Published in Bioinformatics on June 19, 2009
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics (2011) 3.51
PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3 (Bethesda) (2013) 2.85
ConDeTri--a content dependent read trimmer for Illumina data. PLoS One (2011) 2.78
Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol (2013) 2.46
Overcoming bias and systematic errors in next generation sequencing data. Genome Med (2010) 1.75
ECHO: a reference-free short-read error correction algorithm. Genome Res (2011) 1.68
Benchmarking short sequence mapping tools. BMC Bioinformatics (2013) 1.48
LoRDEC: accurate and efficient long read error correction. Bioinformatics (2014) 1.36
Three-stage quality control strategies for DNA re-sequencing data. Brief Bioinform (2013) 1.30
Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform (2015) 1.22
Estimation of sequencing error rates in short reads. BMC Bioinformatics (2012) 1.22
Prospects and limitations of full-text index structures in genome analysis. Nucleic Acids Res (2012) 1.20
Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol (2014) 1.16
Reference-free validation of short read data. PLoS One (2010) 1.13
Probabilistic error correction for RNA sequencing. Nucleic Acids Res (2013) 1.08
Next-generation sequence assembly: four stages of data processing and computational challenges. PLoS Comput Biol (2013) 1.07
Fulcrum: condensing redundant reads from high-throughput sequencing studies. Bioinformatics (2012) 1.03
Repeat-aware modeling and correction of short read errors. BMC Bioinformatics (2011) 1.00
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. BMC Bioinformatics (2011) 0.95
A bioinformatician's guide to the forefront of suffix array construction algorithms. Brief Bioinform (2014) 0.95
Fiona: a parallel and automatic strategy for read error correction. Bioinformatics (2014) 0.91
Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly. BMC Res Notes (2016) 0.86
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC Bioinformatics (2014) 0.85
Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation. BMC Bioinformatics (2012) 0.82
Querying large read collections in main memory: a versatile data structure. BMC Bioinformatics (2011) 0.82
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. Gigascience (2015) 0.82
Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly. Brief Bioinform (2016) 0.80
Empirical estimation of sequencing error rates using smoothing splines. BMC Bioinformatics (2016) 0.78
DRISEE overestimates errors in metagenomic sequencing data. Brief Bioinform (2013) 0.77
Jabba: hybrid error correction for long sequencing reads. Algorithms Mol Biol (2016) 0.77
Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief Funct Genomics (2014) 0.77
Sequencing error correction without a reference genome. BMC Bioinformatics (2013) 0.77
CRCDA--Comprehensive resources for cancer NGS data analysis. Database (Oxford) (2015) 0.75
In search of perfect reads. BMC Bioinformatics (2015) 0.75
ADEPT, a dynamic next generation sequencing data error-detection program with trimming. BMC Bioinformatics (2016) 0.75
Indexing Arbitrary-Length k-Mers in Sequencing Reads. PLoS One (2015) 0.75
From next-generation resequencing reads to a high-quality variant data set. Heredity (Edinb) (2016) 0.75
RecountDB: a database of mapped and count corrected transcribed sequences. Nucleic Acids Res (2011) 0.75
A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis. Hum Genomics (2016) 0.75
EC: an efficient error correction algorithm for short reads. BMC Bioinformatics (2015) 0.75
DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing. PLoS One (2017) 0.75
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinformatics (2010) 2.53
CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Res Notes (2009) 1.96
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics (2012) 1.73
A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware. J Comput Biol (2010) 1.68
Reproducibility of intratumor distribution of (18)F-fluoromisonidazole in head and neck cancer. Int J Radiat Oncol Biol Phys (2008) 1.64
CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions. BMC Res Notes (2010) 1.60
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinformatics (2012) 1.59
Long read alignment based on maximal exact match seeds. Bioinformatics (2012) 1.54
CBESW: sequence alignment on the Playstation 3. BMC Bioinformatics (2008) 1.48
Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. Bioinformatics (2005) 1.43
A fast hybrid short read fragment assembly algorithm. Bioinformatics (2009) 1.33
CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. BMC Bioinformatics (2013) 1.24
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics (2010) 1.11
Molecular layering of fluorinated ionic liquids at a charged sapphire (0001) surface. Science (2008) 1.11
Parallelized short read assembly of large genomes using de Bruijn graphs. BMC Bioinformatics (2011) 1.08
Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. BMC Bioinformatics (2007) 1.05
Multiple protein sequence alignment with MSAProbs. Methods Mol Biol (2014) 1.03
High-resolution in situ x-ray study of the hydrophobic gap at the water-octadecyl-trichlorosilane interface. Proc Natl Acad Sci U S A (2006) 0.97
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. BMC Bioinformatics (2011) 0.95
CUDA-BLASTP: accelerating BLASTP on CUDA-enabled graphics hardware. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.93
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.91
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC Bioinformatics (2014) 0.85
Layering of [BMIM]+-based ionic liquids at a charged sapphire interface. J Chem Phys (2009) 0.84
DySC: software for greedy clustering of 16S rRNA reads. Bioinformatics (2012) 0.83
High speed biological sequence analysis with hidden Markov models on reconfigurable platforms. IEEE Trans Inf Technol Biomed (2008) 0.82
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures. Bioinformatics (2010) 0.81
A hybrid short read mapping accelerator. BMC Bioinformatics (2013) 0.81
Water and ice in contact with octadecyl-trichlorosilane functionalized surfaces: a high resolution x-ray reflectivity study. J Chem Phys (2008) 0.81
RepMaestro: scalable repeat detection on disk-based genome sequences. Bioinformatics (2010) 0.80
High-speed multiple sequence alignment on a reconfigurable platform. Int J Bioinform Res Appl (2006) 0.80
CellMinerHCC: a microarray-based expression database for hepatocellular carcinoma cell lines. Liver Int (2013) 0.80
Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment. BMC Bioinformatics (2008) 0.79
Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.78
A hybrid computational grid architecture for comparative genomics. IEEE Trans Inf Technol Biomed (2008) 0.77
Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.76
PREDNOD, a prediction server for peptide binding to the H-2g7 haplotype of the non-obese diabetic mouse. Autoimmunity (2006) 0.76
All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing. BMC Genomics (2014) 0.76
Parallel mutual information estimation for inferring gene regulatory networks on GPUs. BMC Res Notes (2011) 0.75
A scanning Kelvin probe for synchrotron investigations: the in situ detection of radiation-induced potential changes. J Synchrotron Radiat (2011) 0.75
Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75
Chemistry-dependent X-ray-induced surface charging. Phys Chem Chem Phys (2014) 0.75