Research output per year
Research output per year
Search results
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2008
An iterative time windowed signature algorith for time-dependent transcription module discovery
Meng, J., Gao, S. J. & Huang, Y., 2008, GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics. 4555659. (GENSIPS'08 - 6th IEEE International Workshop on Genomic Signal Processing and Statistics).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
Open Access -
2009
Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules
Meng, J., Gao, S. J. & Huang, Y., 2009, In: Bioinformatics. 25, 12, p. 1521-1527 7 p.Research output: Contribution to journal › Article › peer-review
Open Access -
2010
An iterated conditional mode solution for Bayesian factor modeling of transcriptional regulatory networks
Meng, J., Zhang, J., Chen, Y. & Huang, Y., 2010, 2010 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2010. 5719679. (2010 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2010).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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An iterated conditional modes solution for sparse Bayesian factor modeling of transcriptional regulatory networks
Meng, J., Zhang, J., Chen, Y. & Huang, Y., 2010, Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010. p. 335-340 6 p. 5706587. (Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Robust inference of the context specific structure and temporal dynamics of gene regulatory network
Meng, J., Lu, M., Chen, Y., Gao, S. J. & Huang, Y., 1 Dec 2010, In: BMC Genomics. 11, SUPPL. 3, S11.Research output: Contribution to journal › Article › peer-review
Open Access -
Uncovering transcriptional regulatory networks by sparse bayesian factor model
Huang, Y., Meng, J., Zhang, J., Qi, Y. & Chen, Y., 2010, In: Eurasip Journal on Advances in Signal Processing. 2010, 538919.Research output: Contribution to journal › Article › peer-review
Open Access -
Uncovering transcriptional regulatory networks by sparse Bayesian factor model
Meng, J., Zhang, J., Chen, Y. & Huang, Y., 2010, ICSP2010 - 2010 IEEE 10th International Conference on Signal Processing, Proceedings. p. 1785-1788 4 p. 5656704. (International Conference on Signal Processing Proceedings, ICSP).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
Open Access -
2011
Bayesian non-negative factor analysis for reconstructing transcriptional regulatory network
Meng, J., Zhang, J., Chen, Y. & Huang, Y., 2011, 2011 IEEE Statistical Signal Processing Workshop, SSP 2011. p. 361-364 4 p. 5967704. (IEEE Workshop on Statistical Signal Processing Proceedings).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks
Meng, J., Zhang, J. M., Chen, Y. & Huang, Y., 14 Oct 2011, In: Proteome Science. 9, SUPPL. 1, S9.Research output: Contribution to journal › Article › peer-review
Open Access -
Clustering DNA methylation expressions using nonparametric beta mixture model
Zhang, L., Meng, J., Liu, H. & Huang, Y., 2011, Proceedings 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11. IEEE Computer Society, p. 170-173 4 p. 6169472. (Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Uncover cooperative gene regulations by microRNAs and transcription factors in glioblastoma using a nonnegative hybrid factor model
Meng, J., Chen, H. I., Zhang, J., Chen, Y. & Huang, Y., 2011, 2011 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Proceedings. p. 6012-6015 4 p. 5947732. (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Uncover transcription factor mediated gene regulations using Bayesian nonnegative factor models
Meng, J., Chen, H. I., Zhang, J., Chen, Y. & Huang, Y., 2011, 2011 IEEE International Conference on Signal Processing, Communications and Computing, ICSPCC 2011. 6061806. (2011 IEEE International Conference on Signal Processing, Communications and Computing, ICSPCC 2011).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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2012
A nonparametric Bayesian approach for clustering bisulfate-based DNA methylation profiles.
Zhang, L., Meng, J., Liu, H. & Huang, Y., 2012, In: BMC Genomics. 13 Suppl 6Research output: Contribution to journal › Article › peer-review
Open Access -
Basis-expansion factor models for uncovering transcription factor regulatory network
Sanchez-Castillo, M., Meng, J., Tienda-Luna, I. M. & Huang, Y., 2012, 2012 IEEE Statistical Signal Processing Workshop, SSP 2012. p. 700-703 4 p. 6319799. (2012 IEEE Statistical Signal Processing Workshop, SSP 2012).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Biclustering of time series microarray data
Meng, J. & Huang, Y., 2012, Next Generation Microarray Bioinformatics: Methods and Protocols. Wang, J., Tian, T. & Tan, A. C. (eds.). p. 87-100 14 p. (Methods in Molecular Biology; vol. 802).Research output: Chapter in Book or Report/Conference proceeding › Chapter › peer-review
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Characterization and Robust Classification of EEG Signal from Image RSVP Events with Independent Time-Frequency Features
Meng, J., Meriño, L. M., Shamlo, N. B., Makeig, S., Robbins, K. & Huang, Y., 18 Sept 2012, In: PLoS ONE. 7, 9, e44464.Research output: Contribution to journal › Article › peer-review
Open Access -
Classification of EEG recordings without perfectly time-locked events
Meng, J., Mauricio Meriño, L., Robbins, K. & Huang, Y., 2012, 2012 IEEE Statistical Signal Processing Workshop, SSP 2012. p. 444-447 4 p. 6319727. (2012 IEEE Statistical Signal Processing Workshop, SSP 2012).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Direct and efficient cellular transformation of primary rat mesenchymal precursor cells by KSHV
Jones, T., Ye, F., Bedolla, R., Huang, Y., Meng, J., Qian, L., Pan, H., Zhou, F., Moody, R., Wagner, B., Arar, M. & Gao, S. J., 1 Mar 2012, In: Journal of Clinical Investigation. 122, 3, p. 1076-1081 6 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Exploiting correlated discriminant features in time frequency and space for characterization and robust classification of image RSVP events with EEG data
Meng, J., Meriño, L. M., Robbins, K. & Huang, Y., 2012, 2012 IEEE Statistical Signal Processing Workshop, SSP 2012. p. 668-671 4 p. 6319790. (2012 IEEE Statistical Signal Processing Workshop, SSP 2012).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Uncover context-specific gene regulation by transcription factors and microRNAs using Bayesian sparse nonnegative factor regression
Meng, J., Chen, Y. & Huang, Y., Dec 2012, In: Journal of Biological Systems. 20, 4, p. 377-402 26 p.Research output: Contribution to journal › Article › peer-review
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Understanding MicroRNA regulation: A computational perspective
Yue, D., Meng, J., Lu, M., Chen, C. L. P., Guo, M. & Huang, Y., Jan 2012, In: IEEE Signal Processing Magazine. 29, 1, p. 77-88 12 p., 6105465.Research output: Contribution to journal › Article › peer-review
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2013
A bag-of-words model for task-load prediction from EEG in complex environments
Merino, L. M., Meng, J., Gordon, S., Lance, B. J., Johnson, T., Paul, V., Robbins, K., Vettel, J. M. & Huang, Y., 18 Oct 2013, 2013 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2013 - Proceedings. p. 1227-1231 5 p. 6637846. (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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A Deep Learning method for classification of images RSVP events with EEG data
Ahmed, S., Mauricio Merino, L., Mao, Z., Meng, J., Robbins, K. & Huang, Y., 2013, 2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings. p. 33-36 4 p. 6736804. (2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Differential analysis of rna methylation sequencing data
Cui, X., Meng, J., Rao, M. K., Chen, Y. & Huang, Y., 2013, 2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings. p. 41-42 2 p. 6736806. (2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Exome-based analysis for RNA epigenome sequencing data
Meng, J., Cui, X., Rao, M. K., Chen, Y. & Huang, Y., 15 Jun 2013, In: Bioinformatics. 29, 12, p. 1565-1567 3 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Integration of gene expression, genome wide DNA methylation, and gene networks for clinical outcome prediction in ovarian cancer
Zhang, L., Liu, H., Meng, J., Wang, X., Chen, Y. & Huangi, Y., 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 535-538 4 p. 6732553. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Tet1 is critical for neuronal activity-regulated gene expression and memory extinction
Rudenko, A., Dawlaty, M. M., Seo, J., Cheng, A. W., Meng, J., Le, T., Faull, K. F., Jaenisch, R. & Tsai, L. H., 18 Sept 2013, In: Neuron. 79, 6, p. 1109-1122 14 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Unveiling the dynamics in RNA epigenetic regulations
Meng, J., Cui, X., Liu, H., Zhang, L., Zhang, S., Rao, M. K., Chen, Y. & Huang, Y., 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 139-144 6 p. 6732477. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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2014
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package
Meng, J., Lu, Z., Liu, H., Zhang, L., Zhang, S., Chen, Y., Rao, M. K. & Huang, Y., 1 Oct 2014, In: Methods. 69, 3, p. 274-281 8 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Classification of imperfectly time-locked image RSVP events with EEG device
Meng, J., Meriño, L. M., Robbins, K. & Huang, Y., Apr 2014, In: Neuroinformatics. 12, 2, p. 261-275 15 p.Research output: Contribution to journal › Article › peer-review
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Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test
Zhang, L., Meng, J., Liu, H., Cui, X., Zhang, S. W., Chen, Y. & Huang, Y., 5 Feb 2014, 2014 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2014. Institute of Electrical and Electronics Engineers Inc., p. 1368-1371 4 p. 7032349. (2014 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2014).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Differential analysis of RNA methylome with improved spatial resolution
Zhang, Y. C., Zhang, S. W., Liu, L., Zhang, L., Liu, H., Cui, X., Huang, Y. & Meng, J., 5 Feb 2014, 2014 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2014. Institute of Electrical and Electronics Engineers Inc., p. 1372-1375 4 p. 7032350. (2014 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2014).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Early remodeling of the neocortex upon episodic memory encoding
Bero, A. W., Meng, J., Cho, S., Shen, A. H., Canter, R. G., Ericsson, M. & Tsai, L. H., 12 Aug 2014, In: Proceedings of the National Academy of Sciences of the United States of America. 111, 32, p. 11852-11857 6 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Epigenetic priming of memory updating during reconsolidation to attenuate remote fear memories
Gräff, J., Joseph, N. F., Horn, M. E., Samiei, A., Meng, J., Seo, J., Rei, D., Bero, A. W., Phan, T. X., Wagner, F., Holson, E., Xu, J., Sun, J., Neve, R. L., Mach, R. H., Haggarty, S. J. & Tsai, L. H., 2014, In: Cell. 156, 1-2, p. 261-276 16 p.Research output: Contribution to journal › Article › peer-review
Open Access298 Citations (Scopus)
- Citations
- Citation Indexes: 298
- Patent Family Citations: 1
- Captures
- Readers: 662
- Mentions
- Blog Mentions: 2
- References: 4
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2015
Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome
Liu, L., Zhang, S. W., Zhang, Y. C., Liu, H., Zhang, L., Chen, R., Huang, Y. & Meng, J., 1 Jan 2015, In: Molecular BioSystems. 11, 1, p. 262-274 13 p.Research output: Contribution to journal › Article › peer-review
Open Access -
HEPeak: An HMM-based exome peak-finding package for RNA epigenome sequencing data
Cui, X., Meng, J., Rao, M. K., Chen, Y. & Huang, Y., 21 Apr 2015, In: BMC Genomics. 16, 4, S2.Research output: Contribution to journal › Article › peer-review
Open Access -
IncRScan-SVM: A tool for predicting long non-coding RNAs using support vector machine
Sun, L., Liu, H., Zhang, L. & Meng, J., 5 Oct 2015, In: PLoS ONE. 10, 10, e0139654.Research output: Contribution to journal › Article › peer-review
Open Access -
MeT-DB: A database of transcriptome methylation in mammalian cells
Liu, H., Flores, M. A., Meng, J., Zhang, L., Zhao, X., Rao, M. K., Chen, Y. & Huang, Y., 28 Jan 2015, In: Nucleic Acids Research. 43, D1, p. D197-D203Research output: Contribution to journal › Article › peer-review
Open Access -
Modeling of replicates variances for detecting RNA methylation site in MERIP-SEQ data
Cui, X., Meng, J., Zhang, S. & Huang, Y., 31 Aug 2015, 2015 IEEE China Summit and International Conference on Signal and Information Processing, ChinaSIP 2015 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 802-806 5 p. 7230515. (2015 IEEE China Summit and International Conference on Signal and Information Processing, ChinaSIP 2015 - Proceedings).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Recent progress and challenges in high throughput RNA methylation sequencing data analysis
Liu, L., Zhang, S. W., Meng, J. & Chen, R. S., Oct 2015, In: Progress in Biochemistry and Biophysics. 42, 10, p. 891-899 9 p.Research output: Contribution to journal › Review article › peer-review
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Sketching the distribution of transcriptomic features on RNA transcripts with Travis coordinates
Cui, X., Wei, Z., Zhang, L., Liu, H., Sun, L., Zhang, S. W., Huang, Y. & Meng, J., 16 Dec 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Schapranow, L. M., Zhou, J., Hu, X. T., Ma, B., Rajasekaran, S., Miyano, S., Yoo, I., Pierce, B., Shehu, A., Gombar, V. K., Chen, B., Pai, V. & Huan, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1536-1542 7 p. 7359904. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
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Spatially Enhanced Differential RNA Methylation Analysis from Affinity-Based Sequencing Data with Hidden Markov Model
Zhang, Y. C., Zhang, S. W., Liu, L., Liu, H., Zhang, L., Cui, X., Huang, Y. & Meng, J., 2015, In: BioMed Research International. 2015, 852070.Research output: Contribution to journal › Article › peer-review
Open Access -
2016
A hierarchical model for clustering m6A methylation peaks in MeRIP-seq data
Cui, X., Meng, J., Zhang, S., Rao, M. K., Chen, Y. & Huang, Y., 22 Aug 2016, In: BMC Genomics. 17, 520.Research output: Contribution to journal › Article › peer-review
Open Access -
A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data
Cui, X., Meng, J., Zhang, S., Chen, Y. & Huang, Y., 15 Jun 2016, In: Bioinformatics. 32, 12, p. i378-i385Research output: Contribution to journal › Article › peer-review
Open Access -
Cortical neurons gradually attain a post-mitotic state
De Anda, F. C., Madabhushi, R., Rei, D., Meng, J., Gräff, J., Durak, O., Meletis, K., Richter, M., Schwanke, B., Mungenast, A. & Tsai, L. H., 1 Sept 2016, In: Cell Research. 26, 9, p. 1033-1047 15 p.Research output: Contribution to journal › Article › peer-review
Open Access -
DRME: Count-based differential RNA methylation analysis at small sample size scenario
Liu, L., Zhang, S. W., Gao, F., Zhang, Y., Huang, Y., Chen, R. & Meng, J., 15 Apr 2016, In: Analytical Biochemistry. 499, p. 15-23 9 p.Research output: Contribution to journal › Article › peer-review
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Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features
Cui, X., Wei, Z., Zhang, L., Liu, H., Sun, L., Zhang, S. W., Huang, Y. & Meng, J., 2016, In: BioMed Research International. 2016, 8367534.Research output: Contribution to journal › Article › peer-review
Open Access -
Histone deacetylase 3 associates with MeCP2 to regulate FOXO and social behavior
Nott, A., Cheng, J., Gao, F., Lin, Y. T., Gjoneska, E., Ko, T., Minhas, P., Zamudio, A. V., Meng, J., Zhang, F., Jin, P. & Tsai, L. H., 26 Oct 2016, In: Nature Neuroscience. 19, 11, p. 1497-1505 9 p.Research output: Contribution to journal › Article › peer-review
Open Access -
m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks
Zhang, S., Zhang, S., Liu, L., Meng, J. & Huang, Y., Dec 2016, In: PLoS Computational Biology. 12, 12, e1005287.Research output: Contribution to journal › Article › peer-review
Open Access -
Novel numerical and computational techniques for remote sensor based monitoring of freshwater quality
Zhu, X., Yue, Y., Wong, P., Zhang, Y. & Meng, J., 17 Sept 2016, Proceedings of 2016 IEEE International Conference of Online Analysis and Computing Science, ICOACS 2016. Chen, G. & Peng, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 91-95 5 p. 7563055. (Proceedings of 2016 IEEE International Conference of Online Analysis and Computing Science, ICOACS 2016).Research output: Chapter in Book or Report/Conference proceeding › Conference Proceeding › peer-review
