Süleyman Cenk Sahinalp

ORCID

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 27

Top Venues

Publications

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)
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)
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) (2022)
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) (2021)
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 G. Gut, David Haan, Arif O. 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) (2020)
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) (2020)
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) (2020)
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) (2020)
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) (2020)
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) (2020)
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) (2019)
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)
Ehsan Haghshenas, Süleyman Cenk Sahinalp, Faraz Hach
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. Bioinform. 35 (1) (2019)
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)
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) (2018)
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) (2018)
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) (2018)
Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
GTED: Graph Traversal Edit Distance. RECOMB (2018)
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)
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) (2017)
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) (2017)
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) (2017)
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)
Ehsan Haghshenas, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve
CoLoRMap: Correcting Long Reads by Mapping short reads. Bioinform. 32 (17) (2016)
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 (2015)
Ibrahim Numanagic, Salem Malikic, Victoria M. Pratt, Todd C. Skaar, David A. Flockhart, Süleyman Cenk Sahinalp
using high-throughput sequencing data. Bioinform. 31 (12) (2015)
Andrew W. McPherson, Andrew Roth, Cédric Chauve, Süleyman Cenk Sahinalp
Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. RECOMB (2015)
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) (2014)
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)
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) (2014)
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) (2012)
Faraz Hach, Ibrahim Numanagic, Can Alkan, Süleyman Cenk Sahinalp
SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinform. 28 (23) (2012)
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) (2012)
Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
Sensitive and fast mapping of di-base encoded reads. Bioinform. 28 (1) (2012)
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)
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)
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)
Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
Sensitive and fast mapping of di-base encoded reads. Bioinform. 27 (14) (2011)
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) (2011)
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) (2011)
Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp
Mirroring co-evolving trees in the light of their topologies CoRR (2011)
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)
Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp
Session Introduction. Pacific Symposium on Biocomputing (2010)
Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler
Session Introduction. Pacific Symposium on Biocomputing (2010)
Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp
Sparsification of RNA structure prediction including pseudoknots. Algorithms Mol. Biol. 5 (2010)
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)
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) (2010)
Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp
Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. J. Comput. Biol. 17 (5) (2010)
Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp
Fast prediction of RNA-RNA interaction. Algorithms Mol. Biol. 5 (2010)
Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp
Periodicity testing with sublinear samples and space. ACM Trans. Algorithms 6 (2) (2010)
Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp
Sparsification of RNA Structure Prediction Including Pseudoknots. WABI (2010)
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) (2010)
Raheleh Salari, Mathias Möhl, Sebastian Will, Süleyman Cenk Sahinalp, Rolf Backofen
Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. RECOMB (2010)
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) (2010)
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) (2010)
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) (2010)
Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. RECOMB (2009)
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)
Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen
A partition function algorithm for interacting nucleic acid strands. Bioinform. 25 (12) (2009)
Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp
biRNA: Fast RNA-RNA Binding Sites Prediction. WABI (2009)
Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp
Fast Prediction of RNA-RNA Interaction. WABI (2009)
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) (2009)
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)
Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp
Biomolecular network motif counting and discovery by color coding. ISMB (2008)
Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. ISMB (2008)
Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp
The Relation between Indel Length and Functional Divergence: A Formal Study. WABI (2008)
Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov
Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. Pacific Symposium on Biocomputing (2007)
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) (2007)
Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp
Novel approaches for small biomolecule classification and structural similarity search. SIGKDD Explor. 9 (1) (2007)
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)
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)
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) (2007)
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)
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) (2006)
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) (2006)
Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp
Distance based algorithms for small biomolecule classification and structural similarity search. ISMB (Supplement of Bioinformatics) (2006)
Süleyman Cenk Sahinalp, Ugur Dogrusöz, S. Muthukrishnan
Preface. Theor. Comput. Sci. 368 (3) (2006)
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) (2006)
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)
Tugkan Batu, Funda Ergün, Süleyman Cenk Sahinalp
Oblivious string embeddings and edit distance approximations. SODA (2006)
Tugkan Batu, Süleyman Cenk Sahinalp
Locally Consistent Parsing and Applications to Approximate String Comparisons. Developments in Language Theory (2005)
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) (2005)
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)
Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur
Optimal Spaced Seeds for Faster Approximate String Matching. ICALP (2005)
Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang
RNA-RNA Interaction Prediction and Antisense RNA Target Search. RECOMB (2005)
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) (2004)
Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp
Sublinear Methods for Detecting Periodic Trends in Data Streams. LATIN (2004)
Süleyman Cenk Sahinalp, Andrey Utis
Hardness of String Similarity Search and Other Indexing Problems. ICALP (2004)
Emre Karakoç, Z. Meral Özsoyoglu, Süleyman Cenk Sahinalp, Murat Tasan, Xiang Zhang
Novel Approaches to Biomolecular Sequence Indexing. IEEE Data Eng. Bull. 27 (3) (2004)
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) (2004)
S. Muthukrishnan, Süleyman Cenk Sahinalp
An efficient algorithm for sequence comparison with block reversals. Theor. Comput. Sci. 321 (1) (2004)
Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp
Comparing Sequences with Segment Rearrangements. FSTTCS (2003)
Süleyman Cenk Sahinalp, Murat Tasan, Jai Macker, Z. Meral Özsoyoglu
Distance Based Indexing for String Proximity Search. ICDE (2003)
S. Muthukrishnan, Süleyman Cenk Sahinalp
An Improved Algorithm for Sequence Comparison with Block Reversals. LATIN (2002)
S. Muthukrishnan, Süleyman Cenk Sahinalp
Simple and Practical Sequence Nearest Neighbors with Block Operations. CPM (2002)
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)
Yossi Matias, Nasir M. Rajpoot, Süleyman Cenk Sahinalp
The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression. ACM J. Exp. Algorithmics 6 (2001)
Funda Ergün, Suvo Mittra, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha
A Dynamic Lookup Scheme for Bursty Access Patterns. INFOCOM (2001)
Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha
Biased Skip Lists for Highly Skewed Access Patterns. ALENEX (2001)
Graham Cormode, S. Muthukrishnan, Süleyman Cenk Sahinalp
Permutation Editing and Matching via Embeddings. ICALP (2001)

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Süleyman Cenk Sahinalp