
@misc{chollet2015,
author = {François Chollet },
title = {keras},
year = {2015},
publisher = {GitHub},
journal = {GitHub repository},
howpublished = {\url{https://github.com/fchollet/keras}},
commit = {5bcac37}
}

@ARTICLE{koon,
  author = {Koonin, E V and Altschul, S F and P Bork},
  title = {{BRCA1 protein products: functional motifs}},
  journal = {Nat Genet},
  year = {1996},
  volume = {13},
  pages = {266-267},
}


@ARTICLE{oreg,
  author = {Orengo, C A and Bray, J E and Hubbard T and LoConte, L and Sillitoe, I},
  title = {{Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction}},
  journal = {Proteins},
  year = {1999},
  volume = {Suppl 3},
  pages = {149-170},
}


@inpress{khar,
  author = {Kharitonov, S A and Barnes, P J},
  title = {{Clinical aspects of exhaled nitric oxide}},
  journal = {Eur Respir J},
  note = {in press},
  year = {2014},
}


@ARTICLE{zvai,
  author = {Zvaifler, N J and Burger, J A and Marinova-Mutafchieva L and Taylor, P and Maini, R N},
  title = {{Mesenchymal cells, stromal derived factor-1 and rheumatoid arthritis [abstract]}},
  journal = {Arthritis Rheum},
  year = {1999},
  volume = {42},
  pages = {s250},
}


@Inproceedings{xjon,
  author = {X Jones},
  title = {{Zeolites and synthetic mechanisms}},
  booktitle = {Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore},
  year = {1996},
  editor = {Y Smith},
  pages = {16-27},
  organization = {Stoneham: Butterworth-Heinemann},
}


@incollection{schn,
  author = {E Schnepf},
  title = {{From prey via endosymbiont to plastids: comparative studies in dinoflagellates}},
  booktitle = {Origins of Plastids},
  editor = {R A Lewin},
  publisher = {Chapman and Hall},
  pages = {53-76},
  year = {1993},
  address = {New York},
  volume = {2},
  edition = {2nd},
}


@wholejournal{pond,
  author = {B Ponder and S Johnston and L Chodosh},
  title = {{Innovative oncology}},
  journal = {Breast Cancer Res},
  year = {1998},
  volume = {10},
  pages = {1-72},
}


@proceedings{smith,
  author = {Y Smith},
  title = {{Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore}},
  year = {1996},
  address = {Stoneham},
  publisher = {Butterworth-Heinemann},
}


@book{marg,
  author = {L Margulis},
  title = {{Origin of Eukaryotic Cells}},
  publisher = {Yale University Press},
  year = {1970},
  address = {New Haven},
}


@incollection{hunn,
  author = {G W Hunninghake and J E Gadek},
  title = {{The alveloar macrophage}},
  booktitle = {Cultured Human Cells and Tissues},
  publisher = {Academic Press},
  year = {1995},
  pages = {54-56},
  editor = {T J R Harris},
  address = {New York},
  note = {Stoner G (Series Editor): Methods and Perspectives in Cell Biology, vol 1},
}


@manual{advi,
  title = {{Annual Report}},
  organization = {Advisory Committee on Genetic Modification},
  address = {London},
  year = {1999},
  author = {Multiple authors},
}


@phdthesis{koha,
  author = {R Kohavi},
  title = {{Wrappers for performance enhancement and obvious decision graphs}},
  school = {Stanford University, Computer Science Department},
  year = {1995},
}


@webpage{mouse,
  author = {J Smith},
  year = {2014},
  title = {{The Mouse Tumor Biology Database}},
  url = {http://tumor.informatics.jax.org/cancer\_links.html},
}


@article{Salimi_2012,
  doi = {10.1111/j.1365-2567.2012.03611.x},
  url = {http://dx.doi.org/10.1111/j.1365-2567.2012.03611.x},
  year = {2012},
  month = {September},
  publisher = {Wiley-Blackwell},
  volume = {137},
  number = {2},
  pages = {117--123},
  author = {Nima Salimi and Ward Fleri and Bjoern Peters and Alessandro Sette},
  title = {{The immune epitope database: a historical retrospective of the first decade}},
  journal = {Immunology},
}


@article{Kim_2014,
  doi = {10.1186/1471-2105-15-241},
  url = {http://dx.doi.org/10.1186/1471-2105-15-241},
  year = {2014},
  publisher = {Springer Science $\mathplus$ Business Media},
  volume = {15},
  number = {1},
  pages = {241},
  author = {Yohan Kim and John Sidney and S{\o}ren Buus and Alessandro Sette and Morten Nielsen and Bjoern Peters},
  title = {{Dataset size and composition impact the reliability of performance benchmarks for peptide-{MHC} binding predictions}},
  journal = {{BMC} Bioinformatics},
}


@article{Troyanskaya_2001,
  doi = {10.1093/bioinformatics/17.6.520},
  url = {http://dx.doi.org/10.1093/bioinformatics/17.6.520},
  year = {2001},
  month = {June},
  publisher = {Oxford University Press ({OUP})},
  volume = {17},
  number = {6},
  pages = {520--525},
  author = {O. Troyanskaya and M. Cantor and G. Sherlock and P. Brown and T. Hastie and R. Tibshirani and D. Botstein and R. B. Altman},
  title = {{Missing value estimation methods for {DNA} microarrays}},
  journal = {Bioinformatics},
}


@article{Mazumder2010SpectralMatrices,
  title = {{Spectral Regularization Algorithms for Learning Large Incomplete Matrices}},
  year = {2010},
  journal = {The Journal of Machine Learning Research},
  author = {Mazumder, Rahul and Hastie, Trevor and Tibshirani, Robert},
  month = {3},
  pages = {2287--2322},
  volume = {11},
  publisher = {JMLR.org},
  url = {http://dl.acm.org/citation.cfm?id=1756006.1859931},
}


@article{Azur_2011,
  doi = {10.1002/mpr.329},
  url = {http://dx.doi.org/10.1002/mpr.329},
  year = {2011},
  month = {February},
  publisher = {Wiley-Blackwell},
  volume = {20},
  number = {1},
  pages = {40--49},
  author = {Melissa J. Azur and Elizabeth A. Stuart and Constantine Frangakis and Philip J. Leaf},
  title = {{Multiple imputation by chained equations: what is it and how does it work?}},
  journal = {International Journal of Methods in Psychiatric Research},
}


@article{lundegaard2008accurate,
  title = {{Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers}},
  author = {Lundegaard, Claus and Lund, Ole and Nielsen, Morten},
  journal = {Bioinformatics},
  volume = {24},
  number = {11},
  pages = {1397--1398},
  year = {2008},
  publisher = {Oxford Univ Press},
}


@article{Anderson_2004,
  doi = {10.4049/jimmunol.172.10.5851},
  url = {http://dx.doi.org/10.4049/jimmunol.172.10.5851},
  year = {2004},
  month = {May},
  publisher = {The American Association of Immunologists},
  volume = {172},
  number = {10},
  pages = {5851--5860},
  author = {M. K. Anderson and R. Pant and A. L. Miracle and X. Sun and C. A. Luer and C. J. Walsh and J. C. Telfer and G. W. Litman and E. V. Rothenberg},
  title = {{Evolutionary Origins of Lymphocytes: Ensembles of T Cell and B Cell Transcriptional Regulators in a Cartilaginous Fish}},
  journal = {The Journal of Immunology},
}


@article{Lund_2011,
  doi = {10.1371/journal.pone.0026494},
  url = {http://dx.doi.org/10.1371/journal.pone.0026494},
  year = {2011},
  month = {October},
  publisher = {Public Library of Science ({PLoS})},
  volume = {6},
  number = {10},
  pages = {e26494},
  author = {Ole Lund and Eduardo J. M. Nascimento and Milton Maciel and Morten Nielsen and Mette Voldby Larsen and Claus Lundegaard and Mikkel Harndahl and Kasper Lamberth and S{\o}ren Buus and J{\'{e}}r{\^{o}}me Salmon and Thomas J. August and Ernesto T. A. Marques},
  editor = {Man-Seong Park},
  title = {{Human Leukocyte Antigen ({HLA}) Class I Restricted Epitope Discovery in Yellow Fewer and Dengue Viruses: Importance of {HLA} Binding Strength}},
  journal = {{PLoS} {ONE}},
}


@article{Snyder_2015,
  doi = {10.1016/j.gde.2014.12.003},
  url = {http://dx.doi.org/10.1016/j.gde.2014.12.003},
  year = {2015},
  month = {February},
  publisher = {Elsevier {BV}},
  volume = {30},
  pages = {7--16},
  author = {Alexandra Snyder and Timothy A Chan},
  title = {{Immunogenic peptide discovery in cancer genomes}},
  journal = {Current Opinion in Genetics {\&} Development},
}


@article{Gubin_2015,
  doi = {10.1172/jci80008},
  url = {http://dx.doi.org/10.1172/jci80008},
  year = {2015},
  month = {August},
  publisher = {American Society for Clinical Investigation},
  volume = {125},
  number = {9},
  pages = {3413--3421},
  author = {Matthew M. Gubin and Maxim N. Artyomov and Elaine R. Mardis and Robert D. Schreiber},
  title = {{Tumor neoantigens: building a framework for personalized cancer immunotherapy}},
  journal = {Journal of Clinical Investigation},
}


@article{Abreu_2012,
  doi = {10.1111/j.1365-2249.2012.04635.x},
  url = {http://dx.doi.org/10.1111/j.1365-2249.2012.04635.x},
  year = {2012},
  month = {September},
  publisher = {Wiley-Blackwell},
  volume = {170},
  number = {1},
  pages = {57--65},
  author = {J. R. F. Abreu and S. Martina and A. A. Verrijn Stuart and Y. E. Filli{\'{e}} and K. L. M. C. Franken and J. W. Drijfhout and B. O. Roep},
  title = {{{CD}8 T cell autoreactivity to preproinsulin epitopes with very low human leucocyte antigen class I binding affinity}},
  journal = {Clinical {\&} Experimental Immunology},
}


@article{Huseby_2005,
  doi = {10.1016/j.cell.2005.05.013},
  url = {http://dx.doi.org/10.1016/j.cell.2005.05.013},
  year = {2005},
  month = {July},
  publisher = {Elsevier {BV}},
  volume = {122},
  number = {2},
  pages = {247--260},
  author = {Eric S. Huseby and Janice White and Frances Crawford and Tibor Vass and Dean Becker and Clemencia Pinilla and Philippa Marrack and John W. Kappler},
  title = {{How the T Cell Repertoire Becomes Peptide and {MHC} Specific}},
  journal = {Cell},
}


@article{Blackman_1990,
  doi = {10.1126/science.1972592},
  url = {http://dx.doi.org/10.1126/science.1972592},
  year = {1990},
  month = {June},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  volume = {248},
  number = {4961},
  pages = {1335--1341},
  author = {M Blackman and J Kappler and P Marrack},
  title = {{The role of the T cell receptor in positive and negative selection of developing T cells}},
  journal = {Science},
}


@article{Cresswell_2005,
  doi = {10.1111/j.0105-2896.2005.00316.x},
  url = {http://dx.doi.org/10.1111/j.0105-2896.2005.00316.x},
  year = {2005},
  month = {October},
  publisher = {Wiley-Blackwell},
  volume = {207},
  number = {1},
  pages = {145--157},
  author = {Peter Cresswell and Anne L. Ackerman and Alessandra Giodini and David R. Peaper and Pamela A. Wearsch},
  title = {{Mechanisms of {MHC} class I-restricted antigen processing and cross-presentation}},
  journal = {Immunol Rev},
}


@article{Lundegaard_2008,
  doi = {10.1093/nar/gkn202},
  url = {http://dx.doi.org/10.1093/nar/gkn202},
  year = {2008},
  month = {May},
  publisher = {Oxford University Press ({OUP})},
  volume = {36},
  number = {Web Server},
  pages = {W509--W512},
  author = {C. Lundegaard and K. Lamberth and M. Harndahl and S. Buus and O. Lund and M. Nielsen},
  title = {{{NetMHC}-3.0: accurate web accessible predictions of human mouse and monkey {MHC} class I affinities for peptides of length 8-11}},
  journal = {Nucleic Acids Research},
}


@article{Nielsen_2007,
  doi = {10.1371/journal.pone.0000796},
  url = {http://dx.doi.org/10.1371/journal.pone.0000796},
  year = {2007},
  month = {August},
  publisher = {Public Library of Science ({PLoS})},
  volume = {2},
  number = {8},
  pages = {e796},
  author = {Morten Nielsen and Claus Lundegaard and Thomas Blicher and Kasper Lamberth and Mikkel Harndahl and Sune Justesen and Gustav R{\o}der and Bjoern Peters and Alessandro Sette and Ole Lund and S{\o}ren Buus},
  editor = {Esper Kallas},
  title = {{{NetMHCpan} a Method for Quantitative Predictions of Peptide Binding to Any {HLA}-A and -B Locus Protein of Known Sequence}},
  journal = {{PLoS} {ONE}},
}


@article{Sette_1989,
  doi = {10.1073/pnas.86.9.3296},
  url = {http://dx.doi.org/10.1073/pnas.86.9.3296},
  year = {1989},
  month = {May},
  publisher = {Proceedings of the National Academy of Sciences},
  volume = {86},
  number = {9},
  pages = {3296--3300},
  author = {A. Sette and S. Buus and E. Appella and J. A. Smith and R. Chesnut and C. Miles and S. M. Colon and H. M. Grey},
  title = {{Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis.}},
  journal = {Proceedings of the National Academy of Sciences},
}


@article{Peters_2003,
  doi = {10.1093/bioinformatics/btg247},
  url = {http://dx.doi.org/10.1093/bioinformatics/btg247},
  year = {2003},
  month = {September},
  publisher = {Oxford University Press ({OUP})},
  volume = {19},
  number = {14},
  pages = {1765--1772},
  author = {B. Peters and W. Tong and J. Sidney and A. Sette and Z. Weng},
  title = {{Examining the independent binding assumption for binding of peptide epitopes to {MHC}-I molecules}},
  journal = {Bioinformatics},
}


@article{Gfeller_2016,
  doi = {10.1080/2162402x.2016.1177691},
  url = {http://dx.doi.org/10.1080/2162402x.2016.1177691},
  year = {2016},
  month = {April},
  publisher = {Informa {UK} Limited},
  pages = {00--00},
  author = {David Gfeller and Michal Bassani-Sternberg and Julien Schmidt and Immanuel F. Luescher},
  title = {{Current tools for predicting cancer-specific T cell immunity}},
  journal = {{OncoImmunology}},
}


@article{Perez_2007,
  doi = {10.1109/mcse.2007.53},
  url = {http://dx.doi.org/10.1109/mcse.2007.53},
  year = {2007},
  publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})},
  volume = {9},
  number = {3},
  pages = {21--29},
  author = {Fernando Perez and Brian E. Granger},
  title = {{{IPython}: A System for Interactive Scientific Computing}},
  journal = {Comput. Sci. Eng.},
}


@article{Srivastava2014,
  abstract = {Deep neural nets with a large number of parameters are very powerful machine learning systems. However, overfitting is a serious problem in such networks. Large networks are also slow to use, making it difficult to deal with overfitting by combining the predictions of many different large neural nets at test time. Dropout is a technique for addressing this problem. The key idea is to randomly drop units (along with their connections) from the neural network during training. This prevents units from co-adapting too much. During training, dropout samples from an exponential number of different “thinned” networks. At test time, it is easy to approximate the effect of averaging the predictions of all these thinned networks by simply using a single unthinned network that has smaller weights. This significantly reduces overfitting and gives major improvements over other regularization methods. We show that dropout improves the performance of neural networks on supervised learning tasks in vision, speech recognition, document classification and computational biology, obtaining state-of-the-art results on many benchmark data sets},
  archiveprefix = {arXiv},
  arxivid = {1102.4807},
  author = {Srivastava, Nitish and Hinton, Geoffrey E. and Krizhevsky, Alex and Sutskever, Ilya and Salakhutdinov, Ruslan},
  doi = {10.1214/12-AOS1000},
  eprint = {1102.4807},
  file = {:Users/tim/Documents/Mendeley Desktop/Hinton/2014/Hinton - 2014 - Dropout A Simple Way to Prevent Neural Networks from Overfitting.pdf:pdf},
  isbn = {1532-4435},
  issn = {15337928},
  journal = {Journal of Machine Learning Research (JMLR)},
  keywords = {deep learning,model combination,neural networks,regularization},
  pages = {1929--1958},
  title = {{Dropout : A Simple Way to Prevent Neural Networks from Overfitting}},
  volume = {15},
  year = {2014},
}


@article{Lundegaard_2007,
  doi = {10.1093/bioinformatics/btm471},
  url = {http://dx.doi.org/10.1093/bioinformatics/btm471},
  year = {2007},
  month = {November},
  publisher = {Oxford University Press ({OUP})},
  volume = {23},
  number = {24},
  pages = {3265--3275},
  author = {C. Lundegaard and O. Lund and C. Kesmir and S. Brunak and M. Nielsen},
  title = {{Modeling the adaptive immune system: predictions and simulations}},
  journal = {Bioinformatics},
}

@misc{fancyimpute-0-0-16,
  author       = { Sergey Feldman and Alex Rubinsteyn},
  title        = {fancyimpute: Version 0.0.16},
  month        = May,
  year         = 2016,
  doi          = {10.5281/zenodo.51773},
  url          = {http://dx.doi.org/10.5281/zenodo.51773}
}
