| Mühendislik ve Doğa Bilimleri Fakültesi

Ogün Adebali Mühendislik ve Doğa Bilimleri Fakültesi Öğretim Üyesi (216) 568 7043 ogunadebalisabanciunivedu

Personal Web

http://adebalilab.org

Jobs

Öğretim Üyesi

Areas of Interest

Hesaplamali Genomik, Protein Enformatiği, Moleküler Evrim, DNA Hasarı ve Onarımı

Memberships

Ekiloji ve Evrimsel Biyoloji Derneği Moleküler Biyoloji Derneği

Kaya, Sezgi and Erdogan, Dugcar Ebrar and Sancar, Aziz and Adebali, Ogün and Oztas, Onur (2024) "Global repair is the primary nucleotide excision repair subpathway for the removal of pyrimidine-pyrimidone (6-4) damage from the Arabidopsis genome", Scientific Reports, Vol.14, No.1 (SCI)

Selçuk, Berkay and Aksu, Tuana and Dereli, Onur and Adebali, Ogün (2023) "Downregulated NPAS4 in multiple brain regions is associated with major depressive disorder", Scientific Reports, Vol.13, No.1 (SCI)

Akköse, Ümit and Adebali, Ogün (2023) "Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis", Turkish Journal of Biology, Vol.47, No.2, 141-157 (SCI)

Akköse, Ümit and Adebali, Ogün (2023) "The interplay of 3D genome organization with UV-induced DNA damage and repair", Journal of Biological Chemistry, Vol.299, No.5 (SCI)

Adebali, Ogün and Yang, Yanyan and Neupane, Pradeep and Dike, Nneka I. and Boltz, Julia L. and Kose, Cansu and Braunstein, Miriam and Selby, Christopher P. and Sancar, Aziz and Lindsey-Boltz, Laura A. (2023) "The Mfd protein is the transcription-repair coupling factor (TRCF) in Mycobacterium smegmatis", Journal of Biological Chemistry, Vol.299, No.3 (SCI)

Nabi, Afshan and Dilekoğlu, Berke and Adebali, Ogün and Taştan, Öznur (2023) "Discovering misannotated lncRNAs using deep learning training dynamics", Bioinformatics (Oxford, England), Vol.39, No.1 (SCI)

Piepoli, Sofia and Barakat, Sarah Mohammed Mohammed and Noğay, Liyne and Şimşek, Büşra and Akköse, Ümit and Taşkıran, Hakan and Tolay, Nazife and Gezen, Melike and Yeşilada, Canberk Yarkın and Tuncay, Mustafa and Adebali, Ogün and Atılgan, Canan and Erman, Batu (2022) "Sibling rivalry among the ZBTB transcription factor family: homodimers versus heterodimers", Life Science Alliance, Vol.5, No.11 (SCI)

Selçuk, Berkay and Erol, İsmail and Durdağı, Serdar and Adebali, Ogün (2022) "Evolutionary association of receptor-wide amino acids with G protein-coupling selectivity in aminergic GPCRs", Life Science Alliance, Vol.5, No.10 (SCI)

Huang, Yanchao and Azgari, Cem and Yin, Mengdie and Chiou, Yi Ying and Lindsey-Boltz, Laura A. and Sancar, Aziz and Hu, Jinchuan and Adebali, Ogün (2022) "Effects of replication domains on genomewide UV-induced DNA damage and repair", PLoS Genetics, Vol.18, No.9 (SCI)

Kuru, Nurdan and Dereli, Onur and Akkoyun, Emrah and Bircan, Aylin and Taştan, Öznur and Adebali, Ogün (2022) "PHACT: phylogeny-aware computing of tolerance for missense mutations", Molecular Biology and Evolution, Vol.39, No.6 (SCI)

Kaya, Sezgi and Adebali, Ogün and Oztas, Onur and Sancar, Aziz (2022) "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 (SI), Vol.98, No.3, 707-712 (SCI)

Deger, Nazli and Cao, Xuemei and Selby, Christopher P. and Gulec, Saygin and Kawara, Hiroaki and Dewey, Evan B. and Wang, Li and Yang, Yanyan and Archibald, Sierra and Selçuk, Berkay and Adebali, Ogün and Sekelsky, Jeff and Sancar, Aziz and Liu, Zhenxing (2022) "CSB-independent, XPC-dependent transcription-coupled repair in Drosophila", Proceedings of the National Academy of Sciences of the United States of America, Vol.119, No.9 (SCI)

Akköse, Ümit and Kaya, Veysel Oğulcan and Lindsey-Boltz, Laura and Karagöz, Zeynep and Brown, Adam D. and Larsen, Peter A. and Yoder, Anne D. and Sancar, Aziz and Adebali, Ogün (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, Vol.22, No.1 (SCI)

Özçelik, Elif and Kuru, Nurdan and Adebali, Ogün (2021) "Phylostat: a web-based tool to analyze paralogous clade divergence in phylogenetic trees", Turkish Journal of Biology, Vol.45, No.6, 667-673 (SCI)

Kose, Melis and Isik, Esra and Aykut, Ayça and Durmaz, Asude and Kose, Engin and Ersoy, Melike and Diniz, Gulden and Adebali, Ogün and Ünalp, Aycan and Yilmaz, Ünsal and Karaoǧlu, Pakize and Edizer, Selvinaz and Tekin, Hande Gazeteci and Özdemir, Taha Reşid and Atik, Tahir and Onay, Hüseyin and Özklnay, Ferda (2021) "The utility of next-generation sequencing technologies in diagnosis of Mendelian mitochondrial diseases and reflections on clinical spectrum", Journal of Pediatric Endocrinology and Metabolism, Vol.34, No.4, 417-430 (SCI)

Azgari, Cem and Kılınç, Zeynep and Turhan, Berk and Çirci, Defne and Adebali, Ogün (2021) "The mutation profile of SARS-CoV-2 is primarily shaped by the host antiviral defense", Viruses, Vol.13, No.3 (SCI)

Kose, Melis and Canda, Ebru and Kagnici, Mehtap and Aykut, Ayça and Adebali, Ogün and Durmaz, Asude and Bircan, Aylin and Diniz, Gulden and Eraslan, Cenk and Kose, Engin and Ünalp, Aycan and Yılmaz, Ünsal and Ozyilmaz, Berk and Özdemir, Taha Reşid and Atik, Tahir and Uçar, Sema Kalkan and McFarland, Robert and Taylor, Robert W. and Brown, Garry K. and Çoker, Mahmut and Özkınay, Ferda (2020) "SURF1 related Leigh syndrome: clinical and molecular findings of 16 patients from Turkey", Molecular Genetics and Metabolism Reports, Vol.25 (SCI)

Piepoli, Sofia and Shamloo, Bahar and Bircan, Aylin and Adebali, Ogün and Erman, Batu (2020) "Molecular biology of sars-cov-2 [Sars-cov-2'nin moleküler biyolojisi]", Turkish Journal of Immunology, Vol.8, No.2, 73-88 (ESCI)

Adebali, Ogün and Bircan, Aylin and Çirci, Defne and İşlek, Burak and Kilinçer, Zeynep and Selçuk, Berkay and Turhan, Berk (2020) "Phylogenetic analysis of sars-cov-2 genomes in Turkey", Turkish Journal of Biology (SI), Vol.44, No.3, 146-156 (SCI)

Gumerov, Vadim M. and Ortega, Davi R. and Adebali, Ogün and Ulrich, Luke E. and Zhulin, Igor B. (2020) "MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems", Nucleic Acid Research, Vol.48, No.D1, D459-D464 (SCI)

Li, Wentao and Liu, Wenjie and Kakoki, Ayano and Wang, Rujin and Adebali, Ogün and Jiang, Yuchao and Sancar, Aziz (2019) "Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells", Journal of Biological Chemistry, Vol.294, No.15, 5914-5922 (SCI)

Askar, Yimit and Adebali, Ogün and Sancar, Aziz and Jiang, Yuchao (2019) "Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs", Nature Communicaitons, Vol.10, No.1 (SCI)

Hu, Jinchuan and Li, Wentao and Adebali, Ogün and Yang, Yanyan and Öztaş, Onur and Selby, Christopher P. and Sancar, Aziz (2019) "Genome-wide mapping of nucleotide excision repair with XR-seq", Nature Protocols, Vol.14, No.1, 248-282 (SCI)

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, 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.

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