| 2012 |
|---|
| 82 | Sensitive and fast mapping of di-base encoded reads. Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan. Bioinformatics (28): 150 (2012). Web SearchBibTeXDownload |
| 81 | Dissect: detection and characterization of novel structural alterations in transcribed sequences. Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin Collins, Inanç Birol, Süleyman Cenk Sahinalp. Bioinformatics (28): 179-187 (2012). Web SearchBibTeXDownload |
| 80 | Mirroring co-evolving trees in the light of their topologies. Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp. Bioinformatics (28): 1202-1208 (2012). Web SearchBibTeXDownload |
| 79 | SCALCE: boosting sequence compression algorithms using locally consistent encoding. Faraz Hach, Ibrahim Numanagic, Can Alkan, Süleyman Cenk Sahinalp. Bioinformatics (28): 3051-3057 (2012). Web SearchBibTeXDownload |
| 78 | Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing. Andrew McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin Collins, Süleyman Cenk Sahinalp. RECOMB 2012, 181-182. Web SearchBibTeXDownload |
| 77 | CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin Collins, Süleyman Cenk Sahinalp. WABI 2012, 178-189. Web SearchBibTeXDownload |
| 2011 |
|---|
| 76 | Sensitive and fast mapping of di-base encoded reads. Farhad Hormozdiari, Faraz Hach, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan. Bioinformatics (27): 1915-1921 (2011). Web SearchBibTeXDownload |
| 75 | Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Andrew McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, Süleyman Cenk Sahinalp. Bioinformatics (27): 1481-1488 (2011). Web SearchBibTeXDownload |
| 74 | Optimally discriminative subnetwork markers predict response to chemotherapy. Phuong Dao, Kendric Wang, Colin Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp. Bioinformatics [ISMB/ECCB] (27): 205-213 (2011). Web SearchBibTeXDownload |
| 73 | Mirroring co-evolving trees in the light of their topologies. Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp. CoRR (abs/1110.5704) (2011). Web SearchBibTeXDownload |
| 72 | deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data. 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. PLoS Computational Biology (7) (2011). Web SearchBibTeXDownload |
| 71 | Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, Süleyman Cenk Sahinalp. RECOMB 2011, 104-105. Web SearchBibTeXDownload |
| 2010 |
|---|
| 70 | Periodicity testing with sublinear samples and space. Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp. ACM Transactions on Algorithms (6) (2010). Web SearchBibTeXDownload |
| 69 | Sparsification of RNA structure prediction including pseudoknots. Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp. Algorithms for Molecular Biology (5): 39 (2010). Web SearchBibTeXDownload |
| 68 | Fast prediction of RNA-RNA interaction. Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp. Algorithms for Molecular Biology (5): 5 (2010). Web SearchBibTeXDownload |
| 67 | Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanç Birol, Evan E. Eichler, Süleyman Cenk Sahinalp. Bioinformatics (26): 1277-1283 (2010). Web SearchBibTeXDownload |
| 66 | PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. 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. Bioinformatics (26): 1608-1615 (2010). Web SearchBibTeXDownload |
| 65 | Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yörükoglu, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp. Bioinformatics [ISMB] (26): 350-357 (2010). Web SearchBibTeXDownload |
| 64 | Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length. Alexander Schönhuth, Raheleh Salari, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp. Journal of Computational Biology (17): 1-20 (2010). Web SearchBibTeXDownload |
| 63 | Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets. Fereydoun Hormozdiari, Raheleh Salari, Vineet Bafna, Süleyman Cenk Sahinalp. Journal of Computational Biology (17): 669-684 (2010). Web SearchBibTeXDownload |
| 62 | Session Introduction. Yves A. Lussier, John Quackenbush, Roy Kerckhoffs, Predrag Radivojac, Marco Punta, Maricel G. Kann, Maricel G. Kann. Pacific Symposium on Biocomputing 2010, 302-304. Web SearchBibTeXDownload |
| 61 | Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. Raheleh Salari, Mathias Möhl, Sebastian Will, Süleyman Cenk Sahinalp, Rolf Backofen. RECOMB 2010, 473-490. Web SearchBibTeXDownload |
| 60 | Sparsification of RNA Structure Prediction Including Pseudoknots. Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp. WABI 2010, 40-51. Web SearchBibTeXDownload |
| 59 | Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties. Alexander Schönhuth, Raheleh Salari, Süleyman Cenk Sahinalp. WABI 2010, 350-361. Web SearchBibTeXDownload |
| 2009 |
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| 58 | A partition function algorithm for interacting nucleic acid strands. Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen. Bioinformatics (25) (2009). Web SearchBibTeXDownload |
| 57 | The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study. Fereydoun Hormozdiari, Raheleh Salari, Michael Hsing, Alexander Schönhuth, Simon K. Chan, Süleyman Cenk Sahinalp, Artem Cherkasov. Journal of Computational Biology (16): 159-167 (2009). Web SearchBibTeXDownload |
| 56 | Dense Graphlet Statistics of Protein Interaction and Random Networks. Recep Colak, Fereydoun Hormozdiari, Flavia Moser, Alexander Schönhuth, J. Holman, Martin Ester, Süleyman Cenk Sahinalp. Pacific Symposium on Biocomputing 2009, 178-189. Web SearchBibTeXDownload |
| 55 | Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp. RECOMB 2009, 218-219. Web SearchBibTeXDownload |
| 54 | Fast Prediction of RNA-RNA Interaction. Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp. WABI 2009, 261-272. Web SearchBibTeXDownload |
| 53 | biRNA: Fast RNA-RNA Binding Sites Prediction. Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp. WABI 2009, 25-36. Web SearchBibTeXDownload |
| 52 | Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester. WABI 2009, 37-48. Web SearchBibTeXDownload |
| 2008 |
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| 51 | Edit Distance Under Block Operations. Süleyman Cenk Sahinalp. Encyclopedia of Algorithms 2008. Web SearchBibTeXDownload |
| 50 | Biomolecular network motif counting and discovery by color coding. Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp. ISMB 2008, 241-249. Web SearchBibTeXDownload |
| 49 | Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol. ISMB 2008, 32-40. Web SearchBibTeXDownload |
| 48 | The Relation between Indel Length and Functional Divergence: A Formal Study. Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp. WABI 2008, 330-341. Web SearchBibTeXDownload |
| 2007 |
|---|
| 47 | Optimal spaced seeds for faster approximate string matching. Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur. J. Comput. Syst. Sci. (73): 1035-1044 (2007). Web SearchBibTeXDownload |
| 46 | taveRNA: a web suite for RNA algorithms and applications. Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan, Süleyman Cenk Sahinalp. Nucleic Acids Research (35): 325-329 (2007). Web SearchBibTeXDownload |
| 45 | Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov. Pacific Symposium on Biocomputing 2007, 133-144. Web SearchBibTeXDownload |
| 44 | Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution. Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, Süleyman Cenk Sahinalp. PLoS Computational Biology (3) (2007). Web SearchBibTeXDownload |
| 43 | Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data. Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, Süleyman Cenk Sahinalp, Evan E. Eichler. PLoS Computational Biology (3) (2007). Web SearchBibTeXDownload |
| 42 | Novel approaches for small biomolecule classification and structural similarity search. Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp. SIGKDD Explorations (9): 14-21 (2007). Web SearchBibTeXDownload |
| 2006 |
|---|
| 41 | Distance based algorithms for small biomolecule classification and structural similarity search. Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp. ISMB (Supplement of Bioinformatics) 2006, 243-251. Web SearchBibTeXDownload |
| 40 | RNA-RNA Interaction Prediction and Antisense RNA Target Search. Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang. Journal of Computational Biology (13): 267-282 (2006). Web SearchBibTeXDownload |
| 39 | RNA Secondary Structure Prediction Via Energy Density Minimization. Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler. RECOMB 2006, 130-142. Web SearchBibTeXDownload |
| 38 | Oblivious string embeddings and edit distance approximations. Tugkan Batu, Funda Ergün, Süleyman Cenk Sahinalp. SODA 2006, 792-801. Web SearchBibTeXDownload |
| 37 | Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation. Fereydoun Hormozdiari, Petra Berenbrink, Natasa Przulj, Süleyman Cenk Sahinalp. Systems Biology and Computational Proteomics 2006, 1-13. Web SearchBibTeXDownload |
| 36 | The degree distribution of the generalized duplication model. Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp. Theor. Comput. Sci. (369): 239-249 (2006). Web SearchBibTeXDownload |
| 2005 |
|---|
| 35 | Locally Consistent Parsing and Applications to Approximate String Comparisons. Tugkan Batu, Süleyman Cenk Sahinalp. Developments in Language Theory 2005, 22-35. Web SearchBibTeXDownload |
| 34 | Optimal Spaced Seeds for Faster Approximate String Matching. Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur. ICALP 2005, 1251-1262. Web SearchBibTeXDownload |
| 33 | Manipulating multiple sequence alignments via MaM and WebMaM. Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp. Nucleic Acids Research (33): 295-298 (2005). Web SearchBibTeXDownload |
| 32 | RNA-RNA Interaction Prediction and Antisense RNA Target Search. Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang. RECOMB 2005, 152-171. Web SearchBibTeXDownload |
| 31 | Improved Duplication Models for Proteome Network Evolution. Gürkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Süleyman Cenk Sahinalp. Systems Biology and Regulatory Genomics 2005, 119-137. Web SearchBibTeXDownload |
| 2004 |
|---|
| 30 | Hardness of String Similarity Search and Other Indexing Problems. Süleyman Cenk Sahinalp, Andrey Utis. ICALP 2004, 1080-1098. Web SearchBibTeXDownload |
| 29 | Novel Approaches to Biomolecular Sequence Indexing. Emre Karakoç, Z. Meral Özsoyoglu, Süleyman Cenk Sahinalp, Murat Tasan, Xiang Zhang. IEEE Data Eng. Bull. (27): 40-47 (2004). Web SearchBibTeX |
| 28 | Identifying Uniformly Mutated Segments within Repeats. Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün. J. Bioinformatics and Computational Biology (2): 657-668 (2004). Web SearchBibTeXDownload |
| 27 | The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis. Can Alkan, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp, Eray Tüzün. Journal of Computational Biology (11): 933-944 (2004). Web SearchBibTeXDownload |
| 26 | Sublinear Methods for Detecting Periodic Trends in Data Streams. Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp. LATIN 2004, 16-28. Cited by 11Web SearchBibTeXDownload |
| 25 | An efficient algorithm for sequence comparison with block reversals. S. Muthukrishnan, Süleyman Cenk Sahinalp. Theor. Comput. Sci. (321): 95-101 (2004). Cited by 2Web SearchBibTeXDownload |
| 2003 |
|---|
| 24 | Comparing Sequences with Segment Rearrangements. Funda Ergün, S. Muthukrishnan, Süleyman Cenk Sahinalp. FSTTCS 2003, 183-194. Cited by 17Web SearchBibTeXDownload |
| 23 | Distance Based Indexing for String Proximity Search. Süleyman Cenk Sahinalp, Murat Tasan, Jai Macker, Z. Meral Özsoyoglu. ICDE 2003, 125-136. Web SearchBibTeXDownload |
| 2002 |
|---|
| 22 | Statistical Identification of Uniformly Mutated Segments within Repeats. Süleyman Cenk Sahinalp, Evan E. Eichler, Paul W. Goldberg, Petra Berenbrink, Tom Friedetzky, Funda Ergün. CPM 2002, 249-261. Web SearchBibTeXDownload |
| 21 | Simple and Practical Sequence Nearest Neighbors with Block Operations. S. Muthukrishnan, Süleyman Cenk Sahinalp. CPM 2002, 262-278. Cited by 15Web SearchBibTeXDownload |
| 20 | An Improved Algorithm for Sequence Comparison with Block Reversals. S. Muthukrishnan, Süleyman Cenk Sahinalp. LATIN 2002, 319-325. Web SearchBibTeXDownload |
| 2001 |
|---|
| 19 | The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression. Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp. ACM Journal of Experimental Algorithmics (6): 10 (2001). Cited by 3Web SearchBibTeXDownload |
| 18 | Biased Skip Lists for Highly Skewed Access Patterns. Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha. ALENEX 2001, 216-230. Web SearchBibTeXDownload |
| 17 | Permutation Editing and Matching via Embeddings. Graham Cormode, S. Muthukrishnan, Süleyman Cenk Sahinalp. ICALP 2001, 481-492. Cited by 11Web SearchBibTeXDownload |
| 16 | A Dynamic Lookup Scheme for Bursty Access Patterns. Funda Ergün, Suvo Mittra, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha. INFOCOM 2001, 1444-1453. Web SearchBibTeXDownload |
| 15 | The Complexity of Gene Placement. Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk. J. Algorithms (41): 225-243 (2001). Web SearchBibTeXDownload |
| 14 | Biased dictionaries with fast insert/deletes. Funda Ergün, Süleyman Cenk Sahinalp, Jonathan Sharp, Rakesh K. Sinha. STOC 2001, 483-491. Web SearchBibTeXDownload |
| 2000 |
|---|
| 13 | On the temporal HZY compression scheme. Z. Cohen, Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv. SODA 2000, 185-186. Cited by 1Web SearchBibTeXDownload |
| 12 | Communication complexity of document exchange. Graham Cormode, Mike Paterson, Süleyman Cenk Sahinalp, Uzi Vishkin. SODA 2000, 197-206. Cited by 83Web SearchBibTeXDownload |
| 11 | Approximate nearest neighbors and sequence comparison with block operations. S. Muthukrishnan, Süleyman Cenk Sahinalp. STOC 2000, 416-424. Cited by 67Web SearchBibTeXDownload |
| 1999 |
|---|
| 10 | The Effect of Flexible Parsing for Dynamic Dictionary Based Data Compression. Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp. Data Compression Conference 1999, 238-246. Web SearchBibTeXDownload |
| 9 | The Complexity of Gene Placement. Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk. SODA 1999, 386-395. Web SearchBibTeXDownload |
| 8 | On the Optimality of Parsing in Dynamic Dictionary Based Data Compression. Yossi Matias, Süleyman Cenk Sahinalp. SODA 1999, 943-944. Cited by 6Web SearchBibTeXDownload |
| 7 | Compact Grid Layouts of Multi-Level Networks. S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp, Torsten Suel. STOC 1999, 455-463. Cited by 21Web SearchBibTeXDownload |
| 1998 |
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| 6 | Implementation and Experimental Evaluation of Flexible Parsing for Dynamic Dictionary Based Data Compression. Yossi Matias, Nasir Rajpoot, Süleyman Cenk Sahinalp. Algorithm Engineering 1998, 49-61. Web SearchBibTeX |
| 5 | Augmenting Suffix Trees, with Applications. Yossi Matias, S. Muthukrishnan, Süleyman Cenk Sahinalp, Jacob Ziv. ESA 1998, 67-78. Cited by 14Web SearchBibTeXDownload |
| 4 | Layout of the Batcher Bitonic Sorter (Extended Abstract). Shimon Even, S. Muthukrishnan, Mike Paterson, Süleyman Cenk Sahinalp. SPAA 1998, 172-181. Cited by 10Web SearchBibTeXDownload |
| 1996 |
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| 3 | Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm (extended abstract). Süleyman Cenk Sahinalp, Uzi Vishkin. FOCS 1996, 320-328. Web SearchBibTeXDownload |
| 1994 |
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| 2 | On a Parallel-Algorithms Method for String Matching Problems. Süleyman Cenk Sahinalp, Uzi Vishkin. CIAC 1994, 22-32. Web SearchBibTeXDownload |
| 1 | Symmetry breaking for suffix tree construction. Süleyman Cenk Sahinalp, Uzi Vishkin. STOC 1994, 300-309. Web SearchBibTeXDownload |
