references.bib

@article{de2004discovery,
  title={Discovery of meaningful associations in genomic data using partial correlation coefficients},
  author={De La Fuente, Alberto and Bing, Nan and Hoeschele, Ina and Mendes, Pedro},
  journal={Bioinformatics},
  volume={20},
  number={18},
  pages={3565--3574},
  year={2004},
  publisher={Oxford Univ Press}
}
@book{jolliffe2005principal,
  title={Principal component analysis},
  author={Jolliffe, Ian},
  year={2005},
  publisher={Wiley Online Library}
}
@article{alter2000singular,
  title={Singular value decomposition for genome-wide expression data processing and modeling},
  author={Alter, Orly and Brown, Patrick O and Botstein, David},
  journal={Proceedings of the National Academy of Sciences},
  volume={97},
  number={18},
  pages={10101--10106},
  year={2000},
  publisher={National Acad Sciences}
}

@book{oppenheim1983signals,
  title={Signals and systems},
  author={Oppenheim, Alan V and Willsky, Alan S and Nawab, Syed Hamid},
  volume={2},
  year={1983},
  publisher={Prentice-Hall Englewood Cliffs, NJ}
}

@article{pakkenberg2003aging,
  title={Aging and the human neocortex},
  author={Pakkenberg, Bente and Pelvig, Dorte and Marner, Lisbeth and Bundgaard, Mads J and Gundersen, Hans J{\o}rgen G and Nyengaard, Jens R and Regeur, Lisbeth},
  journal={Experimental gerontology},
  volume={38},
  number={1},
  pages={95--99},
  year={2003},
  publisher={Elsevier}
}
@article{kaiser1977data,
  title={Data smoothing using low-pass digital filters},
  author={Kaiser, JF and Reed, WA},
  journal={Review of Scientific Instruments},
  volume={48},
  number={11},
  pages={1447--1457},
  year={1977},
  publisher={AIP Publishing}
}

@book{shipley2002cause,
  title={Cause and correlation in biology: a user's guide to path analysis, structural equations and causal inference},
  author={Shipley, Bill},
  year={2002},
  publisher={Cambridge University Press}
}

@phdthesis{louppe2014understanding,
title={Understanding random forests},
author={Louppe, Gilles},
year={2014},
school={University of Liège}
}

@article{stetter2012model,
  title={Model-free reconstruction of excitatory neuronal connectivity from calcium imaging signals},
  author={Stetter, Olav and Battaglia, Demian and Soriano, Jordi and Geisel, Theo},
  journal={PLoS computational biology},
  volume={8},
  number={8},
  pages={e1002653},
  year={2012},
  publisher={Public Library of Science}
}

@article{schrynemackers2013protocols,
  title={On protocols and measures for the validation of supervised methods for the inference of biological networks},
  author={Schrynemackers, Marie and K{\"u}ffner, Robert and Geurts, Pierre},
  journal={Frontiers in genetics},
  volume={4},
  year={2013},
  publisher={Frontiers Media SA}
}

@article{huynhthu2010inferring,
  title={Inferring regulatory networks from expression data using tree-based methods},
  author = {Huynh-Thu, Vân Anh AND Irrthum, Alexandre AND Wehenkel, Louis AND Geurts, Pierre},
  journal={PloS one},
  volume={5},
  number={9},
  pages={e12776},
  year={2010},
  publisher={Public Library of Science}
}

@inproceedings{louppe2013understanding,
  title={Understanding variable importances in forests of randomized trees},
  author={Louppe, Gilles and Wehenkel, Louis and Sutera, Antonio and Geurts, Pierre},
  booktitle={Advances in Neural Information Processing Systems},
  pages={431--439},
  year={2013}
}

@book{koller2009probabilistic,
  title={Probabilistic graphical models: principles and techniques},
  author={Koller, Daphne and Friedman, Nir},
  year={2009},
  publisher={MIT press}
}

# [in Stetter, [6]]
@article{lichtman2011big,
  title={The big and the small: challenges of imaging the brain’s circuits},
  author={Lichtman, Jeff W and Denk, Winfried},
  journal={Science},
  volume={334},
  number={6056},
  pages={618--623},
  year={2011},
  publisher={American Association for the Advancement of Science}
}

@article{breiman2001random,
  title={Random forests},
  author={Breiman, Leo},
  journal={Machine learning},
  volume={45},
  number={1},
  pages={5--32},
  year={2001},
  publisher={Springer}
}

@book{bishop2006pattern,
  title={Pattern recognition and machine learning},
  author={Bishop, Christopher M},
  volume={1},
  year={2006},
  publisher={Springer New York}
}

@article{baba2004partial,
  title={Partial correlation and conditional correlation as measures of conditional independence},
  author={Baba, Kunihiro and Shibata, Ritei and Sibuya, Masaaki},
  journal={Australian \& New Zealand Journal of Statistics},
  volume={46},
  number={4},
  pages={657--664},
  year={2004},
  publisher={Wiley Online Library}
}

@Article{marbach2012,
  author = 	 {Marbach, Daniel and Costello, James C. and K\"uffner, Robert and Vega, Nicole and Prill, Robert J. and Camacho, Diogo M. and Allison, Kyle R. and The DREAM5 Consortium and Kellis, Manolis and Collins, James J. and Stolovitzky, Gustavo},
  title = 	 {Wisdom of crowds for robust network inference},
  journal = 	 {Nature methods},
  year = 	 2012,
  volume = 	 9,
  number = 	 8,
  pages = 	 {794-804}}

@article{Schafer:2005,
author = {Sch\"afer, Juliane and Strimmer, Korbinian}, 
journal = {Statistical applications in genetics and molecular biology},
title = {A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics},
number = {32},
pages = {1175},
volume = {4},
year = {2005}
}