@article{morgulis06,
  title={A fast and symmetric {DUST} implementation to mask low-complexity DNA sequences},
  year={2006},
  author={A. Morgulis and E.M. Gertz and A.A. Schaffer and R. Agarwala},
  journal={Journal of Computational Biology},
  volume={13},
  pages={1028--1040},
}

@article{orlov04,
  title={Complexity: an internet resource for analysis of {DNA} sequence complexity},
  year={2004},
  author={Y.L. Orlov and V.N. Potapov},
  journal={Nucleic Acids Research},
  volume={32},
  pages={W628--W633},
}

@incollection{trifonov90,
  title={Making sense of the human genome},
  author={E.N. Trifonov},
  year={1990},
  editor={R.H. Sarma},
  booktitle={Structure \& Methods},
  publisher={Adenine Press},
  address={Albany},
  pages={69--77},
}

@article{wootton93,
  title={Statistics of local complexity in amino acid sequences and sequence databases},
  year={1993},
  author={J.C. Wootton and S. Federhen},
  journal={Computers \& Chemistry},
  volume={17},
  pages={149--163},
}

@article{biophys03,
  title={A Biophysical Approach to Transcription Factor Binding Site Discovery},
  year={2003},
  author={M. Djordjevic and A.M. Sengupta and B.I. Shraiman},
  journal={Genome Research},
  volume={13},
  number={11},
  pages={2381--2390},
}

@article{ruan17,
  title={Inherent limitations of probabilistic models for protein-DNA binding specificity},
  year={2017},
  author={S. Ruan and G.D. Stormo},
  journal={PLoS Computational Biology},
  volume={13},
  number={7},
  pages={e1005638},
}

@article{mahony,
  title={DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies},
  year={2007},
  author={S. Mahony and P.E. Auron and P.V. Benos},
  journal={PLoS Computational Biology},
  volume={3},
  number={3},
  pages={e61},
}

@article{bhatt,
  title={On a measure of divergence between two statistical populations defined by their probability distributions},
  year={1943},
  author={A. Bhattacharyya},
  journal={Bulletin of the Calcutta Mathematical Society},
  volume={35},
  pages={99--109},
}

@Article{wasserman,
  title = {Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics},
  author = {A. Sandelin and W.W. Wasserman},
  year = {2004},
  journal = {Journal of Molecular Biology},
  volume = {338},
  number = {2},
  pages = {207--215},
}

@article{hellinger,
  title={Neue Begr\"undung der Theorie quadratischer Formen von unendlichvielen Ver\"anderlichen},
  author={Ernst Hellinger},
  year={1909},
  journal={Journal f\"ur die reine und angewandte Mathematik},
  volume={136},
  pages={210--271},
}

@article{roepcke,
  title={T-Reg Comparator: an analysis tool for the comparison of position weight matrices},
  year={2005},
  author={S. Roepcke and S. Grossmann and S. Rahmann and M. Vingron},
  journal={Nucleic Acids Research},
  volume={33},
  number={suppl_2},
  pages={W438--W441},
}

@article{wang,
  title={Combining phylogenetic data with co-regulated genes to identify motifs},
  year={2003},
  author={T. Wang and G.D. Stormo},
  journal={Bioinformatics},
  volume={19},
  number={18},
  pages={2369--2380},
}

@article{pietrokovski,
  year={1996},
  author={S. Pietrokovski},
  title={Searching databases of conserved sequence regions by aligning protein multiple-alignments},
  journal={Nucleic Acids Research},
  volume={24},
  number={19},
  pages={3836--3845},
}

@inproceedings{ISdist,
  title={Analysis synthesis telephony based on the maximum likelihood method},
  year={1968},
  author={F. Itakura and S. Saito},
  address={Los Alamitos, CA},
  pages={C-17--C-20},
  booktitle={6th International Congress on Acoustics},
  publisher={IEEE},
}

@article{markovmodel,
  title = {Random sequences},
  author = {Walter M. Fitch},
  year = {1983},
  journal = {Journal of Molecular Biology},
  volume = {163},
  issue = {2},
  pages = {171-176},
}

@article{markovmodel2,
  title = {Significance of Nucleotide Sequence Alignments: A Method for Random Sequence Permutation That Preserves Dinucleotide and Codon Usage},
  author = {Stephen F. Altschul and Bruce W. Erickson},
  year = {1985},
  journal = {Molecular Biology and Evolution},
  volume = {2},
  issue = {6},
  pages= {526-538},
}

@Article{eulerAlgo,
  author={J.G. Propp and D.W. Wilson},
  title={How to get a perfectly random sample from a generic markov chain and generate a random spanning tree of a directed graph},
  journal={Journal of Algorithms},
  volume={27},
  pages={170--217},
  year={1998},
}

@article{meme3,
  title={Fitting a mixture model by expectation maximization to discover motifs in biopolymers},
  author={T.L. Bailey and C. Elkan},
  journal={Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology},
  volume={2},
  year={1994},
  pages={28--36},
}

@article{ushuffle,
  title={{uS}huffle: A useful tool for shuffling biological sequences while preserving k-let counts},
  author={M. Jiang and J. Anderson and J. Gillespie and M. Mayne},
  year={2008},
  journal={BMC Bioinformatics},
  volume={9},
  issue={192},
}

@article{pwm,
  title = {Use of the Perceptron algorithm to distinguish translational initiation sites in E. {c}oli},
  author = {Gary D. Stormo and Thomas D. Schneider and Larry Gold and Andrzej Ehrenfeucht},
  year = {1982},
  journal = {Nucleic Acids Research},
  volume = {10},
  issue = {9},
  pages = {2997-3011},
}

@article{motifhist,
  author={G. D. Stormo},
  title={DNA binding sites: representation and discovery},
  journal={Bioinformatics},
  volume={16},
  number={1},
  year={2000},
  pages={16--23}
}

@article{pval,
  author = {H. Touzet and J.-S. Varre},
  title = {Efficient and accurate P-value computation for Position Weight Matrices},
  journal = {Algorithms for Molecular Biology},
  volume = {2},
  pages = {15},
  year = {2007}
}

@article{correction,
  title = {Information content of binding sites on nucleotide sequences},
  author = {Thomas D. Schneider and Gary D. Stormo and Larry Gold and Andrzej Ehrenfeucht},
  year = {1986},
  journal = {Journal of Molecular Biology},
  volume = {188},
  issue = {3},
  pages = {415-431},
}

@article{icm,
  title = {Sequence Logos: A New Way to Display Consensus Sequences},
  author = {T. D. Schneider and R. M. Stephens},
  year = {1990},
  journal = {Nucleic Acids Research},
  volume = {18},
  issue = {20},
  pages = {6097-6100},
}

@article{shannon,
  title = {A Mathematical Theory of Communication},
  author = {Claude E. Shannon},
  year = {1948},
  journal = {Bell System Technical Journal},
  volume = {27},
  issue = {3},
  pages = {379-423},
}

@article{bits,
  title = {Theory of Molecular Machines. II. Energy Dissipation from Molecular Machines},
  author = {T. D. Schneider},
  year = {1991},
  journal = {Journal of Theoretical Biology},
  volume = {148},
  issue = {1},
  pages = {125-137},
}

@article{kl,
  title = {On information and sufficiency},
  author = {S. Kullback and R. A. Leibler},
  year = {1951},
  journal = {The Annals of Mathematical Statistics},
  volume = {22},
  pages = {79-86},
}

@Article{cisbp,
  title = {Determination and inference of eukaryotic transcription factor sequence specificity.},
  author = {M.T. Weirauch and A. Yang and M. Albu and A.G. Cote and A. Montenegro-Montero and P. Drewe and H.S. Najafabadi and S.A. Lambert and I. Mann and K. Cook and H. Zheng and A. Goity and H. van Bakel and J.C. Lozano and M. Galli and M.G. Lewsey and E. Huang and T. Mukherjee and X. Chen and J.S. Reece-Hoyes and S. Govindarajan and G. Shaulsky and A.J. Walhout and F.Y. Bouget and G. Ratsch and L.F. Larrondo and J.R. Ecker and T.R. Hughes},
  journal = {Cell},
  volume = {158},
  issue = {6},
  pages = {1431-1443},
  year = {2014},
}

@Article{homer,
  title = {Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.},
  author = {S. Heinz and C. Benner and N. Spann and E. Bertolino and Y.C. Lin and P. Laslo and J.X. Cheng and C. Murre and H. Singh and C.K. Glass},
  journal = {Molecular Cell},
  volume = {38},
  issue = {4},
  pages = {576-589},
  year = {2010},
}

@article{meme,
  title = {MEME SUITE: tools for motif discovery and searching},
  author = {T.L. Bailey and M. Boden and F.A. Buske and M. Frith and C.E. Grant and L. Clementi and J. Ren and W.W. Li and W.S. Noble},
  journal = {Nucleic Acids Research},
  volume = {37},
  pages = {W202-W208},
  year = {2009},
}

@article{transfac,
  title = {TRANSFAC: A Database on Transcription Factors and Their DNA Binding Sites},
  author = {E. Wingender and P. Dietze and H. Karas and R. Knuppel},
  journal = {Nucleic Acids Research},
  volume = {24},
  issue = {1},
  pages = {238-241},
  year = {1996},
}

@article{uniprobe,
  title = {UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.},
  author = {M.A. Hume and L.A. Barrera and S.S. Gisselbrecht and M.L. Bulyk},
  journal = {Nucleic Acids Research},
  volume = {43},
  pages = {D117-D122},
  year = {2015},
}

@article{jaspar,
  title = {JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.},
  author = {A. Khan and O. Fornes and A. Stigliani and M. Gheorghe and J.A. Castro-Mondragon and R. van der Lee and A. Bessy and J. Cheneby and S. R. Kulkarni and G. Tan and D. Baranasic and D.J. Arenillas and A. Sandelin and K. Vandepoele and B. Lenhard and B. Ballester and W.W. Wasserman and F. Parcy and A. Mathelier},
  journal = {Nucleic Acids Research},
  volume = {46},
  issue = {D1},
  year = {2018},
  pages = {D260-D266},
}

@article{tffm,
  title = {The Next Generation of Transcription Factor Binding Site Prediction},
  author = {A. Mathelier and W.W. Wasserman},
  journal = {PLoS Computational Biology},
  volume = {9},
  issue = {9},
  year = {2013},
  pages = {e1003214}
}

@article{bamm,
  title = {Bayesian Markov models consistently outperform {PWM}s at predicting motifs in nucleotide sequences},
  author = {M. Siebert and J. Soding},
  journal = {Nucleic Acids Research},
  volume = {44},
  issue = {13},
  year = {2016},
  pages = {6055--6069}
}

@article{ksm,
  title = {A novel k-mer set memory ({KSM}) motif representation improves regulatory variant prediction},
  author = {Y. Guo and K. Tian and H. Zeng and X. Guo and D.K. Gifford},
  journal = {Genome Research},
  volume = {28},
  year = {2018},
  pages = {891--900}
}

@article{pvalues,
  title = {The {XX}motif web server for e{X}haustive, weight matri{X}-based motif discovery in nucleotide sequences.},
  author = {S. Luehr and H. Hartmann and J. S\"oding},
  year = {2012},
  journal = {Nucleic Acids Research},
  volume = {40},
  pages = {W104--W109},
}

@article{noble09,
  title={How does multiple testing correction work?},
  author = {William S. Noble},
  year={2009},
  journal={Nature Biotechnology},
  volume={27},
  issue={12},
  pages={1135--1137},
}

@article{grant11,
  title={FIMO: scanning for occurrences of a given motif},
  author={C.E. Grant and T.L. Bailey and W.S. Noble},
  year={2011},
  journal={Bioinformatics},
  volume={27},
  pages={1017--1018},
}

@article{gupta07,
  title={Quantifying similarity between motifs},
  author={S. Gupta and J.A. Stamatoyannopoulos and T.L. Bailey and W.S. Noble},
  year={2007},
  journal={Genome Biology},
  volume={8},
  pages={R24},
}
