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51

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences

Sahinalp, Suleyman Cenk, Muthukrishnan, S., Dogrusoz, Ugur

Year:

2004

Language:

english

File:

PDF, 242 KB

english, 2004

52

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

Haghshenas, Ehsan, Sahinalp, S Cenk, Hach, Faraz

Journal:

Year:

2018

Language:

english

File:

PDF, 465 KB

english, 2018

53

Identification of conserved evolutionary trajectories in tumors

Hodzic, Ermin, Shrestha, Raunak, Malikic, Salem, Collins, Colin C, Litchfield, Kevin, Turajlic, Samra, Sahinalp, S Cenk

Journal:

Year:

2020

File:

PDF, 460 KB

2020

54

The intelligence in developing systems for molecular biology

S Cenk Sahinalp

Journal:

Year:

2007

Language:

english

File:

PDF, 57 KB

english, 2007

55

SSMART: Sequence-structure motif identification for RNA-binding proteins

Munteanu, Alina, Mukherjee, Neelanjan, Ohler, Uwe, Sahinalp, Cenk

Journal:

Year:

2018

Language:

english

File:

PDF, 4.63 MB

english, 2018

56

Graph Traversal Edit Distance and Extensions

Ebrahimpour Boroojeny, Ali, Shrestha, Akash, Sharifi-Zarchi, Ali, Gallagher, Suzanne Renick, Sahinalp, S. Cenk, Chitsaz, Hamidreza

Journal:

Journal of Computational Biology

Year:

2020

Language:

english

File:

PDF, 378 KB

english, 2020

57

Optimal spaced seeds for faster approximate string matching

Martin Farach-Colton, Gad M. Landau, S. Cenk Sahinalp, Dekel Tsur

Journal:

Journal of Computer and System Sciences

Year:

2007

Language:

english

File:

PDF, 221 KB

english, 2007

58

Preface

Suleyman Cenk Sahinalp, Ugur Dogrusoz, S. Muthukrishnan

Journal:

Theoretical Computer Science

Year:

2006

Language:

english

File:

PDF, 82 KB

english, 2006

59

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 6577 || Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks

Bafna, Vineet, Sahinalp, S. Cenk

Year:

2011

Language:

english

File:

PDF, 291 KB

english, 2011

60

The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study

Hormozdiari, Fereydoun, Salari, Raheleh, Hsing, Michael, Schönhuth, Alexander, Chan, Simon K., Sahinalp, S. Cenk, Cherkasov, Artem

Journal:

Journal of Computational Biology

Year:

2009

Language:

english

File:

PDF, 314 KB

english, 2009

61

Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data

Numanagić, Ibrahim, Malikić, Salem, Pratt, Victoria M., Skaar, Todd C., Flockhart, David A., Sahinalp, S. Cenk

Journal:

Year:

2015

Language:

english

File:

PDF, 697 KB

english, 2015

62

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Approximate Labelled Subtree Homeomorphism

Sahinalp, Suleyman Cenk, Muthukrishnan, S., Dogrusoz, Ugur

Year:

2004

Language:

english

File:

PDF, 392 KB

english, 2004

63

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || Towards Recovering Allele-Specific Cancer Genome Graphs

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 470 KB

english, 2017

64

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Average-Case Analysis of Approximate Trie Search

Sahinalp, Suleyman Cenk, Muthukrishnan, S., Dogrusoz, Ugur

Year:

2004

Language:

english

File:

PDF, 213 KB

english, 2004

65

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Multi-seed Lossless Filtration

Sahinalp, Suleyman Cenk, Muthukrishnan, S., Dogrusoz, Ugur

Year:

2004

Language:

english

File:

PDF, 226 KB

english, 2004

66

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 663 KB

english, 2017

67

A multi-labeled tree dissimilarity measure for comparing “clonal trees” of tumor progression

Karpov, Nikolai, Malikic, Salem, Rahman, Md. Khaledur, Sahinalp, S. Cenk

Journal:

Algorithms for Molecular Biology

Year:

2019

Language:

english

File:

PDF, 3.23 MB

english, 2019

68

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || New Results for the 2-Interval Pattern Problem

Sahinalp, Suleyman Cenk, Muthukrishnan, S., Dogrusoz, Ugur

Year:

2004

Language:

english

File:

PDF, 252 KB

english, 2004

69

Enabling Privacy-Preserving GWASs in Heterogeneous Human Populations

Simmons, Sean, Sahinalp, Cenk, Berger, Bonnie

Journal:

Year:

2016

Language:

english

File:

PDF, 1.22 MB

english, 2016

70

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || Dynamic Alignment-Free and Reference-Free Read Compression

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 488 KB

english, 2017

71

Optimal compressed representation of high throughput sequence data via light assembly

Ginart, Antonio A., Hui, Joseph, Zhu, Kaiyuan, Numanagić, Ibrahim, Courtade, Thomas A., Sahinalp, S. Cenk, Tse, David N.

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.00 MB

english, 2018

72

Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA

Gawroński, Alexander R, Lin, Yen-Yi, McConeghy, Brian, LeBihan, Stephane, Asghari, Hossein, Koçkan, Can, Orabi, Baraa, Adra, Nabil, Pili, Roberto, Collins, Colin C, Sahinalp, S Cenk, Hach, Faraz

Journal:

Nucleic Acids Research

Year:

2019

Language:

english

File:

PDF, 714 KB

english, 2019

73

CoLoRMap: Correcting Long Reads by Mapping short reads

Haghshenas, Ehsan, Hach, Faraz, Sahinalp, S. Cenk, Chauve, Cedric

Journal:

Year:

2016

Language:

english

File:

PDF, 208 KB

english, 2016

74

Comparison of high-throughput sequencing data compression tools

Numanagić, Ibrahim, Bonfield, James K, Hach, Faraz, Voges, Jan, Ostermann, Jörn, Alberti, Claudio, Mattavelli, Marco, Sahinalp, S Cenk

Journal:

Year:

2016

Language:

english

File:

PDF, 330 KB

english, 2016

75

Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data

Alkan, Can, Ventura, Mario, Archidiacono, Nicoletta, Rocchi, Mariano, Sahinalp, S. Cenk, Eichler, Evan E.

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 1.07 MB

english, 2007

76

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 6577 || A Three-Dimensional Model of the Yeast Genome

Bafna, Vineet, Sahinalp, S. Cenk

Year:

2011

Language:

english

File:

PDF, 40 KB

english, 2011

77

DeeZ: reference-based compression by local assembly

Hach, Faraz, Numanagic, Ibrahim, Sahinalp, S Cenk

Journal:

Year:

2014

Language:

english

File:

PDF, 125 KB

english, 2014

78

IDENTIFYING UNIFORMLY MUTATED SEGMENTS WITHIN REPEATS

SAHINALP, S. CENK, EICHLER, EVAN, GOLDBERG, PAUL, BERENBRINK, PETRA, FRIEDETZKY, TOM, ERGUN, FUNDA

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2004

Language:

english

File:

PDF, 190 KB

english, 2004

79

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 6577 || Rich Parameterization Improves RNA Structure Prediction

Bafna, Vineet, Sahinalp, S. Cenk

Year:

2011

Language:

english

File:

PDF, 346 KB

english, 2011

80

The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression

Matias, Yossi, Rajpoot, Nasir, Sahinalp, Cenk

Journal:

Journal of Experimental Algorithmics

Year:

2001

Language:

english

File:

PDF, 355 KB

english, 2001

81

[ACM Press the thirty-second annual ACM symposium - Portland, Oregon, United States (2000.05.21-2000.05.23)] Proceedings of the thirty-second annual ACM symposium on Theory of computing - STOC '00 - Approximate nearest neighbors and sequence comparison with block operations

Muthukrishnan, S., Sahinalp, Süleyman Cenk

Year:

2000

Language:

english

File:

PDF, 842 KB

english, 2000

82

Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data

Donmez, Nilgun, Malikic, Salem, Wyatt, Alexander W., Gleave, Martin E., Collins, Colin C., Sahinalp, S. Cenk

Journal:

Journal of Computational Biology

Year:

2017

Language:

english

File:

PDF, 621 KB

english, 2017

83

Correction to: ReMixT: clone-specific genomic structure estimation in cancer

McPherson, Andrew W., Roth, Andrew, Ha, Gavin, Chauve, Cedric, Steif, Adi, de Souza, Camila P. E., Eirew, Peter, Bouchard-Côté, Alexandre, Aparicio, Sam, Sahinalp, S. Cenk, Shah, Sohrab P.

Journal:

Year:

2017

Language:

english

File:

PDF, 214 KB

english, 2017

84

Sparsification of RNA structure prediction including pseudoknots

Möhl, Mathias, Salari, Raheleh, Will, Sebastian, Backofen, Rolf, Sahinalp, S Cenk

Journal:

Algorithms for Molecular Biology

Year:

2010

Language:

english

File:

PDF, 605 KB

english, 2010

85

SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA

Kockan, Can, Hach, Faraz, Sarrafi, Iman, Bell, Robert H., McConeghy, Brian, Beja, Kevin, Haegert, Anne, Wyatt, Alexander W., Volik, Stanislav V., Chi, Kim N., Collins, Colin C., Sahinalp, S. Cenk

Journal:

Year:

2016

Language:

english

File:

PDF, 367 KB

english, 2016

86

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 6577 || T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome

Bafna, Vineet, Sahinalp, S. Cenk

Year:

2011

Language:

english

File:

PDF, 92 KB

english, 2011

87

RNA–RNA Interaction Prediction and Antisense RNA Target Search

Alkan, Can, Karakoç, Emre, Nadeau, Joseph H., Sahinalp, S. Cenk, Zhang, Kaizhong

Journal:

Journal of Computational Biology

Year:

2006

Language:

english

File:

PDF, 362 KB

english, 2006

88

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 993 KB

english, 2017

89

Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes Using Long Reads

Ford, Michael, Haghshenas, Ehsan, Watson, Corey T., Sahinalp, S. Cenk

Journal:

Year:

2020

Language:

english

File:

PDF, 2.04 MB

english, 2020

90

Tumor Phylogeny Topology Inference via Deep Learning

Sadeqi Azer, Erfan, Haghir Ebrahimabadi, Mohammad, MalikiÄ, Salem, Khardon, Roni, Sahinalp, S. Cenk

Journal:

Year:

2020

File:

PDF, 376 KB

2020

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