Journal Articles

  1. Akkose U., Adebali O. (2023)
    The interplay of 3D genome organization with UV-induced DNA damage and repair
    Journal of Biological Chemistry.

  2. Akkose U., Adebali O. (2023)
    Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis
    Turkish Journal of Biology.

  3. Adebali O., Yang Y., Neupane P., Dike N.I., Boltz J.L., Kose C., Braunstein M., Selby C.P., Sancar A., Lindsey-Boltz L.A. (2023)
    The Mfd protein is the Transcription-Repair Coupling Factor (TRCF) in Mycobacterium smegmatis
    Journal of Biological Chemistry, 299(3), 103009.

  4. Nabi A., Dilekoglu B., Adebali O., Tastan O. (2022)
    Discovering Misannotated lncRNAs using Deep Learning Training Dynamics
    Bioinformatics, 39(1), btac821.

  5. Huang Y., Azgari C., Yin M., Chiou Y., Lindsey-Boltz L.A., Sancar A., Hu J., Adebali O. (2022)
    Effects of replication domains on genome-wide UV-induced DNA damage and repair
    PLOS Genetics, 9(18), e1010426.

  6. Piepoli S., Barakat S., Nogay L., Simsek B., Akkose U., Taskiran H., Tolay N., Gezen M., Yesilada C.Y., Tuncay M., Adebali O., Atilgan C., Erman B. (2022)
    Sibling rivalry among the ZBTB transcription factor family: homodimers versus heterodimers
    Life Science Alliance, 5(11), e202201474.

  7. Kuru N, Dereli O, Akkoyun E, Bircan A, Tastan O, Adebali O. (2022)
    PHACT: Phylogeny-Aware Computing of Tolerance for Missense Mutations
    Molecular Biology and Evolution, 39(6), msac114.

  8. Selcuk B., Erol I., Durdagi S., Adebali O. (2022)
    Evolutionary association of receptor-wide amino acids with G protein-coupling selectivity in aminergic GPCRs
    Life Science Alliance, 5(10), e202201439.

  9. Deger N, Cao X, Selby CP, Gulec S, Kawara H, Dewey EB, Wang L, Yang Y, Archibald S, Selcuk B, Adebali O, Sekelsky J, Sancar A, Liu Z. (2022)
    CSB-independent, XPC-dependent transcription-coupled repair in Drosophila.
    Proc Natl Acad Sci U S A., 119(9), e2123163119.

  10. Ozcelik E., Kuru N., Adebali O. (2021)
    Phylostat: a web-based tool to analyze paralogous clade divergence in phylogenetic trees
    Turkish Journal of Biology, 45, 667-673.

  11. 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).

  12. 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.

  13. Kose M., Isik E., Aykut A., Durmaz A., Kose E., Ersoy M., Diniz G., Adebali O., Ünalp A., Yilmaz Ü., Karaoğlu P., Edizer S., Tekin H.G., Özdemir T.R., Atik T., Onay H., Özkınay F. (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, 34(4), 417-430.

  14. 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, 25, 100657.

  15. Piepoli S., Shamloo B., Bircan A., Adebali O., Erman B. (2020)
    Molecular Biology of SARS-CoV-2
    Turkish Journal of Immunology, 2(8), 73-88.

  16. 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.

  17. 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 Acids Research, 48(D1), D459–D464.

  18. 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, 15(294), 5914–5922.

  19. 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.

  20. 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 (Featured: From the Cover), 14(1), 248-282.

  21. 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.
    Proceedings of the National Academy of Sciences of the United States Of America, 21(115), E4777-E4785.

  22. 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.

  23. 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.
    Proceedings of the National Academy of Sciences of the United States Of America, 115(15), E3408-E3415.

  24. 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.

  25. 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.

  26. Hu J., Adebali O., Adar S., Sancar A. (2017)
    Dynamic maps of UV damage formation and repair.
    Proceedings of the National Academy of Sciences of the United States Of America, 114(26), 6758-6763.

  27. 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.
    Proceedings of the National Academy of Sciences of the United States Of America, 114(26), 6752-6757.

  28. 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.

  29. 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.

  30. 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 - Structure Function and Bioinformatics, 85(1), 72-77.

  31. 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).

  32. 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.

  33. 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.

# Equal Contribution | * Corresponding Author