CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units Y Liu, D Maskell, B Schmidt BMC Research Notes 2 (1), 73, 2009 | 359 | 2009 |
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data Y Liu, J Schröder, B Schmidt Bioinformatics 29 (3), 308-315, 2013 | 332 | 2013 |
CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions Y Liu, A Wirawan, B Schmidt BMC Bioinformatics 14 (1), 117, 2013 | 293 | 2013 |
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities Y Liu, B Schmidt, DL Maskell Bioinformatics 26 (16), 1958-1964, 2010 | 280 | 2010 |
CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions Y Liu, B Schmidt, D Maskell BMC Research Notes 3 (1), 93, 2010 | 262 | 2010 |
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform Y Liu, B Schmidt, DL Maskell Bioinformatics 28 (14), 1830-1837, 2012 | 218 | 2012 |
Long read alignment based on maximal exact match seeds Y Liu, B Schmidt Bioinformatics 28 (18), i318-i324, 2012 | 137 | 2012 |
MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA Y Liu, B Schmidt, DL Maskell 20th IEEE International Conference on Application-specific Systems …, 2009 | 116 | 2009 |
Parallelized short read assembly of large genomes using de Bruijn graphs Y Liu, B Schmidt, D Maskell BMC Bioinformatics 12 (1), 354, 2011 | 107 | 2011 |
CUDA-MEME: accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units Y Liu, B Schmidt, W Liu, DL Maskell Pattern Recognition Letters 31 (14), 2170-2177, 2010 | 98 | 2010 |
CUSHAW2-GPU: empowering faster gapped short-read alignment using GPU computing Y Liu, B Schmidt IEEE Design & Test 31 (1), 31-39, 2013 | 91 | 2013 |
SWAPHI: Smith-Waterman protein database search on Xeon Phi coprocessors Y Liu, B Schmidt 2014 IEEE 25th International Conference on Application-Specific Systems …, 2014 | 86 | 2014 |
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI Y Liu, B Schmidt, D Maskell BMC Bioinformatics 12 (1), 85, 2011 | 82 | 2011 |
CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding Y Liu, B Popp, B Schmidt PloS one 9 (1), e86869, 2014 | 77 | 2014 |
LightSpMV: faster CSR-based sparse matrix-vector multiplication on CUDA-enabled GPUs Y Liu, B Schmidt 2015 IEEE 26th International Conference on Application-specific Systems …, 2015 | 71 | 2015 |
SWAPHI-LS: Smith-Waterman algorithm on Xeon Phi coprocessors for long DNA sequences Y Liu, TT Tran, F Lauenroth, B Schmidt 2014 IEEE International Conference on Cluster Computing, 257-265, 2014 | 69 | 2014 |
All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing F Ripp, CF Krombholz, Y Liu, M Weber, A Schäfer, B Schmidt, R Köppel, ... BMC Genomics 15 (1), 639, 2014 | 64 | 2014 |
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments L Kuttippurathu, M Hsing, Y Liu, B Schmidt, DL Maskell, K Lee, A He, ... Bioinformatics 27 (5), 715, 2011 | 60 | 2011 |
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data A Wirawan, RS Harris, Y Liu, B Schmidt, J Schröder BMC Bioinformatics 15 (1), 131, 2014 | 45 | 2014 |
Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA Y Liu, B Schmidt, DL Maskell 2009 IEEE International Symposium on Parallel & Distributed Processing, 1-8, 2009 | 43 | 2009 |