B2G in Papers

Citing Blast2GO

  • Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Tim D. Williams, María José Nueda, Montserrat Robles, Manuel Talón, Joaquín Dopazo and Ana Conesa
    High-throughput functional annotation and data mining with the Blast2GO suite.
    Nucleic Acids Res. 2008 June; 36(10): 3420–3435.
    Supplementary Material
  • Ana Conesa and Stefan Götz
    Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
    Int J Plant Genomics. 2008; 2008: 619832.
  • Ana Conesa, Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Manuel Talón and Montserrat Robles \\Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
    Bioinformatics 2005 21: 3674-3676 LINK

Blast2GO in Papers


donde nos cintan
issue):D223-6
2010

  1. Rattei T, Tischler P, Götz S, Jehl MA, Hoser J, Arnold R, Conesa A, Mewes HW
    SIMAP–a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D223-6

2009

  1. Hocher V, Auguy F, Bogusz D, et al.
    Actinorhizal nitrogen fixing symbiosis: An example of adaptation against soil abiotic stresses
    CAHIERS AGRICULTURES 2009,18 (6): 498-505
  2. GPaxton Payton et al.
    Gene expression profiling in peanut using high density oligonucleotide microarrays
    BMC Genomics 2009, 10:265
  3. Sapriel G, Quinet M, Heijde M, Jourdren L, Tanty V, et al.
    Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters
    PLoS ONE 4(10): e7458. doi:10.1371/journal.pone.0007458
  4. PW Laffy, K Benkendorff, CA Abbott
    Annotating a partial transcriptome of the marine snail Dicathais orbita’s hypobranchial gland using suppressive subtractive hybridization and BLAST2GO
  5. Bhatia VN, Perlman DH, Costello CE, et al.
    Software Tool for Researching Annotations of Proteins: Open-Source Protein
    ANALYTICAL CHEMISTRY 2009, 81(23): 9819-9823
  6. Bishwo N Adhikari et al. Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora\\BMC Genomics 2009, 10:609
  7. Fiorilli V, Catoni M, Miozzi L, et al \\Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus
    NEW PHYTOLOGIST 2009, 184(4): 975-987
  8. Catoni M, Miozzi L, Fiorilli V, et al.
    Comparative Analysis of Expression Profiles in Shoots and Roots of Tomato Systemically Infected by Tomato spotted wilt virus Reveals Organ-Specific Transcriptional Responses
    MOLECULAR PLANT-MICROBE INTERACTIONS 2009, 22(12): 1504-1513
  9. Karim N, Jones JT, Okada H, et al.
    Analysis of expressed sequence tags and identification of genes encoding cell-wall-degrading enzymes from the fungivorous nematode Aphelenchus avenae
    BMC GENOMICS 2009,10:525
  10. Barret M, Frey-Klett P, Guillerm-Erckelboudt AY, et al.
    Effect of Wheat Roots Infected with the Pathogenic Fungus Gaeumannomyces graminis var. tritici on Gene Expression of the Biocontrol Bacterium Pseudomonas fluorescens Pf29Arp
    MOLECULAR PLANT-MICROBE INTERACTIONS 2009, 22(12): 1611-1623
  11. Andreassen R, Lunner S, Hoyheim B
    Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)
    BMC GENOMICS 2009, 10:502
  12. Galla G, Barcaccia G, Ramina A, et al.
    Computational annotation of genes differentially expressed along olive fruit development
    BMC PLANT BIOLOGY 2009, 9: 128
  13. María José Nueda, Patricia Sebastián, Sonia Tarazona, Francisco García-García, Joaquín Dopazo, Alberto Ferrer and Ana Conesa
    Functional assessment of time course microarray data
    BMC Bioinformatics 2009, 10(Suppl 6):S9 doi:10.1186/1471-2105-10-S6-S9
  14. Ma L-J, Ibrahim AS, Skory C, Grabherr MG, Burger G, et al.
    Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication
    PLoS Genet 5(7):e1000549. doi:10.1371/journal.pgen.1000549
  15. Paul J. Seear, Stephen N. Carmichael, Richard Talbot, John B. Taggart, James E. Bron and Glen E. Sweeney
    Differential Gene Expression During Smoltification of Atlantic Salmon (Salmo salar L.): a First Large-Scale Microarray Study
    Marine Biotechnology 2009, doi:10.1007/s10126-009-9218-x
  16. Jong-Min Kim, Byung-Gee Kim and S. June Oh
    Evolutionary Signature of Information Transfer Complexity in Cellular Membrane Proteomes
    Genomics & Informatics 2009, 7(2) 111-121
  17. Dacheng Liang, Chui E. Wong, Mohan B. Singh, Christine A. Beveridge, Belinda Phipson, Gordon K. Smyth and Prem L. Bhalla
    Molecular dissection of the pea shoot apical meristem
    Journal of Experimental Botany 2009, doi:10.1093/jxb/erp254
  18. Kalaiselvi Senthil, Neha G. Wasnik, Yu-Jin Kim and Deok-Chun Yang
    Generation and analysis of expressed sequence tags from leaf and root of Withania somnifera (Ashwgandha)
    Molecular Biology Reports 2009, doi:10.1007/s11033-009-9696-y
  19. Christiane Tröße, Rune Waagbø, Olav Breck, Anne-Kristin Stavrum, Kjell Petersen and Pål A. Olsvik
    Genome-wide transcription analysis of histidine-related cataract in Atlantic salmon (Salmo salar L)
    Molecular Vision, 2009 15:1332–1350 PMCID:PMC2709424
  20. Nuno A. Fonseca, Vitor Santos Costa, Rui Camacho, Cristina Vieira and Jorge Vieira
    Partitional Clustering of Protein Sequences – An Inductive Logic Programming Approach
    Lecture Notes in Computer Science 2009, 5518 doi:10.1007/978-3-642-02481-8_152
  21. Liang D, Wong CE, Singh MB, et al. \\Molecular dissection of the pea shoot apical meristem
    JOURNAL OF EXPERIMENTAL BOTANY , 2009, 60 (14): 4201-4213
  22. Jones JT, Kumar A, Pylypenko LA, et al.
    Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida \\MOLECULAR PLANT PATHOLOGY 2009, 10(6):815-828
  23. Laura Pascual, Jose M Blanca, Joaquin Cañizares and Fernado Nuez
    Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set
    BMC Plant Biology 2009, 9:67 doi:10.1186/1471-2229-9-67
  24. D. Yang, Z. H. Tang, L. P. Zhang, C. P. Zhao and Y. L. Zheng
    Construction, Characterization, and Expressed Sequence Tag (EST) Analysis of Normalized cDNA Library of Thermo-Photoperiod-Sensitive Genic Male Sterile (TPGMS) Wheat from Spike Developmental Stages
    Plant Molecular Biology Reporter 2009, 27:2 doi:10.1007/s11105-008-0050-7
  25. Deepak P Patil, Santosh Atanur, Dhiraj P Dhotre, D Anantharam, Vineet S Mahajan, Sandeep A Walujkar, Rakesh K Chandode, Girish J Kulkarni, Pankaj S Ghate, Abhishek Srivastav, Kannayakanahalli M Dayananda, Neha Gupta, Bhakti Bhagwat, Rajendra R Joshi, Devendra T Mourya, Milind S Patole and Yogesh S Shouche
    Generation, annotation, and analysis of ESTs from midgut tissue of adult female Anopheles stephensi mosquitoes
    BMC Genomics 2009, 10:386 doi:10.1186/1471-2164-10-386
  26. Pål A Olsvik and Elisabeth Holen
    Characterization of an Atlantic cod (Gadus morhua) embryonic stem cell cDNA library
    BMC Research Notes 2009, 2:74 doi:10.1186/1756-0500-2-74
  27. Tangphatsornruang S, Somta P, Uthaipaisanwong P, et al.
    Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek)
    BMC PLANT BIOLOGY 2009, 9:137
  28. Vizoso P, Meisel LA, Tittarelli A, et al.
    Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality
    BMC GENOMICS 2009,10:423
  29. Paxton Payton et al.
    Gene expression profiling in peanut using high density oligonucleotide microarray
    BMC Genomics 2009, 10:265
  30. Chacko E, Ranganathan S
    Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases
    BMC GENOMICS 2009,10: S11,Suppl. 3
  31. Andres F, Galbraith DW, Talon M, et al.
    Analysis of PHOTOPERIOD SENSITIVITY5 Sheds Light on the Role of Phytochromes in Photoperiodic Flowering in Rice
    PLANT PHYSIOLOGY 2009, 151(2) 681-690
  32. Dapeng Zhang
    Defining Global Neuroendocrine Gene Expression Patterns Associated with Reproductive Seasonality in Fish
    PLoS ONE. 2009; 4(6): e5816.
  33. Szymon Kaczanowski et al.
    The High Throughput Sequence Annotation Service (HT-SAS) - the shortcut from sequence to true Medline words
    BMC Bioinformatics 2009, 10:148
  34. Pedro J. Alcolea et al.
    Genome-wide analysis reveals increased levels of transcripts related with infectivity in peanut lectin non-agglutinated promastigotes of Leishmania infantum
    Genomics, 2009 93(6) doi:10.1016/j.ygeno
  35. C. Cantacessi et al.
    Bioinformatic analysis of abundant, gender-enriched transcripts of adult Ascaris suum (Nematoda) using a semi-automated workflow platform
    Molecular and Cellular Probes 2009, doi:10.1016/j.mcp.2009.03.003
  36. Benjamin Nota et al.
    Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene
    BMC Genomics 2009, 10:236
  37. James W. Borrone
    An EST-SSR-based linkage map for Persea americana Mill. (avocado)
    Tree Genetics & Genomes, 2009 , 10.1007/s11295-009-0208-y
  38. Rajat Aggarwal et al.
    A BAC-based physical map of the Hessian fly genome anchored to polytene chromosomes
    BMC Genomics 2009, 10:293
  39. Yong Wang and Frederick C. C. Leung
    In Silico Prediction of Two Classes of Honeybee Genes with CpG Deficiency or CpG Enrichment and Sorting According to Gene Ontology Classes
    Journal of Molecular Evolution 2009 , 68:700:705
  40. Chitvan Khajuria et al.
    Expressed sequence tags from larval gut of the European corn borer (Ostrinia nubilalis): Exploring candidate genes potentially involved in Bacillus thuringiensis toxicity and resistance.
    BMC Genomics 2009, 10:286
  41. Stefano Capomaccio, Pierluigi Barone, Lara Reale, Fabio Veronesi and Daniele Rosellini
    Isolation of genes from female sterile flowers in Medicago sativa
    Sexual Plant Reproduction, 2009, Volume 22, Number 2, 97:107
  42. Gravato C, Guimarães L and Guilhermino L
    Effects of pollutants on estuarine and coastal animals: from genes to populations
    ICES CM 2007/I:18 2009
  43. Maria Domenica Moccia, Christine Oger-Desfeux, Gabriel AB Marais and Alex Widmer
    A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping
    BMC Genomics 2009, 10:243
  44. Kumar C.
    Bioinformatics analysis of mass spectrometry-based proteomics data sets
    FEBS Letters, Volume 583, Issue 11, Pages 1703-1712
  45. Zuojian Tang, Jeong-Hyeon Choi, Chris Hemmerich, Ankita Sarangi, John K. Colbourne and Qunfeng Don
    ESTPiper- a web-based analysis pipeline for expressed sequence tag
    BMC Genomics 2009, 10:174
  46. Elena Sarropoulou, Pilar Sepulcre, Laura Poisa-Beiro, Victoriano Mulero, José Meseguer, Antonio Figueras, Beatriz Novoa, Vasso Terzoglou, Richard Reinhardt, Antonios Magoulas and Georgios Kotoulas
    Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax
    BMC Genomics 2009, 10:157
  47. Ming-Kuem Lin, Young-Jin Lee, Tony J. Lough, Brett S. Phinney and William J. Lucas
    Analysis of the Pumpkin Phloem Proteome Provides Insights into Angiosperm Sieve Tube Function
    Molecular & Cellular Proteomics 8:343-356, 2009
  48. Joshua A. Udall
    The Gossypium Transcriptome
    IN: Genetics and Genomics of Cotton, 2009 pags 1-29, Springer New York
  49. Penny M. Hopkin
    Crustacean Ecdysteroids and Their Receptors
    IN: Ecdysone: Structures and Functions, 2009 pags 93-97, Springer Netherlands
  50. Christopher J. Martyniuk, Sophie Alvarez, Scott McClung, Daniel L. Villeneuve, Gerald T. Ankley and Nancy D. Denslow
    Quantitative proteomic profiles of androgen receptor signaling in the liver of fathead minnow
    J. Proteome Res., 2009, 8 (5), pp 2186–2200
  51. Liraz Levi, Irena Pekarski, Ellen Gutman, Paolo Fortina, Terry Hyslop, Jakob Biran, Berta Levavi-Sivan and Esther Lubzen
    Revealing genes associated with vitellogenesis in the liver of the zebrafish (Danio rerio) by transcriptome profiling
    BMC Genomics 2009, 10:141
  52. Shoba Ranganathan, Ranjeeta Menon and Robin B. Gasser
    Advanced in silico analysis of expressed sequence tag (EST) data for parasitic nematodes of major socio-economic importance — Fundamental insights toward biotechnological outcomes
    Biotechnology Advances,Volume 27, Issue 4, July-August 2009, Pages 439-448
  53. Ryan A Rapp, Joshua A Udal and Jonathan F Wendel
    Genomic expression dominance in allopolyploids
    BMC Biology 2009, 7:18
  54. Inmaculada Osuna-Jiménez, Timothy D. Williams, María-José Prieto-Álamo, Nieves Abril,J. Kevin Chipman and Carmen Pueyo
    Immune- and stress-related transcriptomic responses of Solea senegalensis stimulated with lipopolysaccharide and copper sulphate using heterologous cDNA microarrays
    Fish & Shellfish Immunology, Volume 26, Issue 5, May 2009, Pages 699-706
  55. B. Altincicek and A. Vilcinskas
    Septic injury-inducible genes in medicinal maggots of the green blow fly Lucilia sericata
    Insect Molecular Biology, Volume 18 Issue 1, Pages 119 - 125
  56. Won Kyong Cho, Xiong-Yan Chen, Nazim Mohamad Uddin, Yeonggil Rima, Juyeon Moon, Jin-Hee Jung, Chunlin Shi, Hyosub Chu, Suwha Kim, Seon-Won Kim, Zee-Yong Park and Jae-Yean Kim
    Comprehensive proteome analysis of lettuce latex using multidimensional protein-identification technology
    Phytochemistry, Volume 70, Issue 5, March 2009, Pages 570-578
  57. Sabine Specht and Achim Hoerauf
    Filarial parasites in the postgenomic era
    Expert Review of Anti-infective Therapy, March 2009, Vol. 7, No. 2, Pages 189-192 , DOI 10.1586/14787210.7.2.189
  58. Annelies Haegeman, Joachim Jacob, Bartel Vanholme, Tina Kyndt, Makedonka Mitreva and Godelieve Gheysen
    Expressed sequence tags of the peanut pod nematode Ditylenchus africanus: The first transcriptome analysis of an Anguinid nematode
    Molecular and Biochemical Parasitology, Article in Press.
  59. Daniel Martins-de-Souza, Wagner F. Gattaz, Andrea Schmitt, José C. Novello,Sérgio Marangoni, Christoph W. Turck and Emmanuel Dias-Neto
    Proteome analysis of schizophrenia patients Wernicke's area reveals an energy metabolism dysregulation
    BMC Psychiatry 2009, 9:17
  60. Tingaud-Sequeira A, Chauvigne F, Lozano J, et al.
    New insights into molecular pathways associated with flatfish ovarian development and atresia revealed by transcriptional analysis
    BMC GENOMICS 2009, 10:434
  61. Takahashi T, McDougall C, Troscianko J, et al.
    An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals
    BMC EVOLUTIONARY BIOLOGY 2009, 9: 240
  62. Nicolas Dauchot, Dominique Mingeot, Bénédicte Purnelle, Céline Muys, Bernard Watillon, Marc Boutry and Pierre Van Cutsem
    Construction of 12 EST libraries and characterization of a 12,226 EST dataset for chicory (Cichorium intybus) root, leaves and nodules in the context of carbohydrate metabolism investigation
    BMC Plant Biology 2009, 9:14
  63. Yannick Paucheta,Paul Wilkinsona, Manuella van Munsterb, Sylvie Augustinc, David Pauronb and Richard H. ffrench-Constanta.
    Pyrosequencing of the midgut transcriptome of the poplar leaf beetle Chrysomela tremulae reveals new gene families in Coleoptera
    Insect Biochemistry and Molecular Biology, Article in Press.
  64. ILI Qing, LI Lin, DAI JingRui, LI JianSheng and YAN JianBing.
    Identification and characterization of CACTA trans-posable elements capturing gene fragments in maize.
    Chinese Science Bulletin, February 2009, vol. 54, no. 4, 642-651
  65. Bishwo N Adhikari, Diana H Wall, Byron J Adams
    Desiccation survival in an Antarctic nematode: Molecular analysis using expressed sequenced tags.
    BMC Genomics 2009, 10:69
  66. Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA.
    Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre.
    Environmental Microbiology, doi: 10.1111/j.1462-2920.2008.01863.
  67. Sabine Specht and Achim Hoerauf
    Filarial parasites in the postgenomic era
    Expert Review of Anti-infective Therapy, March 2009, Vol. 7, No. 2, Pages 189-192 , DOI 10.1586/14787210.7.2.189
  68. Yong Wang and Frederick C. C. Leung
    A study on genomic distribution and sequence features of human long inverted repeats reveals species-specific intronic inverted repeats
    FEBS Journal, Volume 276 Issue 7, Pages 1986 - 1998
  69. A. S. TAFT, J. J. VERMEIRE, J. BERNIER, S. R. BIRKELAND, M. J. CIPRIANO, A. R. PAPA, A. G. McARTHUR and T. P. YOSHINO
    Transcriptome analysis of Schistosoma mansoni larval development using serial analysis of gene expression (SAGE)
    Parasitolog, doi:10.1017/S0031182009005733
  70. Dauchot N. et al.
    Construction of 12 EST libraries and characterization of a 12,226 EST dataset for chicory (Cichorium intybus) root, leaves and nodules in the context of carbohydrate metabolism investigation
    BMC Plant Biology 2009, 9:14
  71. Rabelo EM, Hall RS, Loukas A, et al.
    Improved insights into the transcriptomes of the human hookworm Necator americanus - Fundamental and biotechnological implications
    BIOTECHNOLOGY ADVANCES,27(2),122-132
  72. Aragon AD, Imani RA, Blackburn VR, et al.
    Towards an understanding of the mechanism of action of praziquantel
    MOLECULAR AND BIOCHEMICAL PARASITOLOGY Volume: 164 Issue: 1 Pages: 57-65
  73. Wen Juan Zhao, Hui Zhanga, Xinwen Bo, Yao Li and Xuping Fu
    Generation and analysis of expressed sequence tags from a cDNA library of Moniezia expansa.
    Molecular and Biochemical Parasitology , volume 164, Issue 1, March 2009, Pages 80-85
  74. Javier Brumos, Jose M. Colmenero-Flores, Ana Conesa, Pedro Izquierdo, Guadalupe Sanchez, Domingo Iglesias, Maria F. Lopez-Climent, Aurelio Sanchez-Cadenas and Manuel Talon.
    Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstock.
    Funct. Integr. Genomics. DOI 10.1007/s10142-008-0107-6
  75. FD Frentiu, M Adamski, E McGraw, MW Blows, SF and Chenoweth SF.
    An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies.
    BMC Genomics 2009, 10:40 , Doi:10.1186/1471-2164-10-40
  76. Bishwo N Adhikari, Diana H Wall AND Byron J Adams. Desiccation survival in an Antarctic nematode: Molecular analysis using expressed sequenced tags. BMC Genomics 2009, 10:69, doi:10.1186/1471-2164-10-69
  77. Paolo Fontana Alessandro Cestaro, Riccardo Velasco, Elide Formentin and Stefano Toppo
    Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology.
    PLoS ONE. 2009; 4(2): e4619.
  78. Rosanna Marino, Maharajah Ponnaiah, Pawel Krajewski, Carla Frova, Luca Gianfranceschi, M. Enrico Pè and Mirella Sari-Gorla
    Addressing drought tolerance in maize by transcriptional profiling and mapping
    Molecular Genetics and Genomics, DOI 10.1007/s00438-008-0401-y
  79. Qing Liu, Andan Zhu, Lijun Chai, Wenjing Zhou, Keqin Yu, Jian Ding, Juan Xu and Xiuxin Deng.
    Transcriptome analysis of a spontaneous mutant in sweet orange [Citrus sinensis (L.) Osbeck] during fruit development.
    Journal of Experimental Botany 2009 60(3):801-813; doi:10.1093/jxb/ern32
  80. Domingo C, Andres F, Tharreau D, et al.
    Constitutive Expression of OsGH3.1 Reduces Auxin Content and Enhances Defense Response and Resistance to a Fungal Pathogen in Rice
    MOLECULAR PLANT-MICROBE INTERACTIONS 22 (2):201-210
  81. Norelli JL, Farrell RE, Bassett CL, et al.
    Rapid transcriptional response of apple to fire blight disease revealed by cDNA suppression subtractive hybridization analysis.
    TREE GENETICS & GENOMES 5(1),27-40
  82. A.G. Gossner and J. Hopkins.
    Incremental generation of an EST set for the analysis of scrapie pathogenesis.
    Small Ruminant Research, Volume 81, Issue 1, January 2009, Pages 75-78

2008

  1. Krzysztof Pawlowski
    Uncharacterized/hypothetical proteins in biomedical ‘omics’ experiments: is novelty being swept under the carpet?
    Briefings in Functional Genomics and Proteomics 2008 7(4):283-290
  2. F. Falciani, A.M. Diab, V. Sabine, T.D. Williams, F. Ortega, S.G. Georg and J.K. Chipman
    Hepatic transcriptomic profiles of European flounder (Platichthys flesus) from field sites and computational approaches to predict site from stress gene responses following exposure to model toxicants
    Aquatic Toxicology, Volume 90, Issue 2, 11 November 2008, Pages 92-101
  3. Hyun Park, In-Young Ahn, Hakjun Kim, Jina Cheon and Meesun Kim
    Analysis of ESTs and expression of two peroxiredoxins in the thermally stressed Antarctic bivalve Laternula elliptica
    Fish & Shellfish Immunology,Volume 25, Issue 5, November 2008, Pages 550-559
  4. Xingfu Zha, Qingyou Xi,Jun Duan Chunyun Wang, Ningjia He and Zhonghuai Xiang
    Dosage analysis of Z chromosome genes using microarray in silkworm, Bombyx mori
    Insect Biochemistry and Molecular Biology, doi:10.1016/j.ibmb.2008.12.003
  5. C Nguyen, M Mannino, K Gardiner, KJ Cios
    ClusFCM: An algorithm for predicting protein functions using homologies and protein interactions
  6. Mbaye Tinea, Julien de Lorgerila, Hélèna D'Cotta, Elodie Pepey, François Bonhomme, Jean François Baroiller and Jean-Dominique Duranda
    Transcriptional responses of the black-chinned tilapia Sarotherodon melanotheron to salinity extremes
    Marine Genomics,Volume 1, Issue 2, June 2008, Pages 37-46
  7. Shamith A. Samarajiwa1, Sam Forster, Katie Auchettl and Paul J. Hertzog
    INTERFEROME: the database of interferon regulated gene
    Nucleic Acids Research, 2009, Vol. 37, Database issue D852-D857
  8. J.K. Chipman, T.D. William, T. Kitan, I. Katsiadaki, M.N. Sanders, J. Leadd, M. Baalousha and E. Cieslak
    Toxicogenomics as an “open” system to detect tissue-specific responses to toxicants: Nanoparticles as a proof of principle in fish
    Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology, Volume 151, Issue 1, Supplement 1, September 2008, Page S37
  9. Matan Oren,Marie-line Escande,Guy Paz, Zvi Fishelson and Baruch Rinkevich
    Urochordate Histoincompatible Interactions Activate Vertebrate-Like Coagulation System Components
    PLoS ONE. 20 08; 3(9): e3
  10. Marijke De Wit Dorien Keil, Noor Remmerie, Karlijn van der Ven, Evert-Jan van den Brandhof, Dries Knapen, Erwin Witters and Wim De Coen
    Molecular targets of TBBPA in zebrafish analysed through integration of genomic and proteomic approaches
    Chemosphere, Volume 74, Issue 1, December 2008, Pages 96-105.
  11. Cerda J, Mercade J, Lozano JJ, et al.
    Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform
    BMC GENOMICS 9 no. 508
  12. Gerald A. Tuskan
    Running head: F-box Genes in Arabidopsis, Oryza, Populus, Carica and Vitis
    Plant Physiology Preview. Published on September 5, 2008, as DOI:10.1104/pp.108.121921
  13. Lambert CM Ngoka
    Dramatic down-regulation of oxidoreductases in human hepatocellular carcinoma hepG2 cells: proteomics and gene ontology unveiling new frontiers in cancer enzymology\\Proteome Science 2008, 6:29.
  14. Liao Q, Shen C, Vouros P.
    GenoMass - a computer software for automated identification of oligonucleotide DNA adducts from LC-MS analysis of DNA digests.
    J Mass Spectrom. 2008 Dec 3.
  15. A Moustafa, CX Chan, M Danforth, D Zear, H Ahmed et al.
    A Phylogenomic Approach for Studying Plastid Endosymbiosis.
    Genome Informatics 21: 165-176 (2008)
  16. Lambert CM Ngoka
    Sample prep for proteomics of breast cancer: proteomics and gene ontology reveal dramatic differences in protein solubilization preferences of radioimmunoprecipitation assay and urea lysis buffers.
    Proteome Sci. 2008; 6: 30.
  17. Waisberg M, Lobo FP, Cerqueira GC, et al.
    Schistosoma mansoni: Microarray analysis of gene expression induced by host sex.
    EXPERIMENTAL PARASITOLOGY 120(4),357-363.
  18. Jury DR, Kaveti S, Duan ZH, et al.
    Effects of calorie restriction on the zebrafish liver proteome.
    COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 3 (4, 275-282
  19. BH Bluhm, B Dhillon, EA Lindquist, GHJ Kema, SB et al.
    Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative,infectious, and reproductive growth.
    BMC Genomics 2008, 9:523
  20. Coates BS, Sumerford DV, Hellmich RL, et al.
    Mining an Ostrinia nubilalis midgut expressed sequence tag (EST) library for candidate genes and single nucleotide polymorphisms (SNPs)
    INSECT MOLECULAR BIOLOGY 17(6): 607-620.
  21. Chan QWT, Foster LJ Changes in protein expression during honey bee larval development. GENOME BIOLOGY, 9(10): R156.
  22. Yovany Moreno and Timothy G. Geary
    Stage- and Gender-Specific Proteomic Analysis of Brugia malayi Excretory-Secretory Products
    PLoS Negl Trop Dis. 2008 October; 2(10): e326.
  23. Mehdi Pirooznia, Tanwir Habib, Edward J. Perkins and Youping Deng.
    GOfetcher: a database with complex searching facility for gene ontology.
    Bioinformatics 2008 24(21):2561-2563
  24. F. Geoghegan, I. Katsiadaki, T. D. Williams J. K. Chipman
    A cDNA microarray for the three-spined stickleback, Gasterosteus aculeatus L., and analysis of the interactive effects of oestradiol and dibenzanthracene exposures.
    Journal of Fish Biology, 2008, 72(9):2133 - 2153
  25. M. Auslander, Y. Yudkovski, V. Chalifa-Caspi, B. Herut1, R. Ophir, R. Reinhardt, P. M. Neumann and M. Tom.
    Pollution-Affected Fish Hepatic Transcriptome and Its Expression Patterns on Exposure to Cadmium.
    Marine Biotechnology, 2008, doi 10.1007/s10126-007-9060-y
  26. Jeroen Gillard, Valerie Devos, Marie J.J. Huysman, Lieven De Veylder, Sofie D'Hondt, Cindy Martens, Pieter Vanormelingen, Katrijn Vannerum, Koen Sabbe, Victor A. Chepurnov, Dirk Inzé, Marnik Vuylsteke, and Wim Vyverman.
    Physiological and Transcriptomic Evidence for a Close Coupling between Chloroplast Ontogeny and Cell Cycle Progression in the Pennate Diatom Seminavis robust.
    Plant Physiol. 2008 November; 148(3): 1394–1411.
  27. Xavier Argout et al.
    Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao generated from various tissues and under various conditions.
    BMC Genomics 2008, 9:512
  28. Hanelt B, Lun CM, Adema CM
    Comparative ORESTES-sampling of transcriptomes of immune-challenged Biomphalaria glabrata snails
    JOURNAL OF INVERTEBRATE PATHOLOGY, 2008, 99(2): 192-203
  29. Botton A, Ferrigo D, Scopel C, et al.
    A cDNA-AFLP approach to study ochratoxin A production in Aspergillus carbonarius.
    INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY, 2008, 127(12): 105-115
  30. Ma'ayan A.
    Network integration and graph analysis in mammalian molecular systems biology.
    IET SYSTEMS BIOLOGY, 2008, 2(5), 206-221
  31. Anthony D. Aragon, Reza A. Imani, Vint R. Blackburn and Charles Cunningham
    Microarray based analysis of temperature and oxidative stress induced messenger RNA in Schistosoma mansoni.
    doi:10.1016/j.molbiopara.2008.08.004
  32. Chaudhary B, Hovav R, Rapp R, et al.
    Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evolution and Development, vol. 10: 567-582 .
  33. NShivashankar H. Nagaraj, Robin B. Gasser, and Shoba Ranganathan.
    Needles in the EST Haystack: Large-Scale Identification and Analysis of Excretory-Secretory (ES) Proteins in Parasitic Nematodes Using Expressed Sequence Tags (ESTs).
    PLoS Negl Trop Dis. 2008 September; 2(9): e301.
  34. Javier Terol, Miguel A Naranjo, Patrick Ollitrault and Manuel Talon.
    Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences.
    BMC Genomics 2008, 9:423doi:10.1186/1471-2164-9-423
  35. Xiaohan Yang , Udaya C. Kalluri , Sara Jawdy , Lee E. Gunter , Tongming Yin , Timothy J. Tschaplinski , David J. Weston , Priya Ranjan , and Gerald A. Tuskan.
    F-box Gene Family is Expanded in Herbaceous Annual Plants Relative to Woody Perennial Plants.
    Plant Physiology, doi:10.1104/pp.108.121921, 2008
  36. Ana Conesa, Rasmus Bro, Francisco García-García, José Manuel Prats, Stefan Götz, Karin Kjeldahl, David Montaner and Joaquín Dopazo.
    Direct functional assessment of the composite phenotype through multivariate projection strategies.
    Genomics, doi:10.1016/j.ygeno.2008.05.015, 2008
  37. Tadeo FR, Cercos M, Colmenero-Flores JM, et al.
    Molecular physiology of development and quality of citrus.
    IN: BOTANICAL RESEARCH: INCORPORATING ADVANCES IN PLANT PATHOLOGY, VOL. 47, 147-223,2008.
  38. J Maxwell Silverman, Simon K Chan, Dale P Robinson, Dennis M Dwyer, Devki Nandan, Leonard J Foster and Neil E Reine.
    Proteomic analysis of the secretome of Leishmania donovani.
    Genome Biology 2008, 9:R35doi:10.1186/gb-2008-9-2-r35
  39. Botton A, Galla G, Conesa A, Bachem C, Ramina A, Barcaccia G.
    Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology.
    BMC Genomics. 2008 Jul 24;9:347.
  40. Ralf Schmid and Mark L Blaxter.
    annot8r: GO, EC and KEGG annotation of EST datasets.
    BMC Bioinformatics. 2008; 9: 180.
  41. Jan Alexander Mennigen, Christopher J Martyniuk, Kate Crump, Huiling Xiong, E Zhao, Jason Popesku, Hymie Anisman, Andrew R. Cossins, Xuhua Xia and Vance L Trudeau.
    The effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus)
    Physiol. Genomics (September 2, 2008). doi:10.1152/physiolgenomics.90263.2008.
  42. Nandan Deshpande, Marc R Wilkins, Nicolle Packer and Helena Nevalainen.
    Protein glycosylation pathways in filamentous fungi.
    Glycobiology 2008 18(8):626-637.
  43. James W. Wynne, Maree G. O’Sullivan, Glenn Stone, Mathew T. Cook, Barbara F. Nowak, David R. Lovell, Richard S. Taylor and Nicholas G. Elliott.
    Resistance to amoebic gill disease (AGD) is characterised by the transcriptional dysregulation of immune and cell cycle pathways.
    Developmental & Comparative Immunology, doi:10.1016/j.dci.2008.05.013.
  44. James W. Wynne, Maree G. O’Sullivan, Mathew T. Cook, Glenn Stone, Barbara F. Nowak, David R. Lovell and Nicholas G. Elliott.
    Transcriptome Analyses of Amoebic Gill Disease-affected Atlantic Salmon ( Salmo salar ) Tissues Reveal Localized Host Gene Suppression.
    Marine Biotechnology, doi:10.1007/s10126-007-9075-4.
  45. Hyoung-Joo Lee, Min-Seok Kwon, Eun-Young Lee, Sang Yun Cho, Young-Ki Paik.
    Establishment of a PF2D-MS/MS platform for rapid profiling and semiquantitative analysis of membrane protein biomarkers.
    Proteomics, 8: Issue 11, Pages 2168 - 217
  46. Klaus Kayser‌, Jürgen Görtler‌, Frederik Giesel‌ & Gian Kayser‌.
    How to implement grid technology in tissue-based diagnosis: diagnostic surgical pathology.
    Expert Opinion on Medical Diagnostics.
    March 2008, Vol. 2, No. 3, Pages 323-337.
  47. Joseph Morris, Eric Rouchka and David Schultz.
    Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags.
    MC Bioinformatics 2008, 9(Suppl 7):P25 doi:10.1186/1471-2105-9-S7-P25.
  48. CE Wong, PL Bhalla, H Ottenhof, M Singh.
    Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance.
    BMC Plant Biology 2008, 8:7.
  49. William Lanier,Ahmed Moustafa, Debashish Bhattacharya,and Josep M. Comeron.
    EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes.
    PLoS ONE. 2008; 3(5): e2171.
  50. A. Hagenaars,D. Knapen, I.J. Meyer, K. van der Ven, P. Hoff and W. De Coen.
    Toxicity evaluation of perfluorooctane sulfonate (PFOS) in the liver of common carp (Cyprinus carpio).
    Aquatic Toxicology, doi:10.1016/j.aquatox.2008.04.002.
  51. Nils Weinhold, Oliver Sander, Francisco S. Domingues, Thomas Lengauer, and Ingolf Sommer.
    Local Function Conservation in Sequence and Structure Space.
    PLoS Comput Biol. 2008 July; 4(7):doi: 10.1371/journal.pcbi.1000105.
  52. Wenchuan Leng, Tao Liu, Rui Li, Jian Yang, Candong Wei, Wenliang Zhang, and Qi Jin.
    Proteomic profile of dormant Trichophyton Rubrum conidia.
    BMC Genomics. 2008; 9: 303.doi: 10.1186/1471-2164-9-303.
  53. Eng-Ti L Low, Halimah Alias, Soo-Heong Boon, Elyana M Shariff,Chi-Yee A Tan, Leslie CL Ooi, Suan-Choo Cheah, Abdul-Rahim Raha, Kiew-Lian Wan and Rajinder Singh.
    Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: Identifying genes associated with callogenesis and embryogenesis.
    BMC Plant Biol. 2008; 8: 62 doi: 10.1186/1471-2229-8-62
  54. Jacob J, Mitreva M, Vanholme B, et al.
    Exploring the transcriptome of the burrowing nematode Radopholus similis.
    MOLECULAR GENETICS AND GENOMICS 280 (1): 1-17 JUL 2008.
  55. Kane; Sringer; Iannotti; Gough; Johns; Schlueter; Sepúlveda.
    Identification of development and tissue-specific gene expression in the fathead minnow Pimephales promelas, Rafinesque using computational and DNA microarray methods.
    Journal of Fish Biology, Volume 72, Number 9, June 2008 , pp. 2341-2353(13).
  56. Taggart; Bron; Martin; Seear; Høyheim; Talbot; Carmichael; Villeneuve; Sweeney; Houlihan; Secombes; Tocher; Teale .
    A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray.
    Journal of Fish Biology, Volume 72, Number 9, June 2008 , pp. 2071-2094(24).
  57. François L Luro, Gilles Costantino, Javier Terol, Xavier Argout, Thierry Allario, Patrick Wincker, Manuel Talon, Patrick Ollitrault and Raphael Morillon.
    Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping.
    BMC Genomics 2008, 9:287doi:10.1186/1471-2164-9-287
  58. Klaus Kayser‌, Jürgen Görtler‌, Frederik Giesel‌ & Gian Kayser.
    How to implement grid technology in tissue-based diagnosis: diagnostic surgical pathology.
    Expert Opinion on Medical Diagnostics, March 2008, Vol. 2, No. 3, Pages 323-337.
  59. Diab; Williams; Sabine; Chipman; George.
    The GENIPOL European flounder Platichthys flesus L. toxicogenomics microarray: application for investigation of the response to furunculosis vaccination.
    Journal of Fish Biology, Volume 72, Number 9, June 2008 , pp. 2154-2169(16).
  60. You-Jin Hao, Rafael Montiel, Gisela Nascimento, Duarte Toubarro1 and Nelson Simoes.
    Identification, characterization of functional candidate genes for host-parasite interactions in entomopathogenetic nematode Steinernema carpocapsae by suppressive subtractive hybridization.
    Parasitology Research, 10.1007/s00436-008-1030-4.
  61. Michael Wisniewski,Carole Bassett, John Norelli, Dumitru Macarisin, Timothy Artlip, Ksenija Gasic and Schuyler Korba.
    Expressed sequence tag analysis of the response of apple (Malus x domestica ‘Royal Gala’) to low temperature and water deficit.
    Physiologia Plantarum. Volume 133 Issue 2 Page 298-317, June 2008
  62. Pacharawongsakda, Eakasit; Yokwai, Sunai; Karoonuthaisiri, Nitsara; Wichadakul, Duangdao; Ingsriswang, Supawadee.
    ESTplus: An Integrative System for Comprehensive and Customized EST Analysis and Proteomic Data Matching.
    Bioinformatics and Biomedical Engineering, 2008. ICBBE 2008, Volume , Issue , 16-18 May 2008 Page(s):29 - 32
  63. Al-Shahrour F, Carbonell J, Minguez P, Goetz S, Conesa A, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J.
    Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
    Nucleic Acids Res. 2008 May 31.
  64. V.L. Marlatt C.J. Martyniuka, D. Zhanga, H. Xionga, J. Watta, X. Xiaa, T. Moona and V.L. Trudeau.
    Auto-regulation of estrogen receptor subtypes and gene expression profiling of 17β-estradiol action in the neuroendocrine axis of male goldfish.
    Molecular and Cellular Endocrinology, doi:10.1016/j.mce.2007.10.013.
  65. Ran Hovav, Joshua A. Udall, Bhupendra Chaudhary, Ryan Rapp, Lex Flagel, and Jonathan F. Wendel
    Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant
    PNAS, April 22, 2008, vol. 105, no. 16, 6191-6195
  66. L Flagel, JA Udall, D Nettleton, JF Wendel
    Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution
    BMC Biology, 2008; 6: 16
  67. Mathieu Fourment and Michael R Gillings
    A comparison of common programming languages used in bioinformatics
    BMC Bioinformatics. 2008; 9: 82
  68. Gerardo D. L. Cervigni, Norma Paniego et al.
    Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula
    Plant Molecular Biology, 2008, 10.1007/s11103-007-9282-4
  69. Hovav R, Udall JA, Chaudhary B, Hovav E, Flagel L, et al
    The Evolution of Spinnable Cotton Fiber Entailed Prolonged Development and a Novel Metabolism
    PLoS Genetics 4(2): e25 doi:10.1371/journal.pgen.0040025, 2008
  70. Cindy Martens, Klaas Vandepoele, and Yves Van de Peer
    Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species
    PNAS | March 4, 2008 | vol. 105 | no. 9 | 3427-3432
  71. Margaret M. Brown, Timothy D. Williams, J. Kevin Chipman, Ioanna Katsiadaki, Matthew Sanders and John A. Craft.
    Construction of subtracted EST and normalised cDNA libraries from liver of chemical-exposed three-spined stickleback (Gasterosteus aculeatus) containing pollutant-responsive genes as a resource for transcriptome analysis.
    Marine Environmental Research. doi:10.1016/j.marenvres.2008.02.043
  72. Yoonseong Parka, Jamie Aikinsa, L.J. Wang, Richard W. Beemanc, Brenda Oppertc, Jeffrey C. Lordc, Susan J. Brownb, Marcé D. Lorenzenc, Stephen Richardsd, George M. Weinstockd and Richard A. Gibbsd.
    Analysis of transcriptome data in the red flour beetle, Tribolium castaneum
    Insect Biochemistry and Molecular Biology. doi:10.1016/j.ibmb.2007.09.008
  73. Kei Nakayama Shin-Ichi Kitamura, Yasunori Murakam, Jun-Young Song, Sung-Ju Jung, Myung-Joo Oh, Hisato Iwata and Shinsuke Tanabe.
    Toxicogenomic analysis of immune system-related genes in Japanese flounder (Paralichthys olivaceus) exposed to heavy oil.
    Marine Pollution Bulletin. doi:10.1016/j.marpolbul.2008.02.021.
  74. Ran Hovav, Joshua A. Udall, Einat Hovav, Ryan Rapp, Lex Flagel and Jonathan F. Wendel
    A majority of cotton genes are expressed in single-celled fibe
    Planta Volume 227, Number 2 / January 2008, 319-329
  75. Bennett J. D. Datu,Robin B. Gasser, Shivashankar H. Nagaraj, Eng K. Ong, Peter O'Donoghue, Russell McInnes, Shoba Ranganathan and Alex Loukas
    Transcriptional Changes in the Hookworm, Ancylostoma caninum, during the Transition from a Free-Living to a Parasitic Larva
    PLoS Negl Trop Dis. 2008 January; 2(1): e130.
  76. Jessica A. Schlueter, Jose Luis Goicoechea, Kristi Collura, et al.
    BAC-end Sequence Analysis and a Draft Physical Map of the Common Bean ( Phaseolus vulgaris L.) Genome
    Tropical Plant Biology, 2008, 1935-9756 (Print) 1935-9764 (Online), Doi 10.1007/s12042-007-9003-9
  77. Shivashankar H Nagaraj, Robin B Gasser, Alasdair J Nisbet and Shoba Ranganathan
    In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches
    BMC Bioinformatics 2008, 9(Suppl 1):S10
  78. Peatman E, Terhune J, Baoprasertkul P, et al.
    Microarray analysis of gene expression in the blue catfish liver reveals early activation of the MHC class I pathway after infection with Edwardsiella ictaluri
    MOLECULAR IMMUNOLOGY 45 (2): 553-566 JAN 2008.

2007

  1. Nils Blüthgen, Szymon M. Kielbasa and Dieter Beule.
    Handling and Interpreting Gene Groups.
    Introduction to Systems Biology.
    Humana Press, ISBN: 978-1-58829-706-8 (Print) 978-1-59745-531-2 (Online). 2007.
  2. Emily Dimmer, Tanya Z. Berardini, Daniel Barrell, Evelyn Camon
    Methods for Gene Ontology Annotation
    Plant Bioinformatics: Methods and Protocols. Series: Methods in Molecular Biology | Volume: 406 | Pub. Date: Dec-01-2007 | Page Range: 495-520
  3. Stan Gaj, Arie van Erk Rachel, IM van Haaften and Chris TA Evelo
    Linking microarray reporters with protein functions
    BMC Bioinformatics. 2007; 8: 360
  4. Melody S Clark, Michael AS Thorne, Jelena Purac', Gordana Grubor-Lajšic', Michael Kube Richard Reinhardt and M Roger Worland
    Surviving extreme polar winters by desiccation: clues from Arctic springtail (Onychiurus arcticus) EST libraries
    BMC Genomics. 2007; 8: 475
  5. Peter van Baarlen1, H. Peter van Esse, Roland J. Siezen, and Bart P.H.J. Thomma.
    Challenges in plant cellular pathway reconstruction based on gene expression profiling.
    Trends in Plant Science, doi:10.1016/j.tplants.2007.11.003.
  6. Brian D Eads,John K Colbourne, Elizabeth Bohuski, and Justen Andrews
    Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex
    BMC Genomics. 2007; 8: 464.
  7. Melanie T. Cushion, A. George Smulian, Bradley E. Slaven, Tom Sesterhenn, Jonathan Arnold, Chuck Staben, Aleksey Porollo, Rafal Adamczak and Jarek Meller
    Transcriptome of Pneumocystis carinii during Fulminate Infection: Carbohydrate Metabolism and the Concept of a Compatible Parasite
    PLoS ONE. 2007; 2(5): e423
  8. Joseph R Shaw, John K Colbourne, Jennifer C Davey, Stephen P Glaholt, Thomas H Hampton, Celia Y Chen, Carol L Folt and Joshua W Hamilton
    Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins
    BMC Genomics. 2007; 8: 477
  9. Alberto Labarga, Franck Valentin, Mikael Anderson and Rodrigo Lopez
    Web Services at the European Bioinformatics Institute
    Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W6-W11
  10. James K. Hanea, Rohan G.T. Lowea, Peter S. Solomona, Kar-Chun Tana et al.
    Dothideomycete–Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum
    The Plant Cell 19:3347-3368 (2007)
  11. Larsen PF, Nielsen EE, Williams TD, et al.
    Adaptive differences in gene expression in European flounder (Platichthys flesus)
    MOLECULAR ECOLOGY 16 (22): 4674-4683 NOV 2007
  12. Stephan A. Osmani and Gustavo H. Goldman
    The Aspergilli: Genomics, Medical Aspects, Biotechnology, and Research Methods
    Taylor and Francis Group. 2007. ISBN-10: 084939080X
  13. S Ranganathan, SH Nagaraj, M Hu, C Strube, T et al.
    A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus
    BMC Genomics, 2007
  14. Yudkovski Y, Shechter A, Chalifa-Caspi V, Auslander M, Ophir R, Dauphin-Villemant C, Waterman M, Sagi A, Tom M.
    Hepatopancreatic multi-transcript expression patterns in the crayfish Cherax quadricarinatus during the moult cycle
    Insect Mol Biol. 2007 Oct 19 [Epub ahead of print]
  15. Gandia M, Conesa A, Ancillo G, Gadea J, Forment J, Pallas V, Flores R, Duran-Vila N, Moreno P, Guerri J.
    Transcriptional response of Citrus aurantifolia to infection by Citrus tristeza virus
    VIROLOGY 367 (2): 298-306 OCT 25 2007
  16. A Rokas, JE Galagan.
    Aspergillus nidulans Genome and a Comparative Analysis of Genome Evolution in Aspergillus.
    Genomics, Medical Applications, Biotechnology and Research, 2007.
  17. Quaggiotti S, Barcaccia G, Schiavon M, et al.
    Phytoremediation of chromium using Salix species: Cloning ESTs and candidate genes involved in the Cr response
    GENE 402 (1-2): 68-80 NOV 1 2007
  18. Yockteng R, Marthey S, Chiapello H, et al.
    Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes
    BMC GENOMICS 8: Art. No. 272 AUG 10 2007
  19. Tang ZL, Li Y, Wan P, et al.
    LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs
    GENOME BIOLOGY 8 (6): Art. No. R115 2007
  20. K. A. Duthie, L. C. Osborne, L. J. Foster, and N. Abraham
    Proteomics Analysis of Interleukin (IL)-7-induced Signaling Effectors Shows Selective Changes in IL-7R{alpha}449F Knock-in T Cell Progenitors
    Mol. Cell. Proteomics, October 1, 2007; 6(10): 1700 - 1710
  21. Chai-Ling Ho, Yen-Yen Kwan et al.
    Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.)
    BMC Genomics. 2007; 8: 381.
  22. G. Lopez, A. Valencia, and M. L. Tress
    Firestar–prediction of functionally important residues using structural templates and alignment reliability
    Nucleic Acids Res., July 13, 2007; 35(suppl_2): W573 - W577
  23. S. A. M. Martin1, J. B. Taggart2, P. Seear
    Interferon type I and type II responses in an Atlantic salmon (Salmo salar) SHK-1 cell line by the salmon TRAITS/SGP microarray
    Physiol. Genomics 32: 33-44, 2007
  24. D. Hackett, H. S. Yoon, S. Li, A. Reyes-Prieto, S. E. Rummele, and D. Bhattacharya
    Phylogenomic Analysis Supports the Monophyly of Cryptophytes and Haptophytes and the Association of Rhizaria with Chromalveolates
    Mol. Biol. Evol., August 1, 2007; 24(8): 1702 - 1713.
  25. S. H. Nagaraj, N. Deshpande, R. B. Gasser, and S. Ranganathan
    ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
    Nucleic Acids Res., July 13, 2007; 35(suppl_2): W143 - W147.
  26. V Sangar, DJ Blankenberg, N Altman, AM Les
    Quantitative sequence-function relationships in proteins based on gene ontology
    BMC BIOINFORMATICS 8: Art. No. 294 AUG 8 2007
  27. Nueda MJ, Conesa A, Westerhuis JA, et al.
    Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA
    BIOINFORMATICS 23 (14): 1792-1800 JUL 15 2007
  28. Vizcaino JA, Redondo J, Suarez MB, et al.
    Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol
    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 75 (4): 853-862 JUN 2007
  29. Dardick C
    Comparative expression profiling of Nicotiana benthamiana leaves systemically infected with three fruit tree viruses
    MOLECULAR PLANT-MICROBE INTERACTIONS 20 (8): 1004-1017 AUG 2007
  30. Waisberg M, Lobo FP, Cerqueira GC, et al.
    Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni
    BMC GENOMICS 8: Art. No. 81 JUN 20 2007
  31. Adachi J, Kumar C, Zhang YL, et al.
    In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics
    MOLECULAR & CELLULAR PROTEOMICS 6 (7): 1257-1273 JUL 2007
  32. Colbourne JK, Eads BD, Shaw J, et al.
    Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes
    BMC GENOMICS 8: Art. No. 217 JUL 6 2007
  33. Quilang J, Wang SL, Li P, et al.
    Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers
    BMC GENOMICS 8: Art. No. 157 JUN 8 2007
  34. Rensing SA, Ick J, Fawcett JA, et al.
    An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens
    BMC EVOLUTIONARY BIOLOGY 7: Art. No. 130 AUG 2 2007
  35. Brisson JA, Davis GK, Stern DL
    Common genome-wide patterns of transcript accumulation underlying the wing polyphenism and polymorphism in the pea aphid (Acyrthosiphon pisum)
    EVOLUTION & DEVELOPMENT 9 (4): 338-346 JUL-AUG 2007
  36. Abernathy JW, Xu P, Li P, et al.
    Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis
    BMC GENOMICS 8: Art. No. 176 JUN 18 2007
  37. Suarez MB, Vizcaino JA, Llobell A, et al.
    Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach
    CURRENT GENETICS 51 (5): 331-342 MAY 2007
  38. Guo W, Cai C, Wang C, Han Z, Song X, Wang K, Niu X, Wang C, Lu K, Shi B, Zhang T.
    A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium
    Genetics. 2007 May;176(1):527-41
  39. Conesa A, Forment J,Gadea J, van Dijk J
    Microarray Technology in Agricultural Research
    In: Microarray Technology Through Applications. Editor. F. Falciani, Taylor & Francis, ISBN 978-0-415-37853-6, MAY 2007
  40. Macek B, Mijakovic I, Olsen JV, et al.
    The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis
    MOLECULAR & CELLULAR PROTEOMICS 6 (4): 697-707 APR 2007
  41. Patrick Lambrix, He Tan, Vaida Jakoniene and Lena Strömbäck
    Semantic Web, Revolutionizing Knowledge Discovery in the Life Sciences
    Springer US, ISBN, 978-0-387-48436-5, APRIL 2007
  42. Valeria Siciliano, Andrea Genre, Raffaella Balestrini, Gilda Cappellazzo, Pierre J.G.M. deWit and Paola Bonfante
    Transcriptome Analysis of Arbuscular Mycorrhizal Roots during Development of the Prepenetration Apparatu
    Plant Physiology 144:1455-1466 (2007)
  43. Terol J, Conesa A, Colmenero JM, et al.
    Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance
    BMC GENOMICS 8: Art. No. 31 JAN 25 2007
  44. Williams TD, Diab AM, George SG, et al.
    Gene expression responses of European flounder (Platichthys flesus) to 17-beta estradiol
    TOXICOLOGY LETTERS 168 (3): 236-248 FEB 5 2007
  45. Nagaraj SH, Gasser RB, Ranganathan S
    A hitchhiker's guide to expressed sequence tag (EST) analysis
    BRIEFINGS IN BIOINFORMATICS 8 (1): 6-21 JAN 2007

2006

  1. Chan QWT, Howes CG, Foster LJ
    Quantitative comparison of caste differences in honeybee hemolymph
    MOLECULAR & CELLULAR PROTEOMICS 5 (12): 2252-2262 DEC 2006
  2. Reyes-Prieto A, Hackett JD, Soares MB, et al.
    Cyanobacterial contribution to algal nuclear genomes a primarily limited to plastid functions
    CURRENT BIOLOGY 16 (23): 2320-2325 DEC 5 2006
  3. Durica DS, Kupfer D, Najar F, et al.
    EST library sequencing of genes expressed during early limb regeneration in the fiddler crab and transcriptional responses to ecdysteroid exposure in limb bud explants
    INTEGRATIVE AND COMPARATIVE BIOLOGY 46 (6): 948-964 DEC 2006
  4. Faria-Campos AC, Moratelli FS, Mendes IK, et al.
    Production of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from Schistosoma mansoni
    MEMORIAS DO INSTITUTO OSWALDO CRUZ 101: 161-165 Suppl. 1 2006
  5. SLAVEN, BRADLEY E.; POROLLO, ALEKSEY; SESTERHENN, THOMAS; SMULIAN, A. GEORGE; CUSHION, MELANIE T.; MELLER, JAROSLAW
    Large-Scale Characterization of Introns in the Pneumocystis carinii Genome
    Journal of Eukaryotic Microbiology, Volume 53, Supplement 1, November 2006 , pp. S151-S153(1)
  6. Williams TD, Diab AM, George SG, et al.
    Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose.
    ENVIRONMENTAL SCIENCE & TECHNOLOGY 40 (20): 6479-6488 OCT 15 2006
  7. Cai ZT, Mao XZ, Li SG, et al.
    Genome comparison using Gene Ontology (GO) with statistical testing
    BMC BIOINFORMATICS 7: Art. No. 374 AUG 11 2006
  8. Nelson RT, Shoemaker R
    Identification and analysis of gene families from the duplicated genome of soybean using EST sequences
    BMC GENOMICS 7: Art. No. 204 AUG 9 2006
  9. Razib M. Othman, Safaai Deris, and Rosli M. Illias
    Computational Method for Annotation of Protein Sequence According to Gene Ontology Terms
    NTERNATIONAL JOURNAL OF BIOMEDICAL SCIENCES VOLUME 1 NUMBER 1 2006 ISSN 1306-1216
  10. Vizcaino JA, Gonzalez FJ, Suarez MB, et al.
    Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413
    BMC GENOMICS 7: Art. No. 193 JUL 27 2006
  11. Bonnet A, O Frappart P, Dehais P, et al.
    Identification of differential gene expression in in vitro FSH treated pig granulosa cells using suppression subtractive hybridization
    REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY 4: Art. No. 35 JUL 7 2006
  12. Wei W, Ding GH, Wang XJ, et al.
    Comparative analysis of whole-genome sequences of Streptococcus suis
    CHINESE SCIENCE BULLETIN 51 (10): 1199-1209 MAY 2006
  13. Aparicio G, Götz S, Conesa A, et al.
    Blast2GO goes Grid: Developing a-Enabled Prototype for Functional Genomics Analysis
    IOS-Press, Studies in Health Technology and Informatics Vol. 120, May 2006
  14. Ma J, Morrow DJ, Fernandes J, et al.
    Comparative profiling of the sense and antisense transcriptome of maize lines
    GENOME BIOLOGY 7 (3): Art. No. R22 2006

2005

  1. ME Aranguren
    Ontology design patterns for the formalisation of biological ontologies
    University of Manchester, Faculty of Engineering and Physical Sciences, 2005
b2g_in_papers.txt · Last modified: 2010/02/14 20:41 by sgoetz
Bioinformatics and Genomics Department
Centro de Investigación Príncipe Felipe
Valencia, SPAIN
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