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51

[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

52

[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

53

SRRM4 Drives Neuroendocrine Transdifferentiation of Prostate Adenocarcinoma Under Androgen Receptor Pathway Inhibition

Li, Yinan, Donmez, Nilgun, Sahinalp, Cenk, Xie, Ning, Wang, Yuwei, Xue, Hui, Mo, Fan, Beltran, Himisha, Gleave, Martin, Wang, Yuzhuo, Collins, Colin, Dong, Xuesen

Journal:

European Urology

Year:

2016

Language:

english

File:

PDF, 4.51 MB

english, 2016

54

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

55

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

56

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

57

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

58

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

59

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 ||

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 18.79 MB

english, 2017

60

[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

61

[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

62

[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

63

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || Resolving Multicopy Duplications de novo Using Polyploid Phasing

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 451 KB

english, 2017

64

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 337 KB

english, 2017

65

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy?

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 496 KB

english, 2017

66

[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

67

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 1012 KB

english, 2017

68

HIT'nDRIVE: Patient-specific multi-driver gene prioritization for precision oncology

Shrestha, Raunak, Hodzic, Ermin, Sauerwald, Thomas, Dao, Phuong, Wang, Kendric, Yeung, Jake, Anderson, Shawn, Vandin, Fabio, Haffari, Gholamreza, Collins, Colin C, Sahinalp, Cenk

Journal:

Genome Research

Year:

2017

Language:

english

File:

PDF, 2.77 MB

english, 2017

69

Mutational Analysis of Gene Fusions Predicts Novel MHC Class I-Restricted T cell Epitopes & Immune Signatures in a Subset of Prostate Cancer

Kalina, Jennifer L., Neilson, David S., Lin, Yen-Yi, Hamilton, Phineas T., Comber, Alexandra Paige, Loy, Emma M.H., Sahinalp, S. Cenk, Collins, Colin C., Hach, Faraz, Lum, Julian J.

Journal:

Clinical Cancer Research

Year:

2017

Language:

english

File:

PDF, 1.75 MB

english, 2017

70

Computational identification of micro-structural variations and their proteogenomic consequences in cancer

Lin, Yen-Yi, Gawronski, Alexander, Hach, Faraz, Li, Sujun, Numanagić, Ibrahim, Sarrafi, Iman, Mishra, Swati, McPherson, Andrew, Collins, Colin, Radovich, Milan, Tang, Haixu, Sahinalp, S Cenk

Journal:

Year:

2017

Language:

english

File:

PDF, 397 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

Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data

Yamada, Makoto, Tang, Jiliang, Lugo-Martinez, Jose, Hodzic, Ermin, Shrestha, Raunak, Ouyang, Hua, Radivojac, Predrag, Sahinalp, Cenk, Menczer, Filippo, Chang, Yi, Saha, Avishek, Mamitsuka, Hiroshi, Yi

Journal:

IEEE Transactions on Knowledge and Data Engineering

Year:

2018

Language:

english

File:

PDF, 3.76 MB

english, 2018

73

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions

Gawronski, Alexander R, Uhl, Michael, Zhang, Yajia, Lin, Yen-Yi, Niknafs, Yashar S, Ramnarine, Varune R, Malik, Rohit, Feng, Felix, Chinnaiyan, Arul M, Collins, Colin C, Sahinalp, S Cenk, Backofen, Ro

Journal:

Year:

2018

Language:

english

File:

PDF, 504 KB

english, 2018

74

Publisher Correction: 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, 240 KB

english, 2018

75

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

76

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

77

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

78

Preface: Selected Articles from RECOMB 2017

Journal:

Journal of Computational Biology

Year:

2018

Language:

english

File:

PDF, 26 KB

english, 2018

79

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Reversal Distance without Hurdles and Fortresses

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

Year:

2004

Language:

english

File:

PDF, 175 KB

english, 2004

80

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Approximate String Matching Using Compressed Suffix Arrays

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

Year:

2004

File:

PDF, 216 KB

2004

81

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

82

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Approximate String Matching Using Compressed Suffix Arrays

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

Year:

2004

Language:

english

File:

PDF, 216 KB

english, 2004

83

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

84

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

85

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

86

[IEEE 2019 IEEE International Conference on Big Data (Big Data) - Los Angeles, CA, USA (2019.12.9-2019.12.12)] 2019 IEEE International Conference on Big Data (Big Data) - SubGraph2Vec: Highly-Vectorized Tree-like Subgraph Counting

Chen, Langshi, Li, Jiayu, Sahinalp, Cenk, Marathe, Madhav, Vullikanti, Anil, Nikolaev, Andrey, Smirnov, Egor, Israfilov, Ruslan, Qiu, Judy

Year:

2019

File:

PDF, 1.39 MB

2019

87

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Small Phylogeny Problem: Character Evolution Trees

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

Year:

2004

File:

PDF, 206 KB

2004

88

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

89

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Improved Single and Multiple Approximate String Matching

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

Year:

2004

File:

PDF, 372 KB

2004

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