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Cenk Sahinalp

Research Profile

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Evolution, Molecular

Genes & Molecular Sequences

Chemicals & Drugs

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Gene Fusion

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Publications

TOP 3
Faraz Hach; Ibrahim Numanagic; Can Alkan; S Cenk Sahinalp
SCALCE: boosting sequence compression algorithms using locally consistent encoding.
Chunxiao Wu; Alexander W Wyatt; Yongjun Zhao; Steven J M Jones; Martin E Gleave; Anna V Lapuk; Dong Lin; Marco A Marra; Brian J McConeghy; Andrew McPherson; Fan Mo; S Cenk Sahinalp; Robert Shukin; Stanislav V Volik; Yuzhuo Wang; Colin C Collins
Poly-gene fusion transcripts and chromothripsis in prostate cancer.
Andrew McPherson; Sohrab Shah; Chunxiao Wu; Alexander W Wyatt; Colin Collins; S Cenk Sahinalp
nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.

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All Publications

2012: Faraz Hach; Ibrahim Numanagic; Can Alkan; S Cenk Sahinalp
SCALCE: boosting sequence compression algorithms using locally consistent encoding.
Bioinformatics (Oxford, England) 2012;28(23):3051-7.
2012: Chunxiao Wu; Alexander W Wyatt; Yongjun Zhao; Steven J M Jones; Martin E Gleave; Anna V Lapuk; Dong Lin; Marco A Marra; Brian J McConeghy; Andrew McPherson; Fan Mo; S Cenk Sahinalp; Robert Shukin; Stanislav V Volik; Yuzhuo Wang; Colin C Collins
Poly-gene fusion transcripts and chromothripsis in prostate cancer.
Genes, chromosomes & cancer 2012;51(12):1144-53.
2012: Andrew McPherson; Sohrab Shah; Chunxiao Wu; Alexander W Wyatt; Colin Collins; S Cenk Sahinalp
nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
Genome research 2012;22(11):2250-61.
2012: Deniz Yorukoglu; Lucas Swanson; Inanc Birol; Colin C Collins; Faraz Hach; S Cenk Sahinalp
Dissect: detection and characterization of novel structural alterations in transcribed sequences.
Bioinformatics (Oxford, England) 2012;28(12):i179-87.
2012: IMAN HAJIRASOULIHA; Alexander Schönhuth; Alfonso Valencia; David de Juan; S Cenk Sahinalp
Mirroring co-evolving trees in the light of their topologies.
Bioinformatics (Oxford, England) 2012;28(9):1202-8.
2012: Chunxiao Wu; Alexander W Wyatt; Shawn Anderson; Robert H Bell; Paul C Boutros; Sonal Brahmbhatt; Robert G Bristow; Yaron S N Butterfield; Arul M Chinnaiyan; Ladan Fazli; Martin E Gleave; Faraz Hach; Anne Haegert; IMAN HAJIRASOULIHA; Martin Hirst; Fereydoun Hormozdiari; Antonio Hurtado-coll; Edward C Jones; Steven Jm Jones; Anna V Lapuk; Estelle Li; Christopher A Maher; Marco A Marra; Brian J McConeghy; Andrew McPherson; Fan Mo; S Cenk Sahinalp; Robert Shukin; Stanislav V Volik; Colin C Collins
Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer.
The Journal of pathology 2012;227(1):53-61.
2011: Fereydoun Hormozdiari; Andrew McPherson; Evan E Eichler; IMAN HAJIRASOULIHA; S Cenk Sahinalp
Simultaneous structural variation discovery among multiple paired-end sequenced genomes.
Genome research 2011;21(12):2203-12.
2011: Farhad Hormozdiari; S Cenk Sahinalp; Evan E Eichler; Faraz Hach; Can Alkan
Sensitive and fast mapping of di-base encoded reads.
Bioinformatics (Oxford, England) 2011;27(14):1915-21.
2011: Phuong Dao; Martin Ester; Anna Lapuk; Colin Collins; Kendric Wang; S Cenk Sahinalp
Optimally discriminative subnetwork markers predict response to chemotherapy.
Bioinformatics (Oxford, England) 2011;27(13):i205-13.
2011: Andrew McPherson; Chunxiao Wu; IMAN HAJIRASOULIHA; Fereydoun Hormozdiari; Faraz Hach; Anna Lapuk; Stanislav Volik; Sohrab Shah; Colin Collins; S Cenk Sahinalp
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
Bioinformatics (Oxford, England) 2011;27(11):1481-8.
2011: Fereydoun Hormozdiari; Can Alkan; Mario Ventura; IMAN HAJIRASOULIHA; Maika Malig; Faraz Hach; Deniz Yorukoglu; Phuong Dao; Marzieh Bakhshi; S Cenk Sahinalp; Evan E Eichler
Alu repeat discovery and characterization within human genomes.
Genome research 2011;21(6):840-9.
2011: Andrew McPherson; Fereydoun Hormozdiari; Abdalnasser Zayed; Ryan Giuliany; Gavin Ha; Mark G F Sun; Malachi Griffith; Alireza Heravi Moussavi; Janine Senz; Nataliya Melnyk; Marina Pacheco; Marco A Marra; Martin Hirst; Torsten O Nielsen; S Cenk Sahinalp; David Huntsman; Sohrab P Shah
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
PLoS computational biology 2011;7(5):e1001138.
2010: Faraz Hach; Fereydoun Hormozdiari; Can Alkan; Farhad Hormozdiari; Inanc Birol; Evan E Eichler; S Cenk Sahinalp
mrsFAST: a cache-oblivious algorithm for short-read mapping.
Nature methods 2010;7(8):576-7.
2010: Nancy Y Yu; James R Wagner; Matthew R Laird; Gabor Melli; Séb REY; Raymond Lo; Phuong Dao; S Cenk Sahinalp; Martin Ester; Leonard J Foster; Fiona S L Brinkman
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Bioinformatics (Oxford, England) 2010;26(13):1608-15.
2010: Fereydoun Hormozdiari; IMAN HAJIRASOULIHA; Phuong Dao; Faraz Hach; Deniz Yorukoglu; Can Alkan; Evan E Eichler; S Cenk Sahinalp
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
Bioinformatics (Oxford, England) 2010;26(12):i350-7.
2010: IMAN HAJIRASOULIHA; Fereydoun Hormozdiari; Can Alkan; Jeffrey M Kidd; Inanc Birol; Evan E Eichler; S Cenk Sahinalp
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.
Bioinformatics (Oxford, England) 2010;26(10):1277-83.
2010: Fereydoun Hormozdiari; Raheleh Salari; Vineet Bafna; S Cenk Sahinalp
Protein-protein interaction network evaluation for identifying potential drug targets.
Journal of computational biology : a journal of computational molecular cell biology 2010;17(5):669-84.
2010: Mathias Möhl; Raheleh Salari; Sebastian Will; Rolf Backofen; S Cenk Sahinalp
Sparsification of RNA structure prediction including pseudoknots.
Algorithms for molecular biology : AMB 2010;5():39.
2010: Alexander Schönhuth; Raheleh Salari; Fereydoun Hormozdiari; Artem Cherkasov; S Cenk Sahinalp
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 2010;17(1):1-20.
2010: Raheleh Salari; Rolf Backofen; S Cenk Sahinalp
Fast prediction of RNA-RNA interaction.
Algorithms for molecular biology : AMB 2010;5():5.
2009: Can Alkan; Jeffrey M Kidd; Tomas Marques-Bonet; Gozde Aksay; Francesca Antonacci; Fereydoun Hormozdiari; Jacob O Kitzman; Carl Baker; Maika Malig; Onur Mutlu; S Cenk Sahinalp; Richard A Gibbs; Evan E Eichler
Personalized copy number and segmental duplication maps using next-generation sequencing.
Nature genetics 2009;41(10):1061-7.
2009: Fereydoun Hormozdiari; Can Alkan; Evan E Eichler; S Cenk Sahinalp
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.
Genome research 2009;19(7):1270-8.
2009: Hamidreza Chitsaz; Raheleh Salari; S Cenk Sahinalp; Rolf Backofen
A partition function algorithm for interacting nucleic acid strands.
Bioinformatics (Oxford, England) 2009;25(12):i365-73.
2009: Fereydoun Hormozdiari; Raheleh Salari; Michael Hsing; Alexander Schönhuth; Simon K Chan; S Cenk Sahinalp; Artem Cherkasov
The effect of insertions and deletions on wirings in protein-protein interaction networks: a large-scale study.
Journal of computational biology : a journal of computational molecular cell biology 2009;16(2):159-67.
2009: Raheleh Salari; Cagri Aksay; Emre Karakoc; peter unrau; IMAN HAJIRASOULIHA; S Cenk Sahinalp
smyRNA: a novel Ab initio ncRNA gene finder.
PloS one 2009;4(5):e5433.
2009: R Colak; F Hormozdiari; F Moser; Alexander Schönhuth; J Holman; M Ester; S Cenk Sahinalp
Dense graphlet statistics of protein interaction and random networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2009;():178-89.
2008: Elena V Dolgosheina; Ryan D Morin; Gozde Aksay; S Cenk Sahinalp; vincent magrini; Elaine R Mardis; Jim Mattsson; peter unrau
Conifers have a unique small RNA silencing signature.
RNA (New York, N.Y.) 2008;14(8):1508-15.
2008: IMAN HAJIRASOULIHA; Fereydoun Hormozdiari; S Cenk Sahinalp; Inanc Birol
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.
Bioinformatics (Oxford, England) 2008;24(13):i32-40.
2008: Noga Alon; Phuong Dao; IMAN HAJIRASOULIHA; Fereydoun Hormozdiari; S Cenk Sahinalp
Biomolecular network motif counting and discovery by color coding.
Bioinformatics (Oxford, England) 2008;24(13):i241-9.
2008: Ryan D Morin; Gozde Aksay; Elena Dolgosheina; H Alexander Ebhardt; vincent magrini; Elaine R Mardis; S Cenk Sahinalp; peter unrau
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa.
Genome research 2008;18(4):571-84.
2007: Can Alkan; ventura Mario; Nicoletta Archidiacono; Mariano Rocchi; S Cenk Sahinalp; Evan E Eichler
Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.
PLoS computational biology 2007;3(9):1807-18.
2007: Fereydoun Hormozdiari; Petra Berenbrink; Natasa Przulj; S Cenk Sahinalp
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution.
PLoS computational biology 2007;3(7):e118.
2007: Cagri Aksay; Raheleh Salari; Emre Karakoc; Can Alkan; S Cenk Sahinalp
taveRNA: a web suite for RNA algorithms and applications.
Nucleic acids research 2007;35(Web Server issue):W325-9.
2007: Emre Karakoc; S Cenk Sahinalp; Artem Cherkasov
Comparative QSAR analysis of bacterial, fungal, plant and human metabolites.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007;():133-44.
2007: S Cenk Sahinalp
The intelligence in developing systems for molecular biology.
Genome biology 2007;8(1):301.
2006: Emre Karakoc; S Cenk Sahinalp; Artem Cherkasov
Comparative QSAR- and fragments distribution analysis of drugs, druglikes, metabolic substances, and antimicrobial compounds.
Journal of chemical information and modeling 2006;46(5):2167-82.
2006: Emre Karakoc; Artem Cherkasov; S Cenk Sahinalp
Distance based algorithms for small biomolecule classification and structural similarity search.
Bioinformatics (Oxford, England) 2006;22(14):e243-51.
2006: Can Alkan; Emre Karakoç; Joseph H Nadeau; S Cenk Sahinalp; Kaizhong Zhang
RNA-RNA interaction prediction and antisense RNA target search.
Journal of computational biology : a journal of computational molecular cell biology 2006;13(2):267-82.
2005: Can Alkan; Eray Tüzün; Jerome Buard; Franck Lethiec; Evan E Eichler; Jeffrey A Bailey; S Cenk Sahinalp
Manipulating multiple sequence alignments via MaM and WebMaM.
Nucleic acids research 2005;33(Web Server issue):W295-8.
2004: S Cenk Sahinalp; Evan E Eichler; Paul Goldberg; Petra Berenbrink; Tom Friedetzky; Funda Ergun
Identifying uniformly mutated segments within repeats.
Journal of bioinformatics and computational biology 2004;2(4):657-68.
2004: Can Alkan; Evan E Eichler; Jeffrey A Bailey; S Cenk Sahinalp; Eray Tüzün
The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(5):933-44.
2003: Ge Liu; Shaying Zhao; Jeffrey A Bailey; S Cenk Sahinalp; Can Alkan; Eray Tuzun; Eric Green; Evan E Eichler
Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome.
Genome research 2003;13(3):358-68.
2002: Can Alkan; Jeffrey A Bailey; Evan E Eichler; S Cenk Sahinalp; Eray Tuzun
An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution.
Genome informatics. International Conference on Genome Informatics 2002;13():93-102.