Süleyman Cenk Sahinalp

	2009
56		Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp: Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. RECOMB 2009: 218-219
55		Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp: biRNA: Fast RNA-RNA Binding Sites Prediction. WABI 2009: 25-36
54		Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp: Fast Prediction of RNA-RNA Interaction. WABI 2009: 261-272
53		Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester: Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. WABI 2009: 37-48
52		Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen: A partition function algorithm for interacting nucleic acid strands. Bioinformatics 25(12): (2009)
	2008
51		Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp: Biomolecular network motif counting and discovery by color coding. ISMB 2008: 241-249
50		Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol: Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. ISMB 2008: 32-40
49		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
48		Süleyman Cenk Sahinalp: Edit Distance Under Block Operations. Encyclopedia of Algorithms 2008
	2007
47		Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov: Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. Pacific Symposium on Biocomputing 2007: 133-144
46		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)
45		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)
44		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
43		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
42		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
41		Tugkan Batu, Funda Ergün, Süleyman Cenk Sahinalp: Oblivious string embeddings and edit distance approximations. SODA 2006: 792-801
40		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
39		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)
38		Süleyman Cenk Sahinalp, Ugur Dogrusöz, S. Muthukrishnan: Preface. Theor. Comput. Sci. 368(3): 195 (2006)
37		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
36		Tugkan Batu, Süleyman Cenk Sahinalp: Locally Consistent Parsing and Applications to Approximate String Comparisons. Developments in Language Theory 2005: 22-35
35		Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur: Optimal Spaced Seeds for Faster Approximate String Matching. ICALP 2005: 1251-1262
34		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
33		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
32		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
31		Süleyman Cenk Sahinalp, S. Muthukrishnan, Ugur Dogrusöz: Combinatorial Pattern Matching, 15th Annual Symposium, CPM 2004, Istanbul,Turkey, July 5-7, 2004, Proceedings Springer 2004
30		Süleyman Cenk Sahinalp, Andrey Utis: Hardness of String Similarity Search and Other Indexing Problems. ICALP 2004: 1080-1098
29		Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp: Sublinear Methods for Detecting Periodic Trends in Data Streams. LATIN 2004: 16-28
28		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)
27		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)
26		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)
25		S. Muthukrishnan, Süleyman Cenk Sahinalp: An efficient algorithm for sequence comparison with block reversals. Theor. Comput. Sci. 321(1): 95-101 (2004)
	2003
24		Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp: Comparing Sequences with Segment Rearrangements. FSTTCS 2003: 183-194
23		Süleyman Cenk Sahinalp, Murat Tasan, Jai Macker, Z. Meral Özsoyoglu: Distance Based Indexing for String Proximity Search. ICDE 2003: 125-
	2002
22		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
21		S. Muthukrishnan, Süleyman Cenk Sahinalp: Simple and Practical Sequence Nearest Neighbors with Block Operations. CPM 2002: 262-278
20		S. Muthukrishnan, Süleyman Cenk Sahinalp: An Improved Algorithm for Sequence Comparison with Block Reversals. LATIN 2002: 319-325
	2001
19		Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha: Biased Skip Lists for Highly Skewed Access Patterns. ALENEX 2001: 216-230
18		Graham Cormode, S. Muthukrishnan, Süleyman Cenk Sahinalp: Permutation Editing and Matching via Embeddings. ICALP 2001: 481-492
17		Funda Ergün, Suvo Mittra, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha: A Dynamic Lookup Scheme for Bursty Access Patterns. INFOCOM 2001: 1444-1453
16		Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha: Biased dictionaries with fast insert/deletes. STOC 2001: 483-491
15		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)
14		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
13		Z. Cohen, Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv: On the temporal HZY compression scheme. SODA 2000: 185-186
12		Graham Cormode, Mike Paterson, Süleyman Cenk Sahinalp, Uzi Vishkin: Communication complexity of document exchange. SODA 2000: 197-206
11		S. Muthukrishnan, Süleyman Cenk Sahinalp: Approximate nearest neighbors and sequence comparison with block operations. STOC 2000: 416-424
	1999
10		Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp: The Effect of Flexible Parsing for Dynamic Dictionary Based Data Compression. Data Compression Conference 1999: 238-246
9		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		Yossi Matias, Süleyman Cenk Sahinalp: On the Optimality of Parsing in Dynamic Dictionary Based Data Compression. SODA 1999: 943-944
7		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		Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv: Augmenting Suffix Trees, with Applications. ESA 1998: 67-78
4		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		Süleyman Cenk Sahinalp, Uzi Vishkin: Symmetry breaking for suffix tree construction. STOC 1994: 300-309

Coauthor Index

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

Colors in the list of coauthors