Diagnostics of viral infections using high-throughput genome sequencing data von Ning, Haochen, Boyes, Ian, Numanagić, Ibrahim, Rott, Michael, Xing, Li, Zhang, Xuekui

Volltext

Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing von Smajlović, Haris, Shajii, Ariya, Berger, Bonnie, Cho, Hyunghoon, Numanagić, Ibrahim

Volltext

A Python-based programming language for high-performance computational genomics von Shajii, Ariya, Numanagić, Ibrahim, Leighton, Alexander T., Greenyer, Haley, Amarasinghe, Saman, Berger, Bonnie

Volltext

SCALCE: boosting sequence compression algorithms using locally consistent encoding von HACH, Faraz, NUMANAGIC, Ibrahim, ALKAN, Can, CENK SAHINALP, S

Volltext

Fast characterization of segmental duplications in genome assemblies von Numanagić, Ibrahim, Gökkaya, Alim S, Zhang, Lillian, Berger, Bonnie, Alkan, Can, Hach, Faraz

Volltext

Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool von Ford, Michael K B, Hari, Ananth, Zhou, Qinghui, Numanagić, Ibrahim, Sahinalp, S Cenk

Volltext

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets von Berger, Emily, Yorukoglu, Deniz, Zhang, Lillian, Nyquist, Sarah K., Shalek, Alex K., Kellis, Manolis, Numanagić, Ibrahim, Berger, Bonnie

Volltext

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

Volltext

Comparison of high-throughput sequencing data compression tools von Numanagić, Ibrahim, Bonfield, James K, Hach, Faraz, Voges, Jan, Ostermann, Jörn, Alberti, Claudio, Mattavelli, Marco, Sahinalp, S Cenk

Volltext

Fast characterization of segmental duplication structure in multiple genome assemblies von Išerić, Hamza, Alkan, Can, Hach, Faraz, Numanagić, Ibrahim

Volltext

An efficient genotyper and star-allele caller for pharmacogenomics von Hari, Ananth, Zhou, Qinghui, Gonzaludo, Nina, Harting, John, Scott, Stuart A, Qin, Xiang, Scherer, Steve, Sahinalp, S Cenk, Numanagić, Ibrahim

Volltext

Discovery and genotyping of novel sequence insertions in many sequenced individuals von Kavak, Pinar, Lin, Yen-Yi, Numanagic, Ibrahim, Asghari, Hossein, Güngör, Tunga, Alkan, Can, Hach, Faraz

Volltext

DeeZ: reference-based compression by local assembly von Hach, Faraz, Numanagic, Ibrahim, Sahinalp, S Cenk

Volltext

Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data von Numanagić, Ibrahim, Malikić, Salem, Pratt, Victoria M, Skaar, Todd C, Flockhart, David A, Sahinalp, S Cenk

Volltext

Optimal compressed representation of high throughput sequence data via light assembly von Ginart, Antonio A., Hui, Joseph, Zhu, Kaiyuan, Numanagić, Ibrahim, Courtade, Thomas A., Sahinalp, S. Cenk, Tse, David N.

Volltext

Computational pharmacogenotype extraction from clinical next-generation sequencing von 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

Volltext

Analytical Validation of a Computational Method for Pharmacogenetic Genotyping from Clinical Whole Exome Sequencing von 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.

Volltext

Statistical Binning for Barcoded Reads Improves Downstream Analyses von Shajii, Ariya, Numanagić, Ibrahim, Whelan, Christopher, Berger, Bonnie

Volltext

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

Volltext

Seq: a high-performance language for bioinformatics von Shajii, Ariya, Numanagić, Ibrahim, Baghdadi, Riyadh, Berger, Bonnie, Amarasinghe, Saman

Volltext