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ORCIDSüleyman Cenk Sahinalp
S. Cenk Sahinalp
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- affiliation: Simon Fraser University, Burnaby, Canada
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2020 – today
- 2024
[c61]Chih Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, Süleyman Cenk Sahinalp, Salem Malikic:
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History. RECOMB 2024: 438-443- 2022
- [j57]Can Kizilkale, Farid Rashidi Mehrabadi
, Erfan Sadeqi Azer, Eva Pérez-Guijarro, Kerrie Marie, Maxwell P. Lee, Chi-Ping Day, Glenn Merlino, Funda Ergün, Aydin Buluç, Süleyman Cenk Sahinalp, Salem Malikic:
Fast intratumor heterogeneity inference from single-cell sequencing data. Nat. Comput. Sci. 2(9): 577-583 (2022) - [c60]Michael Ford, Ananth Hari, Oscar Rodriguez, Junyan Xu, Justin Lack, Cihan Oguz, Yu Zhang, Sarah Weber, Mary Magliocco, Jason Barnett, Sandhya Xirasagar, Smilee Samuel, Luisa Imberti, Paolo Bonfanti, Andrea Biondi, Clifton L. Dalgard, Stephen J. Chanock, Lindsey Rosen, Steven Holland, Helen Su, Luigi Notarangelo, Uzi Vishkin, Corey Watson, Süleyman Cenk Sahinalp:
ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes Using Short Read Data. RECOMB 2022: 382-384 - 2021
- [j56]Salem Malikic, Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, Mohammad Haghir Ebrahim-Abadi, Süleyman Cenk Sahinalp:
Studying the History of Tumor Evolution from Single-Cell Sequencing Data by Exploring the Space of Binary Matrices. J. Comput. Biol. 28(9): 857-879 (2021) - 2020
- [j55]Erfan Sadeqi Azer, Farid Rashidi Mehrabadi, Salem Malikic, Xuan Cindy Li, Osnat Bartok, Kevin Litchfield, Ronen Levy, Yardena Samuels, Alejandro A. Schäffer, E. Michael Gertz, Chi-Ping Day, Eva Pérez-Guijarro, Kerrie Marie, Maxwell P. Lee, Glenn Merlino, Funda Ergün, Süleyman Cenk Sahinalp:
PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. Bioinform. 36(Supplement-1): i169-i176 (2020) - [j54]Ermin Hodzic, Raunak Shrestha, Salem Malikic, Colin C. Collins, Kevin Litchfield, Samra Turajlic, Süleyman Cenk Sahinalp:
Identification of conserved evolutionary trajectories in tumors. Bioinform. 36(Supplement-1): i427-i435 (2020) - [j53]Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz:
Graph Traversal Edit Distance and Extensions. J. Comput. Biol. 27(3): 317-329 (2020) - [j52]Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz:
PyGTED: Python Application for Computing Graph Traversal Edit Distance. J. Comput. Biol. 27(3): 436-439 (2020) - [j51]Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j50]Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit G. Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff MacIntyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven E. Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. L. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, Süleyman Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D. Morris, David J. Adams, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie, Yupeng Cun, Kevin J. Dawson, Ruben M. Drews, Roland Eils, Matthew Fittall, Dale W. Garsed, Gavin Ha, Henry Lee-Six, Iñigo Martincorena, Layla Oesper, Myron Peto, Benjamin J. Raphael, Daniel T. Rosebrock, Adriana Salcedo, Ruian Shi, Seung Jun Shin, Oliver Spiro, Lincoln D. Stein, Shankar Vembu, David A. Wheeler, Tsun-Po Yang, Paul T. Spellman, David C. Wedge, Peter Van Loo:
The evolutionary history of 2,658 cancers. Nat. 578(7793): 122-128 (2020) - [i3]Langshi Chen, Jiayu Li, Ariful Azad, S. Cenk Sahinalp, Madhav V. Marathe, Anil Vullikanti, Andrey Nikolaev, Egor Smirnov, Ruslan Israfilov, Judy Qiu:
SubGraph2Vec: Highly-Vectorized Tree-likeSubgraph Counting. CoRR abs/2009.11665 (2020)
2010 – 2019
- 2019
- [j49]Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, Süleyman Cenk Sahinalp:
A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression. Algorithms Mol. Biol. 14(1): 17:1-17:18 (2019) - [j48]Ehsan Haghshenas, Süleyman Cenk Sahinalp, Faraz Hach:
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. Bioinform. 35(1): 20-27 (2019) - [c59]Langshi Chen, Jiayu Li, S. Cenk Sahinalp, Madhav V. Marathe, Anil Vullikanti, Andrey Nikolaev, Egor Smirnov, Ruslan Israfilov, Judy Qiu:
SubGraph2Vec: Highly-Vectorized Tree-like Subgraph Counting. IEEE BigData 2019: 483-492 - [c58]Sean Simmons, Bonnie Berger, S. Cenk Sahinalp:
Protecting Genomic Data Privacy with Probabilistic Modeling. PSB 2019: 403-414 - [c57]Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, M. Oguzhan Külekci, David P. Woodruff, Süleyman Cenk Sahinalp:
Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave. RECOMB 2019: 302-304 - [r3]Kaiyuan Zhu, Ibrahim Numanagic, Süleyman Cenk Sahinalp:
Genomic Data Compression. Encyclopedia of Big Data Technologies 2019 - 2018
- [j47]Yen-Yi Lin, Alexander Gawronski, Faraz Hach, Sujun Li, Ibrahim Numanagic, Iman Sarrafi, Swati Mishra, Andrew W. McPherson, Colin C. Collins, Milan Radovich, Haixu Tang, Süleyman Cenk Sahinalp:
Computational identification of micro-structural variations and their proteogenomic consequences in cancer. Bioinform. 34(10): 1672-1681 (2018) - [j46]Alexander Gawronski, Michael Uhl, Yajia Zhang, Yen-Yi Lin, Yashar S. Niknafs, Varune R. Ramnarine, Rohit Malik, Felix Feng, Arul M. Chinnaiyan, Colin C. Collins, Süleyman Cenk Sahinalp, Rolf Backofen:
MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. Bioinform. 34(18): 3101-3110 (2018) - [j45]S. Cenk Sahinalp:
Preface: Selected Articles from RECOMB 2017. J. Comput. Biol. 25(7): 623 (2018) - [j44]Makoto Yamada, Jiliang Tang, Jose Lugo-Martinez, Ermin Hodzic, Raunak Shrestha, Avishek Saha, Hua Ouyang, Dawei Yin, Hiroshi Mamitsuka, Süleyman Cenk Sahinalp, Predrag Radivojac, Filippo Menczer, Yi Chang:
Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. IEEE Trans. Knowl. Data Eng. 30(7): 1352-1365 (2018) - [c56]Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz:
GTED: Graph Traversal Edit Distance. RECOMB 2018: 37-53 - [c55]Salem Malikic, Katharina Jahn, Jack Kuipers, Süleyman Cenk Sahinalp, Niko Beerenwinkel:
Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. RECOMB 2018: 269-270 - [c54]Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, Süleyman Cenk Sahinalp:
A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression. WABI 2018: 22:1-22:19 - 2017
- [j43]Can Kockan, Faraz Hach, Iman Sarrafi, Robert H. Bell, Brian McConeghy, Kevin Beja, Anne Haegert, Alexander W. Wyatt, Stanislav Volik, Kim N. Chi, Colin C. Collins, Süleyman Cenk Sahinalp:
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA. Bioinform. 33(1): 26-34 (2017) - [j42]Feng Chen, Shuang Wang, Xiaoqian Jiang, Sijie Ding, Yao Lu, Jihoon Kim, Süleyman Cenk Sahinalp, Chisato Shimizu, Jane C. Burns, Victoria J. Wright, Eileen Png, Martin L. Hibberd, David D. Lloyd, Hai Yang, Amalio Telenti, Cinnamon S. Bloss, Dov Fox, Kristin E. Lauter, Lucila Ohno-Machado:
PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. Bioinform. 33(6): 871-878 (2017) - [j41]Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp:
Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data. J. Comput. Biol. 24(6): 515-523 (2017) - [e3]Süleyman Cenk Sahinalp:
Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Hong Kong, China, May 3-7, 2017, Proceedings. Lecture Notes in Computer Science 10229, 2017, ISBN 978-3-319-56969-7 [contents] - 2016
- [j40]Ehsan Haghshenas, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve:
CoLoRMap: Correcting Long Reads by Mapping short reads. Bioinform. 32(17): 545-551 (2016) - [c53]Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp:
Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data. RECOMB 2016: 83-94 - [c52]Sean Simmons, S. Cenk Sahinalp, Bonnie Berger:
Enabling Privacy Preserving GWAS in Heterogeneous Human Populations. RECOMB 2016: 246-247 - [r2]Süleyman Cenk Sahinalp:
Edit Distance Under Block Operations. Encyclopedia of Algorithms 2016: 611-614 - 2015
- [j39]Salem Malikic, Andrew W. McPherson, Nilgun Donmez, S. Cenk Sahinalp:
Clonality inference in multiple tumor samples using phylogeny. Bioinform. 31(9): 1349-1356 (2015) - [j38]Ibrahim Numanagic, Salem Malikic, Victoria M. Pratt, Todd C. Skaar, David A. Flockhart, Süleyman Cenk Sahinalp:
Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data. Bioinform. 31(12): 27-34 (2015) - [c51]Andrew W. McPherson, Andrew Roth, Cédric Chauve, Süleyman Cenk Sahinalp:
Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. RECOMB 2015: 256-258 - [i2]Andrew W. McPherson, Andrew Roth, Gavin Ha, Sohrab P. Shah, Cédric Chauve, Süleyman Cenk Sahinalp:
Joint Inference of Genome Structure and Content in Heterogeneous Tumour Samples. CoRR abs/1504.03080 (2015) - 2014
- [j37]Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp:
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Bioinform. 30(5): 644-651 (2014) - [j36]Faraz Hach, Iman Sarrafi, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp:
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Res. 42(Webserver-Issue): 494-500 (2014) - [c50]Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin, Colin C. Collins, Gholamreza Haffari, Süleyman Cenk Sahinalp:
HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time. RECOMB 2014: 293-306 - 2012
- [j35]Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan:
Sensitive and fast mapping of di-base encoded reads. Bioinform. 28(1): 150 (2012) - [j34]Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp:
Mirroring co-evolving trees in the light of their topologies. Bioinform. 28(9): 1202-1208 (2012) - [j33]Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin C. Collins, Inanç Birol, Süleyman Cenk Sahinalp:
Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinform. 28(12): 179-187 (2012) - [j32]Faraz Hach, Ibrahim Numanagic, Can Alkan, Süleyman Cenk Sahinalp:
SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinform. 28(23): 3051-3057 (2012) - [c49]Andrew W. McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp:
Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing. RECOMB 2012: 181-182 - [c48]Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp:
CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. WABI 2012: 178-189 - 2011
- [j31]Andrew W. McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp:
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinform. 27(11): 1481-1488 (2011) - [j30]Phuong Dao, Kendric Wang, Colin C. Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp:
Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinform. 27(13): 205-213 (2011) - [j29]Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan:
Sensitive and fast mapping of di-base encoded reads. Bioinform. 27(14): 1915-1921 (2011) - [j28]Andrew W. McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G. F. Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A. Marra, Martin Hirst, Torsten O. Nielsen, Süleyman Cenk Sahinalp, David G. Huntsman, Sohrab P. Shah:
deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data. PLoS Comput. Biol. 7(5) (2011) - [c47]Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew W. McPherson, Evan E. Eichler, Süleyman Cenk Sahinalp:
Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. RECOMB 2011: 104-105 - [e2]Vineet Bafna, Süleyman Cenk Sahinalp:
Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings. Lecture Notes in Computer Science 6577, Springer 2011, ISBN 978-3-642-20035-9 [contents] - [i1]Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp:
Mirroring co-evolving trees in the light of their topologies. CoRR abs/1110.5704 (2011) - 2010
- [j27]Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp:
Fast prediction of RNA-RNA interaction. Algorithms Mol. Biol. 5: 5 (2010) - [j26]Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp:
Sparsification of RNA structure prediction including pseudoknots. Algorithms Mol. Biol. 5: 39 (2010) - [j25]Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp:
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinform. 26(10): 1277-1283 (2010) - [j24]Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp:
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinform. 26(12): 350-357 (2010) - [j23]Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, Süleyman Cenk Sahinalp, Martin Ester, Leonard J. Foster, Fiona S. L. Brinkman:
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinform. 26(13): 1608-1615 (2010) - [j22]Alexander Schönhuth, Raheleh Salari, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp:
Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length. J. Comput. Biol. 17(1): 1-20 (2010) - [j21]Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp:
Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. J. Comput. Biol. 17(5): 669-684 (2010) - [j20]Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Artem Cherkasov, Jiazhong Li, Paola Gramatica, Katja Hansen, Timon Schroeter, Klaus-Robert Müller, Lili Xi, Huanxiang Liu, Xiaojun Yao, Tomas Öberg, Farhad Hormozdiari, Phuong Dao, Süleyman Cenk Sahinalp, Roberto Todeschini, Pavel G. Polishchuk, Anatoly G. Artemenko, Victor Kuzmin, Todd Martin, Douglas M. Young, Denis Fourches, Eugene N. Muratov, Alexander Tropsha, Igor I. Baskin, Dragos Horvath, Gilles Marcou, Christophe Muller, Alexandre Varnek, Volodymyr V. Prokopenko, Igor V. Tetko:
Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. J. Chem. Inf. Model. 50(12): 2094-2111 (2010) - [j19]Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp:
Periodicity testing with sublinear samples and space. ACM Trans. Algorithms 6(2): 43:1-43:14 (2010) - [c46]Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler:
Session Introduction. Pacific Symposium on Biocomputing 2010: 54-56 - [c45]Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp:
Session Introduction. Pacific Symposium on Biocomputing 2010: 302-304 - [c44]Raheleh Salari, Mathias Möhl, Sebastian Will, Süleyman Cenk Sahinalp, Rolf Backofen:
Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. RECOMB 2010: 473-490 - [c43]Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp:
Sparsification of RNA Structure Prediction Including Pseudoknots. WABI 2010: 40-51 - [c42]Alexander Schönhuth, Raheleh Salari, Süleyman Cenk Sahinalp:
Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties. WABI 2010: 350-361
2000 – 2009
- 2009
- [j18]Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen:
A partition function algorithm for interacting nucleic acid strands. Bioinform. 25(12) (2009) - [j17]Fereydoun Hormozdiari, Raheleh Salari, Michael Hsing, Alexander Schönhuth, Simon K. Chan, Süleyman Cenk Sahinalp, Artem Cherkasov:
The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study. J. Comput. Biol. 16(2): 159-167 (2009) - [c41]Recep Colak, Fereydoun Hormozdiari, Flavia Moser, Alexander Schönhuth, J. Holman, Martin Ester, Süleyman Cenk Sahinalp:
Dense Graphlet Statistics of Protein Interaction and Random Networks. Pacific Symposium on Biocomputing 2009: 178-189 - [c40]Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp:
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. RECOMB 2009: 218-219 - [c39]Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp:
biRNA: Fast RNA-RNA Binding Sites Prediction. WABI 2009: 25-36 - [c38]Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester:
Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. WABI 2009: 37-48 - [c37]Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp:
Fast Prediction of RNA-RNA Interaction. WABI 2009: 261-272 - 2008
- [c36]Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol:
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. ISMB 2008: 32-40 - [c35]Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp:
Biomolecular network motif counting and discovery by color coding. ISMB 2008: 241-249 - [c34]Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp:
The Relation between Indel Length and Functional Divergence: A Formal Study. WABI 2008: 330-341 - [r1]Süleyman Cenk Sahinalp:
Edit Distance Under Block Operations. Encyclopedia of Algorithms 2008 - 2007
- [j16]Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur:
Optimal spaced seeds for faster approximate string matching. J. Comput. Syst. Sci. 73(7): 1035-1044 (2007) - [j15]Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp:
taveRNA: a web suite for RNA algorithms and applications. Nucleic Acids Res. 35(Web-Server-Issue): 325-329 (2007) - [j14]Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, Süleyman Cenk Sahinalp:
Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution. PLoS Comput. Biol. 3(7) (2007) - [j13]Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Süleyman Cenk Sahinalp, Evan E. Eichler:
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data. PLoS Comput. Biol. 3(9) (2007) - [j12]Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp:
Novel approaches for small biomolecule classification and structural similarity search. SIGKDD Explor. 9(1): 14-21 (2007) - [c33]Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov:
Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. Pacific Symposium on Biocomputing 2007: 133-144 - 2006
- [j11]Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang:
RNA-RNA Interaction Prediction and Antisense RNA Target Search. J. Comput. Biol. 13(2): 267-282 (2006) - [j10]Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov:
Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds. J. Chem. Inf. Model. 46(5): 2167-2182 (2006) - [j9]Süleyman Cenk Sahinalp, Ugur Dogrusöz, S. Muthukrishnan:
Preface. Theor. Comput. Sci. 368(3): 195 (2006) - [j8]Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp:
The degree distribution of the generalized duplication model. Theor. Comput. Sci. 369(1-3): 239-249 (2006) - [c32]Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp:
Distance based algorithms for small biomolecule classification and structural similarity search. ISMB (Supplement of Bioinformatics) 2006: 243-251 - [c31]Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, Süleyman Cenk Sahinalp:
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation. Systems Biology and Computational Proteomics 2006: 1-13 - [c30]Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler:
RNA Secondary Structure Prediction Via Energy Density Minimization. RECOMB 2006: 130-142 - [c29]Tugkan Batu, Funda Ergün, Süleyman Cenk Sahinalp:
Oblivious string embeddings and edit distance approximations. SODA 2006: 792-801 - 2005
- [j7]Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp:
Manipulating multiple sequence alignments via MaM and WebMaM. Nucleic Acids Res. 33(Web-Server-Issue): 295-298 (2005) - [c28]Tugkan Batu, Süleyman Cenk Sahinalp:
Locally Consistent Parsing and Applications to Approximate String Comparisons. Developments in Language Theory 2005: 22-35 - [c27]Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur:
Optimal Spaced Seeds for Faster Approximate String Matching. ICALP 2005: 1251-1262 - [c26]Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp:
Improved Duplication Models for Proteome Network Evolution. Systems Biology and Regulatory Genomics 2005: 119-137 - [c25]Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang:
RNA-RNA Interaction Prediction and Antisense RNA Target Search. RECOMB 2005: 152-171 - 2004
- [j6]Emre Karakoç, Z. Meral Özsoyoglu, Süleyman Cenk Sahinalp, Murat Tasan, Xiang Zhang:
Novel Approaches to Biomolecular Sequence Indexing. IEEE Data Eng. Bull. 27(3): 40-47 (2004) - [j5]Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün:
Identifying Uniformly Mutated Segments within Repeats. J. Bioinform. Comput. Biol. 2(4): 657-668 (2004) - [j4]Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp, Eray Tüzün:
The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis. J. Comput. Biol. 11(5): 933-944 (2004) - [j3]S. Muthukrishnan, Süleyman Cenk Sahinalp:
An efficient algorithm for sequence comparison with block reversals. Theor. Comput. Sci. 321(1): 95-101 (2004) - [c24]Süleyman Cenk Sahinalp, Andrey Utis:
Hardness of String Similarity Search and Other Indexing Problems. ICALP 2004: 1080-1098 - [c23]Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp:
Sublinear Methods for Detecting Periodic Trends in Data Streams. LATIN 2004: 16-28 - [e1]Süleyman Cenk Sahinalp, S. Muthukrishnan, Ugur Dogrusöz:
Combinatorial Pattern Matching, 15th Annual Symposium, CPM 2004, Istanbul,Turkey, July 5-7, 2004, Proceedings. Lecture Notes in Computer Science 3109, Springer 2004, ISBN 3-540-22341-X [contents] - 2003
- [c22]Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp:
Comparing Sequences with Segment Rearrangements. FSTTCS 2003: 183-194 - [c21]Süleyman Cenk Sahinalp, Murat Tasan, Jai Macker, Z. Meral Özsoyoglu:
Distance Based Indexing for String Proximity Search. ICDE 2003: 125-136 - 2002
- [c20]Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün:
Statistical Identification of Uniformly Mutated Segments within Repeats. CPM 2002: 249-261 - [c19]S. Muthukrishnan, Süleyman Cenk Sahinalp:
Simple and Practical Sequence Nearest Neighbors with Block Operations. CPM 2002: 262-278 - [c18]S. Muthukrishnan, Süleyman Cenk Sahinalp:
An Improved Algorithm for Sequence Comparison with Block Reversals. LATIN 2002: 319-325 - 2001
- [j2]Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk:
The Complexity of Gene Placement. J. Algorithms 41(2): 225-243 (2001) - [j1]Yossi Matias, Nasir M. Rajpoot, Süleyman Cenk Sahinalp:
The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression. ACM J. Exp. Algorithmics 6: 10 (2001) - [c17]Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha:
Biased Skip Lists for Highly Skewed Access Patterns. ALENEX 2001: 216-230 - [c16]Graham Cormode, S. Muthukrishnan, Süleyman Cenk Sahinalp:
Permutation Editing and Matching via Embeddings. ICALP 2001: 481-492 - [c15]Funda Ergün, Suvo Mittra, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha:
A Dynamic Lookup Scheme for Bursty Access Patterns. INFOCOM 2001: 1444-1453 - [c14]Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha:
Biased dictionaries with fast insert/deletes. STOC 2001: 483-491 - 2000
- [c13]Z. Cohen, Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv:
On the temporal HZY compression scheme. SODA 2000: 185-186 - [c12]Graham Cormode, Mike Paterson, Süleyman Cenk Sahinalp, Uzi Vishkin:
Communication complexity of document exchange. SODA 2000: 197-206 - [c11]S. Muthukrishnan, Süleyman Cenk Sahinalp:
Approximate nearest neighbors and sequence comparison with block operations. STOC 2000: 416-424
1990 – 1999
- 1999
- [c10]Yossi Matias, Nasir M. Rajpoot, Süleyman Cenk Sahinalp:
The Effect of Flexible Parsing for Dynamic Dictionary Based Data Compression. Data Compression Conference 1999: 238-246 - [c9]Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk:
The Complexity of Gene Placement. SODA 1999: 386-395 - [c8]Yossi Matias, Süleyman Cenk Sahinalp:
On the Optimality of Parsing in Dynamic Dictionary Based Data Compression. SODA 1999: 943-944 - [c7]S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp, Torsten Suel:
Compact Grid Layouts of Multi-Level Networks. STOC 1999: 455-463 - 1998
- [c6]Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv:
Augmenting Suffix Trees, with Applications. ESA 1998: 67-78 - [c5]Shimon Even, S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp:
Layout of the Batcher Bitonic Sorter (Extended Abstract). SPAA 1998: 172-181 - [c4]Yossi Matias, Nasir M. Rajpoot, Süleyman Cenk Sahinalp:
Implementation and Experimental Evaluation of Flexible Parsing for Dynamic Dictionary Based Data Compression. WAE 1998: 49-61 - 1996
- [c3]Süleyman Cenk Sahinalp, Uzi Vishkin:
Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm (extended abstract). FOCS 1996: 320-328 - 1994
- [c2]Süleyman Cenk Sahinalp, Uzi Vishkin:
On a Parallel-Algorithms Method for String Matching Problems. CIAC 1994: 22-32 - [c1]Süleyman Cenk Sahinalp, Uzi Vishkin:
Symmetry breaking for suffix tree construction. STOC 1994: 300-309
Coauthor Index
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