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Robert R Clarke

1981 …2021

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  • 2014

    A Markov random field-based Bayesian model to identify genes with differential methylation

    Wang, X., Gu, J., Xuan, J., Clarke, R. & Hilakivi-Clarke, L., 2014, 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2014. IEEE Computer Society, 6845515. (2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2014).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • BSSV: Bayesian based somatic structural variation identification with whole genome DNA-seq data

    Chen, X., Shi, X., Shajahan, A. N., Hilakivi-Clarke, L., Clarke, R. & Xuan, J., Nov 2 2014, 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014. Institute of Electrical and Electronics Engineers Inc., p. 3937-3940 4 p. 6944485. (2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Statistical identification of co-regulatory gene modules using multiple ChIP-Seq experiments

    Chen, X., Shi, X., Shajahan-Haq, A. N., Hilakivi-Clarke, L., Clarke, R. & Xuan, J., 2014, BIOINFORMATICS 2014 - 5th Int. Conf. on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 7th Int. Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2014. SciTePress, p. 109-116 8 p. (BIOINFORMATICS 2014 - 5th Int. Conf. on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 7th Int. Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2014).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • 2013

    A novel statistical approach to identify co-regulatory gene modules

    Chen, X., Xuan, J., Shi, X., Shajahan-Haq, A. N., Hilakivi-Clarke, L. & Clarke, R., 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 16-18 3 p. 6732746. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Reconstructing transcriptional regulatory networks by probabilistic network component analysis

    Gu, J., Xuan, J., Wang, X., Shajahan, A. N., Hilakivi-Clarke, L. & Clarke, R., 2013, 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013. p. 96-105 10 p. (2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • 2012

    Accurate identification of significant aberrations in contaminated cancer genome

    Hou, X., Yu, G., Yuan, X., Zhang, B., Shih, I. M., Zhang, Z., Clarke, R. & Madhavan, S., 2012, Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012. p. 74-77 4 p. 6507730. (Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Reconstruction of transcription regulatory networks by stability-based network component analysis

    Chen, X., Wang, C., Shajahan, A. N., Riggins, R. B., Clarke, R. & Xuan, J., 2012, Bioinformatics Research and Applications - 8th International Symposium, ISBRA 2012, Proceedings. p. 36-47 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7292 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Sampling-based subnetwork identification from microarray data and protein-protein interaction network

    Wang, X., Gu, J., Xuan, J., Shajahan, A. N., Clarke, R. & Chen, L., 2012, Proceedings - 2012 11th International Conference on Machine Learning and Applications, ICMLA 2012. p. 158-163 6 p. 6406744. (Proceedings - 2012 11th International Conference on Machine Learning and Applications, ICMLA 2012; vol. 2).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2011

    GIST: A Gibbs sampler to identify intracellular signal transduction pathways

    Gu, J., Wang, C., Shih, I. M., Wang, T. L., Wang, Y., Clarke, R. & Xuan, J., 2011, 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011. p. 2434-2437 4 p. 6090677. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2010

    Identification of transcriptional regulatory networks by learning the marginal function of outlier sum statistic

    Gu, J., Xuan, J., Wang, Y., Riggins, R. B. & Clarke, R., 2010, Proceedings - 9th International Conference on Machine Learning and Applications, ICMLA 2010. p. 281-286 6 p. 5708845. (Proceedings - 9th International Conference on Machine Learning and Applications, ICMLA 2010).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Module-based biomarker discovery in breast cancer

    Zhang, Y., Xuan, J. J., Clarke, R. & Ressom, H. W., 2010, Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010. p. 352-356 5 p. 5706590. (Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • 2009

    A systems biology approach to identify affected regulatory and signaling circuits in protein interaction networks

    Gong, T., Xuan, J., Reggins, R. B. & Clarke, R., 2009, Proceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009. p. 297-300 4 p. 5260659. (Proceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Learning a highly resolved tree of phenotypes using genomic data clustering

    Feng, Y., Miller, D. J., Clarke, R., Hoffman, E. P. & Wang, Y., 2009, Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009. p. 355 1 p. 5332074. (Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2008

    Exploring transcriptional modules through integrative gene clustering guided by transcription factor binding information

    Gong, T., Xuan, J., Riggins, R. B., Wang, Y., Hoffman, E. P. & Clarke, R., 2008, Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008. p. 191-197 7 p. (Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Identification of condition-specific regulatory modules by multi-level motif and mRNA expression analysis

    Chen, L., Xuan, J., Riggins, R. B., Wang, Y., Hoffman, E. P. & Clarke, R., 2008, Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008. p. 23-28 6 p. (Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Inferring condition-specific miRNA-Gene modules from miRNA and mRNA profiling data

    Xiong, J., Wang, C., Zhang, B., Wang, Y., Hoffman, E. P., Clarke, R. & Xuan, J., 2008, International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2008, BCBGC 2008. p. 49-55 7 p. (International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2008, BCBGC 2008).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Integrative network component analysis for regulatory network reconstruction

    Wang, C., Xuan, J., Chen, L., Zhao, P., Wang, Y., Clarke, R. & Hoffman, E. P., 2008, Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings. p. 196-207 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4983 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Network-constrained support vector machine for classification

    Chen, L., Xuan, J., Wang, Y., Riggins, R. B. & Clarke, R., 2008, Proceedings - 7th International Conference on Machine Learning and Applications, ICMLA 2008. p. 60-65 6 p. 4724956. (Proceedings - 7th International Conference on Machine Learning and Applications, ICMLA 2008).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Network motif-based identification of breast cancer susceptibility genes

    Zhang, Y., Xuan, J., De Los Reyes, B. G., Clarke, R. & Ressom, H. W., 2008, Proceedings of the 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'08. IEEE Computer Society, p. 5696-5699 4 p. 4650507. (Proceedings of the 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'08 - "Personalized Healthcare through Technology").

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    28 Scopus citations
  • Reliability analysis of transcriptional regulatory networks

    Wang, C., Xuan, J., Chen, L., Hoffman, E. P. & Clarke, R., 2008, International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2008, BCBGC 2008. p. 42-48 7 p. (International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2008, BCBGC 2008).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Reverse engineering module networks by PSO-RNN hybrid modeling

    Zhang, Y., Xuan, J., De Los Reyes, B. G., Clarke, R. & Ressom, H. W., 2008, Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008. p. 401-407 7 p. (Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Sparse decomposition of gene expression data to infer transcriptional modules guided by motif information

    Gong, T., Xuan, J., Chen, L., Riggins, R. B., Wang, Y., Hoffman, E. P. & Clarke, R., 2008, Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings. p. 244-255 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4983 LNBI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2007

    Biomarker identification by knowledge-driven multi-level ICA and motif analysis

    Chen, L., Wang, C., Shih, I. M., Wang, T. L., Zhang, Z., Wang, Y., Clarke, R., Hoffman, E. & Xuan, J., 2007, Proceedings - 6th International Conference on Machine Learning and Applications, ICMLA 2007. p. 560-566 7 p. 4457289. (Proceedings - 6th International Conference on Machine Learning and Applications, ICMLA 2007).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Biomarker identification by knowledge-driven multi-scale independent component analysis

    Chen, L., Xuan, J., Clarke, R. & Wang, Y., 2007, 2007 IEEE/NIH Life Science Systems and Applications Workshop, LISA. IEEE Computer Society, p. 261-264 4 p. 4400934. (2007 IEEE/NIH Life Science Systems and Applications Workshop, LISA).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Integrating multi-source biological data for transcriptional regulatory module discovery

    Ressom, H. W., Zhang, Y., Xuan, J., Wang, Y. & Clarke, R., 2007, 2007 IEEE/NIH Life Science Systems and Applications Workshop, LISA. IEEE Computer Society, p. 184-187 4 p. 4400915. (2007 IEEE/NIH Life Science Systems and Applications Workshop, LISA).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2006

    Composite gene module discovery using non-negative independent component analysis

    Gong, T., Xuan, J., Zhu, Y., Li, H., Clarke, R., Hoffman, E. P. & Wang, Y., 2006, 2006 IEEE/NLM Life Science Systems and Applications Workshop, LiSA 2006. 4015835. (2006 IEEE/NLM Life Science Systems and Applications Workshop, LiSA 2006).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence

    Ressom, H. W., Zhang, Y., Xuan, J., Wang, Y. & Clarke, R., 2006, Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06. p. 435-442 8 p. 4133205. (Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    11 Scopus citations
  • Inferring network interactions using recurrent neural networks and swarm intelligence

    Ressom, H. W., Zhang, Y., Xuan, J., Wang, Y. & Clarke, R., 2006, 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06. p. 4241-4244 4 p. 4029512. (Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • Latent variable and nICA modeling of pathway gene module composite

    Gong, T., Zhu, Y., Xuan, J., Li, H., Clarke, R., Hoffman, E. P. & Wang, Y., 2006, 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06. p. 5872-5875 4 p. 4029667. (Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • Learning the tree of phenotypes using genomic data and VISDA

    Feng, Y., Wang, Z., Zhu, Y., Xuan, J., Miller, D. J., Clarke, R., Hoffman, E. P. & Wang, Y., 2006, Proceedings - Sixth IEEE Symposium on BioInformatics and BioEngineering, BIBE 2006. p. 165-170 6 p. 4019655. (Proceedings - Sixth IEEE Symposium on BioInformatics and BioEngineering, BIBE 2006).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    2 Scopus citations
  • ModVis: An information visualization tool for gene module discovery

    Molineaux, J., Xuan, J., Gong, T., Zhu, Y., Hoffman, E., Clarke, R. & Wang, Y., 2006, 19th International Conference on Computer Applications in Industry and Engineering, CAINE 2006. p. 24-31 8 p. (19th International Conference on Computer Applications in Industry and Engineering, CAINE 2006).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • 2005

    Normalization of microarray data by iterative nonlinear regression

    Xuan, J., Huffman, E., Clarke, R. & Wang, Y., 2005, Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering. p. 267-270 4 p. 1544478. (Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering; vol. 2005).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    4 Scopus citations
  • 2004

    Optimizing multilayer perceptrons by discriminatory component analysis

    Wang, Y., Wang, Z., Xuan, J., Zhang, J., Hoffman, E. P., Clarke, R. & Khan, J., 2004, Machine Learning for Signal Processing XIV - Proceedings of 2004 IEEE Signal Processing Society Workshop. Barros, A., Principe, J., Larsen, J., Adali, T. & Douglas, S. (eds.). p. 273-282 10 p. (Machine Learning for Signal Processing XIV - Proceedings of the 2004 IEEE Signal Processing Society Workshop).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Robust feature selection by weighted fisher criterion for multiclass prediction in gene expression profiling

    Xuan, J., Dong, Y., Khan, J., Hoffman, E., Clarke, R. & Wang, Y., 2004, Proceedings of the 17th International Conference on Pattern Recognition, ICPR 2004. Kittler, J., Petrou, M. & Nixon, M. (eds.). p. 291-294 4 p. (Proceedings - International Conference on Pattern Recognition; vol. 2).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    8 Scopus citations
  • 2003

    Partially-independent component analysis for tissue heterogeneity correction in microarray gene expression analysis

    Wang, Y., Zhang, J., Khan, J., Clarke, R. & Gu, Z., 2003, 2003 IEEE 13th Workshop on Neural Networks for Signal Processing, NNSP 2003. Institute of Electrical and Electronics Engineers Inc., p. 23-32 10 p. 1318001. (Neural Networks for Signal Processing - Proceedings of the IEEE Workshop; vol. 2003-January).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    6 Scopus citations
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