Publications

2017

Mutational Analysis of Gene Fusions Predicts Novel MHC Class I-Restricted T cell Epitopes and Immune Signatures in a Subset of Prostate Cancer

Kalina JL, Neilson DS, Lin YY, Hamilton PT, Comber AP, Loy EMH, Sahinalp SC, Collins CC, Hach F, Lum JJ

Clin Cancer Res, Sep 27 2017.
Journal link

PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension

Chen F, Wang C, Dai W, Jiang X, Mohammed N, Al Aziz MM, Sadat MN, Sahinalp C, Lauter K, Wang S

BMC Med Genomics, Jul 26 2017.
Journal link

HIT'nDRIVE: Patient-specific multi-driver gene prioritization for precision oncology

Raunak Shrestra, Ermin Hodzic, Thomas Sauerwald, Phuong Dao, Kendric Wang, Jake Yeung, Shawn Anderson, Fabio Vandin, Gholamreza Haffari, Colin C. Collins, Cenk S. Sahinalp

Genome Research, July 18 2017.
Journal link

ReMixT: clone-specific genomic structure estimation in cancer

McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Cote A, Aparicio S, Sahinalp SC, Shah SP

Genome Biol, Jul 27 2017.
Journal link

Stromal Gene Expression is Predictive for Metastatic Primary Prostate Cancer

Mo F, Lin D, Takhar M, Ramnarine VR, Dong X, Bell RH, Volik SV, Wang K, Xue H, Wang Y, Haegert A, Anderson S, Brahmbhatt S, Erho N, Wang X, Gout PW, Morris J, Karnes RJ, Den RB, Klein EA, Schaeffer EM, Ross A, Ren S, Sahinalp SC, Li Y, Xu X, Wang J, Wang J, Gleave ME, Davicioni E, Sun Y, Wang Y, Collins CC

Eur Urol, Mar 19 2017.
Journal link

Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data

Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, S. Cenk Sahinalp

Journal of Computational Biology. June 2017, 24(6): 515-523.
Journal link

SRRM4 Drives Neuroendocrine Transdifferentiation of Prostate Adenocarcinoma Under Androgen Receptor Pathway Inhibition

Yinan Li, Nilgun Donmez, S. Cenk Sahinalp, Ning Xie, Yuwei Wang, Hui Xue, Fan Mo, Himisha Beltran, Martin Gleave, Yuzhuo Wang, Colin Collins, Xuesen Dong

European Urology. 2017 Jan 31
Journal link

Genomic Hallmarks of Localized, Non-Indolent Prostate Cancer

Michael Fraser, Veronica Y. Sabelnykoca, Takafumi N. Yamaguchi, Lawrence E. Heisler, Julie Livingstone, Vincent Huang, Yu-Jia Shiah, Fouad Yousif, Xihui Lin, Andre P. Masella, Natalie S. Fox, Michale Xie, Stephenie D. Prokopec, Alejandro Berlin, Emilie Lalonde, Musaddeque Ahmed, Dominique Trudel, Xuemei Luo, Timothy A. Beck, Alice Meng, Junyan Zhang, Alister D'Costa, Robert E. Denroche, Haiying Kong, Shadrielle Melijah G. Espiritu, Melvin L.K. Chua, Ada Wong , S. Cenk Sahinalp et. al.

Nature. 2017 Jan 9
Journal link

PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software Guard extensionS

Feng Chen, Shuang Wang, Xiaoqian Jiang, Sijie Ding, Yao Lu, Jihoon Kim, S. Cenk Sahinalp, Chisato Shimizu, Jane C. Burns, Victoria J. Wright, Eileen Png, Martin L. Hibberd, David D. Lloyd, Hai Yang, Amalio Telenti, Cinnamon S. Bloss, Dov Fox, Kristin Lauter, Licila Ohno-Machado

Bioinformatics. 2017 Jan 8
Journal link

Prostate Cancer Focal Therapy: Just Because You Can Does Not Mean You Should

Olivier Rouviere, Jean-Yves Chapelon, Sebastien Crouzet, Albert Gelet, S. Cenk Sahinalp et. al.

European Urology. 2017 Jan 1
Journal link

2016

Comparison of High-Throughput Sequencing Data Compression Tools

Ibrahim Numanagic, James K. Bonfield, Faraz Hach, Jan Voges, Jorn Ostermann, Claudio Alberti, Marco Mattavelli, S. Cenk Sahinalp

Nature Methods. 2016 Oct 24
Journal link

The lncRNA Landscape of Breast Cancer Reveals a Role for DSCAM-AS1 in Breast Cancer Progression

Yashar S. Niknafs, Sumin Han, Teng Ma, Corey Speers, Chao Zhang, Kari Wilder-Romans, Matthew K. Iyer, Sethuramasundaram Pitchiaya, Rohit Malik, Yasuyuki Hosono, John R. Prensner, Anton Poliakov, Udit Singhal, Lanbo Xiao, Steven Kregel, Ronald F. Siebenaler, Shuang G. Zhao, Michael Uhl, Alexander Gawronski, Daniel F. Hayes, Lori J. Pierce, Xuhong Cao, Colin Collins, Rolf Backofen, S. Cenk Sahinalp, James M. Rae, Arul M. Chinnaiyan, Felix Y. Feng

Nature Communications. 2016 Sep 26
Journal link

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

Enabling Privacy-Preserving GWAS in Heterogeneous Human Populations

Sean Simmons, S. Cenk Sahinalp, Bonnie Berger

Cell Systems. 2016 Jul 17
Journal link

ICGC in the Cloud

Christina K. Yung, Guillaume Bourque, Paul C. Boutros, Khaled El Emam, Vincent Ferretti, Bartha M. Knoppers, Brian O'Connor, B.F. Francis Ouellette, S. Cenk Sahinalp, Sohrab P. Shah, Lincoln D. Stein, Cancer Genome Collaboratory Consortium

Cancer Research. 2016 Jul 15
Journal link

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

Robustness of Massively Parallel Sequencing Platforms

Pinar Kavak, Bayram Yuksel, Soner Aksu, M. Oguzhan Kulekci, Tunga Gungor, Faraz Hach, S. Cenk Sahinalp

PLoS One. 2015 Sep 18
Journal link

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 |