
@Article{chow:68,
  author = 	 {C. K. Chow and C. N. Liu},
  title = 	 {Approximating discrete probability distributions with dependence trees},
  journal = 	 {IEEE Transactions on Information Theory},
  year = 	 {1968},
  volume = 	 {IT-14},
  number = 	 {3},
  pages = 	 {462--467}}


@Book{pearl:88,
  author = 	 {Judea Pearl},
  title = 	 {Probabilistic {R}easoning in {I}ntelligent {S}ystems: 
		  {N}etworks of {P}lausible {I}nference},
  publisher = 	 {Morgan Kaufman Publishers},
  year = 	 {1988},
  address = 	 {San Mateo, CA}
}

@article{DBLP:journals/corr/abs-1911-05656,
  author       = {Aditi Laddha and
                  Yin Tat Lee and
                  Santosh S. Vempala},
  title        = {Strong Self-Concordance and Sampling},
  journal      = {CoRR},
  volume       = {abs/1911.05656},
  year         = {2019},
  url          = {http://arxiv.org/abs/1911.05656},
  eprinttype    = {arXiv},
  eprint       = {1911.05656},
  timestamp    = {Mon, 02 Dec 2019 13:44:01 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-1911-05656.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2202-01908,
  author       = {Yunbum Kook and
                  Yin Tat Lee and
                  Ruoqi Shen and
                  Santosh S. Vempala},
  title        = {Sampling with Riemannian Hamiltonian Monte Carlo in a Constrained
                  Space},
  journal      = {CoRR},
  volume       = {abs/2202.01908},
  year         = {2022},
  url          = {https://arxiv.org/abs/2202.01908},
  eprinttype    = {arXiv},
  eprint       = {2202.01908},
  timestamp    = {Wed, 09 Feb 2022 15:43:34 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2202-01908.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{JMLR:v19:18-158,
  author  = {Yuansi Chen and Raaz Dwivedi and Martin J. Wainwright and Bin Yu},
  title   = {Fast MCMC Sampling Algorithms on Polytopes},
  journal = {Journal of Machine Learning Research},
  year    = {2018},
  volume  = {19},
  number  = {55},
  pages   = {1--86},
  url     = {http://jmlr.org/papers/v19/18-158.html}
}

@article{drusvyatskiy2017many,
	author = {Drusvyatskiy, Dmitriy and Wolkowicz, Henry and others},
	date-added = {2022-11-20 21:00:56 -0500},
	date-modified = {2022-11-20 21:00:56 -0500},
	journal = {Foundations and Trends{\textregistered} in Optimization},
	number = {2},
	pages = {77--170},
	publisher = {Now Publishers, Inc.},
	title = {The many faces of degeneracy in conic optimization},
	volume = {3},
	year = {2017}}

@article{DBLP:journals/corr/SachdevaV15,
  author       = {Sushant Sachdeva and
                  Nisheeth K. Vishnoi},
  title        = {A Simple Analysis of the Dikin Walk},
  journal      = {CoRR},
  volume       = {abs/1508.01977},
  year         = {2015},
  url          = {http://arxiv.org/abs/1508.01977},
  eprinttype    = {arXiv},
  eprint       = {1508.01977},
  timestamp    = {Mon, 13 Aug 2018 16:46:57 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/SachdevaV15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{vempala2005,
  author       = {Santosh Vempala},
  title        = {Geometric Random Walks: A Survey},
  journal      = {Combinatorial and Computational Geometry},
  volume       = {52},
  year         = {2005},
  url          = {https://faculty.cc.gatech.edu/~vempala/papers/survey.pdf}
}

@article{lovasz1999,
  author       = {László Lovász},
  title        = {Hit-and-run mixes fast},
  journal      = {Mathematical Programming},
  volume       = {86},
  year         = {1999},
  url          = {https://link.springer.com/content/pdf/10.1007/s101070050099.pdf}
}

@article{Simonovits2003,
  author       = {Mikl´os Simonovits},
  title        = {How to compute the volume in high dimension?},
  journal      = {Mathematical Programming},
  volume       = {97},
  year         = {2003},
  url          = {https://link.springer.com/article/10.1007/s10107-003-0447-x}
}

@article{DBLP:journals/corr/abs-1803-05861,
  author       = {Ludovic Cal{\`{e}}s and
                  Apostolos Chalkis and
                  Ioannis Z. Emiris and
                  Vissarion Fisikopoulos},
  title        = {Practical volume computation of structured convex bodies, and an application
                  to modeling portfolio dependencies and financial crises},
  journal      = {CoRR},
  volume       = {abs/1803.05861},
  year         = {2018},
  url          = {http://arxiv.org/abs/1803.05861},
  eprinttype    = {arXiv},
  eprint       = {1803.05861},
  timestamp    = {Mon, 13 Aug 2018 16:45:57 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-1803-05861.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}


@misc{COBRA,
      title={Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0}, 
      author={Laurent Heirendt and Sylvain Arreckx and Thomas Pfau and Sebastián N. Mendoza and Anne Richelle and Almut Heinken and Hulda S. Haraldsdóttir and Jacek Wachowiak and Sarah M. Keating and Vanja Vlasov and Stefania Magnusdóttir and Chiam Yu Ng and German Preciat and Alise Žagare and Siu H. J. Chan and Maike K. Aurich and Catherine M. Clancy and Jennifer Modamio and John T. Sauls and Alberto Noronha and Aarash Bordbar and Benjamin Cousins and Diana C. El Assal and Luis V. Valcarcel and Iñigo Apaolaza and Susan Ghaderi and Masoud Ahookhosh and Marouen Ben Guebila and Andrejs Kostromins and Nicolas Sompairac and Hoai M. Le and Ding Ma and Yuekai Sun and Lin Wang and James T. Yurkovich and Miguel A. P. Oliveira and Phan T. Vuong and Lemmer P. El Assal and Inna Kuperstein and Andrei Zinovyev and H. Scott Hinton and William A. Bryant and Francisco J. Aragón Artacho and Francisco J. Planes and Egils Stalidzans and Alejandro Maass and Santosh Vempala and Michael Hucka and Michael A. Saunders and Costas D. Maranas and Nathan E. Lewis and Thomas Sauter and Bernhard Ø. Palsson and Ines Thiele and Ronan M. T. Fleming},
      year={2018},
      eprint={1710.04038},
      archivePrefix={arXiv},
      primaryClass={q-bio.QM}
}

@article{10.1093/nar/gkv1049,
    author = {King, Zachary A. and Lu, Justin and Dräger, Andreas and Miller, Philip and Federowicz, Stephen and Lerman, Joshua A. and Ebrahim, Ali and Palsson, Bernhard O. and Lewis, Nathan E.},
    title = "{BiGG Models: A platform for integrating, standardizing and sharing genome-scale models}",
    journal = {Nucleic Acids Research},
    volume = {44},
    number = {D1},
    pages = {D515-D522},
    year = {2015},
    month = {10},
    abstract = "{Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkv1049},
    url = {https://doi.org/10.1093/nar/gkv1049},
    eprint = {https://academic.oup.com/nar/article-pdf/44/D1/D515/16661243/gkv1049.pdf},
}


@article{im2023revisiting,
	author = {Im, Haesol and Wolkowicz, Henry},
	date-added = {2023-11-15 15:48:48 -0500},
	date-modified = {2023-11-15 15:48:48 -0500},
	journal = {European Journal of Operational Research},
	number = {2},
	pages = {495--510},
	publisher = {Elsevier},
	title = {Revisiting degeneracy, strict feasibility, stability, in linear programming},
	volume = {310},
	year = {2023}}


@article{Chalkis_2021,
   title={volesti: Volume Approximation and Sampling for Convex Polytopes in R},
   volume={13},
   ISSN={2073-4859},
   url={http://dx.doi.org/10.32614/RJ-2021-077},
   DOI={10.32614/rj-2021-077},
   number={2},
   journal={The R Journal},
   publisher={The R Foundation},
   author={Chalkis, Apostolos and Fisikopoulos, Vissarion},
   year={2021},
   pages={561} }

@article{Yao2017, doi = {10.21105/joss.00061}, url = {https://doi.org/10.21105/joss.00061}, year = {2017}, publisher = {The Open Journal}, volume = {2}, number = {11}, pages = {61}, author = {Andy Yu Zhu Yao and David Kane}, title = {walkr: MCMC Sampling from Non-Negative Convex Polytopes}, journal = {Journal of Open Source Software} }


@article{CIOMEK2021100659,
	author = {Krzysztof Ciomek and Mi{\l}osz Kadzi{\'n}ski},
	journal = {SoftwareX},
	pages = {100659},
	title = {Polyrun: A Java library for sampling from the bounded convex polytopes},
	volume = {13},
	year = {2021}}

@article {Emanuel:2007,
    author = "Kerry Emanuel",
    title = "Environmental Factors Affecting Tropical Cyclone Power Dissipation",
    journal = "Journal of Climate",
    year = "2007",
    publisher = "American Meteorological Society",
    address = "Boston MA, USA",
    volume = "20",
    number = "22",
    doi = "10.1175/2007JCLI1571.1",
    pages= "5497 - 5509",
    url = "https://journals.ametsoc.org/view/journals/clim/20/22/2007jcli1571.1.xml"
}