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ORCIDBibTeX records: Süleyman Cenk Sahinalp
@article{DBLP:journals/ncs/KizilkaleMAPMLD22,
author = {Can Kizilkale and
Farid Rashidi Mehrabadi and
Erfan Sadeqi Azer and
Eva P{\'{e}}rez{-}Guijarro and
Kerrie Marie and
Maxwell P. Lee and
Chi{-}Ping Day and
Glenn Merlino and
Funda Erg{\"{u}}n and
Aydin Bulu{\c{c}} and
S{\"{u}}leyman Cenk Sahinalp and
Salem Malikic},
title = {Fast intratumor heterogeneity inference from single-cell sequencing
data},
journal = {Nat. Comput. Sci.},
volume = {2},
number = {9},
pages = {577--583},
year = {2022},
url = {https://doi.org/10.1038/s43588-022-00298-x},
doi = {10.1038/S43588-022-00298-X},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ncs/KizilkaleMAPMLD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/FordHRXLOZWMBXS22,
author = {Michael Ford and
Ananth Hari and
Oscar Rodriguez and
Junyan Xu and
Justin Lack and
Cihan Oguz and
Yu Zhang and
Sarah Weber and
Mary Magliocco and
Jason Barnett and
Sandhya Xirasagar and
Smilee Samuel and
Luisa Imberti and
Paolo Bonfanti and
Andrea Biondi and
Clifton L. Dalgard and
Stephen J. Chanock and
Lindsey Rosen and
Steven Holland and
Helen Su and
Luigi Notarangelo and
Uzi Vishkin and
Corey Watson and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Itsik Pe'er},
title = {ImmunoTyper-SR: {A} Novel Computational Approach for Genotyping Immunoglobulin
Heavy Chain Variable Genes Using Short Read Data},
booktitle = {Research in Computational Molecular Biology - 26th Annual International
Conference, {RECOMB} 2022, San Diego, CA, USA, May 22-25, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13278},
pages = {382--384},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-04749-7\_37},
doi = {10.1007/978-3-031-04749-7\_37},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/FordHRXLOZWMBXS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MalikicMAES21,
author = {Salem Malikic and
Farid Rashidi Mehrabadi and
Erfan Sadeqi Azer and
Mohammad Haghir Ebrahim{-}Abadi and
S{\"{u}}leyman Cenk Sahinalp},
title = {Studying the History of Tumor Evolution from Single-Cell Sequencing
Data by Exploring the Space of Binary Matrices},
journal = {J. Comput. Biol.},
volume = {28},
number = {9},
pages = {857--879},
year = {2021},
url = {https://doi.org/10.1089/cmb.2020.0595},
doi = {10.1089/CMB.2020.0595},
timestamp = {Wed, 03 Nov 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/MalikicMAES21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AzerMMLBLLSSGDP20,
author = {Erfan Sadeqi Azer and
Farid Rashidi Mehrabadi and
Salem Malikic and
Xuan Cindy Li and
Osnat Bartok and
Kevin Litchfield and
Ronen Levy and
Yardena Samuels and
Alejandro A. Sch{\"{a}}ffer and
E. Michael Gertz and
Chi{-}Ping Day and
Eva P{\'{e}}rez{-}Guijarro and
Kerrie Marie and
Maxwell P. Lee and
Glenn Merlino and
Funda Erg{\"{u}}n and
S{\"{u}}leyman Cenk Sahinalp},
title = {PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor
phylogeny reconstruction problem},
journal = {Bioinform.},
volume = {36},
number = {Supplement-1},
pages = {i169--i176},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa464},
doi = {10.1093/BIOINFORMATICS/BTAA464},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AzerMMLBLLSSGDP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HodzicSMCLTS20,
author = {Ermin Hodzic and
Raunak Shrestha and
Salem Malikic and
Colin C. Collins and
Kevin Litchfield and
Samra Turajlic and
S{\"{u}}leyman Cenk Sahinalp},
title = {Identification of conserved evolutionary trajectories in tumors},
journal = {Bioinform.},
volume = {36},
number = {Supplement-1},
pages = {i427--i435},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa453},
doi = {10.1093/BIOINFORMATICS/BTAA453},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HodzicSMCLTS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BoroojenySSGSC20,
author = {Ali Ebrahimpour Boroojeny and
Akash Shrestha and
Ali Sharifi{-}Zarchi and
Suzanne Renick Gallagher and
S{\"{u}}leyman Cenk Sahinalp and
Hamidreza Chitsaz},
title = {Graph Traversal Edit Distance and Extensions},
journal = {J. Comput. Biol.},
volume = {27},
number = {3},
pages = {317--329},
year = {2020},
url = {https://doi.org/10.1089/cmb.2019.0511},
doi = {10.1089/CMB.2019.0511},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/BoroojenySSGSC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BoroojenySSGSC20a,
author = {Ali Ebrahimpour Boroojeny and
Akash Shrestha and
Ali Sharifi{-}Zarchi and
Suzanne Renick Gallagher and
S{\"{u}}leyman Cenk Sahinalp and
Hamidreza Chitsaz},
title = {PyGTED: Python Application for Computing Graph Traversal Edit Distance},
journal = {J. Comput. Biol.},
volume = {27},
number = {3},
pages = {436--439},
year = {2020},
url = {https://doi.org/10.1089/cmb.2019.0510},
doi = {10.1089/CMB.2019.0510},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/BoroojenySSGSC20a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/RheinbayNAWSTHH20,
author = {Esther Rheinbay and
Morten Muhlig Nielsen and
Federico Abascal and
Jeremiah Wala and
Ofer Shapira and
Grace Tiao and
Henrik Hornsh{\o}j and
Julian M. Hess and
Randi Istrup Juul and
Ziao Lin and
Lars Feuerbach and
Radhakrishnan Sabarinathan and
Tobias Madsen and
Jaegil Kim and
Loris Mularoni and
Shimin Shuai and
Andr{\'{e}}s Lanz{\'{o}}s and
Carl Herrmann and
Yosef E. Maruvka and
Ciyue Shen and
Samirkumar B. Amin and
Pratiti Bandopadhayay and
Johanna Bertl and
Keith A. Boroevich and
John Busanovich and
Joana Carlevaro{-}Fita and
Dimple Chakravarty and
Calvin Wing Yiu Chan and
David Craft and
Priyanka Dhingra and
Klev Diamanti and
Nuno A. Fonseca and
Abel Gonzalez{-}Perez and
Qianyun Guo and
Mark P. Hamilton and
Nicholas J. Haradhvala and
Chen Hong and
Keren Isaev and
Todd A. Johnson and
Malene Juul and
Andr{\'{e}} Kahles and
Abdullah Kahraman and
Youngwook Kim and
Jan Komorowski and
Kiran Kumar and
Sushant Kumar and
Donghoon Lee and
Kjong{-}Van Lehmann and
Yilong Li and
Eric Minwei Liu and
Lucas Lochovsky and
Keunchil Park and
Oriol Pich and
Nicola D. Roberts and
Gordon Saksena and
Steven E. Schumacher and
Nikos Sidiropoulos and
Lina Sieverling and
Nasa Sinnott{-}Armstrong and
Chip Stewart and
David Tamborero and
Jose M. C. Tubio and
Husen M. Umer and
Liis Uusk{\"{u}}la{-}Reimand and
Claes Wadelius and
Lina Wadi and
Xiaotong Yao and
Cheng{-}Zhong Zhang and
Jing Zhang and
James E. Haber and
Asger Hobolth and
Marcin Imielinski and
Manolis Kellis and
Michael S. Lawrence and
Christian von Mering and
Hidewaki Nakagawa and
Benjamin J. Raphael and
Mark A. Rubin and
Chris Sander and
Lincoln D. Stein and
Joshua M. Stuart and
Tatsuhiko Tsunoda and
David A. Wheeler and
Rory Johnson and
J{\"{u}}ri Reimand and
Mark Gerstein and
Ekta Khurana and
Peter J. Campbell and
N{\'{u}}ria L{\'{o}}pez{-}Bigas and
Gary D. Bader and
Jonathan Barenboim and
Rameen Beroukhim and
S{\o}ren Brunak and
Ken Chen and
Jung Kyoon Choi and
Jordi Deu{-}Pons and
J. Lynn Fink and
Joan Frigola and
Carlo Gambacorti Passerini and
Dale W. Garsed and
Gad Getz and
Ivo Glynne Gut and
David Haan and
Arif Ozgun Harmanci and
Mohamed Helmy and
Ermin Hodzic and
Jos{\'{e}} M. G. Izarzugaza and
Jong K. Kim and
Jan O. Korbel and
Erik Larsson and
Shantao Li and
Xiaotong Li and
Shaoke Lou and
Kathleen Marchal and
I{\~{n}}igo Martincorena and
Alexander Mart{\'{\i}}nez{-}Fundichely and
Patrick D. McGillivray and
William Meyerson and
Ferran Mui{\~{n}}os and
Marta Paczkowska and
Kiejung Park and
Jakob Skou Pedersen and
Tirso Pons and
Sergio Pulido{-}Tamayo and
Iker Reyes{-}Salazar and
Matthew A. Reyna and
Carlota Rubio{-}Perez and
S{\"{u}}leyman Cenk Sahinalp and
Leonidas Salichos and
Mark Shackleton and
Raunak Shrestha and
Alfonso Valencia and
Miguel Vazquez and
Lieven P. C. Verbeke and
Jiayin Wang and
Jonathan Warrell and
Sebastian M. Waszak and
Joachim Weischenfeldt and
Guanming Wu and
Jun Yu and
Xuanping Zhang and
Yan Zhang and
Zhongming Zhao and
Lihua Zou and
Kadir C. Akdemir and
Eva G. Alvarez and
Adrian Baez{-}Ortega and
Paul C. Boutros and
David D. L. Bowtell and
Benedikt Brors and
Kathleen H. Burns and
Kin Chan and
Isidro Cort{\'{e}}s{-}Ciriano and
Ana Dueso{-}Barroso and
Andrew J. Dunford and
Paul A. Edwards and
Xavier Estivill and
Dariush Etemadmoghadam and
Milana Frenkel{-}Morgenstern and
Dmitry A. Gordenin and
Barbara Hutter and
David T. W. Jones and
Young Seok Ju and
Marat D. Kazanov and
Leszek J. Klimczak and
Youngil Koh and
Eunjung Alice Lee and
Jake June{-}Koo Lee and
Andy G. Lynch and
Geoff MacIntyre and
Florian Markowetz and
Matthew Meyerson and
Satoru Miyano and
Fabio C. P. Navarro and
Stephan Ossowski and
Peter J. Park and
John V. Pearson and
Montserrat Puiggr{\`{o}}s and
Karsten Rippe and
Steven A. Roberts and
Bernardo Rodriguez{-}Martin and
Ralph Scully and
David Torrents and
Izar Villasante and
Nicola Waddell and
Jeremiah A. Wala and
Lixing Yang and
Sung{-}Soo Yoon and
Jorge Zamora},
title = {Analyses of non-coding somatic drivers in 2,658 cancer whole genomes},
journal = {Nat.},
volume = {578},
number = {7793},
pages = {102--111},
year = {2020},
url = {https://doi.org/10.1038/s41586-020-1965-x},
doi = {10.1038/S41586-020-1965-X},
timestamp = {Thu, 11 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/RheinbayNAWSTHH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/GerstungJLDGRMR20,
author = {Moritz Gerstung and
Clemency Jolly and
Ignaty Leshchiner and
Stefan C. Dentro and
Santiago Gonzalez and
Thomas J. Mitchell and
Yulia Rubanova and
Pavana Anur and
Kaixian Yu and
Maxime Tarabichi and
Amit G. Deshwar and
Jeff Wintersinger and
Kortine Kleinheinz and
Ignacio V{\'{a}}zquez{-}Garc{\'{\i}}a and
Kerstin Haase and
Lara Jerman and
Subhajit Sengupta and
Geoff MacIntyre and
Salem Malikic and
Nilgun Donmez and
Dimitri G. Livitz and
Marek Cmero and
Jonas Demeulemeester and
Steven E. Schumacher and
Yu Fan and
Xiaotong Yao and
Juhee Lee and
Matthias Schlesner and
Paul C. Boutros and
David D. L. Bowtell and
Hongtu Zhu and
Gad Getz and
Marcin Imielinski and
Rameen Beroukhim and
S{\"{u}}leyman Cenk Sahinalp and
Yuan Ji and
Martin Peifer and
Florian Markowetz and
Ville Mustonen and
Ke Yuan and
Wenyi Wang and
Quaid D. Morris and
David J. Adams and
Peter J. Campbell and
Shaolong Cao and
Elizabeth L. Christie and
Yupeng Cun and
Kevin J. Dawson and
Ruben M. Drews and
Roland Eils and
Matthew Fittall and
Dale W. Garsed and
Gavin Ha and
Henry Lee{-}Six and
I{\~{n}}igo Martincorena and
Layla Oesper and
Myron Peto and
Benjamin J. Raphael and
Daniel T. Rosebrock and
Adriana Salcedo and
Ruian Shi and
Seung Jun Shin and
Oliver Spiro and
Lincoln D. Stein and
Shankar Vembu and
David A. Wheeler and
Tsun{-}Po Yang and
Paul T. Spellman and
David C. Wedge and
Peter Van Loo},
title = {The evolutionary history of 2,658 cancers},
journal = {Nat.},
volume = {578},
number = {7793},
pages = {122--128},
year = {2020},
url = {https://doi.org/10.1038/s41586-019-1907-7},
doi = {10.1038/S41586-019-1907-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/GerstungJLDGRMR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KarpovMRS19,
author = {Nikolai Karpov and
Salem Malikic and
Md. Khaledur Rahman and
S{\"{u}}leyman Cenk Sahinalp},
title = {A multi-labeled tree dissimilarity measure for comparing "clonal
trees" of tumor progression},
journal = {Algorithms Mol. Biol.},
volume = {14},
number = {1},
pages = {17:1--17:18},
year = {2019},
url = {https://doi.org/10.1186/s13015-019-0152-9},
doi = {10.1186/S13015-019-0152-9},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/KarpovMRS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HaghshenasSH19,
author = {Ehsan Haghshenas and
S{\"{u}}leyman Cenk Sahinalp and
Faraz Hach},
title = {lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy
Read sequencing Data},
journal = {Bioinform.},
volume = {35},
number = {1},
pages = {20--27},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty544},
doi = {10.1093/BIOINFORMATICS/BTY544},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HaghshenasSH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/0001BS19,
author = {Sean Simmons and
Bonnie Berger and
Cenk S. Sahinalp},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Marylyn D. Ritchie and
Teri E. Klein},
title = {Protecting Genomic Data Privacy with Probabilistic Modeling},
booktitle = {Biocomputing 2019: Proceedings of the Pacific Symposium, The Big Island
of Hawaii, Hawaii, USA, January 3-7, 2019},
pages = {403--414},
year = {2019},
url = {http://psb.stanford.edu/psb-online/proceedings/psb19/simmons.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/0001BS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/KockanZDKKWS19,
author = {Can Kockan and
Kaiyuan Zhu and
Natnatee Dokmai and
Nikolai Karpov and
M. Oguzhan K{\"{u}}lekci and
David P. Woodruff and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Lenore J. Cowen},
title = {Sketching Algorithms for Genomic Data Analysis and Querying in a Secure
Enclave},
booktitle = {Research in Computational Molecular Biology - 23rd Annual International
Conference, {RECOMB} 2019, Washington, DC, USA, May 5-8, 2019, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {11467},
pages = {302--304},
publisher = {Springer},
year = {2019},
url = {https://link.springer.com/content/pdf/bbm\%3A978-3-030-17083-7\%2F1.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/KockanZDKKWS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/bdt/ZhuNS19,
author = {Kaiyuan Zhu and
Ibrahim Numanagic and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Sherif Sakr and
Albert Y. Zomaya},
title = {Genomic Data Compression},
booktitle = {Encyclopedia of Big Data Technologies},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-319-63962-8\_55-1},
doi = {10.1007/978-3-319-63962-8\_55-1},
timestamp = {Thu, 14 Feb 2019 16:03:55 +0100},
biburl = {https://dblp.org/rec/reference/bdt/ZhuNS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LinGHLNSMMCRTS18,
author = {Yen{-}Yi Lin and
Alexander Gawronski and
Faraz Hach and
Sujun Li and
Ibrahim Numanagic and
Iman Sarrafi and
Swati Mishra and
Andrew W. McPherson and
Colin C. Collins and
Milan Radovich and
Haixu Tang and
S{\"{u}}leyman Cenk Sahinalp},
title = {Computational identification of micro-structural variations and their
proteogenomic consequences in cancer},
journal = {Bioinform.},
volume = {34},
number = {10},
pages = {1672--1681},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx807},
doi = {10.1093/BIOINFORMATICS/BTX807},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LinGHLNSMMCRTS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GawronskiUZLNRM18,
author = {Alexander Gawronski and
Michael Uhl and
Yajia Zhang and
Yen{-}Yi Lin and
Yashar S. Niknafs and
Varune R. Ramnarine and
Rohit Malik and
Felix Feng and
Arul M. Chinnaiyan and
Colin C. Collins and
S{\"{u}}leyman Cenk Sahinalp and
Rolf Backofen},
title = {MechRNA: prediction of lncRNA mechanisms from {RNA-RNA} and RNA-protein
interactions},
journal = {Bioinform.},
volume = {34},
number = {18},
pages = {3101--3110},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty208},
doi = {10.1093/BIOINFORMATICS/BTY208},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GawronskiUZLNRM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Sahinalp18,
author = {Cenk S. Sahinalp},
title = {Preface: Selected Articles from {RECOMB} 2017},
journal = {J. Comput. Biol.},
volume = {25},
number = {7},
pages = {623},
year = {2018},
url = {https://doi.org/10.1089/cmb.2018.29017.cs},
doi = {10.1089/CMB.2018.29017.CS},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/Sahinalp18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tkde/YamadaTLHSSOYMS18,
author = {Makoto Yamada and
Jiliang Tang and
Jose Lugo{-}Martinez and
Ermin Hodzic and
Raunak Shrestha and
Avishek Saha and
Hua Ouyang and
Dawei Yin and
Hiroshi Mamitsuka and
S{\"{u}}leyman Cenk Sahinalp and
Predrag Radivojac and
Filippo Menczer and
Yi Chang},
title = {Ultra High-Dimensional Nonlinear Feature Selection for Big Biological
Data},
journal = {{IEEE} Trans. Knowl. Data Eng.},
volume = {30},
number = {7},
pages = {1352--1365},
year = {2018},
url = {https://doi.org/10.1109/TKDE.2018.2789451},
doi = {10.1109/TKDE.2018.2789451},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tkde/YamadaTLHSSOYMS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BoroojenySSGSC18,
author = {Ali Ebrahimpour Boroojeny and
Akash Shrestha and
Ali Sharifi{-}Zarchi and
Suzanne Renick Gallagher and
S{\"{u}}leyman Cenk Sahinalp and
Hamidreza Chitsaz},
editor = {Benjamin J. Raphael},
title = {{GTED:} Graph Traversal Edit Distance},
booktitle = {Research in Computational Molecular Biology - 22nd Annual International
Conference, {RECOMB} 2018, Paris, France, April 21-24, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10812},
pages = {37--53},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-319-89929-9\_3},
doi = {10.1007/978-3-319-89929-9\_3},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BoroojenySSGSC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/MalikicJKSB18,
author = {Salem Malikic and
Katharina Jahn and
Jack Kuipers and
S{\"{u}}leyman Cenk Sahinalp and
Niko Beerenwinkel},
editor = {Benjamin J. Raphael},
title = {Integrative Inference of Subclonal Tumour Evolution from Single-Cell
and Bulk Sequencing Data},
booktitle = {Research in Computational Molecular Biology - 22nd Annual International
Conference, {RECOMB} 2018, Paris, France, April 21-24, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10812},
pages = {269--270},
publisher = {Springer},
year = {2018},
url = {https://link.springer.com/content/pdf/bbm\%3A978-3-319-89929-9\%2F1.pdf},
timestamp = {Thu, 09 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/MalikicJKSB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/KarpovMRS18,
author = {Nikolai Karpov and
Salem Malikic and
Md. Khaledur Rahman and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Laxmi Parida and
Esko Ukkonen},
title = {A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees"
of Tumor Progression},
booktitle = {18th International Workshop on Algorithms in Bioinformatics, {WABI}
2018, August 20-22, 2018, Helsinki, Finland},
series = {LIPIcs},
volume = {113},
pages = {22:1--22:19},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2018},
url = {https://doi.org/10.4230/LIPIcs.WABI.2018.22},
doi = {10.4230/LIPICS.WABI.2018.22},
timestamp = {Tue, 11 Feb 2020 15:52:14 +0100},
biburl = {https://dblp.org/rec/conf/wabi/KarpovMRS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KockanHSBMBHWVC17,
author = {Can Kockan and
Faraz Hach and
Iman Sarrafi and
Robert H. Bell and
Brian McConeghy and
Kevin Beja and
Anne Haegert and
Alexander W. Wyatt and
Stanislav Volik and
Kim N. Chi and
Colin C. Collins and
S{\"{u}}leyman Cenk Sahinalp},
title = {SiNVICT: ultra-sensitive detection of single nucleotide variants and
indels in circulating tumour {DNA}},
journal = {Bioinform.},
volume = {33},
number = {1},
pages = {26--34},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw536},
doi = {10.1093/BIOINFORMATICS/BTW536},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KockanHSBMBHWVC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenWJDLKSSBWPH17,
author = {Feng Chen and
Shuang Wang and
Xiaoqian Jiang and
Sijie Ding and
Yao Lu and
Jihoon Kim and
S{\"{u}}leyman Cenk Sahinalp and
Chisato Shimizu and
Jane C. Burns and
Victoria J. Wright and
Eileen Png and
Martin L. Hibberd and
David D. Lloyd and
Hai Yang and
Amalio Telenti and
Cinnamon S. Bloss and
Dov Fox and
Kristin E. Lauter and
Lucila Ohno{-}Machado},
title = {{PRINCESS:} Privacy-protecting Rare disease International Network
Collaboration via Encryption through Software guard extensionS},
journal = {Bioinform.},
volume = {33},
number = {6},
pages = {871--878},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw758},
doi = {10.1093/BIOINFORMATICS/BTW758},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenWJDLKSSBWPH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/DonmezMWGCS17,
author = {Nilgun Donmez and
Salem Malikic and
Alexander W. Wyatt and
Martin E. Gleave and
Colin C. Collins and
S{\"{u}}leyman Cenk Sahinalp},
title = {Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence
Data},
journal = {J. Comput. Biol.},
volume = {24},
number = {6},
pages = {515--523},
year = {2017},
url = {https://doi.org/10.1089/cmb.2016.0148},
doi = {10.1089/CMB.2016.0148},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/DonmezMWGCS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/recomb/2017,
editor = {S{\"{u}}leyman Cenk Sahinalp},
title = {Research in Computational Molecular Biology - 21st Annual International
Conference, {RECOMB} 2017, Hong Kong, China, May 3-7, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10229},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-56970-3},
doi = {10.1007/978-3-319-56970-3},
isbn = {978-3-319-56969-7},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/2017.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HaghshenasHSC16,
author = {Ehsan Haghshenas and
Faraz Hach and
S{\"{u}}leyman Cenk Sahinalp and
C{\'{e}}dric Chauve},
title = {CoLoRMap: Correcting Long Reads by Mapping short reads},
journal = {Bioinform.},
volume = {32},
number = {17},
pages = {545--551},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw463},
doi = {10.1093/BIOINFORMATICS/BTW463},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HaghshenasHSC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/DonmezMWGCS16,
author = {Nilgun Donmez and
Salem Malikic and
Alexander W. Wyatt and
Martin E. Gleave and
Colin C. Collins and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Mona Singh},
title = {Clonality Inference from Single Tumor Samples Using Low Coverage Sequence
Data},
booktitle = {Research in Computational Molecular Biology - 20th Annual Conference,
{RECOMB} 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9649},
pages = {83--94},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-31957-5\_6},
doi = {10.1007/978-3-319-31957-5\_6},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/DonmezMWGCS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/0001SB16,
author = {Sean Simmons and
Cenk S. Sahinalp and
Bonnie Berger},
editor = {Mona Singh},
title = {Enabling Privacy Preserving {GWAS} in Heterogeneous Human Populations},
booktitle = {Research in Computational Molecular Biology - 20th Annual Conference,
{RECOMB} 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9649},
pages = {246--247},
publisher = {Springer},
year = {2016},
url = {https://link.springer.com/content/pdf/bbm\%3A978-3-319-31957-5\%2F1.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/0001SB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/algo/Sahinalp16,
author = {S{\"{u}}leyman Cenk Sahinalp},
title = {Edit Distance Under Block Operations},
booktitle = {Encyclopedia of Algorithms},
pages = {611--614},
year = {2016},
url = {https://doi.org/10.1007/978-1-4939-2864-4\_122},
doi = {10.1007/978-1-4939-2864-4\_122},
timestamp = {Wed, 12 Jul 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/algo/Sahinalp16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MalikicMDS15,
author = {Salem Malikic and
Andrew W. McPherson and
Nilgun Donmez and
Cenk S. Sahinalp},
title = {Clonality inference in multiple tumor samples using phylogeny},
journal = {Bioinform.},
volume = {31},
number = {9},
pages = {1349--1356},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv003},
doi = {10.1093/BIOINFORMATICS/BTV003},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MalikicMDS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NumanagicMPSFS15,
author = {Ibrahim Numanagic and
Salem Malikic and
Victoria M. Pratt and
Todd C. Skaar and
David A. Flockhart and
S{\"{u}}leyman Cenk Sahinalp},
title = {Cypiripi: exact genotyping of \emph{CYP2D6} using high-throughput
sequencing data},
journal = {Bioinform.},
volume = {31},
number = {12},
pages = {27--34},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv232},
doi = {10.1093/BIOINFORMATICS/BTV232},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NumanagicMPSFS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/McPhersonRCS15,
author = {Andrew W. McPherson and
Andrew Roth and
C{\'{e}}dric Chauve and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Teresa M. Przytycka},
title = {Joint Inference of Genome Structure and Content in Heterogeneous Tumor
Samples},
booktitle = {Research in Computational Molecular Biology - 19th Annual International
Conference, {RECOMB} 2015, Warsaw, Poland, April 12-15, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9029},
pages = {256--258},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-16706-0\_25},
doi = {10.1007/978-3-319-16706-0\_25},
timestamp = {Thu, 10 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/McPhersonRCS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/McPhersonRHSCS15,
author = {Andrew W. McPherson and
Andrew Roth and
Gavin Ha and
Sohrab P. Shah and
C{\'{e}}dric Chauve and
S{\"{u}}leyman Cenk Sahinalp},
title = {Joint Inference of Genome Structure and Content in Heterogeneous Tumour
Samples},
journal = {CoRR},
volume = {abs/1504.03080},
year = {2015},
url = {http://arxiv.org/abs/1504.03080},
eprinttype = {arXiv},
eprint = {1504.03080},
timestamp = {Thu, 10 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/McPhersonRHSCS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DaoNLHKDCES14,
author = {Phuong Dao and
Ibrahim Numanagic and
Yen{-}Yi Lin and
Faraz Hach and
Emre Karako{\c{c}} and
Nilgun Donmez and
Colin C. Collins and
Evan E. Eichler and
S{\"{u}}leyman Cenk Sahinalp},
title = {{ORMAN:} Optimal resolution of ambiguous RNA-Seq multimappings in
the presence of novel isoforms},
journal = {Bioinform.},
volume = {30},
number = {5},
pages = {644--651},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt591},
doi = {10.1093/BIOINFORMATICS/BTT591},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DaoNLHKDCES14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HachSHAES14,
author = {Faraz Hach and
Iman Sarrafi and
Farhad Hormozdiari and
Can Alkan and
Evan E. Eichler and
S{\"{u}}leyman Cenk Sahinalp},
title = {mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing
applications},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Webserver-Issue},
pages = {494--500},
year = {2014},
url = {https://doi.org/10.1093/nar/gku370},
doi = {10.1093/NAR/GKU370},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HachSHAES14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ShresthaHYWSDABRCHS14,
author = {Raunak Shrestha and
Ermin Hodzic and
Jake Yeung and
Kendric Wang and
Thomas Sauerwald and
Phuong Dao and
Shawn Anderson and
Himisha Beltran and
Mark A. Rubin and
Colin C. Collins and
Gholamreza Haffari and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Roded Sharan},
title = {HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time},
booktitle = {Research in Computational Molecular Biology - 18th Annual International
Conference, {RECOMB} 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8394},
pages = {293--306},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-05269-4\_23},
doi = {10.1007/978-3-319-05269-4\_23},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ShresthaHYWSDABRCHS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HormozdiariHSEA12,
author = {Farhad Hormozdiari and
Faraz Hach and
S{\"{u}}leyman Cenk Sahinalp and
Evan E. Eichler and
Can Alkan},
title = {Sensitive and fast mapping of di-base encoded reads},
journal = {Bioinform.},
volume = {28},
number = {1},
pages = {150},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/btr647},
doi = {10.1093/BIOINFORMATICS/BTR647},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HormozdiariHSEA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HajirasoulihaSJVS12,
author = {Iman Hajirasouliha and
Alexander Sch{\"{o}}nhuth and
David de Juan and
Alfonso Valencia and
S{\"{u}}leyman Cenk Sahinalp},
title = {Mirroring co-evolving trees in the light of their topologies},
journal = {Bioinform.},
volume = {28},
number = {9},
pages = {1202--1208},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts109},
doi = {10.1093/BIOINFORMATICS/BTS109},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HajirasoulihaSJVS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YorukogluHSCBS12,
author = {Deniz Y{\"{o}}r{\"{u}}koglu and
Faraz Hach and
Lucas Swanson and
Colin C. Collins and
Inan{\c{c}} Birol and
S{\"{u}}leyman Cenk Sahinalp},
title = {Dissect: detection and characterization of novel structural alterations
in transcribed sequences},
journal = {Bioinform.},
volume = {28},
number = {12},
pages = {179--187},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts214},
doi = {10.1093/BIOINFORMATICS/BTS214},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YorukogluHSCBS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HachNAS12,
author = {Faraz Hach and
Ibrahim Numanagic and
Can Alkan and
S{\"{u}}leyman Cenk Sahinalp},
title = {{SCALCE:} boosting sequence compression algorithms using locally consistent
encoding},
journal = {Bioinform.},
volume = {28},
number = {23},
pages = {3051--3057},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts593},
doi = {10.1093/BIOINFORMATICS/BTS593},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HachNAS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/McPhersonWWSCS12,
author = {Andrew W. McPherson and
Chunxiao Wu and
Alexander Wyatt and
Sohrab P. Shah and
Colin C. Collins and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Benny Chor},
title = {Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput
Sequencing},
booktitle = {Research in Computational Molecular Biology - 16th Annual International
Conference, {RECOMB} 2012, Barcelona, Spain, April 21-24, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7262},
pages = {181--182},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-29627-7\_17},
doi = {10.1007/978-3-642-29627-7\_17},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/McPhersonWWSCS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/LinDHBMLCS12,
author = {Yen{-}Yi Lin and
Phuong Dao and
Faraz Hach and
Marzieh Bakhshi and
Fan Mo and
Anna Lapuk and
Colin C. Collins and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Benjamin J. Raphael and
Jijun Tang},
title = {{CLIIQ:} Accurate Comparative Detection and Quantification of Expressed
Isoforms in a Population},
booktitle = {Algorithms in Bioinformatics - 12th International Workshop, {WABI}
2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7534},
pages = {178--189},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33122-0\_14},
doi = {10.1007/978-3-642-33122-0\_14},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/LinDHBMLCS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/McPhersonWHHHLVSCS11,
author = {Andrew W. McPherson and
Chunxiao Wu and
Iman Hajirasouliha and
Fereydoun Hormozdiari and
Faraz Hach and
Anna Lapuk and
Stanislav Volik and
Sohrab P. Shah and
Colin C. Collins and
S{\"{u}}leyman Cenk Sahinalp},
title = {Comrad: detection of expressed rearrangements by integrated analysis
of RNA-Seq and low coverage genome sequence data},
journal = {Bioinform.},
volume = {27},
number = {11},
pages = {1481--1488},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr184},
doi = {10.1093/BIOINFORMATICS/BTR184},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/McPhersonWHHHLVSCS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DaoWCELS11,
author = {Phuong Dao and
Kendric Wang and
Colin C. Collins and
Martin Ester and
Anna Lapuk and
S{\"{u}}leyman Cenk Sahinalp},
title = {Optimally discriminative subnetwork markers predict response to chemotherapy},
journal = {Bioinform.},
volume = {27},
number = {13},
pages = {205--213},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr245},
doi = {10.1093/BIOINFORMATICS/BTR245},
timestamp = {Tue, 08 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DaoWCELS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HormozdiariHSEA11,
author = {Farhad Hormozdiari and
Faraz Hach and
S{\"{u}}leyman Cenk Sahinalp and
Evan E. Eichler and
Can Alkan},
title = {Sensitive and fast mapping of di-base encoded reads},
journal = {Bioinform.},
volume = {27},
number = {14},
pages = {1915--1921},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr303},
doi = {10.1093/BIOINFORMATICS/BTR303},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HormozdiariHSEA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/McPhersonHZGHSGMSMPMHNSHS11,
author = {Andrew W. McPherson and
Fereydoun Hormozdiari and
Abdalnasser Zayed and
Ryan Giuliany and
Gavin Ha and
Mark G. F. Sun and
Malachi Griffith and
Alireza Heravi Moussavi and
Janine Senz and
Nataliya Melnyk and
Marina Pacheco and
Marco A. Marra and
Martin Hirst and
Torsten O. Nielsen and
S{\"{u}}leyman Cenk Sahinalp and
David G. Huntsman and
Sohrab P. Shah},
title = {deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {5},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1001138},
doi = {10.1371/JOURNAL.PCBI.1001138},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/McPhersonHZGHSGMSMPMHNSHS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/HormozdiariHMES11,
author = {Fereydoun Hormozdiari and
Iman Hajirasouliha and
Andrew W. McPherson and
Evan E. Eichler and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {Simultaneous Structural Variation Discovery in Multiple Paired-End
Sequenced Genomes},
booktitle = {Research in Computational Molecular Biology - 15th Annual International
Conference, {RECOMB} 2011, Vancouver, BC, Canada, March 28-31, 2011.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6577},
pages = {104--105},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-20036-6\_11},
doi = {10.1007/978-3-642-20036-6\_11},
timestamp = {Thu, 10 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/HormozdiariHMES11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/recomb/2011,
editor = {Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {Research in Computational Molecular Biology - 15th Annual International
Conference, {RECOMB} 2011, Vancouver, BC, Canada, March 28-31, 2011.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6577},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-20036-6},
doi = {10.1007/978-3-642-20036-6},
isbn = {978-3-642-20035-9},
timestamp = {Mon, 13 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/2011.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1110-5704,
author = {Iman Hajirasouliha and
Alexander Sch{\"{o}}nhuth and
David de Juan and
Alfonso Valencia and
S{\"{u}}leyman Cenk Sahinalp},
title = {Mirroring co-evolving trees in the light of their topologies},
journal = {CoRR},
volume = {abs/1110.5704},
year = {2011},
url = {http://arxiv.org/abs/1110.5704},
eprinttype = {arXiv},
eprint = {1110.5704},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1110-5704.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SalariBS10,
author = {Raheleh Salari and
Rolf Backofen and
S{\"{u}}leyman Cenk Sahinalp},
title = {Fast prediction of {RNA-RNA} interaction},
journal = {Algorithms Mol. Biol.},
volume = {5},
pages = {5},
year = {2010},
url = {https://doi.org/10.1186/1748-7188-5-5},
doi = {10.1186/1748-7188-5-5},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/SalariBS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MohlSWBS10,
author = {Mathias M{\"{o}}hl and
Raheleh Salari and
Sebastian Will and
Rolf Backofen and
S{\"{u}}leyman Cenk Sahinalp},
title = {Sparsification of {RNA} structure prediction including pseudoknots},
journal = {Algorithms Mol. Biol.},
volume = {5},
pages = {39},
year = {2010},
url = {https://doi.org/10.1186/1748-7188-5-39},
doi = {10.1186/1748-7188-5-39},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/MohlSWBS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HajirasoulihaHAKBES10,
author = {Iman Hajirasouliha and
Fereydoun Hormozdiari and
Can Alkan and
Jeffrey M. Kidd and
Inan{\c{c}} Birol and
Evan E. Eichler and
S{\"{u}}leyman Cenk Sahinalp},
title = {Detection and characterization of novel sequence insertions using
paired-end next-generation sequencing},
journal = {Bioinform.},
volume = {26},
number = {10},
pages = {1277--1283},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq152},
doi = {10.1093/BIOINFORMATICS/BTQ152},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HajirasoulihaHAKBES10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HormozdiariHDHYAES10,
author = {Fereydoun Hormozdiari and
Iman Hajirasouliha and
Phuong Dao and
Faraz Hach and
Deniz Y{\"{o}}r{\"{u}}koglu and
Can Alkan and
Evan E. Eichler and
S{\"{u}}leyman Cenk Sahinalp},
title = {Next-generation VariationHunter: combinatorial algorithms for transposon
insertion discovery},
journal = {Bioinform.},
volume = {26},
number = {12},
pages = {350--357},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq216},
doi = {10.1093/BIOINFORMATICS/BTQ216},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HormozdiariHDHYAES10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuWLMRLDSEFB10,
author = {Nancy Y. Yu and
James R. Wagner and
Matthew R. Laird and
Gabor Melli and
S{\'{e}}bastien Rey and
Raymond Lo and
Phuong Dao and
S{\"{u}}leyman Cenk Sahinalp and
Martin Ester and
Leonard J. Foster and
Fiona S. L. Brinkman},
title = {PSORTb 3.0: improved protein subcellular localization prediction with
refined localization subcategories and predictive capabilities for
all prokaryotes},
journal = {Bioinform.},
volume = {26},
number = {13},
pages = {1608--1615},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq249},
doi = {10.1093/BIOINFORMATICS/BTQ249},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuWLMRLDSEFB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SchonhuthSHCS10,
author = {Alexander Sch{\"{o}}nhuth and
Raheleh Salari and
Fereydoun Hormozdiari and
Artem Cherkasov and
S{\"{u}}leyman Cenk Sahinalp},
title = {Towards Improved Assessment of Functional Similarity in Large-Scale
Screens: {A} Study on Indel Length},
journal = {J. Comput. Biol.},
volume = {17},
number = {1},
pages = {1--20},
year = {2010},
url = {https://doi.org/10.1089/cmb.2009.0031},
doi = {10.1089/CMB.2009.0031},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SchonhuthSHCS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/HormozdiariSBS10,
author = {Fereydoun Hormozdiari and
Raheleh Salari and
Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {Protein-Protein Interaction Network Evaluation for Identifying Potential
Drug Targets},
journal = {J. Comput. Biol.},
volume = {17},
number = {5},
pages = {669--684},
year = {2010},
url = {https://doi.org/10.1089/cmb.2009.0032},
doi = {10.1089/CMB.2009.0032},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/HormozdiariSBS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SushkoNKPCLGHSMXLYOHDSTPAKMYFMTBHMMVPT10,
author = {Iurii Sushko and
Sergii Novotarskyi and
Robert K{\"{o}}rner and
Anil Kumar Pandey and
Artem Cherkasov and
Jiazhong Li and
Paola Gramatica and
Katja Hansen and
Timon Schroeter and
Klaus{-}Robert M{\"{u}}ller and
Lili Xi and
Huanxiang Liu and
Xiaojun Yao and
Tomas {\"{O}}berg and
Farhad Hormozdiari and
Phuong Dao and
S{\"{u}}leyman Cenk Sahinalp and
Roberto Todeschini and
Pavel G. Polishchuk and
Anatoly G. Artemenko and
Victor Kuzmin and
Todd Martin and
Douglas M. Young and
Denis Fourches and
Eugene N. Muratov and
Alexander Tropsha and
Igor I. Baskin and
Dragos Horvath and
Gilles Marcou and
Christophe Muller and
Alexandre Varnek and
Volodymyr V. Prokopenko and
Igor V. Tetko},
title = {Applicability Domains for Classification Problems: Benchmarking of
Distance to Models for Ames Mutagenicity Set},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {12},
pages = {2094--2111},
year = {2010},
url = {https://doi.org/10.1021/ci100253r},
doi = {10.1021/CI100253R},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SushkoNKPCLGHSMXLYOHDSTPAKMYFMTBHMMVPT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/talg/ErgunMS10,
author = {Funda Erg{\"{u}}n and
S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp},
title = {Periodicity testing with sublinear samples and space},
journal = {{ACM} Trans. Algorithms},
volume = {6},
number = {2},
pages = {43:1--43:14},
year = {2010},
url = {https://doi.org/10.1145/1721837.1721859},
doi = {10.1145/1721837.1721859},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/talg/ErgunMS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/BackofenCHSS10,
author = {Rolf Backofen and
Hamidreza Chitsaz and
Ivo L. Hofacker and
S{\"{u}}leyman Cenk Sahinalp and
Peter F. Stadler},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela,
Hawaii, USA, 4-8 January 2010},
pages = {54--56},
publisher = {World Scientific Publishing},
year = {2010},
url = {http://psb.stanford.edu/psb-online/proceedings/psb10/intro-rna.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/BackofenCHSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/AlkanBEKS10,
author = {Can Alkan and
Michael Brudno and
Evan E. Eichler and
Maricel G. Kann and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela,
Hawaii, USA, 4-8 January 2010},
pages = {302--304},
publisher = {World Scientific Publishing},
year = {2010},
url = {http://psb.stanford.edu/psb-online/proceedings/psb10/intro-personal.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/AlkanBEKS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SalariMWSB10,
author = {Raheleh Salari and
Mathias M{\"{o}}hl and
Sebastian Will and
S{\"{u}}leyman Cenk Sahinalp and
Rolf Backofen},
editor = {Bonnie Berger},
title = {Time and Space Efficient {RNA-RNA} Interaction Prediction via Sparse
Folding},
booktitle = {Research in Computational Molecular Biology, 14th Annual International
Conference, {RECOMB} 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6044},
pages = {473--490},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-12683-3\_31},
doi = {10.1007/978-3-642-12683-3\_31},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SalariMWSB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MohlSWBS10,
author = {Mathias M{\"{o}}hl and
Raheleh Salari and
Sebastian Will and
Rolf Backofen and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Vincent Moulton and
Mona Singh},
title = {Sparsification of {RNA} Structure Prediction Including Pseudoknots},
booktitle = {Algorithms in Bioinformatics, 10th International Workshop, {WABI}
2010, Liverpool, UK, September 6-8, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6293},
pages = {40--51},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-15294-8\_4},
doi = {10.1007/978-3-642-15294-8\_4},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/MohlSWBS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SchonhuthSS10,
author = {Alexander Sch{\"{o}}nhuth and
Raheleh Salari and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Vincent Moulton and
Mona Singh},
title = {Pair {HMM} Based Gap Statistics for Re-evaluation of Indels in Alignments
with Affine Gap Penalties},
booktitle = {Algorithms in Bioinformatics, 10th International Workshop, {WABI}
2010, Liverpool, UK, September 6-8, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6293},
pages = {350--361},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-15294-8\_29},
doi = {10.1007/978-3-642-15294-8\_29},
timestamp = {Thu, 25 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SchonhuthSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChitsazSSB09,
author = {Hamidreza Chitsaz and
Raheleh Salari and
S{\"{u}}leyman Cenk Sahinalp and
Rolf Backofen},
title = {A partition function algorithm for interacting nucleic acid strands},
journal = {Bioinform.},
volume = {25},
number = {12},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp212},
doi = {10.1093/BIOINFORMATICS/BTP212},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChitsazSSB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/HormozdiariSHSCSC09,
author = {Fereydoun Hormozdiari and
Raheleh Salari and
Michael Hsing and
Alexander Sch{\"{o}}nhuth and
Simon K. Chan and
S{\"{u}}leyman Cenk Sahinalp and
Artem Cherkasov},
title = {The Effect of Insertions and Deletions on Wirings in Protein-Protein
Interaction Networks: {A} Large-Scale Study},
journal = {J. Comput. Biol.},
volume = {16},
number = {2},
pages = {159--167},
year = {2009},
url = {https://doi.org/10.1089/cmb.2008.03TT},
doi = {10.1089/CMB.2008.03TT},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/HormozdiariSHSCSC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/ColakHMSHES09,
author = {Recep Colak and
Fereydoun Hormozdiari and
Flavia Moser and
Alexander Sch{\"{o}}nhuth and
J. Holman and
Martin Ester and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Dense Graphlet Statistics of Protein Interaction and Random Networks},
booktitle = {Biocomputing 2009: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, 5-9 January 2009},
pages = {178--189},
year = {2009},
url = {http://psb.stanford.edu/psb-online/proceedings/psb09/colak.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/ColakHMSHES09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/HormozdiariAES09,
author = {Fereydoun Hormozdiari and
Can Alkan and
Evan E. Eichler and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Serafim Batzoglou},
title = {Combinatorial Algorithms for Structural Variation Detection in High
Throughput Sequenced Genomes},
booktitle = {Research in Computational Molecular Biology, 13th Annual International
Conference, {RECOMB} 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5541},
pages = {218--219},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02008-7\_16},
doi = {10.1007/978-3-642-02008-7\_16},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/HormozdiariAES09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/ChitsazBS09,
author = {Hamidreza Chitsaz and
Rolf Backofen and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Steven Salzberg and
Tandy J. Warnow},
title = {biRNA: Fast {RNA-RNA} Binding Sites Prediction},
booktitle = {Algorithms in Bioinformatics, 9th International Workshop, {WABI} 2009,
Philadelphia, PA, USA, September 12-13, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5724},
pages = {25--36},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04241-6\_3},
doi = {10.1007/978-3-642-04241-6\_3},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/ChitsazBS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/DaoSHHSE09,
author = {Phuong Dao and
Alexander Sch{\"{o}}nhuth and
Fereydoun Hormozdiari and
Iman Hajirasouliha and
S{\"{u}}leyman Cenk Sahinalp and
Martin Ester},
editor = {Steven Salzberg and
Tandy J. Warnow},
title = {Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored
{PPI} Networks},
booktitle = {Algorithms in Bioinformatics, 9th International Workshop, {WABI} 2009,
Philadelphia, PA, USA, September 12-13, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5724},
pages = {37--48},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04241-6\_4},
doi = {10.1007/978-3-642-04241-6\_4},
timestamp = {Thu, 25 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/DaoSHHSE09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SalariBS09,
author = {Raheleh Salari and
Rolf Backofen and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Steven Salzberg and
Tandy J. Warnow},
title = {Fast Prediction of {RNA-RNA} Interaction},
booktitle = {Algorithms in Bioinformatics, 9th International Workshop, {WABI} 2009,
Philadelphia, PA, USA, September 12-13, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5724},
pages = {261--272},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04241-6\_22},
doi = {10.1007/978-3-642-04241-6\_22},
timestamp = {Thu, 25 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SalariBS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/HajirasoulihaHSB08,
author = {Iman Hajirasouliha and
Fereydoun Hormozdiari and
S{\"{u}}leyman Cenk Sahinalp and
Inan{\c{c}} Birol},
title = {Optimal pooling for genome re-sequencing with ultra-high-throughput
short-read technologies},
booktitle = {Proceedings 16th International Conference on Intelligent Systems for
Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008},
pages = {32--40},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn173},
doi = {10.1093/BIOINFORMATICS/BTN173},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/HajirasoulihaHSB08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/AlonDHHS08,
author = {Noga Alon and
Phuong Dao and
Iman Hajirasouliha and
Fereydoun Hormozdiari and
S{\"{u}}leyman Cenk Sahinalp},
title = {Biomolecular network motif counting and discovery by color coding},
booktitle = {Proceedings 16th International Conference on Intelligent Systems for
Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008},
pages = {241--249},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn163},
doi = {10.1093/BIOINFORMATICS/BTN163},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/AlonDHHS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SalariSHCS08,
author = {Raheleh Salari and
Alexander Sch{\"{o}}nhuth and
Fereydoun Hormozdiari and
Artem Cherkasov and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Keith A. Crandall and
Jens Lagergren},
title = {The Relation between Indel Length and Functional Divergence: {A} Formal
Study},
booktitle = {Algorithms in Bioinformatics, 8th International Workshop, {WABI} 2008,
Karlsruhe, Germany, September 15-19, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5251},
pages = {330--341},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-87361-7\_28},
doi = {10.1007/978-3-540-87361-7\_28},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SalariSHCS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/algo/Sahinalp08,
author = {S{\"{u}}leyman Cenk Sahinalp},
editor = {Ming{-}Yang Kao},
title = {Edit Distance Under Block Operations},
booktitle = {Encyclopedia of Algorithms - 2008 Edition},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-0-387-30162-4\_122},
doi = {10.1007/978-0-387-30162-4\_122},
timestamp = {Thu, 27 Jun 2019 16:25:31 +0200},
biburl = {https://dblp.org/rec/reference/algo/Sahinalp08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcss/Farach-ColtonLST07,
author = {Martin Farach{-}Colton and
Gad M. Landau and
S{\"{u}}leyman Cenk Sahinalp and
Dekel Tsur},
title = {Optimal spaced seeds for faster approximate string matching},
journal = {J. Comput. Syst. Sci.},
volume = {73},
number = {7},
pages = {1035--1044},
year = {2007},
url = {https://doi.org/10.1016/j.jcss.2007.03.007},
doi = {10.1016/J.JCSS.2007.03.007},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcss/Farach-ColtonLST07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AksaySKAS07,
author = {Cagri Aksay and
Raheleh Salari and
Emre Karako{\c{c}} and
Can Alkan and
S{\"{u}}leyman Cenk Sahinalp},
title = {taveRNA: a web suite for {RNA} algorithms and applications},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Web-Server-Issue},
pages = {325--329},
year = {2007},
url = {https://doi.org/10.1093/nar/gkm303},
doi = {10.1093/NAR/GKM303},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AksaySKAS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/HormozdiariBPS07,
author = {Fereydoun Hormozdiari and
Petra Berenbrink and
Natasa Przulj and
S{\"{u}}leyman Cenk Sahinalp},
title = {Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph
in {PPI} Network Evolution},
journal = {PLoS Comput. Biol.},
volume = {3},
number = {7},
year = {2007},
url = {https://doi.org/10.1371/journal.pcbi.0030118},
doi = {10.1371/JOURNAL.PCBI.0030118},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/HormozdiariBPS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/AlkanVARSE07,
author = {Can Alkan and
Mario Ventura and
Nicoletta Archidiacono and
Mariano Rocchi and
S{\"{u}}leyman Cenk Sahinalp and
Evan E. Eichler},
title = {Organization and Evolution of Primate Centromeric {DNA} from Whole-Genome
Shotgun Sequence Data},
journal = {PLoS Comput. Biol.},
volume = {3},
number = {9},
year = {2007},
url = {https://doi.org/10.1371/journal.pcbi.0030181},
doi = {10.1371/JOURNAL.PCBI.0030181},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/AlkanVARSE07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sigkdd/KarakocCS07,
author = {Emre Karako{\c{c}} and
Artem Cherkasov and
S{\"{u}}leyman Cenk Sahinalp},
title = {Novel approaches for small biomolecule classification and structural
similarity search},
journal = {{SIGKDD} Explor.},
volume = {9},
number = {1},
pages = {14--21},
year = {2007},
url = {https://doi.org/10.1145/1294301.1294307},
doi = {10.1145/1294301.1294307},
timestamp = {Tue, 29 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/sigkdd/KarakocCS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KarakocSC07,
author = {Emre Karako{\c{c}} and
S{\"{u}}leyman Cenk Sahinalp and
Artem Cherkasov},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Comparative {QSAR} Analysis of Bacterial-, Fungalplant- and Human
Metabolites},
booktitle = {Biocomputing 2007, Proceedings of the Pacific Symposium, Maui, Hawaii,
USA, 3-7 January 2007},
pages = {133--144},
publisher = {World Scientific},
year = {2007},
url = {http://psb.stanford.edu/psb-online/proceedings/psb07/karakoc.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KarakocSC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/AlkanKNSZ06,
author = {Can Alkan and
Emre Karako{\c{c}} and
Joseph H. Nadeau and
S{\"{u}}leyman Cenk Sahinalp and
Kaizhong Zhang},
title = {{RNA-RNA} Interaction Prediction and Antisense {RNA} Target Search},
journal = {J. Comput. Biol.},
volume = {13},
number = {2},
pages = {267--282},
year = {2006},
url = {https://doi.org/10.1089/cmb.2006.13.267},
doi = {10.1089/CMB.2006.13.267},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/AlkanKNSZ06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KarakocSC06,
author = {Emre Karako{\c{c}} and
S{\"{u}}leyman Cenk Sahinalp and
Artem Cherkasov},
title = {Comparative {QSAR-} and Fragments Distribution Analysis of Drugs,
Druglikes, Metabolic Substances, and Antimicrobial Compounds},
journal = {J. Chem. Inf. Model.},
volume = {46},
number = {5},
pages = {2167--2182},
year = {2006},
url = {https://doi.org/10.1021/ci0601517},
doi = {10.1021/CI0601517},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/KarakocSC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/SahinalpDM06,
author = {S{\"{u}}leyman Cenk Sahinalp and
Ugur Dogrus{\"{o}}z and
S. Muthukrishnan},
title = {Preface},
journal = {Theor. Comput. Sci.},
volume = {368},
number = {3},
pages = {195},
year = {2006},
url = {https://doi.org/10.1016/j.tcs.2006.09.011},
doi = {10.1016/J.TCS.2006.09.011},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/SahinalpDM06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/BebekBCFNS06,
author = {G{\"{u}}rkan Bebek and
Petra Berenbrink and
Colin Cooper and
Tom Friedetzky and
Joseph H. Nadeau and
S{\"{u}}leyman Cenk Sahinalp},
title = {The degree distribution of the generalized duplication model},
journal = {Theor. Comput. Sci.},
volume = {369},
number = {1-3},
pages = {239--249},
year = {2006},
url = {https://doi.org/10.1016/j.tcs.2006.08.045},
doi = {10.1016/J.TCS.2006.08.045},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/BebekBCFNS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KarakocCS06,
author = {Emre Karako{\c{c}} and
Artem Cherkasov and
S{\"{u}}leyman Cenk Sahinalp},
title = {Distance based algorithms for small biomolecule classification and
structural similarity search},
booktitle = {Proceedings 14th International Conference on Intelligent Systems for
Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006},
pages = {243--251},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl259},
doi = {10.1093/BIOINFORMATICS/BTL259},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/KarakocCS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/HormozdiariBPS06,
author = {Fereydoun Hormozdiari and
Petra Berenbrink and
Natasa Przulj and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Trey Ideker and
Vineet Bafna},
title = {Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph
in {PPI} Network Emulation},
booktitle = {Systems Biology and Computational Proteomics, Joint {RECOMB} 2006
Satellite Workshops on Systems Biology and on Computational Proteomics,
San Diego, CA, USA, December 1-3, 2006, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {4532},
pages = {1--13},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/978-3-540-73060-6\_1},
doi = {10.1007/978-3-540-73060-6\_1},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/HormozdiariBPS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/AlkanKSUEZB06,
author = {Can Alkan and
Emre Karako{\c{c}} and
S{\"{u}}leyman Cenk Sahinalp and
Peter J. Unrau and
H. Alexander Ebhardt and
Kaizhong Zhang and
Jeremy Buhler},
editor = {Alberto Apostolico and
Concettina Guerra and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {{RNA} Secondary Structure Prediction Via Energy Density Minimization},
booktitle = {Research in Computational Molecular Biology, 10th Annual International
Conference, {RECOMB} 2006, Venice, Italy, April 2-5, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3909},
pages = {130--142},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11732990\_12},
doi = {10.1007/11732990\_12},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/AlkanKSUEZB06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/soda/BatuES06,
author = {Tugkan Batu and
Funda Erg{\"{u}}n and
S{\"{u}}leyman Cenk Sahinalp},
title = {Oblivious string embeddings and edit distance approximations},
booktitle = {Proceedings of the Seventeenth Annual {ACM-SIAM} Symposium on Discrete
Algorithms, {SODA} 2006, Miami, Florida, USA, January 22-26, 2006},
pages = {792--801},
publisher = {{ACM} Press},
year = {2006},
url = {http://dl.acm.org/citation.cfm?id=1109557.1109644},
timestamp = {Fri, 07 Dec 2012 17:02:08 +0100},
biburl = {https://dblp.org/rec/conf/soda/BatuES06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AlkanTBLEBS05,
author = {Can Alkan and
Eray T{\"{u}}z{\"{u}}n and
Jerome Buard and
Franck Lethiec and
Evan E. Eichler and
Jeffrey A. Bailey and
S{\"{u}}leyman Cenk Sahinalp},
title = {Manipulating multiple sequence alignments via MaM and WebMaM},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Web-Server-Issue},
pages = {295--298},
year = {2005},
url = {https://doi.org/10.1093/nar/gki406},
doi = {10.1093/NAR/GKI406},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AlkanTBLEBS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dlt/BatuS05,
author = {Tugkan Batu and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Clelia de Felice and
Antonio Restivo},
title = {Locally Consistent Parsing and Applications to Approximate String
Comparisons},
booktitle = {Developments in Language Theory, 9th International Conference, {DLT}
2005, Palermo, Italy, July 4-8, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3572},
pages = {22--35},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11505877\_3},
doi = {10.1007/11505877\_3},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/dlt/BatuS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/Farach-ColtonLST05,
author = {Martin Farach{-}Colton and
Gad M. Landau and
S{\"{u}}leyman Cenk Sahinalp and
Dekel Tsur},
editor = {Lu{\'{\i}}s Caires and
Giuseppe F. Italiano and
Lu{\'{\i}}s Monteiro and
Catuscia Palamidessi and
Moti Yung},
title = {Optimal Spaced Seeds for Faster Approximate String Matching},
booktitle = {Automata, Languages and Programming, 32nd International Colloquium,
{ICALP} 2005, Lisbon, Portugal, July 11-15, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3580},
pages = {1251--1262},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11523468\_101},
doi = {10.1007/11523468\_101},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icalp/Farach-ColtonLST05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BebekBCFNS05,
author = {G{\"{u}}rkan Bebek and
Petra Berenbrink and
Colin Cooper and
Tom Friedetzky and
Joseph H. Nadeau and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Eleazar Eskin and
Trey Ideker and
Benjamin J. Raphael and
Christopher T. Workman},
title = {Improved Duplication Models for Proteome Network Evolution},
booktitle = {Systems Biology and Regulatory Genomics, Joint Annual {RECOMB} 2005
Satellite Workshops on Systems Biology and on Regulatory Genomics,
San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {4023},
pages = {119--137},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/978-3-540-48540-7\_11},
doi = {10.1007/978-3-540-48540-7\_11},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BebekBCFNS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/AlkanKNSZ05,
author = {Can Alkan and
Emre Karako{\c{c}} and
Joseph H. Nadeau and
S{\"{u}}leyman Cenk Sahinalp and
Kaizhong Zhang},
editor = {Satoru Miyano and
Jill P. Mesirov and
Simon Kasif and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {{RNA-RNA} Interaction Prediction and Antisense {RNA} Target Search},
booktitle = {Research in Computational Molecular Biology, 9th Annual International
Conference, {RECOMB} 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3500},
pages = {152--171},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11415770\_12},
doi = {10.1007/11415770\_12},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/AlkanKNSZ05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/debu/KarakocOSTZ04,
author = {Emre Karako{\c{c}} and
Z. Meral {\"{O}}zsoyoglu and
S{\"{u}}leyman Cenk Sahinalp and
Murat Tasan and
Xiang Zhang},
title = {Novel Approaches to Biomolecular Sequence Indexing},
journal = {{IEEE} Data Eng. Bull.},
volume = {27},
number = {3},
pages = {40--47},
year = {2004},
url = {http://sites.computer.org/debull/A04sept/bulletin.ps},
timestamp = {Wed, 19 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/debu/KarakocOSTZ04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/SahinalpEGBFE04,
author = {S{\"{u}}leyman Cenk Sahinalp and
Evan E. Eichler and
Paul W. Goldberg and
Petra Berenbrink and
Tom Friedetzky and
Funda Erg{\"{u}}n},
title = {Identifying Uniformly Mutated Segments within Repeats},
journal = {J. Bioinform. Comput. Biol.},
volume = {2},
number = {4},
pages = {657--668},
year = {2004},
url = {https://doi.org/10.1142/S0219720004000788},
doi = {10.1142/S0219720004000788},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/SahinalpEGBFE04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/AlkanEBST04,
author = {Can Alkan and
Evan E. Eichler and
Jeffrey A. Bailey and
S{\"{u}}leyman Cenk Sahinalp and
Eray T{\"{u}}z{\"{u}}n},
title = {The Role of Unequal Crossover in Alpha-Satellite {DNA} Evolution:
{A} Computational Analysis},
journal = {J. Comput. Biol.},
volume = {11},
number = {5},
pages = {933--944},
year = {2004},
url = {https://doi.org/10.1089/cmb.2004.11.933},
doi = {10.1089/CMB.2004.11.933},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/AlkanEBST04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/MuthukrishnanS04,
author = {S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp},
title = {An efficient algorithm for sequence comparison with block reversals},
journal = {Theor. Comput. Sci.},
volume = {321},
number = {1},
pages = {95--101},
year = {2004},
url = {https://doi.org/10.1016/j.tcs.2003.05.005},
doi = {10.1016/J.TCS.2003.05.005},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/MuthukrishnanS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/SahinalpU04,
author = {S{\"{u}}leyman Cenk Sahinalp and
Andrey Utis},
editor = {Josep D{\'{\i}}az and
Juhani Karhum{\"{a}}ki and
Arto Lepist{\"{o}} and
Donald Sannella},
title = {Hardness of String Similarity Search and Other Indexing Problems},
booktitle = {Automata, Languages and Programming: 31st International Colloquium,
{ICALP} 2004, Turku, Finland, July 12-16, 2004. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3142},
pages = {1080--1098},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-27836-8\_90},
doi = {10.1007/978-3-540-27836-8\_90},
timestamp = {Tue, 14 May 2019 10:00:44 +0200},
biburl = {https://dblp.org/rec/conf/icalp/SahinalpU04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/latin/ErgunMS04,
author = {Funda Erg{\"{u}}n and
S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Martin Farach{-}Colton},
title = {Sublinear Methods for Detecting Periodic Trends in Data Streams},
booktitle = {{LATIN} 2004: Theoretical Informatics, 6th Latin American Symposium,
Buenos Aires, Argentina, April 5-8, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2976},
pages = {16--28},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-24698-5\_6},
doi = {10.1007/978-3-540-24698-5\_6},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/latin/ErgunMS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/cpm/2004,
editor = {S{\"{u}}leyman Cenk Sahinalp and
S. Muthukrishnan and
Ugur Dogrus{\"{o}}z},
title = {Combinatorial Pattern Matching, 15th Annual Symposium, {CPM} 2004,
Istanbul,Turkey, July 5-7, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3109},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/b98377},
doi = {10.1007/B98377},
isbn = {3-540-22341-X},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/2004.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fsttcs/ErgunMS03,
author = {Funda Erg{\"{u}}n and
S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Paritosh K. Pandya and
Jaikumar Radhakrishnan},
title = {Comparing Sequences with Segment Rearrangements},
booktitle = {{FST} {TCS} 2003: Foundations of Software Technology and Theoretical
Computer Science, 23rd Conference, Mumbai, India, December 15-17,
2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2914},
pages = {183--194},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/978-3-540-24597-1\_16},
doi = {10.1007/978-3-540-24597-1\_16},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fsttcs/ErgunMS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icde/SahinalpTMO03,
author = {S{\"{u}}leyman Cenk Sahinalp and
Murat Tasan and
Jai Macker and
Z. Meral {\"{O}}zsoyoglu},
editor = {Umeshwar Dayal and
Krithi Ramamritham and
T. M. Vijayaraman},
title = {Distance Based Indexing for String Proximity Search},
booktitle = {Proceedings of the 19th International Conference on Data Engineering,
March 5-8, 2003, Bangalore, India},
pages = {125--136},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/ICDE.2003.1260787},
doi = {10.1109/ICDE.2003.1260787},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icde/SahinalpTMO03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/SahinalpEGBFE02,
author = {S{\"{u}}leyman Cenk Sahinalp and
Evan E. Eichler and
Paul W. Goldberg and
Petra Berenbrink and
Tom Friedetzky and
Funda Erg{\"{u}}n},
editor = {Alberto Apostolico and
Masayuki Takeda},
title = {Statistical Identification of Uniformly Mutated Segments within Repeats},
booktitle = {Combinatorial Pattern Matching, 13th Annual Symposium, {CPM} 2002,
Fukuoka, Japan, July 3-5, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2373},
pages = {249--261},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45452-7\_21},
doi = {10.1007/3-540-45452-7\_21},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/SahinalpEGBFE02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/MuthukrishnanS02,
author = {S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Alberto Apostolico and
Masayuki Takeda},
title = {Simple and Practical Sequence Nearest Neighbors with Block Operations},
booktitle = {Combinatorial Pattern Matching, 13th Annual Symposium, {CPM} 2002,
Fukuoka, Japan, July 3-5, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2373},
pages = {262--278},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45452-7\_22},
doi = {10.1007/3-540-45452-7\_22},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/MuthukrishnanS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/latin/MuthukrishnanS02,
author = {S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Sergio Rajsbaum},
title = {An Improved Algorithm for Sequence Comparison with Block Reversals},
booktitle = {{LATIN} 2002: Theoretical Informatics, 5th Latin American Symposium,
Cancun, Mexico, April 3-6, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2286},
pages = {319--325},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45995-2\_30},
doi = {10.1007/3-540-45995-2\_30},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/latin/MuthukrishnanS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jal/GoldbergGPPSS01,
author = {Leslie Ann Goldberg and
Paul W. Goldberg and
Mike Paterson and
Pavel A. Pevzner and
S{\"{u}}leyman Cenk Sahinalp and
Elizabeth Sweedyk},
title = {The Complexity of Gene Placement},
journal = {J. Algorithms},
volume = {41},
number = {2},
pages = {225--243},
year = {2001},
url = {https://doi.org/10.1006/jagm.2001.1172},
doi = {10.1006/JAGM.2001.1172},
timestamp = {Sun, 28 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jal/GoldbergGPPSS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jea/MatiasRS01,
author = {Yossi Matias and
Nasir M. Rajpoot and
S{\"{u}}leyman Cenk Sahinalp},
title = {The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression},
journal = {{ACM} J. Exp. Algorithmics},
volume = {6},
pages = {10},
year = {2001},
url = {https://doi.org/10.1145/945394.945404},
doi = {10.1145/945394.945404},
timestamp = {Thu, 25 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jea/MatiasRS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alenex/ErgunSSS01,
author = {Funda Erg{\"{u}}n and
S{\"{u}}leyman Cenk Sahinalp and
Jonathan Sharp and
Rakesh K. Sinha},
editor = {Adam L. Buchsbaum and
Jack Snoeyink},
title = {Biased Skip Lists for Highly Skewed Access Patterns},
booktitle = {Algorithm Engineering and Experimentation, Third International Workshop,
{ALENEX} 2001, Washington, DC, USA, January 5-6, 2001, Revised Papers},
series = {Lecture Notes in Computer Science},
volume = {2153},
pages = {216--230},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44808-X\_18},
doi = {10.1007/3-540-44808-X\_18},
timestamp = {Tue, 14 May 2019 10:00:46 +0200},
biburl = {https://dblp.org/rec/conf/alenex/ErgunSSS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/CormodeMS01,
author = {Graham Cormode and
S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Fernando Orejas and
Paul G. Spirakis and
Jan van Leeuwen},
title = {Permutation Editing and Matching via Embeddings},
booktitle = {Automata, Languages and Programming, 28th International Colloquium,
{ICALP} 2001, Crete, Greece, July 8-12, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2076},
pages = {481--492},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-48224-5\_40},
doi = {10.1007/3-540-48224-5\_40},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icalp/CormodeMS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/infocom/ErgunMSSS01,
author = {Funda Erg{\"{u}}n and
Suvo Mittra and
S{\"{u}}leyman Cenk Sahinalp and
Jonathan Sharp and
Rakesh K. Sinha},
title = {A Dynamic Lookup Scheme for Bursty Access Patterns},
booktitle = {Proceedings {IEEE} {INFOCOM} 2001, The Conference on Computer Communications,
Twentieth Annual Joint Conference of the {IEEE} Computer and Communications
Societies, Twenty years into the communications odyssey, Anchorage,
Alaska, USA, April 22-26, 2001},
pages = {1444--1453},
publisher = {{IEEE} Comptuer Society},
year = {2001},
url = {https://doi.org/10.1109/INFCOM.2001.916640},
doi = {10.1109/INFCOM.2001.916640},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/infocom/ErgunMSSS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stoc/ErgunSSS01,
author = {Funda Erg{\"{u}}n and
S{\"{u}}leyman Cenk Sahinalp and
Jonathan Sharp and
Rakesh K. Sinha},
editor = {Jeffrey Scott Vitter and
Paul G. Spirakis and
Mihalis Yannakakis},
title = {Biased dictionaries with fast insert/deletes},
booktitle = {Proceedings on 33rd Annual {ACM} Symposium on Theory of Computing,
July 6-8, 2001, Heraklion, Crete, Greece},
pages = {483--491},
publisher = {{ACM}},
year = {2001},
url = {https://doi.org/10.1145/380752.380843},
doi = {10.1145/380752.380843},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/stoc/ErgunSSS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/soda/CohenMMSZ00,
author = {Z. Cohen and
Yossi Matias and
S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp and
Jacob Ziv},
editor = {David B. Shmoys},
title = {On the temporal {HZY} compression scheme},
booktitle = {Proceedings of the Eleventh Annual {ACM-SIAM} Symposium on Discrete
Algorithms, January 9-11, 2000, San Francisco, CA, {USA}},
pages = {185--186},
publisher = {{ACM/SIAM}},
year = {2000},
url = {http://dl.acm.org/citation.cfm?id=338219.338250},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/soda/CohenMMSZ00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/soda/CormodePSV00,
author = {Graham Cormode and
Mike Paterson and
S{\"{u}}leyman Cenk Sahinalp and
Uzi Vishkin},
editor = {David B. Shmoys},
title = {Communication complexity of document exchange},
booktitle = {Proceedings of the Eleventh Annual {ACM-SIAM} Symposium on Discrete
Algorithms, January 9-11, 2000, San Francisco, CA, {USA}},
pages = {197--206},
publisher = {{ACM/SIAM}},
year = {2000},
url = {http://dl.acm.org/citation.cfm?id=338219.338252},
timestamp = {Fri, 07 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/soda/CormodePSV00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stoc/MuthukrishnanS00,
author = {S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp},
editor = {F. Frances Yao and
Eugene M. Luks},
title = {Approximate nearest neighbors and sequence comparison with block operations},
booktitle = {Proceedings of the Thirty-Second Annual {ACM} Symposium on Theory
of Computing, May 21-23, 2000, Portland, OR, {USA}},
pages = {416--424},
publisher = {{ACM}},
year = {2000},
url = {https://doi.org/10.1145/335305.335353},
doi = {10.1145/335305.335353},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/stoc/MuthukrishnanS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dcc/MatiasRS99,
author = {Yossi Matias and
Nasir M. Rajpoot and
S{\"{u}}leyman Cenk Sahinalp},
title = {The Effect of Flexible Parsing for Dynamic Dictionary Based Data Compression},
booktitle = {Data Compression Conference, {DCC} 1999, Snowbird, Utah, USA, March
29-31, 1999},
pages = {238--246},
publisher = {{IEEE} Computer Society},
year = {1999},
url = {https://doi.org/10.1109/DCC.1999.755673},
doi = {10.1109/DCC.1999.755673},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/dcc/MatiasRS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/soda/GoldbergGPPSS99,
author = {Leslie Ann Goldberg and
Paul W. Goldberg and
Mike Paterson and
Pavel A. Pevzner and
S{\"{u}}leyman Cenk Sahinalp and
Elizabeth Sweedyk},
editor = {Robert Endre Tarjan and
Tandy J. Warnow},
title = {The Complexity of Gene Placement},
booktitle = {Proceedings of the Tenth Annual {ACM-SIAM} Symposium on Discrete Algorithms,
17-19 January 1999, Baltimore, Maryland, {USA}},
pages = {386--395},
publisher = {{ACM/SIAM}},
year = {1999},
url = {http://dl.acm.org/citation.cfm?id=314500.314591},
timestamp = {Thu, 05 Jul 2018 07:29:57 +0200},
biburl = {https://dblp.org/rec/conf/soda/GoldbergGPPSS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/soda/MatiasS99,
author = {Yossi Matias and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Robert Endre Tarjan and
Tandy J. Warnow},
title = {On the Optimality of Parsing in Dynamic Dictionary Based Data Compression},
booktitle = {Proceedings of the Tenth Annual {ACM-SIAM} Symposium on Discrete Algorithms,
17-19 January 1999, Baltimore, Maryland, {USA}},
pages = {943--944},
publisher = {{ACM/SIAM}},
year = {1999},
url = {http://dl.acm.org/citation.cfm?id=314500.314935},
timestamp = {Fri, 07 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/soda/MatiasS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stoc/MuthukrishnanPSS99,
author = {S. Muthukrishnan and
Mike Paterson and
S{\"{u}}leyman Cenk Sahinalp and
Torsten Suel},
editor = {Jeffrey Scott Vitter and
Lawrence L. Larmore and
Frank Thomson Leighton},
title = {Compact Grid Layouts of Multi-Level Networks},
booktitle = {Proceedings of the Thirty-First Annual {ACM} Symposium on Theory of
Computing, May 1-4, 1999, Atlanta, Georgia, {USA}},
pages = {455--463},
publisher = {{ACM}},
year = {1999},
url = {https://doi.org/10.1145/301250.301372},
doi = {10.1145/301250.301372},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/stoc/MuthukrishnanPSS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/esa/MatiasMSZ98,
author = {Yossi Matias and
S. Muthukrishnan and
S{\"{u}}leyman Cenk Sahinalp and
Jacob Ziv},
editor = {Gianfranco Bilardi and
Giuseppe F. Italiano and
Andrea Pietracaprina and
Geppino Pucci},
title = {Augmenting Suffix Trees, with Applications},
booktitle = {Algorithms - {ESA} '98, 6th Annual European Symposium, Venice, Italy,
August 24-26, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1461},
pages = {67--78},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/3-540-68530-8\_6},
doi = {10.1007/3-540-68530-8\_6},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/esa/MatiasMSZ98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spaa/EvenMPS98,
author = {Shimon Even and
S. Muthukrishnan and
Mike Paterson and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Gary L. Miller and
Phillip B. Gibbons},
title = {Layout of the Batcher Bitonic Sorter (Extended Abstract)},
booktitle = {Proceedings of the Tenth Annual {ACM} Symposium on Parallel Algorithms
and Architectures, {SPAA} '98, Puerto Vallarta, Mexico, June 28 -
July 2, 1998},
pages = {172--181},
publisher = {{ACM}},
year = {1998},
url = {https://doi.org/10.1145/277651.277683},
doi = {10.1145/277651.277683},
timestamp = {Fri, 07 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/spaa/EvenMPS98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wae/MatiasRS98,
author = {Yossi Matias and
Nasir M. Rajpoot and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Kurt Mehlhorn},
title = {Implementation and Experimental Evaluation of Flexible Parsing for
Dynamic Dictionary Based Data Compression},
booktitle = {Algorithm Engineering, 2nd International Workshop, {WAE} '92, Saarbr{\"{u}}cken,
Germany, August 20-22, 1998, Proceedings},
pages = {49--61},
publisher = {Max-Planck-Institut f{\"{u}}r Informatik},
year = {1998},
timestamp = {Mon, 10 May 2021 14:22:35 +0200},
biburl = {https://dblp.org/rec/conf/wae/MatiasRS98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/focs/SahinalpV96,
author = {S{\"{u}}leyman Cenk Sahinalp and
Uzi Vishkin},
title = {Efficient Approximate and Dynamic Matching of Patterns Using a Labeling
Paradigm (extended abstract)},
booktitle = {37th Annual Symposium on Foundations of Computer Science, {FOCS} '96,
Burlington, Vermont, USA, 14-16 October, 1996},
pages = {320--328},
publisher = {{IEEE} Computer Society},
year = {1996},
url = {https://doi.org/10.1109/SFCS.1996.548491},
doi = {10.1109/SFCS.1996.548491},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/focs/SahinalpV96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ciac/SahinalpV94,
author = {S{\"{u}}leyman Cenk Sahinalp and
Uzi Vishkin},
editor = {Maurizio A. Bonuccelli and
Pierluigi Crescenzi and
Rossella Petreschi},
title = {On a Parallel-Algorithms Method for String Matching Problems},
booktitle = {Algorithms and Complexity, Second Italian Conference, {CIAC} '94,
Rome, Italy, February 23-25, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {778},
pages = {22--32},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-57811-0\_3},
doi = {10.1007/3-540-57811-0\_3},
timestamp = {Fri, 17 Jul 2020 16:12:46 +0200},
biburl = {https://dblp.org/rec/conf/ciac/SahinalpV94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stoc/SahinalpV94,
author = {S{\"{u}}leyman Cenk Sahinalp and
Uzi Vishkin},
editor = {Frank Thomson Leighton and
Michael T. Goodrich},
title = {Symmetry breaking for suffix tree construction},
booktitle = {Proceedings of the Twenty-Sixth Annual {ACM} Symposium on Theory of
Computing, 23-25 May 1994, Montr{\'{e}}al, Qu{\'{e}}bec,
Canada},
pages = {300--309},
publisher = {{ACM}},
year = {1994},
url = {https://doi.org/10.1145/195058.195164},
doi = {10.1145/195058.195164},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/stoc/SahinalpV94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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