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PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.

Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC.

Genome Res. 2019 Nov;29(11):1860-1877. doi: 10.1101/gr.234435.118. Epub 2019 Oct 18.


A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression.

Karpov N, Malikic S, Rahman MK, Sahinalp SC.

Algorithms Mol Biol. 2019 Jul 27;14:17. doi: 10.1186/s13015-019-0152-9. eCollection 2019.


Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data.

Malikic S, Jahn K, Kuipers J, Sahinalp SC, Beerenwinkel N.

Nat Commun. 2019 Jun 21;10(1):2750. doi: 10.1038/s41467-019-10737-5.


BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma.

Shrestha R, Nabavi N, Lin YY, Mo F, Anderson S, Volik S, Adomat HH, Lin D, Xue H, Dong X, Shukin R, Bell RH, McConeghy B, Haegert A, Brahmbhatt S, Li E, Oo HZ, Hurtado-Coll A, Fazli L, Zhou J, McConnell Y, McCart A, Lowy A, Morin GB, Chen T, Daugaard M, Sahinalp SC, Hach F, Le Bihan S, Gleave ME, Wang Y, Churg A, Collins CC.

Genome Med. 2019 Feb 18;11(1):8. doi: 10.1186/s13073-019-0620-3.


Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA.

Gawroński AR, Lin YY, McConeghy B, LeBihan S, Asghari H, Koçkan C, Orabi B, Adra N, Pili R, Collins CC, Sahinalp SC, Hach F.

Nucleic Acids Res. 2019 Apr 23;47(7):e38. doi: 10.1093/nar/gkz067.


lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data.

Haghshenas E, Sahinalp SC, Hach F.

Bioinformatics. 2019 Jan 1;35(1):20-27. doi: 10.1093/bioinformatics/bty544.


Publisher Correction: Optimal compressed representation of high throughput sequence data via light assembly.

Ginart AA, Hui J, Zhu K, Numanagić I, Courtade TA, Sahinalp SC, Tse DN.

Nat Commun. 2018 Apr 26;9(1):1755. doi: 10.1038/s41467-018-03711-0.


MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions.

Gawronski AR, Uhl M, Zhang Y, Lin YY, Niknafs YS, Ramnarine VR, Malik R, Feng F, Chinnaiyan AM, Collins CC, Sahinalp SC, Backofen R.

Bioinformatics. 2018 Sep 15;34(18):3101-3110. doi: 10.1093/bioinformatics/bty208.


Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes.

Numanagić I, Malikić S, Ford M, Qin X, Toji L, Radovich M, Skaar TC, Pratt VM, Berger B, Scherer S, Sahinalp SC.

Nat Commun. 2018 Feb 26;9(1):828. doi: 10.1038/s41467-018-03273-1.


Optimal compressed representation of high throughput sequence data via light assembly.

Ginart AA, Hui J, Zhu K, Numanagić I, Courtade TA, Sahinalp SC, Tse DN.

Nat Commun. 2018 Feb 8;9(1):566. doi: 10.1038/s41467-017-02480-6. Erratum in: Nat Commun. 2018 Apr 26;9(1):1755.


Computational identification of micro-structural variations and their proteogenomic consequences in cancer.

Lin YY, Gawronski A, Hach F, Li S, Numanagic I, Sarrafi I, Mishra S, McPherson A, Collins CC, Radovich M, Tang H, Sahinalp SC.

Bioinformatics. 2018 May 15;34(10):1672-1681. doi: 10.1093/bioinformatics/btx807.


Correction to: ReMixT: clone-specific genomic structure estimation in cancer.

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

Genome Biol. 2017 Oct 6;18(1):188. doi: 10.1186/s13059-017-1327-7. No abstract available.


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. 2017 Dec 15;23(24):7596-7607. doi: 10.1158/1078-0432.CCR-17-0618. Epub 2017 Sep 27.


HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology.

Shrestha R, Hodzic E, Sauerwald T, Dao P, Wang K, Yeung J, Anderson S, Vandin F, Haffari G, Collins CC, Sahinalp SC.

Genome Res. 2017 Sep;27(9):1573-1588. doi: 10.1101/gr.221218.117. Epub 2017 Jul 18.


ReMixT: clone-specific genomic structure estimation in cancer.

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

Genome Biol. 2017 Jul 27;18(1):140. doi: 10.1186/s13059-017-1267-2. Erratum in: Genome Biol. 2017 Oct 6;18(1):188.


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. 2018 Apr;73(4):524-532. doi: 10.1016/j.eururo.2017.02.038. Epub 2017 Mar 19.


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

Chen F, Wang S, Jiang X, Ding S, Lu Y, Kim J, Sahinalp SC, Shimizu C, Burns JC, Wright VJ, Png E, Hibberd ML, Lloyd DD, Yang H, Telenti A, Bloss CS, Fox D, Lauter K, Ohno-Machado L.

Bioinformatics. 2017 Mar 15;33(6):871-878. doi: 10.1093/bioinformatics/btw758.


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

Donmez N, Malikic S, Wyatt AW, Gleave ME, Collins CC, Sahinalp SC.

J Comput Biol. 2017 Jun;24(6):515-523. doi: 10.1089/cmb.2016.0148. Epub 2017 Jan 5.


Comparison of high-throughput sequencing data compression tools.

Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J, Alberti C, Mattavelli M, Sahinalp SC.

Nat Methods. 2016 Dec;13(12):1005-1008. doi: 10.1038/nmeth.4037. Epub 2016 Oct 24.


CoLoRMap: Correcting Long Reads by Mapping short reads.

Haghshenas E, Hach F, Sahinalp SC, Chauve C.

Bioinformatics. 2016 Sep 1;32(17):i545-i551. doi: 10.1093/bioinformatics/btw463.


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. 2017 Jan 1;33(1):26-34. doi: 10.1093/bioinformatics/btw536. Epub 2016 Aug 16.


Robustness of Massively Parallel Sequencing Platforms.

Kavak P, Yüksel B, Aksu S, Kulekci MO, Güngör T, Hach F, Şahinalp SC; Turkish Human Genome Project, Alkan C, Sağıroğlu MŞ.

PLoS One. 2015 Sep 18;10(9):e0138259. doi: 10.1371/journal.pone.0138259. eCollection 2015.


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

Numanagić I, Malikić S, Pratt VM, Skaar TC, Flockhart DA, Sahinalp SC.

Bioinformatics. 2015 Jun 15;31(12):i27-34. doi: 10.1093/bioinformatics/btv232.


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.


DeeZ: reference-based compression by local assembly.

Hach F, Numanagić I, Sahinalp SC.

Nat Methods. 2014 Nov;11(11):1082-4. doi: 10.1038/nmeth.3133. No abstract available.


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

Hach F, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W494-500. doi: 10.1093/nar/gku370. Epub 2014 May 8.


ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

Dao P, Numanagić I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC.

Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15.


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.


SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Hach F, Numanagic I, Alkan C, Sahinalp SC.

Bioinformatics. 2012 Dec 1;28(23):3051-7. doi: 10.1093/bioinformatics/bts593. Epub 2012 Oct 9.


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, 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. doi: 10.1002/gcc.21999. Epub 2012 Aug 25.


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 Nov;22(11):2250-61. doi: 10.1101/gr.136572.111. Epub 2012 Jun 28.


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. doi: 10.1093/bioinformatics/bts214.


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. doi: 10.1002/path.4047.


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

Hajirasouliha I, Schönhuth A, de Juan D, Valencia A, Sahinalp SC.

Bioinformatics. 2012 May 1;28(9):1202-8. doi: 10.1093/bioinformatics/bts109. Epub 2012 Mar 6.


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. 2012 May;227(1):53-61. doi: 10.1002/path.3987. Epub 2012 Mar 21.


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

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

Genome Res. 2011 Dec;21(12):2203-12. doi: 10.1101/gr.120501.111. Epub 2011 Nov 2.


Optimally discriminative subnetwork markers predict response to chemotherapy.

Dao P, Wang K, Collins C, Ester M, Lapuk A, Sahinalp SC.

Bioinformatics. 2011 Jul 1;27(13):i205-13. doi: 10.1093/bioinformatics/btr245.


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. doi: 10.1371/journal.pcbi.1001138. Epub 2011 May 19.


Sensitive and fast mapping of di-base encoded reads.

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

Bioinformatics. 2011 Jul 15;27(14):1915-21. doi: 10.1093/bioinformatics/btr303. Epub 2011 May 17. Erratum in: Bioinformatics. 2012 Jan 1;28(1):150.


Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.

McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC.

Bioinformatics. 2011 Jun 1;27(11):1481-8. doi: 10.1093/bioinformatics/btr184. Epub 2011 Apr 9.


Sparsification of RNA structure prediction including pseudoknots.

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

Algorithms Mol Biol. 2010 Dec 31;5:39. doi: 10.1186/1748-7188-5-39.


Alu repeat discovery and characterization within human genomes.

Hormozdiari F, 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. doi: 10.1101/gr.115956.110. Epub 2010 Dec 3.


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

Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC.

Nat Methods. 2010 Aug;7(8):576-7. doi: 10.1038/nmeth0810-576. No abstract available.


Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.

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

Bioinformatics. 2010 Jun 15;26(12):i350-7. doi: 10.1093/bioinformatics/btq216.


Protein-protein interaction network evaluation for identifying potential drug targets.

Hormozdiari F, Salari R, Bafna V, Sahinalp SC.

J Comput Biol. 2010 May;17(5):669-84. doi: 10.1089/cmb.2009.0032.


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 FS.

Bioinformatics. 2010 Jul 1;26(13):1608-15. doi: 10.1093/bioinformatics/btq249. Epub 2010 May 13.


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

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

Bioinformatics. 2010 May 15;26(10):1277-83. doi: 10.1093/bioinformatics/btq152. Epub 2010 Apr 12.


Towards improved assessment of functional similarity in large-scale screens: a study on indel length.

Schönhuth A, Salari R, Hormozdiari F, Cherkasov A, Sahinalp SC.

J Comput Biol. 2010 Jan;17(1):1-20. doi: 10.1089/cmb.2009.0031.


Fast prediction of RNA-RNA interaction.

Salari R, Backofen R, Sahinalp SC.

Algorithms Mol Biol. 2010 Jan 4;5:5. doi: 10.1186/1748-7188-5-5.


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

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

Nat Genet. 2009 Oct;41(10):1061-7. doi: 10.1038/ng.437. Epub 2009 Aug 30.

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