@article{BrubakerLostPAMI2016,
  author = {Marcus A. Brubaker and Andreas Geiger and Raquel Urtasun},
  title = {{Map-based Probabilistic Visual Self-Localization}},
  journal = {{IEEE Transactions on Pattern Analysis and Machine Intelligence}},
  year = {2016},
  url_Paper = {BrubakerLostPAMI2016.pdf}
}

@inproceedings{WangDeepGPAISTATS2016,
  author = {Yali Wang and Marcus A. Brubaker and Brahim Chaib-draa and Raquel Urtasun},
  title = {{Sequential Inference for Deep Gaussian Process}},
  booktitle = {{Proceedings of Nineteenth International Conference on Artificial Intelligence and Statistics (AISTATS)}},
  year = {2016},
  url_Paper = {WangDeepGPAISTATS2016.pdf},
}

@inproceedings{BrubakerCryoEMCVPR2015,
  author = {Marcus A. Brubaker and Ali Punjani and David J. Fleet},
  title = {{Building Proteins in a Day: Efficient 3D Molecular Reconstruction}},
  booktitle = {{Proceedings of IEEE Conference on Computer Vision and Pattern Recognition}},
  year = {2015},
  url_Paper = {BrubakerCryoEMCVPR2015.pdf},
  url_arXiv = {http://arxiv.org/abs/1504.03573},
  url_Extended_Abstract = {BrubakerCryoEMCVPR2015-ExtAbs.pdf},
  url_GitHub = {https://github.com/mbrubake/cryoem-cvpr2015},
  url_Presentation = {http://techtalks.tv/talks/building-proteins-in-a-day-efficient-3d-molecular-reconstruction/61603/}
}

@article{WellerAFTEJournal2015,
  author = {Todd Weller and Marcus A. Brubaker and Pierre Duez and Ryan Lilien},
  title = {{Introduction and Initial Evaluation of a Novel Three-Dimensional Imaging and Analysis System for Firearm Forensics}},
  journal = {{Association of Firearm and Tool Mark Examiners (AFTE) Journal}},
  volume = {47},
  number = {4},
  pages = {198 -- 208},
  year = {2015},
  url_Journal = {https://afte.org/afte-journal}
}

@article{CarpenterJSS2016,
  author = {Bob Carpenter and Andrew Gelman and Matt Hoffman and Daniel Lee and Ben Goodrich and Michael Betancourt and Marcus A. Brubaker and Jiqiang Guo and Peter Li and Allen Riddell},
  title = {{Stan: A Probabilistic Programming Language}},
  journal = {{Journal of Statistical Software (to appear)}},
  year = {2016}
}

@article{RubinsteinCryoEMAlignment2015,
  author = {John L. Rubinstein and Marcus A. Brubaker},
  title = {{Alignment of cryo-EM movies of individual particles by optimization of image translations}},
  journal = {{Journal of Structural Biology}},
  volume = {192},
  number = {2},
  pages = {188 -- 195},
  year = {2015},
  url_arXiv = {http://arxiv.org/abs/1409.6789},
  url_Paper = {http://dx.doi.org/10.1016/j.jsb.2015.08.007},
}

@article{ZhaoJSBAnisotropy2015,
  title = {{Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images}},
  author = {Jianhua  Zhao and Marcus A. Brubaker and Samir Benlekbir and John L. Rubinstein},
  journal = {{Journal of Structural Biology}},
  volume = {192},
  number = {2},
  pages = {209 -- 215},
  year = {2015},
  url_arXiv = {http://arxiv.org/abs/1501.05928},
  url_Paper = {http://dx.doi.org/10.1016/j.jsb.2015.06.014},
}

@article{Cao2015,
  author = {Yanshuai Cao and Marcus A. Brubaker and David J. Fleet and Aaron Hertzmann},
  title = {{Efficient Optimization for Sparse Gaussian Process Regression}},
  journal = {{IEEE Transactions on Pattern Analysis and Machine Intelligence}},
  volume = {37},
  number = {12},
  pages = {2415 -- 2427},
  year = {2015},
  url_Paper = {Cao2015.pdf},
}

@INPROCEEDINGS{Wang2014,
  author = {Yali Wang and Marcus A. Brubaker and Brahim Chaib-draa and Raquel Urtasun},
  title = {{Bayesian Filtering with Online Gaussian Process Latent Variable Models}},
  booktitle = {{Proceedings of Conference on Uncertainty in Artificial Intelligence}},
  year = {2014},
  url_Paper = {Wang2014.pdf},
}

@INPROCEEDINGS{Cao2013,
  author = {Yanshuai Cao and Marcus A. Brubaker and Aaron Hertzmann and David J. Fleet},
  title = {{Efficient Optimization for Sparse Gaussian Process Regression}},
  booktitle = {{Proceedings of Neural Information Processing Systems}},
  year = {2013},
  url_Paper = {Cao2013.pdf},
  url_arXiv = {http://arxiv.org/abs/1310.6007},
  url_Website = {http://www.cs.toronto.edu/~caoy/opt_sgpr},
  url_Proceedings = {http://papers.nips.cc/paper/5087-efficient-optimization-for-sparse-gaussian-process-regression}
}

@INPROCEEDINGS{Brubaker2013,
  author = {Marcus A. Brubaker and Andreas Geiger and Raquel Urtasun},
  title = {{Lost! Leveraging the Crowd for Probabilistic Visual Self-Localization}},
  booktitle = {{Proceedings of IEEE Conference on Computer Vision and Pattern Recognition}},
  year = {2013},
  url_Paper = {Brubaker2013.pdf},
  url_Supplemental = {Brubaker2013-Supplemental.pdf},
  url_Poster = {Brubaker2013-Poster.pdf},
  url_Slides = {Brubaker2013-Slides.pdf},
  url_Presentation = {http://techtalks.tv/talks/lost-leveraging-the-crowd-for-probabilistic-visual-self-localization/58677/},
  url_Video = {Brubaker2013-Video.mp4},
  url_YouTube = {http://youtu.be/4Z3shNPOdQA},
  url_Website = {http://www.cs.toronto.edu/~mbrubake/projects/map},
}

@INPROCEEDINGS{Brubaker2013WS,
  author = {Marcus A. Brubaker  and Andreas Geiger and Raquel Urtasun},
  title = {{Probabilistic Map Localization Through Visual Odometry}},
  booktitle = {{Proceedings of SUNw: Scene Understanding Workshop at IEEE Conference on Computer Vision and Pattern Recognition}},
  year = {2013},
  url_Paper = {Brubaker2013WS.pdf},
  url_Workshop = {http://sunw.csail.mit.edu/2013},
}

@ARTICLE{Zhao2013,
  author = {Jianhua Zhao and Marcus A. Brubaker and John L. Rubinstein},
  title = {{TMaCS: A hybrid template matching and classification system for partially-automated particle selection}},
  journal = {Journal of Structural Biology},
  volume = {181},
  number = {3},
  pages = {234 -- 242},
  year = {2013},
  url_Paper = {http://dx.doi.org/10.1016/j.jsb.2012.12.010},
  url_Code = {http://www.sickkids.ca/Research/Rubinstein/Software/index.html},
}
 
@INPROCEEDINGS{BrubakerAISTATS2012,
  author = {Marcus A. Brubaker and Mathieu Salzmann and Raquel Urtasun},
  title = {{A Family of {MCMC} Methods on Implicitly Defined Manifolds}},
  booktitle = {Proceedings of the Fifteenth International Conference on Artificial
	Intelligence and Statistics (AISTATS)},
  year = {2012},
  url_Paper = {BrubakerAISTATS2012.pdf},
  url_Poster = {BrubakerAISTATS2012-Poster.pdf},
  url_Website = {http://www.cs.toronto.edu/~mbrubake/projects/cmcmc}
}

@ARTICLE{BrubakerIJCV2010,
  author = {Marcus A. Brubaker and David J. Fleet and Aaron Hertzmann},
  title = {{Physics-based Person Tracking using the Anthropomorphic Walker}},
  journal = {International Journal of Computer Vision},
  volume = {87},
  pages = {140--155},
  number = {1},
  year = {2010},
  url_Paper = {BrubakerIJCV2010.pdf},
  url_Website = {http://www.cs.toronto.edu/~mbrubake/permanent/awalker}
}

@ARTICLE{Jaitly2010,
  author = {Navdeep Jaitly and Marcus A. Brubaker and John Rubinstein and Ryan
	H. Lilien},
  title = {{A Bayesian Method for 3-D Macromolecular Structure Inference using
	Class Average Images from Single Particle Electron Microscopy}},
  journal = {Bioinformatics},
  year = {2010},
  volume = {26},
  pages = {2406-2415},
  url_Paper = {http://bioinformatics.oxfordjournals.org/cgi/reprint/btq456?ijkey=TR5pnBrtbyXdqN6&keytype=ref},
  url_Website = {http://compbio.cs.toronto.edu/cryoem/}
}

@INCOLLECTION{BrubakerAISE2009,
  author = {Marcus A. Brubaker and Leonid Sigal and David J. Fleet},
  title = {{Video-based People Tracking}},
  booktitle = {Handbook on Ambient Intelligence and Smart Environments},
  publisher = {Springer Verlag},
  editor = {H. Nakashima and H. Aghajan and J.C. Augusto},
  year = {2009},
  url_Paper = {BrubakerAISE2009.pdf},
}

@INPROCEEDINGS{BrubakerICCV2009,
  author = {Marcus A. Brubaker and Leonid Sigal and David J. Fleet},
  title = {{Estimating Contact Dynamics}},
  booktitle = {Proceedings of IEEE International Conference on Computer Vision},
  year = {2009},
  url_Paper = {BrubakerICCV2009.pdf},
  url_MocapResults = {BrubakerICCV2009-MocapResults.avi},
  url_MocapYouTube = {http://youtu.be/RbL0zx53DQg},
  url_VideoResults = {BrubakerICCV2009-VideoResults.avi},
  url_VideoYouTube = {http://youtu.be/NZ4U8oO--6M},
}

@INPROCEEDINGS{BrubakerCVPR2008,
  author = {Marcus A. Brubaker and David J. Fleet},
  title = {{The Kneed Walker for Human Pose Tracking}},
  booktitle = {Proceedings of IEEE Conference on Computer Vision and Pattern Recognition},
  year = {2008},
  url_Paper = {BrubakerCVPR2008.pdf},
  url_Video = {BrubakerCVPR2008-Results.avi},
  url_YouTube = {http://youtu.be/-rUM4ZxCD0I},
}

@INPROCEEDINGS{Brubaker2007,
  author = {Marcus A. Brubaker and David J. Fleet and Aaron Hertzmann},
  title = {Physics-based person tracking using simplified lower-body dynamics},
  booktitle = {Proceedings of IEEE Conference on Computer Vision and Pattern Recognition},
  year = {2007},
  url_Paper = {BrubakerCVPR2007.pdf},
  url_Video = {BrubakerCVPR2007-Results.avi},
  url_YouTube = {http://youtu.be/IZhl9Fo7eUI},
}


@article{CarpenterStanAD2015,
  author = {Bob Carpenter and Matthew D. Hoffman and Marcus A. Brubaker and Daniel Lee and Peter Li and Michael Betancourt},
  title = {{The Stan Math Library: Reverse-Mode Automatic Differentiation in C++}},
  journal = {ArXiv e-prints},
  volume = {cs.MS/1509.07164},
  archivePrefix = "arXiv",
  eprinttype={arxiv},
  eprint = {1509.07164},
  primaryClass = "cs.MS",
  year = 2015,
  month = sep,
  url = {http://arxiv.org/abs/1509.07164},
}

@article{PunjaniStochOptCryoEM2015,
  author = {Ali Punjani and Marcus A. Brubaker},
  title = {{Microscopic Advances with Large-Scale Learning: Stochastic Optimization for Cryo-EM}},
  journal = {ArXiv e-prints},
  volume = {stat.ML/1501.04656},
  archivePrefix = "arXiv",
  eprinttype={arxiv},
  eprint = {1501.04656},
  primaryClass = "stat.ML",
  year = 2015,
  month = jan,
  url = {http://arxiv.org/abs/1501.04656},
}

@PHDTHESIS{BrubakerPhD2011,
  author = {Marcus A. Brubaker},
  title = {{Physical Models of Human Motion for Estimation and Scene Analysis}},
  school = {University of Toronto},
  year = {2011},
}

@misc{BrubakerICCVTut2009,
  author = {Marcus A. Brubaker and Leonid Sigal and David J. Fleet},
  title = {{Physics-based Human Motion Modelling for people tracking: A short tutorial}},
  howpublished = {Tutorial at IEEE International Conference of Computer Vision, Kyoto,
	Japan},
  year = {2009},
}

@MASTERSTHESIS{BrubakerMSc2006,
  author = {Marcus A. Brubaker},
  title = {Physics-Based Priors for Human Pose Tracking},
  school = {University of Toronto},
  year = {2006},
}


@inproceedings{CarpenterADMB2016,
  author = {Bob Carpenter and Matthew D. Hoffman and Marcus A. Brubaker and Daniel Lee and Michael Betancourt and Sebastian Weber and Rob Trangucci},
  title = {{Algorithmic Differentiation in the Stan Math C++ Library}},
  booktitle = {{ADMB Developers Workshop}},
  month = {June},
  year = {2016}
}

@inproceedings{BrubakerCryoEMBIC2015,
  author = {Marcus A. Brubaker and Ali Punjani and David J. Fleet},
  title = {{Efficient 3D Macromolecular Reconstruction with Electron Cryomicroscopy}},
  booktitle = {{BioImage Computing Workshop at IEEE Conference on Computer Vision and Pattern Recognition}},
  month = {June},
  year = {2015}
}

@inproceedings{BrubakerCryoEMNIPS2014,
  author = {Ali Punjani and Marcus A. Brubaker},
  title = {{Microscopic Advances with Large-Scale Learning: Stochastic Optimization for Cryo-EM}},
  booktitle = {{Neural Information Processing Systems Workshop: Machine Learning in Computational Biology (MLCB)}},
  month = {December},
  year = {2014}
}

@inproceedings{LilienAFTE2014,
  author = {Ryan Lilien and Marcus A. Brubaker and Todd Weller},
  title = {{Progress Towards a Novel 3D-Topography Imaging and Analysis System for Firearm Identification, TopMatch-GS, and Results of a Large-Scale Study}},
  booktitle = {The Association of Firearm and Tool Mark Examiners Annual Training Seminar},
  month = {May},
  year = {2014},
}

@inproceedings{LilienAFTE2013,
  author = {Ryan Lilien and Marcus A. Brubaker and Todd Weller},
  title = {{Development of a 3D-Topography Imaging and Analysis System for Firearm Identification using GelSight and Feature Based Case Matching}},
  booktitle = {The Association of Firearm and Tool Mark Examiners Annual Training Seminar},
  month = {June},
  year = {2013},
}

@inproceedings{LilienIPES2012,
  author = {Ryan Lilien and Marcus A. Brubaker and Todd Weller and Micah Johnson},
  title = {{Three-Dimensional Topography System for Firearm Identification using GelSight}},
  booktitle = {NIJ and FBI Impression and Pattern Evidence Symposium, Clearwater, Florida},
  month = {August},
  year = {2012},
}

@inproceedings{BrubakerNIST2012,
  author = {Marcus A. Brubaker and Ryan Lilien and Todd Weller and Micah Johnson},
  title = {{Surface Topography Measurement using GelSight Elastomeric Sensor for Firearm Forensics}},
  booktitle = {NIST Conference on Measurement Science and Standards in Forensic Firearms Analysis, Gaithersburg, Maryland},
  month = {July},
  year = {2012},
}

@inproceedings{Jaitly2009,
  author = {Navdeep Jaitly and Marcus A. Brubaker and John Rubinstein and Ryan Lilien},
  title = {{A Bayesian method for 3D reconstruction of macromolecular structure using class averages from single particle electron microscopy}},
  booktitle = {Neural Information Processing Systems Workshop: Machine Learning in Computational Biology (MLCB)},
  month = {December},
  year = {2009},
}

@inproceedings{Brubaker2006,
  author = {Marcus A. Brubaker and David J. Fleet and Aaron Hertzmann},
  title = {{Physics-based Human Pose Tracking}},
  booktitle = {Neural Information Processing Systems Workshop: Evaluation of Articulated Human Motion and Pose Estimation (EHuM)},
  month = {December},
  year = {2006},
}