Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer.

Süleyman Cenk Sahinalp S. Cenk Sahinalp Simon Fraser University, Burnaby, Canada http://www.cs.sfu.ca/~cenk/ https://orcid.org/0000-0002-5050-0682

Xuan Cindy Li Yuelin Liu Alejandro A. Schäffer Stephen M. Mount S. Cenk Sahinalp Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer. i150-i159 2025 41 Bioinform. Supplement_1 https://doi.org/10.1093/bioinformatics/btaf237 db/journals/bioinformatics/bioinformatics41.html#LiLSMS25

Natnatee Dokmai Kaiyuan Zhu S. Cenk Sahinalp Hyunghoon Cho TX-Phase: Secure Phasing of Private Genomes in a Trusted Execution Environment. 325-329 2025 RECOMB https://doi.org/10.1007/978-3-031-90252-9_32 conf/recomb/2025 db/conf/recomb/recomb2025.html#DokmaiZSC25 streams/conf/recomb Farid Rashidi Mehrabadi Erfan Sadeqi Azer John D. Bridgers Eva Pérez-Guijarro Kerrie Marie Howard H. Yang Charli Gruen Chih Hao Wu Welles Robinson Huaitian Liu Can Kizilkale Michael C. Kelly Cari Smith Sung Chin Jessica Ebersole Sandra Burkett Aydin Buluç Maxwell P. Lee Erin K. Molloy Teresa M. Przytycka Glenn Merlino Chi-Ping Day Salem Malikic Funda Ergün S. Cenk Sahinalp A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data. 409-413 2025 RECOMB https://doi.org/10.1007/978-3-031-90252-9_50 conf/recomb/2025 db/conf/recomb/recomb2025.html#MehrabadiABPMYGWRLKKSCE25 streams/conf/recomb John D. Bridgers Jan Hoinka S. Cenk Sahinalp Salem Malikic Teresa M. Przytycka Funda Ergün Improved Algorithms for Bi-Partition Function Computation. 5:1-5:18 2025 WABI https://doi.org/10.4230/LIPIcs.WABI.2025.5 conf/wabi/2025 db/conf/wabi/wabi2025.html#BridgersHSMPE25

Michael K. B. Ford Ananth Hari Qinghui Zhou Ibrahim Numanagic S. Cenk Sahinalp Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool. 2024 40 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btae622 db/journals/bioinformatics/bioinformatics40.html#FordHZNS24

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. 438-443 2024 RECOMB https://doi.org/10.1007/978-1-0716-3989-4_48 conf/recomb/2024 db/conf/recomb/recomb2024.html#WuJRRSSM24

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. 577-583 2022 2 Nat. Comput. Sci. 9 https://doi.org/10.1038/s43588-022-00298-x db/journals/ncs/ncs2.html#KizilkaleMAPMLD22

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 ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes Using Short Read Data. 382-384 2022 RECOMB https://doi.org/10.1007/978-3-031-04749-7_37 https://www.wikidata.org/entity/Q128021053 conf/recomb/2022 db/conf/recomb/recomb2022.html#FordHRXLOZWMBXS22

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. 857-879 2021 28 J. Comput. Biol. 9 https://doi.org/10.1089/cmb.2020.0595 db/journals/jcb/jcb28.html#MalikicMAES21

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. i169-i176 2020 36 Bioinform. Supplement-1 https://doi.org/10.1093/bioinformatics/btaa464 https://www.wikidata.org/entity/Q97542007 db/journals/bioinformatics/bioinformatics36.html#AzerMMLBLLSSGDP20

Ermin Hodzic Raunak Shrestha Salem Malikic Colin C. Collins Kevin Litchfield Samra Turajlic Süleyman Cenk Sahinalp Identification of conserved evolutionary trajectories in tumors. i427-i435 2020 36 Bioinform. Supplement-1 https://doi.org/10.1093/bioinformatics/btaa453 https://www.wikidata.org/entity/Q97542145 db/journals/bioinformatics/bioinformatics36.html#HodzicSMCLTS20

Ali Ebrahimpour Boroojeny Akash Shrestha Ali Sharifi-Zarchi Suzanne Renick Gallagher Süleyman Cenk Sahinalp Hamidreza Chitsaz Graph Traversal Edit Distance and Extensions. 317-329 2020 27 J. Comput. Biol. 3 https://doi.org/10.1089/cmb.2019.0511 https://www.wikidata.org/entity/Q89716723 db/journals/jcb/jcb27.html#BoroojenySSGSC20

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. 436-439 2020 27 J. Comput. Biol. 3 https://doi.org/10.1089/cmb.2019.0510 https://www.wikidata.org/entity/Q90234897 db/journals/jcb/jcb27.html#BoroojenySSGSC20a

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 0006 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 0062 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 0032 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. 102-111 2020 578 Nat. 7793 https://doi.org/10.1038/s41586-020-1965-x https://www.wikidata.org/entity/Q89557100 db/journals/nature/nature578.html#RheinbayNAWSTHH20

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 0001 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. 122-128 2020 578 Nat. 7793 https://doi.org/10.1038/s41586-019-1907-7 https://www.wikidata.org/entity/Q89556915 db/journals/nature/nature578.html#GerstungJLDGRMR20

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. 2020 abs/2009.11665 CoRR https://arxiv.org/abs/2009.11665 db/journals/corr/corr2009.html#abs-2009-11665

Nikolai Karpov Salem Malikic Md. Khaledur Rahman Süleyman Cenk Sahinalp A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression. 17:1-17:18 2019 14 Algorithms Mol. Biol. 1 https://doi.org/10.1186/s13015-019-0152-9 https://www.wikidata.org/entity/Q92355631 db/journals/almob/almob14.html#KarpovMRS19

Ehsan Haghshenas Süleyman Cenk Sahinalp Faraz Hach lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. 20-27 2019 35 Bioinform. 1 https://doi.org/10.1093/bioinformatics/bty544 https://www.wikidata.org/entity/Q90609863 db/journals/bioinformatics/bioinformatics35.html#HaghshenasSH19

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. 483-492 2019 IEEE BigData https://doi.org/10.1109/BigData47090.2019.9006037 conf/bigdataconf/2019 db/conf/bigdataconf/bigdataconf2019.html#ChenLSMVNSIQ19 Sean Simmons 0001 Bonnie Berger S. Cenk Sahinalp Protecting Genomic Data Privacy with Probabilistic Modeling. 403-414 2019 PSB http://psb.stanford.edu/psb-online/proceedings/psb19/simmons.pdf conf/psb/2019 db/conf/psb/psb2019.html#0001BS19 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. 302-304 2019 RECOMB https://link.springer.com/content/pdf/bbm%3A978-3-030-17083-7%2F1.pdf conf/recomb/2019 db/conf/recomb/recomb2019.html#KockanZDKKWS19 Kaiyuan Zhu Ibrahim Numanagic Süleyman Cenk Sahinalp Genomic Data Compression. 2019 Encyclopedia of Big Data Technologies https://doi.org/10.1007/978-3-319-63962-8_55-1 https://www.wikidata.org/entity/Q124796869 reference/bdt/2019 db/reference/bdt/1.html#ZhuNS19

Yen-Yi Lin Alexander Gawronski Faraz Hach Sujun Li Ibrahim Numanagic Iman Sarrafi Swati Mishra 0006 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. 1672-1681 2018 34 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btx807 https://www.wikidata.org/entity/Q47264953 db/journals/bioinformatics/bioinformatics34.html#LinGHLNSMMCRTS18

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. 3101-3110 2018 34 Bioinform. 18 https://doi.org/10.1093/bioinformatics/bty208 https://www.wikidata.org/entity/Q52607047 db/journals/bioinformatics/bioinformatics34.html#GawronskiUZLNRM18

S. Cenk Sahinalp Preface: Selected Articles from RECOMB 2017. 623 2018 25 J. Comput. Biol. 7 https://doi.org/10.1089/cmb.2018.29017.cs https://www.wikidata.org/entity/Q90241437 db/journals/jcb/jcb25.html#Sahinalp18

Makoto Yamada Jiliang Tang Jose Lugo-Martinez Ermin Hodzic Raunak Shrestha Avishek Saha Hua Ouyang Dawei Yin 0001 Hiroshi Mamitsuka Süleyman Cenk Sahinalp Predrag Radivojac Filippo Menczer Yi Chang 0001 Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. 1352-1365 2018 30 IEEE Trans. Knowl. Data Eng. 7 https://doi.org/10.1109/TKDE.2018.2789451 http://doi.ieeecomputersociety.org/10.1109/TKDE.2018.2789451 db/journals/tkde/tkde30.html#YamadaTLHSSOYMS18

Ali Ebrahimpour Boroojeny Akash Shrestha Ali Sharifi-Zarchi Suzanne Renick Gallagher Süleyman Cenk Sahinalp Hamidreza Chitsaz GTED: Graph Traversal Edit Distance. 37-53 2018 RECOMB https://doi.org/10.1007/978-3-319-89929-9_3 conf/recomb/2018 db/conf/recomb/recomb2018.html#BoroojenySSGSC18 Salem Malikic Katharina Jahn 0001 Jack Kuipers Süleyman Cenk Sahinalp Niko Beerenwinkel Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. 269-270 2018 RECOMB https://link.springer.com/content/pdf/bbm%3A978-3-319-89929-9%2F1.pdf conf/recomb/2018 db/conf/recomb/recomb2018.html#MalikicJKSB18 Nikolai Karpov Salem Malikic Md. Khaledur Rahman Süleyman Cenk Sahinalp A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression. 22:1-22:19 2018 WABI https://doi.org/10.4230/LIPIcs.WABI.2018.22 conf/wabi/2018 db/conf/wabi/wabi2018.html#KarpovMRS18

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. 26-34 2017 33 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btw536 https://www.wikidata.org/entity/Q39484267 db/journals/bioinformatics/bioinformatics33.html#KockanHSBMBHWVC17

Feng Chen 0016 Shuang Wang 0002 Xiaoqian Jiang Sijie Ding Yao Lu 0006 Jihoon Kim 0001 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. 871-878 2017 33 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btw758 https://www.wikidata.org/entity/Q39033087 db/journals/bioinformatics/bioinformatics33.html#ChenWJDLKSSBWPH17

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. 515-523 2017 24 J. Comput. Biol. 6 https://doi.org/10.1089/cmb.2016.0148 https://www.wikidata.org/entity/Q31152930 db/journals/jcb/jcb24.html#DonmezMWGCS17

Süleyman Cenk Sahinalp Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Hong Kong, China, May 3-7, 2017, Proceedings RECOMB 2017 Lecture Notes in Computer Science 10229 978-3-319-56969-7 978-3-319-56970-3 https://doi.org/10.1007/978-3-319-56970-3 https://www.wikidata.org/entity/Q88509423 db/conf/recomb/recomb2017.html

Ehsan Haghshenas Faraz Hach Süleyman Cenk Sahinalp Cédric Chauve CoLoRMap: Correcting Long Reads by Mapping short reads. 545-551 2016 32 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btw463 https://www.wikidata.org/entity/Q39429396 db/journals/bioinformatics/bioinformatics32.html#HaghshenasHSC16

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. 83-94 2016 RECOMB https://doi.org/10.1007/978-3-319-31957-5_6 conf/recomb/2016 db/conf/recomb/recomb2016.html#DonmezMWGCS16 Sean Simmons 0001 S. Cenk Sahinalp Bonnie Berger Enabling Privacy Preserving GWAS in Heterogeneous Human Populations. 246-247 2016 RECOMB https://link.springer.com/content/pdf/bbm%3A978-3-319-31957-5%2F1.pdf conf/recomb/2016 db/conf/recomb/recomb2016.html#0001SB16 Süleyman Cenk Sahinalp Edit Distance Under Block Operations. 611-614 2016 Encyclopedia of Algorithms https://doi.org/10.1007/978-1-4939-2864-4_122 db/reference/algo/algo2016.html#Sahinalp16

Salem Malikic Andrew W. McPherson Nilgun Donmez S. Cenk Sahinalp Clonality inference in multiple tumor samples using phylogeny. 1349-1356 2015 31 Bioinform. 9 https://doi.org/10.1093/bioinformatics/btv003 https://www.wikidata.org/entity/Q41610580 db/journals/bioinformatics/bioinformatics31.html#MalikicMDS15

Ibrahim Numanagic Salem Malikic Victoria M. Pratt Todd C. Skaar David A. Flockhart Süleyman Cenk Sahinalp Cypiripi: exact genotyping of <i>CYP2D6</i> using high-throughput sequencing data. 27-34 2015 31 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btv232 https://www.wikidata.org/entity/Q30971296 db/journals/bioinformatics/bioinformatics31.html#NumanagicMPSFS15

Andrew W. McPherson Andrew Roth Cédric Chauve Süleyman Cenk Sahinalp Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. 256-258 2015 RECOMB https://doi.org/10.1007/978-3-319-16706-0_25 conf/recomb/2015 db/conf/recomb/recomb2015.html#McPhersonRCS15

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. 2015 abs/1504.03080 CoRR http://arxiv.org/abs/1504.03080 db/journals/corr/corr1504.html#McPhersonRHSCS15

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. 644-651 2014 30 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btt591 https://www.wikidata.org/entity/Q43826516 db/journals/bioinformatics/bioinformatics30.html#DaoNLHKDCES14

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. 494-500 2014 42 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gku370 https://www.wikidata.org/entity/Q33860843 db/journals/nar/nar42.html#HachSHAES14

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. 293-306 2014 RECOMB https://doi.org/10.1007/978-3-319-05269-4_23 https://www.wikidata.org/entity/Q57693305 conf/recomb/2014 db/conf/recomb/recomb2014.html#ShresthaHYWSDABRCHS14

Farhad Hormozdiari Faraz Hach Süleyman Cenk Sahinalp Evan E. Eichler Can Alkan Sensitive and fast mapping of di-base encoded reads. 150 2012 28 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btr647 https://www.wikidata.org/entity/Q93547169 db/journals/bioinformatics/bioinformatics28.html#HormozdiariHSEA12

Iman Hajirasouliha Alexander Schönhuth David de Juan Alfonso Valencia Süleyman Cenk Sahinalp Mirroring co-evolving trees in the light of their topologies. 1202-1208 2012 28 Bioinform. 9 https://doi.org/10.1093/bioinformatics/bts109 https://www.wikidata.org/entity/Q48003918 db/journals/bioinformatics/bioinformatics28.html#HajirasoulihaSJVS12

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. 179-187 2012 28 Bioinform. 12 https://doi.org/10.1093/bioinformatics/bts214 https://www.wikidata.org/entity/Q36022127 db/journals/bioinformatics/bioinformatics28.html#YorukogluHSCBS12

Faraz Hach Ibrahim Numanagic Can Alkan Süleyman Cenk Sahinalp SCALCE: boosting sequence compression algorithms using locally consistent encoding. 3051-3057 2012 28 Bioinform. 23 https://doi.org/10.1093/bioinformatics/bts593 https://www.wikidata.org/entity/Q28276638 db/journals/bioinformatics/bioinformatics28.html#HachNAS12

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. 181-182 2012 RECOMB https://doi.org/10.1007/978-3-642-29627-7_17 conf/recomb/2012 db/conf/recomb/recomb2012.html#McPhersonWWSCS12 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. 178-189 2012 WABI https://doi.org/10.1007/978-3-642-33122-0_14 conf/wabi/2012 db/conf/wabi/wabi2012.html#LinDHBMLCS12

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. 1481-1488 2011 27 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btr184 https://www.wikidata.org/entity/Q33866899 db/journals/bioinformatics/bioinformatics27.html#McPhersonWHHHLVSCS11

Phuong Dao Kendric Wang Colin C. Collins Martin Ester Anna Lapuk Süleyman Cenk Sahinalp Optimally discriminative subnetwork markers predict response to chemotherapy. 205-213 2011 27 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btr245 https://www.wikidata.org/entity/Q42762256 db/journals/bioinformatics/bioinformatics27.html#DaoWCELS11

Farhad Hormozdiari Faraz Hach Süleyman Cenk Sahinalp Evan E. Eichler Can Alkan Sensitive and fast mapping of di-base encoded reads. 1915-1921 2011 27 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btr303 https://www.wikidata.org/entity/Q35086028 db/journals/bioinformatics/bioinformatics27.html#HormozdiariHSEA11

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. 2011 7 PLoS Comput. Biol. 5 https://doi.org/10.1371/journal.pcbi.1001138 https://www.wikidata.org/entity/Q33916606 db/journals/ploscb/ploscb7.html#McPhersonHZGHSGMSMPMHNSHS11

Fereydoun Hormozdiari Iman Hajirasouliha Andrew W. McPherson Evan E. Eichler Süleyman Cenk Sahinalp Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. 104-105 2011 RECOMB https://doi.org/10.1007/978-3-642-20036-6_11 conf/recomb/2011 db/conf/recomb/recomb2011.html#HormozdiariHMES11 Vineet Bafna Süleyman Cenk Sahinalp Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings 6577 2011 https://doi.org/10.1007/978-3-642-20036-6 978-3-642-20035-9 RECOMB Lecture Notes in Computer Science Springer db/conf/recomb/recomb2011.html

Iman Hajirasouliha Alexander Schönhuth David de Juan Alfonso Valencia Süleyman Cenk Sahinalp Mirroring co-evolving trees in the light of their topologies http://arxiv.org/abs/1110.5704 2011 CoRR abs/1110.5704 db/journals/corr/corr1110.html#abs-1110-5704

Raheleh Salari Rolf Backofen Süleyman Cenk Sahinalp Fast prediction of RNA-RNA interaction. 5 2010 5 Algorithms Mol. Biol. https://doi.org/10.1186/1748-7188-5-5 https://www.wikidata.org/entity/Q39270386 db/journals/almob/almob5.html#SalariBS10

Mathias Möhl Raheleh Salari Sebastian Will Rolf Backofen Süleyman Cenk Sahinalp Sparsification of RNA structure prediction including pseudoknots. 39 2010 5 Algorithms Mol. Biol. https://doi.org/10.1186/1748-7188-5-39 https://www.wikidata.org/entity/Q38259402 db/journals/almob/almob5.html#MohlSWBS10

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. 1277-1283 2010 26 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btq152 https://www.wikidata.org/entity/Q33834741 db/journals/bioinformatics/bioinformatics26.html#HajirasoulihaHAKBES10

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. 350-357 2010 26 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btq216 https://www.wikidata.org/entity/Q24599569 db/journals/bioinformatics/bioinformatics26.html#HormozdiariHDHYAES10

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. 1608-1615 2010 26 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btq249 https://www.wikidata.org/entity/Q41126055 db/journals/bioinformatics/bioinformatics26.html#YuWLMRLDSEFB10

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. 1-20 2010 17 J. Comput. Biol. 1 https://doi.org/10.1089/cmb.2009.0031 https://www.wikidata.org/entity/Q38507685 db/journals/jcb/jcb17.html#SchonhuthSHCS10

Fereydoun Hormozdiari Raheleh Salari Vineet Bafna Süleyman Cenk Sahinalp Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. 669-684 2010 17 J. Comput. Biol. 5 https://doi.org/10.1089/cmb.2009.0032 https://www.wikidata.org/entity/Q51694945 db/journals/jcb/jcb17.html#HormozdiariSBS10

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 Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. 2094-2111 2010 50 J. Chem. Inf. Model. 12 https://doi.org/10.1021/ci100253r https://www.wikidata.org/entity/Q54376695 db/journals/jcisd/jcisd50.html#SushkoNKPCLGHSMXLYOHDSTPAKMYFMTBHMMVPT10

Funda Ergün S. Muthukrishnan 0001 Süleyman Cenk Sahinalp Periodicity testing with sublinear samples and space. 2010 6 ACM Trans. Algorithms 2 https://doi.org/10.1145/1721837.1721859 db/journals/talg/talg6.html#ErgunMS10 43:1-43:14

Rolf Backofen Hamidreza Chitsaz Ivo L. Hofacker Süleyman Cenk Sahinalp Peter F. Stadler Session Introduction. 54-56 2010 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb10/intro-rna.pdf conf/psb/2010 db/conf/psb/psb2010.html#BackofenCHSS10 Can Alkan Michael Brudno Evan E. Eichler Maricel G. Kann Süleyman Cenk Sahinalp Session Introduction. 302-304 2010 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb10/intro-personal.pdf conf/psb/2010 db/conf/psb/psb2010.html#AlkanBEKS10 Raheleh Salari Mathias Möhl Sebastian Will Süleyman Cenk Sahinalp Rolf Backofen Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. 473-490 2010 RECOMB https://doi.org/10.1007/978-3-642-12683-3_31 conf/recomb/2010 db/conf/recomb/recomb2010.html#SalariMWSB10 Mathias Möhl Raheleh Salari Sebastian Will Rolf Backofen Süleyman Cenk Sahinalp Sparsification of RNA Structure Prediction Including Pseudoknots. 40-51 2010 WABI https://doi.org/10.1007/978-3-642-15294-8_4 conf/wabi/2010 db/conf/wabi/wabi2010.html#MohlSWBS10 Alexander Schönhuth Raheleh Salari Süleyman Cenk Sahinalp Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties. 350-361 2010 WABI https://doi.org/10.1007/978-3-642-15294-8_29 conf/wabi/2010 db/conf/wabi/wabi2010.html#SchonhuthSS10

Hamidreza Chitsaz Raheleh Salari Süleyman Cenk Sahinalp Rolf Backofen A partition function algorithm for interacting nucleic acid strands. 2009 25 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btp212 https://www.wikidata.org/entity/Q24654098 db/journals/bioinformatics/bioinformatics25.html#ChitsazSSB09

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. 159-167 2009 16 J. Comput. Biol. 2 https://doi.org/10.1089/cmb.2008.03TT https://www.wikidata.org/entity/Q51840296 db/journals/jcb/jcb16.html#HormozdiariSHSCSC09

Recep Colak Fereydoun Hormozdiari Flavia Moser Alexander Schönhuth J. Holman Martin Ester Süleyman Cenk Sahinalp Dense Graphlet Statistics of Protein Interaction and Random Networks. 178-189 2009 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb09/colak.pdf conf/psb/2009 db/conf/psb/psb2009.html#ColakHMSHES09 Fereydoun Hormozdiari Can Alkan Evan E. Eichler Süleyman Cenk Sahinalp Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. 218-219 2009 RECOMB https://doi.org/10.1007/978-3-642-02008-7_16 conf/recomb/2009 db/conf/recomb/recomb2009.html#HormozdiariAES09 Hamidreza Chitsaz Rolf Backofen Süleyman Cenk Sahinalp biRNA: Fast RNA-RNA Binding Sites Prediction. 25-36 2009 WABI https://doi.org/10.1007/978-3-642-04241-6_3 conf/wabi/2009 db/conf/wabi/wabi2009.html#ChitsazBS09 Phuong Dao Alexander Schönhuth Fereydoun Hormozdiari Iman Hajirasouliha Süleyman Cenk Sahinalp Martin Ester Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. 37-48 2009 WABI https://doi.org/10.1007/978-3-642-04241-6_4 conf/wabi/2009 db/conf/wabi/wabi2009.html#DaoSHHSE09 Raheleh Salari Rolf Backofen Süleyman Cenk Sahinalp Fast Prediction of RNA-RNA Interaction. 261-272 2009 WABI https://doi.org/10.1007/978-3-642-04241-6_22 conf/wabi/2009 db/conf/wabi/wabi2009.html#SalariBS09 Iman Hajirasouliha Fereydoun Hormozdiari Süleyman Cenk Sahinalp Inanç Birol Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. 32-40 2008 ISMB https://doi.org/10.1093/bioinformatics/btn173 https://www.wikidata.org/entity/Q42132757 conf/ismb/2008 db/conf/ismb/ismb2008.html#HajirasoulihaHSB08 Noga Alon Phuong Dao Iman Hajirasouliha Fereydoun Hormozdiari Süleyman Cenk Sahinalp Biomolecular network motif counting and discovery by color coding. 241-249 2008 ISMB https://doi.org/10.1093/bioinformatics/btn163 https://www.wikidata.org/entity/Q34789976 conf/ismb/2008 db/conf/ismb/ismb2008.html#AlonDHHS08 Raheleh Salari Alexander Schönhuth Fereydoun Hormozdiari Artem Cherkasov Süleyman Cenk Sahinalp The Relation between Indel Length and Functional Divergence: A Formal Study. 330-341 2008 WABI https://doi.org/10.1007/978-3-540-87361-7_28 conf/wabi/2008 db/conf/wabi/wabi2008.html#SalariSHCS08 Süleyman Cenk Sahinalp Edit Distance Under Block Operations. 2008 Encyclopedia of Algorithms https://doi.org/10.1007/978-0-387-30162-4_122 reference/algo/2008 db/reference/algo/algo2008.html#Sahinalp08

Martin Farach-Colton Gad M. Landau Süleyman Cenk Sahinalp Dekel Tsur Optimal spaced seeds for faster approximate string matching. 1035-1044 2007 73 J. Comput. Syst. Sci. 7 https://doi.org/10.1016/j.jcss.2007.03.007 db/journals/jcss/jcss73.html#Farach-ColtonLST07

Cagri Aksay Raheleh Salari Emre Karakoç Can Alkan Süleyman Cenk Sahinalp taveRNA: a web suite for RNA algorithms and applications. 325-329 2007 35 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gkm303 https://www.wikidata.org/entity/Q41862019 db/journals/nar/nar35.html#AksaySKAS07

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. 2007 3 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.0030118 https://www.wikidata.org/entity/Q33290222 db/journals/ploscb/ploscb3.html#HormozdiariBPS07

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. 2007 3 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.0030181 https://www.wikidata.org/entity/Q31131695 db/journals/ploscb/ploscb3.html#AlkanVARSE07

Emre Karakoç Artem Cherkasov Süleyman Cenk Sahinalp Novel approaches for small biomolecule classification and structural similarity search. 14-21 2007 9 SIGKDD Explor. 1 https://doi.org/10.1145/1294301.1294307 db/journals/sigkdd/sigkdd9.html#KarakocCS07

Emre Karakoç Süleyman Cenk Sahinalp Artem Cherkasov Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. 133-144 2007 conf/psb/2007 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb07/karakoc.pdf db/conf/psb/psb2007.html#KarakocSC07

Can Alkan Emre Karakoç Joseph H. Nadeau Süleyman Cenk Sahinalp Kaizhong Zhang RNA-RNA Interaction Prediction and Antisense RNA Target Search. 267-282 2006 13 J. Comput. Biol. 2 https://doi.org/10.1089/cmb.2006.13.267 https://www.wikidata.org/entity/Q51944572 db/journals/jcb/jcb13.html#AlkanKNSZ06

Emre Karakoç Süleyman Cenk Sahinalp Artem Cherkasov Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds. 2167-2182 2006 46 J. Chem. Inf. Model. 5 https://doi.org/10.1021/ci0601517 https://www.wikidata.org/entity/Q51932936 db/journals/jcisd/jcisd46.html#KarakocSC06

Süleyman Cenk Sahinalp Ugur Dogrusöz S. Muthukrishnan 0001 Preface. 195 2006 368 Theor. Comput. Sci. 3 https://doi.org/10.1016/j.tcs.2006.09.011 db/journals/tcs/tcs368.html#SahinalpDM06

Gürkan Bebek Petra Berenbrink Colin Cooper Tom Friedetzky Joseph H. Nadeau Süleyman Cenk Sahinalp The degree distribution of the generalized duplication model. 239-249 2006 369 Theor. Comput. Sci. 1-3 https://doi.org/10.1016/j.tcs.2006.08.045 db/journals/tcs/tcs369.html#BebekBCFNS06

Emre Karakoç Artem Cherkasov Süleyman Cenk Sahinalp Distance based algorithms for small biomolecule classification and structural similarity search. 243-251 2006 conf/ismb/2006 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/btl259 https://www.wikidata.org/entity/Q48437512 db/conf/ismb/ismb2006.html#KarakocCS06 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. 1-13 2006 conf/recomb/2006sbcp Systems Biology and Computational Proteomics https://doi.org/10.1007/978-3-540-73060-6_1 db/conf/recomb/sbcp2006.html#HormozdiariBPS06 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. 130-142 2006 conf/recomb/2006 RECOMB https://doi.org/10.1007/11732990_12 db/conf/recomb/recomb2006.html#AlkanKSUEZB06 Tugkan Batu Funda Ergün Süleyman Cenk Sahinalp Oblivious string embeddings and edit distance approximations. 792-801 2006 conf/soda/2006 SODA http://dl.acm.org/citation.cfm?id=1109557.1109644 db/conf/soda/soda2006.html#BatuES06

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. 295-298 2005 33 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gki406 https://www.wikidata.org/entity/Q24812546 db/journals/nar/nar33.html#AlkanTBLEBS05

Tugkan Batu Süleyman Cenk Sahinalp Locally Consistent Parsing and Applications to Approximate String Comparisons. 22-35 2005 conf/dlt/2005 Developments in Language Theory https://doi.org/10.1007/11505877_3 db/conf/dlt/dlt2005.html#BatuS05 Martin Farach-Colton Gad M. Landau Süleyman Cenk Sahinalp Dekel Tsur Optimal Spaced Seeds for Faster Approximate String Matching. 1251-1262 2005 conf/icalp/2005 ICALP https://doi.org/10.1007/11523468_101 db/conf/icalp/icalp2005.html#Farach-ColtonLST05 Gürkan Bebek Petra Berenbrink Colin Cooper Tom Friedetzky Joseph H. Nadeau Süleyman Cenk Sahinalp Improved Duplication Models for Proteome Network Evolution. 119-137 2005 conf/recomb/2005sbrg Systems Biology and Regulatory Genomics https://doi.org/10.1007/978-3-540-48540-7_11 db/conf/recomb/sbrg2005.html#BebekBCFNS05 Can Alkan Emre Karakoç Joseph H. Nadeau Süleyman Cenk Sahinalp Kaizhong Zhang RNA-RNA Interaction Prediction and Antisense RNA Target Search. 152-171 2005 conf/recomb/2005 RECOMB https://doi.org/10.1007/11415770_12 db/conf/recomb/recomb2005.html#AlkanKNSZ05

Emre Karakoç Z. Meral Özsoyoglu Süleyman Cenk Sahinalp Murat Tasan Xiang Zhang 0001 Novel Approaches to Biomolecular Sequence Indexing. 40-47 2004 27 IEEE Data Eng. Bull. 3 http://sites.computer.org/debull/A04sept/bulletin.ps db/journals/debu/debu27.html#KarakocOSTZ04

Süleyman Cenk Sahinalp Evan E. Eichler Paul W. Goldberg Petra Berenbrink Tom Friedetzky Funda Ergün Identifying Uniformly Mutated Segments within Repeats. 657-668 2004 2 J. Bioinform. Comput. Biol. 4 https://doi.org/10.1142/S0219720004000788 https://www.wikidata.org/entity/Q51981501 db/journals/jbcb/jbcb2.html#SahinalpEGBFE04

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. 933-944 2004 11 J. Comput. Biol. 5 https://doi.org/10.1089/cmb.2004.11.933 https://www.wikidata.org/entity/Q81380591 db/journals/jcb/jcb11.html#AlkanEBST04

S. Muthukrishnan 0001 Süleyman Cenk Sahinalp An efficient algorithm for sequence comparison with block reversals. 95-101 2004 321 Theor. Comput. Sci. 1 https://doi.org/10.1016/j.tcs.2003.05.005 db/journals/tcs/tcs321.html#MuthukrishnanS04

Süleyman Cenk Sahinalp Andrey Utis Hardness of String Similarity Search and Other Indexing Problems. 1080-1098 https://doi.org/10.1007/978-3-540-27836-8_90 2004 conf/icalp/2004 ICALP db/conf/icalp/icalp2004.html#SahinalpU04 Funda Ergün S. Muthukrishnan 0001 Süleyman Cenk Sahinalp Sublinear Methods for Detecting Periodic Trends in Data Streams. 16-28 https://doi.org/10.1007/978-3-540-24698-5_6 2004 conf/latin/2004 LATIN db/conf/latin/latin2004.html#ErgunMS04 Süleyman Cenk Sahinalp S. Muthukrishnan 0001 Ugur Dogrusöz Combinatorial Pattern Matching, 15th Annual Symposium, CPM 2004, Istanbul,Turkey, July 5-7, 2004, Proceedings 3-540-22341-X CPM Lecture Notes in Computer Science 3109 Springer 2004 https://doi.org/10.1007/b98377 db/conf/cpm/cpm2004.html Funda Ergün S. Muthukrishnan 0001 Süleyman Cenk Sahinalp Comparing Sequences with Segment Rearrangements. 183-194 https://doi.org/10.1007/978-3-540-24597-1_16 2003 conf/fsttcs/2003 FSTTCS db/conf/fsttcs/fsttcs2003.html#ErgunMS03 Süleyman Cenk Sahinalp Murat Tasan Jai Macker Z. Meral Özsoyoglu Distance Based Indexing for String Proximity Search. 125-136 https://doi.org/10.1109/ICDE.2003.1260787 https://doi.ieeecomputersociety.org/10.1109/ICDE.2003.1260787 2003 conf/icde/2003 ICDE db/conf/icde/icde2003.html#SahinalpTMO03 Süleyman Cenk Sahinalp Evan E. Eichler Paul W. Goldberg Petra Berenbrink Tom Friedetzky Funda Ergün Statistical Identification of Uniformly Mutated Segments within Repeats. 249-261 2002 conf/cpm/2002 CPM https://doi.org/10.1007/3-540-45452-7_21 db/conf/cpm/cpm2002.html#SahinalpEGBFE02 S. Muthukrishnan 0001 Süleyman Cenk Sahinalp Simple and Practical Sequence Nearest Neighbors with Block Operations. 262-278 2002 conf/cpm/2002 CPM https://doi.org/10.1007/3-540-45452-7_22 db/conf/cpm/cpm2002.html#MuthukrishnanS02 S. Muthukrishnan 0001 Süleyman Cenk Sahinalp An Improved Algorithm for Sequence Comparison with Block Reversals. 319-325 2002 conf/latin/2002 LATIN https://doi.org/10.1007/3-540-45995-2_30 db/conf/latin/latin2002.html#MuthukrishnanS02

Leslie Ann Goldberg Paul W. Goldberg Mike Paterson Pavel A. Pevzner Süleyman Cenk Sahinalp Elizabeth Sweedyk The Complexity of Gene Placement. 225-243 2001 41 J. Algorithms 2 https://doi.org/10.1006/jagm.2001.1172 db/journals/jal/jal41.html#GoldbergGPPSS01

Yossi Matias Nasir M. Rajpoot Süleyman Cenk Sahinalp The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression. 10 2001 6 ACM J. Exp. Algorithmics db/journals/jea/jea6.html#MatiasRS01 https://doi.org/10.1145/945394.945404 https://www.wikidata.org/entity/Q57737196

Funda Ergün Süleyman Cenk Sahinalp Jonathan Sharp Rakesh K. Sinha Biased Skip Lists for Highly Skewed Access Patterns. 216-230 2001 conf/alenex/2001 ALENEX https://doi.org/10.1007/3-540-44808-X_18 db/conf/alenex/alenex2001.html#ErgunSSS01 Graham Cormode S. Muthukrishnan 0001 Süleyman Cenk Sahinalp Permutation Editing and Matching via Embeddings. 481-492 2001 conf/icalp/2001 ICALP https://doi.org/10.1007/3-540-48224-5_40 db/conf/icalp/icalp2001.html#CormodeMS01 Funda Ergün Suvo Mittra Süleyman Cenk Sahinalp Jonathan Sharp Rakesh K. Sinha A Dynamic Lookup Scheme for Bursty Access Patterns. 1444-1453 2001 conf/infocom/2001 INFOCOM https://doi.org/10.1109/INFCOM.2001.916640 https://doi.ieeecomputersociety.org/10.1109/INFCOM.2001.916640 db/conf/infocom/infocom2001-3.html#ErgunMSSS01 Funda Ergün Süleyman Cenk Sahinalp Jonathan Sharp Rakesh K. Sinha Biased dictionaries with fast insert/deletes. 483-491 2001 conf/stoc/2001 STOC https://doi.org/10.1145/380752.380843 db/conf/stoc/stoc2001.html#ErgunSSS01 Z. Cohen Yossi Matias S. Muthukrishnan 0001 Süleyman Cenk Sahinalp Jacob Ziv On the temporal HZY compression scheme. 185-186 2000 conf/soda/2000 SODA http://dl.acm.org/citation.cfm?id=338219.338250 db/conf/soda/soda2000.html#CohenMMSZ00 Graham Cormode Mike Paterson Süleyman Cenk Sahinalp Uzi Vishkin Communication complexity of document exchange. 197-206 2000 conf/soda/2000 SODA http://dl.acm.org/citation.cfm?id=338219.338252 db/conf/soda/soda2000.html#CormodePSV00 S. Muthukrishnan 0001 Süleyman Cenk Sahinalp Approximate nearest neighbors and sequence comparison with block operations. 416-424 2000 conf/stoc/2000 STOC https://doi.org/10.1145/335305.335353 db/conf/stoc/stoc2000.html#MuthukrishnanS00 Yossi Matias Nasir M. Rajpoot Süleyman Cenk Sahinalp The Effect of Flexible Parsing for Dynamic Dictionary Based Data Compression. 238-246 1999 conf/dcc/1999 Data Compression Conference https://doi.org/10.1109/DCC.1999.755673 https://doi.ieeecomputersociety.org/10.1109/DCC.1999.755673 db/conf/dcc/dcc99.html#MatiasRS99 Leslie Ann Goldberg Paul W. Goldberg Mike Paterson Pavel A. Pevzner Süleyman Cenk Sahinalp Elizabeth Sweedyk The Complexity of Gene Placement. 386-395 1999 conf/soda/1999 SODA http://dl.acm.org/citation.cfm?id=314500.314591 db/conf/soda/soda99.html#GoldbergGPPSS99 Yossi Matias Süleyman Cenk Sahinalp On the Optimality of Parsing in Dynamic Dictionary Based Data Compression. 943-944 1999 conf/soda/1999 SODA http://dl.acm.org/citation.cfm?id=314500.314935 db/conf/soda/soda99.html#MatiasS99 S. Muthukrishnan 0001 Mike Paterson Süleyman Cenk Sahinalp Torsten Suel Compact Grid Layouts of Multi-Level Networks. 455-463 1999 conf/stoc/1999 STOC https://doi.org/10.1145/301250.301372 db/conf/stoc/stoc1999.html#MuthukrishnanPSS99 Yossi Matias S. Muthukrishnan 0001 Süleyman Cenk Sahinalp Jacob Ziv Augmenting Suffix Trees, with Applications. 67-78 https://doi.org/10.1007/3-540-68530-8_6 1998 conf/esa/1998 ESA db/conf/esa/esa98.html#MatiasMSZ98 Shimon Even S. Muthukrishnan 0001 Mike Paterson Süleyman Cenk Sahinalp Layout of the Batcher Bitonic Sorter (Extended Abstract). 172-181 1998 conf/spaa/1998 SPAA https://doi.org/10.1145/277651.277683 db/conf/spaa/spaa98.html#EvenMPS98 Yossi Matias Nasir M. Rajpoot Süleyman Cenk Sahinalp Implementation and Experimental Evaluation of Flexible Parsing for Dynamic Dictionary Based Data Compression. 49-61 1998 conf/wae/1998 WAE db/conf/wae/wae1998.html#MatiasRS98 Süleyman Cenk Sahinalp Uzi Vishkin Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm (extended abstract). 320-328 1996 conf/focs/1996 FOCS db/conf/focs/focs96.html#SahinalpV96 https://doi.org/10.1109/SFCS.1996.548491 https://doi.ieeecomputersociety.org/10.1109/SFCS.1996.548491 Süleyman Cenk Sahinalp Uzi Vishkin On a Parallel-Algorithms Method for String Matching Problems. 22-32 1994 conf/ciac/1994 CIAC db/conf/ciac/ciac1994.html#SahinalpV94 https://doi.org/10.1007/3-540-57811-0_3 Süleyman Cenk Sahinalp Uzi Vishkin Symmetry breaking for suffix tree construction. 300-309 1994 conf/stoc/STOC26 STOC https://doi.org/10.1145/195058.195164 db/conf/stoc/stoc1994.html#SahinalpV94 Federico Abascal David J. Adams Kadir C. Akdemir Cagri Aksay Can Alkan Noga Alon Eva G. Alvarez Samirkumar B. Amin Shawn Anderson Pavana Anur Nicoletta Archidiacono Anatoly G. Artemenko Ariful Azad Erfan Sadeqi Azer Rolf Backofen Gary D. Bader Adrian Baez-Ortega Vineet Bafna Jeffrey A. Bailey Marzieh Bakhshi Pratiti Bandopadhayay Jonathan Barenboim Jason Barnett Osnat Bartok Igor I. Baskin Tugkan Batu Gürkan Bebek Niko Beerenwinkel Kevin Beja Robert H. Bell Himisha Beltran Petra Berenbrink Bonnie Berger Rameen Beroukhim Johanna Bertl Andrea Biondi Inanç Birol Cinnamon S. Bloss Paolo Bonfanti Keith A. Boroevich Ali Ebrahimpour Boroojeny Paul C. Boutros David D. L. Bowtell John D. Bridgers Fiona S. L. Brinkman Benedikt Brors Michael Brudno Søren Brunak Jerome Buard Jeremy Buhler Aydin Buluç Sandra Burkett Jane C. Burns Kathleen H. Burns John Busanovich Peter J. Campbell Shaolong Cao Joana Carlevaro-Fita Dimple Chakravarty Calvin Wing Yiu Chan Kin Chan Simon K. Chan Yi Chang 0001 Stephen J. Chanock Cédric Chauve Feng Chen 0016 Ken Chen Langshi Chen Artem Cherkasov Kim N. Chi Sung Chin Arul M. Chinnaiyan Hamidreza Chitsaz Hyunghoon Cho Jung Kyoon Choi Elizabeth L. Christie Marek Cmero Z. Cohen Recep Colak Colin C. Collins Colin Cooper Graham Cormode Isidro Cortes-CirianoIsidro Cortés-Ciriano David Craft Yupeng Cun Clifton L. Dalgard Phuong Dao Kevin J. Dawson Chi-Ping Day Jonas Demeulemeester Stefan C. Dentro Amit G. Deshwar Jordi Deu-Pons Priyanka Dhingra Klev Diamanti Sijie Ding Ugur DogrusozUgur Dogrusöz Natnatee Dokmai Nilgun Donmez Ruben M. Drews Ana Dueso-Barroso Andrew J. Dunford Jessica Ebersole H. Alexander Ebhardt Mohammad Haghir Ebrahim-Abadi Paul A. Edwards Evan E. Eichler Roland Eils Funda Ergün Martin Ester Xavier Estivill Dariush Etemadmoghadam Shimon Even Yu Fan Martin Farach-Colton Felix Feng Lars Feuerbach J. Lynn Fink Matthew Fittall David A. Flockhart Nuno A. Fonseca Michael K. B. Ford Leonard J. Foster Denis Fourches Dov Fox Milana Frenkel-Morgenstern Tom Friedetzky Joan Frigola Suzanne Renick Gallagher Dale W. Garsed Alexander Gawronski Mark Gerstein Moritz Gerstung E. Michael Gertz Gad Getz Ryan Giuliany Martin E. Gleave Leslie Ann Goldberg Paul W. Goldberg Santiago Gonzalez Abel González-Pérez Dmitry A. Gordenin Paola Gramatica Malachi Griffith Charli Gruen Qianyun Guo Ivo Glynne Gut Gavin Ha David Haan Kerstin Haase James E. Haber Faraz Hach Anne Haegert Gholamreza Haffari Ehsan Haghshenas Iman Hajirasouliha Mark P. Hamilton Katja Hansen Nicholas J. Haradhvala Ananth Hari Arif Ozgun Harmanci Mohamed Helmy Carl Herrmann Julian M. Hess Martin L. Hibberd Martin Hirst Asger Hobolth Ermin Hodzic Ivo L. Hofacker Jan Hoinka Steven Holland J. Holman Chen Hong Farhad Hormozdiari Fereydoun Hormozdiari Henrik Hornshøj Dragos Horvath Michael Hsing David G. Huntsman Barbara Hutter Luisa Imberti Marcin Imielinski Keren Isaev Ruslan Israfilov José M. G. Izarzugaza Katharina Jahn 0001 Lara Jerman Yuan Ji Xiaoqian Jiang Rory Johnson Todd A. Johnson Clemency Jolly David T. W. Jones Suraj Joshi Young Seok Ju David de Juan Malene Juul Randi Istrup Juul André Kahles Abdullah Kahraman Maricel G. Kann Emre Karakoç Nikolai Karpov Marat D. Kazanov Manolis Kellis Michael C. Kelly Ekta Khurana Jeffrey M. Kidd Jaegil Kim Jihoon Kim 0001 Jong K. Kim Youngwook Kim Can Kizilkale Kortine Kleinheinz Leszek J. Klimczak Can Kockan Youngil Koh Jan Komorowski Jan O. Korbel Robert Körner Jack Kuipers M. Oguzhan Külekci Kiran Kumar Sushant Kumar Victor Kuzmin Justin Lack Matthew R. Laird Gad M. Landau Andrés Lanzós Anna Lapuk Erik Larsson Kristin E. Lauter Michael S. Lawrence Donghoon Lee 0006 Eunjung Alice Lee Jake June-Koo Lee Juhee Lee Maxwell P. Lee Henry Lee-Six Kjong-Van Lehmann Ignaty Leshchiner Franck Lethiec Ronen Levy Jiayu Li Jiazhong Li Shantao Li Sujun Li Xiaotong Li Xuan Cindy Li Yilong Li Yen-Yi Lin Ziao Lin Kevin Litchfield Eric Minwei Liu Huaitian Liu Huanxiang Liu Yuelin Liu Dimitri G. Livitz David D. Lloyd Raymond Lo Lucas Lochovsky Peter Van Loo Núria López-Bigas Shaoke Lou Yao Lu 0006 Jose Lugo-Martinez Andy G. Lynch Geoff MacIntyre Jai Macker Tobias Madsen Mary Magliocco Rohit Malik Salem Malikic Hiroshi Mamitsuka Madhav V. Marathe Kathleen Marchal Gilles Marcou Kerrie Marie Florian Markowetz Marco A. Marra Todd M. Martin Iñigo Martincorena Alexander Martínez-Fundichely Yosef E. Maruvka Yossi Matias Brian McConeghy Patrick D. McGillivray Andrew W. McPherson Farid Rashidi Mehrabadi Gabor Melli Nataliya Melnyk Filippo Menczer Christian von Mering Glenn Merlino Matthew Meyerson William Meyerson Swati Mishra 0006 Tom Mitchell 0001Thomas J. Mitchell Suvo Mittra Satoru Miyano Fan Mo Mathias Möhl Erin K. Molloy Quaid MorrisQuaid D. Morris Flavia Moser Stephen M. Mount Alireza Heravi Moussavi Ferran Muiños Loris Mularoni Christophe Muller Klaus-Robert Müller Eugene N. Muratov Ville Mustonen S. Muthukrishnan 0001 Joseph H. Nadeau Hidewaki Nakagawa Fabio C. P. Navarro Morten Muhlig Nielsen Torsten O. Nielsen Yashar S. Niknafs Andrey Nikolaev Luigi Notarangelo Sergii Novotarskyi Ibrahim Numanagic Tomas Öberg Layla Oesper Cihan Oguz Lucila Ohno-Machado Stephan Ossowski Hua Ouyang Z. Meral Özsoyoglu Marina Pacheco Marta Paczkowska Anil Kumar Pandey Keunchil Park Kiejung Park Peter J. Park Carlo Gambacorti Passerini Mike Paterson John V. Pearson Jakob Skou Pedersen Martin Peifer Eva Pérez-Guijarro Myron Peto Pavel A. Pevzner Oriol Pich Eileen Png Pavel G. Polishchuk Tirso Pons Victoria M. Pratt Volodymyr V. Prokopenko Natasa Przulj Teresa M. Przytycka Montserrat Puiggròs Sergio Pulido-Tamayo Judy Qiu Predrag Radivojac Milan Radovich Md. Khaledur Rahman Nasir M. Rajpoot Varune R. Ramnarine Benjamin J. Raphael Jüri Reimand Sébastien Rey Iker Reyes-Salazar Matthew A. Reyna Esther Rheinbay Karsten Rippe Paul F. Robbins Nicola D. Roberts Steven A. Roberts Welles Robinson Mariano Rocchi Oscar Rodriguez Bernardo Rodriguez-Martin Daniel T. Rosebrock Lindsey Rosen Andrew Roth Yulia Rubanova Mark A. Rubin Carlota Rubio-Perez Radhakrishnan Sabarinathan Avishek Saha Gordon Saksena Raheleh Salari Adriana Salcedo Leonidas Salichos Smilee Samuel Yardena Samuels Chris Sander Iman Sarrafi Thomas Sauerwald Alejandro A. Schäffer Matthias Schlesner Alexander Schönhuth Timon Schroeter Steven E. Schumacher Russell Schwartz Ralph Scully Subhajit Sengupta Janine Senz Mark Shackleton Sohrab P. Shah Ofer Shapira Ali Sharifi-Zarchi Jonathan Sharp Ciyue Shen Ruian Shi Chisato Shimizu Seung Jun Shin Akash Shrestha Raunak Shrestha Shimin Shuai Nikos Sidiropoulos Lina Sieverling Sean Simmons 0001 Rakesh K. Sinha Nasa Sinnott-Armstrong Todd C. Skaar Egor Smirnov Cari Smith Paul T. Spellman Oliver Spiro Peter F. Stadler Lincoln SteinLincoln D. Stein Chip Stewart Joshua M. Stuart Helen Su Torsten Suel Mark G. F. Sun Iurii Sushko Lucas Swanson Elizabeth Sweedyk David Tamborero Haixu Tang Jiliang Tang Maxime Tarabichi Murat Tasan Amalio Telenti Igor V. Tetko Grace Tiao Roberto Todeschini David Torrents Alexander Tropsha Tatsuhiko Tsunoda Dekel Tsur Jose M. C. Tubio Samra Turajlic Eray Tüzün Michael Uhl Husen M. Umer Peter J. Unrau Andrey Utis Liis Uusküla-Reimand Alfonso Valencia Alexandre Varnek Miguel Vazquez Ignacio Vázquez-García Shankar Vembu Mario Ventura Lieven P. C. Verbeke Izar Villasante Uzi Vishkin Stanislav Volik Anil Vullikanti Nic WaddellNicola Waddell Claes Wadelius Lina Wadi James R. Wagner Jeremiah Wala Jeremiah A. Wala Jiayin Wang Kendric Wang Shuang Wang 0002 Wenyi Wang 0001 Jonathan Warrell Sebastian M. Waszak Corey Watson Sarah Weber David C. Wedge Joachim Weischenfeldt David A. Wheeler Sebastian Will Jeff Wintersinger David P. Woodruff Victoria J. Wright Chih Hao Wu Chunxiao Wu Guanming Wu Alexander WyattAlexander W. Wyatt Lili Xi Sandhya Xirasagar Junyan Xu Makoto Yamada Hai Yang Howard H. Yang Lixing Yang Tsun-Po Yang Xiaojun Yao Xiaotong Yao Jake Yeung Dawei Yin 0001 Sung-Soo Yoon Deniz Yörükoglu Douglas M. Young Jun Yu Kaixian Yu Nancy Y. Yu Ke Yuan Jorge Zamora Abdalnasser Zayed Cheng-Zhong Zhang Jing Zhang 0062 Kaizhong Zhang Xiang Zhang 0001 Xuanping Zhang Yajia Zhang Yan Zhang 0032 Yu Zhang Zhongming Zhao Qinghui Zhou Hongtu Zhu Kaiyuan Zhu Jacob Ziv Lihua Zou