Ogün Adebali, PhD

Principle Investigator

oadebali@sabanciuniv.edu

Education

2015 Ph.D. University of Tennessee, Knoxville - USA
- Major: Life Sciences - Genome Science & Technology
- Minor: Computational Science
2011 B.S. Middle East Technical University, Ankara - Turkey
- Major: Molecular Biology and Genetics

Work Experience


2018 - now	Assistant Professor	Sabanci University
2016 - 2018	Postdoctoral Research Associate	University of North Carolina, Aziz Sancar Lab
2015 - 2016	Postdoctoral Research Associate	Oak Ridge National Laboratory, Igor Zhulin Lab
2011 - 2015	Graduate Research/Teaching Assistant	University of Tennessee

Publications

Ozcelik E., Kuru N., Adebali O.* (2021)

Phylostat: A Web-based Tool to Analyze Paralogous Clade Divergence in Phylogenetic Trees Turkish Journal of Biology - In press
Kaya S., Adebali O., Oztas O., Sancar A. (2021)

Genome-wide Excision Repair Map of Cyclobutane Pyrimidine Dimers in Arabidopsis and the Roles of CSA1 and CSA2 Proteins in Transcription-Coupled Repair Photochemistry and Photobiology.
Akkose U., Kaya V.O., Lindsey-Boltz L., Karagoz Z., Brown A.D, Larsen P.A., Yoder A.D., Sancar A., Adebali O.* (2021)

Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events BMC Genomics, 1(22).
Azgari C., Kilinc Z., Turhan B., Circi D., Adebali O.* (2021)

The mutation profile of SARS-CoV-2 is primarily shaped by the host antiviral defense Viruses, 13(3)394.
Kose M.*, Canda E., Kagnici M., Aykut A., Adebali O., Durmaz A., Bircan A., Diniz G., Eraslan C., Kose E., Ünalp A., Yılmaz U., Ozyilmaz B., Özdemir T.R., Atik T., Uçar S.K., McFarland R., Taylor R.W., Brown G.K., Çoker M., Özkınay F. (2020)

SURF1-related Leigh Syndrome: Clinical and molecular findings of 16 patients from Turkey Molecular Genetics and Metabolism Reports
Piepoli S., Shamloo B., Bircan A., Adebali O., Erman B.* (2020)

Molecular Biology of SARS-CoV-2. Turkish Journal of Immunology
Adebali O.*, Bircan A., Circi D., Islek B., Kilinc Z., Selcuk B., Turhan B. (2020)

Phylogenetic analysis of SARS-CoV-2 genomes in Turkey Turkish Journal of Biology, 44(3), 146-156.
Gumerov V.M., Ortega D.R., Adebali O., Ulrich L., Zhulin I.B. (2020)

MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems. Nucleic Acid Research
Li W., Liu W., Kakoki A., Wang R., Adebali O., Sancar A., Jiang Y. (2019)

Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells Journal of Biological Chemistry
Yimit A., Adebali O., Sancar A.*, Jiang Y.* (2019)

Differential damage and repair of anti-cancer drug cisplatin induced DNA-adducts across mouse organs. Nature Communications, 10(1), 309
Hu J., Li W., Adebali O., Yang Y., Oztas O., Selby C.P., Sancar A.* (2019)

Genome-wide mapping of nucleotide excision repair with XR-seq. Nature Protocols, 14(1), 248-282.
Yang Y., Adebali O., Wu G., Selby C.P., Rashid N., Hogenesch J.B., Sancar A.* (2018)

Cisplatin-DNA adduct repair of transcribed genes is controlled by two circadian programs in mouse tissues. PNAS, 21(115), E4777-E4785.
Oztas O., Selby C.P., Sancar A.*, Adebali O.* (2018)

Genome-wide Excision Repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns. Nature Communications, 9(1), 1503.
Li W., Adebali O., Yang Y., Selby C.P., Sancar A.* (2018)

Single-nucleotide resolution dynamic repair maps of UV damage in Saccharomyces cerevisiae genome. PNAS, 115(15), E3408-E3415.
Adebali O., Sancar A.*, Selby C.P.* (2017)

Mfd translocase is necessary and sufficient for transcription-coupled repair in Escherichia coli. The Journal of Biological Chemistry, 292(45), 18386-18391.
Hu J., Selby C.P., Adar S., Adebali O., Sancar A.* (2017)

Molecular mechanism of DNA excision repair and excision repair maps of the human and E. coli genomes. The Journal of Biological Chemistry, 292(38), 15588-15597.
Hu J.#, Adebali O.#, Adar S., Sancar A.* (2017)

Dynamic maps of UV damage formation and repair. PNAS, 114(26), 6758-6763.
Li W., Hu J., Adebali O., Adar S., Yang Y., Chiou Y., Sancar A.* (2017)

Human genome-wide repair map of DNA damage caused by the cigarette smoke carcinogen benzo[a]pyrene. PNAS, 114(26), 6752-6757.
Adebali O., Petukh M., Reznik A., Tishkov A., Upadhyay A., Zhulin I.B.* (2017)

Class III histidine kinases: a recently accessorized kinase domain in putative modulators of type IV pili based motility. Journal of Bacteriology, 199(18), e00218-17.
Adebali O., Chiou Y., Hu J., Sancar A.*, Selby C.P.* (2017)

Genome-wide transcription-coupled repair in Escherichia coli is mediated by the Mfd translocase. PNAS (Featured: From the Cover), 114(11), E2116-E2125.
Adebali O.*, Zhulin I.B. (2016)

Aquerium: a web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree. Proteins, 85(1), 72-77.
Upadhyay A.A., Fleetwood A.D., Adebali O., Finn R., Zhulin I.B.* (2016)

Cache domains are dominant extracellular sensors for signal transduction in prokaryotes. PLOS Computational Biology , 12(4).
Adebali O., Reznik A.O., Ory D.S., Zhulin, I.B.* (2016)

Establishing the precise evolutionary history of a gene improves predicting disease-causing missense mutations. Genetics in Medicine, 18(10), 1029-1036.
Adebali O.*, Ortega D.R., Zhulin I.B.* (2015)

CDvist: a webserver for identification and visualization of conserved domains in protein sequences. Bioinformatics, 31(9), 1475–1477.

*Corresponding author | #Equal contribution

Preprints

Selcuk B., Erol I., Durdagi S., Adebali O.* (2021)

Receptor-wide Determinants of G Protein Coupling Selectivity in Aminergic GPCRs BioRxiv.
Nabi A., Adebali O., Tastan O.* (2021)

Detecting Misannotated Long Non-coding RNAs with Training Dynamics of Deep Sequence Classification. BioRxiv.

Awards and Honors


2022	Mustafa Parlar Research Incentive Award
2021	Young Scientist Award (TÜBA-GEBIP) Turkish Academy of Sciences
2019	Young Scientist Award (BAGEP) Science Academy of Turkey
2018	EMBO Installation Grant Award
2015	University of Tennessee – Division of Biology Cokkinias Research Excellence Award
2011	Graduation with Honors, Middle East Technical University
2006	Undergraduate scholarship for 5 years from “The Scientific and Technological Research Council of Turkey”

Travel awards


2018	ASBMB Travel Award
2014	Travel award for RECOMB Comparative Genomics meeting, Cold Spring Harbor, New York, awarded by Graduate Student Senate, University of Tennessee

Funding

Years	Program	Role	Duration
2022-2025	TUBITAK 3501 - Career Development Program	PI	36 Months
2020-2022	TUSEB - Systems Biology and Bioinformatics Strategic R&D	PI	24 Months
2020-2023	TUBITAK 2232 - International Fellowship for Outstanding Researchers	PI	36 Months
2020-2023	TUBITAK 1001 - The Grant Program for Scientific and Technological Research Projects	Researcher	36 Months
2019-2022	EMBO Installation Grant	PI	36 Months
2019-2021	BAGEP Award	PI	36 Months
2019-2020	Sabanci University Starting Grant	PI	12 Months
2018-2019	TUBITAK - Return Fellowship Program	PI	18 Months

Presentations and Seminars

Year	Event	Location	Title	Type
2021	EMBO Young Scientists Forum	Poland, Warsahw	Phylogeny-Aware Amino Acid Substitution Scoring	Invited Talk
2021	EMBO Evolution Meeting	Online	Phylogeny-based analyses of protein functions at molecular level	Seminar
2021	ERNEST Meeting	Online	G-protein selective activation mechanisms in GPCRs	Talk
2021	EMBO Young Investigator Meeting	Online	Unraveling signaling mechanisms of GPCRs through molecular evolution	Talk
2021	EuroCC Seminars	Online	Using workflow managers in HPC systems	Seminar
2021	EuroCC Winter School	Online	Batch Computations in Genomics	Invited Talk
2021	Bogazici University Biotech Conference	Online	Computational Genomics	Invited Talk
2020	Medical Biology and Genetics Association	Online	To understand genome-wide DNA repair	Seminar
2020	Kadir Has University (HASGEN Student Club)	Online	Associations between heterogeneous DNA repair and uneven genomic distribution of cancer mutations	Seminar
2020	Data Science Summer School	Online	What we learn from SARS-CoV-2 Evolution	Invited talk
2020	Ecology and Evolutionary Biology Society of Turkey	Online	What Molecular Evolution Provides and SARS-CoV-2 Genome analyses	Seminar
2020	IRB Barcelona	Barcelona, Spain	Genomic factors involved in genome-wide DNA repair efficacy	Seminar
2020	BAU School of Medicine Basic Science Seminars	Bahcesehir University, Istanbul	When and where to target? DNA and protein informatics as a preliminary step into medical applications.	Seminar
2019	BAU Drug Design Congress	Bahcesehir University, Istanbul	High-resolution evolutionary analysis of membrane proteins in health context	Invited talk
2019	Evolution Conference	Gebze Technical University, Kocaeli	Molecular biology in the light of evolution	Invited talk
2019	EMBO Genome Integrity Meeting	University of Zurich, Switzerland	Heterogeneous genome-wide DNA repair	Talk
2019	Molecular Biology Congress	Istanbul Technical University, Istanbul	Heterogeneous genome-wide DNA repair	Invited talk
2019	Biological databases and data analysis symposium	Koc University, Istanbul	Evolutionary analysis of proteins involved in signal transduction	Invited talk
2019	Organelle Biogenesis and Function in Cell Physiology and in Disease	Koc University, Istanbul	Precise evolutionary history sheds light into molecular features of human receptors	Invited talk
2019	Kadir Has University Science Seminars	Kadir Has University, Istanbul	Circadian clock-controlled nucleotide excision repair maps	Invited seminar
2019	Aykut Kence Evolution Conference	Middle East Technical University, Ankara	Evolutionary Bioinformatics in Biomedical and Basic Research	Invited talk
2018	11th International Symposium on Health Informatics and Bioinformatics	Antalya Bilim University, Antalya	Circadian clock-controlled nucleotide excision repair maps	Talk
2018	MRC Laboratory of Molecular Biology Science Seminars	MRC Laboratory of Molecular Biology, Cambridge, UK	Gaining insights into proteins and associated phenotypes through the accurate lens of evolution	Seminar
2018	Ecology and Evolutionary Biology Symposium	Dokuz Eylul University, Izmir	Identifying functionally equivalent orthologs in the context of predicting disease-causing mutations	Talk
2018	ASBMB Meeting	San Diego, California, USA	High-resolution maps of genome-wide human damage and repair	Talk
2017	10th International Symposium on Health Informatics and Bioinformatics	Middle East Technical University, Cyprus	Genomics of DNA damage, repair and mutation in health and disease	Invited talk
2016	Gordon Research Conference: Human Single Nucleotide Polymorphisms & Disease	South Hadley, MA	Establishing precise evolutionary history in predicting variant effects	Talk
2016	UT Hospital Seminars	Knoxville, TN	The Importance of precise evolutionary information in health and disease	Seminar
2016	Max Planck Institute Seminars	Max Planck Institute, Dresden, Germany	Applications of protein informatics in basic and biomedical research	Seminar
2011	6th International Symposium on Health Informatics and Bioinformatics	Izmir Institute of Technology, Izmir	Applications of Bioinformatics for Synthetic Biology	Talk

Organizations

Co-chair of HIBIT2020 - 13th The International Symposium on Health Informatics and Bioinformatics
Program Committee member for HIBIT2017, HIBI2018, HIBIT2019

Teaching

Year	Course
2018-2021	Science of Nature
2018-2021	Computational Biology
2020	Genome-wide Sequencing Techniques and Analysis

Peer service

Editorial Board of Turkish Journal of Biology
Peer reviewer for Genome Research, Bioinformatics, Journal of Bacteriology, PLOS, PeerJ, Experimental Neurology, Current Microbiology

Memberships

Molecular Biology Association of Turkey
Ecology and Evolutionary Biology Association

Services

CDvist: Comprehensive Domain Visualization Tool - cdvist.adebalilab.org
Aquerium: Architecture Querying Podium - aquerium.adebalilab.org
SAVER: Single Amino Acid Variant Evaluator (NPC1) – saver.adebalilab.org
MiST: Microbial Signal Transduction Database – mistdb.com
Phylostat: Phylogenetic analysis of paralogous clade divergence – phylostat.adebalilab.org

Press and Media

2021

GazeteSu (Turkish)

2020

GazeteSu (Turkish)
Column Article by Sedat Ergin (Turkish)
Interview - HaberTurk (Turkish)
Interview - NTV (Turkish)

2019

Interview - Milliyet

| Milliyet (Turkish) |
Scientific Homecoming | En bilimsel geri dönüş

| Sabah (Turkish) |
Science Academy 2019 Young Scientist Award | Sabancı Üniversitesi Öğretim Üyelerine 2019 Yılı Bilim Akademisi BAGEP Ödülü

| GazeteSu (Turkish) |
Against Brain Drain | Beyin göçüne inat, Nobel alacak bilim insanları yetiştirmek için Türkiye’ye döndü!..

| Sozcu (Turkish) |
Interview | #AkademisyeneSor’un yeni konuğu Ogün Adebali

| GazeteSu (Turkish) |

2018

Öğretim Üyemize Avrupa Moleküler Biyoloji Örgütü (EMBO) Yerleşim Desteği Ödülü

| GazeteSu (Turkish) |
Could Reading our Circadian Clocks According to DNA Repair Optimize Chemotherapy?

| UNC |
How does plant DNA avoid the ravages of UV radiation?

| Science Daily |

2017

Where Cigarette Smoking’s Damage is Done … Down to Your DNA

| UNC News | Science Daily |
How Life Survives: UNC researchers confirm basic mechanism of DNA repair

| UNC News | Genetic Engineering News | Natural Science News | Phys.org | Bilim Dili (Turkish) |

2016

Researchers Develop Way to Better Predict Disease-Causing Mutations in Human Genes

| Tennessee Today | News Medical | Science Daily | Medical Express | Science Newsline |

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