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At least 811 records · Page 45Linked to original sources
PubMed2005

A human-curated annotation of the Candida albicans genome.

Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.

Journal Article↗
PubMed2004

Expressed sequence tags: analysis and annotation.

Expressed sequence tags (ESTs) present a special set of problems for bioinformatic analysis. They are partial and error-prone, and large datasets can have significant internal redundancy. To facilitate analysis of small EST datasets from in-house projects, we present an integrated "pipeline" of tools that take EST data from sequence trace to database submission. These tools also can be used to provide clustering of ESTs into putative genes and to annotate these genes with preliminary sequence similarity searches. The systems are written to use the public-domain LINUX environment and other openly available analytical tools.

Computational Biology↗
PubMed2006

Microarray RNA transcriptional profiling: part II. Analytical considerations and annotation.

This review summarizes the various data filtration, transformation and normalization processes for different array platforms (cDNA, oligos, one- and two-color), data analysis methods and their validation, and databases and annotation for RNA transcriptional profiling microarrays. This review is intended to introduce the beginner to the analyses and interpretation of gene expression studies using a nonmathematical approach for easier comprehension. Microarray analysis is not a trivial undertaking as there is no single method that works well for all, and results obtained from these analyses should be considered as a complement to other approaches.

Computational Biology↗
PubMed2006

Genome annotating proteomics pipelines: available tools.

Proteomics based on tandem mass spectrometry is a powerful tool for identifying novel biomarkers and drug targets. Previously, a major bottleneck in high-throughput proteomics has been that the computational techniques needed to reliably identify proteins from proteomic data lagged behind the ability to collect the immense quantity of data generated. This is no longer the case, as fully automated pipelines for peptide and protein identification exist, and these are publicly and privately accessible. Such pipelines can automatically and rapidly generate high-confidence protein identifications from large datasets in a searchable format covering multiple experimental runs. However, the main challenge for the community now is to use these resources as they are, by taking full advantage of the pooling of information, so that the next barrier in our understanding of biology may be broken. There are currently two pipelines in the public domain that provide such potential: PeptideAtlas and the Genome Annotating Proteomic Pipeline. This review will introduce their features in the context of high-throughput proteomics, and provide indicative results as to their usefulness and usability through a side-by-side comparison of results obtained when processing a set of human plasma samples.

Animals↗
PubMed2001

House dust mites in Brazil--an annotated bibliography.

House dust mites have been reported to be the most important allergen in human dwellings. Several articles had already shown the presence of different mite species at homes in Brazil, being Pyroglyphidae, Glycyphagidae and Cheyletidae the most important families found. This paper is an annotated bibliography that will lead to a better knowledge of house dust mite fauna in Brazil.

Animals↗
PubMed2002

In vivo functional proteomics: mammalian genome annotation using CD-tagging.

A self-inactivating CD-tagging retroviral vector was used to introduce epitope and GFP tags into genes and proteins in NIH 3T3 cells. Several hundred cell clones, each expressing GFP fluorescence in a distinctive pattern, were isolated. Molecular analysis showed that a wide variety of genes and proteins, some known and some newly discovered, had been tagged. The analysis also revealed that, in the great majority of instances, the abundance and cellular location of the tagged protein mirrored that of its untagged counterpart. This approach provides a systematic means for the functional annotation of mammalian genomes and proteomes in living cells.

3T3 Cells↗
PubMed1998

An editing environment for DNA sequence analysis and annotation (extended abstract).

This paper presents a computer system for analyzing and annotating large-scale genomic sequences. The core of the system is a multiple-gene structure identification program, which predicts the most "probable" gene structures based on the given evidence, including pattern recognition, EST and protein homology information. A graphics-based user interface provides an environment which allows the user to interactively control the evidence to be used in the gene identification process. To overcome the computational bottleneck in the database similarity search used in the gene identification process, we have developed an effective way to partition a database into a set of sub-databases of "related" sequences, and reduced the search problem on a large database to a signature identification problem and a search problem on a much smaller sub-database. This reduces the number of sequences to be searched from N to O ([square root of] N) on average, and hence greatly reduces the search time, where N is the number of sequences in the original database. The system provides the user with the ability to facilitate and modify the analysis and modeling in real time.

Base Sequence↗
PubMed1977

Marijuana and human performance: an annotated bibliography (1970-1975).

A bibliography of 199 annotated references was compiled to aid the reader in determining the impact of marijuana on psychomotor, cognitive, and physiological factors considered pertinent to flight performance. The bibliography contains an index which categorizes the references into the following major areas: (1) reviews or overviews of issues, literature or research; (2) psychological effects of marijuana use; (3) physiological and pharmacological research; (4) medical comments and research critiques; and (5) additional reference sources. The basic period of coverage is 1970 to 1975, although selected studies from earlier years are also included.

Aerospace Medicine↗
PubMed2005

An annotated chronology of the history of AIDS in Toronto: the first five years, 1981-1986.

The purpose of this annotated chronology is to help provide a framework for research into the history of the first five years of the AIDS epidemic in Canada but especially as it unfolded in Toronto, Canada. The chronological entries can be used to identify the order and relationship of particular themes, while the sources listed in the chronology can be used as points of reference for further investigations. This chronology is primarily derived from reports in key newspapers based in the Toronto region. Each chronological entry lists the sources which reported on the particular event.

Acquired Immunodeficiency Syndrome↗
PubMed2001

VIDANN: a video annotation system.

VIDANN is a computer program that allows participants to watch a video on a standard TV and to write their annotations (thought/feeling entries) on paper attached to a writing tablet. The system is designed as a Microsoft ActiveX module. It can be further adapted by the individual researcher through the use of a VBScript. All data, including the participant's handwriting, are stored in an XML database. An accompanying Wizard has been designed that enables researchers to generate VBScripts for standard configurations.

Humans↗
PubMedDate not supplied

Atherectomy, stents and lasers. An annotated bibliography of recent references.

This is an annotated bibliography of selected references on atherectomy, stents and lasers that have appeared in the literature since the particular issue of the Journal of Invasive Cardiology covering that device was published. It has been structured to include pertinent details about each citation, including the site at which the device was used (coronary or peripheral), the type of article in which the research was reported (clinical paper, case report, abstract, review, editorial), the number of subjects or procedures and lesions treated, the design of the study (case study, single group, group comparison, or randomized trial), acute and late results, and comments about the study and its findings.

Angioplasty, Laser↗
PubMed1999

Spirituality and prayer research: a select annotated bibliography.

As the world has become more complex, so too have our ethical conceptualizations about it. In the 1970s, ethical theories and principle-based bioethics dominated. Then clinicians and scholars began to experience the limitations of these two approaches when used alone. In the 1980s, women's voices began to be heard through both feminist ethics and the ethic of care. In addition, virtue ethics and casuistry again gained recognition. During the 1990s and as we are about to enter the 21st century, ethics has expanded to capture the concepts of narrative ethics and spirituality. This select annotated bibliography focuses on spirituality and on prayer research.

Ethics, Nursing↗
PubMed2001

Annotation: Recent research examining the role of peer relationships in the development of psychopathology.

This Annotation highlights recent research on the role of peer group and friendship factors in the development of psychopathology in childhood and adolescence. Several processes are considered. including peer rejection (e.g., exclusion and victimization), social withdrawal and avoidance of peer interaction, and the socialization of deviant behavior and internalizing problems. The mediating influences of several proximal components are examined, including cognitive-perceptual factors and emotion regulation. In addition, the moderating influences of close friendship, age, gender, ethnicity, and group norms are considered. Several promising avenues for future directions in research are highlighted, including the examination of heterogeneity in developmental processes, further investigation of gender-based norms, and the application of multi-level modeling techniques and gene-environment process models.

Adaptation, Psychological↗
PubMed2000

[Analysis and investigation on annotations on synopsis of Jade book of golden chamber (Jin gui yi han yao lue shu yi)].

It is claimed that this Annotations on Synopsis of Jade Book of Golden Chamber written by the Japanese Kitamura Tadahiro may possibly recover, to a great extent, the original face of Jingui (Synopsis of Golden Chamber) through textual research. This is supported by the author's own study. It is also held that Kitamura's expounding on Jingui's theory is unique, based on his rich medical practice. This is of significant reference value to both clinical practice and textual research.

China↗
PubMed2001

Use of word processors to support written communication: an annotated bibliography.

When children with disabilities have difficulty with written communication, members of their educational teams, including occupational therapists and physical therapists, often recommend use of a word processor. This annotated bibliography summarizes a variety of articles that describe the use of word processing technology with school-aged children. The articles include research reports, descriptions of special features used with word processing programs, and guidelines for using word processing with students. Implications for occupational therapists and physical therapists working with students who have written communication problems are discussed.

Child↗
PubMedDate not supplied

[Comparative approach to correction of annotated gene starts in complete bacterial genomes].

A method for refining the beginnings of genes and a search for shifts of the reading frame is proposed. The method is based on a comparison of nucleotide and amino acid sequences of homologous genes of related organisms. The algorithm is based on the fact that the rate of changes in the protein-coding regions of the genome is substantially lower than that of noncoding regions. A modification of the Smith-Waterman algorithm is proposed, which makes it possible to align the amino acid sequences obtained by formal translation of the starting nucleotide sequences by taking into account a possible shift of the reading frame. The algorithm has been implemented in the package of ORTOLOGATOR-GeneCorrector programs. Testing the program showed that the approach enables one to detect a wrong annotation of the beginnings in 1% of genes (even in well-studied organisms such as Escherichia coli) and identify several (approximately 10) shifts of the open reading frame. Thus, the algorithm can be used at both the initial and final stages of analysis of the genome.

Algorithms↗