@article{carhart1985apm,
  title={{Atom pairs as molecular features in structure-activity studies: definition and applications}},
  author={Carhart, R.E. and Smith, D.H. and Venkataraghavan, R.},
  journal={Journal of Chemical Information and Computer Sciences},
  volume={25},
  number={2},
  pages={64--73},
  year={1985},
  publisher={American Chemical Society}
}
@article{chen2002psm,
  title={{Performance of Similarity Measures in 2D Fragment-Based Similarity Searching: Comparison of Structural Descriptors and Similarity Coefficients}},
  author={Chen, X. and Reynolds, C.H.},
  journal={Journal of Chemical Information and Computer Sciences},
  volume={42},
  number={6},
  pages={1407--1414},
  year={2002}
}

@Article{girke2005ccm,
author = "Girke, T and Cheng, L C and Raikhel, N",
title = {{C}hem{M}ine. {A} compound mining database for chemical genomics},
abstract = {},
journal = "Plant Physiol",
year = "2005",
volume = "138",
number = "2",
pages = "573-577",
pmid = "15955920",
doi = "10.1104/pp.105.062687"
}

@Article{Cao2008c,
author = "Cao, Y and Charisi, A and Cheng, L C and Jiang, T and Girke, T",
title = {{ChemmineR: a compound mining framework for R}},
journal = "Bioinformatics",
year = "2008",
volume = "24",
number = "15",
pages = "1733-1734",
month = "Aug",
pmid = "18596077",
url = "http://www.hubmed.org/display.cgi?uids=18596077",
doi = "10.1093/bioinformatics/btn307",
}
@Article{Backman2011a,
author = "Backman, T W and Cao, Y and Girke, T",
title = {{ChemMine tools: an online service for analyzing and clustering small molecules}},
journal = "Nucleic Acids Res",
year = "2011",
volume = "39",
number = "Web Server issue",
pages = "486-491",
month = "Jul",
pmid = "21576229",
url = "http://www.hubmed.org/display.cgi?uids=21576229",
doi = "10.1093/nar/gkr320"
}
@Article{Hanser1996a,
author = {Hanser, Th. and Jauffret, Ph. and Kaufmann, G.},
title = {A New Algorithm for Exhaustive Ring Perception in a Molecular Graph},
journal = {Journal of Chemical Information and Computer Sciences},
volume = {36},
number = {6},
pages = {1146-1152},
year = {1996},
url = {http://pubs.acs.org/doi/abs/10.1021/ci960322f},
mycat = "<<<cheminformatics>>> <<ring perception>>",
doi = {10.1021/ci960322f}
}
@Article{Jarvis1973a,
title={{Clustering using a similarity measure based on shared near neighbors}},
author={Jarvis, R.A. and Patrick, E.A.},
journal={IEEE Transactions on Computers},
volume={22},
number={11},
pages={1025--1034},
year={1973},
url = {http://davide.eynard.it/teaching/2012_PAMI/JP.pdf},  
publisher={IEEE Computer Society Washington, DC, USA}
}
@Article{Wang2013a,
author = "Wang, Y and Backman, T W and Horan, K and Girke, T",
title = {{fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R}},
journal = "Bioinformatics",
year = "2013",
volume = "",
number = "",
pages = "",
month = "Aug",
pmid = "23962615",
url = "http://www.hubmed.org/display.cgi?uids=23962615",
doi = "10.1093/bioinformatics/btt475"
}
@Article{OBoyle2011a,
author = "O'Boyle, N M and Banck, M and James, C A and Morley, C and Vandermeersch, T and Hutchison, G R",
title = {{Open Babel: An open chemical toolbox}},
journal = "J Cheminform",
year = "2011",
volume = "3",
number = "",
pages = "33-33",
month = "",
pmid = "21982300",
url = "http://www.hubmed.org/display.cgi?uids=21982300",
doi = "10.1186/1758-2946-3-33"
}
@Article{OBoyle2008a,
author = "O'Boyle, N M and Morley, C and Hutchison, G R",
title = {{Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit}},
journal = "Chem Cent J",
year = "2008",
volume = "2",
number = "1",
pages = "5-5",
month = "Mar",
pmid = "18328109",
pmcid = "PMC2270842",
url = "http://www.hubmed.org/display.cgi?uids=18328109",
doi = "10.1186/1752-153X-2-5",
}
