Publications

Thesis:

• Söylev, Arda (2018),“Structural variation discovery using multiple sequence signatures”, Doctoral Dissertation, Bilkent University

• Söylev, Arda (2013),“Biyolojik Veritabanlarında Etkin Benzerlik Hesaplama”, Master of Science Thesis, TOBB Economy and Technology University

Unpublished preprints:

• Complex genetic variation in nearly complete human genomes Glennis A Logsdon, Peter Ebert, Peter A Audano, Mark Loftus, David Porubsky, Jana Ebler, Feyza Yilmaz, Pille Hallast, Timofey Prodanov, DongAhn Yoo, Carolyn A Paisie, William T Harvey, Xuefang Zhao, Gianni V Martino, Mir Henglin, Katherine M Munson, Keon Rabbani, Chen-Shan Chin, Bida Gu, Hufsah Ashraf, Olanrewaju Austine-Orimoloye, Parithi Balachandran, Marc Jan Bonder, Haoyu Cheng, Zechen Chong, Jonathan Crabtree, Mark Gerstein, Lisbeth A Guethlein, Patrick Hasenfeld, Glenn Hickey, Kendra Hoekzema, Sarah E Hunt, Matthew Jensen, Yunzhe Jiang, Sergey Koren, Youngjun Kwon, Chong Li, Heng Li, Jiaqi Li, Paul J Norman, Keisuke K Oshima, Benedict Paten, Adam M Phillippy, Nicholas R Pollock, Tobias Rausch, Mikko Rautiainen, Stephan Scholz, Yuwei Song, Arda Söylev, Arvis Sulovari, Likhitha Surapaneni, Vasiliki Tsapalou, Weichen Zhou, Ying Zhou, Qihui Zhu, Michael C Zody, Ryan E Mills, Scott E Devine, Xinghua Shi, Mike E Talkowski, Mark JP Chaisson, Alexander T Dilthey, Miriam K Konkel, Jan O Korbel, Charles Lee, Christine R Beck, Evan E Eichler, Tobias Marschall. bioRxiv (2024): 2024-09.

• Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project Siegfried Schloissnig, Samarendra Pani, Bernardo Rodriguez-Martin, Jana Ebler, Carsten Hain, Vasiliki Tsapalou, Arda Söylev, Patrick Hüther, Hufsah Ashraf, Timofey Prodanov, Mila Asparuhova, Sarah Hunt, Tobias Rausch, Tobias Marschall, Jan O. Korbel. bioRxiv (2024): 2024-04.

• SVarp: pangenome-based structural variant discovery Arda Söylev, Jana Ebler, Samarendra Pani, Tobias Rausch, Jan Korbel, Tobias Marschall. bioRxiv (2024): 2024-02.

Peer-Reviewed Journal Articles:

• Metabolic independence drives gut microbial colonization and resilience in health and disease. Andrea R. Watson, Jessika Füssel, Iva Veseli, Johanna Zaal DeLongchamp, Marisela Silva, Florian Trigodet, Karen Lolans, Alon Shaiber, Emily Fogarty, Joseph M. Runde, Christopher Quince, Michael K. Yu, Arda Söylev, Hilary G. Morrison, Sonny Lee, Dina Kao, David T. Rubin, Bana Jabri, Thomas Louie, A. Murat Eren. Genome Biology 24, no. 1 (2023): 1-21.

• MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes Atağ, Gözde, Kıvılcım Başak Vural, Damla Kaptan, Mustafa Özkan, Dilek Koptekin, Ekin Sağlıcan, Sevcan Doğramacı, Mevlüt Köz, Ardan Yılmaz, Arda Söylev, İnci Togan, Mehmet Somel, Füsun Özer. [version 3; peer review: 2 approved]. Open Res Europe 2023, 2:100.

• CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data. Arda Söylev, Sevim Seda Cokoglu, Dilek Koptekin, Can Alkan, and Mehmet Somel. PLOS Computational Biology 18, no. 12 (2022): e1010788.

• A comprehensive benchmarking of WGS-based deletion structural variant callers. Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Sei Chang, Angela Lu, Nicholas Darci-Maher, Russell Littman, Karishma Chhugani, Arda Soylev, Zoia Comarova, Emily Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G. Distler, Eleazar Eskin, Jonathan Flint, Serghei Mangul. Briefings in Bioinformatics 23, no. 4 (2022)

• An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. Ann M. Mc Cartney, Medhat Mahmoud, Michael Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev, Hakeem Almabrazi, Ahmed Arslan, Advait Balaji, Sairam Behera, Kimberley Billingsley, Daniel L Cameron, Joyjit Daw, Eric T. Dawson, Wouter De Coster, Haowei Du, Christopher Dunn, Rocio Esteban, Angad Jolly, Divya Kalra, Chunxiao Liao, Yunxi Liu, Tsung-Yu Lu, James M Havrilla, Michael M Khayat, Maximillian Marin, Jean Monlong, Stephen Price, Alejandro Rafael Gener, Jingwen Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Soylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J Sedlazeck. F1000Research (2021): 10(246), 246.

• A robust benchmark for germline large deletion and insertion detection. Justin M. Zook, Nancy F. Hansen, Nathan D. Olson, Lesley M. Chapman, James C. Mullikin, Chunlin Xiao, Stephen Sherry, Sergey Koren, Adam M, Phillippy, Paul C. Boutros, Sayed Mohammad E. Sahraeian, Vincent Huang, Alexandre Rouette, Noah Alexander, Christopher E. Mason, Iman Hajirasouliha, Camir Ricketts, Joyce Lee, Rick Tearle, Ian T. Fiddes, Alvaro Martinez-Barrio, Jeremiah Wala, Andrew Carroll, Noushin Ghaffari, Oscar L. Rodriguez, Ali Bashir, Shaun Jackman, John J. Farrell, Aaron M. Wenger, Can Alkan, Arda Soylev, Michael C. Schatz, Shilpa Garg, George Church, Tobias Marschall, Ken Chen, Xian Fan, Adam C. English, Jeffrey A. Rosenfeld, Weichen Zhou, Ryan E. Mills, Jay M. Sage, Jennifer R. Davis, Michael D. Kaiser, John S. Oliver, Anthony P. Catalano, Mark J.P. Chaisson, Noah Spies, Fritz J. Sedlazeck, Mark Salit. Nature Biotechnology (2020): 1-9.

• Discovery of tandem and interspersed segmental duplications using high throughput sequencing. Arda Soylev, Thong Le, Hajar Amini, Can Alkan and Fereydoun Hormozdiari. Bioinformatics (2019).

• Toolkit for automated and rapid discovery of structural variants. Arda Soylev, Can Kockan, Fereydoun Hormozdiari, and Can Alkan. Methods 129 (2017): 3-7.

• MOOCs 2.0: The Social Era of Education. Arda Soylev. Turkish Online Journal of Distance Education 18, no. 2 (2017): 56-67.

• Ses yalıtımında ses azaltım indisi modellerinin karşılaştırmalı olarak incelenmesi. Aksoylu, Ceyhun, Engin Mendi, and Arda Söylev. Journal of the Faculty of Engineering and Architecture of Gazi University 31.4 (2016): 961-970.