Fungal genomics : methods and protocols / edited by Jin-Rong Xu, Burton H. Bluhm.

Contributor(s): Xu, Jin-Rong | Bluhm, Burton H
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 722.Publisher: New York : Humana Press, ©2011Description: 1 online resource (xi, 285 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9781617790409; 1617790400; 1617790397; 9781617790393Subject(s): Fungi -- Genetics | Genomics | Eukaryota | Biology | Publication Formats | Genome | Biological Science Disciplines | Organisms | Genetic Structures | Publication Characteristics | Natural Science Disciplines | Genetic Phenomena | Disciplines and Occupations | Phenomena and Processes | Fungi | Genetics | Laboratory Manuals | Genome, Fungal | Fungi -- Genetics | Genomics | schimmels | fungi | genexpressie | gene expression | genexpressieanalyse | genomics | genetica | genetics | eiwitexpressieanalyse | proteomics | laboratoriummethoden | laboratory methods | protocollen | protocols | Fungi | Genome informatics | Biological Techniques | Schimmels | Genoominformatica | Biologische techniekenGenre/Form: Electronic books. Additional physical formats: Print version:: Fungal genomics.DDC classification: 579/.135 LOC classification: QK602 | .F86 2011Online resources: Click here to access online
Contents:
Genome sequencing and assembly / Manfred G. Grabherr, Evan Mauceli, and Li-Jun Ma -- Targeted cloning of fungal telomeres / Mark L. Farman -- Identification and annotation of repetitive sequences in fungal genomes / Braham Dhillon and Stephen B. Goodwin -- Next-generation sequencing and potential applications in fungal genomics / Phillip SanMiguel -- Getting the most out of your fungal microarray data : two cost- and time-effective methods / Sandra M. Mathioni [and others] -- Fusarium graminearum from expression analysis to functional assays / Heather E. Hallen-Adams, Brad L. Cavinder, and Frances Trail -- EST analysis pipeline : use of distributed computing resources / Francisco Javier Gonzalez and Juan Antonio Vizcaino -- Application of ChIP-chip analysis in the rice blast pathogen / Soonok Kim and Thomas K. Mitchell -- Proteome studies of filamentous fungi / Scott E. Baker and Ellen A. Panisko -- Bioinformatics pipeline for sequence-based analyses of fungal biodiversity / D. Lee Taylor and Shawn Houston -- Identifying protein complexes by affinity purification and mass spectrometry analysis in the rice blast fungus / Wende Liu [and others] -- Large scale identification of genes involved in plant-fungal interactions using Illumina's sequencing-by-synthesis technology / R.C. Venu [and others] -- High-throughput production of gene replacement mutants in Neurospora crassa / Gyungsoon Park [and others] -- Phenotypic analysis of Neurospora crassa gene deletion strains / Gloria E. Turner -- Efficient approaches for generating GFP fusion and epitope-tagging constructs in filamentous fungi / Xiaoying Zhou, Guotian Li, and Jin-Rong Xu -- Large-scale insertional mutagenesis in Magnaporthe oryzae by Agrobacterium tumefaciens-mediated transformation / Xiao-Lin Chen, Jun Yang, and You-Liang Peng -- Molecular methods for studying the Cryphonectria parasitica -- hypovirus experimental system / Angus L. Dawe [and others] -- Metabolic fingerprinting in Fusarium verticillioides to determine gene function / Jonathon E. Smith and Burton H. Bluhm -- Tapping genomics to unravel ectomycorrhizal symbiosis / Jonathan M. Plett [and others].
Summary: Having experienced unprecedented growth since the turn of the millennium, the dramatic expansion of resources and techniques in fungal genomics is poised to fundamentally redefine the study of fungal biology. In Fungal Genomics: Methods and Protocols, expert researchers explore the three most likely fronts upon which the field will advance: the sequencing of more and more fungal genomes, the mining of sequenced genomes for useful information, and most importantly, the use of genomics sequences to provide a foundation for powerful techniques to explain biological processes. Much of the book is dedicated to explaining established and emerging genomics-based technologies in filamentous fungi, including gene expression profiling techniques, techniques for fungal proteomics as well as various case studies that could be adapted to a wide range of fungi. Written in the highly successful Methods in Molecular Biology series format, protocol chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step laboratory protocols, and key unpublished tips, potential pitfalls, common mistakes, and special considerations based on the unique experiences of the contributors. Authoritative and cutting-edge, Fungal Genomics: Methods and Protocols provides fungal biologists at any stage of their careers a user-friendly resource for fungal genomics, especially as readers branch out into unfamiliar but exciting new areas of study.
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Includes bibliographical references and index.

Genome sequencing and assembly / Manfred G. Grabherr, Evan Mauceli, and Li-Jun Ma -- Targeted cloning of fungal telomeres / Mark L. Farman -- Identification and annotation of repetitive sequences in fungal genomes / Braham Dhillon and Stephen B. Goodwin -- Next-generation sequencing and potential applications in fungal genomics / Phillip SanMiguel -- Getting the most out of your fungal microarray data : two cost- and time-effective methods / Sandra M. Mathioni [and others] -- Fusarium graminearum from expression analysis to functional assays / Heather E. Hallen-Adams, Brad L. Cavinder, and Frances Trail -- EST analysis pipeline : use of distributed computing resources / Francisco Javier Gonzalez and Juan Antonio Vizcaino -- Application of ChIP-chip analysis in the rice blast pathogen / Soonok Kim and Thomas K. Mitchell -- Proteome studies of filamentous fungi / Scott E. Baker and Ellen A. Panisko -- Bioinformatics pipeline for sequence-based analyses of fungal biodiversity / D. Lee Taylor and Shawn Houston -- Identifying protein complexes by affinity purification and mass spectrometry analysis in the rice blast fungus / Wende Liu [and others] -- Large scale identification of genes involved in plant-fungal interactions using Illumina's sequencing-by-synthesis technology / R.C. Venu [and others] -- High-throughput production of gene replacement mutants in Neurospora crassa / Gyungsoon Park [and others] -- Phenotypic analysis of Neurospora crassa gene deletion strains / Gloria E. Turner -- Efficient approaches for generating GFP fusion and epitope-tagging constructs in filamentous fungi / Xiaoying Zhou, Guotian Li, and Jin-Rong Xu -- Large-scale insertional mutagenesis in Magnaporthe oryzae by Agrobacterium tumefaciens-mediated transformation / Xiao-Lin Chen, Jun Yang, and You-Liang Peng -- Molecular methods for studying the Cryphonectria parasitica -- hypovirus experimental system / Angus L. Dawe [and others] -- Metabolic fingerprinting in Fusarium verticillioides to determine gene function / Jonathon E. Smith and Burton H. Bluhm -- Tapping genomics to unravel ectomycorrhizal symbiosis / Jonathan M. Plett [and others].

Having experienced unprecedented growth since the turn of the millennium, the dramatic expansion of resources and techniques in fungal genomics is poised to fundamentally redefine the study of fungal biology. In Fungal Genomics: Methods and Protocols, expert researchers explore the three most likely fronts upon which the field will advance: the sequencing of more and more fungal genomes, the mining of sequenced genomes for useful information, and most importantly, the use of genomics sequences to provide a foundation for powerful techniques to explain biological processes. Much of the book is dedicated to explaining established and emerging genomics-based technologies in filamentous fungi, including gene expression profiling techniques, techniques for fungal proteomics as well as various case studies that could be adapted to a wide range of fungi. Written in the highly successful Methods in Molecular Biology series format, protocol chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step laboratory protocols, and key unpublished tips, potential pitfalls, common mistakes, and special considerations based on the unique experiences of the contributors. Authoritative and cutting-edge, Fungal Genomics: Methods and Protocols provides fungal biologists at any stage of their careers a user-friendly resource for fungal genomics, especially as readers branch out into unfamiliar but exciting new areas of study.

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