Süleyman Cenk Sahinalp

121 papers A* 15A 4B 23C 10Misc 4Journal 57Unranked 5

Year	Rank	Type	Title / Venue / Authors
2024	B	`conf`	Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History. RECOMB Chih Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, Süleyman Cenk Sahinalp, Salem Malikic
2022	J	`jnl`	Fast intratumor heterogeneity inference from single-cell sequencing data. Nat. Comput. Sci. 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
2022	B	`conf`	ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes Using Short Read Data. RECOMB Michael K. B. 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
2021	J	`jnl`	Studying the History of Tumor Evolution from Single-Cell Sequencing Data by Exploring the Space of Binary Matrices. J. Comput. Biol. Salem Malikic, Farid Rashidi Mehrabadi, Erfan Sadeqi Azer, Mohammad Haghir Ebrahim-Abadi, Süleyman Cenk Sahinalp
2020	J	`jnl`	Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 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 González-Pérez, 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
2020	J	`jnl`	Graph Traversal Edit Distance and Extensions. J. Comput. Biol. Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
2020	J	`jnl`	Identification of conserved evolutionary trajectories in tumors. Bioinform. Ermin Hodzic, Raunak Shrestha, Salem Malikic, Colin C. Collins, Kevin Litchfield, Samra Turajlic, Süleyman Cenk Sahinalp
2020	J	`jnl`	PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. Bioinform. 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
2020	J	`jnl`	PyGTED: Python Application for Computing Graph Traversal Edit Distance. J. Comput. Biol. Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
2020	J	`jnl`	The evolutionary history of 2,658 cancers. Nat. 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
2019	J	`jnl`	A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression. Algorithms Mol. Biol. Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, Süleyman Cenk Sahinalp
2019	—	`ch.`	Genomic Data Compression. Encyclopedia of Big Data Technologies Kaiyuan Zhu, Ibrahim Numanagic, Süleyman Cenk Sahinalp
2019	B	`conf`	Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave. RECOMB Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, M. Oguzhan Külekci, David P. Woodruff, Süleyman Cenk Sahinalp
2019	J	`jnl`	lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. Bioinform. Ehsan Haghshenas, Süleyman Cenk Sahinalp, Faraz Hach
2018	C	`conf`	A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression. WABI Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, Süleyman Cenk Sahinalp
2018	J	`jnl`	Computational identification of micro-structural variations and their proteogenomic consequences in cancer. Bioinform. 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
2018	B	`conf`	GTED: Graph Traversal Edit Distance. RECOMB Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
2018	B	`conf`	Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. RECOMB Salem Malikic, Katharina Jahn, Jack Kuipers, Süleyman Cenk Sahinalp, Niko Beerenwinkel
2018	J	`jnl`	MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. Bioinform. 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
2018	J	`jnl`	Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. IEEE Trans. Knowl. Data Eng. 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
2017	J	`jnl`	Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data. J. Comput. Biol. Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp
2017	J	`jnl`	PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. Bioinform. 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
2017	B	`ed.`	Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Hong Kong, China, May 3-7, 2017, Proceedings RECOMB Süleyman Cenk Sahinalp
2017	J	`jnl`	SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA. Bioinform. 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
2016	B	`conf`	Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data. RECOMB Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp
2016	J	`jnl`	CoLoRMap: Correcting Long Reads by Mapping short reads. Bioinform. Ehsan Haghshenas, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve
2016	—	`ch.`	Edit Distance Under Block Operations. Encyclopedia of Algorithms Süleyman Cenk Sahinalp
2015	J	`jnl`	Cypiripi: exact genotyping of Bioinform. Ibrahim Numanagic, Salem Malikic, Victoria M. Pratt, Todd C. Skaar, David A. Flockhart, Süleyman Cenk Sahinalp
2015	B	`conf`	Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. RECOMB Andrew W. McPherson, Andrew Roth, Cédric Chauve, Süleyman Cenk Sahinalp
2015	J	`jnl`	Joint Inference of Genome Structure and Content in Heterogeneous Tumour Samples. CoRR Andrew W. McPherson, Andrew Roth, Gavin Ha, Sohrab P. Shah, Cédric Chauve, Süleyman Cenk Sahinalp
2014	B	`conf`	HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time. RECOMB 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
2014	J	`jnl`	ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Bioinform. Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp
2014	J	`jnl`	mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Res. Faraz Hach, Iman Sarrafi, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
2012	C	`conf`	CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. WABI Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp
2012	B	`conf`	Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing. RECOMB Andrew W. McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp
2012	J	`jnl`	Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinform. Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin C. Collins, Inanç Birol, Süleyman Cenk Sahinalp
2012	J	`jnl`	Mirroring co-evolving trees in the light of their topologies. Bioinform. Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp
2012	J	`jnl`	SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinform. Faraz Hach, Ibrahim Numanagic, Can Alkan, Süleyman Cenk Sahinalp
2012	J	`jnl`	Sensitive and fast mapping of di-base encoded reads. Bioinform. Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
2011	J	`jnl`	Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinform. Andrew W. McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp
2011	J	`jnl`	Mirroring co-evolving trees in the light of their topologies CoRR Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp
2011	J	`jnl`	Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinform. Phuong Dao, Kendric Wang, Colin C. Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp
2011	B	`ed.`	Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings RECOMB Vineet Bafna, Süleyman Cenk Sahinalp
2011	J	`jnl`	Sensitive and fast mapping of di-base encoded reads. Bioinform. Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan
2011	B	`conf`	Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. RECOMB Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew W. McPherson, Evan E. Eichler, Süleyman Cenk Sahinalp
2011	J	`jnl`	deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data. PLoS Comput. Biol. 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
2010	J	`jnl`	Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. J. Chem. Inf. Model. 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 M. 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
2010	J	`jnl`	Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinform. Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp
2010	J	`jnl`	Fast prediction of RNA-RNA interaction. Algorithms Mol. Biol. Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp
2010	J	`jnl`	Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinform. Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
2010	J	`jnl`	PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinform. 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
2010	C	`conf`	Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties. WABI Alexander Schönhuth, Raheleh Salari, Süleyman Cenk Sahinalp
2010	J	`jnl`	Periodicity testing with sublinear samples and space. ACM Trans. Algorithms Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp
2010	J	`jnl`	Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. J. Comput. Biol. Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp
2010	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp
2010	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler
2010	C	`conf`	Sparsification of RNA Structure Prediction Including Pseudoknots. WABI Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp
2010	J	`jnl`	Sparsification of RNA structure prediction including pseudoknots. Algorithms Mol. Biol. Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp
2010	B	`conf`	Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. RECOMB Raheleh Salari, Mathias Möhl, Sebastian Will, Süleyman Cenk Sahinalp, Rolf Backofen
2010	J	`jnl`	Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length. J. Comput. Biol. Alexander Schönhuth, Raheleh Salari, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp
2009	J	`jnl`	A partition function algorithm for interacting nucleic acid strands. Bioinform. Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen
2009	B	`conf`	Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. RECOMB Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp
2009	Misc	`conf`	Dense Graphlet Statistics of Protein Interaction and Random Networks. Pacific Symposium on Biocomputing Recep Colak, Fereydoun Hormozdiari, Flavia Moser, Alexander Schönhuth, J. Holman, Martin Ester, Süleyman Cenk Sahinalp
2009	C	`conf`	Fast Prediction of RNA-RNA Interaction. WABI Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp
2009	C	`conf`	Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. WABI Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester
2009	J	`jnl`	The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study. J. Comput. Biol. Fereydoun Hormozdiari, Raheleh Salari, Michael Hsing, Alexander Schönhuth, Simon K. Chan, Süleyman Cenk Sahinalp, Artem Cherkasov
2009	C	`conf`	biRNA: Fast RNA-RNA Binding Sites Prediction. WABI Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp
2008	A	`conf`	Biomolecular network motif counting and discovery by color coding. ISMB Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp
2008	—	`ch.`	Edit Distance Under Block Operations. Encyclopedia of Algorithms Süleyman Cenk Sahinalp
2008	A	`conf`	Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. ISMB Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol
2008	C	`conf`	The Relation between Indel Length and Functional Divergence: A Formal Study. WABI Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp
2007	Misc	`conf`	Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. Pacific Symposium on Biocomputing Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov
2007	J	`jnl`	Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution. PLoS Comput. Biol. Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, Süleyman Cenk Sahinalp
2007	J	`jnl`	Novel approaches for small biomolecule classification and structural similarity search. SIGKDD Explor. Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp
2007	J	`jnl`	Optimal spaced seeds for faster approximate string matching. J. Comput. Syst. Sci. Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur
2007	J	`jnl`	Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data. PLoS Comput. Biol. Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Süleyman Cenk Sahinalp, Evan E. Eichler
2007	J	`jnl`	taveRNA: a web suite for RNA algorithms and applications. Nucleic Acids Res. Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp
2006	J	`jnl`	Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds. J. Chem. Inf. Model. Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov
2006	—	`conf`	Distance based algorithms for small biomolecule classification and structural similarity search. ISMB (Supplement of Bioinformatics) Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp
2006	—	`conf`	Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation. Systems Biology and Computational Proteomics Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, Süleyman Cenk Sahinalp
2006	A*	`conf`	Oblivious string embeddings and edit distance approximations. SODA Tugkan Batu, Funda Ergün, Süleyman Cenk Sahinalp
2006	J	`jnl`	Preface. Theor. Comput. Sci. Süleyman Cenk Sahinalp, Ugur Dogrusöz, S. Muthukrishnan
2006	B	`conf`	RNA Secondary Structure Prediction Via Energy Density Minimization. RECOMB Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler
2006	J	`jnl`	RNA-RNA Interaction Prediction and Antisense RNA Target Search. J. Comput. Biol. Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang
2006	J	`jnl`	The degree distribution of the generalized duplication model. Theor. Comput. Sci. Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp
2005	—	`conf`	Improved Duplication Models for Proteome Network Evolution. Systems Biology and Regulatory Genomics Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp
2005	C	`conf`	Locally Consistent Parsing and Applications to Approximate String Comparisons. Developments in Language Theory Tugkan Batu, Süleyman Cenk Sahinalp
2005	J	`jnl`	Manipulating multiple sequence alignments via MaM and WebMaM. Nucleic Acids Res. Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp
2005	A*	`conf`	Optimal Spaced Seeds for Faster Approximate String Matching. ICALP Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur
2005	B	`conf`	RNA-RNA Interaction Prediction and Antisense RNA Target Search. RECOMB Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang
2004	J	`jnl`	An efficient algorithm for sequence comparison with block reversals. Theor. Comput. Sci. S. Muthukrishnan, Süleyman Cenk Sahinalp
2004	B	`ed.`	Combinatorial Pattern Matching, 15th Annual Symposium, CPM 2004, Istanbul,Turkey, July 5-7, 2004, Proceedings CPM Süleyman Cenk Sahinalp, S. Muthukrishnan, Ugur Dogrusöz
2004	A*	`conf`	Hardness of String Similarity Search and Other Indexing Problems. ICALP Süleyman Cenk Sahinalp, Andrey Utis
2004	J	`jnl`	Identifying Uniformly Mutated Segments within Repeats. J. Bioinform. Comput. Biol. Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün
2004	J	`jnl`	Novel Approaches to Biomolecular Sequence Indexing. IEEE Data Eng. Bull. Emre Karakoç, Z. Meral Özsoyoglu, Süleyman Cenk Sahinalp, Murat Tasan, Xiang Zhang
2004	B	`conf`	Sublinear Methods for Detecting Periodic Trends in Data Streams. LATIN Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp
2004	J	`jnl`	The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis. J. Comput. Biol. Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp, Eray Tüzün
2003	—	`conf`	Comparing Sequences with Segment Rearrangements. FSTTCS Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp
2003	A*	`conf`	Distance Based Indexing for String Proximity Search. ICDE Süleyman Cenk Sahinalp, Murat Tasan, Jai Macker, Z. Meral Özsoyoglu
2002	B	`conf`	An Improved Algorithm for Sequence Comparison with Block Reversals. LATIN S. Muthukrishnan, Süleyman Cenk Sahinalp
2002	B	`conf`	Simple and Practical Sequence Nearest Neighbors with Block Operations. CPM S. Muthukrishnan, Süleyman Cenk Sahinalp
2002	B	`conf`	Statistical Identification of Uniformly Mutated Segments within Repeats. CPM Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün
2001	A*	`conf`	A Dynamic Lookup Scheme for Bursty Access Patterns. INFOCOM Funda Ergün, Suvo Mittra, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha
2001	A	`conf`	Biased Skip Lists for Highly Skewed Access Patterns. ALENEX Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha
2001	A*	`conf`	Biased dictionaries with fast insert/deletes. STOC Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha
2001	A*	`conf`	Permutation Editing and Matching via Embeddings. ICALP Graham Cormode, S. Muthukrishnan, Süleyman Cenk Sahinalp
2001	J	`jnl`	The Complexity of Gene Placement. J. Algorithms Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk
2001	J	`jnl`	The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression. ACM J. Exp. Algorithmics Yossi Matias, Nasir M. Rajpoot, Süleyman Cenk Sahinalp
2000	A*	`conf`	Approximate nearest neighbors and sequence comparison with block operations. STOC S. Muthukrishnan, Süleyman Cenk Sahinalp
2000	A*	`conf`	Communication complexity of document exchange. SODA Graham Cormode, Mike Paterson, Süleyman Cenk Sahinalp, Uzi Vishkin
2000	A*	`conf`	On the temporal HZY compression scheme. SODA Z. Cohen, Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv
1999	A*	`conf`	Compact Grid Layouts of Multi-Level Networks. STOC S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp, Torsten Suel
1999	A*	`conf`	On the Optimality of Parsing in Dynamic Dictionary Based Data Compression. SODA Yossi Matias, Süleyman Cenk Sahinalp
1999	A*	`conf`	The Complexity of Gene Placement. SODA Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk
1999	B	`conf`	The Effect of Flexible Parsing for Dynamic Dictionary Based Data Compression. Data Compression Conference Yossi Matias, Nasir M. Rajpoot, Süleyman Cenk Sahinalp
1998	A	`conf`	Augmenting Suffix Trees, with Applications. ESA Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv
1998	—	`conf`	Implementation and Experimental Evaluation of Flexible Parsing for Dynamic Dictionary Based Data Compression. WAE Yossi Matias, Nasir M. Rajpoot, Süleyman Cenk Sahinalp
1998	B	`conf`	Layout of the Batcher Bitonic Sorter (Extended Abstract). SPAA Shimon Even, S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp
1996	A*	`conf`	Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm (extended abstract). FOCS Süleyman Cenk Sahinalp, Uzi Vishkin
1994	C	`conf`	On a Parallel-Algorithms Method for String Matching Problems. CIAC Süleyman Cenk Sahinalp, Uzi Vishkin
1994	A*	`conf`	Symmetry breaking for suffix tree construction. STOC Süleyman Cenk Sahinalp, Uzi Vishkin