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S Cenk Sahinalp - Publications

Affiliations: 
Case Western Reserve University, Cleveland Heights, OH, United States 
Area:
Computer Science, Genetics, Biostatistics Biology
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Hari A, Zhou Q, Gonzaludo N, Harting J, Scott SA, Qin X, Scherer S, Sahinalp SC, Numanagić I. An efficient genotyper and star-allele caller for pharmacogenomics. Genome Research. 33: 61-70. PMID 36657977 DOI: 10.1101/gr.277075.122  0.314
2022 Zhu K, Schäffer AA, Robinson W, Xu J, Ruppin E, Ergun AF, Ye Y, Sahinalp SC. Strain level microbial detection and quantification with applications to single cell metagenomics. Nature Communications. 13: 6430. PMID 36307411 DOI: 10.1038/s41467-022-33869-7  0.34
2022 Ford MKB, Hari A, Rodriguez O, Xu J, Lack J, Oguz C, Zhang Y, Weber S, Magliocco M, Barnett J, Xirasagar S, Samuel S, Imberti L, Bonfanti P, Biondi A, ... ... Sahinalp SC, et al. ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data. Cell Systems. 13: 808-816.e5. PMID 36265467 DOI: 10.1016/j.cels.2022.08.008  0.307
2022 Ford M, Hari A, Rodriguez O, Xu J, Lack J, Oguz C, Zhang Y, Weber S, Magglioco M, Barnett J, Xirasagar S, Samuel S, Imberti L, Bonfanti P, Biondi A, ... ... Sahinalp SC, et al. ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data. Biorxiv : the Preprint Server For Biology. PMID 35132409 DOI: 10.1101/2022.01.31.478564  0.317
2020 Kockan C, Zhu K, Dokmai N, Karpov N, Kulekci MO, Woodruff DP, Sahinalp SC. Sketching algorithms for genomic data analysis and querying in a secure enclave. Nature Methods. 17: 295-301. PMID 32132732 DOI: 10.1038/s41592-020-0761-8  0.31
2019 Haghshenas E, Sahinalp SC, Hach F. lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data. Bioinformatics (Oxford, England). 35: 20-27. PMID 30561550 DOI: 10.1093/Bioinformatics/Bty544  0.458
2017 Lin YY, Gawronski A, Hach F, Li S, Numanagic I, Sarrafi I, Mishra S, McPherson A, Collins C, Radovich M, Tang H, Sahinalp SC. Computational identification of micro-structural variations and their proteogenomic consequences in cancer. Bioinformatics (Oxford, England). PMID 29267878 DOI: 10.1093/Bioinformatics/Btx807  0.417
2017 McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP. Correction to: ReMixT: clone-specific genomic structure estimation in cancer. Genome Biology. 18: 188. PMID 28985744 DOI: 10.1186/S13059-017-1327-7  0.358
2017 Kalina JL, Neilson DS, Lin YY, Hamilton PT, Comber AP, Loy EMH, Sahinalp SC, Collins CC, Hach F, Lum JJ. Mutational Analysis of Gene Fusions Predicts Novel MHC Class I-Restricted T cell Epitopes & Immune Signatures in a Subset of Prostate Cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 28954787 DOI: 10.1158/1078-0432.Ccr-17-0618  0.325
2017 Shrestha R, Hodzic E, Sauerwald T, Dao P, Wang K, Yeung J, Anderson S, Vandin F, Haffari G, Collins CC, Sahinalp SC. HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology. Genome Research. PMID 28768687 DOI: 10.1101/Gr.221218.117  0.37
2017 McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP. ReMixT: clone-specific genomic structure estimation in cancer. Genome Biology. 18: 140. PMID 28750660 DOI: 10.1186/S13059-017-1267-2  0.385
2017 Donmez N, Malikic S, Wyatt AW, Gleave ME, Collins CC, Sahinalp SC. Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 28056180 DOI: 10.1089/Cmb.2016.0148  0.328
2016 Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J, Alberti C, Mattavelli M, Sahinalp SC. Comparison of high-throughput sequencing data compression tools. Nature Methods. PMID 27776113 DOI: 10.1038/Nmeth.4037  0.321
2016 Haghshenas E, Hach F, Sahinalp SC, Chauve C. CoLoRMap: Correcting Long Reads by Mapping short reads. Bioinformatics (Oxford, England). 32: i545-i551. PMID 27587673 DOI: 10.1093/Bioinformatics/Btw463  0.381
2016 Kockan C, Hach F, Sarrafi I, Bell RH, McConeghy B, Beja K, Haegert A, Wyatt AW, Volik SV, Chi KN, Collins CC, Sahinalp SC. SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA. Bioinformatics (Oxford, England). PMID 27531099 DOI: 10.1093/Bioinformatics/Btw536  0.425
2015 Kavak P, Yüksel B, Aksu S, Kulekci MO, Güngör T, Hach F, Şahinalp SC, Alkan C, Sağıroğlu MŞ. Robustness of Massively Parallel Sequencing Platforms. Plos One. 10: e0138259. PMID 26382624 DOI: 10.1371/Journal.Pone.0138259  0.327
2015 Numanagić I, Malikić S, Pratt VM, Skaar TC, Flockhart DA, Sahinalp SC. Cypiripi: Exact genotyping of CYP2D6 using high-throughput sequencing data Bioinformatics. 31: i27-i34. PMID 26072492 DOI: 10.1093/Bioinformatics/Btv232  0.348
2014 Alkan C, Kavak P, Somel M, Gokcumen O, Ugurlu S, Saygi C, Dal E, Bugra K, Güngör T, Sahinalp SC, Özören N, Bekpen C. Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa. Bmc Genomics. 15: 963. PMID 25376095 DOI: 10.1186/1471-2164-15-963  0.335
2014 Hach F, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Research. 42: W494-500. PMID 24810850 DOI: 10.1093/Nar/Gku370  0.369
2014 Dao P, Numanagi? I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC. ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Bioinformatics (Oxford, England). 30: 644-51. PMID 24130305 DOI: 10.1093/Bioinformatics/Btt591  0.362
2013 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, ... ... Sahinalp SC, et al. Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. Bmc Genomics. 14: 550. PMID 23941359 DOI: 10.1186/1471-2164-14-550  0.368
2012 Hach F, Numanagic I, Alkan C, Sahinalp SC. SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinformatics (Oxford, England). 28: 3051-7. PMID 23047557 DOI: 10.1093/Bioinformatics/Bts593  0.393
2012 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, et al. Poly-gene fusion transcripts and chromothripsis in prostate cancer. Genes, Chromosomes & Cancer. 51: 1144-53. PMID 22927308 DOI: 10.1002/Gcc.21999  0.417
2012 McPherson A, Wu C, Wyatt AW, Shah S, Collins C, Sahinalp SC. nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing. Genome Research. 22: 2250-61. PMID 22745232 DOI: 10.1101/Gr.136572.111  0.464
2012 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, ... ... Sahinalp SC, et al. From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. The Journal of Pathology. 227: 286-97. PMID 22553170 DOI: 10.1002/Path.4047  0.354
2012 Hajirasouliha I, Schönhuth A, de Juan D, Valencia A, Sahinalp SC. Mirroring co-evolving trees in the light of their topologies. Bioinformatics (Oxford, England). 28: 1202-8. PMID 22399677 DOI: 10.1093/Bioinformatics/Bts109  0.309
2012 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, ... ... Sahinalp SC, et al. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. The Journal of Pathology. 227: 53-61. PMID 22294438 DOI: 10.1002/Path.3987  0.424
2012 McPherson A, Wu C, Wyatt A, Shah S, Collins C, Sahinalp SC. Discovery of complex genomic rearrangements in cancer using high-throughput sequencing Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7262: 181-182. DOI: 10.1007/978-3-642-29627-7_17  0.327
2011 Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC. Simultaneous structural variation discovery among multiple paired-end sequenced genomes. Genome Research. 21: 2203-12. PMID 22048523 DOI: 10.1101/Gr.120501.111  0.46
2011 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, et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. Plos Computational Biology. 7: e1001138. PMID 21625565 DOI: 10.1371/Journal.Pcbi.1001138  0.417
2011 Hormozdiari F, Hach F, Sahinalp SC, Eichler EE, Alkan C. Sensitive and fast mapping of di-base encoded reads. Bioinformatics (Oxford, England). 27: 1915-21. PMID 21586516 DOI: 10.1093/Bioinformatics/Btr303  0.421
2011 McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC. Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinformatics (Oxford, England). 27: 1481-8. PMID 21478487 DOI: 10.1093/Bioinformatics/Btr184  0.457
2011 Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, Eichler EE. Alu repeat discovery and characterization within human genomes. Genome Research. 21: 840-9. PMID 21131385 DOI: 10.1101/Gr.115956.110  0.438
2011 Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC. Simultaneous structural variation discovery in multiple paired-end sequenced genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 104-105. DOI: 10.1007/978-3-642-20036-6_11  0.345
2010 Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. mrsFAST: a cache-oblivious algorithm for short-read mapping. Nature Methods. 7: 576-7. PMID 20676076 DOI: 10.1038/Nmeth0810-576  0.401
2010 Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics (Oxford, England). 26: i350-7. PMID 20529927 DOI: 10.1093/Bioinformatics/Btq216  0.424
2010 Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics (Oxford, England). 26: 1277-83. PMID 20385726 DOI: 10.1093/Bioinformatics/Btq152  0.462
2010 Schönhuth A, Salari R, Hormozdiari F, Cherkasov A, Sahinalp SC. Towards improved assessment of functional similarity in large-scale screens: a study on indel length. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1-20. PMID 20078394 DOI: 10.1089/Cmb.2009.0031  0.365
2010 Salari R, Backofen R, Sahinalp SC. Fast prediction of RNA-RNA interaction. Algorithms For Molecular Biology : Amb. 5: 5. PMID 20047661 DOI: 10.1186/1748-7188-5-5  0.33
2009 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. Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genetics. 41: 1061-7. PMID 19718026 DOI: 10.1038/Ng.437  0.439
2009 Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Research. 19: 1270-8. PMID 19447966 DOI: 10.1101/Gr.088633.108  0.474
2009 Salari R, Aksay C, Karakoc E, Unrau PJ, Hajirasouliha I, Sahinalp SC. smyRNA: a novel Ab initio ncRNA gene finder. Plos One. 4: e5433. PMID 19415115 DOI: 10.1371/Journal.Pone.0005433  0.458
2009 Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. Combinatorial algorithms for structural variation detection in high throughput sequenced genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: 218-219. DOI: 10.1007/978-3-642-02008-7_16  0.327
2008 Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics (Oxford, England). 24: i32-40. PMID 18586730 DOI: 10.1093/bioinformatics/btn173  0.335
2008 Dolgosheina EV, Morin RD, Aksay G, Sahinalp SC, Magrini V, Mardis ER, Mattsson J, Unrau PJ. Conifers have a unique small RNA silencing signature Rna. 14: 1508-1515. PMID 18566193 DOI: 10.1261/Rna.1052008  0.313
2008 Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Research. 18: 571-84. PMID 18323537 DOI: 10.1101/Gr.6897308  0.41
2007 Alkan C, Ventura M, Archidiacono N, Rocchi M, Sahinalp SC, Eichler EE. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. Plos Computational Biology. 3: 1807-18. PMID 17907796 DOI: 10.1371/Journal.Pcbi.0030181  0.451
2005 Alkan C, Tüzün E, Buard J, Lethiec F, Eichler EE, Bailey JA, Sahinalp SC. Manipulating multiple sequence alignments via MaM and WebMaM. Nucleic Acids Research. 33: W295-8. PMID 15980474 DOI: 10.1093/Nar/Gki406  0.429
2004 Sahinalp SC, Eichler E, Goldberg P, Berenbrink P, Friedetzky T, Ergun F. Identifying uniformly mutated segments within repeats. Journal of Bioinformatics and Computational Biology. 2: 657-68. PMID 15617159 DOI: 10.1142/S0219720004000788  0.373
2004 Muthukrishnan S, Sahinalp SC. An efficient algorithm for sequence comparison with block reversals Theoretical Computer Science. 321: 95-101. DOI: 10.1016/J.Tcs.2003.05.005  0.343
2003 Liu G, Zhao S, Bailey JA, Sahinalp SC, Alkan C, Tuzun E, Green ED, Eichler EE. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Research. 13: 358-68. PMID 12618366 DOI: 10.1101/Gr.923303  0.42
2002 Alkan C, Bailey JA, Eichler EE, Sahinalp SC, Tuzun E. An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution. Genome Informatics. International Conference On Genome Informatics. 13: 93-102. PMID 14571378 DOI: 10.11234/Gi1990.13.93  0.312
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