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IEEE transactions on evolutionary computation, ISSN 1941-0026, 2015, Volume 19, Issue 1, pp. 118 - 135
We show that the genetic improvement of programs (GIP) can scale by evolving increased performance in a widely-used and highly complex 50000 line system.... 
Software | Complexity theory | Grammar | Semantics | Genetic programming | DNA | Automatic software reengineering | genetic programming (GP) | Bowtie2 | search based software engineering (SBSE) | multiple objective exploration | Bowtie2(GP) | COMPUTER SCIENCE, THEORY & METHODS | COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE
Journal Article
Journal Article
G3-GENES GENOMES GENETICS, ISSN 2160-1836, 05/2020, Volume 10, Issue 5, pp. 1775 - 1783
Alignment of scRNA-Seq data are the first and one of the most critical steps of the scRNA-Seq analysis workflow, and thus the choice of proper aligners is of... 
single nuclei RNA-Seq | Drop-seq | STAR | Bowtie2 | Fluidigm | GENETICS & HEREDITY | Kallisto | accuracy | alignment | 10x genomics | single cell RNA-Seq | kallisto | bowtie2 | fluidigm | single cell rna-seq | star | drop-seq | single nuclei rna-seq
Journal Article
2019 International Conference on Innovation and Intelligence for Informatics, Computing, and Technologies (3ICT), 09/2019, pp. 1 - 6
The recent advancements in Next-generation sequencing technologies have resulted in an enormous amount of sequencing data with newer properties. An important... 
Sequential analysis | Bowtie2 | BWA MEM | Genomics | DNA | Tools | Throughput | Bioinformatics | Next-generation Sequencing | Next generation networking | Alignment Problem
Conference Proceeding
2019 International Conference on Innovative Trends in Computer Engineering (ITCE), 02/2019, pp. 130 - 135
This paper presents a comparative study of CPU and GPU performance in sequence alignments for the Next Generation Sequencing (NGS), specifically in the context... 
Sequence Mapping | Instruction sets | Bowtie2 | Software algorithms | Graphics processing units | Genomics | CPU | NVBowtie | GPU | BWA | BarraCUDA | Sequential analysis | Price | Efficiency | DNA | Sequence Alignment Tools | Bioinformatics
Conference Proceeding
Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, SYNASC 2014, 02/2015, pp. 14 - 19
Conference Proceeding
08/2015, ISBN 9780128026465
Insertions and deletions (indels) are one of the most common class of mutations in the human genome. Correctly detecting and identifying indels is important in... 
Indel calling | SHRIMP FreeBayes | Bowtie2 | Pipelines | Dindel | BFAST | BWA | SNVer
Book Chapter
2015, ISBN 9780128026465
Insertions and deletions (indels) are one of the most common class of mutations in the human genome. Correctly detecting and identifying indels is important in... 
Indel calling | pipelines | SHRIMP FreeBayes | Bowtie2 | Dindel | BFAST | BWA | SNVer
Book Chapter
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