个人主页——彭绍亮

2019

[113] J Li, Y Li, W Li, H Luo, Y Xi, S Dong, M Gao, ... S Peng*, F Wu and W Yu(2018). Guide Positioning Sequencingidentifies aberrant DNA methylation patterns that alter cell identity andtumor-immune surveillance networks. Genome Research（影响因子10.101）. February 2019, 29 (2).（并列通讯作者）

[112] Benyun Shi, Guangliang Liu, Hongjun Qiu, Yu-Wang Chen, Shaoliang Peng*. Voluntary Vaccination through Perceiving Epidemic Severity in Social Networks. Complexity 2019: 3901218:1-3901218:13 (2019).

[111] Xinguo Lu, Xin Qian, Xing Li, Qiumai Miao, Shaoliang Peng*. DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters. Bioinformatics( Volume 35, Issue 3, 01 February 2019).（通讯作者）

[110] Gaole An, Jiaqi Sun, Chao Ren, Zhangyi Ouyang, Lingyun Zhu, Xiaochen Bo, Shaoliang Peng*, Wenjie Shu. LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs. Database 2019( 13 February 2019 ).

[109] Shaoliang Peng* , Yingbo Cui , Shunyun Yang , Wenhe Su , Xiaoyu Zhang , Tenglilang Zhang , et al. A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer. IEEE/ACM Transactions on Computational Biology and Bioinformatics ( Volume: 16, Issue: 2, March-April 1 2019 ).（第一作者、通讯作者）

[108] T Huang, W Lin, Y Li, LG He, SL Peng. A Latency-Aware Multiple Data Replicas Placement Strategy for Fog Computing. Journal of Signal Processing Systems: 1-14 (22 February 2019)

2018

[107] Bu, D., Peng, S.*, Luo, H., Li, X., Li, H., Sun, L., ... & Yi, Z. (2018). From big data to knowledge in precision medicine. Science. 02 Feb 2018: Vol. 359, Issue 6375, pp. 598（P35-38） DOI: 10.1126/science.359.6375.598-b（并列第一作者）

[106] S Peng* , Cheng M , Huang K , et al. .(2018). Efficient computation of motif discovery on Intel Many Integrated Core (MIC) Architecture[J]. BMC Bioinformatics, 2018, 19(9):282.（第一作者、通讯作者）

[105] D Dong, Z Xu, W Zhong, S Peng* .(2018). Parallelization of Molecular Docking: A Review, Current Topics in Medicinal Chemistry, 2018, 18(12): 1015–1028.（通讯作者）

[104] Z Zhang, Y Lu, S Peng* .(2018). A dictionary learning algorithm for gene expression profile classification based on feature selection, 2018 International Conference on Intelligent Robotic and Control Engineering.（通讯作者）

[103] X Xie, Q Sun, X Liao, Y Tong, S Peng* .(2018). Complete genomes of two novel active prophages discovered by bioinformatics methods from high-throughput sequencing data, ITA 2018.（通讯作者）

[102] R Guo, X Xie, B Shi, S Li, K Li, X Liao, S Peng* .(2018). Review of Bioinformatics Application on Intel MIC Architecture, Interdisciplinary Sciences: Computational Life Sciences, 2018.（通讯作者）

[101] R Guo, Y Wang, W Shu, S Peng* .(2018). Accurate identification of RNA editing sites from primitive sequence with recurrent neural network, Current Gene Therapy, 2018.（通讯作者）

[100] Zhang, Z.,Zhao, Y., Liao, X., Shi, W., Li, K., Zou, Q*., Peng, S.*..(2018). Deep Learning in omics: a survey and guideline. Briefings in Functional Genomics, 00(00), 2018, 1–17.（并列通讯作者）

[99] Zhang, X., Liao, X., Zhu, H., Li, K., Shi, B., Peng, S.. (2018). COPCOP: A Novel Algorithm and Parallel Optimization Framework for Co-Evolutionary Domain Detection. IEEE/ACM Transactions on Computational Biology and Bioinformatics..

[98] Peng, S., Zhang, X.,Lu, Y., Liao, X., Lu, K., Yang, C., ... & Wei, D. (2018). High-scalable Collaborated Parallel Framework for Large-scale Molecular Dynamic Simulation on Tianhe-2 Supercomputer. IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[97] Cui, Y., Peng, S.*,Lu, Y., Zhu, X., Wang, B., Wu, C., & Liao, X. (2018). mSNP: A Massively Parallel Algorithm for Large-Scale SNP Detection. IEEE Transactions on Parallel and Distributed Systems. （通讯作者）

[96] Guo, R., Zhao, Y., Zou Q., Fang X., & Peng, S.* (2018). Bioinformatics applications on Apache Spark. GigaScience. （通讯作者）

[95] Dong, D., Su, W., Shi, W.,Zou, Q., & Peng, S.* (2018). VCSRA: A fast and accurate multiple sequence alignment algorithm with a high degree of parallelism. Journal of Genetics and Genomics. （通讯作者）

[94] Lu, X., Qian, X., Li, X.,Miao, Q., Peng, S.*, & Berger, B. (2018). DMCM: A Data-adaptive Mutation Clustering Method to Identify Cancer-related Mutation Clusters. Bioinformatics. （并列通讯作者）

[93] Yang, S., Guo, R., Liu, R.,Liao, X., Zou, Q., Shi, B., & Peng, S.* (2018). cmFSM: ascalable CPU-MIC coordinated drug-finding tool by frequent subgraphmining. BMC bioinformatics, 19(4), 98. （通讯作者）

[92] Cui, Y., Xu, J., Cheng, M.,Liao, X., & Peng, S.* (2018). Review of CRISPR/Cas9 sgRNA DesignTools. Interdisciplinary Sciences: Computational Life Sciences, 1-11. （通讯作者）

[91] Lu,X., Li, X., Liu, P., Qian, X., Miao, Q., & Peng, S.* (2018). The Integrative Method Based on the Module-Network for Identifying Driver Genes in Cancer Subtypes. Molecules, 23(2), 183. （并列通讯作者）

[90] Bai,L. Y., Dai, H., Xu, Q., Junaid, M., Peng, S. L. , Zhu, X., ... &Wei, D. Q. (2018). Prediction of Effective Drug Combinations by an Improved Naive Bayesian Algorithm. International journal of molecular sciences, 19(2), 467.

2017

[89] Peng, S., Yang, S.,Bo, X., & Li, F. (2017). paraGSEA: a scalable approach for large-scale gene expression profiling. Nucleic acids research, 45(17), e155-e155.

[88] Peng, S., Yang, S.,Su, W., Zhang, X., Zhang, T., Liu, W., & Zhao, X. (2017). A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer. IEEE/ACM transactions on computational biology and bioinformatics.

[87] Peng, S., Zhang, X.,Yang, S., Su, W., Zhang, Z., Dong, D., ... & Zhu, W. (2017, May). mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. In Cluster, Cloud and Grid Computing (CCGRID), 2017 17th IEEE/ACM International Symposium on (pp. 671-676). IEEE.

[86] Peng, S., Yang, S.,Gao, M., Liao, X., Liu, J., Yang, C., ... & Yu, W. (2017). P-Hint-Hunt: adeep parallelized whole genome DNA methylation detection tool. BMC genomics, 18(2), 134.

[85] Zhang, H. Y., Xu, Q., Xiong,Y., Peng, S. L., Kumari, K. M., & Wei, D. Q. (2017). Membrane defectand water leakage caused by passive calcium permeation. Journal of Molecular Liquids.

[84] Su, W., Liao, X., Lu, Y.,Zou, Q., & Peng, S.* (2017). Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: A Linear Method for Multiple Nucleotide Sequence Alignment on Spark Parallel Framework. Journal of Computational Biology, 24(12), 1230-1242.（并列通讯作者）

[83] Shi, B., Wang, W., Qiu, H.,Chen, Y. W., & Peng, S. (2017). Exploring Voluntary Vaccinating Behaviors using Evolutionary N-person Threshold Games. Scientificreports, 7(1), 16355.

[82] Zhang, X., Liao, X., Zhu,H., Li, K., Shi, B., & Peng, S.*(2017, November). A novel algorithm for detecting co-evolutionary domains in protein and nucleotide sequences. In 2017 IEEE International Conference on Bioinformatics and Biomedicine(BIBM) (pp. 56-61). IEEE.（并列通讯作者）

2016

[81] Xiao, M., Li, J., Li, W.,Wang, Y., Wu, F., Xi, Y., ... & Peng, S. (2017). MicroRNAs activategene transcription epigenetically as an enhancer trigger. RNAbiology, 14(10), 1326-1334.

[80] Peng, S. (2016, December). High performance computational biology and drug design on TianHe Supercomputers. In Bioinformatics and Biomedicine (BIBM), 2016 IEEE International Conference on (pp. 7-7). IEEE.

[79] Peng, S., Zhang, X.,Lu, Y., Liao, X., Lu, K., Yang, C., ... & Wei, D. (2016, December). mAMBER: A CPU/MIC collaborated parallel framework for AMBER on Tianhe-2 supercomputer.In Bioinformatics and Biomedicine (BIBM), 2016 IEEE International Conference on (pp. 651-657). IEEE.

[78] Zhang, F., Liao, X., Peng,S.*, Cui, Y., Wang, B., Zhu, X., & Liu, J. (2016). A Hybrid Parallel Strategy Based on String Graph Theory to Improve De Novo DNA Assembly on theTianHe-2 Supercomputer. Interdisciplinary Sciences: Computational Life Sciences, 8(2), 169-176.（并列通讯作者）

[77] Lan, H., Chan, Y., Xu, K.,Schmidt, B., Peng, S., & Liu, W. (2016). Parallel algorithms forlarge-scale biological sequence alignment on Xeon-Phi based clusters. BMC bioinformatics, 17(9), 267.

[76] Cui, Y., Liao, X., Zhu, X.,Wang, B., & Peng, S.* (2016). B-MIC: an ultrafast three-level parallel sequence aligner using MIC. Interdisciplinary Sciences:Computational Life Sciences, 8(1), 28-34.（并列通讯作者）

[75] Li, X., Wu, W. K., Xing, R.,Wong, S. H., Liu, Y., Fang, X., ... & Peng, S. (2016). Distinct subtypes of gastric cancer defined by molecular characterization include novel mutational signatures with prognostic capability. Cancer research.

[74] Cheng, C., Zhou, Y., Li, H.,Xiong, T., Li, S., Bi, Y., ... & Peng, S. (2016). Whole-genome sequencing reveals diverse models of structural variations in esophageal squamous cell carcinoma. The American Journal of Human Genetics, 98(2), 256-274.

2015

[73] Peng, S., Liao, X.,Yang, C., Lu, Y., Liu, J., Cui, Y., ... & Wang, B. (2015, May). The Challenge of Scaling Genome Big Data Analysis Software on TH-2 Supercomputer. In Cluster, Cloud and Grid Computing (CCGrid), 2015 15th IEEE/ACM International Symposium on (pp. 823-828). IEEE.

[72] Wang, H., Peng, S.*,Zhu, X., Wu, C., Liu, X., Chen, Q., ... & Yang, H. (2015, May). A method toaccelerate GROMACS in offload mode on Tianhe-2 supercomputer. In Cluster, Cloud and Grid Computing (CCGrid), 2015 15th IEEE/ACM International Symposiumon (pp. 781-784). IEEE.（通讯作者）

[71] Liu, X., Peng, S.*,Yang, C., Wu, C., Wang, H., Cheng, Q., ... & Wang, J. (2015, May). mAMBER:Accelerating explicit solvent molecular dynamic with Intel Xeon Phimany-integrated core coprocessors. In Cluster, Cloud and Grid Computing(CCGrid), 2015 15th IEEE/ACM International Symposium on(pp. 729-732). IEEE.（通讯作者）

[70] Cheng, Q., Peng, S.*,Lu, Y., Zhu, W., Xu, Z., & Zhang, X. (2015, May). mD3DOCKxb: a deepparallel optimized software for molecular docking with Intel Xeon Phicoprocessors. In Cluster, Cloud and Grid Computing (CCGrid), 2015 15th IEEE/ACM International Symposium on(pp. 725-728). IEEE.（通讯作者）

[69] Zhu, X., Peng, S.*,Liu, S., Cui, Y., Gu, X., Gao, M., ... & Fang, X. (2015). A Massively Parallel Computational Method of Reading Index Files for SOAPsnv. Interdisciplinary Sciences: Computational LifeSciences, 7(4), 397-404.（通讯作者）

[68] Wang, H., Peng, S.*,Lu, Y., Wu, C., Wen, J., Liu, J., & Zhu, X. (2015, July). BWTCP: A parallel method for constructing BWT in large collection of genomic reads. In International Conference on High Performance Computing (pp.171-178). Springer, Cham.（通讯作者）

[67] Liao, X., Peng, S.,Lu, Y., Cui, Y., Wu, C., Wang, H., & Wen, J. (2015). Neo-hetergeneous Programmingand Parallelized Optimization of a Human Genome Re-sequencing Analysis Software Pipeline on TH-2 Supercomputer. Supercomputing Frontiers and Innovations, 2(1), 73-83.

[66] Cui, Y., Liao, X., Peng,S.*, Lu, Y., Yang, C., Wang, B., & Wu, C. (2015, July). Large-scale neo-heterogeneous programming and optimization of SNP detection on Tianhe-2. In International Conference on High Performance Computing(pp. 74-86). Springer, Cham.（通讯作者）

[65] Zhang, J., Li, S., Liao, X.,Peng, S., Liu, X., & Jia, Z. (2015). Hematch: a redundancy layout placement scheme for erasure-coded storages in practical heterogeneous failure patterns. Science China Information Sciences, 58(6), 1-11.

[64] Wu, C., Schwartz, J. M.,Brabant, G., Peng, S. L., & Nenadic, G. (2015). Constructing amolecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events. BMC systems biology, 9(6), S5.

[63] Luo, R., Cheung, J., Wu, E.,Wang, H., Chan, S. H., Law, W. C., ... & Peng, S. (2015). MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC). BMC bioinformatics, 16(7), S10.

[62] Fang, X., Nevo, E., Han, L.,Levanon, E. Y., Zhao, J., Avivi, A., ... & Peng, S. (2015). Corrigendum: Genome-wide adaptive complexes to underground stresses in blindmole rats Spalax. Nature communications, 6, 8051.

2014

[61] Murabito, E., Colombo, R.,Wu, C., Verma, M., Rehman, S., Snoep, J., ... & Peng, S. (2015). Supra Biology 2014: Promoting UK-China collaboration on Systems Biology and High Performance Computing.

[60] Wang, J., Peng, S., Cossins, B. P., Liao, X., Chen, K., Shao, Q., ... & Zhu, W. (2014). Mapping central α-Helix linker mediated conformational transition pathway of calmodulin via simple computational approach. The Journal of Physical Chemistry B, 118(32), 9677-9685.

[59] Liu, X., Li, S., Liao, X., Peng,S., Wang, L., & Kong, Z. (2014). Know by a handful the whole sack: efficient sampling for top-k influential user identification in largegraphs. World Wide Web, 17(4), 627-647.

[58] Liu, X., Li, M., Li, S., Peng,S*., Liao, X., & Lu, X. (2014). IMGPU: GPU-accelerated influence maximization in large-scale social networks. IEEE Transactions on Paralleland Distributed Systems, 25(1), 136-145.（并列通讯作者）

[57] Cui, Y., Liao, X., Zhu, X.,Wang, B., & Peng, S. (2014). mBWA: A massively parallel sequencereads aligner. In 8th International Conference on Practical Applicationsof Computational Biology & Bioinformatics (PACBB 2014) (pp. 113-120).Springer, Cham.

[56] Fang, X., Nevo, E., Han, L., Levanon, E. Y., Zhao, J., Avivi, A., ... & Peng, S. (2015).Corrigendum: Genome-wide adaptive complexes to underground stresses in blindmole rats Spalax. Nature communications, 6, 8051.

2013

[55] Li, S., Peng, S.*, Chen,W., & Lu, X. (2013). INCOME: Practical land monitoring in precision agriculture with sensor networks. Computer Communications, 36(4),459-467.（并列通讯作者）

[54] Huang, H., Liao, X., Li, S.,Peng, S.*, Liu, X., & Lin, B. (2013, August). The architecture and traffic management of wireless collaborated hybrid data center network.In ACM SIGCOMM Computer Communication Review (Vol. 43, No. 4, pp.511-512). ACM.（并列通讯作者）

[53] Liang, C. P., Fan, J. L.,Gong, H. R., Liao, X., Zhu, X., & Peng, S. (2013). Interface structure and work function of W-Cu interfaces. Applied PhysicsLetters, 103(21), 211604.

[52] LU, X., DONG, D., LIAO, X.,& PENG, S. (2013). P-Zone: Connectivity-based Packet Path Tracing in Wireless Sensor Networks. Chinese Journal of Electronics, 22(3),477-482.

[51] Luo, R., Wong, T., Zhu, J.,Liu, C. M., Zhu, X., Wu, E., ... & Peng, S. (2013). SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner. PloS one, 8(5), e65632.

[50] Jia, W., Qiu, K., He, M.,Song, P., Zhou, Q., Zhou, F., ... & Peng, S. (2013). SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seqdata. Genome biology, 14(2), R12.

2012

[49] Luo, R., Liu, B., Xie, Y.,Li, Z., Huang, W., Yuan, J., ... & Peng, S. (2012). SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1(1), 18.（被引用次数：1769）

[48] Peng, S., Li, S.,Liao, X., Peng, Y., & Xiao, N. (2012). A scalable code dissemination protocol in heterogeneous wireless sensor networks. Science ChinaInformation Sciences, 55(6), 1323-1336.

[47] Peng, S., Xing, G.,Li, S., Jia, W., & Peng, Y. (2012). Fast release/capture sampling inlarge-scale sensor networks. IEEE Transactions on Mobile Computing, 11(8), 1274-1286.

[46] Liu, B., Yao, Y., Jiang, Z.,Yan, L., Qu, Q., & Peng, S. (2012, July). HLA-based parallel simulation: A case study. In Principles of Advanced and Distributed Simulation (PADS), 2012 ACM/IEEE/SCS 26th Workshop on (pp. 65-67). IEEE.

2011

[45] Hou, B., Yao, Y., & Peng,S.* (2011, June). Empirical study on entity interaction graph oflarge-scale parallel simulations. In Proceedings of the 2011 IEEE Workshopon Principles of Advanced and Distributed Simulation (pp. 1-6). IEEE Computer Society.（并列通讯作者）

[44] Chen, L. L., Lu, Y. S., Yao,Y. P., & Peng, S. L.* (2011, June). A well-balanced time warp systemon multi-core environments. In Principles of Advanced and Distributed Simulation (PADS), 2011 IEEE Workshop on (pp. 1-9). IEEE.（并列通讯作者）