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Tag synteny [81 articles]

Recent papers classified by the tag synteny.
  • Synteny and Collinearity in Plant Genomes
    Science, Vol. 320, No. 5875. (25 April 2008), pp. 486-488.
    by Haibao Tang, John E Bowers, Xiyin Wang, Ray Ming, Maqsudul Alam, Andrew H Paterson
    posted to collinearity comparative genomics plant synteny by tanghaibao on 2008-04-25 04:07:21 as ** along with 4 people and 1 group natstreet biomcgary ArtemPankin bpcusack Khavkin's lab
  • Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses
    Proceedings of the National Academy of Sciences, Vol. 102, No. 37. (13 September 2005), pp. 13206-13211.
    by John E Bowers, Miguel A Arias, Rochelle Asher, Jennifer A Avise, Robert T Ball, Gene A Brewer, Ryan W Buss, Amy H Chen, Thomas M Edwards, James C Estill, Heather E Exum, Valorie H Goff, Kristen L Herrick, Cassie L Steele, Santhosh Karunakaran, Gmerice K Lafayette, Cornelia Lemke, Barry S Marler, Shelley L Masters, Joana M Mcmillan, Lisa K Nelson, Graham A Newsome, Chike C Nwakanma, Rosana N Odeh, Cynthia A Phelps, Elizabeth A Rarick, Carl J Rogers, Sean P Ryan, Keimun A Slaughter, Carol A Soderlund, Haibao Tang, Rod A Wing, Andrew H Paterson
    posted to grasses heterochromatin map physical rearrangement sorghum synteny by tanghaibao on 2008-04-25 04:19:08 as **
  • Automatic genome-wide reconstruction of phylogenetic gene trees.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev
    posted to evolution genome phylogenetics synteny yeast by stajich on 2007-12-02 23:47:19 as read along with 3 people and 1 group shigepong seitentaisei tharris Berkeley Mycology
  • DAGchainer: a tool for mining segmental genome duplications and synteny.
    Bioinformatics, Vol. 20, No. 18. (12 December 2004), pp. 3643-3646.
    by BJ Haas, AL Delcher, JR Wortman, SL Salzberg
    posted to duplication genome_evolution synteny by stajich on 2007-12-02 23:43:45 as ** along with 3 people and 2 groups jwortman indigoviolet AaronDarling EisenLab Berkeley Mycology
  • The UniMarker (UM) method for synteny mapping of large genomes.
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 3156-3165.
    by BY Liao, YJ Chang, JM Ho, MJ Hwang
    posted to evolution genome synteny by stajich on 2007-12-02 23:47:49 as ** along with 1 person and 1 group indigoviolet EisenLab
  • The determinants of gene order conservation in yeasts
    Genome Biology, Vol. 8 (05 November 2007), R233.
    by Juan F Poyatos, Laurence D Hurst
    posted to genome_evolution synteny yeast by stajich on 2007-12-02 23:35:07 as ** along with 3 people and 1 group cjeans maximilianh hpaces Berkeley Mycology
  • Natural history and evolutionary principles of gene duplication in fungi
    Nature, Vol. 449, No. 7158., pp. 54-61.
    by Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev
    posted to evolution gene synteny yeast by stajich on 2007-09-05 20:39:04 as ** along with 13 people and 4 groups aheilbut dpollard tny dchughes djkt zwang biomcgary lp2 tzhughes maximilianh pkm bpcusack dandaman EisenLab G4ID Genetics-of-Gambling Berkeley Mycology
  • Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms
    BMC Bioinformatics, Vol. 8 (08 March 2007), 82.
    by Amit U Sinha, Jaroslaw Meller
    posted to algorithm synteny by stajich on 2007-12-04 06:31:32 as ** along with 3 people and 2 groups druvus natstreet indigoviolet EisenLab Berkeley Mycology
  • Are There Rearrangement Hotspots in the Human Genome?
    PLoS Comput Biol, Vol. 3, No. 11. (9 November 2007)
    by Max A A Alekseyev, Pavel A A Pevzner
    posted to genome_evolution synteny by stajich on 2007-12-03 05:28:50 as ** along with 1 person ealloza
  • Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History.
    PLoS genetics, Vol. 3, No. 7. (20 July 2007)
    by Fusheng Wei, Ed Coe, William Nelson, Arvind K K Bharti, Fred Engler, Ed Butler, Hyeran Kim, Jose Luis L Goicoechea, Mingsheng Chen, Seunghee Lee, Galina Fuks, Hector Sanchez-Villeda, Steven Schroeder, Zhiwei Fang, Michael McMullen, Georgia Davis, John E E Bowers, Andrew H H Paterson, Mary Schaeffer, Jack Gardiner, Karen Cone, Joachim Messing, Carol Soderlund, Rod A A Wing
    posted to genome genome_evolution maize synteny by stajich on 2008-06-09 05:37:06 as ** along with 1 person and 1 group kengg Berkeley Mycology
  • How Malleable is the Eukaryotic Genome? Extreme Rate of Chromosomal Rearrangement in the Genus Drosophila
    Genome Res., Vol. 11, No. 2. (1 February 2001), pp. 230-239.
    by Jose M Ranz, Ferran Casals, Alfredo Ruiz
    posted to evolution gene order synteny by sharpton on 2008-05-19 22:26:35 as **
  • Measures of Synteny Conservation Between Species Pairs
    Genetics, Vol. 162, No. 1. (1 September 2002), pp. 441-448.
    by Elizabeth A Housworth, John Postlethwait
    posted to evolution gene order synteny by sharpton on 2008-05-19 22:28:37 as **
  • Naturally occurring circular permutations in proteins
    Protein Eng., Vol. 14, No. 8. (1 August 2001), pp. 533-542.
    by Shai Uliel, Amit Fliess, Ron Unger
    posted to algorithm bioinformatics circular gene genome order permutation screen synteny by sharpton on 2008-02-18 18:16:52 as read
  • GENETICS: Why Genomes in Pieces?
    Science, Vol. 318, No. 5849. (19 October 2007), pp. 405-407.
    by Laura F Landweber
    posted to circular evolution gene genome order permutation synteny by sharpton on 2008-02-18 18:17:32 as ** along with 3 people operon gulsacan smbe2008
  • Prevalence of small inversions in yeast gene order evolution
    Proceedings of the National Academy of Sciences, Vol. 97, No. 26. (19 December 2000), pp. 14433-14437.
    by Cathal Seoighe, Nancy Federspiel, Ted Jones, Nancy Hansen, Vesna Bivolarovic, Ray Surzycki, Raquel Tamse, Caridad Komp, Lucas Huizar, Ronald W Davis, Stewart Scherer, Evelyn Tait, Duncan J Shaw, David Harris, Lee Murphy, Karen Oliver, Kate Taylor, Marie-Adele Rajandream, Bart G Barrell, Kenneth H Wolfe
    posted to evolution gene order synteny by sharpton on 2008-05-19 22:25:20 as **
  • On the Structure of Syntenic Distance
    Journal of Computational Biology, Vol. 8, No. 1. (2001), pp. 53-67.
    by David L Nowell
    posted to evolution gene order synteny by sharpton on 2008-05-19 22:30:26 as **
  • Expected Gene Order Distances and Model Selection in Bacteria.
    Bioinformatics (Oxford, England) (1 April 2008)
    by Daniel Dalevi, Niklas Eriksen
    posted to bacteria gene genome microbe order synteny by sharpton on 2008-05-19 19:15:15 as ** along with 3 people and 1 group maximilianh Ema cisevol BergmanLab
  • Fourfold Faster Rate of Genome Rearrangement in Nematodes Than in Drosophila
    Genome Res., Vol. 12, No. 6. (1 June 2002), pp. 857-867.
    by Avril Coghlan, Kenneth H Wolfe
    posted to evolution gene order synteny by sharpton on 2008-05-19 22:29:35 as ** along with 2 people and 1 group tharris hausen C. elegans / WormBase
  • Algorithmic approaches for genome rearrangement: a review
    Systems, Man, and Cybernetics, Part C: Applications and Reviews, IEEE Transactions on, Vol. 36, No. 5. (2006), pp. 636-648.
    by Zimao Li, Lusheng Wang, Kaizhong Zhang
    posted to evolution gene order review synteny by sharpton on 2008-05-19 22:31:53 as **
  • Structural dynamics of eukaryotic chromosome evolution.
    Science, Vol. 301, No. 5634. (8 August 2003), pp. 793-797.
    by EE Eichler, D Sankoff
    posted to evolution gene order synteny by sharpton on 2008-05-19 22:27:42 as ** along with 2 people david_parsons timflutre
  • Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
    PLoS Computational Biology, Vol. 2, No. 9. (1 September 2006), e133.
    by Leo Goodstadt, Chris P Ponting
    posted to eukaryotic evolution genomics ortholog paralog phylogenetics synteny by operon on 2007-07-23 21:11:47 as ***** along with 1 person and 1 group indigoviolet EisenLab
  • Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.
    Proc Natl Acad Sci U S A, Vol. 100, No. 20. (30 September 2003), pp. 11484-11489.
    by WJ Kent, R Baertsch, A Hinrichs, W Miller, D Haussler
    posted to human mouse synteny by nuin on 2008-08-27 21:19:12 as ** along with 5 people and 1 group bryankr pcahan1 djkt gjuggler Auger Dead 60's
  • Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements.
    Hum Mol Genet, Vol. 12, No. 17. (1 September 2003), pp. 2201-2208.
    by L Armengol, MA Pujana, J Cheung, SW Scherer, X Estivill
    posted to human mouse synteny by nuin on 2008-08-27 21:18:24 as ** along with 1 person pcahan1
  • SynBlast: assisting the analysis of conserved Synteny information
    BMC Bioinformatics, Vol. 9 (24 August 2008), 351.
    by Jorg Lehmann, Peter F Stadler, Sonja J Prohaska
    posted to human mouse synteny by nuin on 2008-08-27 21:41:36 as ** along with 2 people grahamc Neeperando
  • PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Christine Fong, Laurence Rohmer, Matthew Radey, Michael Wasnick, Mitchell Brittnacher
    posted to bioinformatics conservation genomics neighbourhood prokaryotic synteny by neils on 2008-03-26 23:50:21 as ** along with 2 people treangen maximilianh
  • i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles.
    Bioinformatics (Oxford, England), Vol. 24, No. 1. (1 January 2008), pp. 127-128.
    by C Simillion, K Janssens, L Sterck, Y Van de Peer
    posted to detection synteny by Neeperando on 2008-08-25 15:15:41 as **
  • LineUp: statistical detection of chromosomal homology with application to plant comparative genomics.
    Genome research, Vol. 13, No. 5. (May 2003), pp. 999-1010.
    by S Hampson, A McLysaght, B Gaut, P Baldi
    posted to detection synteny by Neeperando on 2008-08-25 15:14:17 as **
  • DAGchainer: a tool for mining segmental genome duplications and synteny
    Bioinformatics, Vol. 20, No. 18., 3643.
    by Brian J Haas, Arthur L Delcher, Steven L Salzberg
    posted to detection synteny by Neeperando on 2008-08-25 15:15:00 as read along with 1 person treangen
  • Statistical detection of chromosomal homology using shared-gene density alone.
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1339-1348.
    by SE Hampson, BS Gaut, P Baldi
    posted to detection synteny by Neeperando on 2008-08-25 15:13:52 as ** along with 1 person AaronDarling
  • Building genomic profiles for uncovering segmental homology in the twilight zone.
    Genome research, Vol. 14, No. 6. (June 2004), pp. 1095-1106.
    by C Simillion, K Vandepoele, Y Saeys, Y Van de Peer
    posted to synteny by Neeperando on 2008-08-26 21:38:52 as **
  • The random versus fragile breakage models of chromosome evolution: a matter of resolution.
    Mol Genet Genomics, Vol. 278, No. 5. (November 2007), pp. 487-491.
    by TS Becker, B Lenhard
    posted to geneorder genomicregulatoryblocks synteny syntenypaper by maximilianh on 2007-11-02 18:36:01 as ** along with 2 people Heute boudinot
  • Genome classification by gene distribution: an overlapping subspace clustering approach
    BMC Evolutionary Biology, Vol. 8 (23 April 2008), 116.
    by Jason Li, Saman K Halgamuge, Sen-Lin Tang
    posted to geneorder synteny syntenypaper by maximilianh on 2008-04-28 10:28:20 as ** along with 1 person cmzmasek
  • Comparison of Pax1/9 Locus Reveals 500-Myr-Old Syntenic Block and Evolutionary Conserved Noncoding Regions
    Molecular Biology and Evolution, Vol. 24, No. 3. (March 2007), pp. 784-791.
    by Wang, Wei, Zhong, Jing, Su, Bing, Zhou, Yan, Wang, Yi-Quan
    posted to genomicregulatoryblocks synteny syntenypaper by maximilianh on 2008-01-15 19:50:49 as ** along with 1 person alhufton
  • OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes.
    Nucleic acids research (2 May 2008)
    by Li-Wei W Jiang, Kuang-Lun L Lin, Chin Lung L Lu
    posted to synteny syntenypaper syntenytools by maximilianh on 2008-05-11 22:20:19 as **
  • Genomic regulatory blocks underlie extensive microsynteny conservation in insects
    Genome Res. (7 November 2007), gr.6669607.
    by Par G Engstrom, Ho, Oyvind Drivenes, Thomas S Becker, Boris Lenhard
    posted to genomicregulatoryblocks synteny syntenypaper by maximilianh on 2007-11-13 18:20:24 as **
  • Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
    Genome Res., Vol. 17, No. 5. (1 May 2007), pp. 545-555.
    by Hiroshi Kikuta, Mary Laplante, Pavla Navratilova, Anna Z Komisarczuk, Par G Engstrom, David Fredman, Altuna Akalin, Mario Caccamo, Ian Sealy, Kerstin Howe, Julien Ghislain, Guillaume Pezeron, Philippe Mourrain, Staale Ellingsen, Andrew C Oates, Christine Thisse, Bernard Thisse, Isabelle Foucher, Birgit Adolf, Andrea Geling, Boris Lenhard, Thomas S Becker
    posted to genomicregulatoryblocks randombreakage synteny syntenypaper by maximilianh on 2008-01-15 17:38:19 as ** along with 3 people and 3 groups dchughes djkt boudinot Bioinformatics G4ID Genetics-of-Gambling
  • Cis- and Trans-Acting Elements Regulate the Mouse Psmb9 Meiotic Recombination Hotspot.
    PLoS Genet, Vol. 3, No. 6. (22 June 2007)
    by Frédéric Baudat, Bernard de Massy
    posted to geneorder randombreakage synteny syntenypaper by maximilianh on 2007-12-07 09:29:17 as ** along with 1 person and 1 group dpollard EisenLab
  • Subfunctionalization of Duplicated Zebrafish pax6 Genes by cis-Regulatory Divergence
    PLoS Genetics, Vol. 4, No. 2. (1 February 2008), e29.
    by Dirk A Kleinjan, Ruth M Bancewicz, Philippe Gautier, Ralf Dahm, Helia B Schonthaler, Giuseppe Damante, Anne Seawright, Ann M Hever, Patricia L Yeyati, Veronica van Heyningen, Pedro Coutinho
    posted to cns-differences duplicates synteny tandem by maximilianh on 2008-06-05 23:41:15 as ** along with 4 people brant gjuggler emptyhb Stew
  • Inversions and the dynamics of eukaryotic gene order.
    Trends Genet, Vol. 17, No. 6. (June 2001), pp. 304-306.
    by MA Huynen, B Snel, P Bork
    posted to geneorder synteny syntenyorientation syntenypaper by maximilianh on 2008-01-15 11:20:12 as **
  • The Fragile Breakage versus Random Breakage Models of Chromosome Evolution.
    PLoS Comput Biol, Vol. 2, No. 2. (24 February 2006)
    by Qian Peng, Pavel A A Pevzner, Glenn Tesler
    posted to genomeregulatoryblocks randombreakage synteny syntenypaper by maximilianh on 2008-01-14 15:54:13 as ** along with 1 person AaronDarling
  • Quantification of insect genome divergence.
    Trends Genet (8 November 2006)
    by Evgeny M M Zdobnov, Peer Bork
    posted to phylogenomics synteny syntenypaper by maximilianh on 2008-01-17 16:59:34 as ** along with 3 people and 1 group nachtalp indigoviolet balicea EisenLab
  • Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps.
    Hum Genomics, Vol. 1, No. 1. (November 2003), pp. 30-40.
    by WJ Murphy, G Bourque, G Tesler, P Pevzner, SJ O'Brien
    posted to randombreakage synteny syntenypaper by maximilianh on 2008-03-05 14:12:58 as ** along with 1 person balajis
  • Genome evolution in yeasts.
    Nature, Vol. 430, No. 6995. (1 July 2004), pp. 35-44.
    by B Dujon, D Sherman, G Fischer, P Durrens, S Casaregola, I Lafontaine, J De Montigny, C Marck, C Neuvéglise, E Talla, N Goffard, L Frangeul, M Aigle, V Anthouard, A Babour, V Barbe, S Barnay, S Blanchin, JM Beckerich, E Beyne, C Bleykasten, A Boisramé, J Boyer, L Cattolico, F Confanioleri, A De Daruvar, L Despons, E Fabre, C Fairhead, H Ferry-Dumazet, A Groppi, F Hantraye, C Hennequin, N Jauniaux, P Joyet, R Kachouri, A Kerrest, R Koszul, M Lemaire, I Lesur, L Ma, H Muller, JM Nicaud, M Nikolski, S Oztas, O Ozier-Kalogeropoulos, S Pellenz, S Potier, GF Richard, ML Straub, A Suleau, D Swennen, F Tekaia, M Wésolowski-Louvel, E Westhof, B Wirth, M Zeniou-Meyer, I Zivanovic, M Bolotin-Fukuhara, A Thierry, C Bouchier, B Caudron, C Scarpelli, C Gaillardin, J Weissenbach, P Wincker, JL Souciet
    posted to geneorder genes synteny by maximilianh on 2007-10-01 12:20:15 as *** along with 5 people and 3 groups evaf indigoviolet dchughes dbenn nklee EisenLab G4ID Genetics-of-Gambling
  • Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps
    Science, Vol. 309, No. 5734. (22 July 2005), pp. 613-617.
    by William J Murphy, Denis M Larkin, Der, Guillaume Bourque, Glenn Tesler, Loretta Auvil, Jonathan E Beever, Bhanu P Chowdhary, Francis Galibert, Lisa Gatzke, Christophe Hitte, Stacey N Meyers, Denis Milan, Elaine A Ostrander, Greg Pape, Heidi G Parker, Terje Raudsepp, Margarita B Rogatcheva, Lawrence B Schook, Loren C Skow, Michael Welge, James E Womack, Stephen J O'Brien, Pavel A Pevzner, Harris A Lewin
    posted to randombreakage synteny by maximilianh on 2008-01-15 10:45:54 as ** along with 2 people balajis mycitation
  • Chromosomal clustering of genes controlled by the aire transcription factor.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 20. (17 May 2005), pp. 7233-7238.
    by JB Johnnidis, ES Venanzi, DJ Taxman, JP Ting, CO Benoist, DJ Mathis
    posted to syntenypaper synteny geneorder genecoregulation by maximilianh on 2008-09-13 16:05:26 as **
  • Chromosome rearrangements in evolution: From gene order to genome sequence and back.
    Proc Natl Acad Sci U S A, Vol. 100, No. 20. (30 September 2003), pp. 11188-11189.
    by D Sankoff, JH Nadeau
    posted to synteny syntenypaper by maximilianh on 2008-01-15 10:38:05 as ** along with 2 people and 1 group operon Auger Dead 60's
  • On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees
    Genome Biology, Vol. 8, No. 10. (2007)
    by Tomas M Bonet, Jesus S Ruiz, Lluis Armengol, Razi Khaja, Jaume Bertranpetit, Mariano Rocchi, Elodie Gazave, Nuria L Bigas, Arcadi Navarro
    posted to geneorder synteny syntenypaper by maximilianh on 2007-11-04 00:16:54 as ** along with 2 people and 1 group djkt hpaces Bioinformatics
  • 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 **
  • 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 **
  • Convergent evolution of clustering of Iroquois homeobox genes across metazoans.
    Molecular biology and evolution (9 May 2008)
    by Manuel Irimia, Ignacio Maeso, Jordi Garcia-Fernàndez
    posted to copy-number-variation duplicates synteny tandem by maximilianh on 2008-05-17 10:01:23 as ** along with 1 person fhsantanna
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