Süleyman Cenk Sahinalp

	2012
78		Andrew McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin Collins, Süleyman Cenk Sahinalp: Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing. RECOMB 2012: 181-182
77		Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan: Sensitive and fast mapping of di-base encoded reads. Bioinformatics 28(1): 150 (2012)
76		Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp: Mirroring co-evolving trees in the light of their topologies. Bioinformatics 28(9): 1202-1208 (2012)
	2011
75		Vineet Bafna, Süleyman Cenk Sahinalp: Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Vancouver, BC, Canada, March 28-31, 2011. Proceedings Springer 2011
74		Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, Süleyman Cenk Sahinalp: Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. RECOMB 2011: 104-105
73		Andrew McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab P. Shah, Colin Collins, Süleyman Cenk Sahinalp: Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinformatics 27(11): 1481-1488 (2011)
72		Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan: Sensitive and fast mapping of di-base encoded reads. Bioinformatics 27(14): 1915-1921 (2011)
71		Phuong Dao, Kendric Wang, Colin Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp: Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinformatics [ISMB/ECCB] 27(13): 205-213 (2011)
70		Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp: Mirroring co-evolving trees in the light of their topologies CoRR abs/1110.5704: (2011)
69		Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G. F. Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A. Marra, Martin Hirst, Torsten O. Nielsen, Süleyman Cenk Sahinalp, David G. Huntsman, Sohrab P. Shah: deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data. PLoS Computational Biology 7(5): (2011)
	2010
68		Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp: Session Introduction. Pacific Symposium on Biocomputing 2010: 302-304
67		Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler: Session Introduction. Pacific Symposium on Biocomputing 2010: 54-56
66		Raheleh Salari, Mathias Möhl, Sebastian Will, Süleyman Cenk Sahinalp, Rolf Backofen: Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. RECOMB 2010: 473-490
65		Alexander Schönhuth, Raheleh Salari, Süleyman Cenk Sahinalp: Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties. WABI 2010: 350-361
64		Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp: Sparsification of RNA Structure Prediction Including Pseudoknots. WABI 2010: 40-51
63		Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp: Periodicity testing with sublinear samples and space. ACM Transactions on Algorithms 6(2): (2010)
62		Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp: Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics 26(10): 1277-1283 (2010)
61		Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, Süleyman Cenk Sahinalp, Martin Ester, Leonard J. Foster, Fiona S. L. Brinkman: PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26(13): 1608-1615 (2010)
60		Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp: Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics [ISMB] 26(12): 350-357 (2010)
	2009
59		Recep Colak, Fereydoun Hormozdiari, Flavia Moser, Alexander Schönhuth, J. Holman, Martin Ester, Süleyman Cenk Sahinalp: Dense Graphlet Statistics of Protein Interaction and Random Networks. Pacific Symposium on Biocomputing 2009: 178-189
58		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
57		Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp: biRNA: Fast RNA-RNA Binding Sites Prediction. WABI 2009: 25-36
56		Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp: Fast Prediction of RNA-RNA Interaction. WABI 2009: 261-272
55		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
54		Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen: A partition function algorithm for interacting nucleic acid strands. Bioinformatics 25(12): (2009)
	2008
53		Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp: Biomolecular network motif counting and discovery by color coding. ISMB 2008: 241-249
52		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
51		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
50		Süleyman Cenk Sahinalp: Edit Distance Under Block Operations. Encyclopedia of Algorithms 2008
	2007
49		Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov: Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. Pacific Symposium on Biocomputing 2007: 133-144
48		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)
47		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)
46		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 Evolution. PLoS Computational Biology 3(7): (2007)
45		Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Süleyman Cenk Sahinalp, Evan E. Eichler: Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data. PLoS Computational Biology 3(9): (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: 125-136
	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	[47]
2	Can Alkan	[26] [32] [34] [39] [42] [45] [47] [58] [60] [62] [68] [72] [77]
3	Noga Alon	[53]
4	Nicoletta Archidiacono	[45]
5	Rolf Backofen	[54] [56] [57] [64] [66] [67]
6	Vineet Bafna	[75]
7	Jeffrey A. Bailey	[26] [32]
8	Tugkan Batu	[36] [41]
9	Gürkan Bebek	[33] [37]
10	Petra Berenbrink	[22] [27] [33] [37] [40] [46]
11	Inanç Birol	[52] [62]
12	Fiona S. L. Brinkman	[61]
13	Michael Brudno	[68]
14	Jerome Buard	[32]
15	Jeremy Buhler (Jeremy D. Buhler)	[42]
16	Artem Cherkasov	[43] [44] [49] [51]
17	Hamidreza Chitsaz	[54] [57] [67]
18	Z. Cohen	[13]
19	Recep Colak	[59]
20	Colin Collins	[71] [73] [78]
21	Colin Cooper	[33] [37]
22	Graham Cormode	[12] [18]
23	Phuong Dao	[53] [55] [60] [61] [71]
24	Ugur Dogrusöz	[31] [38]
25	H. Alexander Ebhardt	[42]
26	Evan E. Eichler	[22] [26] [27] [32] [45] [58] [60] [62] [68] [72] [74] [77]
27	Funda Ergün	[16] [17] [19] [22] [24] [27] [29] [41] [63]
28	Martin Ester	[55] [59] [61] [71]
29	Shimon Even	[4]
30	Martin Farach-Colton (Martin Farach)	[35] [48]
31	Leonard J. Foster	[61]
32	Tom Friedetzky	[22] [27] [33] [37]
33	Ryan Giuliany	[69]
34	Leslie Ann Goldberg	[9] [14]
35	Paul W. Goldberg	[9] [14] [22] [27]
36	Malachi Griffith	[69]
37	Gavin Ha	[69]
38	Faraz Hach	[60] [72] [73] [77]
39	Iman Hajirasouliha	[52] [53] [55] [60] [62] [70] [73] [74] [76]
40	Martin Hirst	[69]
41	Ivo L. Hofacker	[67]
42	J. Holman	[59]
43	Farhad Hormozdiari	[72] [77]
44	Fereydoun Hormozdiari	[40] [46] [51] [52] [53] [55] [58] [59] [60] [62] [69] [73] [74]
45	David G. Huntsman	[69]
46	David de Juan	[70] [76]
47	Maricel G. Kann	[68]
48	Emre Karakoç	[28] [34] [39] [42] [43] [44] [47] [49]
49	Jeffrey M. Kidd	[62]
50	Matthew R. Laird	[61]
51	Gad M. Landau	[35] [48]
52	Anna Lapuk	[71] [73]
53	Franck Lethiec	[32]
54	Raymond Lo	[61]
55	Jai Macker	[23]
56	Marco A. Marra	[69]
57	Yossi Matias	[5] [6] [8] [10] [13] [15]
58	Andrew McPherson	[69] [73] [74] [78]
59	Gabor Melli	[61]
60	Nataliya Melnyk	[69]
61	Suvo Mittra	[17]
62	Mathias Möhl	[64] [66]
63	Flavia Moser	[59]
64	Alireza Heravi Moussavi	[69]
65	S. Muthukrishnan (S. Muthu Muthukrishnan)	[4] [5] [7] [11] [13] [18] [20] [21] [24] [25] [29] [31] [38] [63]
66	Joseph H. Nadeau	[33] [34] [37] [39]
67	Torsten O. Nielsen	[69]
68	Z. Meral Özsoyoglu	[23] [28]
69	Marina Pacheco	[69]
70	Mike Paterson	[4] [7] [9] [12] [14]
71	Pavel A. Pevzner	[9] [14]
72	Natasa Przulj	[40] [46]
73	Nasir Rajpoot (Nasir M. Rajpoot)	[6] [10] [15]
74	Sébastien Rey	[61]
75	Mariano Rocchi	[45]
76	Raheleh Salari	[47] [51] [54] [56] [64] [65] [66]
77	Alexander Schönhuth	[51] [55] [59] [65] [70] [76]
78	Janine Senz	[69]
79	Sohrab P. Shah	[69] [73] [78]
80	Jonathan Sharp	[16] [17] [19]
81	Rakesh K. Sinha	[16] [17] [19]
82	Peter F. Stadler	[67]
83	Torsten Suel	[7]
84	Mark G. F. Sun	[69]
85	Elizabeth Sweedyk	[9] [14]
86	Murat Tasan	[23] [28]
87	Dekel Tsur	[35] [48]
88	Eray Tüzün	[26] [32]
89	Peter J. Unrau	[42]
90	Andrey Utis	[30]
91	Alfonso Valencia	[70] [76]
92	Mario Ventura	[45]
93	Uzi Vishkin	[1] [2] [3] [12]
94	Stanislav Volik	[73]
95	James R. Wagner	[61]
96	Kendric Wang	[71]
97	Sebastian Will	[64] [66]
98	Chunxiao Wu	[73] [78]
99	Alexander Wyatt	[78]
100	Deniz Yörükoglu	[60]
101	Nancy Y. Yu	[61]
102	Abdalnasser Zayed	[69]
103	Kaizhong Zhang	[34] [39] [42]
104	Xiang Zhang	[28]
105	Jacob Ziv	[5] [13]

Colors in the list of coauthors

Last update Fri May 25 01:42:58 2012 CET by the DBLP Team — Data released under the ODC-BY 1.0 license — See also our legal information page