nlapalu's library 89 articles Export

	Analysis of loss of pathogenicity mutants reveals that repeat-induced point mutations can occur in the Dothideomycete Leptosphaeria maculans [My Copy] Fungal Genetics and Biology, Vol. 39, No. 1. (June 2003), pp. 31-37. by Alexander Idnurm, Barbara J. Howlett posted to silencing restriction pathogenicity napus mutagenesis mediated integration gene fungi enzyme brassica by nlapalu on 2009-11-18 08:59:42 as
	Repeat-Induced Point Mutation (RIP) as an Alternative Mechanism of Evolution Toward Virulence in Leptosphaeria maculans [My Copy] Molecular Plant-Microbe Interactions, Vol. 22, No. 8. (1 August 2009), pp. 932-941. by Isabelle Fudal, Simon Ross, Hortense Brun, et al.Anne-Laure Besnard, Magali Ermel, Marie-Line Kuhn, Marie-Hélène Balesdent, Thierry Rouxel posted to virulence rip leptosphaeria_maculans evolution by nlapalu on 2009-11-18 08:50:56 as
	Truncated and RIP-degenerated copies of the LTR retrotransposon Pholy are clustered in a pericentromeric region of the Leptosphaeria maculans genome [My Copy] Fungal Genetics and Biology, Vol. 42, No. 1. (January 2005), pp. 30-41. by Agnès Attard, Lilian Gout, Simon Ross, et al.Francis Parlange, Laurence Cattolico, Marie-Hélène Balesdent, Thierry Rouxel posted to rip retrotransposon leptosphaeria_maculans genome by nlapalu on 2009-11-18 08:44:59 as
	Repeat induced point mutation in two asexual fungi, Aspergillus niger and Penicillium chrysogenum [My Copy] Current Genetics, Vol. 53, No. 5. (May 2008), pp. 287-297. by Braumann, Ilka, Berg, Marco, Kempken, Frank posted to rip penicillium_chrysogenum genome gene fungi fungal_genomes aspergillus_niger by nlapalu on 2009-11-18 08:38:38 as along with 1 person jamselem
	Genomic Perl: From Bioinformatics Basics to Working Code [My Copy] (15 July 2002) by Rex A. Dwyer posted to books perl_books bioinformatic_books by nlapalu on 2009-11-11 11:46:34 as along with 2 people antonkratz quianominorleo
	Bioinformatics: The Machine Learning Approach, Second Edition (Adaptive Computation and Machine Learning) [My Copy] (01 August 2001) by Pierre Baldi, Sã¸ren Brunak posted to books machine_learning bioinformatic_books by nlapalu on 2009-11-11 11:38:55 as along with 2 people npt11tpn ujh
	Indexing genomic sequence libraries [My Copy] Information Processing & Management, Vol. 41, No. 2. (March 2005), pp. 265-274. by Kevin C. O'Kane, Matthew J. Lockner posted to perl indexing genome_sequences databank data c by nlapalu on 2009-11-11 11:33:43 as along with 1 person sriks6711
	ANNIE: integrated de novo protein sequence annotation [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W435-440. by Hong S. Ooi, Chia Y. Kwo, Michael Wildpaner, et al.Fernanda L. Sirota, Birgit Eisenhaber, Sebastian Maurer-Stroh, Wing C. Wong, Alexander Schleiffer, Frank Eisenhaber, Georg Schneider posted to web pipeline genome fungal_genomes functional families annotation algorithm by nlapalu on 2009-11-03 12:50:46 as along with 5 people Thaverkamp druvus dullhunk guhjy renatomilani
	RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (12 November 2008), 478. by James Hane, Richard Oliver posted to tool rip genome fungal_genomes alignment by nlapalu on 2009-10-30 17:07:17 as along with 2 people operon jamselem
	Genomic Resources of Magnaporthe oryzae (GROMO): A comprehensive and integrated database on rice blast fungus [My Copy] BMC Genomics, Vol. 10, No. 1. (2009), 316. by Shalabh Thakur, Sanjay Jha, Subhankar R. Barman, Bharat Chattoo posted to user_interface sequence blast annotation by nlapalu on 2009-10-30 17:04:39 as along with 1 person druvus
	The Gene Wiki: community intelligence applied to human gene annotation [My Copy] Nucl. Acids Res. (15 September 2009), gkp760. by Jon W. Huss, Pierre Lindenbaum, Michael Martone, et al.Donabel Roberts, Angel Pizarro, Faramarz Valafar, John B. Hogenesch, Andrew I. Su posted to wikipedia wiki online_encyclopedia human_genes genomes genome_sequences genome gene community_intelligence annotation by nlapalu on 2009-10-15 13:02:04 as along with 11 people and 2 groups operon fgibson daforerog jobadge jgill thomaskelder timhubbard VGreiff druvus ppgardne dullhunk eLearning in Leicester Journal picks
	The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_1. (1 January 2004), pp. D262-266. by Evelyn Camon, Michele Magrane, Daniel Barrell, et al.Vivian Lee, Emily Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, Rolf Apweiler posted to ontology goa genome gene by nlapalu on 2009-10-15 13:00:42 as along with 4 people miguel balajis sgoetz marck
	A fungal phylogeny based on 82 complete genomes using the composition vector method [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (10 August 2009), 195. by Hao Wang, Zhao Xu, Lei Gao, Bailin Hao posted to vector_method molecular_phylogenetics genomes genome fungi fungal_systematics fungal_genomes by nlapalu on 2009-10-14 15:25:23 as along with 4 people and 1 group tomt21 jamselem stajich druvus Mycology
	The fungus Ustilago maydis and humans share disease-related proteins that are not found in Saccharomyces cerevisiae [My Copy] BMC Genomics, Vol. 8, No. 1. (20 December 2007), 473. by Martin Munsterkotter, Gero Steinberg posted to ustilago proteome model_system maydis homology homologue comparative_analysis by nlapalu on 2009-10-14 15:16:38 as along with 3 people and 1 group stajich GustavoLacerda seitentaisei Mycology
	Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis [My Copy] PLoS ONE, Vol. 3, No. 6. (4 June 2008), e2300. by Darren M. Soanes, Intikhab Alam, Mike Cornell, et al.Han M. Wong, Cornelia Hedeler, Norman W. Paton, Magnus Rattray, Simon J. Hubbard, Stephen G. Oliver, Nicholas J. Talbot posted to protein_families pathogenic_fungi genome_sequences fungal_pathogenesis filamentous_fungi comparative_genome_analysis by nlapalu on 2009-10-14 15:15:06 as along with 3 people and 1 group bcondon stajich GustavoLacerda Mycology
	The secretome of the maize pathogen Ustilago maydis [My Copy] Fungal Genetics and Biology In Thematic Issue: Ustilago maydis, Vol. 45, No. Supplement 1. (August 2008), pp. S63-S70. by Olaf Mueller, Regine Kahmann, Guillermo Aguilar, Blanca Trejo-Aguilar, Andy Wu, Ronald P. de Vries posted to ustilago secreted proteins pathogen maydis maize genome by nlapalu on 2009-10-14 15:04:51 as
	Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 47. (20 November 2007), pp. 18730-18735. by Jun Xu, Charles W. Saunders, Ping Hu, et al.Raymond A. Grant, Teun Boekhout, Eiko E. Kuramae, James W. Kronstad, Yvonne M. DeAngelis, Nancy L. Reeder, Kevin R. Johnstone, Meredith Leland, Angela M. Fieno, William M. Begley, Yiping Sun, Martin P. Lacey, Tanuja Chaudhary, Thomas Keough, Lien Chu, Russell Sears, Bo Yuan, Thomas L. Dawson posted to protein genomes gene fungi by nlapalu on 2009-10-14 15:01:55 as along with 1 person stajich
	HMM-based databases in InterPro [My Copy] Brief Bioinform, Vol. 3, No. 3. (1 January 2002), pp. 236-245. by Alex Bateman, Daniel H. Haft posted to signature protein pattern motif interproscan hmm domain database databank bank annotation by nlapalu on 2009-10-09 16:46:40 as
	Applications of InterPro in protein annotation and genome analysis [My Copy] Brief Bioinform, Vol. 3, No. 3. (1 January 2002), pp. 285-295. by Margaret Biswas, John F. O'Rourke, Evelyn Camon, et al.Gill Fraser, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia Kriventseva, Virginie Mittard, Nicola Mulder, Isabelle Phan, Florence Servant, Rolf Apweiler posted to signature prosite prediction pattern motif interproscan functional domain database databank annotation by nlapalu on 2009-10-09 16:43:47 as
	ProRule: a new database containing functional and structural information on PROSITE profiles [My Copy] Bioinformatics, Vol. 21, No. 21. (1 November 2005), pp. 4060-4066. by Christian J. A. Sigrist, Edouard De Castro, Petra S. Langendijk-Genevaux, Virginie Le Saux, Amos Bairoch, Nicolas Hulo posted to signature protein prosite pattern motif functional domain database databank bank by nlapalu on 2009-10-09 16:41:31 as
	ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins [My Copy] Nucl. Acids Res., Vol. 34, No. suppl_2. (1 July 2006), pp. W362-365. by Edouard de Castro, Christian J. A. Sigrist, Alexandre Gattiker, et al.Virginie Bulliard, Petra S. Langendijk-Genevaux, Elisabeth Gasteiger, Amos Bairoch, Nicolas Hulo posted to signature protein prosite pattern motif functional database databank bank by nlapalu on 2009-10-09 16:39:14 as along with 3 people Copper_Calcio niallhaslam fbristow
	PROSITE: A documented database using patterns and profiles as motif descriptors [My Copy] Brief Bioinform, Vol. 3, No. 3. (1 January 2002), pp. 265-274. by Christian J. A. Sigrist, Lorenzo Cerutti, Nicolas Hulo, et al.Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher posted to protein prosite pattern motif functional domain database databank bank by nlapalu on 2009-10-09 16:37:11 as along with 4 people jwm siebertm shung jteyra
	PROSITE: a dictionary of sites and patterns in proteins [My Copy] Nucleic Acids Research, Vol. 19 (1991), pp. 2241-2245. by Amos Bairoch posted to signature prosite pattern motif domain database databank bank by nlapalu on 2009-10-07 17:51:27 as
	The 20 years of PROSITE [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_1. (11 January 2008), pp. D245-249. by Nicolas Hulo, Amos Bairoch, Virginie Bulliard, et al.Lorenzo Cerutti, Beatrice A. Cuche, Edouard de Castro, Corinne Lachaize, Petra S. Langendijk-Genevaux, Christian J. A. Sigrist posted to signature prosite motif domain database databank bank by nlapalu on 2009-10-07 17:47:20 as along with 8 people and 1 group gwallau Zoltan_Barczikay fbristow ojabado reyez dullhunk hplatero Evangelia LabDros
	Biological Profiling of Gene Groups utilizing Gene Ontology [My Copy] Japanese Society for Bioinformatics, Vol. 16, No. 1. by Nils Blüthgen[1], Karsten Brand[2], Branka Cajavec[1], Maciej Swat[1], Hanspeter Herzel[1], Dieter Beule[3] posted to statistics ontology by nlapalu on 2009-09-21 10:03:02 as
	A general method applicable to the search for similarities in the amino acid sequence of two proteins [My Copy] Journal of Molecular Biology, Vol. 48, No. 3. (28 March 1970), pp. 443-453. by Saul B. Needleman, Christian D. Wunsch posted to similarity sequence protein algorithm by nlapalu on 2009-09-01 10:30:37 as
	TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 18. (15 September 2009), pp. 2440-2441. by Lin Himmelmann, Dirk Metzler posted to tool phylogeny molecular_clock c by nlapalu on 2009-09-01 08:45:42 as along with 2 people and 1 group nuin djkt iSEEM
	PROTICdb: A web-based application to store, track, query, and compare plant proteome data [My Copy] PROTEOMICS, Vol. 5, No. 8. (2005), pp. 2069-2081. by Hélène Ferry-Dumazet, Gwenn Houel, Pierre Montalent, et al.Luc Moreau, Olivier Langella, Luc Negroni, Delphine Vincent, Céline Lalanne, Antoine de Daruvar, Christophe Plomion, Michel Zivy, Johann Joets posted to web protein plant fungi by nlapalu on 2009-08-27 10:04:47 as
	A CitationRank algorithm inheriting Google technology designed to highlight genes responsible for serious adverse drug reaction. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 17. (1 September 2009), pp. 2244-2250. by Lun Yang, Langlai Xu, Lin He posted to text gene algorithm by nlapalu on 2009-08-20 08:49:24 as along with 4 people ashishanand reyez ylem guhjy
	SOLpro: accurate sequence-based prediction of protein solubility [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2200-2207. by Christophe N. Magnan, Arlo Randall, Pierre Baldi posted to solubility protein prediction by nlapalu on 2009-08-20 08:45:25 as
	GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events [My Copy] Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2188-2193. by Te-Chin Chu, Tsunglin Liu, D. T. Lee, Greg C. Lee, Arthur C. Shih posted to genomes alignment algorithm by nlapalu on 2009-08-20 08:34:09 as along with 2 people torfinnnome jmeppley
	MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes [My Copy] Genome Research, Vol. 18, No. 1. (19 January 2008), pp. 188-196. by Brandi L. Cantarel, Ian Korf, Sofia M. C. Robb, et al.Genis Parra, Eric Ross, Barry Moore, Carson Holt, Alejandro Sánchez Alvarado, Mark Yandell posted to prediction maker genomes gene annotation by nlapalu on 2009-08-12 13:32:13 as along with 10 people thegoose2 natstreet Thaverkamp timflutre stajich GustavoLacerda urgi tharris jamselem orzenil
	The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions [My Copy] Nucl. Acids Res. (12 October 2007), gkm846. by Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, et al.Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides posted to annotation database functional by nlapalu on 2009-08-05 11:06:27 as along with 3 people azazello druvus tbudnik
	DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis. [My Copy] Genome research, Vol. 19, No. 7. (15 July 2009), pp. 1243-1253. by Yaniv Erlich, Kenneth Chang, Assaf Gordon, et al.Roy Ronen, Oron Navon, Michelle Rooks, Gregory J. Hannon posted to high-throughput sequencing by nlapalu on 2009-07-23 11:00:29 as along with 19 people and 1 group hzoltan orzenil heliopais qayub jandot pkonings jcbarret guhjy fenghezi dandaman xingxu djkt ppgardne daforerog n00c rpatward jbhiatt natstreet samgj Journal picks
	Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing [My Copy] Genome Research, Vol. 19, No. 7. (4 July 2009), pp. 1309-1315. by Wei Qu, Shin-ichi Hashimoto, Shinichi Morishita posted to sequencing short-read by nlapalu on 2009-07-23 10:58:00 as along with 8 people heliopais druvus n00c megraw dakelley djkt operon natstreet
	High-throughput functional annotation and data mining with the Blast2GO suite [My Copy] Nucl. Acids Res., Vol. 36, No. 10. (1 June 2008), pp. 3420-3435. by Stefan Gotz, Juan M. Garcia-Gomez, Javier Terol, et al.Tim D. Williams, Shivashankar H. Nagaraj, Maria J. Nueda, Montserrat Robles, Manuel Talon, Joaquin Dopazo, Ana Conesa posted to annotation blast2go functional by nlapalu on 2009-07-03 17:04:33 as along with 8 people seb1 margamvm kiekyon karinlag Keywan guhjy barriot sgoetz
	Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research [My Copy] Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3674-3676. by Ana Conesa, Stefan Gotz, Juan M. Garcia-Gomez, Javier Terol, Manuel Talon, Montserrat Robles posted to annotation blast2go functional genomes tool by nlapalu on 2009-07-03 17:00:00 as along with 10 people seb1 Thaverkamp karinlag bertelsen fbristow Garamonfok sgoetz talponer imelda aconesa
	Genome-scale approaches to resolving incongruence in molecular phylogenies [My Copy] Nature, Vol. 425, No. 6960. (23 October 2003), pp. 798-804. by Antonis Rokas, Barry L. Williams, Nicole King, Sean B. Carroll posted to evolution families fungi phylogeny tree by nlapalu on 2009-05-11 16:39:29 as along with 7 people and 1 group skembel biomcgary druvus knaseanka aprasad AaronDarling srfairclough iSEEM
	Estimating the tempo and mode of gene family evolution from comparative genomic data [My Copy] Genome Res., Vol. 15, No. 8. (1 August 2005), pp. 1153-1160. by Matthew W. Hahn, Tijl De Bie, Jason E. Stajich, Chi Nguyen, Nello Cristianini posted to algorithm cafe evolution genomes phylogenetic phylogeny by nlapalu on 2009-05-07 17:06:21 as along with 1 person Ema
	Accelerated Rate of Gene Gain and Loss in Primates [My Copy] Genetics, Vol. 177, No. 3. (1 November 2007), pp. 1941-1949. by Matthew W. Hahn, Jeffery P. Demuth, Sang-Gook Han posted to cafe phylogeny by nlapalu on 2009-05-07 17:00:35 as
	Identifying protein-coding genes in genomic sequences [My Copy] Genome Biology, Vol. 10, No. 1. (30 January 2009), 201. by Jennifer Harrow, Alinda Nagy, Alexandre Reymond, et al.Tyler Alioto, Laszlo Patthy, Stylianos Antonarakis, Roderic Guigo posted to annotation gene pipeline protein by nlapalu on 2009-04-30 09:26:39 as along with 14 people and 2 groups jfr antonkratz robfsouza renatomilani ArtemPankin hpaces guhjy michaelbarton idoerg jm12 pawelszczesny natstreet barriot druvus Bioinformatics Khavkin's lab
	Annotating genomes with massive-scale RNA sequencing. [My Copy] Genome biology, Vol. 9, No. 12. (2008), R175. by France Denoeud, Jean-Marc M. Aury, Corinne Da Silva, et al.Benjamin Noel, Odile Rogier, Massimo Delledonne, Michele Morgante, Giorgio Valle, Patrick Wincker, Claude Scarpelli, Olivier Jaillon, François Artiguenave posted to annotation genomes rna sequencing by nlapalu on 2009-04-30 09:13:46 as along with 20 people and 1 group hzoltan cthachuk GustavoLacerda jamselem n00c jonilaserson ghattem jmcq dandaman abizar dakelley inesdesantiago mhamada pengchy balicea fhalbrit GeeSharpMinor natstreet druvus neils SIMR bioinformatics
	Funybase: a Fungal phylogenomic database [My Copy] BMC Bioinformatics, Vol. 9 (27 October 2008), 456. by Sylvain Marthey, Gabriela Aguileta, Francois Rodolphe, et al.Annie Gendrault, Tatiana Giraud, Elisabeth Fournier, Manuela Lopez-Villavicencio, Angelique Gautier, Marc-Henri Lebrun, Helene Chiapello posted to database fungi funybase phylogeny by nlapalu on 2009-02-24 09:14:06 as along with 6 people and 1 group GustavoLacerda fungal ojabado druvus stajich nklee Mycology
	PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference. [My Copy] Nucleic acids research, Vol. 33, No. Web Server issue. (1 July 2005) by S. Guindon, F. Lethiec, P. Duroux, O. Gascuel posted to likelihood phylogeny phyml web by nlapalu on 2009-02-19 08:56:00 as along with 3 people chica treangen fhsantanna
	A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood [My Copy] Syst Biol, Vol. 52, No. 5. (1 October 2003), pp. 696-704. by Stephane Guindon, Olivier Gascuel posted to algorithm likelihood phylogeny by nlapalu on 2009-02-19 08:53:52 as along with 2 people timflutre urgi
	Phylogeny.fr: robust phylogenetic analysis for the non-specialist [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W465-469. by A. Dereeper, V. Guignon, G. Blanc, et al.S. Audic, S. Buffet, F. Chevenet, J. F. Dufayard, S. Guindon, V. Lefort, M. Lescot, J. M. Claverie, O. Gascuel posted to phylogeny by nlapalu on 2009-02-19 08:40:25 as along with 7 people biovils BioNica Eduvernois treangen operon druvus sanchezbuelna
	Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies [My Copy] Systematic Biology, Vol. 57, No. 4. (August 2008), pp. 613-627. by Aguileta, G., Marthey, et al. S., Chiapello, H., Lebrun, -H, Rodolphe, F., Fournier, E., Gendrault-Jacquemard, A., Giraud, T. posted to evolution gene phylogeny systematic by nlapalu on 2009-02-19 08:37:36 as along with 2 people and 1 group dbensasson stajich Mycology
	CAFE: a computational tool for the study of gene family evolution [My Copy] Bioinformatics, Vol. 22, No. 10. (15 May 2006), pp. 1269-1271. by Tijl De Bie, Nello Cristianini, Jeffery P. Demuth, Matthew W. Hahn posted to cafe evolution families multi-genic ortholog phylogenetic tree by nlapalu on 2009-02-18 15:26:19 as
	Evaluation of annotation strategies using an entire genome sequence [My Copy] Bioinformatics, Vol. 19, No. 6. (12 April 2003), pp. 717-726. by Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, et al.Anton J. Enright, Mark Carroll, Patrick Poullet, Vassilis Promponas, Theodore Liakopoulos, Giorgos Palaios, Claude Pasquier, Stavros Hamodrakas, Javier Tamames, Asutosh T. Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A. Ouzounis posted to annotation functional prediction protein by nlapalu on 2009-02-10 11:36:35 as along with 1 person stharward
	ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database [My Copy] Bioinformatics, Vol. 19, No. 5. (22 March 2003), pp. 675-676. by Andrew Kossenkov, Frank J. Manion, Eugene Korotkov, Thomas D. Moloshok, Michael F. Ochs posted to annotation pipeline by nlapalu on 2009-02-10 11:35:00 as

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