Publications

This folder holds the following references to publications, sorted by year and author.

There are 39 references in this bibliography folder.

Liu, Y, Schroeder, J, and Schmidt, B (2013).
Musket: a multistage k-mer spectrum based error corrector for Illumina sequence data
Bioinformatics, 29(3):308-315.

Liu, Y, Wirawan, A, and Schmidt, B (2013).
CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions
BMC Bioinformatics, 14(117).

Dang, H and Schmidt, B (2012).
The Sliced COO format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs
In: International Conference on Computational Science.

Lim, KG, Kwoh, CK, Hsu, LY, and Wirawan, A (2012).
Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance
Briefings in Bioinformatics.

Liu, Y and Schmidt, B (2012).
Evaluation of GPU-based seed generation for computational genomics using Burrows-Wheeler transform
In: 11th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2012), pp. 684-690, IEEE.

Liu, Y and Schmidt, B (2012).
Long read alignment based on maximal exact match seeds
Bioinformatics, 28(18):i318-i324.

Liu, Y, Schmidt, B, and Maskell, DL (2012).
A fast CUDA compatible short read aligner to large genomes
In: GPU Technology Conference 2012 (GTC 2012), Poster.

Liu, Y, Schmidt, B, and Maskell, DL (2012).
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
Bioinformatics, 28(14):1830-1837.

Nguyen, TD, Schmidt, B, Zheng, Z, and Kwoh, CK (2012).
Large-Scale Clustering of Short Reads for Metagenomics on GPUs
In: Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, ed. by Mourad Elloumi and Albert Y. Zomaya. Wiley-Blackwell, chap. to appear, pp. .

Schmidt, B, Aribowo, H, and Dang, H (2012).
Iterative Sparse Matrix-Vector Multiplication for Accelerating the Block Wiedemann Algorithm over GF(2) on Multi-GPU Systems
Concurrency and Computation: Practice and Experience.

Wirawan, A, Kwoh, CK, Chew, PTK, Aquino, MCD, Loon, SC, See, J, Zheng, C, and Lin, W (2012).
Feature Selection for Computer-Aided Angle Closure Glaucoma Mechanism Detection
Journal of Medical Imaging and Health Informatics , 2(4):438-444.

Giraud, M, Schmidt, B, Janot, S, and Varre, JS (2011).
M. Giraud, B. Schmidt, S. Janot, J.S. Varre: Many-core high-performance computing in Bioinformatics
In: Advances in Genomic Sequence Analysis and Pattern Discovery, ed. by Laura Elnitski, Helen Piontkivska, Lonnie R Welch. World Scientific, chap. 8, pp. 179-208.

Kuttippurathu, L, Hsing, M, Liu, Y, Schmidt, B, Maskell, DL, Lee, K, He, A, Pu, WT, and Kong, SW (2011).
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.
Bioinformatics, 27(5):715-7.

Ligowski, L, Rudnicki, W, Liu, Y, and Schmidt, B (2011).
Accurate scanning of sequence databases with the Smith-Waterman algorithm
GPU Computing Gems:155-172.

Liu, W, Schmidt, B, Liu, Y, and Müller-Wittig, W (2011).
Mapping of the BLASTP algorithm onto GPU clusters
17th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2011):236-243.

Liu, Y, Schmidt, B, and Maskell, DL (2011).
Parallelized short read assembly of large genomes using de Bruijn graphs.
BMC Bioinformatics, 12:354.

Liu, Y, Schmidt, B, and Maskell, DL (2011).
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI.
BMC Bioinformatics, 12:85.

Liu, Y, Schmidt, B, and Maskell, DL (2011).
An ultrafast scalable many-core motif discovery algorithm for multiple GPUs
10th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2011):428-434.

Schmidt, B, Aribowo, H, and Dang, H (2011).
Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs
In: Euro-Par 2011 Parallel Processing - 17th International Conference, Euro-Par 2011, Bordeaux, France, August 29 - September 2, 2011, vol. 6853, pp. 413-424, Springer. Lecture Notes in Computer Science.

Zhang, Z, Kwoh, CK, Liu, J, Yin, F, Wirawan, A, Cheung, C, Baskarang, M, Aung, T, and Wong, TY (2011).
MRMR Optimized Classification for Automatic Glaucoma Diagnosis
In: IEEE Engineering in Medicine and Biology Society, pp. 6228 - 6231 .

Liu, Y, Schmidt, B, and Maskell, DL (2010).
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.
Bioinformatics, 26(16):1958-64.

Liu, Y, Schmidt, B, and Maskell, DL (2010).
CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions.
BMC Res Notes, 3:93.

Liu, Y, Schmidt, B, and Maskell, DL (2010).
Parallel bioinformatics algorithms for CUDA-enabled GPUs
Bioinformatics: High Performance Parallel Computer Architectures:117–137.

Liu, Y, Schmidt, B, Liu, W, and Maskell, DL (2010).
CUDA-MEME: accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units
Pattern Recognition Letters, 31(14):2170 - 2177.

Schmidt, B (2010).
Bioinformatics: High Performance Parallel Computer Architectures
Taylor & Francis/CRC Press.