Süleyman Cenk Sahinalp

2008
52	EE	Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp: Biomolecular network motif counting and discovery by color coding. ISMB 2008: 241-249
51	EE	Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanc Birol: Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. ISMB 2008: 32-40
50	EE	Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp: The Relation between Indel Length and Functional Divergence: A Formal Study. WABI 2008: 330-341
49	EE	Süleyman Cenk Sahinalp: Edit Distance Under Block Operations. Encyclopedia of Algorithms 2008
2007
48	EE	Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov: Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. Pacific Symposium on Biocomputing 2007: 133-144
47	EE	Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur: Optimal spaced seeds for faster approximate string matching. J. Comput. Syst. Sci. 73(7): 1035-1044 (2007)
46	EE	Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp: taveRNA: a web suite for RNA algorithms and applications. Nucleic Acids Research 35(Web-Server-Issue): 325-329 (2007)
45	EE	Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp: Novel approaches for small biomolecule classification and structural similarity search. SIGKDD Explorations 9(1): 14-21 (2007)
2006
44	EE	Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp: Distance based algorithms for small biomolecule classification and structural similarity search. ISMB (Supplement of Bioinformatics) 2006: 243-251
43	EE	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. RECOMB 2006: 130-142
42	EE	Tugkan Batu, Funda Ergün, Süleyman Cenk Sahinalp: Oblivious string embeddings and edit distance approximations. SODA 2006: 792-801
41	EE	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. Systems Biology and Computational Proteomics 2006: 1-13
40	EE	Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang: RNA-RNA Interaction Prediction and Antisense RNA Target Search. Journal of Computational Biology 13(2): 267-282 (2006)
39	EE	Süleyman Cenk Sahinalp, Ugur Dogrusöz, S. Muthukrishnan: Preface. Theor. Comput. Sci. 368(3): 195 (2006)
38	EE	Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp: The degree distribution of the generalized duplication model. Theor. Comput. Sci. 369(1-3): 239-249 (2006)
2005
37	EE	Tugkan Batu, Süleyman Cenk Sahinalp: Locally Consistent Parsing and Applications to Approximate String Comparisons. Developments in Language Theory 2005: 22-35
36	EE	Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur: Optimal Spaced Seeds for Faster Approximate String Matching. ICALP 2005: 1251-1262
35	EE	Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang: RNA-RNA Interaction Prediction and Antisense RNA Target Search. RECOMB 2005: 152-171
34	EE	Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp: Improved Duplication Models for Proteome Network Evolution. Systems Biology and Regulatory Genomics 2005: 119-137
33	EE	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. Nucleic Acids Research 33(Web-Server-Issue): 295-298 (2005)
2004
32		Süleyman Cenk Sahinalp, S. Muthukrishnan, Ugur Dogrusöz: Combinatorial Pattern Matching, 15th Annual Symposium, CPM 2004, Istanbul,Turkey, July 5-7, 2004, Proceedings Springer 2004
31	EE	Süleyman Cenk Sahinalp, Andrey Utis: Hardness of String Similarity Search and Other Indexing Problems. ICALP 2004: 1080-1098
30	EE	Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp: Sublinear Methods for Detecting Periodic Trends in Data Streams. LATIN 2004: 16-28
29	EE	Emre Karakoç, Z. Meral Özsoyoglu, Süleyman Cenk Sahinalp, Murat Tasan, Xiang Zhang: Novel Approaches to Biomolecular Sequence Indexing. IEEE Data Eng. Bull. 27(3): 40-47 (2004)
28	EE	Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün: Identifying Uniformly Mutated Segments within Repeats. J. Bioinformatics and Computational Biology 2(4): 657-668 (2004)
27	EE	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. Journal of Computational Biology 11(5): 933-944 (2004)
26	EE	S. Muthukrishnan, Süleyman Cenk Sahinalp: An efficient algorithm for sequence comparison with block reversals. Theor. Comput. Sci. 321(1): 95-101 (2004)
2003
25	EE	Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp: Comparing Sequences with Segment Rearrangements. FSTTCS 2003: 183-194
24	EE	Süleyman Cenk Sahinalp, Murat Tasan, Jai Macker, Z. Meral Özsoyoglu: Distance Based Indexing for String Proximity Search. ICDE 2003: 125-
2002
23	EE	Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün: Statistical Identification of Uniformly Mutated Segments within Repeats. CPM 2002: 249-261
22	EE	S. Muthukrishnan, Süleyman Cenk Sahinalp: Simple and Practical Sequence Nearest Neighbors with Block Operations. CPM 2002: 262-278
21	EE	S. Muthukrishnan, Süleyman Cenk Sahinalp: An Improved Algorithm for Sequence Comparison with Block Reversals. LATIN 2002: 319-325
2001
20	EE	Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha: Biased Skip Lists for Highly Skewed Access Patterns. ALENEX 2001: 216-230
19	EE	Graham Cormode, S. Muthukrishnan, Süleyman Cenk Sahinalp: Permutation Editing and Matching via Embeddings. ICALP 2001: 481-492
18	EE	Funda Ergün, Suvo Mittra, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha: A Dynamic Lookup Scheme for Bursty Access Patterns. INFOCOM 2001: 1444-1453
17	EE	Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha: Biased dictionaries with fast insert/deletes. STOC 2001: 483-491
16		Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp: The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression. ACM Journal of Experimental Algorithmics 6: 10 (2001)
15	EE	Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk: The Complexity of Gene Placement. J. Algorithms 41(2): 225-243 (2001)
2000
14	EE	Z. Cohen, Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv: On the temporal HZY compression scheme. SODA 2000: 185-186
13	EE	Graham Cormode, Mike Paterson, Süleyman Cenk Sahinalp, Uzi Vishkin: Communication complexity of document exchange. SODA 2000: 197-206
12	EE	S. Muthukrishnan, Süleyman Cenk Sahinalp: Approximate nearest neighbors and sequence comparison with block operations. STOC 2000: 416-424
1999
11	EE	Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp: The Effect of Flexible Parsing for Dynamic Dictionary Based Data Compression. Data Compression Conference 1999: 238-246
10	EE	Andrew V. Goldberg, Paul W. Goldberg, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk, Andrew V. Goldberg, Kostas Tsioutsiouliklis: Cut Tree Algorithms. SODA 1999: 376-385
9	EE	Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk: The Complexity of Gene Placement. SODA 1999: 386-395
8	EE	Yossi Matias, Süleyman Cenk Sahinalp: On the Optimality of Parsing in Dynamic Dictionary Based Data Compression. SODA 1999: 943-944
7	EE	S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp, Torsten Suel: Compact Grid Layouts of Multi-Level Networks. STOC 1999: 455-463
1998
6		Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp: Implementation and Experimental Evaluation of Flexible Parsing for Dynamic Dictionary Based Data Compression. Algorithm Engineering 1998: 49-61
5	EE	Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv: Augmenting Suffix Trees, with Applications. ESA 1998: 67-78
4	EE	Shimon Even, S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp: Layout of the Batcher Bitonic Sorter (Extended Abstract). SPAA 1998: 172-181
1996
3		Süleyman Cenk Sahinalp, Uzi Vishkin: Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm (extended abstract). FOCS 1996: 320-328
1994
2		Süleyman Cenk Sahinalp, Uzi Vishkin: On a Parallel-Algorithms Method for String Matching Problems. CIAC 1994: 22-32
1	EE	Süleyman Cenk Sahinalp, Uzi Vishkin: Symmetry breaking for suffix tree construction. STOC 1994: 300-309

Coauthor Index

1	Cagri Aksay	[46]
2	Can Alkan	[27] [33] [35] [40] [43] [46]
3	Noga Alon	[52]
4	Jeffrey A. Bailey	[27] [33]
5	Tugkan Batu	[37] [42]
6	Gürkan Bebek	[34] [38]
7	Petra Berenbrink	[23] [28] [34] [38] [41]
8	Inanc Birol	[51]
9	Jerome Buard	[33]
10	Jeremy Buhler (Jeremy D. Buhler)	[43]
11	Artem Cherkasov	[44] [45] [48] [50]
12	Z. Cohen	[14]
13	Colin Cooper	[34] [38]
14	Graham Cormode	[13] [19]
15	Phuong Dao	[52]
16	Ugur Dogrusöz	[32] [39]
17	H. Alexander Ebhardt	[43]
18	Evan E. Eichler	[23] [27] [28] [33]
19	Funda Ergün	[17] [18] [20] [23] [25] [28] [30] [42]
20	Shimon Even	[4]
21	Martin Farach-Colton (Martin Farach)	[36] [47]
22	Tom Friedetzky	[23] [28] [34] [38]
23	Andrew V. Goldberg	[10]
24	Leslie Ann Goldberg	[9] [15]
25	Paul W. Goldberg	[9] [10] [15] [23] [28]
26	Iman Hajirasouliha	[51] [52]
27	Fereydoun Hormozdiari	[41] [50] [51] [52]
28	Emre Karakoç	[29] [35] [40] [43] [44] [45] [46] [48]
29	Gad M. Landau	[36] [47]
30	Franck Lethiec	[33]
31	Jai Macker	[24]
32	Yossi Matias	[5] [6] [8] [11] [14] [16]
33	Suvo Mittra	[18]
34	S. Muthukrishnan (S. Muthu Muthukrishnan)	[4] [5] [7] [12] [14] [19] [21] [22] [25] [26] [30] [32] [39]
35	Joseph H. Nadeau	[34] [35] [38] [40]
36	Z. Meral Özsoyoglu	[24] [29]
37	Mike Paterson	[4] [7] [9] [13] [15]
38	Pavel A. Pevzner	[9] [10] [15]
39	Natasa Przulj	[41]
40	Nasir Rajpoot (Nasir M. Rajpoot)	[6] [11] [16]
41	Raheleh Salari	[46] [50]
42	Alexander Schönhuth	[50]
43	Jonathan Sharp	[17] [18] [20]
44	Rakesh K. Sinha	[17] [18] [20]
45	Torsten Suel	[7]
46	Elizabeth Sweedyk	[9] [10] [15]
47	Murat Tasan	[24] [29]
48	Kostas Tsioutsiouliklis	[10]
49	Dekel Tsur	[36] [47]
50	Eray Tüzün	[27] [33]
51	Peter J. Unrau	[43]
52	Andrey Utis	[31]
53	Uzi Vishkin	[1] [2] [3] [13]
54	Kaizhong Zhang	[35] [40] [43]
55	Xiang Zhang	[29]
56	Jacob Ziv	[5] [14]

Colors in the list of coauthors