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1. Full Text Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes
by Winsor, Geoffrey L and Van Rossum, Thea and Lo, Raymond and Khaira, Bhavjinder and Whiteside, Matthew D and Hancock, Robert E. W and Brinkman, Fiona S. L
Nucleic Acids Research, ISSN 0305-1048, 1/2009, Volume 37, Issue suppl_1, pp. D483 - D488
Pseudomonas aeruginosa is a well-studied opportunistic pathogen that is particularly known for its intrinsic antimicrobial resistance, diverse metabolic... 
SYSTEM | AERUGINOSA PAO1 | ALIGNMENT | MUTANT LIBRARY | BIOCHEMISTRY & MOLECULAR BIOLOGY | PROTEIN SUBCELLULAR-LOCALIZATION | SEQUENCE | COG DATABASE | PREDICTION | RESOURCE | INSIGHTS | Genes, Bacterial | User-Computer Interface | Genome, Bacterial | Pseudomonas aeruginosa - genetics | Genomics | Bacterial Proteins - genetics | Databases, Genetic | Bacterial Proteins - classification | Bacterial Proteins - analysis | Pseudomonas - genetics
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2. Full Text Toolbox: Creating a systematic database of secretory pathway proteins uncovers new cargo for COPI
by Weill, Uri and Arakel, Eric C and Goldmann, Omer and Golan, Matan and Chuartzman, Silvia and Munro, Sean and Schwappach, Blanche and Schuldiner, Maya
Traffic, ISSN 1398-9219, 05/2018, Volume 19, Issue 5, pp. 370 - 379
A third of yeast genes encode for proteins that function in the endomembrane system. However, the precise localization for many of these proteins is still... 
endomembrane | Lam5 | COPI | SWAT library | cargo | yeast | UBIQUITIN LIGASE | PROTEOME | ALPHA-COP | DISTINCT | TRAFFICKING | GLOBAL ANALYSIS | GOLGI | CELL BIOLOGY | TRANSPORT | COG COMPLEX | Proteins | Fluorescence | Databases | Analysis | Yeast | Functional morphology | Green fluorescent protein | Localization | Endoplasmic reticulum | Golgi apparatus | Toolbox
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3. Full Text Development of a unified clinical trial database for Alzheimer's disease
by Neville, Jon and Kopko, Steve and Broadbent, Steve and Avilés, Enrique and Stafford, Robert and Solinsky, Christine M and Bain, Lisa J and Cisneroz, Martin and Romero, Klaus and Stephenson, Diane and Coalition Major Dis and Coalition Against Major Diseases
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, ISSN 1552-5260, 2015, Volume 11, Issue 10, pp. 1212 - 1221
Abstract Introduction Data obtained in completed Alzheimer's disease (AD) clinical trials can inform decision making for future trials. Recognizing the... 
Neurology | Placebo data | Data standardization | Facilitated access | Alzheimer's disease | Data integration | Clinical trials database | DRUG | ADAS-COG | PATIENT-LEVEL | CLINICAL NEUROLOGY | Decision Making | Reference Standards | Humans | Alzheimer Disease - drug therapy | Clinical Trials as Topic | Cognition | Statistics as Topic | Internet | Databases, Factual | Clinical trials | Drug therapy
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4. Full Text Disease progression model for cognitive deterioration from Alzheimer's Disease Neuroimaging Initiative database
by Ito, Kaori and Corrigan, Brian and Zhao, Qinying and French, Jonathan and Miller, Raymond and Soares, Holly and Katz, Elyse and Nicholas, Timothy and Billing, Bill and Anziano, Richard and Fullerton, Terence and Alzheimers Dis Neuroimaging Initia and Alzheimer's Disease Neuroimaging Initiative
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, ISSN 1552-5260, 2011, Volume 7, Issue 2, pp. 151 - 160
Abstract Background A mathematical model was developed to describe the longitudinal response in Alzheimer's Disease Assessment Scale-cognitive (ADAS-cog)... 
Neurology | MCI | APOE ɛ4 genotype | ADAS-cog | Alzheimer's disease | Disease progression model | Natural history | Age | APOE ε4 genotype | TRIALS | RISK-FACTORS | DEMENTIA | METAANALYSIS | SEX | CLINICAL NEUROLOGY | IMPAIRMENT | DECLINE | APOE epsilon 4 genotype | CLINICAL PREDICTORS | Models, Theoretical | Alzheimer Disease - complications | Apolipoprotein E4 - genetics | Humans | Middle Aged | Risk Factors | Male | Disease Progression | Aged, 80 and over | Female | Aged | Models, Neurological | Alzheimer Disease - genetics | Databases, Factual
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5. Full Text Plant-PrAS: A database of physicochemical and structural properties and novel functional regions in plant proteomes
by Kurotani, Atsushi and Yamada, Yutaka and Shinozaki, Kazuo and Kuroda, Yutaka and Sakurai, Tetsuya
Plant and Cell Physiology, ISSN 0032-0781, 01/2015, Volume 56, Issue 1, pp. e11 - e11
Arabidopsis thaliana is an important model species for studies of plant gene functions. Research on Arabidopsis has resulted in the generation of high-quality... 
Database | Plant protein | Protein property | Gene function | Physicochemical property | INTRINSIC DISORDER | GENE ANNOTATION | INFORMATION | COG DATABASE | IDENTIFICATION | PREDICTION | PLANT SCIENCES | CELL BIOLOGY | GENOME SEQUENCE | INTEGRATION | PROTEIN-PROTEIN INTERACTIONS | EXPRESSION | Oryza - metabolism | Molecular Sequence Annotation | Open Reading Frames | Information Storage and Retrieval | Proteome | Chromosome Mapping | Populus - genetics | Rhodophyta - genetics | Arabidopsis - metabolism | Arabidopsis - genetics | Bryopsida - metabolism | Rhodophyta - metabolism | Bryopsida - genetics | Plant Proteins - genetics | Plants - metabolism | Oryza - genetics | Plants - genetics | Plant Proteins - chemistry | Databases, Protein | Populus - metabolism | Plant Proteins - metabolism | Internet | Special Online Collection – Database Papers
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6. Full Text Understanding placebo responses in Alzheimer's disease clinical trials from the literature meta-data and CAMD database
by Ito, Kaori and Corrigan, Brian and Romero, Klaus and Anziano, Richard and Neville, Jon and Stephenson, Diane and Lalonde, Richard
Journal of Alzheimer's Disease, ISSN 1387-2877, 2013, Volume 37, Issue 1, pp. 173 - 183
Background: The placebo response and the underlying disease progression is difficult to differentiate in longitudinal Alzheimer's disease (AD) studies, yet it... 
meta-analysis | Coalition Against Major Diseases (CAMD) | disease progression | placebo response | ADAS-cog | Alzheimer's disease | METAANALYSIS | MODEL | SIMULATION | NEUROSCIENCES | PROGRESSION | Alzheimer Disease - diagnosis | Clinical Trials as Topic - trends | Placebo Effect | Humans | Alzheimer Disease - therapy | Alzheimer Disease - epidemiology | Databases, Factual - trends | Clinical Trials as Topic - methods | Comprehension
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7. Full Text Clostridium -DTDB : A comprehensive database for potential drug targets of Clostridium difficile
by Jadhav, Ankush and Ezhilarasan, Vijayalakshmi and Prakash Sharma, Om and Pan, Archana
Computers in Biology and Medicine, ISSN 0010-4825, 2013, Volume 43, Issue 4, pp. 362 - 367
Abstract Clostridium difficile is considered to be one of the most important causes of health care-associated infections currently. The prevalence and severity... 
Internal Medicine | Other | Clostridium | Database | Drug targets | Choke point analysis | Homology modeling | MYCOBACTERIUM-TUBERCULOSIS | PROTEIN | ENGINEERING, BIOMEDICAL | METABOLIC PATHWAYS | COG DATABASE | IDENTIFICATION | ORTHOMCL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | GENOMICS | COMPUTER | BIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Proteins | Health facilities | Candidates | Genomics | Genetics | Genomes | Metabolism | Drug resistance | Comparative analysis | Gene expression | Methods | Bioinformatics
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8. Full Text PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
by Hulsen, T and Groenen, P.M.A and Vlieg, J. de and Alkema, W
Nucleic Acids Research, ISSN 0305-1048, 2009, Volume 37, Issue suppl_1, pp. D731 - 737
Phylogenetic patterns show the presence or absence of certain genes in a set of full genomes derived from different species. They can also be used to determine... 
SEARCH | INFORMATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | ONTOLOGY | TREE | COG DATABASE | TOOL | User-Computer Interface | Algorithms | Genes | Databases, Genetic | Internet | Phylogeny | Evolution, Molecular
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9. Full Text GoSynthetic database tool to analyse natural and engineered molecular processes
by Liang, Chunguang and Krug̈er, Beate and Dandekar, Thomas
Database, ISSN 1758-0463, 2013, Volume 2013, p. bat043
An essential topic for synthetic biologists is to understand the structure and function of biological processes and involved proteins and plan experiments... 
GENE | GENOME DATABASE | INFORMATION | MATHEMATICAL & COMPUTATIONAL BIOLOGY | COMPREHENSIVE RESOURCE | NETWORKS | COG DATABASE | EXPRESSION | Metabolic Engineering | Amino Acid Sequence | User-Computer Interface | Signal Transduction | Growth Hormone - metabolism | Databases as Topic | Synthetic Biology | Animals | Protein Engineering | Glycolysis | Search Engine | Mice | Software
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10. Full Text Genome Cluster Database. A Sequence Family Analysis Platform for Arabidopsis and Rice
by Kevin Horan and Josh Lauricha and Julia Bailey-Serres and Natasha Raikhel and Thomas Girke
Plant Physiology, ISSN 0032-0889, 5/2005, Volume 138, Issue 1, pp. 47 - 54
The genome-wide protein sequences from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) spp. japonica were clustered into families using sequence... 
Datasets | Databases | Genes | Online searching | Genomes | Biology | Nucleic acids | Plants | Bioinformatics | Rice | ALIGNMENT | PERSPECTIVE | METABOLISM | ANNOTATION | PROTEIN FAMILIES | GENES | ALGORITHM | COMPLEXITY | COG DATABASE | TOOL | PLANT SCIENCES | Amino Acid Sequence | Arabidopsis Proteins - genetics | Multigene Family | Molecular Sequence Data | Genome, Plant | Sequence Homology, Nucleic Acid | Arabidopsis - genetics | Sequence Homology, Amino Acid | Plant Proteins - genetics | Sequence Alignment | Algorithms | Arabidopsis Proteins - chemistry | Oryza - genetics | Plant Proteins - chemistry | Base Sequence | Arabidopsis thaliana | Protein research | Genetic aspects | Research | Gene expression | Computational biology
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11. Full Text EGGNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
by Huerta-Cepas, Jaime and Szklarczyk, Damian and Forslund, Kristoffer and Cook, Helen and Heller, Davide and Walter, Mathias C and Rattei, Thomas and Mende, Daniel R and Sunagawa, Shinichi and Kuhn, Michael and Jensen, Lars Juhl and Von Mering, Christian and Bork, Peer
Nucleic Acids Research, ISSN 0305-1048, 2016, Volume 44, Issue 1, pp. D286 - D293
eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional... 
PERFORMANCE | BIOCHEMISTRY & MOLECULAR BIOLOGY | PROTEIN FAMILIES | GENES | REPRESENTATION | GENOME-WIDE | TREE | DUPLICATION | COG DATABASE | SOFTWARE | ALIGNMENTS | Sequence Analysis, Protein | Algorithms | Eukaryota | Viral Proteins - chemistry | Databases, Protein | Molecular Sequence Annotation | Archaeal Proteins - chemistry | Bacterial Proteins - chemistry | Phylogeny | Proteome - chemistry | Database Issue
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12. Full Text CEGMA: a pipeline to accurately annotate core genes in eukaryotic genornes
by Parra, G and Bradnam, K and Korf, I
BIOINFORMATICS, ISSN 1367-4803, 05/2007, Volume 23, Issue 9, pp. 1061 - 1067
Motivation: The numbers of finished and ongoing genome projects are increasing at a rapid rate, and providing the catalog of genes for these new genomes is a... 
COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | RECOGNITION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEQUENCE ALIGNMENT | DNA | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | STATISTICS & PROBABILITY | COG DATABASE | GENOME | PREDICTION
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13. Full Text PHOG: A database of supergenomes built from proteome complements
by Merkeev, Igor V and Novichkov, Pavel S and Mironov, Andrey A
BMC Evolutionary Biology, ISSN 1471-2148, 06/2006, Volume 6, Issue 1, pp. 52 - 52
Background: Orthologs and paralogs are widely used terms in modern comparative genomics. Existing procedures for resolving orthologous/paralogous relationships... 
EVOLUTIONARY BIOLOGY | ALIGNMENT | GENOMES | SEARCH | SEQUENCE | GENES | GENETICS & HEREDITY | SITES | BACTERIAL | COG DATABASE | PROTEINS | TOOL | Databases, Genetic | Proteome - genetics | Phylogeny | Genomics | Genome - genetics | Proteomics
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14. Full Text The quantitative and condition-dependent Escherichia coli proteome
by Schmidt, Alexander and Kochanowski, Karl and Vedelaar, Silke and Ahrné, Erik and Volkmer, Benjamin and Callipo, Luciano and Knoops, Kèvin and Bauer, Manuel and Aebersold, Ruedi and Heinemann, Matthias
Nature Biotechnology, ISSN 1087-0156, 2016, Volume 34, Issue 1, pp. 104 - 110
Measuring precise concentrations of proteins can provide insights into biological processes. Here we use efficient protein extraction and sample fractionation,... 
RATES | ACETYLATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | EVOLUTIONARY CONSERVATION | GROWTH-RATE | B-R | GENE-EXPRESSION | COG DATABASE | PROTEINS | MASS-SPECTROMETRY | REVEALS | Escherichia coli Proteins - metabolism | Proteome | Mass Spectrometry | Escherichia coli - metabolism | Physiological aspects | Cellular proteins | Escherichia coli | E coli | Bacterial proteins | Proteomics
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15. Full Text BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
by Hulsen, T and Vlieg, J. de and Alkema, W
BMC Genomics, ISSN 1471-2164, 2008, Volume 9, Issue 1, pp. 488 - 488
BACKGROUND: In many genomics projects, numerous lists containing biological identifiers are produced. Often it is useful to see the overlap between different... 
COG DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENES | GENETICS & HEREDITY | TOOL | Software | Animals | Internet | Humans | Computational Biology | Genetic research | Web applications | Usage | Analysis | Methods | Venn diagrams
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16. Full Text Comparative Genomics of the Lactic Acid Bacteria
by K. Makarova and A. Slesarev and Y. Wolf and A. Sorokin and B. Mirkin and E. Koonin and A. Pavlov and N. Pavlov and V. Karamychev and N. Polouchine and V. Shakhova and I. Grigoriev and Y. Lou and D. Rohksar and S. Lucas and K. Huang and D. M. Goodstein and T. Hawkins and V. Plengvidhya and D. Welker and J. Hughes and Y. Goh and A. Benson and K. Baldwin and J. -H. Lee and I. Díaz-Muñiz and B. Dosti and V. Smeianov and W. Wechter and R. Barabote and G. Lorca and E. Altermann and R. Barrangou and B. Ganesan and Y. Xie and H. Rawsthorne and D. Tamir and C. Parker and F. Breidt and J. Broadbent and R. Hutkins and D. O'Sullivan and J. Steele and G. Unlu and M. Saier and T. Klaenhammer and P. Richardson and S. Kozyavkin and B. Weimer and D. Mills and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2006, Volume 103, Issue 42, pp. 15611 - 15616
Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We... 
Enzymes | Lactic acid bacteria | Phylogenetics | Cogs | Evolution | Genomes | Biosynthesis | Food science | Bacteriocins | Lactobacillus | Evolutionary genomics | Fermentation | LACTOBACILLUS-PLANTARUM | MULTIDISCIPLINARY SCIENCES | COG DATABASE | ARCHAEAL | RADIATION-RESISTANCE | evolutionary genomics | EVOLUTION | SEQUENCE | fermentation | TRANSFER-RNA | HORIZONTAL GENE-TRANSFER | LACTOCOCCUS-LACTIS | MOLECULAR CLOCK | Lactobacillus - genetics | Genome, Bacterial | Genomics | Lactic Acid - metabolism | Bacterial Proteins - genetics | Gene Transfer, Horizontal | Streptococcaceae - genetics | Phylogeny | Food Microbiology | Biological Evolution | Lactobacillus - classification | Animals | Bacterial Proteins - metabolism | Bacterial Proteins - classification |