Publications


Book Chapters

  1. Yongchao Liu and Bertil Schmidt: "CUSHAW Suite: parallel and efficient algorithms for next generation sequencing read alignment". Algorithms for Next-Generations Sequencing Data: Techniques, Approaches and Applications, edited by Mourad Elloumi, Springer, 2017, in press.
  2. Yongchao Liu and Bertil Schmidt: "Pairwise DNA sequence alignment optimization". High Performance Parallelism Pearls Volume Two - Multicore and Many-core Programming Approaches, edited by James Reinders and Jim Jeffers, 2015, pp. 43-54
  3. Yongchao Liu and Bertil Schmidt: "Multiple protein sequence alignment with MSAProbs". Methods in Molecular Biology, Edited by David Russell, Springer, 2014, 1079: 211-218
  4. Lukasz Ligowski, Witold Rudnicki, Yongchao Liu, and Bertil Schmidt: "Accurate scanning of sequence databases with the Smith-Waterman algorithm". GPU Computing Gems, Edited by Wen-mei W. Hwu, Elsevier 2011, Pages 155-172
  5. Yongchao Liu, Bertil Schmidt , and Douglas L. Maskell: "Parallel bioinformatics algorithms for CUDA-enabled GPUs". Bioinformatics: High Performance Parallel Computer Architectures, Edited by Bertil Schmidt, CRC Press 2010, Pages 117-137

Journal Articles

  1. Yongchao Liu, Tony Pan, Oded Green and Srinivas Aluru: "Parallelized Kendall's tau coefficient computation via SIMD vectorized sorting on many-integrated-core processors". Journal of Parallel and Distributed Computing (impact factor 1.320), 2017, under review [arXiv].
  2. Tony C Pan, Patrick Flick, Chirag Jain, Yongchao Liu and Srinivas Aluru: "Kmerind: a exible parallel library for k-mer indexing of biological sequences on distributed memory systems". IEEE/ACM Transactions on Computational Biology and Bioinformatics (impact factor 1.609), 2017, under review
  3. Yongchao Liu, Fabian Ripp, Rene Koeppe, Hanno Schmidt, Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt and Thomas Hankeln: "AFS: identification and quantification of species composition by metagenomic sequencing". Bioinformatics (impact factor 7.307), 2017, 33 (9): 1396-1398.
  4. Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru: "A greedy alignment-free distance estimator for phylogenetic inference". BMC Bioinformatics (impact factor 2.58), 2017, 18(Suppl 8):238.
  5. Yongchao Liu and Bertil Schmidt: "LightSpMV: faster CUDA-compatible sparse matrix-vector multiplication using compressed sparse rows". Journal of Signal Processing Systems (impact factor 0.508), 2017, doi:10.1007/s11265-016-1216-4.
  6. Jorge Gonzalez-Dominguez, Yongchao Liu, Juan Tourino and Bertil Schmidt: "MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems". Bioinformatics (impact factor 5.766), 2016, 32(24): 3826-3828
  7. Yongchao Liu, Martin Loewer, Srinivas Aluru and Bertil Schmidt: "SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations". BMC Systems Biology (impact factor 2.435), 2016, 10(suppl 2): 47
  8. Jorge González-Domínguez, Yongchao Liu, Bertil Schmidt: "Parallel and scalable short-read alignment on multi-core clusters using UPC++". PLoS One (impact factor 3.234), 2016, 11(1): e0145490.
  9. Tuan Tu Tran, Yongchao Liu, Bertil Schmidt: "Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi". Parallel Computing (impact factor 1.511), 2016, 54: 128-138.
  10. Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Alberto Apostolico and Srinivas Aluru: "ALFRED: a practical method for alignment-free distance computation". Journal of Computational Biology (impact factor 1.737), 2016, 23(6): 452-460
  11. Yongchao Liu, Thomas Hankeln, and Bertil Schmidt: "Parallel and space-efficient construction of Burrows-Wheeler transform and suffix array for big genome data". IEEE Transactions on Computational Biology and Bioinformatics (impact factor 1.536), 2016, 13(3): 592-598.
  12. Yongchao Liu, Bertil Schmidt: "GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences". Concurrency and Computation: Practice and Experience (impact factor 0.784), 2015, 27: 958-972
  13. Fabian Ripp, Christopher F Krombholz, Yongchao Liu, Mathias Weber, Anne Sch?fer, Bertil Schmidt, Rene K?ppel and Thomas Hankeln: "All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing". BMC Genomics (impact factor 4.40), 2014, 15:639 [Reported by Austrilian Food News]
  14. Adrianto Wirawan, Robert S Harris, Yongchao Liu, Bertil Schmidt and Jan Schr?der: "HECTOR: A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data." BMC Bioinformatics (impact factor 3.02), 2014, 15:131
  15. Yongchao Liu, Bernt Popp, and Bertil Schmidt: "CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding." PLOS ONE (impact factor 3.730), 2014, 9(1): e86869
  16. Yongchao Liu and Bertil Schmidt: "CUSHAW2-GPU: empowering faster gapped short-read alignment using GPU computing". IEEE Design & Test (impact factor 1.623), 2014, 31(1): 31-39
  17. Yongchao Liu, Adrianto Wirawan and Bertil Schmidt: "CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions". BMC Bioinformatics (impact factor 3.02), 2013, 14:117.
  18. Yongchao Liu, Jan Schr?der, and Bertil Schmidt: "Musket: a multistage k-mer spectrum based error corrector for Illumina sequence data". Bioinformatics (impact factor 5.323), 2013, 29(3): 308-315
  19. Yongchao Liu and Bertil Schmidt: "Long read alignment based on maximal exact match seeds". Bioinformatics(impact factor 5.468), 2012, 28(18): i318-i324 (also from ECCB 2012)
  20. Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform". Bioinformatics (impact factor 5.468), 2012, 28(14): 1830-1837
  21. Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "Parallelized short read assembly of large genomes using de Bruijn graphs". BMC Bioinformatics (impact factor 3.43), 2011, 12:354
  22. Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI". BMC Bioinformatics (impact factor 3.43), 2011, 12:85 [Reported by GenomeWeb]
  23. Lakshmi Kuttippurathu, Michael Hsing, Yongchao Liu, Bertil Schmidt, Douglas L.Maskell, Kyungjoon Lee, Aibin He, William T. Pu, and Sek Won Kong: "CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments". Bioinformatics (impact factor 4.926), 2011, 27(5): 715-717
  24. Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities". Bioinformatics (impact factor 4.926), 2010, 26(16): 1958 -1964
  25. Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions". BMC Research Notes, 2010, 3:93
  26. Yongchao Liu, Bertil Schmidt, Weiguo Liu, and Douglas L. Maskell: "CUDA-MEME: accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units". Pattern Recognition Letters (impact factor 1.559), 2010, 31(14): 2170 - 2177
  27. Yongchao Liu, Douglas L. Maskell, and Bertil Schmidt: "CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units". BMC Research Notes, 2009, 2:73
  28. 李庆诚, 刘永超(Yongchao Liu), 刘嘉鑫: "平台无关的PDF嵌入式高性价比解析器设计与实现(Design and implementation of a platform-independent, high-performance-cost-ratio, embedded PDF format parser*)". 计算机应用(Computer Applications), 2007, 27(z1). [*translated by myself]

Conference/Workshop Papers

  1. Shuozhi Xu, Thomas Payne,Yongchao Liu, Liming Xiong, Youping Chen and David McDowell: ”PyCAC: The concurrent atomistic-continuum simulator with a Python scripting interface”. 2018 TMS Annual Meeting & Exhibition (TMS 2018), under review
  2. Yuandong Chan, Kai Xu, Haidong Lan, Weiguo Liu, Yongchao Liu and Bertil Schmidt: ”PUNAS: a parallel ungapped-alignment-featured seed verification for next-generation sequencing read alignment”. 31st IEEE International Parallel and Distributed Processing Symposium (IPDPS 2017), 2017, pp. 52-61.
  3. Haidong Lan, Weiguo Liu, Yongchao Liu and Bertil Schmidt: ”SWhybrid: a hybrid parallel framework for large-scale protein sequence database search”. 31st IEEE International Parallel and Distributed Processing Symposium (IPDPS 2017), 2017, pp. 42-51.
  4. Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu and Srinivas Aluru: "Kmerind: A flexible parallel library for k-mer indexing of biological sequences on distributed memory systems". 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2016), 2016, pp. 422-433
  5. Yongchao Liu, Tony Pan, and Srinivas Aluru: "Parallel pairwise correlation computation on Intel Xeon Phi clusters". 28th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD 2016), 2016, pp. 141-149
  6. Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt: "SNVSniffer: an integrated caller for germline and somatic SNVs based on Bayesian models". 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM15), 2015, pp. 83-90.
  7. Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru: "A greedy alignment-free distance estimator for phylogenetic inference (extended abstract)". 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2015), 2015, pp. 1-1.
  8. Yongchao Liu and Bertil Schmidt: "LightSpMV: faster CSR-based sparse matrix-vector multiplication on CUDA-enabled GPUs". 26th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2015), 2015, pp. 82-89 (Best Paper Award)
  9. Yongchao Liu, Jorge González-Domínguez, Bertil Schmidt: "Faster compressed sparse row (CSR)-based sparse matrix-vector multiplication using CUDA". GPU Technology Conference 2015 (GTC 2015), San Jose, USA, 2015
  10. Tuan Tu Tran, Simon Schindel, Yongchao Liu and Bertil Schmidt: "Bit-Parallel approximate pattern matching on the Xeon Phi coprocessor". 26th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD 2014), 2014, pp. 81-88
  11. Yongchao Liu, Tuan-Tu Tran, Felix Lauenroth and Bertil Schmidt: "SWAPHI-LS: Smith-Waterman algorithm on Xeon Phi coprocessors for long DNA sequences". 2014 IEEE International Conference on Cluster Computing (Cluster 2014), 2014, pp. 257-265 (Best Paper Award Recommendation)
  12. Yongchao Liu and Bertil Schmidt: "SWAPHI: Smith-Waterman protein database search on Xeon Phi coprocessors". 25th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2014), 2014, pp. 184-185 [full version at arXiv]
  13. Yongchao Liu and Bertil Schmidt: "CUSHAW Software Package: harnessing CUDA-enabled GPUs for next generation sequencing read alignment". GPU Technology Conference 2014 (GTC 2014), San Jose, USA, 2014
  14. Yongchao Liu and Bertil Schmidt: "Faster GPU-accelerated Smith-Waterman algorithm with alignment backtracking for short DNA sequences". 10th International Conference on Parallel Processing and Applied Mathematics (PPAM 2013), appear in Lecture Notes in Computer Science 8385, pp. 247-257
  15. Yongchao Liu and Bertil Schmidt: "Long read alignment based on maximal exact match seeds". 11th European Conference on Computational Biology (ECCB 2012), Basel, Switzerland (also published in the Bioinformatics journal)
  16. Yongchao Liu and Bertil Schmidt: Evaluation of GPU-based seed generation for computational genomics using Burrows-Wheeler transform". 26th IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW 2012), 684-690
  17. Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "A fast CUDA compatible short read aligner to large genomes". GPU Technology Conference 2012 (GTC 2012), San Jose, USA, 2012
  18. Weiguo Liu, Bertil Schmidt, Yongchao Liu, and Wolfgang Müller-Wittig: "Mapping of the BLASTP algorithm onto GPU clusters". 17th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2011), 2011, 236-243
  19. Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "An ultrafast scalable many-core motif discovery algorithm for multiple GPUs". 25th IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW 2011), 428-434
  20. Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA". 20th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2009), 2009, 121-128 (Best Paper Award)
  21. Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "Parallel reconstruction of neighbor-Joining trees for large multiple sequence alignments using CUDA". 23th IEEE International Symposium on Parallel and Distributed Processing (IPDPS 2009), 2009, 1-8.

Informal Publications

  1. Yongchao Liu and Srinivas Aluru: "LightScan: faster scan primitive on CUDA compatible manycore processors". arXiv:1604.04815 [Cs.DC], 2016.
  2. Yongchao Liu: "Research statement for assistant professorship application". ResearchGate, 2016, doi: 10.13140/RG.2.2.28828.90243/1
  3. Yongchao Liu: "OpenGraphAssembly: abstract, modularize and parallelize fundamental building blocks for graph-based genome assembly". ResearchGate, 2015, doi: 10.13140/RG.2.2.11212.825
  4. Yongchao Liu, Bernt Popp, and Bertil Schmidt: "High-speed and accurate color-space short-read alignment with CUSHAW2". arXiv:1304.4766 [q-bio.GN], 2013