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@article{Chang2011,
	Author = {Chang, Chih-Chung and Lin, Chih-Jen},
	Date-Added = {2014-12-18 15:12:12 +0000},
	Date-Modified = {2014-12-18 15:12:12 +0000},
	Issue = {3},
	Journal = {ACM Transactions on Intelligent Systems and Technology},
	Note = {Software available at \url{http://www.csie.ntu.edu.tw/~cjlin/libsvm}},
	Pages = {27:1--27:27},
	Title = {{LIBSVM}: A library for support vector machines},
	Volume = {2},
	Year = {2011}}

@article{Fan2008,
	Author = {Rong-En Fan and Kai-Wei Chang and Cho-Jui Hsieh and Xiang-Rui Wang and Chih-Jen Lin},
	Date-Added = {2014-12-18 15:12:12 +0000},
	Date-Modified = {2014-12-18 15:12:12 +0000},
	Journal = {Journal of Machine Learning Research},
	Pages = {1871--1874},
	Title = {{LIBLINEAR}: A Library for Large Linear Classification},
	Volume = {9},
	Year = {2008}}

@manual{Pages2014,
	Author = {H. Pages and P. Aboyoun and R. Gentleman and S. DebRoy},
	Date-Added = {2014-12-18 14:57:08 +0000},
	Date-Modified = {2014-12-18 14:57:34 +0000},
	Note = {R package version 2.34.0},
	Title = {Biostrings: String objects representing biological sequences, and matching algorithms}}

@article{Karatzoglou2004,
	Author = {Alexandros Karatzoglou and Alex Smola and Kurt Hornik and Achim Zeileis},
	Date-Added = {2014-12-18 14:55:52 +0000},
	Date-Modified = {2014-12-18 14:55:52 +0000},
	Journal = {Journal of Statistical Software},
	Number = {9},
	Pages = {1--20},
	Title = {kernlab -- An {S4} Package for Kernel Methods in {R}},
	Url = {http://www.jstatsoft.org/v11/i09/},
	Volume = {11},
	Year = {2004},
	Bdsk-Url-1 = {http://www.jstatsoft.org/v11/i09/}}

@article{Gorodkin2004,
	Author = {Jan Gorodkin},
	Date-Added = {2014-12-03 21:41:05 +0000},
	Date-Modified = {2014-12-03 21:41:05 +0000},
	Journal = {Computational Biology and Chemistry},
	Number = {5-6},
	Pages = {367--374},
	Title = {Comparing two K-category assignments by a K-category correlation coefficient},
	Volume = {28},
	Year = {2004}}

@article{Suykens1999,
	Author = {Johan A. K. Suykens and Joos Vandewalle},
	Date-Added = {2014-09-24 12:36:40 +0200},
	Date-Modified = {2014-09-24 12:40:14 +0200},
	Journal = {Neural Processing Letters},
	Number = {3},
	Pages = {293--300},
	Title = {Least Squares Support Vector Machine Classifiers},
	Volume = {9},
	Year = {1999}}

@article{Tipping2001,
	Author = {Micheal E. Tipping},
	Date-Added = {2014-09-24 12:32:40 +0200},
	Date-Modified = {2014-09-24 12:34:35 +0200},
	Journal = {Journal of Machine Learning Research},
	Number = {211--244},
	Title = {Sparse Bayesian Learning and the {Relevance Vector Machine}},
	Volume = {1},
	Year = {2001}}

@article{Ben-Hur2003,
	Author = {Asa Ben-Hur and Douglas L. Brutlag},
	Date-Added = {2014-08-21 10:43:23 +0200},
	Date-Modified = {2014-08-21 10:47:03 +0200},
	Journal = {Bioinformatics},
	Pages = {26-33},
	Title = {Remote homology detection: a motif based approach},
	Volume = {19},
	Year = {2003}}

@inproceedings{Bodenhofer2009,
	Address = {Lisbon},
	Author = {Ulrich Bodenhofer and Karin Schwarzbauer and Mihaela Ionescu and Sepp Hochreiter},
	Booktitle = {Proc. Joint 13th IFSA World Congress and 6th EUSFLAT Conference},
	Date-Added = {2014-08-24 12:53:37 +0200},
	Date-Modified = {2014-08-24 12:56:43 +0200},
	Editor = {J. P. Carvalho and D. Dubois and U. Kaymak and J. M. C. Sousa},
	Month = {July},
	Pages = {1376-1381},
	Title = {Modelling Position Specificity in Sequence Kernels by Fuzzy Equivalence Relations},
	Year = {2009}}

@article{Bodenhofer2011a,
	Author = {Ulrich Bodenhofer and Andreas Kothmeier and Sepp Hochreiter},
	Date-Modified = {2014-09-03 10:05:03 +0200},
	Doi = {10.1093/bioinformatics/btr406},
	Journal = {Bioinformatics},
	Pages = {2463--2464},
	Title = {{APCluster: an R package for affinity propagation clustering}},
	Volume = {27},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1093/bioinformatics/btr406}}

@electronic{Bodenhofer2011b,
	Author = {Ulrich Bodenhofer},
	Date-Added = {2014-09-03 09:58:18 +0200},
	Date-Modified = {2014-09-03 10:16:38 +0200},
	Title = {PrOCoil --- A Web Service and an R Package for Predicting the Oligomerization of Coiled Coil Proteins},
	Urldate = {2014-09-03},
	Bdsk-Url-1 = {http://www.bioconductor.org/packages/release/bioc/html/procoil.html}}

@article{Frey2007,
	Author = {Brendan J. Frey and Delbert Dueck},
	Doi = {10.1126/science.1136800},
	Journal = {Science},
	Pages = {972--977},
	Title = {Clustering by passing messages between data points},
	Volume = {315},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1136800}}

@article{Hochreiter2006,
	Abstract = {We describe a new technique for the analysis of
                  dyadic data, where two sets of objects (row and
                  column objects) are characterized by a matrix of
                  numerical values that describe their mutual
                  relationships.  The new technique, called potential
                  support vector machine (P-SVM), is a large-margin
                  method for the construction of classifiers and
                  regression functions for the column
                  objects. Contrary to standard support vector machine
                  approaches, the P-SVM minimizes a scale-invariant
                  capacity measure and requires a new set of
                  constraints. As a result, the P-SVM method leads to
                  a usually sparse expansion of the classification and
                  regression functions in terms of the row rather than
                  the column objects and can handle data and kernel
                  matrices that are neither positive definite nor
                  square. We then describe two complementary
                  regularization schemes. The first scheme improves
                  generalization performance for classification and
                  regression tasks; the second scheme leads to the
                  selection of a small, informative set of row support
                  objects and can be applied to feature
                  selection. Benchmarks for classification,
                  regression, and feature selection tasks are
                  performed with toy data as well as with several
                  real-world data sets. The results show that the new
                  method is at least competitive with but often
                  performs better than the benchmarked standard
                  methods for standard vectorial as well as true
                  dyadic data sets. In addition, a theoretical
                  justification is provided for the new approach.},
	Author = {Sepp Hochreiter and Klaus Obermayer},
	Date-Modified = {2014-09-02 08:08:45 +0200},
	Doi = {10.1162/neco.2006.18.6.1472},
	Institution = {Department of Electrical Engineering and Computer Science, Technische Universit{\"a}t, Berlin, Germany. hochreit@cs.tu-berlin.de},
	Journal = {Neural Comput},
	Language = {eng},
	Medline-Pst = {ppublish},
	Month = {Jun},
	Number = {6},
	Pages = {1472--1510},
	Pmid = {16764511},
	Timestamp = {2011.04.29},
	Title = {Support vector machines for dyadic data.},
	Url = {http://dx.doi.org/10.1162/neco.2006.18.6.1472},
	Volume = {18},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1162/neco.2006.18.6.1472}}

@inproceedings{Kuksa2008,
	Address = {Las Vegas, NV},
	Author = {Pavel Kuksa and Pai-Hsi Huang and Vladimir Pavlovic},
	Booktitle = {8th Int. Workshop on Data Mining in Bioinformatics},
	Date-Added = {2014-09-20 19:31:34 +0200},
	Date-Modified = {2014-09-20 19:34:33 +0200},
	Pages = {29--37},
	Title = {A fast, large-scale learning method for protein sequence classification},
	Year = {2008}}

@inproceedings{KuksaHuangPavlovic2008,
	Author = {Pavel Kuksa and Pai-Hsi Huang and Vladimir Pavlovic},
	Booktitle = {Computational SystemBioinformatics: Proceedings of the CSB2008 Conference},
	Date-Added = {2014-09-20 19:31:34 +0200},
	Date-Modified = {2014-09-20 19:34:33 +0200},
	Pages = {133-143},
	Title = {Fast and accurate multi-class protein fold recognition with spatial sample kernels},
	Year = {2008}}

@article{Lee2011,
	Author = {Dongwon Lee and Rachel Karchin and Michael A. Beer.},
	Date-Added = {2014-09-02 07:37:26 +0200},
	Date-Modified = {2014-09-19 17:50:30 +0200},
	Journal = {Genome Research},
	Month = {December},
	Number = {12},
	Pages = {2167-2180},
	Title = {{Discriminative prediction of mammalian enhancers from DNA sequence.}},
	Volume = {21},
	Year = {2011}}

@article{Leslie2003,
	Author = {Christina S. Leslie and Eleazar Eskin and Adiel Cohen and Jason Weston and William Stafford Noble},
	Date-Added = {2014-08-21 10:41:02 +0200},
	Date-Modified = {2014-09-24 13:05:07 +0200},
	Journal = {Bioinformatics},
	Number = {1},
	Pages = {1--10},
	Title = {Mismatch string kernels for discriminative protein classification},
	Volume = {1},
	Year = {2003}}

@inproceedings{Leslie2002,
	Author = {Christina S. Leslie and Eleazar Eskin and William Stafford Noble},
	Booktitle = {Pacific Symposium on Biocomputing},
	Date-Added = {2014-08-21 10:31:10 +0200},
	Date-Modified = {2014-09-24 13:05:15 +0200},
	Editor = {R. B. Altman and A. K. Dunker and L. Hunter and K. Lauderdale and T. E. D. Klein},
	Journal = {Pacific Symposium on Biocomputing 2002},
	Pages = {566-575},
	Publisher = {World Scientific},
	Title = {The Spectrum Kernel: A String Kernel for {SVM} Protein Classification},
	Year = {2002}}

@article{Mahrenholz2011,
	Author = {Carsten C. Mahrenholz and Ingrid G. Abfalter and Ulrich Bodenhofer and Rudolf Volkmer and Sepp Hochreiter},
	Date-Added = {2014-08-21 10:58:32 +0200},
	Date-Modified = {2014-09-19 18:28:41 +0200},
	Journal = {Mol Cell Proteomics},
	Number = {5},
	Pages = {M110.004994},
	Title = {Complex networks govern coiled-coil oligomerizations - predicting and profiling by means of a machine learning approach.},
	Volume = {10},
	Year = {2011}}

@article{Raetsch2005,
	Author = {Gunnar R\"{a}tsch and S\"{o}ren Sonnenburg and Bernhard Sch\"{o}lkopf},
	Date-Added = {2014-08-21 11:26:24 +0200},
	Date-Modified = {2014-09-19 18:37:10 +0200},
	Journal = {Bioinformatics},
	Number = {suppl1},
	Pages = {i369-i377},
	Title = {{RASE}: Recognition of alternatively spliced exons in {C. elegans}},
	Volume = {21},
	Year = {2005}}

@inbook{Raetsch2004,
	Address = {Cambridge, MA},
	Author = {Gunnar R\"{a}tsch and S\"{o}ren Sonnenburg},
	Chapter = {Accurate Splice Site Prediction for Caenorhabditis elegans},
	Date-Added = {2014-08-21 11:09:31 +0200},
	Date-Modified = {2014-08-21 11:34:56 +0200},
	Pages = {277-298},
	Publisher = {MIT},
	Title = {Kernel Methods in Computational Biology},
	Year = {2004}}

@article{Visel2009,
	Abstract = {{A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover because they are scattered among the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases demonstrated reproducible enhancer activity in the tissues that were predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities, and suggest that such data sets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.}},
	Author = {Visel, Axel and Blow, Matthew J. and Li, Zirong and Zhang, Tao and Akiyama, Jennifer A. and Holt, Amy and Plajzer-Frick, Ingrid and Shoukry, Malak and Wright, Crystal and Chen, Feng and Afzal, Veena and Ren, Bing and Rubin, Edward M. and Pennacchio, Len A.},
	Date-Added = {2014-09-02 08:03:32 +0200},
	Date-Modified = {2014-09-02 08:07:56 +0200},
	Day = {12},
	Doi = {10.1038/nature07730},
	Issn = {1476-4687},
	Journal = {Nature},
	Linkout_Ncbi = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745234/},
	Linkout_Pubmed = {http://view.ncbi.nlm.nih.gov/pubmed/19212405},
	Month = feb,
	Number = {7231},
	Pages = {854--858},
	Pmcid = {PMC2745234},
	Pmid = {19212405},
	Posted-At = {2010-10-29 08:00:56},
	Priority = {2},
	Publisher = {Nature Publishing Group},
	Title = {{ChIP-seq accurately predicts tissue-specific activity of enhancers.}},
	Url = {http://dx.doi.org/10.1038/nature07730},
	Volume = {457},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature07730}}

@misc{klib2011,
	Author = {{AttractiveChaos}},
	Date-Added = {2014-09-19 19:36:06 +0200},
	Date-Modified = {2014-09-21 14:03:20 +0200},
	Howpublished = {\url{https://github.com/attractivechaos/klib}},
	Title = {klib -- A standalone and lightweight C library},
	Year = {2011},
	Bdsk-Url-1 = {https://github.com/attractivechaos/klib}}

@misc{procoil2011,
	Author = {Ulrich Bodenhofer},
	Date-Added = {2014-09-19 19:28:31 +0200},
	Date-Modified = {2014-09-21 14:00:40 +0200},
	Howpublished = {\url{http://www.bioconductor.org/packages/release/html/procoil.html}},
	Title = {PrOCoil --- A Web Service and an R Package for Predicting the Oligomerization of Coiled Coil Proteins},
	Year = {2011},
	Bdsk-Url-1 = {http://www.bioconductor.org/packages/release/html/procoil.html}}
