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Author Danchin [40 articles]

Recent papers posted to CiteULike by the author Danchin.
  • Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
    Nature biotechnology (27 July 2008)
    by Pierre Abad, Jérôme Gouzy, Jean-Marc M Aury, Philippe Castagnone-Sereno, Etienne G J G Danchin, Emeline Deleury, Laetitia Perfus-Barbeoch, Véronique Anthouard, François Artiguenave, Vivian C C Blok, Marie-Cécile C Caillaud, Pedro M M Coutinho, Corinne Dasilva, Francesca De Luca, Florence Deau, Magali Esquibet, Timothé Flutre, Jared V V Goldstone, Noureddine Hamamouch, Tarek Hewezi, Olivier Jaillon, Claire Jubin, Paola Leonetti, Marc Magliano, Tom R R Maier, Gabriel V V Markov, Paul McVeigh, Graziano Pesole, Julie Poulain, Marc Robinson-Rechavi, Erika Sallet, Béatrice Ségurens, Delphine Steinbach, Tom Tytgat, Edgardo Ugarte, Cyril van Ghelder, Pasqua Veronico, Thomas J J Baum, Mark Blaxter, Teresa Bleve-Zacheo, Eric L L Davis, Jonathan J J Ewbank, Bruno Favery, Eric Grenier, Bernard Henrissat, John T T Jones, Vincent Laudet, Aaron G G Maule, Hadi Quesneville, Marie-Noëlle N Rosso, Thomas Schiex, Geert Smant, Jean Weissenbach, Patrick Wincker
    posted to sequence genome gene by zwang on 2008-08-15 09:59:55 as ** along with 1 person timflutre
  • Oligonucleotide bias in Bacillus subtilis: General trends and taxonomic comparisons
    Nucleic Acids Research, Vol. 26, No. 12. (1998), pp. 2971-2980.
    by EPC Rocha, A Viari, A Danchin
    posted to rarewords by aaronsmith on 2008-08-07 16:03:54 as **
  • The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
    Nature, Vol. 452, No. 7183. (6 March 2008), pp. 88-92.
    by F Martin, A Aerts, D Ahren, A Brun, EGJ Danchin, F Duchaussoy, J Gibon, A Kohler, E Lindquist, V Pereda, A Salamov, HJ Shapiro, J Wuyts, D Blaudez, M Buee, P Brokstein, B Canback, D Cohen, PE Courty, PM Coutinho, C Delaruelle, JC Detter, A Deveau, S Difazio, S Duplessis, L Fraissinet-Tachet, E Lucic, P Frey-Klett, C Fourrey, I Feussner, G Gay, J Grimwood, PJ Hoegger, P Jain, S Kilaru, J Labbe, YC Lin, V Legue, F Le Tacon, R Marmeisse, D Melayah, B Montanini, M Muratet, U Nehls, H Niculita-Hirzel, Oudot-Le MP Secq, M Peter, H Quesneville, B Rajashekar, M Reich, N Rouhier, J Schmutz, T Yin, M Chalot, B Henrissat, U Kues, S Lucas, Y Van de Peer, GK Podila, A Polle, PJ Pukkila, PM Richardson, P Rouze, IR Sanders, JE Stajich, A Tunlid, G Tuskan, IV Grigoriev
    posted to genoms by manzanita on 2008-06-20 13:00:40 as ** along with 6 people jamselem neils alexl biomcgary cmzmasek urgi
  • Persistent biases in the amino acid composition of prokaryotic proteins.
    BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 28, No. 7. (July 2006), pp. 726-738.
    by G Pascal, C Médigue, A Danchin
    posted to amino-acid-usage 2008-2-mdb 2008-1-mdb by michaelbarton on 2008-06-17 10:21:59 as ****
  • An analysis of determinants of amino acids substitution rates in bacterial proteins.
    Mol Biol Evol, Vol. 21, No. 1. (January 2004), pp. 108-116.
    by EP Rocha, A Danchin
    posted to subtilis substitution molevoltestis expression escherichia coli bacillus amino acid by skumagai on 2008-06-06 16:02:41 as read along with 4 people and 1 group bjorns tny penka jpoyatos Nie
  • Essential Bacillus subtilis genes.
    Proc Natl Acad Sci U S A, Vol. 100, No. 8. (15 April 2003), pp. 4678-4683.
    by K Kobayashi, SD Ehrlich, A Albertini, G Amati, KK Andersen, M Arnaud, K Asai, S Ashikaga, S Aymerich, P Bessieres, F Boland, SC Brignell, S Bron, K Bunai, J Chapuis, LC Christiansen, A Danchin, M Débarbouille, E Dervyn, E Deuerling, K Devine, SK Devine, O Dreesen, J Errington, S Fillinger, SJ Foster, Y Fujita, A Galizzi, R Gardan, C Eschevins, T Fukushima, K Haga, CR Harwood, M Hecker, D Hosoya, MF Hullo, H Kakeshita, D Karamata, Y Kasahara, F Kawamura, K Koga, P Koski, R Kuwana, D Imamura, M Ishimaru, S Ishikawa, I Ishio, D Le Coq, A Masson, C Mauël, R Meima, RP Mellado, A Moir, S Moriya, E Nagakawa, H Nanamiya, S Nakai, P Nygaard, M Ogura, T Ohanan, M O'Reilly, M O'Rourke, Z Pragai, HM Pooley, G Rapoport, JP Rawlins, LA Rivas, C Rivolta, A Sadaie, Y Sadaie, M Sarvas, T Sato, HH Saxild, E Scanlan, W Schumann, JF Seegers, J Sekiguchi, A Sekowska, SJ Séror, M Simon, P Stragier, R Studer, H Takamatsu, T Tanaka, M Takeuchi, HB Thomaides, V Vagner, JM van Dijl, K Watabe, A Wipat, H Yamamoto, M Yamamoto, Y Yamamoto, K Yamane, K Yata, K Yoshida, H Yoshikawa, U Zuber, N Ogasawara
    posted to no-tag by alanrw on 2008-06-02 13:52:53 as ** along with 3 people and 2 groups hryk ana Serkalem structural_bioinformatics Bioinformatics
  • Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)
    Nature Biotechnology, Vol. 26, No. 5. (04 May 2008), pp. 553-560.
    by Diego Martinez, Randy M Berka, Bernard Henrissat, Markku Saloheimo, Mikko Arvas, Scott E Baker, Jarod Chapman, Olga Chertkov, Pedro M Coutinho, Dan Cullen, Etienne GJ Danchin, Igor V Grigoriev, Paul Harris, Melissa Jackson, Christian P Kubicek, Cliff S Han, Isaac Ho, Luis F Larrondo, Alfredo L de Leon, Jon K Magnuson, Sandy Merino, Monica Misra, Beth Nelson, Nicholas Putnam, Barbara Robbertse, Asaf A Salamov, Monika Schmoll, Astrid Terry, Nina Thayer, Ann Westerholm-Parvinen, Conrad L Schoch, Jian Yao, Ravi Barbote, Mary A Nelson, Chris Detter, David Bruce, Cheryl R Kuske, Gary Xie, Paul Richardson, Daniel S Rokhsar, Susan M Lucas, Edward M Rubin, Nigel Dunn-Coleman, Michael Ward, Thomas S Brettin
    posted to genome fungi by jamselem on 2008-05-19 07:56:30 as **
  • The genome sequence of the model ascomycete fungus Podospora anserina
    Genome Biology, Vol. 9 (06 May 2008), R77.
    by Eric Espagne, Olivier Lespinet, Fabienne Malagnac, Corinne Da Silva, Olivier Jaillon, Betina M Porcel, Arnaud Couloux, Jean-Marc Aury, Béatrice Ségurens, Julie Poulain, Véronique Anthouard, Sandrine Grossetete, Hamid Khalili, Evelyne Coppin, Michelle Déquard-Chablat, Marguerite Picard, Véronique Contamine, Sylvie Arnaise, Anne Bourdais, Véronique Berteaux-Lecellier, Daniel Gautheret, Ronald P de Vries, Evy Battaglia, Pedro M Coutinho, Etienne GJ Danchin, Bernard Henrissat, Riyad EL Khoury, Annie Sainsard-Chanet, Antoine Boivin, Bérangère Pinan-Lucarré, Carole H Sellem, Robert Debuchy, Patrick Wincker, Jean Weissenbach, Philippe Silar
    posted to genome fungi_te fungi by jamselem on 2008-05-17 18:25:46 as ** along with 1 person and 1 group stajich Berkeley Mycology
  • Genomics of an extreme psychrophile, Psychromonas ingrahamii
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Monica Riley, James Staley, Antoine Danchin, Tingzhang Wang, Thomas Brettin, Loren Hauser, Miriam Land, Linda Thompson
    posted to psychrophily psychromonas genomics genome bacteria by neils on 2008-05-06 15:00:02 as **
  • Exploring the Penicillium marneffei genome.
    Archives of microbiology, Vol. 179, No. 5. (May 2003), pp. 339-353.
    by KY Yuen, G Pascal, SS Wong, P Glaser, PC Woo, F Kunst, JJ Cai, EY Cheung, C Médigue, A Danchin
    posted to no-tag by PetrovLab on 2008-05-02 19:17:24 as **
  • Persistence drives gene clustering in bacterial genomes
    BMC Genomics, Vol. 9 (07 January 2008), 4.
    by Gang Fang, Eduardo PC Rocha, Antoine Danchin
    posted to no-tag by saraballouz on 2008-04-30 14:24:03 as ** along with 2 people barriot evodeva
  • Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125.
    Genome Res, Vol. 15, No. 10. (October 2005), pp. 1325-1335.
    by C Médigue, E Krin, G Pascal, V Barbe, A Bernsel, PN Bertin, F Cheung, S Cruveiller, S D'Amico, A Duilio, G Fang, G Feller, C Ho, S Mangenot, G Marino, J Nilsson, E Parrilli, EP Rocha, Z Rouy, A Sekowska, ML Tutino, D Vallenet, G von Heijne, A Danchin
    posted to cold-adaptation by min013 on 2008-04-23 13:54:13 as ** along with 1 person gilda
  • Base composition bias might result from competition for metabolic resources
    Trends in Genetics, Vol. 18, No. 6. (1 June 2002), pp. 291-294.
    by Eduardo P Rocha, Antoine Danchin
    posted to master by operon on 2008-04-17 04:36:58 as ** along with 1 person karfunkel
  • Functional and evolutionary roles of long repeats in prokaryotes.
    Res Microbiol, Vol. 150, No. 9-10. (c 1999), pp. 725-733.
    by EP Rocha, A Danchin, A Viari
    posted to master by operon on 2008-03-16 21:03:54 as **
  • Gene essentiality determines chromosome organisation in bacteria.
    Nucleic Acids Res, Vol. 31, No. 22. (15 November 2003), pp. 6570-6577.
    by EP Rocha, A Danchin
    posted to master by operon on 2008-03-09 23:59:29 as ** along with 2 people bjorns BarrosH
  • Conservation of the MHC-like region throughout evolution.
    Immunogenetics, Vol. 55, No. 3. (June 2003), pp. 141-148.
    by EG Danchin, L Abi-Rached, A Gilles, P Pontarotti
    posted to synteny syntenypaper by maximilianh on 2008-03-05 10:34:18 as **
  • Molecular diagnosis of human cancer type by gene expression profiles and independent component analysis
    European Journal of Human Genetics, Vol. aop, No. current.
    by Xue W Zhang, Yee L Yap, Dong Wei, Feng Chen, Antoine Danchin,
    posted to ica microarray by ghattem on 2008-03-03 20:03:24 as **
  • Specialized microbial databases for inductive exploration of microbial genome sequences.
    BMC Genomics, Vol. 6, No. 1. (2005)
    by G Fang, C Ho, Y Qiu, V Cubas, Z Yu, C Cabau, F Cheung, I Moszer, A Danchin
    posted to gang-fang nar-database by dullhunk on 2008-02-19 13:36:29 as **
  • Statistical evidence for a more than 800-million-year-old evolutionarily conserved genomic region in our genome.
    J Mol Evol, Vol. 59, No. 5. (November 2004), pp. 587-597.
    by EG Danchin, P Pontarotti
    posted to synteny syntenypaper by maximilianh on 2008-01-14 12:16:51 as **
  • Effect of mild acid pH on the functioning of bacterial membranes in Vibrio cholerae.
    Proteomics, Vol. 2, No. 5. (May 2002), pp. 571-579.
    by F Hommais, C Laurent-Winter, V Labas, E Krin, C Tendeng, O Soutourina, A Danchin, P Bertin
    posted to no-tag by victoranaya on 2007-12-04 10:39:30 as **
  • Nucleotide sequence database policies.
    Science, Vol. 298, No. 5597. (15 November 2002)
    by S Brunak, A Danchin, M Hattori, H Nakamura, K Shinozaki, T Matise, D Preuss
    posted to all data-sharing embl example genbank history policy sequencing timing by hpiwowar on 2007-11-24 18:10:40 as read along with 1 person moborg
  • Public Information: From Nosy Neighbors to Cultural Evolution
    Science, Vol. 305, No. 5683. (23 July 2004), pp. 487-491.
    by Etienne Danchin, Luc-Alain Giraldeau, Thomas J Valone, Richard H Wagner
    posted to communication dominance evolution by adriandefroment on 2007-10-25 20:35:25 as **
  • Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes.
    Nucleic Acids Res, Vol. 35, No. 6. (2007)
    by RM Watt, J Wang, M Leong, HF Kung, KS Cheah, D Liu, A Danchin, JD Huang
    posted to proteomegfpflouroscenceproteomicsbacteria by bala on 2007-04-26 16:14:58 as ** along with 1 group DictyosteliumGroup
  • Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence.
    Genome Res, Vol. 9, No. 11. (November 1999), pp. 1116-1127.
    by C Médigue, M Rose, A Viari, A Danchin
    posted to frame_shift by alexl on 2007-04-20 19:20:33 as read
  • Codon Usage Domains over Bacterial Chromosomes
    PLoS Computational Biology, Vol. 2, No. 4. (1 April 2006), e37.
    by Marc Bailly-Bechet, Antoine Danchin, Mudassar Iqbal, Matteo Marsili, Massimo Vergassola
    posted to no-tag by gpalidwor on 2007-04-15 00:17:54 as **
  • A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.
    BMC Genomics, Vol. 6, No. 1. (4 November 2005)
    by Nathalie Balandraud, Philippe Gouret, Etienne G Danchin, Mathieu Blanc, David Zinn, Jean Roudier, Pierre Pontarotti
    posted to no-tag by felixroudier on 2007-04-12 10:44:27 as ** along with 1 person jwortman
  • Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
    Nature Biotechnology, Vol. 25, No. 2. (28 January 2007), pp. 221-231.
    by Herman J Pel, Johannes H de Winde, David B Archer, Paul S Dyer, Gerald Hofmann, Peter J Schaap, Geoffrey Turner, Ronald P de Vries, Richard Albang, Kaj Albermann, Mikael R Andersen, Jannick D Bendtsen, Jacques AE Benen, Marco van den Berg, Stefaan Breestraat, Mark X Caddick, Roland Contreras, Michael Cornell, Pedro M Coutinho, Etienne GJ Danchin, Alfons JM Debets, Peter Dekker, Piet WM van Dijck, Alard van Dijk, Lubbert Dijkhuizen, Arnold JM Driessen, Christophe D'enfert, Steven Geysens, Coenie Goosen, Gert SP Groot, Piet WJ de Groot, Thomas Guillemette, Bernard Henrissat, Marga Herweijer, Johannes PTW van den Hombergh, Cees AMJJ van den Hondel, Rene TJM van der Heijden, Rachel M van der Kaaij, Frans M Klis, Harrie J Kools, Christian P Kubicek, Patricia A van Kuyk, Jürgen Lauber, Xin Lu, Marc JEC van der Maarel, Rogier Meulenberg, Hildegard Menke, Martin A Mortimer, Jens Nielsen, Stephen G Oliver, Maurien Olsthoorn, Karoly Pal, Noël NME van Peij, Arthur FJ Ram, Ursula Rinas, Johannes A Roubos, Cees MJ Sagt, Monika Schmoll, Jibin Sun, David Ussery, Janos Varga, Wouter Vervecken, Peter JJ van de Vondervoort, Holger Wedler, Han AB Wösten, An-Ping Zeng, Albert JJ van Ooyen, Jaap Visser, Hein Stam
    posted to fungi by alexl on 2007-03-22 16:41:53 as **
  • Imagene: an integrated computer environment for sequence annotation and analysis.
    Bioinformatics, Vol. 15, No. 1. (January 1999), pp. 2-15.
    by C Médigue, F Rechenmann, A Danchin, A Viari
    posted to imagene preprocessing by jeremymiller on 2007-02-21 02:16:16 as ** along with 1 person and 1 group plofje GeschwindLab
  • Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
    BMC Bioinformatics, Vol. 8 (08 February 2007), 47.
    by Yuko Makita, Michiel JL de Hoon, Antoine Danchin
    posted to prokaryotes geneprediction baysian by dquest on 2007-02-09 15:20:51 as ** along with 1 person eckart_bindewald
  • Classification between normal and tumor tissues based on the pair-wise gene expression ratio
    BMC Cancer, Vol. 4, No. 1. (2004)
    by Yeeleng Yap, Xuewu Zhang, MT Ling, Xianghong Wang, YC Wong, Antoine Danchin
    posted to microarray cancer by bedo on 2007-01-31 03:09:20 as **
  • The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens
    Nat Biotech, Vol. 21, No. 11. (November 2003), pp. 1307-1313.
    by Eric Duchaud, Christophe Rusniok, Lionel Frangeul, Carmen Buchrieser, Alain Givaudan, Sead Taourit, Stephanie Bocs, Caroline Boursaux-Eude, Michael Chandler, Jean-Francois Charles, Elie Dassa, Richard Derose, Sylviane Derzelle, Georges Freyssinet, Sophie Gaudriault, Claudine Medigue, Anne Lanois, Kerrie Powell, Patricia Siguier, Rachel Vincent, Vincent Wingate, Mohamed Zouine, Philippe Glaser, Noel Boemare, Antoine Danchin, Frank Kunst
    posted to genome by gelack on 2006-12-06 18:03:00 as **
  • Proteomic identification of a two-component regulatory system in Pseudoalteromonas haloplanktis TAC125.
    Extremophiles (22 June 2006)
    by Rosanna Papa, Susanne Glagla, Antoine Danchin, Thomas Schweder, Gennaro Marino, Angela Duilio
    posted to tac by gilda on 2006-10-13 17:46:52 as **
  • Essentiality, not expressiveness, drives gene-strand bias in bacteria.
    Nat Genet, Vol. 34, No. 4. (August 2003), pp. 377-378.
    by EP Rocha, A Danchin
    posted to essentialgenes gene_organization by bjorns on 2006-09-25 07:16:43 as **
  • Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human
    PNAS, Vol. 102, No. 7. (15 February 2005), pp. 2430-2435.
    by Huai-Dong Song, Chang-Chun Tu, Guo-Wei Zhang, Sheng-Yue Wang, Kui Zheng, Lian-Cheng Lei, Qiu-Xia Chen, Yu-Wei Gao, Hui-Qiong Zhou, Hua Xiang, Hua-Jun Zheng, Shur-Wern W Chern, Feng Cheng, Chun-Ming Pan, Hua Xuan, Sai-Juan Chen, Hui-Ming Luo, Duan-Hua Zhou, Yu-Fei Liu, Jian-Feng He, Peng-Zhe Qin, Ling-Hui Li, Yu-Qi Ren, Wen-Jia Liang, Ye-Dong Yu, Larry Anderson, Ming Wang, Rui-Heng Xu, Xin-Wei Wu, Huan-Ying Zheng, Jin-Ding Chen, Guodong Liang, Yang Gao, Ming Liao, Ling Fang, Li-Yun Jiang, Hui Li, Fang Chen, Biao Di, Li-Juan He, Jin-Yan Lin, Suxiang Tong, Xiangang Kong, Lin Du, Pei Hao, Hua Tang, Andrea Bernini, Xiao-Jing Yu, Ottavia Spiga, Zong-Ming Guo, Hai-Yan Pan, Wei-Zhong He, Jean-Claude Manuguerra, Arnaud Fontanet, Antoine Danchin, Neri Niccolai, Yi-Xue Li, Chung-I Wu, Guo-Ping Zhao
    posted to epidemiology evolution x-evolutionary-ecology z-class-evoeco by jmeppley on 2006-03-24 20:54:34 as read
  • Towards the reconstruction of the bilaterian ancestral pre-MHC region.
    Trends Genet, Vol. 20, No. 12. (December 2004), pp. 587-591.
    by EG Danchin, P Pontarotti
    posted to no-tag by balajis on 2006-01-13 22:06:08 as **
  • Imagene: an integrated computer environment for sequence annotation and analysis
    Bioinformatics, Vol. 15, No. 1. (January 1999), pp. 2-15.
    by Claudine Medigue, Francois Rechenmann, Antoine Danchin, Alain Viari
    posted to software by eweaver on 2005-12-29 19:13:30 as **
  • FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform.
    BMC Bioinformatics, Vol. 6 (5 August 2005)
    by P Gouret, V Vitiello, N Balandraud, A Gilles, P Pontarotti, EG Danchin
    posted to algorithm annotation by jwortman on 2005-11-21 01:11:31 as ***
  • The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
    Nature, Vol. 390, No. 6657. (20 November 1997), pp. 249-256.
    by F Kunst, N Ogasawara, I Moszer, AM Albertini, G Alloni, V Azevedo, MG Bertero, P Bessières, A Bolotin, S Borchert, R Borriss, L Boursier, A Brans, M Braun, SC Brignell, S Bron, S Brouillet, CV Bruschi, B Caldwell, V Capuano, NM Carter, SK Choi, JJ Codani, IF Connerton, A Danchin
    posted to genome by Cortel on 2005-07-21 09:31:05 as **
  • A strand-specific model for chromosome segregation in bacteria.
    Mol Microbiol, Vol. 49, No. 4. (August 2003), pp. 895-903.
    by EP Rocha, J Fralick, G Vediyappan, A Danchin, V Norris
    posted to gene_organization theory by bjorns on 2005-07-05 15:35:31 as ***
  • Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes.
    BMC Bioinformatics, Vol. 3, No. 1. (2002)
    by S Bocs, A Danchin, C Médigue
    posted to bioinformatics re-annotation by ziquje on 2005-02-08 17:49:49 as ****
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