Items where Author is "Adebali, Ogün"

Article

Zhang, Jing and Kinch, Lisa and Katsonis, Panagiotis and Lichtarge, Olivier and Jagota, Milind and Song, Yun S. and Sun, Yuanfei and Shen, Yang and Kuru, Nurdan and Dereli, Onur and Adebali, Ogün and Alladin, Muttaqi Ahmad and Pal, Debnath and Capriotti, Emidio and Turina, Maria Paola and Savojardo, Castrense and Martelli, Pier Luigi and Babbi, Giulia and Casadio, Rita and Pucci, Fabrizio and Rooman, Marianne and Cia, Gabriel and Tsishyn, Matsvei and Strokach, Alexey and Hu, Zhiqiang and van Loggerenberg, Warren and Roth, Frederick P. and Radivojac, Predrag and Brenner, Steven E. and Cong, Qian and Grishin, Nick V. (2024) Assessing predictions on fitness effects of missense variants in HMBS in CAGI6. Human Genetics . ISSN 0340-6717 (Print) 1432-1203 (Online) Published Online First https://dx.doi.org/10.1007/s00439-024-02680-3

Bous, Julien and Kinsolving, Julia and Grätz, Lukas and Scharf, Magdalena M. and Voss, Jan Hendrik and Selçuk, Berkay and Adebali, Ogün and Schulte, Gunnar (2024) Structural basis of frizzled 7 activation and allosteric regulation. Nature Communications, 15 (1). ISSN 2041-1723

Dereli, Onur and Kuru, Nurdan and Akkoyun, Emrah and Bircan, Aylin and Taştan, Öznur and Adebali, Ogün (2024) PHACTboost: a phylogeny-aware pathogenicity predictor for missense mutations via boosting. Molecular Biology and Evolution, 41 (7). ISSN 0737-4038 (Print) 1537-1719 (Online)

Jain, Shantanu and Bakolitsa, Constantina and Brenner, Steven E. and Radivojac, Predrag and Moult, John and Repo, Susanna and Hoskins, Roger A. and Andreoletti, Gaia and Barsky, Daniel and Chellapan, Ajithavalli and Chu, Hoyin and Dabbiru, Navya and Kollipara, Naveen K. and Ly, Melissa and Neumann, Andrew J. and Pal, Lipika R. and Odell, Eric and Pandey, Gaurav and Peters-Petrulewicz, Robin C. and Srinivasan, Rajgopal and Yee, Stephen F. and Yeleswarapu, Sri Jyothsna and Zuhl, Maya and Adebali, Ogün and Patra, Ayoti and Beer, Michael A. and Hosur, Raghavendra and Peng, Jian and Bernard, Brady M. and Berry, Michael and Dong, Shengcheng and Boyle, Alan P. and Adhikari, Aashish and Chen, Jingqi and Hu, Zhiqiang and Wang, Robert and Wang, Yaqiong and Miller, Maximilian and Wang, Yanran and Bromberg, Yana and Turina, Paola and Capriotti, Emidio and Han, James J. and Ozturk, Kivilcim and Carter, Hannah and Babbi, Giulia and Bovo, Samuele and Di Lena, Pietro and Martelli, Pier Luigi and Savojardo, Castrense and Casadio, Rita and Cline, Melissa S. and De Baets, Greet and Bonache, Sandra and Díez, Orland and Gutiérrez-Enríquez, Sara and Fernández, Alejandro and Montalban, Gemma and Ootes, Lars and Özkan, Selen and Padilla, Natàlia and Riera, Casandra and De la Cruz, Xavier and Diekhans, Mark and Huwe, Peter J. and Wei, Qiong and Xu, Qifang and Dunbrack, Roland L. and Gotea, Valer and Elnitski, Laura and Margolin, Gennady and Fariselli, Piero and Kulakovskiy, Ivan V. and Makeev, Vsevolod J. and Penzar, Dmitry D. and Vorontsov, Ilya E. and Favorov, Alexander V. and Forman, Julia R. and Hasenahuer, Marcia and Fornasari, Maria S. and Parisi, Gustavo and Avsec, Ziga and Çelik, Muhammed H. and Nguyen, Thi Yen Duong and Gagneur, Julien and Shi, Fang Yuan and Edwards, Matthew D. and Guo, Yuchun and Tian, Kevin and Zeng, Haoyang and Gifford, David K. and Göke, Jonathan and Zaucha, Jan and Gough, Julian and Ritchie, Graham R.S. and Frankish, Adam and Mudge, Jonathan M. and Harrow, Jennifer and Young, Erin L. and Yu, Yao and Huff, Chad D. and Murakami, Katsuhiko and Nagai, Yoko and Imanishi, Tadashi and Mungall, Christopher J. and Jacobsen, Julius O.B. and Kim, Dongsup and Jeong, Chan Seok and Jones, David T. and Li, Mulin Jun and Guthrie, Violeta Beleva and Bhattacharya, Rohit and Chen, Yun Ching and Douville, Christopher and Fan, Jean and Kim, Dewey and Masica, David and Niknafs, Noushin and Sengupta, Sohini and Tokheim, Collin and Turner, Tychele N. and Yeo, Hui Ting Grace and Karchin, Rachel and Shin, Sunyoung and Welch, Rene and Keles, Sunduz and Li, Yue and Kellis, Manolis and Corbi-Verge, Carles and Strokach, Alexey V. and Kim, Philip M. and Klein, Teri E. and Mohan, Rahul and Sinnott-Armstrong, Nicholas A. and Wainberg, Michael and Kundaje, Anshul and Gonzaludo, Nina and Mak, Angel C.Y. and Chhibber, Aparna and Lam, Hugo Y.K. and Dahary, Dvir and Fishilevich, Simon and Lancet, Doron and Lee, Insuk and Bachman, Benjamin and Katsonis, Panagiotis and Lua, Rhonald C. and Wilson, Stephen J. and Lichtarge, Olivier and Bhat, Rajendra R. and Sundaram, Laksshman and Viswanath, Vivek and Bellazzi, Riccardo and Nicora, Giovanna and Rizzo, Ettore and Limongelli, Ivan and Mezlini, Aziz M. and Chang, Ray and Kim, Serra and Lai, Carmen and O’Connor, Robert and Topper, Scott and van den Akker, Jeroen and Zhou, Alicia Y. and Zimmer, Anjali D. and Mishne, Gilad and Bergquist, Timothy R. and Breese, Marcus R. and Guerrero, Rafael F. and Jiang, Yuxiang and Kiga, Nikki and Li, Biao and Mort, Matthew and Pagel, Kymberleigh A. and Pejaver, Vikas and Stamboulian, Moses H. and Thusberg, Janita and Mooney, Sean D. and Teerakulkittipong, Nuttinee and Cao, Chen and Kundu, Kunal and Yin, Yizhou and Yu, Chen Hsin and Kleyman, Michael and Lin, Chiao Feng and Stackpole, Mary and Mount, Stephen M. and Eraslan, Gökcen and Mueller, Nikola S. and Naito, Tatsuhiko and Rao, Aliz R. and Azaria, Johnathan R. and Brodie, Aharon and Ofran, Yanay and Garg, Aditi and Pal, Debnath and Hawkins-Hooker, Alex and Kenlay, Henry and Reid, John and Mucaki, Eliseos J. and Rogan, Peter K. and Schwarz, Jana M. and Searls, David B. and Lee, Gyu Rie and Seok, Chaok and Krämer, Andreas and Shah, Sohela and Huang, Cheng Lai V. and Kirsch, Jack F. and Shatsky, Maxim and Cao, Yue and Chen, Haoran and Karimi, Mostafa and Moronfoye, Oluwaseyi and Sun, Yuanfei and Shen, Yang and Shigeta, Ron and Ford, Colby T. and Nodzak, Conor and Uppal, Aneeta and Shi, Xinghua and Joseph, Thomas and Kotte, Sujatha and Rana, Sadhna and Rao, Aditya and Saipradeep, V. G. and Sivadasan, Naveen and Sunderam, Uma and Stanke, Mario and Su, Andrew and Adzhubey, Ivan and Jordan, Daniel M. and Sunyaev, Shamil and Rousseau, Frederic and Schymkowitz, Joost and Van Durme, Joost and Tavtigian, Sean V. and Carraro, Marco and Giollo, Manuel and Tosatto, Silvio C.E. and Adato, Orit and Carmel, Liran and Cohen, Noa E. and Fenesh, Tzila and Holtzer, Tamar and Juven-Gershon, Tamar and Unger, Ron and Niroula, Abhishek and Olatubosun, Ayodeji and Väliaho, Jouni and Yang, Yang and Vihinen, Mauno and Wahl, Mary E. and Chang, Billy and Chong, Ka Chun and Hu, Inchi and Sun, Rui and Wu, William Ka Kei and Xia, Xiaoxuan and Zee, Benny C. and Wang, Maggie H. and Wang, Meng and Wu, Chunlei and Lu, Yutong and Chen, Ken and Yang, Yuedong and Yates, Christopher M. and Kreimer, Anat and Yan, Zhongxia and Yosef, Nir and Zhao, Huying and Wei, Zhipeng and Yao, Zhaomin and Zhou, Fengfeng and Folkman, Lukas and Zhou, Yaoqi and Daneshjou, Roxana and Altman, Russ B. and Inoue, Fumitaka and Ahituv, Nadav and Arkin, Adam P. and Lovisa, Federica and Bonvini, Paolo and Bowdin, Sarah and Gianni, Stefano and Mantuano, Elide and Minicozzi, Velia and Novak, Leonore and Pasquo, Alessandra and Pastore, Annalisa and Petrosino, Maria and Puglisi, Rita and Toto, Angelo and Veneziano, Liana and Chiaraluce, Roberta and Ball, Mad P. and Bobe, Jason R. and Church, George M. and Consalvi, Valerio and Cooper, David N. and Buckley, Bethany A. and Sheridan, Molly B. and Cutting, Garry R. and Scaini, Maria Chiara and Cygan, Kamil J. and Fredericks, Alger M. and Glidden, David T. and Neil, Christopher and Rhine, Christy L. and Fairbrother, William G. and Alontaga, Aileen Y. and Fenton, Aron W. and Matreyek, Kenneth A. and Starita, Lea M. and Fowler, Douglas M. and Löscher, Britt Sabina and Franke, Andre and Adamson, Scott I. and Graveley, Brenton R. and Gray, Joe W. and Malloy, Mary J. and Kane, John P. and Kousi, Maria and Katsanis, Nicholas and Schubach, Max and Kircher, Martin and Mak, Angel C.Y. and Tang, Paul L.F. and Kwok, Pui Yan and Lathrop, Richard H. and Clark, Wyatt T. and Yu, Guoying K. and LeBowitz, Jonathan H. and Benedicenti, Francesco and Bettella, Elisa and Bigoni, Stefania and Cesca, Federica and Mammi, Isabella and Marino-Buslje, Cristina and Milani, Donatella and Peron, Angela and Polli, Roberta and Sartori, Stefano and Stanzial, Franco and Toldo, Irene and Turolla, Licia and Aspromonte, Maria C. and Bellini, Mariagrazia and Leonardi, Emanuela and Liu, Xiaoming and Marshall, Christian and McCombie, W. Richard and Elefanti, Lisa and Menin, Chiara and Meyn, M. Stephen and Murgia, Alessandra and Nadeau, Kari C.Y. and Neuhausen, Susan L. and Nussbaum, Robert L. and Pirooznia, Mehdi and Potash, James B. and Dimster-Denk, Dago F. and Rine, Jasper D. and Sanford, Jeremy R. and Snyder, Michael and Cote, Atina G. and Sun, Song and Verby, Marta W. and Weile, Jochen and Roth, Frederick P. and Tewhey, Ryan and Sabeti, Pardis C. and Campagna, Joan and Refaat, Marwan M. and Wojciak, Julianne and Grubb, Soren and Schmitt, Nicole and Shendure, Jay and Spurdle, Amanda B. and Stavropoulos, Dimitri J. and Walton, Nephi A. and Zandi, Peter P. and Ziv, Elad and Burke, Wylie and Chen, Flavia and Carr, Lawrence R. and Martinez, Selena and Paik, Jodi and Harris-Wai, Julie and Yarborough, Mark and Fullerton, Stephanie M. and Koenig, Barbara A. and McInnes, Gregory and Shigaki, Dustin and Chandonia, John Marc and Furutsuki, Mabel and Kasak, Laura and Yu, Changhua and Chen, Rui and Friedberg, Iddo and Getz, Gad A. and Cong, Qian and Kinch, Lisa N. and Zhang, Jing and Grishin, Nick V. and Voskanian, Alin and Kann, Maricel G. and Tran, Elizabeth and Ioannidis, Nilah M. and Hunter, Jesse M. and Udani, Rupa and Cai, Binghuang and Morgan, Alexander A. and Sokolov, Artem and Stuart, Joshua M. and Minervini, Giovanni and Monzon, Alexander M. and Batzoglou, Serafim and Butte, Atul J. and Greenblatt, Marc S. and Hart, Reece K. and Hernandez, Ryan and Hubbard, Tim J.P. and Kahn, Scott and O’Donnell-Luria, Anne and Ng, Pauline C. and Shon, John and Veltman, Joris and Zook, Justin M. (2024) CAGI, the critical assessment of genome interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology, 25 (1). ISSN 1474-7596 (Print) 1474-760X (Online)

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, 14 (1). ISSN 2045-2322

Kose, Cansu and Cao, Xuemei and Dewey, Evan B. and Malkoç, Mustafa and Adebali, Ogün and Sekelsky, Jeff and Lindsey-Boltz, Laura A. and Sancar, Aziz (2024) Cross-species investigation into the requirement of XPA for nucleotide excision repair. Nucleic Acids Research, 52 (2). pp. 677-689. ISSN 0305-1048 (Print) 1362-4962 (Online)

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, 13 (1). ISSN 2045-2322

Akköse, Ümit and Adebali, Ogün (2023) Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis. Turkish Journal of Biology, 47 (2). pp. 141-157. ISSN 1300-0152 (Print) 1303-6092 (Online)

Akköse, Ümit and Adebali, Ogün (2023) The interplay of 3D genome organization with UV-induced DNA damage and repair. Journal of Biological Chemistry, 299 (5). ISSN 0021-9258 (Print) 1083-351X (Online)

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, 299 (3). ISSN 0021-9258 (Print) 1083-351X (Online)

Nabi, Afshan and Dilekoğlu, Berke and Adebali, Ogün and Taştan, Öznur (2023) Discovering misannotated lncRNAs using deep learning training dynamics. Bioinformatics (Oxford, England), 39 (1). ISSN 1367-4803 (Print) 1367-4811 (Online)

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, 5 (11). ISSN 2575-1077

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, 5 (10). ISSN 2575-1077

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, 18 (9). ISSN 1553-7390 (Print) 1553-7404 (Online)

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, 39 (6). ISSN 0737-4038 (Print) 1537-1719 (Online)

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), 98 (3). pp. 707-712. ISSN 0031-8655 (Print) 1751-1097 (Online)

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, 119 (9). ISSN 0027-8424 (Print) 1091-6490 (Online)

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, 22 (1). ISSN 1471-2164 (Print) 1471-2164 (Online)

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, 45 (6). pp. 667-673. ISSN 1300-0152 (Print) 1303-6092 (Online)

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, 34 (4). pp. 417-430. ISSN 0334-018X (Print) 2191-0251 (Online)

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, 13 (3). ISSN 1999-4915

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, 25 . ISSN 2214-4269

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, 8 (2). pp. 73-88. ISSN 1301-109X

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), 44 (3). pp. 146-156. ISSN 1300-0152 (Print) 1303-6092 (Online)

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, 48 (D1). D459-D464. ISSN 0305-1048 (Print) 1362-4962 (Online)

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, 294 (15). pp. 5914-5922. ISSN 0021-9258 (Print) 1083-351X (Online)

Li, Wentao and Liu, Wenjie and Kakoki, Ayano and Wang, Rujin and Adebali, Ogün and Jiang, Yuchao and Sancar, Aziz (2019) Differential damage and repair of anti-cancer drug cisplatin induced DNA-adducts across mouse organs. (Accepted)

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, 10 (1). ISSN 2041-1723

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, 14 (1). pp. 248-282. ISSN 1754-2189 (Print) 1750-2799 (Online)

Book Section / Chapter

Selçuk, Berkay and Adebali, Ogün (2022) Common and selective signal transduction mechanisms of GPCRs. Progress in Molecular Biology and Translational Science. Elsevier.