% bmc_article.bib
% 
%  An example of bibtex entries.
%  Entries taken from BMC instructions for authors page.


@article{MHCLam,
	author  = {Lam, E T and Hastie, A and Lin, C and Ehrlich, D and Das, S K and Austin, M D and Deshpande, P and Cao, H and Nagarajan, N and Xiao, M and Kwok, P},
	title   = {Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly},
	journal = {Nature Biotechnology},
	year  = {2012},
	  month = {AUGUST},
	  volume= {30},
	  number= {8},
	  pages = {},
	  note  = {doi:10.1038/nbt.2303},
}
@article{Beetle2008,
	author  = {Richards, S and Gibbs, R A and Weinstock, G M and Brown, S J and Denell, R and Beeman, R W and Gibbs, R and Bucher, G and Friedrich, M and Grimmelikhuijzen, C J et al.},
	title   = {The genome of the model beetle and pest Tribolium castaneum},
	journal = {Nature},
	year  = {2008},
	month = {APRIL},
	volume= {452},
	number= {},
	pages = {949-955},
	note  = {http://dx.doi.org/10.1038/nature06784},
}

@article{BeetleGenMap2005,
author  = {Lorenzen, M D and Doyungan, Z and Savard, J and Snow, K and Crumly, L R and Shippy, T D and Stuart, J J and Brown, S J and Beeman, R W},
title   = {Genetic linkage maps of the red flour beetle, Tribolium castaneum, based on bacterial artificial chromosomes and expressed sequence tags.},
journal = {Genetics},
year  = {2005},
month = {APRIL},
volume= {170},
number= {2},
pages = {741-747},
note  = {doi:  10.1534/genetics.104.032227},
}


@article{Assem22013,
author  = {Bradnam, K and Faas, J and Alexandrov, A and Baranay, P and Bechner, M and Birol, I and Boisvert, S and Chapman, J and Chapuis, G and Chikhi, R and Chitsaz, H and Chou, W and Corbeil, J and Del Fabbro, C and Docking, T R and Durbin, R and Earl, D E and Emrich, S and Fedotov, P and Fonseca, N A and Ganapathy, G and Gibbs, R A and Gnerre, S and Godzaridis, E and Goldstein, S and Haimel, M and Hall, G and Haussler, D and Hiatt, J B and Ho, I Y and Howard, J and Hunt, M and Jackman, S D and Jaffe, D B and Jarvis, E and Jiang, H et al.},
title   = {Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species},
journal = {GigaScience},
year  = {2013},
month = {JUNE},
volume= {2},
number= {10},
pages = {},
note  = {10.1186/2047-217X-2-10},
}

@article{Moleculo2014,
author  = {McCoy, R C and Taylor, R W and Blauwkamp, T A and Kelley, J L and Kertesz, M and Pushkarev, D and Petrov, D A and Fiston-Lavier A},
title   = {Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements},
journal = {PLoS ONE},
year  = {2014},
month = {SEPTEMBER},
volume= {9},
number= {9},
pages = {},
note  = {DOI: 10.1371/journal.pone.0106689},
}

@article{Nanopore2014,
author  = {Quick, J and Quinlan, A R and Loman N J},
title   = {A reference bacterial genome dataset generated on the MinION portable single-molecule nanopore sequencer},
journal = {GigaScience},
year  = {2014},
month = {SEPTEMBER},
volume= {3},
number= {22},
pages = {},
note  = {doi:10.1186/2047-217X-3-22},
}

@article{Gage2012,
author  = {Salzberg, S L and Phillippy, A M and Zimin, A and Puiu, D and Magoc, T and Koren, S and Treangen, T J and Schatz, M C and Delcher, A L and Roberts, M and Marçais, G and Pop, M and Yorke J A},
title   = {GAGE: A critical evaluation of genome assemblies and assembly algorithms},
journal = {Genome Research},
year  = {2012},
month = {JUNE},
volume= {22},
number= {6},
pages = {},
note  = {doi: 10.1101/gr.131383.111},
}

@article{Feature-by-F2012,
author  = {Vezzi, F and Narzisi, G and Mishra, B},
title   = {Feature-by-Feature – Evaluating De Novo Sequence Assembly},
journal = {PLoS ONE},
year  = {2012},
month = {FEB},
volume= {7},
number= {2},
pages = {},
note  = {DOI: 10.1371/journal.pone.0031002},
}

@article{Argos2009,
author  = {Teague, B and Waterman, M S and Goldstein, S and Potamousis, K and Zhou, S and Reslewic, S and Sarkar, D and Valouev, A and Churas, C and Kidd, J M and Kohn, S and Runnheim, R and Lamers, C and Forrest, D and Newton, M A and Eichler, E E and Kent-First, M and Surti, U and Livny, M and Schwartz, D C},
title   = {High-resolution human genome structure by single-molecule analysis},
journal = {PNAS},
year  = {2012},
month = {DEC},
volume= {107},
number= {24},
pages = {},
note  = {doi: 10.1073/pnas.0914638107},
}

@article{OpGenAnalysis2014,
author  = {Mendelowitz, L and Pop, M},
title   = {Computational methods for optical mapping},
journal = {GigaScience},
year  = {2014},
month = {DEC},
volume= {3},
number= {33},
pages = {},
note  = {doi:10.1186/2047-217X-3-33},
}

@article{SeqBias2013,
author  = {Ross, M G and Russ, C and Costello, M and Hollinger, A and Lennon, N J and Hegarty, R and Nusbaum, C and Jaffe, D B},
title   = {Characterizing and measuring bias in sequence data},
journal = {Genome Biology},
year  = {2013},
month = {MAY},
volume= {14},
number= {R51},
pages = {},
note  = {doi:10.1186/gb-2013-14-5-r51},
}

@article{BioNano2010,
author  = {Das, S K and Austin, M D and Akana, M C and Deshpande, P and Cao, H and Xiao, M},
title   = {Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes.},
journal = {Nucleic Acids Research},
year  = {2010},
month = {JUL},
volume= {38},
number= {e177},
pages = {},
note  = {doi: 10.1093/nar/gkq673},
}

@article{BioNanoSV2014,
author  = {Cao, H and Hastie, A R and Cao, D and Lam, E T and Sun, Y and Huang, H and Liu, X and Lin, L and Andrews, W and Chan, S and Huang, S and Tong, X and Requa, M and Anantharaman, T and Krogh, A and Yang, H and Cao, H and Xu, X},
title   = {Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology},
journal = {GigaScience},
year  = {2014},
month = {DEC},
volume= {3},
number= {34},
pages = {},
note  = {doi:10.1186/2047-217X-3-34},
}

@article{blank,
author  = {},
title   = {},
journal = {},
year  = {},
month = {},
volume= {},
number= {},
pages = {},
note  = {},
}


% Article within a journal
@ARTICLE{koon,
	author  = {Koonin, E V and Altschul, S F and P Bork}, 
	title   = {BRCA1 protein products: functional motifs}, 
	journal = {Nat Genet}, 
	year    = {1996},
	volume  = {13}, 
	pages   = {266-267}
}	

% Article within a journal supplement
@ARTICLE{oreg,
	author  = {Orengo, C A and Bray, J E and Hubbard, 
		   T and LoConte, L and Sillitoe, I}, 
	title   = {Analysis and assessment of ab initio 
		   three-dimensional prediction, secondary 
		   structure, and contacts prediction},
	journal = {Proteins}, 
	year    = {1999},
	volume  = {Suppl 3}, 
	pages   = {149-170}
}	

% In press article
@inpress{khar,
	author  = {Kharitonov, S A and Barnes, P J}, 
	title   = {Clinical aspects of exhaled nitric oxide},
	journal = {Eur Respir J}, 
	note    = {in press} 
}	

%
% Published abstract
%
@ARTICLE{zvai,
	author  = {Zvaifler, N J and Burger, J A and Marinova-Mutafchieva, 
		   L and Taylor, P and Maini, R N},
	title   = {Mesenchymal cells, stromal derived factor-1 and 
		   rheumatoid arthritis [abstract]},
	journal = {Arthritis Rheum}, 
	year    = {1999},
	volume  = {42}, 
	pages   = {s250},
}	


%
% Article within conference proceedings
%
@Inproceedings{check,
	author    = {X Jones}, 
	title     = {Zeolites and synthetic mechanisms},
	booktitle = {Proceedings of the First National Conference on 
		     Porous Sieves: 27-30 June 1996; Baltimore},
	year      = {1996},
	  editor  = {Y Smith}, 
	  pages   = {16-27},
	  organization  = {Stoneham: Butterworth-Heinemann}
}
@Inproceedings{ProbFP,
author  = {Anantharaman, T and Mishra, B},
title   = {A Probabilistic Analysis of False Positives in Optical Map Alignment and Validation},
journal = {WABI2001},
year  = {2001},
month = {AUGUST},
note  = {https://cs.nyu.edu/mishra/PUBLICATIONS/01.falsepos.ps}
}

%%%%%%%%
%  Book chapter, or article within a book
%
@incollection{schn,
	author    = {E Schnepf}, 
	title     = {From prey via endosymbiont to plastids: 
		     comparative studies in dinoflagellates},
	booktitle = {Origins of Plastids}, 
	editor    = {R A Lewin}, 
	publisher = {Chapman and Hall},
	pages     = {53-76}, 
	year      = {1993},
	  address = {New York}, 
	  volume  = {2}, 
	  edition = {2nd} 
}	

%%%%%%%%
% Whole issue of journal
%
@wholejournal{pond,
	editor  = {B Ponder and S Johnston and L Chodosh}, 
	title   = {Innovative oncology},
	journal = {Breast Cancer Res}, 
	year  = {1998},
	  volume= {10}, 
	  pages = {1-72}
}	


%%%%%%%%
% Whole conference proceedings
%
@proceedings{smith,
	editor  = {Y Smith}, 
	title   = {Proceedings of the First National Conference
		   on Porous Sieves: 27-30 June 1996; Baltimore},
	year = 1996,
	  address= {Stoneham}, 
	  publisher = {Butterworth-Heinemann},
}	


%%%%%%%%
% Complete book
%
@book{marg,
	author    = {L Margulis}, 
	title     = {Origin of Eukaryotic Cells},
	publisher = {Yale University Press}, 
	year      = {1970},
	address   = {New Haven} 
}



%%%%%%%%
% Monograph or book in series 
%
@incollection{hunn,
	author    = {G W Hunninghake and J E Gadek}, 
	title     = {The alveloar macrophage},
	booktitle = {Cultured Human Cells and Tissues},
	publisher = {Academic Press}, 
	year      = {1995},
  pages      = {54-56},
	  editor   = {T J R Harris}, 
	  address  = {New York}, 
	  note     = {Stoner G (Series Editor): Methods and Perspectives in Cell Biology, vol 1} 
}


%%%%%%%%
% Book with institutional author
@manual{advi,
	  title   = {Annual Report}, 
	    organization  = {Advisory Committee on Genetic Modification}, 
	    address = {London},
	    year    = {1999}
}


%%%%%%%%
% PHD Thesis
%
@phdthesis{koha,
	author = {R Kohavi}, 
	title  = {Wrappers for performance enhancement and
		  obvious decision graphs},
	school = {Stanford University, Computer Science Department},
	year   = {1995}
}

%%%%%%%%
% Webpage Link / URL
%
@webpage{mouse,
	title  = {The Mouse Tumor Biology Database},
	url = {http://tumor.informatics.jax.org/cancer\_links.html}
}
%%%%%%%%
% Webpage Link / URL
%
@webpage{BioNanoSpecs,
key  = {BioNano IrysChips specifications},
title  = {BioNano IrysChips specifications},
url = {http://www.bionanogenomics.com/wp-content/uploads/2015/01/datasheet-web.pdf}
}

%%%%%%%%
% Webpage Link / URL
%
@webpage{PacBioSpecs,
key = {PacBio P6-C4 chemistry specifications},
title  = {PacBio P6-C4 chemistry specifications},
url = {http://investor.pacificbiosciences.com/releasedetail.cfm?ReleaseID=876252}
}

%%%%%%%%
% Webpage Link / URL
%
@webpage{OpgenSpecs,
key  = {Opgen Argus MapCard specifications},
title  = {Opgen Argus MapCard specifications},
url = {http://www.tgac.ac.uk/sequencing-platforms/}
}

%%%%%%%%
% Webpage Link / URL
%
@webpage{MoleculoSpecs,
key  = {Illumina TruSeq synthetic long-read specifications},
title  = {Illumina TruSeq synthetic long-read specifications},
url = {http://investor.pacificbiosciences.com/releasedetail.cfm?ReleaseID=876252}
}
%%%%%%%%
% Webpage Link / URL
%
@webpage{LDJSpecs,
key  = {Illumina Long Distance Jump Library specifications},
title  = {Illumina Long Distance Jump Library specifications},
url = {http://www.operon.com/services/next-generation-sequencing/illumina/libraries.aspx}
}


