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1

PyGTED: Python Application for Computing Graph Traversal Edit Distance

Ebrahimpour Boroojeny, Ali, Shrestha, Akash, Sharifi-zarchi, Ali, Gallagher, Suzanne Renick, Sahinalp, SÃ¼leyman Cenk, Chitsaz, Hamidreza

Journal:

Journal of Computational Biology

Year:

2020

Language:

english

File:

PDF, 74 KB

english, 2020

2

PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS

Chen, Feng, Wang, Shuang, Jiang, Xiaoqian, Ding, Sijie, Lu, Yao, Kim, Jihoon, Sahinalp, S. Cenk, Shimizu, Chisato, Burns, Jane C., Wright, Victoria J., Png, Eileen, Hibberd, Martin L., Lloyd, David D.

Journal:

Year:

2017

Language:

english

File:

PDF, 490 KB

english, 2017

3

Conifers have a unique small RNA silencing signature

Dolgosheina, E. V., Morin, R. D., Aksay, G., Sahinalp, S. C., Magrini, V., Mardis, E. R., Mattsson, J., Unrau, P. J.

Journal:

Year:

2008

Language:

english

File:

PDF, 842 KB

english, 2008

4

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || A Fast Set Intersection Algorithm for Sorted Sequences

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

Year:

2004

Language:

english

File:

PDF, 162 KB

english, 2004

5

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || A Bayesian Active Learning Experimental Design for Inferring Signaling Networks

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 746 KB

english, 2017

6

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 10229 || AllSome Sequence Bloom Trees

Sahinalp, S. Cenk

Year:

2017

Language:

english

File:

PDF, 1.53 MB

english, 2017

7

PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension

Chen, Feng, Wang, Chenghong, Dai, Wenrui, Jiang, Xiaoqian, Mohammed, Noman, Al Aziz, Md Momin, Sadat, Md Nazmus, Sahinalp, Cenk, Lauter, Kristin, Wang, Shuang

Journal:

BMC Medical Genomics

Year:

2017

Language:

english

File:

PDF, 1.22 MB

english, 2017

8

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Numanagić, Ibrahim, Malikić, Salem, Ford, Michael, Qin, Xiang, Toji, Lorraine, Radovich, Milan, Skaar, Todd C., Pratt, Victoria M., Berger, Bonnie, Scherer, Steve, Sahinalp, S. Cenk

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 694 KB

english, 2018

9

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, 1.80 MB

english, 2017

10

Sketching algorithms for genomic data analysis and querying in a secure enclave

Kockan, Can, Zhu, Kaiyuan, Dokmai, Natnatee, Karpov, Nikolai, Kulekci, M. Oguzhan, Woodruff, David P., Sahinalp, S. Cenk

Journal:

Year:

2020

File:

PDF, 3.02 MB

2020

11

The Complexity of Gene Placement

Leslie Ann Goldberg, Paul W Goldberg, Mike Paterson, Pavel Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk

Journal:

Journal of Algorithms

Year:

2001

Language:

english

File:

PDF, 138 KB

english, 2001

12

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

13

An efficient algorithm for sequence comparison with block reversals

S. Muthukrishnan, S. Cenk Sahinalp

Journal:

Theoretical Computer Science

Year:

2004

Language:

english

File:

PDF, 192 KB

english, 2004

14

The degree distribution of the generalized duplication model

G. Bebek, P. Berenbrink, C. Cooper, T. Friedetzky, J. Nadeau, S.C. Sahinalp

Journal:

Theoretical Computer Science

Year:

2006

Language:

english

File:

PDF, 282 KB

english, 2006

15

Preface

Suleyman Cenk Sahinalp, Ugur Dogrusoz, S. Muthukrishnan

Journal:

Theoretical Computer Science

Year:

2006

Language:

english

File:

PDF, 82 KB

english, 2006

16

Fast prediction of RNA-RNA interaction

Raheleh Salari, Rolf Backofen, S Cenk Sahinalp

Journal:

Algorithms for Molecular Biology

Year:

2010

Language:

english

File:

PDF, 438 KB

english, 2010

17

mrsFAST: a cache-oblivious algorithm for short-read mapping

Sahinalp, S Cenk, Hach, Faraz, Hormozdiari, Fereydoun, Alkan, Can, Hormozdiari, Farhad, Birol, Inanc, Eichler, Evan E

Journal:

Year:

2010

Language:

english

File:

PDF, 97 KB

english, 2010

18

[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

19

[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

20

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 6577 || Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers

Bafna, Vineet, Sahinalp, S. Cenk

Year:

2011

Language:

english

File:

PDF, 374 KB

english, 2011

21

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 6577 || IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

Bafna, Vineet, Sahinalp, S. Cenk

Year:

2011

Language:

english

File:

PDF, 613 KB

english, 2011

22

PP-011 DIFFERENTIAL DIAGNOSIS OF TROMBOPHILIA, LEMIERRE SYNDROME: CASE REPORT

Ertan Yucel, Aydan Eroglu, Isik Conkbayir, Sahin Sahinalp

Journal:

International Journal of Cardiology

Year:

2010

Language:

english

File:

PDF, 56 KB

english, 2010

23

[Lecture Notes in Computer Science] Research in Computational Molecular Biology Volume 6577 || Constrained De Novo Sequencing of Peptides with Application to Conotoxins

Bafna, Vineet, Sahinalp, S. Cenk

Year:

2011

Language:

english

File:

PDF, 364 KB

english, 2011

24

The intelligence in developing systems for molecular biology

S Cenk Sahinalp

Journal:

Year:

2007

Language:

english

File:

PDF, 57 KB

english, 2007

25

[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

26

[IEEE Comput. Soc. Press 37th Conference on Foundations of Computer Science - Burlington, VT, USA (14-16 Oct. 1996)] Proceedings of 37th Conference on Foundations of Computer Science - Efficient approximate and dynamic matching of patterns using a labeling paradigm

Sahinalp, S.C., Vishkin, U.

Year:

1996

Language:

english

File:

PDF, 817 KB

english, 1996

27

[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

28

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

Yu, N. Y., Wagner, J. R., Laird, M. R., Melli, G., Rey, S., Lo, R., Dao, P., Sahinalp, S. C., Ester, M., Foster, L. J., Brinkman, F. S. L.

Journal:

Year:

2010

Language:

english

File:

PDF, 298 KB

english, 2010

29

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || On the Average Sequence Complexity

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

Year:

2004

Language:

english

File:

PDF, 260 KB

english, 2004

30

[Lecture Notes in Computer Science] Combinatorial Pattern Matching Volume 3109 || Finding Biclusters by Random Projections

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

Year:

2004

Language:

english

File:

PDF, 267 KB

english, 2004

31

[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

32

Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds

Karakoc, Emre, Sahinalp, S. Cenk, Cherkasov, Artem

Journal:

Journal of Chemical Information and Modeling

Year:

2006

Language:

english

File:

PDF, 807 KB

english, 2006

33

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

Hormozdiari, F., Alkan, C., Eichler, E. E., Sahinalp, S. C.

Journal:

Genome Research

Year:

2009

Language:

english

File:

PDF, 397 KB

english, 2009

34

[IEEE IEEE INFOCOM 2001. Conference on Computer Communications. Twentieth Annual Joint Conference of the IEEE Computer and Communications Society - Anchorage, AK, USA (22-26 April 2001)] Proceedings IEEE INFOCOM 2001. Conference on Computer Communications. Twentieth Annual Joint Conference of the IEEE Computer and Communications Society (Cat. No.01CH37213) - A dynamic lookup scheme for bursty access patterns

Ergun, F., Mittra, S., Sahinalp, S.C., Sharp, J., Sinha, R.K.

Year:

2001

Language:

english

File:

PDF, 239 KB

english, 2001

35

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

36

[IEEE 19th International Conference on Data Engineering - Bangalore, India (5-8 March 2003)] Proceedings 19th International Conference on Data Engineering (Cat. No.03CH37405) - Distance based indexing for string proximity search

Sahinalp, S.C., Tasan, M., Macker, J., Ozsoyoglu, Z.M.

Year:

2003

Language:

english

File:

PDF, 898 KB

english, 2003

37

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

38

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

39

Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets

Hormozdiari, Fereydoun, Salari, Raheleh, Bafna, Vineet, Sahinalp, S. Cenk

Journal:

Journal of Computational Biology

Year:

2010

Language:

english

File:

PDF, 753 KB

english, 2010

40

The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis

Alkan, Can, Eichler, Evan E., Bailey, Jeffrey A., Cenk Şahinalp, S., Tüzün, Eray

Journal:

Journal of Computational Biology

Year:

2004

Language:

english

File:

PDF, 310 KB

english, 2004

41

Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length

Schönhuth, Alexander, Salari, Raheleh, Hormozdiari, Fereydoun, Cherkasov, Artem, Cenk Sahinalp, S.

Journal:

Journal of Computational Biology

Year:

2010

Language:

english

File:

PDF, 328 KB

english, 2010

42

Clonality inference in multiple tumor samples using phylogeny

Malikic, S., McPherson, A. W., Donmez, N., Sahinalp, C. S.

Journal:

Year:

2015

Language:

english

File:

PDF, 352 KB

english, 2015

43

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data

McPherson, A., Wu, C., Hajirasouliha, I., Hormozdiari, F., Hach, F., Lapuk, A., Volik, S., Shah, S., Collins, C., Sahinalp, S. C.

Journal:

Year:

2011

Language:

english

File:

PDF, 385 KB

english, 2011

44

Divergent Origins and Concerted Expansion of Two Segmental Duplications on Chromosome 16

Eichler, E. E., Johnson, M. E., Alkan, C., Tuzun, E., Sahinalp, C., Misceo, D., Archidiacono, N., Rocchi, M.

Journal:

Journal of Heredity

Year:

2001

Language:

english

File:

PDF, 284 KB

english, 2001

45

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa

Alkan, Can, Kavak, Pinar, Somel, Mehmet, Gokcumen, Omer, Ugurlu, Serkan, Saygi, Ceren, Dal, Elif, Bugra, Kuyas, Güngör, Tunga, Sahinalp, S, Özören, Nesrin, Bekpen, Cemalettin

Journal:

Year:

2014

Language:

english

File:

PDF, 2.15 MB

english, 2014

46

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

Morin, R. D., Aksay, G., Dolgosheina, E., Ebhardt, H. A., Magrini, V., Mardis, E. R., Sahinalp, S. C., Unrau, P. J.

Journal:

Genome Research

Year:

2008

Language:

english

File:

PDF, 1.01 MB

english, 2008

47

Mirroring co-evolving trees in the light of their topologies

Hajirasouliha, I., Schonhuth, A., de Juan, D., Valencia, A., Sahinalp, S. C.

Journal:

Year:

2012

Language:

english

File:

PDF, 414 KB

english, 2012

48

taveRNA: a web suite for RNA algorithms and applications

Aksay, C., Salari, R., Karakoc, E., Alkan, C., Sahinalp, S. C.

Journal:

Nucleic Acids Research

Year:

2007

Language:

english

File:

PDF, 2.03 MB

english, 2007

49

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

McPherson, A., Wu, C., Wyatt, A. W., Shah, S., Collins, C., Sahinalp, S. C.

Journal:

Genome Research

Year:

2012

Language:

english

File:

PDF, 972 KB

english, 2012

50

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

Hajirasouliha, I., Hormozdiari, F., Alkan, C., Kidd, J. M., Birol, I., Eichler, E. E., Sahinalp, S. C.

Journal:

Year:

2010

Language:

english

File:

PDF, 497 KB

english, 2010

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