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Publications
RANKPROP: a web server for protein remote homology detection. (2009)
Bioinformatics. 2009 Jan 1;25(1):121-2.
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Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. (2009)
J Mol Biol. 2009 Apr 10;387(4):1040-53.
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Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. (2009)
Nat Biotechnol. 2009 Jun;27(6):549-55.
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Combining classifiers for improved classification of proteins from sequence or structure. (2008)
BMC Bioinformatics. 2008;9:389.
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A predictive model of the oxygen and heme regulatory network in yeast. (2008)
PLoS Comput Biol. 2008 Nov;4(11):e1000224.
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SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. (2007)
BMC Bioinformatics. 2007;8 Suppl 4:S2.
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Multi-class protein classification using adaptive codes (2007)
Journal of Machine Learning Research 2007;8:1557-1581
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Learning regulatory programs that accurately predict differential expression with MEDUSA. (2007)
Ann N Y Acad Sci. 2007 Dec;1115:178-202.
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A classification-based framework for predicting and analyzing gene regulatory response. (2006)
BMC Bioinformatics. 2006;7 Suppl 1:S5.
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Protein ranking by semi-supervised network propagation. (2006)
BMC Bioinformatics. 2006;7 Suppl 1:S10.
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Motif-based protein ranking by network propagation. (2005)
Bioinformatics. 2005 Oct 1;21(19):3711-8.
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Profile-based string kernels for remote homology detection and motif extraction. (2005)
J Bioinform Comput Biol. 2005 Jun;3(3):527-50.
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Identifying remote protein homologs by network propagation. (2005)
FEBS J. 2005 Oct;272(20):5119-28.
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Multi-class protein fold recognition using adaptive codes (2005)
Proceedings of the Twenty-Second International Conference (ICML 2005), Bonn, Germany, August 7-11, 2005. ACM 2005. pp. 329-336.
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Combining sequence and time series expression data to learn transcriptional modules. (2005)
IEEE/ACM Trans Comput Biol Bioinform. 2005;2(3):194-202.
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Semi-supervised protein classification using cluster kernels. (2005)
Bioinformatics. 2005 Aug 1;21(15):3241-7.
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Motif Discovery Through Predictive Modeling of Gene Regulation (2005)
Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), Cambridge, MA, USA, May 14-18, 2005. Lecture Notes in Computer Science 3500 Springer 2005. pp. 538-552.
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Dichotomous splicing signals in exon flanks. (2005)
Genome Res. 2005 Jun;15(6):768-79.
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Profile-based string kernels for remote homology detection and motif extraction. (2004)
Proc IEEE Comput Syst Bioinform Conf. 2004;152-60.
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Mismatch string kernels for discriminative protein classification. (2004)
Bioinformatics. 2004 Mar 1;20(4):467-76.
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Protein backbone angle prediction with machine learning approaches. (2004)
Bioinformatics. 2004 Jul 10;20(10):1612-21.
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Protein ranking: from local to global structure in the protein similarity network. (2004)
Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6559-63.
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Fast String Kernels using Inexact Matching for Protein Sequences (2004)
Journal of Machine Learning Research 2004;5(Nov):1435-1455
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Semi-supervised Protein Classification Using Cluster Kernels (2004)
Advances in Neural Information Processing Systems 16. Proceedings of Neural Information Processing Systems (NIPS 2003), December 8-13, 2003, Vancouver and Whistler, British Columbia, Canada. MIT Press 2004.
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Predicting genetic regulatory response using classification. (2004)
Bioinformatics. 2004 Aug 4;20 Suppl 1:i232-40.
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Sequence information for the splicing of human pre-mRNA identified by support vector machine classification. (2003)
Genome Res. 2003 Dec;13(12):2637-50.
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Fast Kernels for Inexact String Matching (2003)
Proceedings of the 16th Annual Conference on Computational Learning Theory and 7th Kernel Workshop (COLT/Kernel 2003), Washington, DC, USA, August 24-27, 2003. Lecture Notes in Computer Science 2777 Springer 2003. pp. 114-128
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Mismatch String Kernels for SVM Protein Classification (2003)
Advances in Neural Information Processing Systems 15. Proceedings of Neural Information Processing Systems (NIPS 2002), December 9-14, 2002, Vancouver, British Columbia, Canada. MIT Press 2003.
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The spectrum kernel: a string kernel for SVM protein classification. (2002)
Pac Symp Biocomput. 2002;564-75.
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