Publications

    2016

  • SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA

    Kockan C, Hach F, Sarrafi I, Bell RH, McConeghy B, Beja K, Haegert A, Wyatt AW, Volik SV, Chi KN, Collins CC, Sahinalp SC

    Bioinformatics. 2016 Aug 16. pii: btw536
    Journal link | PubMed ID: 27531099

  • CoLoRMap: Correcting Long Reads by Mapping short reads

    Haghshenas E, Hach F, Sahinalp SC, Chauve C

    Bioinformatics. 2016 Sep 1;32(17):i545-i551
    Presented at ECCB’16 (The 15th European Conference on Computational Biology),The Hague, Netherlands, Septemeber 3-7 2016
    Journal link | PubMed ID: 27587673 |

  • 2015

  • Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data

    Numanagic I, Malikic S, Pratt VM, Skaar TC, Flockhart DA, Sahinalp SC.

    Bioinformatics. 2015 Jun 15;31(12):i27-34
    Journal link | PubMed ID: 26072492 |

  • Spatial genomic heterogeneity within localized, multifocal prostate cancer

    Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, Meng A, Hennings-Yeomans PH, McPherson A, Sabelnykova VY, Zia A, Fox NS, Livingstone J, Shiah YJ, Wang J, Beck TA, Have CL, Chong T, Sam M, Johns J, Timms L, Buchner N, Wong A, Watson JD, Simmons TT, P’ng C, Zafarana G, Nguyen F, Luo X, Chu KC, Prokopec SD, Sykes J, Dal Pra A, Berlin A, Brown A, Chan-Seng-Yue MA, Yousif F, Denroche RE, Chong LC, Chen GM, Jung E, Fung C, Starmans MH, Chen H, Govind SK, Hawley J, D’Costa A, Pintilie M, Waggott D, Hach F, Lambin P, Muthuswamy LB, Cooper C, Eeles R, Neal D, Tetu B, Sahinalp CS, Stein LD, Fleshner N, Shah SP, Collins CC, Hudson TJ, McPherson JD, van der Kwast T, Bristow RG.

    Nature Genetics. 2015 May doi:10.1038/ng.3315
    Journal link | PubMed ID: 26005866

  • Clonality Inference in Multiple Tumor Samples using Phylogeny

    Malikic S, McPherson AW, Donmez N, Sahinalp CS.

    Bioinformatics. 2015 May 1;31(9):1349-56
    Journal link | PubMed ID: 25568283

  • 2014

  • Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa

    Alkan C, Kavak P, Somel M, Gokcumen O, Ugurlu S, Saygi C, Dal E, Bugra K, Güngör T, Sahinalp SC, Özören N, Bekpen C

    BMC Genomics. 2014 Nov 7;15:963. doi: 10.1186/1471-2164-15-963
    Journal link | PubMed ID: 25376095 |

  • DeeZ: reference-based compression by local assembly

    Hach F, Numanagic I, Sahinalp SC

    Nature Methods, 2014 Nov; 11(11):1082–4
    Journal link | PubMed ID: 25357237

  • mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications

    Hach F, Sarrafi I, Farhad Hormozdiari, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp

    Nucl. Acids Res. (1 July 2014) 42 (W1): W494-W500.
    Journal link | PubMed ID: 24810850

  • HIT’nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time

    Shrestha R, Hodzic E, Yeung J, Wang K, Sauerwald T, Dao P, Anderson S, Beltran H, Rubin MA, Collins C, Haffari G, Sahinalp SC

    Proc. of RECOMB 2014:293-306
    Presented at RECOMB’14 (18th Annual International Conference on Research in Computational Molecular Biology), Pittsburgh, Pennsylvania, April 2-5 2014
    Journal link

  • 2013

  • Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms

    Dao P, Numanagic I, Lin Y, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC

    Bioinformatics. 2014 Mar 1;30(5):644-51
    Journal link | PubMed ID: 24130305

  • Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies

    Swanson L, Robertson G, Mungall KL, Butterfield YS, Chiu R, Corbett RD, Docking TR, Hogge D, Jackman SD, Moore RA, Mungall AJ, Nip KM, Parker JD, Qian JQ, Raymond A, Sung S, Tam A, Thiessen N, Varhol R, Wang S, Yorukoglu D, Zhao Y, Hoodless PA, Sahinalp SC, Karsan A, Birol I

    BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550.
    Journal link | PubMed ID: 23941359 |

  • 2012

  • SCALCE: boosting Sequence Compression Algorithms using Locally Consistent Encoding

    Hach F, Numanagic I, Alkan C, Sahinalp SC

    Bioinformatics (2012) 28 (23): 3051-3057.
    Presented at RECOMB-Seq’12 (2nd Annual RECOMB Satellite Workshop on Massively Parallel Sequencing), Barcelona, Spain, April 19-20 2012
    Journal link | PubMed ID: 23047557

  • nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

    McPherson A, Wu C, Wyatt AW, Shah S, Collins C, Sahinalp SC

    Genome Res. 2012. 22: 2250-2261
    Presented at RECOMB’12 (16th Annual International Conference on Research in Computational Molecular Biology), Barcelona, Spain, April 21-24 2012
    Journal link | PubMed ID: 22745232

  • Poly-gene fusion transcripts and chromothripsis in prostate cancer

    Wu C, Wyatt AW, McPherson A, Lin D, McConeghy BJ, Mo F, Shukin R, Lapuk AV, M Jones SJ, Zhao Y, Marra MA, Gleave ME, Volik SV, Wang Y, Sahinalp SC, Collins CC

    Genes Chromosomes Cancer. 2012 Dec;51(12):1144-53
    Journal link | PubMed ID: 22927308

  • CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population

    Lin Y, Dao P, Hach F, Bakhshi M, Mo F, Lapuk A, Collins C, Sahinalp SC

    Proc. of WABI 2012: 178-189
    Presented at WABI’12 (12th Workshop on Algorithms in Bioinformatics), September 10-12, Ljubljana, Slovenia
    Journal link

  • Dissect: detection and characterization of novel structural alterations in transcribed sequences

    Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC

    Bioinformatics. 2012 Jun 15;28(12):i179-87
    Presented at ISMB’12 (20th Annual International Conference on Intelligent Systems for Molecular Biology), Long Beach, USA, July 19-23 2012
    Won Ian Lawson Van Toch Memorial Award for Outstanding Student Paper
    Journal link | PubMed ID: 22689759

  • From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer

    Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, Volik SV, Collins CC

    J Pathol. 2012 Jul;227(3):286-97
    Journal link | PubMed ID: 22553170

  • The 1000 Genomes Project: data management and community access

    Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium.

    Nat Methods. 2012 Apr 27;9(5):459-62
    Journal link | PubMed ID: 22543379 |

  • Mirroring co-evolving trees in the light of their topologies

    Hajirasouliha I, Schonhuth A, de Juan D, Valencia A, Sahinalp SC

    Bioinformatics. 2012 May 1;28(9):1202-8
    Journal link | PubMed ID: 22399677

  • Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer

    Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Mo F, Li E, Fazli L, Hurtado-Coll A, Jones EC, Butterfield YS, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Jones SJ, Hirst M, Marra MA, Maher CA, Chinnaiyan AM, Sahinalp SC, Gleave ME, Volik SV, Collins CC.

    J Pathol. Volume 227, Issue 1, pages 53-61, May 2012
    Journal link | PubMed ID: 22294438

  • 2011

  • Simultaneous structural variation discovery among multiple paired-end sequenced genomes

    Hormozdiari Fe, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC.

    Genome Res. 2011. 21: 2203-2212
    Presented at RECOMB’11 (15th Annual International Conference on Research in Computational Molecular Biology), Vancouver, Canada, March 28-31 2011
    Featured on the cover
    Highlighted in: Nature Biotechnology, 29, 1101 (2011)
    Journal link | PubMed ID: 22048523 |

  • Optimally Discriminative Subnetwork Markers Predict Response To Chemotherapy

    Dao P, Wang K, Collins CC, Ester M, Lapuk AV, Sahinalp SC

    Bioinformatics (2011) 27 (13): i205-i213
    Presented at ISMB’11 (19th Annual International Conference on Intelligent Systems for Molecular Biology), Vienna, Austria, July 17-19 2011
    Journal link | PubMed ID: 21685072 |

  • deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

    McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP.

    PLoS Comput Biol. 2011 May;7(5):e1001138. Epub 2011 May 19.
    Journal link | PubMed ID: 21625565 |

  • Sensitive and fast mapping of di-base encoded reads

    Hormozdiari Fe, Hach F, Sahinalp SC, Eichler EE, Alkan C.

    Bioinformatics. 2011 Jul 15;27(14):1915-21.
    Erratum in: Bioinformatics. 2012 Jan 1;28(1):150
    Journal link | PubMed ID: 21586516 |

  • Mapping copy number variation by population-scale genome sequencing

    Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari Fe, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, St?otz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.

    Nature. 2011 Feb 3;470(7332):59-65.
    Journal link | PubMed ID: 21293372

  • Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data

    McPherson A, Wu C, Hajirasouliha I, Hormozdiari Fe, Hach F, Lapuk AV, Volik S, Shah SP, Collins CC, Sahinalp SC

    Bioinformatics (2011) 27 (11): 1481-1488
    Presented at ISMB-HitSeq’11 (High Throughput Sequencing Analysis and Algorithms, Special Interest Group of ISMB’11), Vienna, Austria, July 15-16 2011
    Won Best Paper Award
    Journal link | PubMed ID: 21478487 |

  • Mapping the Protein Interaction Network in Methicillin-Resistant Staphylococcus aureus

    Cherkasov A, Hsing M, Zoraghi R, Foster LJ, See RH, Stoynov N, Jiang J, Kaur S, Lian T, Jackson L, Gong H, Swayze R, Amandoron E, Hormozdiari F, Dao P, Sahinalp C, Santos-Filho O, Axerio-Cilies P, Byler K, McMaster WR, Brunham RC, Finlay BB, Reiner NE.

    J Proteome Res. 2011 Mar 4;10(3):1139-50
    Journal link | PubMed ID: 21166474

  • Alu repeat discovery and characterization within human genomes

    Hormozdiari Fe, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, Eichler EE.

    Genome Res. 2011 Jun;21(6):840-9
    Journal link | PubMed ID: 21131385 |

  • 2010

  • Sparsification of RNA structure prediction including pseudoknots

    Mohl M, Salari R, Will S, Backofen R, Sahinalp SC.

    Algorithms Mol Biol. 2010 Dec 31;5(1):39.
    Journal link | PubMed ID: 21194463 |

  • Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set

    Sushko I, Novotarskyi S, Korner R, Pandey AK, Cherkasov A, Li J, Gramatica P, Hansen K, Schroeter T, Muller KR, Xi L, Liu H, Yao X, Oberg T, Hormozdiari F, Dao P, Sahinalp C, Todeschini R, Polishchuk P, Artemenko A, Kuz’min V, Martin TM, Young DM, Fourches D, Muratov E, Tropsha A, Baskin I, Horvath D, Marcou G, Varnek A, Prokopenko VV, Tetko IV.

    J. Chem. Inf. Model., 2010, 50 (12), pp 2094–2111
    Journal link | PubMed ID: 21033656

  • A map of human genome variation from population-scale sequencing

    1000 Genomes Project Consortium, (Hajirasouliha I, Hormozdiari F, Sahinalp SC – Contributors to structural variation analyses of the manuscript)

    Nature, 2010 Oct 28;467(7319):1061-73
    Journal link | PubMed ID: 20981092 |

  • Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties

    Schonhuth A, Salari R, Sahinalp SC

    Proc. of WABI 2010: 350-361
    Presented at WABI’11 (11th Workshop on Algorithms in Bioinformatics), September 5-7, Saarbrucken, Germany
    Journal link

  • Sparsification of RNA Structure Prediction Including Pseudoknots

    Mohl M, Salari R, Will S, Backofen R, Sahinalp SC

    Proc. of WABI 2010: 40-51
    Presented at WABI’11 (11th Workshop on Algorithms in Bioinformatics), September 5-7, Saarbrucken, Germany
    Journal link

  • mrsFAST: a cache-oblivious algorithm for short-read mapping

    Hach F, Hormozdiari Fe, Alkan C, Hormozdiar Fa, Birol I, Eichler EE, Sahinalp SC

    Nature Methods, 2010 Aug;7(8):576-7
    Journal link | PubMed ID: 20676076

  • Next Generation VariationHunter: Combinatorial Algorithms for Transposon Insertion Discovery

    Hormozdiari Fe, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC

    Bioinformatics 2010 Jun 15;26(12):i350-i357
    Presented at ISMB’10 (18th Annual International Conference Intelligent Systems for Molecular Biology), Boston, USA, July 11-13 2010
    Journal link | PubMed ID: 20529927 |

  • Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

    Hajirasouliha I, Hormozdiari Fe, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC

    Bioinformatics 2010 26(10):1277-1283
    Presented at ISMB-HiTSeq’10 (High Throughput Sequencing Analysis and Algorithms, Special Interest Group of ISMB’10), Boston, USA, July 9-10 2010
    Journal link | PubMed ID: 20385726 |

  • Periodicity testing with sublinear samples and space

    Ergun F, Muthukrishnan S, Sahinalp SC

    ACM Transactions on Algorithms 6(2): (2010)
    Journal link

  • Protein protein interaction network evaluation for identifying potential drug targets

    Hormozdiari Fe, Salari R, Bafna V, Sahinalp SC

    Journal of Computational Biology, 2010 May;17(5):669-84.
    Journal link | PubMed ID: 20500021 |

  • PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

    Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FSL

    Bioinformatics 26(13): 1608-1615 (2010).
    Journal link | PubMed ID: 20472543 |

  • Time and space efficient RNA-RNA interaction prediction via sparse folding

    Salari R, Mohl M, Will S, Sahinalp SC, Backofen R

    Proc. of RECOMB 2010: 473-490
    Presented at RECOMB’10 (14th Annual International Conference on Research in Computational Molecular Biology), Lisbon, Portugal, August 12-15 2012
    Journal link |

  • Towards improved assessment of functional similarity in large-scale screens: an indel study

    Schonhuth A, Salari R, Hormozdiari Fe, Cherkasov A, Sahinalp SC

    Journal of Computational Biology, 2010 Jan;17(1):1-20.
    Journal link | PubMed ID: 20078394 |

  • 2009

  • Personalized copy number and segmental duplication maps using next-generation sequencing

    Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari Fe, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE.

    Nature Genetics,Oct, 41(10):1061-1067, 2009
    Journal link | PubMed ID: 19718026 |

  • Quantifying systemic evolutionary changes by color coding confidence-sored PPI networks

    Dao P, Schonhuth A, Hormozdiari Fe, Hajirasouliha I, Sahinalp SC, Ester M.

    Proc. of WABI 2009: 37-48
    Presented at WABI’09 (9th Workshop on Algorithms in Bioinformatics), Philadelphia, USA, September 12-13 2009.
    Journal link |

  • Fast prediction of RNA-RNA interaction

    Salari R, Backofen R, Sahinalp SC.

    Algorithms for Molecular Biology 2010, 5:5
    Presented at WABI’09 (9th Workshop on Algorithms in Bioinformatics), Philadelphia, USA, September 12-13 2009.
    Journal link | PubMed ID: 20047661 |

  • biRNA: Fast RNA-RNA Binding Sites Prediction

    Chitsaz H, Backofen R, Sahinalp SC

    Proc. of WABI 2009: 25-36
    Presented at WABI’09 (9th Workshop on Algorithms in Bioinformatics), Philadelphia, USA, September 12-13 2009.
    Journal link |

  • Improved Small Molecule Activity Determination via Centroid Nearest Neighbors Classification

    Dao P, Hormozdiari Fa, Jowhari H, Byler K, Cherkasov A, Sahinalp SC

    Proc. of LSS Comput Syst Bioinform Conf. August, 2009. Vol. 8, p. 251-262
    Presented at CSB’09 (The 8th Annual Conference on Computational Systems Bioinformatics), Standford University, USA, August 10-12.

  • smyRNA: A novel ab initio ncRNA gene finder

    Salari R, Aksay C, Karakoc E, Unrau P, Hajirasouliha I, Sahinalp SC

    PLoS ONE 4(5): e5433, 2009.
    Journal link | PubMed ID: 19415115 |

  • A Partition Function Algorithm for Interacting Nucleic Acid Strands

    Chitsaz H, Salari R, Sahinalp SC, Backofen R

    Bioinformatics 25(12):i365-i373
    Presented at ISMB’09 (17th Annual International Conference Intelligent Systems for Molecular Biology), June 27-July 2nd, Stockholm, Sweden.
    Journal link | PubMed ID: 19478011 |

  • Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes

    Hormozdiari Fe, Alkan C, Eichler E, Sahinalp SC.

    Genome Research, Jul, 19(7):1270-8, 2009.
    Presented at RECOMB’09 (13th Annual International Conference on Research in Computational Molecular Biology), Tucson, AZ, USA, May 18-21
    Journal link | PubMed ID: 19447966 |

  • Dense graphlet statistics of protein interaction networks and random networks

    Colak R, Hormozdiari Fe, Moser F, Schonhuth A, Holman J, Ester M, Sahinalp SC.

    Proc. of Pac Symp Biocomput. 2009:178-89
    Presented at PSB’09 (Pacific Symposium on Biocomputing), Big Island of Hawaii, January 5-9
    Journal link | PubMed ID: 19213135 |

  • 2008

  • Edit distance under block operations

    Sahinalp SC.

    Encyclopedia of Algorithms 2008
    Journal link |

  • The effect of insertion and deletions (indels) on wirings in protein interaction networks: a large scale study

    Hormozdiari Fe, Hsing M, Salari R, Schonhuth A, Sahinalp SC, Cherkasov A.

    Journal of Computational Biology, February 1, 2009, 16(2): 159-167
    Presented at RECOMB’08 (12th Annual International Conference on Research in Computational Molecular Biology), Singapore, March 30th-April 2nd
    Journal link | PubMed ID: 19193143 |

  • The relation between indel length and functional divergence: a formal study

    Salari R, Schonhuth A, Hormozdiari Fe, Cherkasov A, Sahinalp SC.

    WABI 2008: 330-341
    Presented at WABI’08 (8th Workshop on Algorithms in Bioinformatics), Karlsruhe, Germany, September 15-17
    Journal link |

  • Biomolecular Network Motif Counting and Discovery by Color Coding

    Alon N, Dao P, Hajirasouliha I, Hormozdiari Fe, Sahinalp SC

    Bioinformatics 2008 24: i241-i249
    Presented at ISMB’08 (16th Annual International Conference Intelligent Systems for Molecular Biology), Toronto, Canada, July 19-23.
    Journal link | PubMed ID: 18586721 |

  • Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies

    Hajirasouliha I, Hormozdiari Fe, Sahinalp SC, Birol I.

    Bioinformatics 2008 24: i32-i40
    Presented at ISMB’08 (16th Annual International Conference Intelligent Systems for Molecular Biology), Toronto, Canada, July 19-23.
    Journal link | PubMed ID: 18586730 |

  • Conifers have a unique small RNA silencing signature

    Dolgosheina EV, Morin RD, Aksay G, Sahinalp SC, Magrini V, Mardis ER, Mattsson J, Unrau PJ.

    RNA 2008. 14: 1508-1515
    Journal link | PubMed ID: 18566193 |

  • Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

    Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ.

    Genome Res. 2008. 18: 571-584
    Journal link | PubMed ID: 18323537 |

  • Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis

    Zhu, H., Tropsha A, Fourches D, Varnek A, Papa E, Gramatica P, Oberg T, Dao P, Cherkasov A, Tetko IV

    J. Chem. Inf. Model., 2008, 48 (4), pp 766–784
    Journal link | PubMed ID: 18311912 |

  • 2007

  • Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data

    Alkan C, Ventura M, Archidiacono N, Rocchi M, Sahinalp SC, Eichler EE.

    PLoS Comput Biol. 2007 Sep;3(9):1807-18.
    Journal link | PubMed ID: 17907796 |

  • Novel Approaches for Small Biomolecule Classification and Structural Similarity Search

    Karakoc E, Cherkasov A, Sahinalp SC.

    ACM SIGKDD Explorations, Volume 9, Issue 1, pages 14-21, June 2007

  • Not all scale-free networks are born equal: The role of the seed graph in PPI network evolution

    Hormozdiari Fe, Berenbrink P, Przulj N, Sahinalp SC.

    PLoS Computational Biology 3(7). July 2007:e118
    Journal link | PubMed ID: 17616981

  • taveRNA: a web suite for RNA algorithms and applications

    Aksay C, Salari R, Karakoc E, Alkan C, Sahinalp SC.

    Nucl. Acids Res. (2007) 35 (suppl 2): W325-W329
    Journal link | PubMed ID: 17488837 |

  • The intelligence in developing systems for molecular biology

    Sahinalp SC.

    Genome Biol. 2007;8(1):301
    Journal link | PubMed ID: 17274837 |

  • Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites

    Karakoc E, Sahinalp SC, Cherkasov A.

    Proc. of Pacific Symposium on Biocomputing, 12:133-144, 2007
    Presented at PSB’07 (Pacific Symposium on Biocomputing), Maui, Hawaii, January 3-7
    Journal link | PubMed ID: 17990487 |

  • Relationship between insertion/deletion (indel) frequency of proteins and essentiality

    Chan SK, Hsing M, Hormozdiari Fe, Cherkasov A.

    BMC Bioinformatics 2007, 8:277
    Journal link | PubMed ID: 17598914 |

  • 2006

  • RNA-RNA Interaction Prediction and Antisense RNA Target Search

    Alkan C, E. Karakoc, J. Nadeau, C. Sahinalp, K. Zhang. **The authors are listed in alphabetical order

    J Comput Biol. 2006 Mar;13(2):267-82.
    Journal link | PubMed ID: 16597239 |

  • Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds

    Karakoc E, Sahinalp SC, Cherkasov A.

    J. Chem. Inf. Model., 2006, 46 (5), pp 2167–2182
    Journal link | PubMed ID: 16995747 |

  • The Degree Distribution of the Generalized Duplication Model

    G. Bebek, Berenbrink P, C. Cooper, Friedetzky T, J. H. Nadeau, S. C. Sahinalp.

    Theor. Comput. Sci. 369(1-3): 239-249 (2006)
    Theoretical Computer Science, Volume 369, Issues 1-3, 15 December 2006, Pages 239-249
    Journal link |

  • Distance Based Algorithms for Small Biomolecule Classification and Structural Similarity Search

    Karakoc E, Cherkasov A, Sahinalp SC.

    Bioinformatics. 2006 Jul 15;22(14):e243-51
    Presented at ISMB’08 (14th Annual International Conference Intelligent Systems for Molecular Biology), , Fortaleza, Brazil, August 6-10
    Journal link | PubMed ID: 16873478 |

  • Not All Scale Free Networks are Born Equal: the Role of the Seed Graph in PPI Network Emulation

    Hormozdiari Fe, Berenbrink P, Przulj N, Sahinalp SC.

    Proc. of Systems Biology and Computational Proteomics 2006: 1-13
    Presented at Systems Biology and Computational Proteomics, Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, San Diego, CA, USA, December 1-3
    Journal link |

  • RNA Secondary Structure Prediction via Energy Density Minimization

    Alkan C, E. Karakoc, C. Sahinalp, P. Unrau, A. Ebhardt, K. Zhang, J. Buhler.

    Proc. of RECOMB 2006: 130-142
    Presented at RECOMB’06 (10th Annual International Conference on Research in Computational Molecular Biology), Venice, Italy, April 2-5
    Journal link |

  • String Embeddings and Edit Distance Approximations

    Batu T, Ergun F, Sahinalp SC.

    Proc of SODA 2006: 792-801
    Presented at SODA’06 (7th Annual ACM-SIAM Symposium on Discrete Algorithms),Miami, Florida, USA, January 22-26
    Journal link |

  • 2005

  • Manipulating Multiple Sequence Alignments via MaM and WebMaM

    Alkan C, Tuzun E, Buard J, Lethiec F, Eichler EE, Bailey JA, Sahinalp SC.

    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W295-8.
    Journal link | PubMed ID: 15980474 |

  • Locally Consistent Parsing and Applications to Approximate String Comparisons

    Batu T, Sahinalp SC.

    Proc. of Developments in Language Theory 2005: 22-35
    Presented at DLT’05 (9th International Conference on Developments in Language Theory), Palermo, Italy, July 4-8
    Journal link |

  • Optimal Spaced Seeds for Faster Approximate String Matching

    Farach-Colton M, Landau G, Sahinalp SC, Tsur D

    Proc. of ICALP 2005: 1251-1262
    Presented at ICALP’05 (Automata, Languages and Programming, 32nd International Colloquium), Lisbon, Portugal, July 11-15
    Journal link |

  • Improved Duplication Models for Proteome Network Evolution

    G. Bebek, Berenbrink P, C. Cooper, Friedetzky T, J. Nadeau, Sahinalp SC.

    Proc. of Systems Biology and Regulatory Genomics 2005: 119-137
    Presented at Systems Biology and Regulatory Genomics, Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA; December 2-4,
    Journal link |

  • RNA-RNA Interaction Prediction and Antisense RNA Target Search

    Alkan C, Karakoc E, Nadeau J, Sahinalp SC, Zhang K. **The authors are listed in alphabetical order

    Proc. of RECOMB 2005: 152-171
    Presented at RECOMB’05 (9th Annual International Conference on Research in Computational Molecular Biology), Cambridge, MA, USA, May 14-18
    Journal link |

  • 2004

  • The structure and evolution of centromeric transition regions within the human genome

    She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE.

    Nature, 2004 Aug 19;430(7002):857-64, (2004)
    Journal link | PubMed ID: 15318213 |

  • Hardness of string similarity search and other indexing problems

    Sahinalp SC, Utis A.

    Proc. of ICALP 2004: 1080-1098
    Presented at ICALP’04 (Automata, Languages and Programming: 31st International Colloquium),Turku, Finland, July 12-16
    Journal link |

  • Identifying uniformly mutated segments within repeats.

    Sahinalp SC, Eichler EE, Goldberg Berenbrink P P, Friedetzky T, Ergun F

    J Bioinform Comput Biol. 2004 Dec;2(4):657-68.
    Journal link | PubMed ID: 15617159 |

  • The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis

    Alkan C, Bailey J, Eichler EE, Sahinalp SC, Tuzun E

    Journal of Computational Biology 11(5): 933-944 (2004)
    Journal link | PubMed ID: 15700410 |

  • Novel approaches to Biomolecular Sequence Indexing

    Karakoc E, Ozsoyoglu M, Sahinalp SC, Tasan M, Zhang X. **The authors are listed in alphabetical order

    IEEE Data Eng. Bull. 27(3): 40-47 (2004)

  • Sublinear methods for detecting periodic trends in data streams

    Ergun F, Muthukrishnan S, Sahinalp SC.

    Proc. of LATIN 2004: 16-28
    Presented at LATIN’04 (Theoretical Informatics, 6th Latin American Symposium), Buenos Aires, Argentina, April 5-8
    Journal link |

  • An Efficient Algorithm for Sequence Comparison with Block Reversals

    Muthukrishnan S, Sahinalp SC.

    Theor. Comput. Sci. 321(1): 95-101 (2004)
    Journal link |

  • 2003

  • Comparing Sequences with Segment Rearrangements

    Ergun F, Muthukrishnan S, Sahinalp SC.

    Proc. of FSTTCS 2003: 183-194
    Presented at FSTTCS’03 (Foundations of Software Technology and Theoretical Computer Science), Mumbai, India, December 15-17
    Journal link |

  • Distance Based Indexing for Sequence Proximity Search

    Tasan M, Macker J, Ozsoyoglu M, Sahinalp SC.

    Proc. of ICDE 2003: 125-136
    Presented at ICDE’03 (19th International Conference on Data Engineering), Bangalore, India, March 5-8
    Journal link |

  • Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome

    Liu G, Zhao S, Bailey J, Sahinalp SC, Alkan C, Tuzun E, Green E, Eichler EE.

    Genome Res. 2003. 13: 358-368
    Journal link | PubMed ID: 12618366 |

  • 2002

  • An algorithmic analysis of the role of unequal crossover in alpha satellite DNA evolution

    Alkan C, Bailey J, Eichler EE, Sahinalp SC, Tuzun E.

    Proc. of Genome Inform. 2002;13:93-102.
    Presented at GIW’02 (The 13th International Conference on Genome Informatics), Tokyo, Japan, December 16-18
    PubMed ID: 14571378 |

  • Statistical Identification of Uniformly Mutated Segments within Repeats

    Sahinalp SC, Eichler EE, Goldberg P, Berenbrink P, Friedetzky T, Ergun F

    Proc. of CPM 2002: 249-261
    Presented at CPM’02 (13th Annual Symposium on Combinatorial Pattern Matching), Fukuoka, Japan, July 3-5
    Journal link |

  • Simple and Practical Sequence Nearest Neighbors Under Block Edit Operations

    Muthukrishnan S, Sahinalp SC.

    Proc. of CPM 2002: 262-278
    Presented at CPM’02 (13th Annual Symposium on Combinatorial Pattern Matching), Fukuoka, Japan, July 3-5
    Journal link |

  • An Improved Algorithm for Sequence Comparison with Block Reversals

    Muthukrishnan S, Sahinalp SC.

    Proc. of LATIN 2002: 319-325
    Presented at LATIN’02 (Theoretical Informatics, 5th Latin American Symposium), Cancun, Mexico, April 3-6
    Journal link |

  • Dictionary Based Data Compression

    Rajpoot N, Sahinalp SC.

    Handbook of Lossless Data Compression, K. Sayood (ed.), Academic Press, (2002).

  • 2001

  • Divergent Origins and Concerted Expansion of Two Segmental Duplications on Chromosome 16

    Eichler EE, Johnson ME, Alkan C, Tuzun E, Sahinalp SC, Viggiano L, Rocchi M

    J Hered. 2001 Nov-Dec;92(6):462-8.
    Journal link |

  • The Complexity of Gene Placement

    Goldberg LA, Goldberg P, Pevzner P, Paterson M, Sahinalp SC, Sweedyk Z

    J. Algorithms 41(2): 225-243 (2001)
    Journal link |

  • The Effect of Flexible Parsing for Dynamic Dictionary-Based Data Compression

    Matias Y, Rajpoot N, Sahinalp SC

    ACM Journal of Experimental Algorithmics 6: 10 (2001)
    Invited paper (2001).
    Journal link

  • Biased Skip Lists for Highly Skewed Access Patterns

    Ergun F, Sahinalp SC, Sharp J, Sinha R.

    Proc. of ALENEX 2001: 216-230
    Presented at ALENEX’01 (Third International Workshop on Algorithm Engineering and Experimentation), Washington, DC, USA, January 5-6
    Journal link

  • Permutation editing and matching via embeddings

    Cormode G, Muthukrishnan S, Sahinalp SC.

    Proc. of ICALP 2001: 481-492
    Presented at ICALP’01 (28th International Colloquium on Automata, Languages and Programming), Crete, Greece, July 8-12
    Journal link |

  • A Dynamic Lookup Scheme for Bursty Access Patterns

    Ergun F, Mitra S, Sahinalp SC, Sharp J, Sinha R. **The authors are listed in alphabetical order

    Proc. of INFOCOM 2001: 1444-1453
    Presented at INFOCOM’01 (The Conference on Computer Communications, Twentieth Annual Joint Conference of the IEEE Computer and Communications Societies, Twenty years into the communications odyssey), Anchorage, Alaska, USA, 22-26 April

  • Biased Dictionaries with Fast Insert/ Deletes

    Ergun F, Sahinalp SC, Sharp J, Sinha R.

    Proc. of STOC 2001: 483-491
    Presented at STOC’01 (33rd Annual ACM Symposium on Theory of Computing), Heraklion, Crete, Greece, July 6-8, 2001
    Journal link |

  • 2000

  • On the temporal HZY data compression scheme

    Cohen Z, Matias Y, Muthukrishan S, Sahinalp SC, Ziv J.

    Proc. of SODA 2000: 185-186
    Presented at SODA’2000 (Eleventh Annual ACM-SIAM Symposium on Discrete Algorithms), San Francisco, CA, USA, January 9-11
    Journal link |

  • Communication complexity of document exchange

    Cormode G, Paterson MS, Sahinalp SC, Vishkin U.

    Proc. of SODA 2000: 197-206
    Presented at SODA’2000 (Eleventh Annual ACM-SIAM Symposium on Discrete Algorithms), San Francisco, CA, USA, January 9-11
    Journal link |

  • Approximate nearest neighbors and sequence comparison with block operations

    Muthukrishnan S, Sahinalp SC.

    Proc. of STOC 2000: 416-424
    Presented at STOC’2000 (Thirty-Second Annual ACM Symposium on Theory of Computing), Portland, OR, USA, May 21-23
    Journal link |

  • 1999

  • The Effect of Flexible Parsing for Lempel-Ziv Dictionary Compression

    Matias Y, Rajpoot N, Sahinalp SC.

    Proc. of Data Compression Conference 1999: 238-246
    Presented at DCC’09 (Data Compression Conference), Snowbird, Utah, USA, March 29-31
    Journal link |

  • The Complexity of Gene Placement

    Goldberg LA, Goldberg P, Pevzner P, Paterson M, Sahinalp SC, Sweedyk Z

    Proc. of SODA 1999: 386-395
    Presented at SODA’09 (Tenth Annual ACM-SIAM Symposium on Discrete Algorithms), Baltimore, Maryland, USA, January 17-19
    Journal link |

  • On the Optimality of Parsing for Dynamic Dictionary Compression

    Matias Y, Sahinalp SC.

    Proc. of SODA 1999: 943-94
    Presented at SODA’09 (Tenth Annual ACM-SIAM Symposium on Discrete Algorithms), Baltimore, Maryland, USA, January 17-19
    Journal link |

  • Compact Grid Layouts of Multi-Level Networks

    Muthukrishnan S, Paterson MS, Sahinalp SC, Suel T.

    Proc. of STOC 1999: 455-463
    Presented at STOC’09 (Thirty-First Annual ACM Symposium on Theory of Computing), Atlanta, Georgia, USA, May 1-4.
    Journal link |

  • 1998

  • Augmenting Suffix Trees with Applications

    Matias Y, Muthukrishnan S, Sahinalp SC, Ziv J.

    Proc. of ESA 1998: 67-78
    Presented at ESA ’98 (6th Annual European Symposium), Venice, Italy, August 24-26
    Journal link |

  • Layout of the Batcher Bitonic Sorter

    Even S, Muthukrishnan S, Paterson MS, Sahinalp SC.

    Proc. of SPAA 1998: 172-181
    Presented at SPAA’98 (Tenth Annual ACM Symposium on Parallel Algorithms and Architectures), Puerto Vallarta, Mexico, June 28-July 2.
    Journal link |

  • Implementation and Experimental Evaluation of Flexible Parsing For Dynamic Dictionary Based Compression

    Matias Y, Rajpoot N, Sahinalp SC.

    Proc. of Algorithm Engineering 1998: 49-61
    Presented at WAE’98 (2nd International Workshop on Algorithm Engineering), Saarbrucken, Germany, Aug 20-22.

  • 1996

  • Performance Evaluation of Approximate Priority Queues

    Matias Y, Sahinalp SC, Young NE.

    Presented at DIMACS Fifth Implementation Challenge: Priority Queues, Dictionaries, and Point Sets, Piscataway, NJ, USA, October 28-30

  • Efficient Approximate and Dynamic Matching of Patterns Using a Labeling Paradigm

    Sahinalp SC, Vishkin U.

    Proc. of FOCS 1996: 320-328
    Presented at FOCS’96 (37th Annual Symposium on Foundations of Computer Science), Burlington, VT, USA, October 14-16
    Journal link |

  • 1994

  • On a parallel-algorithms method for string matching problems

    Sahinalp SC, Vishkin U.

    Proc. of CIAC 1994: 22-32
    Presented at CIAC’94 (Second Italian Conference on Algorithms and Complexity), Rome, Italy, February 23-25
    invited paper
    Journal link

  • Symmetry Breaking In Suffix Tree Construction

    Sahinalp SC, Vishkin U.

    Proc. of STOC 1994: 300-309
    Presented at STOC’94 (Twenty-Sixth Annual ACM Symposium on Theory of Computing), Montreal, QC Canada, May 23-25
    Journal link |