Foundations of Comparative Genomics. by Mushegian, Arcady R.

Table of Contents: “…Cover -- Foundations of Comparative Genomics -- Copyright Page -- Contents -- Dedication Page -- Preface -- Chapter 1: The Beginning of Computational Genomics -- Chapter 2: Finding Sequence Similarities -- Chapter 3: Homology: Can We Get It Right? …”
Full text (MCPHS users only)

Comparative genomics [electronic resource] /

Full text (Open Access)

Comparative genomics and proteomics in drug discovery /

Table of Contents: “…Comparative genomics and drug discovery in trypanosomatids -- The practical implications of comparative kinetoplastid genomics -- The relevance of host genes in malaria -- Nicotinic acetylcholine receptors as drug/chemical targets, contributions from comparative genomics, forward and reverse genetics -- Discovery of novel sodium channel inhibitors : a gene family-based approach -- 'Omics' in translational medicine : are they lost in translation? …”
Table of contents only

Malaria parasites : comparative genomics, evolution and molecular biology /

Subjects: Full text (MCPHS users only)

Sequence - evolution - function computational approaches in comparative genomics / by Koonin, Eugene V.

“…Computational approaches in comparative genomics…”
Full text

The evolution of the genome

Table of Contents: Full text (MCPHS users only)

Chimpanzees in biomedical and behavioral research : assessing the necessity

Table of Contents: Full text (MCPHS users only)

Principles of Genome Analysis and Genomics. by Primrose, Sandy B.

Table of Contents: “…Detecting open-reading frames Software programs for finding genes; Using homology to find genes; Analysis of non-coding RNA and extragenic DNA; Identifying the function of a new gene; Secondary databases of functional domains; Gene ontology; Analyses not based on homology; Genome annotation; Molecular phylogenetics; Suggested reading; Useful websites; CHAPTER 7 Comparative genomics; Introduction; Orthologues,paralogues and gene displacement; Protein evolution by exon shuffing; Comparative genomics of prokaryotes; Comparative genomics of organelles; Comparative genomics of eukaryotes…”
Full text (MCPHS users only)

Aspergillus and penicillium in the post-genomic era

Table of Contents: “…Approaches for Comparative Genomics in Aspergillus and Penicillium -- Introduction -- Current status of genomics -- Available genome databases with comparative genomics capabilities -- General methods for comparative genomics -- Primary metabolism -- Secondary metabolism -- Secretome analysis and plant polysaccharide degradation -- Other comparative 'omics' -- Future perspectives -- what can we learn from bacteria? …”
Full text (MCPHS users only)

Burkholderia : from genomes to function

Table of Contents: “…1: Genomic Taxonomy and Biodiversity of the Burkholderia cepacia Complex -- 2: Comparative Genomics in the Genus Burkholderia -- 3: Molecular epidemiology and population structure of clinically relevant Burkholderia species -- 4: Comparative transcriptomics in Burkholderia -- 5: Burkholderia Proteomics: methodologies, challenges and applications -- 6: Molecular Mechanisms of Virulence in Burkholderia pseudomallei and Burkholderia mallei -- 7: Molecular Mechanisms of Burkholderia cepacia complex intracellular survival in phagocytic cells -- 8: The phytopathogenic Burkholderia -- 9: Molecular Basis for Antibiotic Resistance in the Genus Burkholderia -- 10: Cell-to-cell Communication and Biofilm Formation of Members of the Genus Burkholderia -- 11: Genomics of Burkholderia phages.…”
Full text (MCPHS users only)

Bioinformatics and data analysis in microbiology

Table of Contents: “…IntroductionGenome annotation; Automated annotation pipelines; Future trends; Conclusions; 5: Comparative Analysis of Microbial Pathogen Genomes to Study Unique Gene Families; Introduction; In silico comparative genomics applications in microbiology; Applications of comparative genomics to the study of Mycobacterium tuberculosis; Conclusions; Future trends; 6: Microbial Community Profiling: Current Approaches and Future Trends; Introduction; Genetic fingerprinting techniques; Data analysis; Unresolved questions and future trends; 7: Metagenomics and Microbiomes; Introduction…”
Full text (MCPHS users only)

Advanced Vaccine Research : Methods for the Decade of Vaccines.

Table of Contents: “…Epigenomics: understanding of inheritable chemical changesMetagenomics: finding new pathogens and strains; Bioinformatics challenges; 3: Comparative Genomics Approaches for Tracking the Emergence and Spread of Disease-associated Bacteria; Background; Comparative genomics of disease-associated bacteria; Assays for identification of disease-associated bacteria based on insights from comparative genomics; Conclusions; 4: Quantitative Proteomics in Vaccine Research; Introduction; Quantitative proteomics based on gel electrophoresis; Quantitative proteomics based on differential mass tag.…”
Full text (MCPHS users only)

Genomics and evolution of microbial eukaryotes

Table of Contents: “…Simpson, David J. Patterson -- Comparative genomics of Plasmodium species / Jane M. Carlton -- The genomes of dinoflagellates / Jermiah D. …”
Full text (MCPHS users only)

Atlas of mammalian chromosomes

Full text (MCPHS users only)

Investigations in yeast functional genomics and molecular biology

Table of Contents: “…Chapter 9: A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many EnzymesChapter 10: Genetic Landscape of Open Chromatin in Yeast; Part IV: Comparative Genomics; Chapter 11: High Quality de novo Sequencing and Assembly of the Saccharomyces Arboricolus Genome; Chapter 12: Comparative Gene Expression between Two Yeast Species; Chapter 13: Whole-Genome Comparison Reveals Novel Genetic Elements that Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae; Author Notes.…”
Full text (MCPHS users only)

Advanced techniques in diagnostic cellular pathology

Table of Contents: “…Virtual microscopy / Jim Diamond and David McCleary -- Cytopathology / Mary Hannon-Fletcher -- Flow cytometry / Ian Dimmick -- Immunocytochemistry / Perry Maxwell and Merdol Ibrahim -- Microarray-based comparative genomic hybridization / David S.P. Tan, Rachael Natrajan and Jorge S. …”
Full text (MCPHS users only)

Forest genetics by White, Timothy L., 1951-

Table of Contents: Full text (MCPHS users only)

Omics in Plant Breeding. by Borém, Aluízio

Table of Contents: “…Cover; Title Page; Copyright; Contents; List of Contributors; Foreword; Chapter 1 Omics: Opening up the ""Black Box"" of the Phenotype; The Post-Genomics Era; The Omics in Plant Breeding; Genomics, Precision Genomics, and RNA Interference; Transcriptomics and Proteomics; Metabolomics and Physiognomics; Phenomics; Bioinformatics; Prospects; References; Chapter 2 Genomics; The Rise of Genomics; DNA Sequencing; Development of Sequence-based Markers; Genetic Mapping; Association Mapping; Genome Wide Selection (GWS); Comparative Genomics; Structural and Comparative Genomics.…”
Full text (MCPHS users only)

Regulatory genomics : proceedings of the 3rd annual RECOMB workshop : National University of Singapore, Singapore 17-18 July 2006

Full text (MCPHS users only)

Reconstructing evolution : new mathematical and computational advances

Full text (MCPHS users only)

Evolution after Gene Duplication. by Dittmar, Katharina

Full text (MCPHS users only)

Bovine genomics

Table of Contents: “…Womack -- Linkage mapping / Stephanie McKay and Robert Schnabel -- The bovine X and Y chromosomes / Abel Ponce DeLeon and Wansheng Liu -- Comparative genomics and evolution / Denis Larkin -- Sequencing the bovine genome / Kim Worley, Richard Gibbs -- Bovine genome architecture / Dave Adelson -- Bovine epigenetics and epigenomics / Xiuchun Tian -- Mapping quantitative trait loci / Joel Weller -- Genome wide association studies and linkage disequilibrium in cattle / M.E. …”
Full text (MCPHS users only)

Statistics and informatics in molecular cancer research

Table of Contents: “…Stephens -- Two methods for comparing genomic data across independent studies in cancer research: Meta-analysis and oncomine concepts map / Wendy Lockwood Banka, Matthew J. …”

Genetics, genomics and breeding of peanuts

Full text (MCPHS users only)

Lactic acid bacteria : biodiversity and taxonomy

Table of Contents: “…Introduction: The Lactic Acid Bacteria in present day context -- Introduction to the LAB -- Physiology of the LAB -- Phylogenetics and Systematics -- Overview on the ecology and biodiversity of the lactic acid bacteria -- Comparative genomics of Lactobacillus and other lactic acid bacteria -- Section II. …”
Full text (MCPHS users only)

Bacterial gene regulation and transcriptional networks

Table of Contents: “…Ch 10: Bacillus subtilis Transcriptional NetworkCh 11: Helicobacter pylori Transcriptional Network; Ch 12: The Transcriptional Regulatory Network of Mycobacteriumtuberculosis; Ch 13: Transcriptional Regulatory Network in Pseudomonas aeruginosa; Ch 14: Transcriptional Regulation Network in Cyanobacteria: a Comparative Genomic View; Appendix; Table A.1 Family-wise list of transcription factors found in P. aeruginosa PAO1; Table A.2 Transcription factor interacting partners; Index…”
Full text (MCPHS users only)

Translational medicine : global concepts, tools and technology

Table of Contents: “…Modeling in Target Identification and ValidationModeling in Lead Identification and Optimization; Modeling in ADME; Use of Modeling and Simulation in Phase 1; Modeling and Simulation in Phases 2, 3, and 4; Impact of Modeling and Simulation on Drug Approvals; Oncology, a Special Case; NEXT LEVEL OF CONTRIBUTION FROM MODELING AND SIMULATION; References; 4 -- Advancements in Omics Sciences; OUTLINE OF THE CHAPTER; INTRODUCTION; GENOMICS; Genomic Technologies; Microarrays; Quantitative PCR; Next-Generation Sequencing; Array-Based Comparative Genome Hybridization; Genome-Wide Association Studies…”
Full text (MCPHS users only)

Parasitic helminths : targets, screens, drugs, and vaccines

Table of Contents: “…; Introduction; Comparative Genome Analysis for the Phylum Nematoda; Functional Characterization of Parasite Genes by Heterologous Expression in C. elegans; Comparative Pharmacology of C. elegans and Parasitic Nematode Neurotransmitter Receptors; C. elegans as a Tool to Understand the Mode of Action of Novel Anthelmintics; C. elegans as a Platform for Target Discovery; Conclusions; References; 3 Integrating and Mining Helminth Genomes to Discover and Prioritize Novel Therapeutic Targets.…”
Full text (MCPHS users only)

Biotechnology of Lactic Acid Bacteria : Novel Applications by Mozzi, Fernanda

Table of Contents: “…LAB Metabolism in Light of Genomics, Comparative Genomics, and Metagenomics; 1.5. Novel Aspects of Metabolism Regulation in the Post-genomic Age; 1.6. …”
Full text (MCPHS users only)

Fish cytogenetic techniques : ray-fin fishes and chondrichthyans

Full text (MCPHS users only)

Computational Systems Bioinformatics - Proceedings Of The Conference Csb 2006. by Xu, Ying

Table of Contents: “…Cover -- Contents -- Committees -- Referees -- Preface -- Keynote Addresses -- Exploring the Ocean's Microbes: Sequencing the Seven Seas -- Don't Know Much About Philosophy: The Confusion Over Bio-Ontologies -- Invited Talks -- Biomedical Informatics Research Network (BIRN): Building a National Collaboratory for BioMedical and Brain Research -- Protein Network Comparative Genomics -- Systems Biology in Two Dimensions: Understanding and Engineering Membranes as Dynamical Systems -- Bioinformatics at Microsoft Research -- Movie Crunching in Biological Dynamic Imaging -- Engineering Nucleic Acid-Based Molecular Sensors for Probing and Programming Cellular Systems -- Reactome: A Knowledgebase of Biological Pathways -- Structural Bioinformatics -- Effective Optimization Algorithms for Fragment-Assembly based Protein Structure Prediction -- Transmembrane Helix and Topology Prediction Using Hierarchical SVM Classifiers and an Alternating Geometric Scoring Function -- Protein Fold Recognition Using the Gradient Boost Algorithm -- A Graph-Based Automated NMR Backbone Resonance Sequential Assignment -- A Data-Driven Systematic Search Algorithm for Structure Determination of Denatured or Disordered Proteins -- Multiple Structure Alignment by Optimal RMSD Implies that the Average Structure is a Consensus -- Identification of a-Helices from Low Resolution Protein Density Maps -- Efficient Annotation of Non-Coding RNA Structures Including Pseudoknots via Automated Filters -- Thermodynamic Matchers: Strengthening the Significance of RNA Folding Energies -- Microarray Data Analysis and Applications -- PEM: A General Statistical Approach for Identifying Differentially Expressed Genes in Time-Course CDNA Microarray Experiment without Replicate -- Efficient Generalized Matrix Approximations for Biomarker Discovery and Visualization in Gene Expression Data -- Computational Genomics and Genetics -- Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes) -- Sorting Genomes by Translocations and Deletions -- Turning Repeats to Advantage: Scaffolding Genomic Contigs Using LTR Retrotransposons -- Whole Genome Composition Distance for HIV-1 Genotyping -- Efficient Recursive Linking Algorithm for Computing the Likelihood of an Order of a Large Number of Genetic Markers -- Optimal Imperfect Phylogeny Reconstruction and Haplotyping (IPPH) -- Toward an Algebraic Understanding of Haplotype Inference by Pure Parsimony -- Global Correlation Analysis Between Redundant Probe Sets Using a Large Collection of Arabidopsis ATH1 Expression Profiling Data -- Motif Sequence identification.…”
Full text (MCPHS users only)

Genetics, genomics and breeding of maize

Table of Contents: “…Prasanna, Raman Babu, Sudha Nair, Kassa Semagn, Vijay Chaikam, Jill Cairns, Xuecai Zhang, Yunbi Xu and Michael Olsen -- 6. Comparative genomics / Ramakrishna Wusirika and Rafi Shaik -- 7. …”
Full text (MCPHS users only)

Evolution of Virulence in Eukaryotic Microbes. by Sibley, L. David

Table of Contents: “…CHAPTER 27: GENETIC, GENOMIC, AND MOLECULAR APPROACHES TO DEFINE VIRULENCE OF ASPERGILLUS FUMIGATUSCHAPTER 28: CRYPTOSPORIDIUM: COMPARATIVE GENOMICS AND PATHOGENESIS; INDEX.…”
Full text (MCPHS users only)

Bioinformatics : a Swiss perspective

Table of Contents: “…Methods for Discovery and Characterization of DNA Sequence Motifs / Philipp Bucher -- Comparative Genome Analysis / Robert M. Waterhouse [and others] -- From Modules to Models: Advanced Analysis Methods for Large-Scale Data / Sven Bergmann -- Integrated Analysis of Gene Expression Profiling Studies: Examples in Breast Cancer / Pratyaksha Wirapati [and others] -- Computational Biology of Small Regulatory RNAs / Mihaela Zavolan and Lukasz Jaskiewicz -- UniProtKB/Swiss-Prot Manual and Automated Annotation of Complete Proteomes: The Dictyostelium discoideum Case Study / Amos Bairoch and Lydie Lane -- Analytical Bioinformatics for Proteomics / Patricia M. …”
Full text (MCPHS users only)

Molecular and Cellular Biology of Pathogenic Trypanosomatids

Table of Contents: “….; The Life Cycle of Trypanosoma cruzi ; The Life Cycle of Trypanosoma brucei ; TAXONOMY OF THE TRITRYPS; GENOME ORGANIZATION; Trypanosomatid Comparative Genomics; Leishmania Genomic Features.…”
Full text (MCPHS users only)

The NCBI handbook

Table of Contents: “…Databases -- GenBank: The Nucleotide Sequence Database -- PubMed: The Bibliographic Database -- Macromolecular Structure Databases -- Taxonomy Project -- Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation -- Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository -- Online Mendelian Inheritance in Man (OMIM): A Directory of Human Genes and Genetic Disorders -- NCBI BookShelf: Searchable Biomedical Books -- PubMed Central (PMC): An Archive for Literature from Life Sciences Journals -- SKY/CGH Database for Spectral Karyotyping and Comparative Genomic Hybridization Data -- Data Flow and Processing -- Sequin: A Sequence Submission and Editing Tool -- Processing of Biological Sequence Data at NCBI -- Genome Assembly and Annotation Process -- Querying and Linking the Data -- Entrez Search and Retrieval System -- BLAST Sequence Anaylysis Tool -- LinkOut: Linking to External Resources from Entrez Databases -- Reference Sequence (RefSeq) Project -- LocusLink: A Directory of Genes -- Using the Map Viewer to Explore Genomes -- UniGene: A Unified View of the Transcriptome -- Clusters of Orthologous Groups (COGs) Database: Phylogenetic Classification of Proteins from Complete Genomes -- User Support -- User Services: Helping You Find Your Way -- Exercises: Using Map Viewer.…”
Full text

Halophiles : genetics and genomes

Table of Contents: “…The origins of the Halobacteria may be rooted in horizontal gene transferHomologous recombination within and between Halobacterial lineages; Geographic isolation and barriers to recombination; 4: Comparative Genomics of Haloarchaeal Viruses; Introduction; Haloarchaeal versus prokaryotic viruses; Infection cycle; Related or not related, that's the problem; The influence of viral genes on their hosts; Haloarchaeal viruses; Conclusions and future prospects; 5: Microbial Adaptation to Saline Environments: Lessons from the Genomes of Natranaerobius thermophilus and Halobacillus halophilus.…”
Full text (MCPHS users only)

Microbiology in dairy processing : challenges and opportunities

Full text (MCPHS users only)

Pharmacogenetics of Breast Cancer : Towards the Individualization of Therapy. by Leyland-Jones, Brian

Table of Contents: “…s of Individualized Therapy""; ""3 Role of Genetic Variability in Breast Cancer Treatment Outcomes""; ""4 The Role of Epigenetics in Breast Cancer: Implications for Diagnosis, Prognosis, and Treatment""; ""5 Comparative Genomic Hybridization and Copy Number Abnormalities in Breast Cancer""…”
Full text (MCPHS users only)

The NCBI handbook.

Table of Contents: “…Databases -- GenBank: The Nucleotide Sequence Database -- PubMed: The Bibliographic Database -- Macromolecular Structure Databases -- Taxonomy Project -- Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation -- Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository -- Online Mendelian Inheritance in Man (OMIM): A Directory of Human Genes and Genetic Disorders -- NCBI BookShelf: Searchable Biomedical Books -- PubMed Central (PMC): An Archive for Literature from Life Sciences Journals -- SKY/CGH Database for Spectral Karyotyping and Comparative Genomic Hybridization Data -- Major histocompatibility complex database dbMHC -- Sequin: A Sequence Submission and Editing Tool -- Processing of Biological Sequence Data at NCBI -- Genome Assembly and Annotation Process -- Querying and Linking the Data -- Entrez Search and Retrieval System -- BLAST Sequence Anaylysis Tool -- LinkOut: Linking to External Resources from Entrez Databases -- Reference Sequence (RefSeq) Project -- Entrez gene: a directory of genes -- Using the Map Viewer to Explore Genomes -- UniGene: A Unified View of the Transcriptome -- Clusters of Orthologous Groups (COGs) Database: Phylogenetic Classification of Proteins from Complete Genomes -- User Support -- User Services: Helping You Find Your Way -- Exercises: Using Map Viewer.…”
Get full text
Full text