bibliography.bib

% Bibliography Entries

#####################################
##### Plant Breeding Entries ########
#####################################

@article{moore1965,
title={Cramming more components onto integrated circuits},
author={Moore, Gordon E},
year={1965},
volume={38},
issue={8},
publisher={Electronics}
}


@article{heffner2010,
title={Plant breeding with genomic selection: {G}ain per unit time and cost},
author={Heffner, Elliot L. and Lorenz, Aaron J. and Jannink, Jean-Luc and Sorrells, Mark E.},
journal={Crop Sci},
volume={50},
number={5},
pages={1681-1690},
year={2010},
}


@article{daetwyler2007,
title={Inbreeding in genome-wide selection},
author={Daetwyler, Hans D. and Villanueva, Beatriz and Bijma, Piter and Woolliams, John A.},
journal={J. Anim. Breed. Genet.},
volume={124},
number={6},
pages={369-376},
year={2007},
}


@article{gianola2008,
title={Reproducing kernel {H}ilbert spaces regression methods for genomic assisted prediction of quantitative traits},
author={Gianola, Daniel and van Kaam, Johannes B. C. H. M.},
journal={PCM},
volume={178},
pages={2289-2303},
year={2008},
}


@article{gianola2009,
title={Additive genetic variability and the {B}ayesian {A}lphabet},
author={Gianola, Daniel and de los Campos, Gustavo and Hill, William G. and Manfredi, Eduardo and Frenando Rohan},
journal={Genetics},
volume={183},
pages={347-363},
year={2009},
}

@article{subasi2005,
title={Classification of {EEG} signals using neural network and logistic regression},
author={Subasi, Abdulhamit and Ercelebi, Ergun},
journal={Comput. Meth. Prog. Bio.},
volume={78},
pages={87-99},
year={2005},
}


@article{lang1990,
title={A time-delay neural network architecture for isolated word recognition},
author={Lang, Kevin J. and Waibel, Alex H. and Hinton, Geoffrey E.},
journal={Neural Networks},
volume={3},
pages={23-43},
year={1990},
}


@article{mnih2013,
title={Playing {A}tari with deep reinforcement learning},
author={Mnih, Volodymyr and Kavukcuoglu, Koray and Silver, David and Graves, Alex and Antonoglou, Ioannis and others},
journal={arXiv preprint arXiv:1312.5602},
year={2013}
}


@article{evenson2003,
author={Evenson, R. E. and Gollin, D.},
title={Assessing the Impact of the Green Revolution, 1960 to 2000},
journal={Science},
year={2003},
volume={300},
pages={758-762}
}

@article{fernandez2012,
title={Revisiting the impact of {B}t corn adoption by {US} farmers},
author={Fernandez-Cornejo, Jorge and Wechsler, Seth and others},
journal={J. Agr. Resour. Econ.},
volume={41},
pages={377},
year={2012}
}

@article{hiremath2012,
title={Large-scale development of cost-effective {SNP} marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes},
author={Hiremath, Pavana J and Kumar, Ashish and Penmetsa, Ramachandra Varma and Farmer, Andrew and Schlueter, Jessica A and others},
journal={Plant Biotech J.},
volume={10},
pages={716-732},
year={2012},
}

@article{heffner2009,
title={Genomic selection for crop improvement},
author={Heffner, Elliot L. and Sorrells, Mark E. and Jannink, Jean-Luc},
journal={Crop Sci.},
volume={49},
pages={1-12},
year={2009},
}

@article{lande1990,
title={Efficiency of marker-assisted selection in the improvement of quantitative traits},
author={Lande, Russell and Thompson, Robin},
journal={Genetics},
volume={124},
pages={743-756},
year={1990},
}

@article{tibshirani1996,
title={Regression shrinkage and selection via the lasso},
author={Tibshirani, Robert},
journal={J. R. Stat. Soc. Series B Stat. Methodol.},
pages={267-288},
year={1996},
}

@article{zou2005,
title={Regularization and variable selection via the elastic net},
author={Zou, Hui and Hastie, Trevor},
journal={J. R. Stat. Soc. Series B Stat. Methodol.},
volume={67},
pages={301-320},
year={2005},
}


@article{hoerl1970,
title={Ridge regression: {B}iased estimation for nonorthogonal problems},
author={Hoerl, Arthur E and Kennard, Robert W},
journal={Technometrics},
volume={12},
pages={55-67},
year={1970},
}


@book{fehr1987,
author={Walter R. Fehr},
title={Principles of Cultivar Development},
publisher={Macmillian Publishing Co.},
year={1987},
volume={1},
note={Reprinted 1993},
}

@article{meuwissen2001,
author={Meuwissen, T. H. E. and Hayes, B. J. and Goddard, M. E.},
title={Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps},
journal={Genetics},
year={2001},
volume={157},
pages={1819-1829},

}

@article{gianola2006,
author={Gianola, Daniel and Fernando, Rohan L. and Stella, Alessandra},
title={Genomic-assisted Prediction of Genetic Value with Semiparametric Procedures},
journal={Genetics},
year={2006},
volume={173},
pages={1761-1776},
}

@article{lorenzana2009,
author={Lorenzana, Robenzon E. and Bernardo, Rex},
title={Accuracy of Genotypic Value Predictions for Marker-based Selection in Biparental Plant Populations},
journal={Theor. Appl. Genet.},
year={2009},
volume={120},
pages={151-161},
}

@article{loudet2002,
author={Loudet, O. and Chaillou, S. and Camilleri, C. and Bouchez, D. and Daniel-Vedele, F.},
title={Bay-0 x {S}hahdara Recombinant Inbred Line Population: {A} Powerful Tool for the Genetic Dissection of Complex Traits in {A}rabidopsis},
journal={Theor. Appl. Genet.},
year={2002},
volume={104},
pages={1173-1184},
}

@article{crossa2010,
author={Crossa, J{\'o}se and de los Campos, Gustavo and P{\'e}rez, Paulino and Gianola, Daniel and Burgue{\~n}o, Juan and others},
title={Prediction of Genetic Values of Quantitative Traits in Plant Breeding Using Pedigree and Molecular Markers},
journal={Genetics},
year={2010},
volume={186},
pages={713-724},
}

@article{resende2012,
author={Resende, M. F. R. and Mu{\~n}oz, P. and Resende, M. D. V. and Garrick, D. J. and Fernando, R. L. and others},
title={Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (\emph{Pinus taeda, L.})},
journal={Genetics},
year={2012},
volume={190},
pages={1503-1510},
}

@article{cleveland2012,
author={Cleveland, Matthew A. and Hickey, John. M. and Forni, Selma},
title={A Common Dataset for Genomic Analysis of Livestock Populations},
journal={G3},
year={2012},
volume={2},
pages={429-435},
}

@article{thavamanikumar2015,
author={Thavamanikumar, Saravanan and Dolferus, Rudy and Thumma, Bala R.},
title={Comparison of Genomic Selection Models to Predict Flowering Time and Spike Grain Number in Two Hexaploid Wheat Doubled Haploid Populations},
journal={G3},
year={2015},
volume={5},
pages={1991-1998},
}

@misc{mcdowell2016,
author={McDowell, Riley},
title={Genomic Neuralnet},
year={2016},
publisher={GitHub},
journal={GitHub Repository},
howpublished={\url{https://github.com/rileymcdowell/genomic_neuralnet}},
commit={65d9269e63ccbb80b3b4826b57d74e49bb39ad4d},
}

@article{gonzalez-recio2014,
author={Gonz{\'a}lez-Recio, Oscar and Rosa, Guilherme J. M. and Gianola, Daniel},
title={Machine learning methods and predictive ability metrics for
    genome-wide prediction of complex traits},
journal={Livest. Sci.},
year={2014},
volume={166},
pages={217-231},
}

@article{gonzalez-camacho2012,
author={Gonzalez-Camacho, J. M. and de los Campos, G. and P{\'e}rez, P. and Gianola, D. and Cairns, J. E. and others},
title={Genome-enabled prediction of genetic values using radial basis function neural networks},
journal={Theor. Appl. Genet.},
year={2012},
volume={125},
pages={759-771},
}

@article{heslot2012,
author={Heslot, Nicolas and Yang, Hsiao-Pei and Sorrells, Mark E. and Jannink, Jean-Luc},
title={Genomic selection in plant breeding: {A} comparison of models},
journal={Crop Sci.},
year={2012},
volume={56},
pages={146-160},
}

@article{miles2008,
author={Miles, C. and Wayne, M.},
title={Quantitative trait locus ({QTL}) analysis},
journal={Nature Education},
year={2008},
volume={1},
pages={208},
}

@article{koning2012,
author={de Koning, Dirk-Jan and McIntyre, Lauren},
title={Setting the standard: {A} special focus on genomic selection in {GENETICS} and {G3}},
journal={Genetics},
year={2012},
volume={190},
pages={1151-1152}
}

#####################################
##### Machine Learning Entries ######
#####################################
# Looks like abbreviation is IJUFKS
#journal={International Journal of Uncertainty, Fuzziness, and Knowledge-Based Systems},

@article{hochreiter1998,
title={The vanishing gradient problem during learning recurrent neural nets and problem solutions},
author={Hochreiter, Sepp},
journal={IJUFKS},
volume={6},
number={02},
pages={107-116},
year={1998},
publisher={World Scientific}
}

@article{chetlur2014,
title={{cuDNN}: {E}fficient primitives for deep learning},
author={Chetlur, Sharan and Woolley, Cliff and Vandermersch, Philippe and Cohen, Jonathan and Tran, John and others},
journal={arXiv preprint arXiv:1410.0759},
year={2014}
}


@inproceedings{sierra2010,
title={Parallel training of a back-propagation neural network using {CUDA}},
author={Sierra-Canto, Xavier and Madera-Ramirez, Francisco and Uc-Cetina, Victor},
booktitle={Machine Learning and Applications (ICMLA), 2010 Ninth International Conference on},
pages={307-312},
year={2010},
organization={IEEE}
}


@inproceedings{sutskever2013,
title={On the importance of initialization and momentum in deep learning},
author={Sutskever, Ilya and Martens, James and Dahl, George and Hinton, Geoffrey},
booktitle={Proceedings of the 30th international conference on machine learning (ICML-13)},
pages={1139-1147},
year={2013}
}

@article{breiman2001,
title={Statistical modeling: The two cultures (with comments and a rejoinder by the author)},
author={Breiman, Leo},
journal={Stat. Sci.},
volume={16},
number={3},
pages={199-231},
year={2001},
publisher={Institute of Mathematical Statistics},
}


@inbook{alpaydin2014,
author={Alpaydin, Ethem},
title={Introduction to machine learning},
chapter={1},
year={2014},
publisher={MIT press}
}


@unpublished{donoho2015,
title={50 years of Data Science},
author={Donoho, David},
year={2015},
note={Tukey Centennial Workshop},
}


@article{hornik1989,
author={Kur, Hornik and Stinchombe, Maxwell and White, Halber},
title={Multilayer Feedforward Networks are Universal Approximators},
journal={Neural Networks},
year={1989},
volume={2},
pages={359-366},
}

@article{rumelhart1986,
author={Rumelhart, David E. and Hinton, Geoffrey E. and Williams, Ronald J.},
title={Learning Representations by Back-propagating Errors},
journal={Nature},
year={1986},
volume={323},
pages={533-536},
}

## Abbreviated as NIPS.
# journal={Advances Neural Inform. Processing Syst.},
@article{krogh1992,
author={Krogh, Anders and Hertz, John A.},
title={A simple weight decay can improve generalization},
year={1992},
journal={NIPS},
volume={4},
pages={950-957},
}

@article{srivastava2014,
author={Srivastava, Nitish and Hinton, Geoffrey and Krizhevsky, Alex and Sutskever, Ilya and Salakhutdinov, Ruslan},
title={Dropout: {A} simple way to prevent neural networks from overfitting},
year={2014},
journal={J. Mach. Learn. Res.},
volume={15},
pages={1929-1958},
}


@article{schmidhuber2015,
author={Schmidhuber, J{\"u}rgen},
title={Deep Learning in Neural Networks: {A}n Overview},
journal={Neural Networks},
year={2015},
volume={61},
pages={85-117},
}


#############################
##### Software Entries ######
#############################

@article{nickolls2008,
title={Scalable parallel programming with {CUDA}},
author={Nickolls, John and Buck, Ian and Garland, Michael and Skadron, Kevin},
journal={Queue},
volume={6},
number={2},
pages={40-53},
year={2008},
publisher={ACM}
}


@article{team2016,
title={Theano: {A} {P}ython framework for fast computation of mathematical expressions},
author={Team, The Theano Development and Al-Rfou, Rami and Alain, Guillaume and Almahairi, Amjad and Angermueller, Christof and others},
journal={arXiv preprint arXiv:1605.02688},
year={2016}
}


@misc{chollet2015,
title={Keras},
author={Chollet, Fran\c{c}ois},
year={2015},
publisher={GitHub},
howpublished={\url{https://github.com/fchollet/keras}},
}

# Straight from http://scikit-learn/stable/about.html.
@article{scikit-learn,
title={Scikit-learn: {M}achine Learning in {P}ython},
author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. and Thirion, B. and others},
journal={J. Mach. Learn. Res.},
volume={12},
pages={2825-2830},
year={2011}
}

# Straight from https://raw.githubusercontent.com/tensorflow/tensorflow/master/tensorflow/g3doc/resources/bib.md
@misc{tensorflow2015,
title={{TensorFlow}: {L}arge-Scale Machine Learning on Heterogeneous Systems},
url={http://tensorflow.org/},
note={Software available from tensorflow.org},
author={
    Mart\'{\i}n~Abadi and
    Ashish~Agarwal and
    Paul~Barham and
    Eugene~Brevdo and
    Zhifeng~Chen and others},
year={2015},
}

@article{lecun2015,
title={Deep learning},
author={LeCun, Yann and Bengio, Yoshua and Hinton, Geoffrey},
journal={Nature},
volume={521},
number={7553},
pages={436-444},
year={2015},
publisher={Nature Publishing Group}
}

@inproceedings{glorot2010,
title={Understanding the difficulty of training deep feedforward neural networks},
author={Glorot, Xavier and Bengio, Yoshua},
booktitle={{AISTATS}},
volume={9},
pages={249-256},
year={2010}
}

@techreport{dozat2015,
title={Incorporating {N}esterov momentum into {A}dam},
author={Dozat, Timothy},
year={2015}, 
institution={Standford University},
url={http://cs229.stanford.edu/proj2015/054_report.pdf}
}