Deniz Yorukoglu
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Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
F Hormozdiari, I Hajirasouliha, P Dao, F Hach, D Yorukoglu, C Alkan, ...
Bioinformatics 26 (12), i350-i357, 2010
2472010
Alu repeat discovery and characterization within human genomes
F Hormozdiari, C Alkan, M Ventura, I Hajirasouliha, M Malig, F Hach, ...
Genome research 21 (6), 840-849, 2011
1062011
HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data
E Berger, D Yorukoglu, J Peng, B Berger
PLoS Comput Biol 10 (3), e1003502, 2014
702014
Quality score compression improves genotyping accuracy
YW Yu, D Yorukoglu, J Peng, B Berger
Nature biotechnology 33 (3), 240-243, 2015
582015
Fast genotyping of known SNPs through approximate k-mer matching
A Shajii, D Yorukoglu, Y William Yu, B Berger
Bioinformatics 32 (17), i538-i544, 2016
272016
Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification
YW Yu, D Yorukoglu, B Berger
International Conference on Research in Computational Molecular Biology, 385-399, 2014
262014
Dissect: detection and characterization of novel structural alterations in transcribed sequences
D Yorukoglu, F Hach, L Swanson, CC Collins, I Birol, SC Sahinalp
Bioinformatics 28 (12), i179-i187, 2012
262012
In vitro model for the treatment of restenosis
S Epstein
US Patent App. 10/230,390, 2003
252003
Compressive mapping for next-generation sequencing
D Yorukoglu, YW Yu, J Peng, B Berger
Nature biotechnology 34 (4), 374-376, 2016
232016
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies
L Swanson, G Robertson, KL Mungall, YS Butterfield, R Chiu, RD Corbett, ...
BMC genomics 14 (1), 550, 2013
152013
Topological signatures for population admixture
L Parida, F Utro, D Yorukoglu, AP Carrieri, D Kuhn, S Basu
International Conference on Research in Computational Molecular Biology, 261-275, 2015
62015
HapTree-X: An integrative Bayesian framework for haplotype reconstruction from transcriptome and genome sequencing data
E Berger, D Yorukoglu, B Berger
International Conference on Research in Computational Molecular Biology, 28-29, 2015
42015
Compressively-accelerated read mapping
BB Leighton, D Yörükoglu
US Patent App. 14/053,387, 2014
32014
Discovery of biomarkers for hexachlorobenzene toxicity using population based methods on gene expression data
C Meydan, A Küçükural, D Yörükoğlu, OU Sezerman
IAPR International Conference on Pattern Recognition in Bioinformatics, 412-423, 2008
32008
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26: i350–i357
F Hormozdiari, I Hajirasouliha, P Dao, F Hach, D Yorukoglu, C Alkan, ...
22010
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
E Berger, D Yorukoglu, L Zhang, SK Nyquist, AK Shalek, M Kellis, ...
Nature Communications 11 (1), 1-9, 2020
2020
Compressively-accelerated read mapping framework for next-generation sequencing
BB Leighton, D Yorukoglu, J Peng
US Patent App. 16/299,263, 2019
2019
Quality score compression for improving downstream genotyping accuracy
BB Leighton, D Yorukoglu, YW Yu, J Peng
US Patent App. 16/267,778, 2019
2019
Compressively-accelerated read mapping framework for next-generation sequencing
BB Leighton, D Yorukoglu, J Peng
US Patent 10,230,390, 2019
2019
Quality score compression for improving downstream genotyping accuracy
BB Leighton, D Yorukoglu, YW Yu, J Peng
US Patent 10,198,454, 2019
2019
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