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Süleyman Cenk Sahinalp: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha
    Biased Skip Lists for Highly Skewed Access Patterns. [Citation Graph (0, 0)][DBLP]
    ALENEX, 2001, pp:216-230 [Conf]
  2. Süleyman Cenk Sahinalp, Uzi Vishkin
    On a Parallel-Algorithms Method for String Matching Problems. [Citation Graph (0, 0)][DBLP]
    CIAC, 1994, pp:22-32 [Conf]
  3. S. Muthukrishnan, Süleyman Cenk Sahinalp
    Simple and Practical Sequence Nearest Neighbors with Block Operations. [Citation Graph (0, 0)][DBLP]
    CPM, 2002, pp:262-278 [Conf]
  4. Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün
    Statistical Identification of Uniformly Mutated Segments within Repeats. [Citation Graph (0, 0)][DBLP]
    CPM, 2002, pp:249-261 [Conf]
  5. Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp
    The Effect of Flexible Parsing for Dynamic Dictionary Based Data Compression. [Citation Graph (0, 0)][DBLP]
    Data Compression Conference, 1999, pp:238-246 [Conf]
  6. Tugkan Batu, Süleyman Cenk Sahinalp
    Locally Consistent Parsing and Applications to Approximate String Comparisons. [Citation Graph (0, 0)][DBLP]
    Developments in Language Theory, 2005, pp:22-35 [Conf]
  7. Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv
    Augmenting Suffix Trees, with Applications. [Citation Graph (0, 0)][DBLP]
    ESA, 1998, pp:67-78 [Conf]
  8. Süleyman Cenk Sahinalp, Uzi Vishkin
    Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm (extended abstract). [Citation Graph (0, 0)][DBLP]
    FOCS, 1996, pp:320-328 [Conf]
  9. Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp
    Comparing Sequences with Segment Rearrangements. [Citation Graph (0, 0)][DBLP]
    FSTTCS, 2003, pp:183-194 [Conf]
  10. Graham Cormode, S. Muthukrishnan, Süleyman Cenk Sahinalp
    Permutation Editing and Matching via Embeddings. [Citation Graph (0, 0)][DBLP]
    ICALP, 2001, pp:481-492 [Conf]
  11. Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur
    Optimal Spaced Seeds for Faster Approximate String Matching. [Citation Graph (0, 0)][DBLP]
    ICALP, 2005, pp:1251-1262 [Conf]
  12. Süleyman Cenk Sahinalp, Andrey Utis
    Hardness of String Similarity Search and Other Indexing Problems. [Citation Graph (0, 0)][DBLP]
    ICALP, 2004, pp:1080-1098 [Conf]
  13. Süleyman Cenk Sahinalp, Murat Tasan, Jai Macker, Z. Meral Özsoyoglu
    Distance Based Indexing for String Proximity Search. [Citation Graph (0, 0)][DBLP]
    ICDE, 2003, pp:125-0 [Conf]
  14. Funda Ergün, Suvo Mittra, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha
    A Dynamic Lookup Scheme for Bursty Access Patterns. [Citation Graph (0, 0)][DBLP]
    INFOCOM, 2001, pp:1444-1453 [Conf]
  15. Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp
    Distance based algorithms for small biomolecule classification and structural similarity search. [Citation Graph (0, 0)][DBLP]
    ISMB (Supplement of Bioinformatics), 2006, pp:243-251 [Conf]
  16. Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp
    Sublinear Methods for Detecting Periodic Trends in Data Streams. [Citation Graph (0, 0)][DBLP]
    LATIN, 2004, pp:16-28 [Conf]
  17. S. Muthukrishnan, Süleyman Cenk Sahinalp
    An Improved Algorithm for Sequence Comparison with Block Reversals. [Citation Graph (0, 0)][DBLP]
    LATIN, 2002, pp:319-325 [Conf]
  18. Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang
    RNA-RNA Interaction Prediction and Antisense RNA Target Search. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2005, pp:152-171 [Conf]
  19. 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. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2006, pp:130-142 [Conf]
  20. Tugkan Batu, Funda Ergün, Süleyman Cenk Sahinalp
    Oblivious string embeddings and edit distance approximations. [Citation Graph (0, 0)][DBLP]
    SODA, 2006, pp:792-801 [Conf]
  21. Z. Cohen, Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv
    On the temporal HZY compression scheme. [Citation Graph (0, 0)][DBLP]
    SODA, 2000, pp:185-186 [Conf]
  22. Graham Cormode, Mike Paterson, Süleyman Cenk Sahinalp, Uzi Vishkin
    Communication complexity of document exchange. [Citation Graph (0, 0)][DBLP]
    SODA, 2000, pp:197-206 [Conf]
  23. Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk
    The Complexity of Gene Placement. [Citation Graph (0, 0)][DBLP]
    SODA, 1999, pp:386-395 [Conf]
  24. Yossi Matias, Süleyman Cenk Sahinalp
    On the Optimality of Parsing in Dynamic Dictionary Based Data Compression. [Citation Graph (0, 0)][DBLP]
    SODA, 1999, pp:943-944 [Conf]
  25. Shimon Even, S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp
    Layout of the Batcher Bitonic Sorter (Extended Abstract). [Citation Graph (0, 0)][DBLP]
    SPAA, 1998, pp:172-181 [Conf]
  26. Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha
    Biased dictionaries with fast insert/deletes. [Citation Graph (0, 0)][DBLP]
    STOC, 2001, pp:483-491 [Conf]
  27. S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp, Torsten Suel
    Compact Grid Layouts of Multi-Level Networks. [Citation Graph (0, 0)][DBLP]
    STOC, 1999, pp:455-463 [Conf]
  28. S. Muthukrishnan, Süleyman Cenk Sahinalp
    Approximate nearest neighbors and sequence comparison with block operations. [Citation Graph (0, 0)][DBLP]
    STOC, 2000, pp:416-424 [Conf]
  29. Süleyman Cenk Sahinalp, Uzi Vishkin
    Symmetry breaking for suffix tree construction. [Citation Graph (0, 0)][DBLP]
    STOC, 1994, pp:300-309 [Conf]
  30. Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp
    Implementation and Experimental Evaluation of Flexible Parsing for Dynamic Dictionary Based Data Compression. [Citation Graph (0, 0)][DBLP]
    Algorithm Engineering, 1998, pp:49-61 [Conf]
  31. Emre Karakoç, Z. Meral Özsoyoglu, Süleyman Cenk Sahinalp, Murat Tasan, Xiang Zhang
    Novel Approaches to Biomolecular Sequence Indexing. [Citation Graph (0, 0)][DBLP]
    IEEE Data Eng. Bull., 2004, v:27, n:3, pp:40-47 [Journal]
  32. Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk
    The Complexity of Gene Placement. [Citation Graph (0, 0)][DBLP]
    J. Algorithms, 2001, v:41, n:2, pp:225-243 [Journal]
  33. Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün
    Identifying Uniformly Mutated Segments within Repeats. [Citation Graph (0, 0)][DBLP]
    J. Bioinformatics and Computational Biology, 2004, v:2, n:4, pp:657-668 [Journal]
  34. 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. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2004, v:11, n:5, pp:933-944 [Journal]
  35. Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp
    The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression. [Citation Graph (0, 0)][DBLP]
    ACM Journal of Experimental Algorithms, 2001, v:6, n:, pp:10- [Journal]
  36. 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. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Web-Server-Issue, pp:295-298 [Journal]
  37. S. Muthukrishnan, Süleyman Cenk Sahinalp
    An efficient algorithm for sequence comparison with block reversals. [Citation Graph (0, 0)][DBLP]
    Theor. Comput. Sci., 2004, v:321, n:1, pp:95-101 [Journal]
  38. Süleyman Cenk Sahinalp, Ugur Dogrusöz, S. Muthukrishnan
    Preface. [Citation Graph (0, 0)][DBLP]
    Theor. Comput. Sci., 2006, v:368, n:3, pp:195- [Journal]
  39. Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp
    The degree distribution of the generalized duplication model. [Citation Graph (0, 0)][DBLP]
    Theor. Comput. Sci., 2006, v:369, n:1-3, pp:239-249 [Journal]
  40. Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp
    Improved Duplication Models for Proteome Network Evolution. [Citation Graph (0, 0)][DBLP]
    Systems Biology and Regulatory Genomics, 2005, pp:119-137 [Conf]
  41. 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. [Citation Graph (0, 0)][DBLP]
    Systems Biology and Computational Proteomics, 2006, pp:1-13 [Conf]
  42. Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur
    Optimal spaced seeds for faster approximate string matching. [Citation Graph (0, 0)][DBLP]
    J. Comput. Syst. Sci., 2007, v:73, n:7, pp:1035-1044 [Journal]
  43. Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp
    Novel approaches for small biomolecule classification and structural similarity search. [Citation Graph (0, 0)][DBLP]
    SIGKDD Explorations, 2007, v:9, n:1, pp:14-21 [Journal]

  44. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. [Citation Graph (, )][DBLP]


  45. Biomolecular network motif counting and discovery by color coding. [Citation Graph (, )][DBLP]


  46. Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. [Citation Graph (, )][DBLP]


  47. Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. [Citation Graph (, )][DBLP]


  48. Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. [Citation Graph (, )][DBLP]


  49. The Relation between Indel Length and Functional Divergence: A Formal Study. [Citation Graph (, )][DBLP]


  50. Fast Prediction of RNA-RNA Interaction. [Citation Graph (, )][DBLP]


  51. biRNA: Fast RNA-RNA Binding Sites Prediction. [Citation Graph (, )][DBLP]


  52. Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. [Citation Graph (, )][DBLP]


  53. Sparsification of RNA Structure Prediction Including Pseudoknots. [Citation Graph (, )][DBLP]


  54. Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties. [Citation Graph (, )][DBLP]


  55. A partition function algorithm for interacting nucleic acid strands. [Citation Graph (, )][DBLP]


  56. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. [Citation Graph (, )][DBLP]


  57. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. [Citation Graph (, )][DBLP]


  58. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. [Citation Graph (, )][DBLP]


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