • Professor, School of Medicine, Department of Biostatistics and Medical Informatics
  • Acıbadem University, Istanbul, Turkey

  • Email: sezermanu@gmail.com

    Phone: +90-542-422-3688

• Emel Timucin, PhD
  • Professor, School of Medicine, Department of Biostatistics and Medical Informatics
  • Acıbadem University, Istanbul, Turkey
  • Email: emeldtimucin@gmail.com
• Oktay I. Kaplan, PhD
  • Assistant Professor, Faculty of Life Science
  • Abdullah Gül University, Kayseri, Turkey

  • Email: oktay.kaplan@agu.edu.tr

    Phone: +90-541-716-5849

• Sebiha Çevik, PhD
  • Assistant Professor, Faculty of Life Science
  • Abdullah Gül University, Kayseri, Turkey

  • Email: sebihacevik@gmail.com

    Phone: +90-352-224-8880

• Takashi Fujita, Prof.
  • Professor, Institute for Virus Research
  • Kyoto University, 53 Shogoin Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan

  • Email: fujita.takashi.86e@st.kyoto-u.ac.jp

    Phone: +81-75-751-4002