• Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs.
    Nat Biotechnol. 2009 Jun;27(6):549-55. [ Web | PDF ]
  • Nimrod G, Szilagyi A, Leslie C, Ben-Tal N. Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.
    J Mol Biol. 2009 Apr 10;387(4):1040-53. [ Web | PDF ]
  • Melvin I, Weston J, Leslie C, Noble WS. RANKPROP: a web server for protein remote homology detection.
    Bioinformatics. 2009 Jan 1;25(1):121-2. [ Web | PDF ]
  • Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C. A predictive model of the oxygen and heme regulatory network in yeast.
    PLoS Comput Biol. 2008 Nov;4(11):e1000224. [ Web | PDF ]
  • Melvin I, Weston J, Leslie CS, Noble WS. Combining classifiers for improved classification of proteins from sequence or structure.
    BMC Bioinformatics. 2008;9:389. [ Web | PDF ]
  • Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L, Leslie C. Learning regulatory programs that accurately predict differential expression with MEDUSA.
    Ann N Y Acad Sci. 2007 Dec;1115:178-202. [ Web | PDF ]
  • Melvin I, Ie E, Weston J, Noble WS, Leslie C. Multi-class protein classification using adaptive codes
    Journal of Machine Learning Research 2007;8:1557-1581 [ Web | PDF ]
  • Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C. SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.
    BMC Bioinformatics. 2007;8 Suppl 4:S2. [ Web | PDF ]
  • Weston J, Kuang R, Leslie C, Noble WS. Protein ranking by semi-supervised network propagation.
    BMC Bioinformatics. 2006;7 Suppl 1:S10. [ Web | PDF ]
  • Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C. A classification-based framework for predicting and analyzing gene regulatory response.
    BMC Bioinformatics. 2006;7 Suppl 1:S5. [ Web | PDF ]
  • Zhang XH, Leslie CS, Chasin LA. Computational searches for splicing signals.
    Methods. 2005 Dec;37(4):292-305. [ Web | PDF ]
  • Zhang XH, Leslie CS, Chasin LA. Dichotomous splicing signals in exon flanks.
    Genome Res. 2005 Jun;15(6):768-79. [ Web | PDF ]
  • Middendorf M, Kundaje A, Shah M, Freund Y, Wiggins CH, Leslie C. Motif Discovery Through Predictive Modeling of Gene Regulation
    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. [ Web | PDF ]
  • Weston J, Leslie C, Ie E, Zhou D, Elisseeff A, Noble WS. Semi-supervised protein classification using cluster kernels.
    Bioinformatics. 2005 Aug 1;21(15):3241-7. [ Web | PDF ]
  • Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C. Combining sequence and time series expression data to learn transcriptional modules.
    IEEE/ACM Trans Comput Biol Bioinform. 2005;2(3):194-202. [ Web | PDF ]
  • Ie E, Weston J, Noble WS, Leslie C. Multi-class protein fold recognition using adaptive codes
    Proceedings of the Twenty-Second International Conference (ICML 2005), Bonn, Germany, August 7-11, 2005. ACM 2005. pp. 329-336. [ Web | PDF ]
  • Noble WS, Kuang R, Leslie C, Weston J. Identifying remote protein homologs by network propagation.
    FEBS J. 2005 Oct;272(20):5119-28. [ Web | PDF ]
  • Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C. Profile-based string kernels for remote homology detection and motif extraction.
    J Bioinform Comput Biol. 2005 Jun;3(3):527-50. [ Web | PDF ]
  • Kuang R, Weston J, Noble WS, Leslie C. Motif-based protein ranking by network propagation.
    Bioinformatics. 2005 Oct 1;21(19):3711-8. [ Web | PDF ]
  • Zhang XH, Leslie CS, Chasin LA. Computational searches for splicing signals.
    Methods. 2005 Dec;37(4):292-305. [ Web | PDF ]
  • Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C. Predicting genetic regulatory response using classification.
    Bioinformatics. 2004 Aug 4;20 Suppl 1:i232-40. [ Web | PDF ]
  • Weston J, Leslie C, Zhou D, Elisseeff A, Noble WS. Semi-supervised Protein Classification Using Cluster Kernels
    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. [ Web | PDF ]
  • Leslie C, Kuang R. Fast String Kernels using Inexact Matching for Protein Sequences
    Journal of Machine Learning Research 2004;5(Nov):1435-1455 [ Web | PDF ]
  • Weston J, Elisseeff A, Zhou D, Leslie CS, Noble WS. Protein ranking: from local to global structure in the protein similarity network.
    Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6559-63. [ Web | PDF ]
  • Kuang R, Leslie CS, Yang AS. Protein backbone angle prediction with machine learning approaches.
    Bioinformatics. 2004 Jul 10;20(10):1612-21. [ Web | PDF ]
  • Leslie CS, Eskin E, Cohen A, Weston J, Noble WS. Mismatch string kernels for discriminative protein classification.
    Bioinformatics. 2004 Mar 1;20(4):467-76. [ Web | PDF ]
  • Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C. Profile-based string kernels for remote homology detection and motif extraction.
    Proc IEEE Comput Syst Bioinform Conf. 2004;152-60. [ Web | PDF ]
  • Leslie C, Eskin E, Weston J, Noble WS . Mismatch String Kernels for SVM Protein Classification
    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. [ Web | PDF ]
  • Leslie C, Kuang R. Fast Kernels for Inexact String Matching
    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 [ Web | PDF ]
  • Zhang XH, Heller KA, Hefter I, Leslie CS, Chasin LA. Sequence information for the splicing of human pre-mRNA identified by support vector machine classification.
    Genome Res. 2003 Dec;13(12):2637-50. [ Web | PDF ]
  • Leslie C, Eskin E, Noble WS. The spectrum kernel: a string kernel for SVM protein classification.
    Pac Symp Biocomput. 2002;564-75. [ Web | PDF ]