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CAREx: context-aware read extension of paired-end sequencing data

BMC bioinformatics, 2024-05, Vol.25 (1), p.186-186, Article 186

2024

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Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

Bioinformatics, 2013-02, Vol.29 (3), p.308-315

2013

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CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

BMC bioinformatics, 2013-04, Vol.14 (1), p.117-117, Article 117

2013

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Long read alignment based on maximal exact match seeds

Bioinformatics, 2012-09, Vol.28 (18), p.i318-i324

2012

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CARE 2.0: reducing false-positive sequencing error corrections using machine learning

BMC bioinformatics, 2022-06, Vol.23 (1), p.227-227, Article 227

2022

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CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows―Wheeler transform

Bioinformatics, 2012-07, Vol.28 (14), p.1830-1837

2012

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MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

Bioinformatics, 2010-08, Vol.26 (16), p.1958-1964

2010

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ParDRe: faster parallel duplicated reads removal tool for sequencing studies

Bioinformatics, 2016-05, Vol.32 (10), p.1562-1564

2016

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CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

BMC research notes, 2010-04, Vol.3 (1), p.93-93, Article 93

2010

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CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding

PloS one, 2014-01, Vol.9 (1), p.e86869-e86869

2014

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RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads

BMC bioinformatics, 2020-07, Vol.21 (1), p.1-274, Article 274

2020

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RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches

Genome Biology, 2023-05, Vol.24 (1), p.121-121, Article 121

2023

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Fast and efficient short read mapping based on a succinct hash index

BMC bioinformatics, 2018-03, Vol.19 (1), p.92-92, Article 92

2018

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Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data

BMC bioinformatics, 2022-07, Vol.23 (1), p.1-287, Article 287

2022

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A big data approach to metagenomics for all-food-sequencing

BMC bioinformatics, 2020-03, Vol.21 (1), p.102-102, Article 102

2020

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Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning

IEEE transactions on parallel and distributed systems, 2022-11, Vol.33 (11), p.2885-2899

2022

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Big Data in metagenomics: Apache Spark vs MPI

PloS one, 2020-10, Vol.15 (10), p.e0239741-e0239741

2020

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Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC

PloS one, 2016, Vol.11 (1), p.e0145490-e0145490

2016

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Parallelized short read assembly of large genomes using de Bruijn graphs

BMC bioinformatics, 2011-08, Vol.12 (1), p.354-354, Article 354

2011

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SHREC: a short-read error correction method

Bioinformatics, 2009-09, Vol.25 (17), p.2157-2163

2009

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Next-generation sequencing: big data meets high performance computing

Drug discovery today, 2017-04, Vol.22 (4), p.712-717

2017

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Deep learning in next-generation sequencing

Drug discovery today, 2021-01, Vol.26 (1), p.173-180

2021

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CLOVE: classification of genomic fusions into structural variation events

BMC bioinformatics, 2017-07, Vol.18 (1), p.346-346, Article 346

2017

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From GPUs to AI and quantum: three waves of acceleration in bioinformatics

Drug discovery today, 2024-06, Vol.29 (6), p.103990-103990, Article 103990

2024

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CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

IEEE/ACM transactions on computational biology and bioinformatics, 2011-11, Vol.8 (6), p.1678-1684

2011

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CAREx: context-aware read extension of paired-end sequencing data

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

Long read alignment based on maximal exact match seeds

CARE 2.0: reducing false-positive sequencing error corrections using machine learning

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows―Wheeler transform

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

ParDRe: faster parallel duplicated reads removal tool for sequencing studies

CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding

RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads

RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches

Fast and efficient short read mapping based on a succinct hash index

Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data

A big data approach to metagenomics for all-food-sequencing

Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning

Big Data in metagenomics: Apache Spark vs MPI

Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC

Parallelized short read assembly of large genomes using de Bruijn graphs

SHREC: a short-read error correction method

Next-generation sequencing: big data meets high performance computing

Deep learning in next-generation sequencing

CLOVE: classification of genomic fusions into structural variation events

From GPUs to AI and quantum: three waves of acceleration in bioinformatics

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

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