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Tag phylogenomics [91 articles]

Recent papers classified by the tag phylogenomics.
  • Bushes in the Tree of Life
    PLoS Biology, Vol. 4, No. 11. (1 November 2006), e352.
    by Antonis Rokas, Sean B Carroll
    posted to bushes evolution homoplasy phylogenomics phylogeny by timothee on 2007-01-01 14:34:17 as read along with 2 people and 4 groups emilyhare kehan biodiversity_conservation Bioinformatics EisenLab GrassBase
  • Phylogenomics: the beginning of incongruence?
    Trends Genet (18 February 2006)
    by Olivier Jeffroy, Henner Brinkmann, Frédéric Delsuc, Hervé Philippe
    posted to genome molecular-evolution phylogenomics phylogeny review by taka on 2007-05-26 14:26:56 as *** along with 4 people and 4 groups aprasad indigoviolet dchughes kinestetika EisenLab G4ID microbiology_nijmegen Genetics-of-Gambling
  • Morphological and molecular phylogenetic context of the angiosperms: contrasting the top-down and bottom-up approaches used to infer the likely characteristics of the first flowers
    Journal of Experimental Botany, Vol. 57, No. 13. (October 2006), pp. 3471-3503.
    by Bateman, M Richard, Hilton, Jason, Rudall, J Paula
    posted to molecular-evolution morphology paleobotany phylogenomics phylogeny plant by taka on 2007-05-26 14:20:05 as *** along with 1 person ArtemPankin
  • Comparative genomics in the Brassicaceae: a family-wide perspective
    Current Opinion in Plant Biology, Vol. 10, No. 2. (April 2007), pp. 168-175.
    by Eric M Schranz, Bao-Hua Song, Aaron J Windsor, Thomas Mitchell-Olds
    posted to chromosome diversity genome molecular-evolution phylogenomics phylogeny plant polyploidy by taka on 2007-05-26 14:12:12 as ***
  • Phylogenomics: Intersection of Evolution and Genomics
    Science, Vol. 300, No. 5626. (13 June 2003), pp. 1706-1707.
    by Jonathan A Eisen, Claire M Fraser
    posted to genome molecular-evolution phylogenomics phylogeny review by taka on 2007-05-26 14:02:39 as *** along with 1 person operon
  • Evaluating Support for the Current Classification of Eukaryotic Diversity
    PLoS Genetics, Vol. 2, No. 12. (1 December 2006), e220.
    by Laura W Parfrey, Erika Barbero, Elyse Lasser, Micah Dunthorn, Debashish Bhattacharya, David J Patterson, Laura A Katz
    posted to eukarytoa phylogenomics phylogeny by stajich on 2006-12-28 03:13:04 as ***** along with 4 people and 1 group rvosa srfairclough dandaman cmzmasek FAB-lab
  • A phylogenomic investigation into the origin of Metazoa
    Mol Biol Evol (9 January 2008), msn006.
    by Inaki Ruiz-Trillo, Andrew J Roger, Gertraud Burger, Michael W Gray, Franz B Lang
    posted to evodevo evolution metazoa metazoan methods multicellular phylogenomics by stajich on 2008-03-05 17:54:57 as ** along with 2 people and 1 group cmzmasek renatomilani Berkeley Mycology
  • Profiling Phylogenetic Informativeness
    Systematic Biology, Vol. 56, No. 2. (2007), pp. 222-231.
    by Jeffrey P Townsend
    posted to evolution phylogenetic_marker_selection phylogenetics phylogenomics by stajich on 2007-12-06 22:46:04 as ** along with 3 people and 2 groups aprasad rvosa Jporci FAB-lab Berkeley Mycology
  • Improved Consensus Network Techniques for Genome-Scale Phylogeny
    Molecular Biology and Evolution, Vol. 23, No. 5. (15 May 2006), pp. 848-855.
    by Barbara R Holland, Lars S Jermiin, Vincent Moulton
    posted to genome_evolution methods phylogenetics phylogenomics by stajich on 2007-08-28 09:23:26 as ** along with 1 person and 1 group rvosa FAB-lab
  • Testing Congruence in Phylogenomic Analysis
    Systematic Biology, Vol. 57, No. 1. (2008), pp. 104-115.
    by Jessica W Leigh, Edward Susko, Manuela Baumgartner, Andrew J Roger
    posted to methods phylogenetics phylogenomics by stajich on 2008-03-14 21:08:27 as ** along with 1 group Berkeley Mycology
  • Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution.
    PLoS ONE, Vol. 2 (2007)
    by M Kullberg, B Hallström, U Arnason, A Janke
    posted to est mammal phylogenetics phylogenomics phylogeny by stajich on 2007-09-04 19:00:30 as **
  • Evaluation of the models handling heterotachy in phylogenetic inference
    BMC Evolutionary Biology, Vol. 7 (01 November 2007), 206.
    by Yan Zhou, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe
    posted to heterotachy methods phylogenetics phylogenomics by stajich on 2007-11-07 04:18:59 as ** along with 1 group Berkeley Mycology
  • Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
    BMC Evolutionary Biology, Vol. 8 (26 March 2008), 95.
    by Stefanie Hartmann, Todd J Vision
    posted to methods phylogenomics by stajich on 2008-04-01 06:19:14 as ** along with 2 people and 1 group aprasad Patola Berkeley Mycology
  • Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom
    BMC Evolutionary Biology, Vol. 7 (09 August 2007), 134.
    by Eiko E Kuramae, Vincent Robert, Carlos Echavarri-Erasun, Teun Boekhout
    posted to fungal phylogenetic_marker_selection phylogenomics phylogeny by stajich on 2007-11-13 17:33:27 as ** along with 1 person and 2 groups rvosa FAB-lab Berkeley Mycology
  • Detecting and overcoming systematic errors in genome-scale phylogenies.
    Syst Biol, Vol. 56, No. 3. (June 2007), pp. 389-399.
    by N Rodríguez-Ezpeleta, H Brinkmann, B Roure, N Lartillot, BF Lang, H Philippe
    posted to methods phylogenetics phylogenomics by stajich on 2007-11-16 20:15:16 as ** along with 3 people and 2 groups aprasad rvosa dandaman FAB-lab Berkeley Mycology
  • New Approaches to Phylogenetic Tree Search and Their Application to Large Numbers of Protein Alignments
    Systematic Biology, Vol. 56, No. 5. (2007), pp. 727-740.
    by Simon Whelan
    posted to methods phylogenetics phylogenomics by stajich on 2007-11-29 17:39:54 as ** along with 1 person and 1 group rvosa FAB-lab
  • Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus.
    Gene, Vol. 383 (15 November 2006), pp. 24-32.
    by RA Cramer, JE Stajich, Y Yamanaka, FS Dietrich, WJ Steinbach, JR Perfect
    posted to aspergillus fungi nrps phylogenomics by stajich on 2006-12-08 21:04:02 as read along with 1 person and 1 group rvosa FAB-lab
  • Automatic Methods for Predicting Functionally Important Residues
    Journal of Molecular Biology, Vol. 326, No. 4. (28 February 2003), pp. 1289-1302.
    by A Del, Florencio Pazos, Alfonso Valencia
    posted to component evolutionary function phylogenomics principal by sriram_s on 2006-04-25 01:09:59 as *** along with 2 people and 1 group mdimmic cjeans TNT
  • An evolutionary trace method defines binding surfaces common to protein families.
    J Mol Biol, Vol. 257, No. 2. (29 March 1996), pp. 342-358.
    by O Lichtarge, HR Bourne, FE Cohen
    posted to evolution functional phylogenomics residues by sriram_s on 2006-03-25 00:37:29 as ** along with 3 people and 1 group lna nickolay cat_worth structural_bioinformatics
  • The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.
    Proteins, Vol. 58, No. 3. (15 February 2005), pp. 610-617.
    by F Glaser, Y Rosenberg, A Kessel, T Pupko, N Ben-Tal
    posted to evolution functional phylogenomics residues by sriram_s on 2006-03-25 00:11:25 as **
  • Protein Molecular Function Prediction by Bayesian Phylogenomics.
    PLoS Comput Biol, Vol. 1, No. 5. (7 October 2005)
    by Barbara EE Engelhardt, Michael II Jordan, Kathryn EE Muratore, Steven EE Brenner
    posted to annotation bayeisan function phylogenomics by sriram_s on 2006-03-24 23:59:45 as ** along with 7 people and 4 groups kentsis ana eoghanharr Einat dlr marcius bootsy structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Phylogenomic inference of protein molecular function: advances and challenges.
    Bioinformatics, Vol. 20, No. 2. (22 January 2004), pp. 170-179.
    by K Sjölander
    posted to phylogenomics by sgoetz on 2008-07-24 23:21:51 as ** along with 3 people ziquje jwortman sriram_s
  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
    Nature, Vol. 428, No. 6982. (1 April 2004), pp. 493-521.
    by RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, S Scherer, G Scott, D Steffen, KC Worley, PE Burch, G Okwuonu, S Hines, L Lewis, C DeRamo, O Delgado, S Dugan-Rocha, G Miner, M Morgan, A Hawes, R Gill, Celera, RA Holt, MD Adams, PG Amanatides, H Baden-Tillson, M Barnstead, S Chin, CA Evans, S Ferriera, C Fosler, A Glodek, Z Gu, D Jennings, CL Kraft, T Nguyen, CM Pfannkoch, C Sitter, GG Sutton, JC Venter, T Woodage, D Smith, HM Lee, E Gustafson, P Cahill, A Kana, L Doucette-Stamm, K Weinstock, K Fechtel, RB Weiss, DM Dunn, ED Green, RW Blakesley, GG Bouffard, PJ De Jong, K Osoegawa, B Zhu, M Marra, J Schein, I Bosdet, C Fjell, S Jones, M Krzywinski, C Mathewson, A Siddiqui, N Wye, J McPherson, S Zhao, CM Fraser, J Shetty, S Shatsman, K Geer, Y Chen, S Abramzon, WC Nierman, PH Havlak, R Chen, KJ Durbin, A Egan, Y Ren, XZ Song, B Li, Y Liu, X Qin, S Cawley, KC Worley, AJ Cooney, LM D'Souza, K Martin, JQ Wu, ML Gonzalez-Garay, AR Jackson, KJ Kalafus, MP McLeod, A Milosavljevic, D Virk, A Volkov, DA Wheeler, Z Zhang, JA Bailey, EE Eichler, E Tuzun, E Birney, E Mongin, A Ureta-Vidal, C Woodwark, E Zdobnov, P Bork, M Suyama, D Torrents, M Alexandersson, BJ Trask, JM Young, H Huang, H Wang, H Xing, S Daniels, D Gietzen, J Schmidt, K Stevens, U Vitt, J Wingrove, F Camara, M Mar Albà, JF Abril, R Guigo, A Smit, I Dubchak, EM Rubin, O Couronne, A Poliakov, N Hübner, D Ganten, C Goesele, O Hummel, T Kreitler, YA Lee, J Monti, H Schulz, H Zimdahl, H Himmelbauer, H Lehrach, HJ Jacob, S Bromberg, J Gullings-Handley, MI Jensen-Seaman, AE Kwitek, J Lazar, D Pasko, PJ Tonellato, S Twigger, CP Ponting, JM Duarte, S Rice, L Goodstadt, SA Beatson, RD Emes, EE Winter, C Webber, P Brandt, G Nyakatura, M Adetobi, F Chiaromonte, L Elnitski, P Eswara, RC Hardison, M Hou, D Kolbe, K Makova, W Miller, A Nekrutenko, C Riemer, S Schwartz, J Taylor, S Yang, Y Zhang, K Lindpaintner, TD Andrews, M Caccamo, M Clamp, L Clarke, V Curwen, R Durbin, E Eyras, SM Searle, GM Cooper, S Batzoglou, M Brudno, A Sidow, EA Stone, JC Venter, BA Payseur, G Bourque, C López-Otín, XS Puente, K Chakrabarti, S Chatterji, C Dewey, L Pachter, N Bray, VB Yap, A Caspi, G Tesler, PA Pevzner, D Haussler, KM Roskin, R Baertsch, H Clawson, TS Furey, AS Hinrichs, D Karolchik, WJ Kent, KR Rosenbloom, H Trumbower, M Weirauch, DN Cooper, PD Stenson, B Ma, M Brent, M Arumugam, D Shteynberg, RR Copley, MS Taylor, H Riethman, U Mudunuri, J Peterson, M Guyer, A Felsenfeld, S Old, S Mockrin, F Collins,
    posted to animals data-mining genetics genome mammals phylogenomics rats rodents sequence vertebrates by rvosa on 2008-02-01 11:08:27 as ** along with 5 people and 4 groups aprasad ccots dchughes djkt stajich FAB-lab G4ID Genetics-of-Gambling Berkeley Mycology
  • Distinguishing protein-coding and noncoding genes in the human genome
    Proceedings of the National Academy of Sciences (26 November 2007), 0709013104.
    by Michele Clamp, Ben Fry, Mike Kamal, Xiaohui Xie, James Cuff, Michael F Lin, Manolis Kellis, Kerstin Lindblad-Toh, Eric S Lander
    posted to algorithms amino-acid animals data-mining genetics genome hominidae homology humans mammals methods phylogenomics primates proteins rna sequence vertebrates by rvosa on 2008-02-01 11:04:06 as ** along with 15 people and 3 groups Ema tmmurali balicea sebastien_vigneau giovanni neils stajich cjeans cabbagezs maximilianh oelemento gjuggler slroberd renatomilani gracio EisenLab FAB-lab Berkeley Mycology
  • Assessing performance of orthology detection strategies applied to eukaryotic genomes.
    PLoS ONE, Vol. 2 (2007)
    by F Chen, AJ Mackey, JK Vermunt, DS Roos
    posted to algorithms databases data-mining genome methods phylogenomics phylogeny phyloinformatics by rvosa on 2008-02-01 10:57:02 as ** along with 8 people and 3 groups cerca natstreet icases operon indigoviolet stajich cjeans winterschlaefer EisenLab FAB-lab TNT
  • Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
    Bioinformatics, Vol. 18, No. 1. (January 2002), pp. 92-99.
    by CE Storm, EL Sonnhammer
    posted to algorithms genetics genome methods phylogenomics phylogeny phyloinformatics by rvosa on 2008-02-01 00:03:38 as ** along with 5 people and 1 group mdimmic operon dlr indigoviolet ninch EisenLab
  • Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs
    Genome Res., Vol. 18, No. 3. (1 March 2008), pp. 489-499.
    by Julie E Horvath, David W Weisrock, Stephanie L Embry, Isabella Fiorentino, James P Balhoff, Peter Kappeler, Gregory A Wray, Huntington F Willard, Anne D Yoder
    posted to phylogeny phylogenomics lemur cladistics by pradiptaray on 2008-07-04 11:33:18 as **
  • SHOT: a web server for the construction of genome phylogenies
    Trends in Genetics, Vol. 18, No. 3. (1 March 2002), pp. 158-162.
    by Jan O Korbel, Berend Snel, Martijn A Huynen, Peer Bork
    posted to phylogenomics synteny by maximilianh on 2007-10-23 16:42:19 as **
  • Rearrangement Rate following the Whole-Genome Duplication in Teleosts
    Mol Biol Evol, Vol. 24, No. 3. (1 March 2007), pp. 860-867.
    by Marie Semon, Kenneth H Wolfe
    posted to phylogenomics syntenypaper by maximilianh on 2008-01-14 16:18:29 as ** along with 1 person and 3 groups dchughes Bioinformatics G4ID Genetics-of-Gambling
  • Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions
    PNAS, Vol. 103, No. 26. (27 June 2006), pp. 9929-9934.
    by Hidenori Nishihara, Masami Hasegawa, Norihiro Okada
    posted to phylogenomics by maximilianh on 2008-01-14 14:32:53 as ** along with 2 people and 1 group aprasad cmm FAB-lab
  • Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data
    PLoS Genetics, Vol. 3, No. 1. (1 January 2007), e2.
    by Sergey Nikolaev, Juan I Montoya-Burgos, Elliott H Margulies, Nisc C Program, Jacques Rougemont, Bruno Nyffeler, Stylianos E Antonarakis
    posted to cns phylogenomics phylogeny syntenypaper by maximilianh on 2007-10-17 15:46:38 as read along with 2 people aprasad Garamonfok
  • Using genomic data to unravel the root of the placental mammal phylogeny.
    Genome Res, Vol. 17, No. 4. (April 2007), pp. 413-421.
    by WJ Murphy, TH Pringle, TA Crider, MS Springer, W Miller
    posted to phylogenomics phylogeny syntenypaper by maximilianh on 2008-01-14 14:26:28 as ** along with 1 person aprasad
  • Rooting the eutherian tree: the power and pitfalls of phylogenomics
    Genome Biology, Vol. 8 (21 September 2007), R199.
    by Hidenori Nishihara, Norihiro Okada, Masami Hasegawa
    posted to phylogeny phylogenomics by maximilianh on 2007-09-26 16:53:32 as * along with 1 person aprasad
  • Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages.
    PLoS Genet, Vol. 2, No. 3. (March 2006)
    by G Fischer, EP Rocha, F Brunet, M Vergassola, B Dujon
    posted to phylogenomics syntenypaper by maximilianh on 2008-01-14 16:11:20 as ** along with 2 people nirfriedman jpoyatos
  • 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
  • A higher-level MRP supertree of placental mammals
    BMC Evolutionary Biology, Vol. 6 (13 November 2006), 93.
    by Robin MD Beck, Olaf RP Bininda-Emonds, Marcel Cardillo, Fu-Guo R Liu, Andy Purvis
    posted to syntenypaper phylogeny phylogenomics mammals by maximilianh on 2007-10-30 14:58:25 as **
  • Inferring genome-scale rearrangement phylogeny and ancestral gene order: A Drosophila case study
    Genome Biology, Vol. 8 (08 November 2007), R236.
    by Arjun Bhutkar, William M Gelbart, Temple F Smith
    posted to genometrees genomicregulatoryblocks phylogenomics synteny syntenypaper by maximilianh on 2007-11-22 18:12:13 as ** along with 5 people and 1 group isimpson indigoviolet dpollard balicea hpaces EisenLab
  • Phylogenomics and the reconstruction of the tree of life
    Nature Reviews Genetics, Vol. 6, No. 5. (01 May 2005), pp. 361-375.
    by Frederic Delsuc, Henner Brinkmann, Herve Philippe
    posted to phylogenomics syntenypaper by maximilianh on 2008-01-14 11:49:07 as ** along with 3 people cmzmasek gjuggler dmc
  • Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
    Genome Res, Vol. 15, No. 1. (January 2005), pp. 98-110.
    by G Bourque, EM Zdobnov, P Bork, PA Pevzner, G Tesler
    posted to phylogenomics syntenypaper by maximilianh on 2008-01-14 23:03:54 as ** along with 1 person Ayest
  • Genome phylogeny based on gene content.
    Nat Genet, Vol. 21, No. 1. (January 1999), pp. 108-110.
    by B Snel, P Bork, MA Huynen
    posted to phylogenomics by maximilianh on 2008-01-14 11:43:39 as **
  • A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study
    BMC Evolutionary Biology, Vol. 7 (20 March 2007), 44.
    by Chenhong Li, Guillermo Orti, Gong Zhang, Guoqing Lu
    posted to phylogenomics phylogeny by maximilianh on 2008-01-17 10:48:38 as **
  • Toward Automatic Reconstruction of a Highly Resolved Tree of Life
    Science, Vol. 311, No. 5765. (3 March 2006), pp. 1283-1287.
    by Francesca D Ciccarelli, Tobias Doerks, Christian von Mering, Christopher J Creevey, Berend Snel, Peer Bork
    posted to phylogenomics syntenypaper by maximilianh on 2008-01-14 15:00:19 as ** along with 12 people and 5 groups diamantis Retchless knaseanka dpollard tny dchughes nirfriedman cmm azazello wenhan cmzmasek lonshy EisenLab FAB-lab G4ID Genetics-of-Gambling MBLAB
  • Assessment of phylogenomic and orthology approaches for phylogenetic inference
    Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 815-824.
    by Dutilh, , Van Noort, , van der Heijden, , Boekhout, , Snel, , Huynen,
    posted to phylogenomics syntenypaper by maximilianh on 2008-01-14 14:36:42 as ** along with 1 person svdate
  • A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data.
    Proc Int Conf Intell Syst Mol Biol, Vol. 8 (2000), pp. 104-115.
    by ME Cosner, RK Jansen, BM Moret, LA Raubeson, LS Wang, T Warnow, S Wyman
    posted to phylogenomics synteny syntenypaper by maximilianh on 2008-01-14 18:29:27 as **
  • Multiple genome rearrangement and breakpoint phylogeny.
    J Comput Biol, Vol. 5, No. 3. (1998), pp. 555-570.
    by D Sankoff, M Blanchette
    posted to phylogenomics by maximilianh on 2008-01-14 18:18:42 as ** along with 1 person balicea
  • Functional genome annotation through phylogenomic mapping
    Nature Biotechnology, Vol. 23, No. 6. (06 June 2005), pp. 691-698.
    by Balaji S Srinivasan, Nora B Caberoy, Garret Suen, Rion G Taylor, Radhika Shah, Farah Tengra, Barry S Goldman, Anthony G Garza, Roy D Welch
    posted to functional_genomics phylogenomics by lyongu on 2005-10-11 22:51:18 as *** along with 11 people and 1 group shoshin operon setar tmmurali pggm aprasad balajis nuke2005 nedwards blobbybirdman kroos Myxo group
  • Data incongruence and the problem of avian louse phylogeny
    Zoologica Scripta, Vol. 33, No. 3. (2004), pp. 239-259.
    by Vincent S Smith, Roderic D Page, Kevin P Johnson
    posted to phylogenomics rodpage splitstree by kehan on 2006-03-14 12:55:53 as ** along with 3 groups biodiversity_conservation Bioinformatics GrassBase
  • Modelling the recent common ancestry of all living humans
    Nature, Vol. 431, No. 7008. (2004), pp. 562-566.
    by Douglas L Rohde, Steve Olson, Joseph T Chang
    posted to evolution homo human phylogenomics phylogeny sapiens by kehan on 2006-07-10 12:05:18 as ** along with 4 people and 4 groups dahnielson balicea bpacker larios biodiversity_conservation Bioinformatics vision-ng GrassBase
  • Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia.
    Mol Biol Evol, Vol. 22, No. 5. (May 2005), pp. 1246-1253.
    by H Philippe, N Lartillot, H Brinkmann
    posted to ecdysozoa phylogenomics by hdopazo on 2006-08-04 17:56:08 as ** along with 1 group BioinfoCIPF
  • Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species.
    Bioinformatics, Vol. 20 Suppl 1 (4 August 2004)
    by H Dopazo, J Santoyo, J Dopazo
    posted to ecdysozoa genomics phylogenomics by hdopazo on 2006-07-20 14:13:01 as ***** along with 1 group BioinfoCIPF
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