Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing
Smajlović, Haris, Shajii, Ariya, Berger, Bonnie, Cho, Hyunghoon, Numanagić, Ibrahim
Published in Genome Biology (11.01.2023)
Published in Genome Biology (11.01.2023)
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A Python-based programming language for high-performance computational genomics
Shajii, Ariya, Numanagić, Ibrahim, Leighton, Alexander T., Greenyer, Haley, Amarasinghe, Saman, Berger, Bonnie
Published in Nature biotechnology (01.09.2021)
Published in Nature biotechnology (01.09.2021)
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Journal Article
SCALCE: boosting sequence compression algorithms using locally consistent encoding
HACH, Faraz, NUMANAGIC, Ibrahim, ALKAN, Can, CENK SAHINALP, S
Published in Bioinformatics (01.12.2012)
Published in Bioinformatics (01.12.2012)
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Journal Article
Fast characterization of segmental duplications in genome assemblies
Numanagić, Ibrahim, Gökkaya, Alim S, Zhang, Lillian, Berger, Bonnie, Alkan, Can, Hach, Faraz
Published in Bioinformatics (01.09.2018)
Published in Bioinformatics (01.09.2018)
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Journal Article
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes
Numanagić, Ibrahim, Malikić, Salem, Ford, Michael, Qin, Xiang, Toji, Lorraine, Radovich, Milan, Skaar, Todd C., Pratt, Victoria M., Berger, Bonnie, Scherer, Steve, Sahinalp, S. Cenk
Published in Nature communications (26.02.2018)
Published in Nature communications (26.02.2018)
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Journal Article
Diagnostics of viral infections using high-throughput genome sequencing data
Ning, Haochen, Boyes, Ian, Numanagić, Ibrahim, Rott, Michael, Xing, Li, Zhang, Xuekui
Published in Briefings in bioinformatics (23.09.2024)
Published in Briefings in bioinformatics (23.09.2024)
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Journal Article
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
Berger, Emily, Yorukoglu, Deniz, Zhang, Lillian, Nyquist, Sarah K., Shalek, Alex K., Kellis, Manolis, Numanagić, Ibrahim, Berger, Bonnie
Published in Nature communications (16.09.2020)
Published in Nature communications (16.09.2020)
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Journal Article
Comparison of high-throughput sequencing data compression tools
Numanagić, Ibrahim, Bonfield, James K, Hach, Faraz, Voges, Jan, Ostermann, Jörn, Alberti, Claudio, Mattavelli, Marco, Sahinalp, S Cenk
Published in Nature methods (01.12.2016)
Published in Nature methods (01.12.2016)
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Journal Article
An efficient genotyper and star-allele caller for pharmacogenomics
Hari, Ananth, Zhou, Qinghui, Gonzaludo, Nina, Harting, John, Scott, Stuart A, Qin, Xiang, Scherer, Steve, Sahinalp, S Cenk, Numanagić, Ibrahim
Published in Genome research (01.01.2023)
Published in Genome research (01.01.2023)
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Journal Article
Fast characterization of segmental duplication structure in multiple genome assemblies
Išerić, Hamza, Alkan, Can, Hach, Faraz, Numanagić, Ibrahim
Published in Algorithms for molecular biology (18.03.2022)
Published in Algorithms for molecular biology (18.03.2022)
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Journal Article
Discovery and genotyping of novel sequence insertions in many sequenced individuals
Kavak, Pinar, Lin, Yen-Yi, Numanagic, Ibrahim, Asghari, Hossein, Güngör, Tunga, Alkan, Can, Hach, Faraz
Published in Bioinformatics (Oxford, England) (15.07.2017)
Published in Bioinformatics (Oxford, England) (15.07.2017)
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Journal Article
Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data
Numanagić, Ibrahim, Malikić, Salem, Pratt, Victoria M, Skaar, Todd C, Flockhart, David A, Sahinalp, S Cenk
Published in Bioinformatics (Oxford, England) (15.06.2015)
Published in Bioinformatics (Oxford, England) (15.06.2015)
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Journal Article
Analytical Validation of a Computational Method for Pharmacogenetic Genotyping from Clinical Whole Exome Sequencing
Ly, Reynold C., Shugg, Tyler, Ratcliff, Ryan, Osei, Wilberforce, Lynnes, Ty C., Pratt, Victoria M., Schneider, Bryan P., Radovich, Milan, Bray, Steven M., Salisbury, Benjamin A., Parikh, Baiju, Sahinalp, S. Cenk, Numanagić, Ibrahim, Skaar, Todd C.
Published in The Journal of molecular diagnostics : JMD (01.06.2022)
Published in The Journal of molecular diagnostics : JMD (01.06.2022)
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Journal Article
Computational pharmacogenotype extraction from clinical next-generation sequencing
Shugg, Tyler, Ly, Reynold C, Osei, Wilberforce, Rowe, Elizabeth J, Granfield, Caitlin A, Lynnes, Ty C, Medeiros, Elizabeth B, Hodge, Jennelle C, Breman, Amy M, Schneider, Bryan P, Sahinalp, S Cenk, Numanagić, Ibrahim, Salisbury, Benjamin A, Bray, Steven M, Ratcliff, Ryan, Skaar, Todd C
Published in Frontiers in oncology (04.07.2023)
Published in Frontiers in oncology (04.07.2023)
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Journal Article
Statistical Binning for Barcoded Reads Improves Downstream Analyses
Shajii, Ariya, Numanagić, Ibrahim, Whelan, Christopher, Berger, Bonnie
Published in Cell systems (22.08.2018)
Published in Cell systems (22.08.2018)
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Journal Article
Computational identification of micro-structural variations and their proteogenomic consequences in cancer
Lin, Yen-Yi, Gawronski, Alexander, Hach, Faraz, Li, Sujun, Numanagić, Ibrahim, Sarrafi, Iman, Mishra, Swati, McPherson, Andrew, Collins, Colin C, Radovich, Milan, Tang, Haixu, Sahinalp, S Cenk
Published in Bioinformatics (15.05.2018)
Published in Bioinformatics (15.05.2018)
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Journal Article
Seq: a high-performance language for bioinformatics
Shajii, Ariya, Numanagić, Ibrahim, Baghdadi, Riyadh, Berger, Bonnie, Amarasinghe, Saman
Published in Proceedings of ACM on programming languages (01.10.2019)
Published in Proceedings of ACM on programming languages (01.10.2019)
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Journal Article
Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses
Shajii, Ariya, Numanagić, Ibrahim, Berger, Bonnie
Published in Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005-) (01.04.2018)
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Published in Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005-) (01.04.2018)
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