Moved into trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@341 636b058d-ea47-450e-bf9e-a15bfbe3eedb

1 files changed, 831 insertions, 0 deletions

diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib
new file mode 100644
index 00000000..eec8c14f
--- /dev/null
+++ b/biblio/bibliography.bib
@@ -0,0 +1,831 @@
+@inproceedings{gudhilibrary_ICMS14,
+  author    = {Cl\'ement Maria and Jean-Daniel Boissonnat and 
+              Marc Glisse and Mariette Yvinec},
+  title     = {The {G}udhi Library: Simplicial Complexes and Persistent Homology},
+  booktitle = {ICMS},
+  year      = {2014},
+}
+
+@inproceedings{zigzag_reflection,
+  author    = {Jean-Daniel Boissonnat and Cl\'ement Maria and Steve Oudot},
+  title     = {Zigzag Persistent Homology Algorithm via Reflections},
+  year      = {2014 $\ \ \ \ \ \ \ \ \ \ \ $ \emph{In Preparation}},
+}
+
+@misc{gudhi_stpcoh,
+  author = {Cl\'ement Maria},
+  title = "\textsc{Gudhi}, Simplex Tree and Persistent Cohomology Packages",
+  note  = "\href{https://project.inria.fr/gudhi/software/}{\url{https://project.inria.fr/gudhi/software/}}"
+}
+
+%ARTICLES
+%------------------------------------------------------------------
+@article{boissonnatmariasimplextreealgorithmica,
+year={2014},
+issn={0178-4617},
+journal={Algorithmica},
+doi={10.1007/s00453-014-9887-3},
+title={\href{http://dx.doi.org/10.1007/s00453-014-9887-3}{The Simplex Tree: An Efficient Data Structure for General Simplicial Complexes}},
+publisher={Springer US},
+keywords={Simplicial complexes; Data structure; Computational topology; Flag complexes; Witness complexes},
+author={Boissonnat, Jean-Daniel and Maria, Cl\'ement},
+pages={1-22},
+language={English}
+}
+
+@article{boissonnatmariacamalgorithmica,
+journal={Submitted to Algorithmica},
+title={The Compressed Annotation Matrix: An Efficient Data Structure for Computing Persistent Cohomology},
+author={Jean-Daniel Boissonnat and Tamal K. Dey and Cl{\'e}ment Maria},
+language={English},
+}
+
+@inproceedings{DBLP:conf/esa/BoissonnatDM13,
+  author    = {Jean-Daniel Boissonnat and
+               Tamal K. Dey and
+               Cl{\'e}ment Maria},
+  title     = {\href{http://dx.doi.org/10.1007/978-3-642-40450-4_59}{The Compressed Annotation Matrix: An Efficient Data Structure
+               for Computing Persistent Cohomology}},
+  booktitle = {ESA},
+  year      = {2013},
+  pages     = {695-706},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+@inproceedings{boissonnatmariaesa2014,
+  author    = {Jean-Daniel Boissonnat and
+               Cl{\'e}ment Maria},
+  title     = {Computing Persistent Homology with Various Coefficient Fields in a Single Pass},
+  booktitle = {ESA},
+  year      = {2014}
+}
+
+@inproceedings{DBLP:conf/esa/BoissonnatM12,
+  author    = {Jean-Daniel Boissonnat and
+               Cl{\'e}ment Maria},
+  title     = {\href{http://dx.doi.org/10.1007/978-3-642-33090-2_63}{The Simplex Tree: An Efficient Data Structure for General
+               Simplicial Complexes}},
+  booktitle = {ESA},
+  year      = {2012},
+  pages     = {731-742},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+
+%% hal-00922572, version 2
+%% http://hal.inria.fr/hal-00922572
+@techreport{boissonnat:hal-00922572,
+    hal_id = {hal-00922572},
+    url = {http://hal.inria.fr/hal-00922572},
+    title = {\href{http://hal.inria.fr/hal-00922572}{Computing Persistent Homology with Various Coefficient Fields in a Single Pass}},
+    author = {Boissonnat, Jean-Daniel and Maria, Cl{\'e}ment},
+    abstract = {{In this article, we introduce the multi-field persistence diagram for the persistence homology of a filtered complex. It encodes compactly the superimposition of the persistence diagrams of the complex with several field coefficients, and provides a substantially more precise description of the topology of the filtered complex. Specifically, the multi-field persistence diagram encodes the Betti numbers of integral homology and the prime divisors of the torsion coefficients of the underlying shape. Moreover, it enjoys similar stability properties as the ones of standard persistence diagrams, with the appropriate notion of distance. These properties make the multi-field persistence diagram a useful tool in computational topology.}},
+    keywords = {Computational Topology, Persistent homology, Modular reconstruction},
+    language = {Anglais},
+    affiliation = {GEOMETRICA - INRIA Sophia Antipolis / INRIA Saclay - Ile de France},
+    pages = {19},
+    type = {Rapport de recherche},
+    institution = {INRIA},
+    number = {RR-8436},
+    year = {2013},
+    month = Dec,
+    pdf = {http://hal.inria.fr/hal-00922572/PDF/RR-8436.pdf},
+}
+
+
+
+
+
+
+@inproceedings{DBLP:conf/compgeom/CarlssonSM09,
+  author    = {Gunnar E. Carlsson and
+               Vin de Silva and
+               Dmitriy Morozov},
+  title     = {Zigzag persistent homology and real-valued functions},
+  booktitle = {Symposium on Computational Geometry},
+  year      = {2009},
+  pages     = {247-256},
+  ee        = {http://doi.acm.org/10.1145/1542362.1542408},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@inproceedings{DBLP:conf/compgeom/Cohen-SteinerEM06,
+  author    = {David Cohen-Steiner and
+               Herbert Edelsbrunner and
+               Dmitriy Morozov},
+  title     = {Vines and vineyards by updating persistence in linear time},
+  booktitle = {Symposium on Computational Geometry},
+  year      = {2006},
+  pages     = {119-126},
+  ee        = {http://doi.acm.org/10.1145/1137856.1137877},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+@article{quiverrepresentations_derksenweyman,
+  author  = {Harm Derksen and Jerzy Weyman},
+  title   = {Quiver Representations},
+  journal = {Notices of the AMS},
+  volume  = {52},
+  number  = {2},
+  year    = {2005},
+  pages   = {200-206}
+}
+@article{DBLP:journals/dcg/SilvaMV11,
+  author    = {Vin de Silva and
+               Dmitriy Morozov and
+               Mikael Vejdemo-Johansson},
+  title     = {Persistent Cohomology and Circular Coordinates},
+  journal   = {Discrete {\&} Computational Geometry},
+  volume    = {45},
+  number    = {4},
+  year      = {2011},
+  pages     = {737-759},
+  ee        = {http://dx.doi.org/10.1007/s00454-011-9344-x},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@article{RS62,
+	author={J. B. Rosser and L. Schoenfeld},
+	title={Approximate Formulas for some Functions of Prime Numbers},
+	journal= ijm,
+	volume= 6,
+	year= 1962,
+	pages={64-94},
+	mrnumber={25 \#1139}
+}
+@article{DBLP:journals/siamcomp/Furer09,
+  author    = {Martin F{\"u}rer},
+  title     = {Faster Integer Multiplication},
+  journal   = {SIAM J. Comput.},
+  volume    = {39},
+  number    = {3},
+  year      = {2009},
+  pages     = {979-1005},
+  ee        = {http://dx.doi.org/10.1137/070711761},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@article{DBLP:journals/dcg/ZomorodianC05,
+  author    = {Afra Zomorodian and
+               Gunnar E. Carlsson},
+  title     = {Computing Persistent Homology},
+  journal   = {Discrete {\&} Computational Geometry},
+  volume    = {33},
+  number    = {2},
+  year      = {2005},
+  pages     = {249-274},
+  ee        = {http://www.springerlink.com/index/10.1007/s00454-004-1146-y},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@article{DBLP:journals/dcg/Cohen-SteinerEH07,
+  author    = {David Cohen-Steiner and
+               Herbert Edelsbrunner and
+               John Harer},
+  title     = {Stability of Persistence Diagrams},
+  journal   = {Discrete {\&} Computational Geometry},
+  volume    = {37},
+  number    = {1},
+  year      = {2007},
+  pages     = {103-120},
+  ee        = {http://dx.doi.org/10.1007/s00454-006-1276-5},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@article{DBLP:journals/siamcomp/HafnerM91,
+  author    = {James L. Hafner and
+               Kevin S. McCurley},
+  title     = {Asymptotically Fast Triangularization of Matrices Over Rings},
+  journal   = {SIAM J. Comput.},
+  volume    = {20},
+  number    = {6},
+  year      = {1991},
+  pages     = {1068-1083},
+  ee        = {http://dx.doi.org/10.1137/0220067},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@article{DBLP:journals/algorithmica/EfratIK01,
+  author    = {Alon Efrat and
+               Alon Itai and
+               Matthew J. Katz},
+  title     = {Geometry Helps in Bottleneck Matching and Related Problems},
+  journal   = {Algorithmica},
+  volume    = {31},
+  number    = {1},
+  year      = {2001},
+  pages     = {1-28},
+  ee        = {http://dx.doi.org/10.1007/s00453-001-0016-8},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@article{DBLP:journals/siamcomp/HopcroftK73,
+  author    = {John E. Hopcroft and
+               Richard M. Karp},
+  title     = {An n$^{\mbox{5/2}}$ Algorithm for Maximum Matchings in Bipartite
+               Graphs},
+  journal   = {SIAM J. Comput.},
+  volume    = {2},
+  number    = {4},
+  year      = {1973},
+  pages     = {225-231},
+  ee        = {http://dx.doi.org/10.1137/0202019},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+%------------------------------------------------------------------
+@article{DBLP:journals/corr/abs-1210-1429,
+  author    = {Pawel Dlotko and
+               Hubert Wagner},
+  title     = {Computing homology and persistent homology using iterated
+               Morse decomposition},
+  journal   = {CoRR},
+  volume    = {abs/1210.1429},
+  year      = {2012},
+  ee        = {http://arxiv.org/abs/1210.1429},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+%BOOKS
+%------------------------------------------------------------------
+@book{DBLP:tibkat_237559129,
+   author              = {Saunders Mac Lane},
+   title               = {Categories for the working mathematician},
+   year                = {1998},
+   ee                  = {http://www.zentralblatt-math.org/zmath/en/search/?an}
+}
+
+
+@book{Hatcher-algebraictopology2001,
+    author = {Hatcher, Allen},
+    day = {03},
+    edition = {1},
+    howpublished = {Paperback},
+    isbn = {0521795400},
+    keywords = {topology},
+    month = dec,
+    posted-at = {2008-06-25 09:53:39},
+    priority = {2},
+    publisher = {Cambridge University Press},
+    title = {{Algebraic Topology}},
+    url = {http://www.math.cornell.edu/\~{}hatcher/AT/AT.pdf},
+    year = {2001}
+}
+@book{Munkres-elementsalgtop1984,
+  author    = {James R. Munkres},
+  title     = {Elements of algebraic topology},
+  publisher = {Addison-Wesley},
+  year      = {1984},
+  isbn      = {978-0-201-04586-4},
+  pages     = {I-IX, 1-454},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@book{DBLP:books/aw/Knuth81,
+  author    = {Donald E. Knuth},
+  title     = {The Art of Computer Programming, Volume II: Seminumerical
+               Algorithms, 2nd Edition},
+  publisher = {Addison-Wesley},
+  year      = {1981},
+  isbn      = {0-201-03822-6},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@book{DBLP:books/daglib/0025666,
+  author    = {Herbert Edelsbrunner and
+               John Harer},
+  title     = {Computational Topology - an Introduction},
+  publisher = {American Mathematical Society},
+  year      = {2010},
+  isbn      = {978-0-8218-4925-5},
+  pages     = {I-XII, 1-241},
+  ee        = {http://www.ams.org/bookstore-getitem/item=MBK-69},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@book{Gathen:2003:MCA:945759,
+ author = {Gathen, Joachim Von Zur and Gerhard, Jurgen},
+ title = {Modern Computer Algebra},
+ year = {2003},
+ isbn = {0521826462},
+ edition = {2},
+ publisher = {Cambridge University Press},
+ address = {New York, NY, USA},
+} 
+@book{DBLP:books/aw/AhoHU74,
+  author    = {Alfred V. Aho and
+               John E. Hopcroft and
+               Jeffrey D. Ullman},
+  title     = {The Design and Analysis of Computer Algorithms},
+  publisher = {Addison-Wesley},
+  year      = {1974},
+  isbn      = {0-201-00029-6},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+%------------------------------------------------------------------
+
+
+
+%INPROCEEDINGS
+%------------------------------------------------------------------
+
+  crossref  = {DBLP:conf/esa/2013},
+
+proceedings{DBLP:conf/esa/2013,
+  editor    = {Hans L. Bodlaender and
+               Giuseppe F. Italiano},
+  title     = {Algorithms - ESA 2013 - 21st Annual European Symposium,
+               Sophia Antipolis, France, September 2-4, 2013. Proceedings},
+  booktitle = {ESA},
+  publisher = {Springer},
+  series    = {Lecture Notes in Computer Science},
+  volume    = {8125},
+  year      = {2013},
+  isbn      = {978-3-642-40449-8},
+  ee        = {http://dx.doi.org/10.1007/978-3-642-40450-4},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@inproceedings{DBLP:conf/issac/StorjohannL96,
+  author    = {Arne Storjohann and
+               George Labahn},
+  title     = {Asymptotically Fast Computation of {H}ermite Normal Forms
+               of Integer Matrices},
+  booktitle = {ISSAC},
+  year      = {1996},
+  pages     = {259-266},
+  ee        = {http://doi.acm.org/10.1145/236869.237083},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}  crossref  = {DBLP:conf/issac/1996},
+@inproceedings{DBLP:conf/issac/Storjohann96,
+  author    = {Arne Storjohann},
+  title     = {Near Optimal Algorithms for Computing Smith Normal Forms
+               of Integer Matrices},
+  booktitle = {ISSAC},
+  year      = {1996},
+  pages     = {267-274},
+  ee        = {http://doi.acm.org/10.1145/236869.237084},
+
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}  crossref  = {DBLP:conf/issac/1996},
+proceedings{DBLP:conf/issac/1996,
+  editor    = {Erwin Engeler and
+               B. F. Caviness and
+               Yagati N. Lakshman},
+  title     = {Proceedings of the 1996 International Symposium on Symbolic
+               and Algebraic Computation, ISSAC '96, Zurich, Switzerland,
+               July 24-26, 1996},
+  booktitle = {ISSAC},
+  publisher = {ACM},
+  year      = {1996},
+  isbn      = {0-89791-796-0},
+  ee        = {http://dl.acm.org/citation.cfm?id=236869},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+%------------------------------------------------------------------
+
+%MISC
+%------------------------------------------------------------------
+@article{DBLP:journals/corr/abs-1208-5018,
+  author    = {Tamal K. Dey and
+               Fengtao Fan and
+               Yusu Wang},
+  title     = {Computing Topological Persistence for Simplicial Maps},
+  journal   = {CoRR},
+  volume    = {abs/1208.5018},
+  year      = {2012},
+  ee        = {http://arxiv.org/abs/1208.5018},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@article{DBLP:journals/corr/abs-1107-5665,
+  author    = {Vin de Silva and
+               Dmitriy Morozov and
+               Mikael Vejdemo-Johansson},
+  title     = {Dualities in persistent (co)homology},
+  journal   = {CoRR},
+  volume    = {abs/1107.5665},
+  year      = {2011},
+  ee        = {http://arxiv.org/abs/1107.5665},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+%------------------------------------------------------------------
+
+%LIBRARY
+
+%------------------------------------------------------------------
+@misc{gmplib_cite,
+title = "GMP, The GNU Multiple Precision Arithmetic Library",
+note = "http://gmplib.org/",
+}
+%------------------------------------------------------------------
+
+
+
+
+%TEMPORARY
+%------------------------------------------------------------------
+@inproceedings{deSilva:2013:GSP:2493132.2462402,
+ author = {de Silva, Vin and Nanda, Vidit},
+ title = {Geometry in the space of persistence modules},
+ booktitle = {Proceedings of the twenty-ninth annual symposium on Computational geometry},
+ series = {SoCG '13},
+ year = {2013},
+ isbn = {978-1-4503-2031-3},
+ location = {Rio de Janeiro, Brazil},
+ pages = {397--404},
+ numpages = {8},
+ url = {http://doi.acm.org/10.1145/2462356.2462402},
+ doi = {10.1145/2462356.2462402},
+ acmid = {2462402},
+ publisher = {ACM},
+ address = {New York, NY, USA},
+ keywords = {discrete and computational geometry, embedding theorem, persistent homology},
+} 
+@article{Fredman:1984:SST:828.1884,
+ author = {Fredman, Michael L. and Koml\'{o}s, J\'{a}nos and Szemer{\'e}di, Endre},
+ title = {Storing a Sparse Table with {O}(1) Worst Case Access Time},
+ journal = {J. ACM},
+ issue_date = {July 1984},
+ volume = {31},
+ number = {3},
+ month = jun,
+ year = {1984},
+ issn = {0004-5411},
+ pages = {538--544},
+ numpages = {7},
+ url = {http://doi.acm.org/10.1145/828.1884},
+ doi = {10.1145/828.1884},
+ acmid = {1884},
+ publisher = {ACM},
+ address = {New York, NY, USA},
+} 
+%------------------------------------------------------------------
+
+
+
+%%%%% TEMP
+article{journals/moc/Moller08,
+  added-at = {2011-04-10T00:00:00.000+0200},
+  author = {M\"oller, Niels},
+  biburl = {http://www.bibsonomy.org/bibtex/2a40c83ae0a723c978ff29ccaec7ff7ee/dblp},
+  ee = {http://dx.doi.org/10.1090/S0025-5718-07-02017-0},
+  interhash = {d2f425fef08e9b3ea347b12cbcf9792f},
+  intrahash = {a40c83ae0a723c978ff29ccaec7ff7ee},
+  journal = {Math. Comput.},
+  keywords = {dblp},
+  number = 261,
+  pages = {589-607},
+  timestamp = {2011-04-10T00:00:00.000+0200},
+  title = {On Sch\"onhage's algorithm and subquadratic integer gcd computation.},
+  url = {http://dblp.uni-trier.de/db/journals/moc/moc77.html#Moller08},
+  volume = 77,
+  year = 2008
+}
+
+@article{DBLP:journals/dcg/EdelsbrunnerLZ02,
+  author    = {Herbert Edelsbrunner and
+               David Letscher and
+               Afra Zomorodian},
+  title     = {Topological Persistence and Simplification},
+  journal   = {Discrete Comput. Geom.},
+  volume    = {28},
+  number    = {4},
+  year      = {2002},
+  pages     = {511-533},
+  ee        = {http://dx.doi.org/10.1007/s00454-002-2885-2},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+
+
+inproceedings{DBLP:conf/esa/2012,
+  editor    = {Leah Epstein and
+               Paolo Ferragina},
+  title     = {Algorithms - ESA 2012 - 20th Annual European Symposium,
+               Ljubljana, Slovenia, September 10-12, 2012. Proceedings},
+  booktitle = {ESA},
+  publisher = {Springer},
+  series    = {Lecture Notes in Computer Science},
+  volume    = {7501},
+  year      = {2012},
+  isbn      = {978-3-642-33089-6},
+  ee        = {http://dx.doi.org/10.1007/978-3-642-33090-2},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+
+@article{SMV11,
+  author    = {V. de Silva and
+               D. Morozov and
+               M. Vejdemo-Johansson},
+  title     = {Persistent cohomology and circular coordinates},
+  journal   = {Discrete Comput. Geom.},
+  volume    = {45},
+  pages = {737-759},
+  year      = {2011},
+}
+@article{SMV211,
+  author    = {V. de Silva and
+               D. Morozov and
+               M. Vejdemo-Johansson},
+  title     = {Dualities in persistent (co)homology},
+  journal   = {Inverse Problems},
+  volume    = {27},
+  year      = {2011},
+  pages     = {124003},
+}
+
+
+
+
+
+inproceedings{DBLP:conf/soda/BentleyS97,
+  author    = {Jon Louis Bentley and
+               Robert Sedgewick},
+  title     = {Fast Algorithms for Sorting and Searching Strings},
+  booktitle = {SODA},
+  year      = {1997},
+  pages     = {360-369},
+  ee        = {http://doi.acm.org/10.1145/314161.314321},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@inproceedings{CO08,
+  author    = {F. Chazal and S. Oudot},
+  title     = {Towards persistence-based reconstruction in Euclidean spaces},
+  booktitle   = {Proc. 24th. Annu. Sympos. Comput. Geom.},
+  year      = {2008},
+  pages = {231-241}
+}
+inproceedings{DBLP:conf/soda/1997,
+  editor    = {Michael E. Saks},
+  title     = {Proceedings of the Eighth Annual ACM-SIAM Symposium on Discrete
+               Algorithms, 5-7 January 1997, New Orleans, Louisiana},
+  booktitle = {SODA},
+  publisher = {ACM/SIAM},
+  year      = {1997},
+  isbn      = {0-89871-390-0},
+  ee        = {http://dl.acm.org/citation.cfm?id=314161},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+
+
+
+inproceedings{attali-rips_approx,
+  author    = {Dominique Attali and
+               Andr{\'e} Lieutier and
+               David Salinas},
+  title     = {Vietoris-rips complexes also provide topologically correct
+               reconstructions of sampled shapes},
+  booktitle = {Symposium on Computational Geometry},
+  year      = {2011},
+  pages     = {491-500},
+  ee        = {http://doi.acm.org/10.1145/1998196.1998276},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+
+
+@article{Carlsson:2008:LBS:1325290.1325300,
+ author = {Carlsson, Gunnar and Ishkhanov, Tigran and Silva, Vin and Zomorodian, Afra},
+ title = {On the Local Behavior of Spaces of Natural Images},
+ journal = {Int. J. Comput. Vision},
+ volume = {76},
+ issue = {1},
+ month = {January},
+ year = {2008},
+ issn = {0920-5691},
+ pages = {1--12},
+ numpages = {12},
+ url = {http://portal.acm.org/citation.cfm?id=1325290.1325300},
+ doi = {10.1007/s11263-007-0056-x},
+ acmid = {1325300},
+ publisher = {Kluwer Academic Publishers},
+ address = {Hingham, MA, USA},
+ keywords = {Filtration, Klein bottle, Manifold, Natural images, Persistent homology, Topology},
+} 
+
+article{DBLP:journals/ijcv/LeePM03,
+  author    = {Ann B. Lee and
+               Kim Steenstrup Pedersen and
+               David Mumford},
+  title     = {The Nonlinear Statistics of High-Contrast Patches in Natural
+               Images},
+  journal   = {International Journal of Computer Vision},
+  volume    = {54},
+  number    = {1-3},
+  year      = {2003},
+  pages     = {83-103},
+  ee        = {http://dx.doi.org/10.1023/A:1023705401078},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+@article{martin2010top,
+title={Topology of cyclo-octane energy landscape.},
+author={Martin, S. and Thompson, A. and Coutsias, E.A. and Watson, J.},
+journal={J Chem Phys},
+volume={132},
+number={23},
+pages={234115},
+year={2010},
+abstract={Understanding energy landscapes is a major challenge in chemistry and biology. Although a wide variety of methods have been invented and applied to this problem, very little is understood about the actual mathematical structures underlying such landscapes. Perhaps the most general assumption is the idea that energy landscapes are low-dimensional manifolds embedded in high-dimensional Euclidean space. While this is a very mild assumption, we have discovered an example of an energy landscape which is nonmanifold, demonstrating previously unknown mathematical complexity. The example occurs in the energy landscape of cyclo-octane, which was found to have the structure of a reducible algebraic variety, composed of the union of a sphere and a Klein bottle, intersecting in two rings.}
+}
+ 
+
+book{hatcher2002algebraic,
+  title={Algebraic Topology},
+  author={Hatcher, A.},
+  isbn={9780521795401},
+  lccn={00065166},
+  url={http://books.google.fr/books?id=BjKs86kosqgC},
+  year={2002},
+  publisher={Cambridge University Press}
+}
+
+
+
+@article{DBLP:journals/cagd/DelfinadoE95,
+  author    = {Cecil Jose A. Delfinado and
+               Herbert Edelsbrunner},
+  title     = {An incremental algorithm for {B}etti numbers of simplicial
+               complexes on the 3-sphere},
+  journal   = {Computer Aided Geometric Design},
+  volume    = {12},
+  number    = {7},
+  year      = {1995},
+  pages     = {771-784},
+  ee        = {http://dx.doi.org/10.1016/0167-8396(95)00016-Y},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+@book{Cormen:2001:IA:580470,
+ author = {Cormen, Thomas H. and Stein, Clifford and Rivest, Ronald L. and Leiserson, Charles E.},
+ title = {Introduction to Algorithms},
+ year = {2001},
+ isbn = {0070131511},
+ edition = {2nd},
+ publisher = {McGraw-Hill Higher Education},
+} 
+
+@article{DBLP:journals/focm/CarlssonS10,
+  author    = {Gunnar E. Carlsson and
+               Vin de Silva},
+  title     = {Zigzag Persistence},
+  journal   = {Foundations of Computational Mathematics},
+  volume    = {10},
+  number    = {4},
+  year      = {2010},
+  pages     = {367-405},
+  ee        = {http://dx.doi.org/10.1007/s10208-010-9066-0},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+@article{ghrist_coverage,
+  author    = {V. de Silva and R. Ghrist},
+  title     = {Coverage in sensor network via persistent homology},
+  journal   = {Algebraic {\&} Geometric Topology},
+  volume    = {7},
+  year      = {2007},
+  pages     = {339-358},
+}
+@article{mischaikow_nanda_morse,
+year={2013},
+issn={0179-5376},
+journal={Discrete {\&} Computational Geometry},
+volume={50},
+number={2},
+doi={10.1007/s00454-013-9529-6},
+title={Morse Theory for Filtrations and Efficient Computation of Persistent Homology},
+url={http://dx.doi.org/10.1007/s00454-013-9529-6},
+publisher={Springer US},
+keywords={Computational topology; Discrete Morse theory; Persistent homology},
+author={Mischaikow, Konstantin and Nanda, Vidit},
+pages={330-353},
+language={English}
+}
+
+
+@inproceedings{DBLP:conf/compgeom/MilosavljevicMS11,
+  author    = {Nikola Milosavljevic and
+               Dmitriy Morozov and
+               Primoz Skraba},
+  title     = {Zigzag persistent homology in matrix multiplication time},
+  booktitle = {Symposium on Comp. Geom.},
+  year      = {2011},
+  ee        = {http://doi.acm.org/10.1145/1998196.1998229},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+proceedings{DBLP:conf/compgeom/2011,
+  editor    = {Ferran Hurtado and
+               Marc J. van Kreveld},
+  title     = {Proceedings of the 27th ACM Symposium on Computational Geometry,
+               Paris, France, June 13-15, 2011},
+  booktitle = {Symposium on Computational Geometry},
+  publisher = {ACM},
+  year      = {2011},
+  isbn      = {978-1-4503-0682-9},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+@article{DBLP:journals/comgeo/ChenK13,
+  author    = {Chao Chen and
+               Michael Kerber},
+  title     = {An output-sensitive algorithm for persistent homology},
+  journal   = {Comput. Geom.},
+  volume    = {46},
+  number    = {4},
+  year      = {2013},
+  pages     = {435-447},
+  ee        = {http://dx.doi.org/10.1016/j.comgeo.2012.02.010},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+
+@incollection{Bauer:arXiv1303.0477,
+year={2014},
+isbn={978-3-319-04098-1},
+booktitle={Topological Methods in Data Analysis and Visualization III},
+doi={10.1007/978-3-319-04099-8_7},
+title={Clear and Compress: Computing Persistent Homology in Chunks},
+url={http://dx.doi.org/10.1007/978-3-319-04099-8_7},
+author={Bauer, Ulrich and Kerber, Michael and Reininghaus, Jan},
+pages={103-117},
+language={English}
+}
+@inproceedings{DBLP:conf/alenex/BauerKR14,
+  author    = {Ulrich Bauer and
+               Michael Kerber and
+               Jan Reininghaus},
+  title     = {Distributed Computation of Persistent Homology},
+  booktitle = {ALENEX},
+  year      = {2014},
+  pages     = {31-38},
+  ee        = {http://dx.doi.org/10.1137/1.9781611973198.4},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+@inproceedings{DBLP:conf/compgeom/DeyFW14,
+  author    = {Tamal K. Dey and
+               Fengtao Fan and
+               Yusu Wang},
+  title     = {Computing Topological Persistence for Simplicial Maps},
+  booktitle = {Symposium on Computational Geometry},
+  year      = {2014},
+  pages     = {345},
+  ee        = {http://doi.acm.org/10.1145/2582112.2582165},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+@INPROCEEDINGS{Chen11persistenthomology,
+    author = {Chao Chen and Michael Kerber},
+    title = {Persistent homology computation with a twist},
+    booktitle = {Proceedings 27th European Workshop on Computational Geometry},
+    year = {2011}
+}
+
+
+@ARTICLE{Morozov05persistencealgorithm,
+    author = {Dmitriy Morozov},
+    title = {Persistence algorithm takes cubic time in worst case},
+    journal = {BioGeometry News, Dept. Comput. Sci., Duke Univ},
+    year = {2005}
+}
+
+@article{DBLP:journals/corr/abs-1205-3669,
+  author    = {Peter Bubenik and
+               Jonathan A. Scott},
+  title     = {Categorification of persistent homology},
+  journal   = {CoRR},
+  volume    = {abs/1205.3669},
+  year      = {2012},
+  ee        = {http://arxiv.org/abs/1205.3669},
+  bibsource = {DBLP, http://dblp.uni-trier.de}
+}
+
+misc{buddha_stanford_scan,
+ author = "",
+   title = "The Stanford 3D Scanning Repository",
+    note  = "http://graphics.stanford.edu/data/3Dscanrep/"
+}
+@misc{dionysus_morozov,
+ author = "Dmitriy Morozov",
+   title = "\textsc{Dionysus}",
+    note  = "http://www.mrzv.org/software/dionysus/"
+}
+
+@misc{phat_lib,
+author={Bauer, Ulrich and Kerber, Michael and Reininghaus, Jan},
+   title = "\textsc{Phat}",
+    note  = "https://code.google.com/p/phat/"
+}
+
+misc{ann_mount,
+author = "David M. Mount
+and Sunil Arya",
+    title = "\textsc{ANN}, {A}pproximate {N}earest {N}eighbors {L}ibrary",
+    note  = "http://www.cs.sunysb.edu/~algorith/implement/ANN/implement.shtml"
+}
+
+misc{jplex_cite,
+  author    = "Sexton, Harlan and Johansson, Mikael Vejdemo",
+  title     = "\textsc{JPlex}",
+  year      = "2009",
+  note = "http://comptop.stanford.edu/programs/jplex/"
+}