Finish correct JF notes

[chloroplast13.git] / biblio.bib

diff --git a/biblio.bib b/biblio.bib
index d5aaff6a148d3f627a6dd2f673e3f70b28e60b42..38ab7d7e9946662941b4249390a094e3a4940cca 100644 (file)
--- a/biblio.bib
+++ b/biblio.bib
@@ -21,6 +21,70 @@ pages={1097--1112},
 DOI={10.1089/cmb.2010.0092}
 }
 
 DOI={10.1089/cmb.2010.0092}
 }
 

+@article{Eisen2007,
+    author = {Eisen, Jonathan A},
+    journal = {PLoS Biol},
+    publisher = {Public Library of Science},
+    title = {Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes},
+    year = {2007},
+    month = {03},
+    volume = {5},
+    url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0050082},
+    pages = {e82},
+    abstract = {
+        <p>Environmental shotgun sequencing promises to reveal novel and fundamental insights into the hidden world of microbes, but the complexity of analysis required to realize this potential poses unique interdisciplinary challenges.</p>
+      },
+    number = {3},
+    doi = {10.1371/journal.pbio.0050082}
+}        
+
+@article{Sayers01012011,
+author = {Sayers, Eric W. and Barrett, Tanya and Benson, Dennis A. and Bolton, Evan and Bryant, Stephen H. and Canese, Kathi and Chetvernin, Vyacheslav and Church, Deanna M. and DiCuccio, Michael and Federhen, Scott and Feolo, Michael and Fingerman, Ian M. and Geer, Lewis Y. and Helmberg, Wolfgang and Kapustin, Yuri and Landsman, David and Lipman, David J. and Lu, Zhiyong and Madden, Thomas L. and Madej, Tom and Maglott, Donna R. and Marchler-Bauer, Aron and Miller, Vadim and Mizrachi, Ilene and Ostell, James and Panchenko, Anna and Phan, Lon and Pruitt, Kim D. and Schuler, Gregory D. and Sequeira, Edwin and Sherry, Stephen T. and Shumway, Martin and Sirotkin, Karl and Slotta, Douglas and Souvorov, Alexandre and Starchenko, Grigory and Tatusova, Tatiana A. and Wagner, Lukas and Wang, Yanli and Wilbur, W. John and Yaschenko, Eugene and Ye, Jian}, 
+title = {Database resources of the National Center for Biotechnology Information},
+volume = {39}, 
+number = {suppl 1}, 
+pages = {D38-D51}, 
+year = {2011}, 
+doi = {10.1093/nar/gkq1172},  
+URL = {http://nar.oxfordjournals.org/content/39/suppl_1/D38.abstract}, 
+eprint = {http://nar.oxfordjournals.org/content/39/suppl_1/D38.full.pdf+html}, 
+journal = {Nucleic Acids Research} 
+}
+
+@Article{RDogma,
+AUTHOR = {Stacia K. Wyman, Robert K. Jansen and Jeffrey L. Boore},
+TITLE = {Automatic annotation of organellar genomes
+with DOGMA},
+JOURNAL = {BIOINFORMATICS, oxford Press},
+VOLUME = {20},
+YEAR = {2004},
+NUMBER = {172004},
+PAGES = {3252-3255},
+URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004.pdf},
+}
+
+@article{de2002comparative,
+  title={Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns},
+  author={De Las Rivas, Javier and Lozano, Juan Jose and Ortiz, Angel R},
+  journal={Genome research},
+  volume={12},
+  number={4},
+  pages={567--583},
+  year={2002},
+  publisher={Cold Spring Harbor Lab}
+}
+
+@article{liu2012cpgavas,
+  title={CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences},
+  author={Liu, Chang and Shi, Linchun and Zhu, Yingjie and Chen, Haimei and Zhang, Jianhui and Lin, Xiaohan and Guan, Xiaojun},
+  journal={BMC genomics},
+  volume={13},
+  number={1},
+  pages={715},
+  year={2012},
+  publisher={BioMed Central Ltd}
+}
+

 @article{parra2007cegma,
   title={CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes},
   author={Parra, Genis and Bradnam, Keith and Korf, Ian},
 @article{parra2007cegma,
   title={CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes},
   author={Parra, Genis and Bradnam, Keith and Korf, Ian},


@@ -54,6 +118,27 @@ DOI={10.1089/cmb.2010.0092}
   publisher={Cold Spring Harbor Lab}
 }
 
   publisher={Cold Spring Harbor Lab}
 }
 

+@article{apweiler1985swiss,
+  title={SWISS-PROT AND ITS COMPUTER-ANNOTATED SUPPLEMENT TREMBL: HOW TO PRODUCE HIGH QUALITY AUTOMATIC ANNOTATION},
+  author={Apweiler, Rolf and O’Donovan, Claire and Martin, Maria Jesus and Fleischmann, Wolfgang and Hermjakob, Henning and Moeller, Steffen and Contrino, Sergio and Junker, Vivien},
+  journal={EUR. J. BIOCHEM},
+  volume={147},
+  pages={9--15},
+  year={1985},
+  url={http://www.ebi.ac.uk/ena/}
+}
+
+@article{sugawara2008ddbj,
+  title={DDBJ with new system and face},
+  author={Sugawara, Hideaki and Ogasawara, Osamu and Okubo, Kousaku and Gojobori, Takashi and Tateno, Yoshio},
+  journal={Nucleic acids research},
+  volume={36},
+  number={suppl 1},
+  pages={D22--D24},
+  year={2008},
+  publisher={Oxford Univ Press}
+}
+

 @article{chapman2000biopython,
   title={Biopython: Python tools for computational biology},
   author={Chapman, Brad and Chang, Jeffrey},
 @article{chapman2000biopython,
   title={Biopython: Python tools for computational biology},
   author={Chapman, Brad and Chang, Jeffrey},


@@ -99,24 +184,11 @@ pages={1-12}
     volume = {7},
     url = {http://dx.doi.org/10.1371%2Fjournal.pone.0052841},
     pages = {e52841},
     volume = {7},
     url = {http://dx.doi.org/10.1371%2Fjournal.pone.0052841},
     pages = {e52841},

-    abstract = {<p>Molecular and phylogeographic studies have led to the definition within the <italic>Mycobacterium tuberculosis</italic> complex (MTBC) of a number of geotypes and ecotypes showing a preferential geographic location or host preference. The MTBC is thought to have emerged in Africa, most likely the Horn of Africa, and to have spread worldwide with human migrations. Under this assumption, there is a possibility that unknown deep branching lineages are present in this region. We genotyped by spoligotyping and multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) 435 MTBC isolates recovered from patients. Four hundred and eleven isolates were collected in the Republic of Djibouti over a 12 year period, with the other 24 isolates originating from neighbouring countries. All major <italic>M. tuberculosis</italic> lineages were identified, with only two <italic>M. africanum</italic> and one <italic>M. bovis</italic> isolates. Upon comparison with typing data of worldwide origin we observed that several isolates showed clustering characteristics compatible with new deep branching. Whole genome sequencing (WGS) of seven isolates and comparison with available WGS data from 38 genomes distributed in the different lineages confirms the identification of ancestral nodes for several clades and most importantly of one new lineage, here referred to as lineage 7. Investigation of specific deletions confirms the novelty of this lineage, and analysis of its precise phylogenetic position indicates that the other three superlineages constituting the MTBC emerged independently but within a relatively short timeframe from the Horn of Africa. The availability of such strains compared to the predominant lineages and sharing very ancient ancestry will open new avenues for identifying some of the genetic factors responsible for the success of the modern lineages. Additional deep branching lineages may be readily and efficiently identified by large-scale MLVA screening of isolates from sub-Saharan African countries followed by WGS analysis of a few selected isolates.</p>},

     number = {12},
     doi = {10.1371/journal.pone.0052841}
 }        
 
     number = {12},
     doi = {10.1371/journal.pone.0052841}
 }        
 

-@article{Sayers01012011,
-author = {Sayers, Eric W. and Barrett, Tanya and Benson, Dennis A. and Bolton, Evan and Bryant, Stephen H. and Canese, Kathi and Chetvernin, Vyacheslav and Church, Deanna M. and DiCuccio, Michael and Federhen, Scott and Feolo, Michael and Fingerman, Ian M. and Geer, Lewis Y. and Helmberg, Wolfgang and Kapustin, Yuri and Landsman, David and Lipman, David J. and Lu, Zhiyong and Madden, Thomas L. and Madej, Tom and Maglott, Donna R. and Marchler-Bauer, Aron and Miller, Vadim and Mizrachi, Ilene and Ostell, James and Panchenko, Anna and Phan, Lon and Pruitt, Kim D. and Schuler, Gregory D. and Sequeira, Edwin and Sherry, Stephen T. and Shumway, Martin and Sirotkin, Karl and Slotta, Douglas and Souvorov, Alexandre and Starchenko, Grigory and Tatusova, Tatiana A. and Wagner, Lukas and Wang, Yanli and Wilbur, W. John and Yaschenko, Eugene and Ye, Jian}, 
-title = {Database resources of the National Center for Biotechnology Information},
-volume = {39}, 
-number = {suppl 1}, 
-pages = {D38-D51}, 
-year = {2011}, 
-doi = {10.1093/nar/gkq1172}, 
-abstract ={In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.}, 
-URL = {http://nar.oxfordjournals.org/content/39/suppl_1/D38.abstract}, 
-eprint = {http://nar.oxfordjournals.org/content/39/suppl_1/D38.full.pdf+html}, 
-journal = {Nucleic Acids Research} 
-}
+

 
 @article{zafar2002coregenes,
   title={CoreGenes: A computational tool for identifying and cataloging},
 
 @article{zafar2002coregenes,
   title={CoreGenes: A computational tool for identifying and cataloging},


@@ -141,33 +213,7 @@ URL = {http://www.biomedsearch.com/nih/Reconstructing-ancestor-Mycobacterium-lep
 PubMedID = {17623808},
 ISSN = {1088-9051}
 }
 PubMedID = {17623808},
 ISSN = {1088-9051}
 }

-@article{Eisen2007,
-    author = {Eisen, Jonathan A},
-    journal = {PLoS Biol},
-    publisher = {Public Library of Science},
-    title = {Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes},
-    year = {2007},
-    month = {03},
-    volume = {5},
-    url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0050082},
-    pages = {e82},
-    abstract = {
-        <p>Environmental shotgun sequencing promises to reveal novel and fundamental insights into the hidden world of microbes, but the complexity of analysis required to realize this potential poses unique interdisciplinary challenges.</p>
-      },
-    number = {3},
-    doi = {10.1371/journal.pbio.0050082}
-}        
-@Article{RDogma,
-AUTHOR = {Stacia K. Wyman, Robert K. Jansen and Jeffrey L. Boore},
-TITLE = {Automatic annotation of organellar genomes
-with DOGMA},
-JOURNAL = {BIOINFORMATICS, oxford Press},
-VOLUME = {20},
-YEAR = {2004},
-NUMBER = {172004},
-PAGES = {3252-3255},
-URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004.pdf},
-}
+

 @article{guindon2005phyml,
   title={PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference},
   author={Guindon, Stephane and Lethiec, Franck and Duroux, Patrice and Gascuel, Olivier},
 @article{guindon2005phyml,
   title={PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference},
   author={Guindon, Stephane and Lethiec, Franck and Duroux, Patrice and Gascuel, Olivier},


@@ -218,9 +264,6 @@ URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004
     volume = {4},
     url = {http://dx.doi.org/10.1371%2Fjournal.pone.0006291},
     pages = {e6291},
     volume = {4},
     url = {http://dx.doi.org/10.1371%2Fjournal.pone.0006291},
     pages = {e6291},

-    abstract = {
-<p>Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited in databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon <italic>Halorhabdus utahensis</italic> to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species-specific consensus ribosome-binding site. Additionally, we conducted laboratory experiments to test <italic>H. utahensis</italic> growth and enzyme activity. Current annotation practices need to improve in order to more accurately reflect a genome's biological potential. We make specific recommendations that could improve the quality of microbial annotation projects.</p>
-},

     number = {7},
     doi = {10.1371/journal.pone.0006291}
 }        
     number = {7},
     doi = {10.1371/journal.pone.0006291}
 }