Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “CATALOGING”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58Linked to original sources
PubMed2002

Functional proteomic analysis of human nucleolus.

The notion of a "plurifunctional" nucleolus is now well established. However, molecular mechanisms underlying the biological processes occurring within this nuclear domain remain only partially understood. As a first step in elucidating these mechanisms we have carried out a proteomic analysis to draw up a list of proteins present within nucleoli of HeLa cells. This analysis allowed the identification of 213 different nucleolar proteins. This catalog complements that of the 271 proteins obtained recently by others, giving a total of approximately 350 different nucleolar proteins. Functional classification of these proteins allowed outlining several biological processes taking place within nucleoli. Bioinformatic analyses permitted the assignment of hypothetical functions for 43 proteins for which no functional information is available. Notably, a role in ribosome biogenesis was proposed for 31 proteins. More generally, this functional classification reinforces the plurifunctional nature of nucleoli and provides convincing evidence that nucleoli may play a central role in the control of gene expression. Finally, this analysis supports the recent demonstration of a coupling of transcription and translation in higher eukaryotes.

Cell Nucleolus↗
PubMed1993

Adenocarcinoma in the lung in patients with breast cancer. A prospective analysis of the discriminatory value of immunohistology.

In some patients with a history of breast cancer who also have masses in the lung, making a clinical distinction between primary pulmonary neoplasia and pulmonary metastasis of mammary carcinoma may be impossible. To ascertain whether immunohistologic studies could contribute to resolving this problem, the authors undertook a prospective study of 30 cases showing synchronous or metachronous adenocarcinomas in these two sites. A predefined panel of antibodies--as derived from published antigenic catalogs for breast and lung cancer--was applied to each case. Tumors were interpreted as metastases if they were positive for gross cystic disease fluid protein-15, estrogen receptor protein, or S-100 protein. Conversely, primary adenocarcinomas of the lung were defined by their expression of carcinoembryonic antigen and a lack of the other three determinants. Using these criteria, 15 lesions were classified as metastatic; 11 were categorized as primary pulmonary adenocarcinomas; and 4 cases were indeterminate in origin. Responses to corresponding therapeutic protocols generally supported the validity of the immunohistologic diagnoses; 8 of 15 patients treated for metastatic breast cancer were well at least contact, as were 5 of 11 patients who received therapy for primary carcinoma of the lung. These data suggest that immunohistology plays a useful role in distinguishing mammary from pulmonary adenocarcinomas.

Adenocarcinoma↗
PubMed1981

Quality assurance for multichannel hematology instruments. Four years' experience with patient mean erythrocyte indices.

Experience using the Bull patient moving average control system over a four-year period to control a Coulter multichannel hematology counting system is described. The system allowed the abandonment of commercial control materials at an annual saving of almost $3,000 without any deterioration in the quality of laboratory data generated. Guidelines or instrument trouble shooting are outlined. A catalog of all major control problem episodes that occurred during the four-year period is included.

Erythrocyte Indices↗
PubMed1991

Multitumor "sausage" blocks in immunohistochemistry. Simplified method of preparation, practical uses, and roles in quality assurance.

This report describes a simplified method for preparing multitumor sausage blocks (MTSBs) for use in immunohistochemical procedures. Rather than relying on previously processed paraffin blocks as a source of material, this procedure involves procuring tissue at the time of gross specimen examination. The tissue is processed along with routine surgical pathologic material, and the paraffinized samples are placed in "storage cassettes" for easy cataloging and storage. Thin strips are cut from the tissue in the "storage cassettes" and combined by dripping liquid paraffin onto them while they are rolled between the thumbs and forefingers, somewhat like making a cigarette. This results in a tissue "log." Transverse sections of the "log" are embedded in paraffin blocks and used as MTSBs. Practical uses of MTSBs are discussed, and their role in quality assurance is stressed.

Histological Techniques↗
PubMed2026

CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts.

MOTIVATION: Variant calling for next-generation sequencing (NGS) data relies on a diverse ecosystem of tools and workflows. Large-scale collaborative studies increasingly adopt federated analysis, where each institution processes sensitive data locally using standardized pipelines. Deploying identical pipelines across multiple centers remains challenging because heterogeneous software environments and computing policies can cause workflow divergence and inconsistent results. RESULTS: We developed CBIcall, a workflow backend-flexible, configuration-driven framework that runs standardized variant-calling pipelines from raw FASTQ files to analysis-ready VCFs. Users define each analysis in a single YAML parameters file, which CBIcall resolves against a controlled workflow registry and resource catalog. The execution driver validates parameters and checks compatibility among pipelines, analysis modes, workflow backends, genome builds, tool versions, and resource bundles. CBIcall supports reproducibility auditing by comparing executions using recorded provenance and output fingerprints. CBIcall dispatches validated workflows natively through Bash, Cromwell, Nextflow and Snakemake backends and provides production-ready pipelines for germline WES, WGS (single-sample or cohort joint genotyping following GATK Best Practices), and mitochondrial DNA analysis. We evaluated analytical performance using public benchmark datasets and validated reproducibility across four computing environments. We further deployed CBIcall in the EU HEREDITARY project, where it processed 1102 samples with both WES and mtDNA pipelines on an institutional HPC system, supporting its suitability for reproducible cohort-scale genomic analyses. AVAILABILITY AND IMPLEMENTATION: CBIcall is open source (GPLv3) and distributed with ready-to-run pipelines; full dependency and installation documentation is available at https://github.com/CNAG-Biomedical-Informatics/cbicall.

Journal Article↗
PubMed2001

Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features.

MOTIVATION: The process of determining the functional sequence content of an organism is confounded by several factors. Large protein coding sequences are relatively easy to find by statistical methods. Smaller proteins however may escape detection due to their size falling below some arbitrary researcher-defined minimum cutoff, or the inability to precisely define a promoter, or translational start (Delcher et al., Nucleic Acids Res., 27, 4636-4641, 1999). Promoter and regulatory sequences themselves are difficult to define due to a significant amount of allowable sequence variation, as well as a probable lack of any completely accurate whole-organismal gene catalogs to date. Finally, certain genes coding functional RNAs may have insufficient structural or sequence constraints to be detectable by normal sequence structure/pattern searching methods (Eddy and Rivas, Bioinformatics, 16, 583-605, 2000). In those cases where there are multiple closely related organisms that have been sequenced, there is additional information that may be used in the investigation of sequence content-that being the possible conserved nature of functional sequences between the organisms. We present a method for the utilization of this conserved information to detect genes and other potentially functional sequences that may be missed by standard ORF-calling, RNA finding, and pattern matching software. The tricross programs produce a multi-way cross comparison of three sets of sequences, determine which are conserved in all three sets, and produce a graphical (Virtual Reality Modelling Language-VRML; (ISO/IEC 14772-1: 1997, VDC), 1997) representation as well as alignments of all sequence triples found. The software can also be applied to a pair of sequence sets, though the noise in the results increases. RESULTS: Tricross has been used to examine the intergenic-sequence content of the three archaeal Pyrococcus genomes to determine the most highly related sequences remaining between the annotated protein and RNA coding sequences. Set to relatively stringent similarity requirements for the search, tricross found 101 intergenic sequences conserved among the three organisms. Interestingly, 29 of these appear to contain members of a family of small RNA molecules (Kiss-Laszlo et al., EMBO J., 17, 797-807, 1998) only recently discovered in the Archaea (Armbruster, OSU, Diss., 1988; Omer et al., Science, 288, 517-522, 2000; Gaspin et al., J. Mol. Biol., 297, 895-906, 2000). While some of the remaining 72 appear to be individual highly conserved promoter sequences, others have no currently known biological significance. Although originally developed to facilitate the examination of intergenic sequences, none of the tricross logic is inherently specific to intergenic sequences. The software can also be applied to gene sequences, and has been used to produce inter-genomic gene order dot-plots for Haemophilus influenzae (Fleischmann et al., Science, 269, 496-512, 1995) versus H.ducreyi (unpublished data), and Neisseria meningiditis Z2491 (serogroup A) (Parkhill et al., Nature, 404, 502-506, 2000) versus Neisseria meningiditis Z58 (serogroup B) (Tettelin et al., Science, 287, 1809-1815, 2000) versus Neisseria gonorrhoeae (Lewis et al., http://micro-gen.ouhsc.edu/, 2000). AVAILABILITY: The tricross software package is available from http://www.biosci.ohio-state.edu/~ray/bioinformatics/tricross.html. CONTACT: ray@biosci.ohio-state.edu; daniels.7@osu.edu; munsonr@pediatrics.ohio-state.edu SUPPLEMENTARY INFORMATION: Additional data from the cross-genomic comparisons examined in the discussion section are linked from http://www.biosci.ohio-state.edu/~ray/bioinformatics/tricross.html.

Base Sequence↗
PubMed2025

Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly.

MOTIVATION: De novo assembly creates reference genomes that underpin many modern biodiversity and conservation studies. Large numbers of new genomes are being assembled by labs around the world. To avoid duplication of efforts and variable data quality, we desire a best-practice assembly process, implemented as an automated portable workflow. RESULTS: Here, we present Colora, a Snakemake workflow that produces chromosome-scale de novo primary or phased genome assemblies complete with organelles using Pacific Biosciences HiFi, Hi-C, and optionally Oxford Nanopore Technologies reads as input. Colora is a user-friendly, versatile, and reproducible pipeline that is ready to use by researchers looking for an automated way to obtain high-quality de novo genome assemblies. AVAILABILITY AND IMPLEMENTATION: The source code of Colora is available on GitHub (https://github.com/LiaOb21/colora) and has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576. Colora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora).

Software↗
PubMed2026

ViralQC: a tool for assessing completeness and contamination of predicted viral contigs.

MOTIVATION: Viruses represent the most abundant biological entities on Earth, playing vital roles in diverse ecosystems. Cataloging viruses across various environments is essential for understanding their properties and functions. Metagenomic sequencing has emerged as the most comprehensive method for virus discovery. However, distinguishing viral sequences from the vast background of microbial organisms in metagenomic data remains a significant challenge. Existing tools experience varying degrees of false positive rates due to noise in sequencing and assembly, and the integration of proviruses into microbial genomes. This highlights the urgent need for an accurate and efficient method to evaluate the quality of viral contigs. RESULTS: To address these challenges, we introduce ViralQC, a tool designed to assess the quality of viral contigs or bins. ViralQC identifies microbial contamination within putative viral sequences using an ensemble framework powered by DNA and protein foundation models and estimates completeness by analyzing protein organization. We evaluated ViralQC on multiple datasets and compared its performance against the state-of-the-art tool, CheckV. Leveraging both DNA and protein foundation models, ViralQC achieves higher sensitivity on contamination detection for contigs longer than 10 kbp while maintaining comparable accuracy. Additionally, ViralQC delivers more accurate estimation on contigs with completeness > 50%. AVAILABILITY: The source code of ViralQC is available via: https://github.com/ChengPENG-wolf/ViralQC.

Software↗
PubMed2026

SNPannotator: automated functional annotation of genetic variants and linked proxies.

SUMMARY: Genome-wide association studies (GWASs) have identified thousands of genetic variants associated with complex traits and diseases. However, explaining the mechanisms underlying phenotypic variation remains challenging. Here, we introduce SNPannotator, an automated post-GWAS analysis software package designed to streamline the interpretation of GWAS findings. Our pipeline implements a multi-step process that identifies proxy variants in high linkage disequilibrium (LD) with associated lead variants, then queries comprehensive resources (including Ensembl, the GTEx Portal, the eQTL Catalog, and STRING DB) for genomic position, deleteriousness, regulatory annotations, clinical significance, trait associations, expression (eQTLs) and splicing quantitative trait loci (sQTLs), and functional enrichment analyses and compiles the results into user-friendly reports. This package is implemented in the R programming language and includes auxiliary functions for variant lookup and LD exploration. SNPannotator provides a practical framework for efficiently deriving biologically meaningful insights from GWAS data and for assisting researchers in prioritizing candidate variants for functional validation. AVAILABILITY AND IMPLEMENTATION: The SNPannotator package is available from the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/SNPannotator. The development version and tutorial is available on GitHub (https://github.com/omicslaboratory/SNPannotator). The online version of the package is available at https://omicslab.org/snpannotator.

Software↗
PubMed2003

Predicting phenotype from patterns of annotation.

MOTIVATION: Predicting the outcome of specific experiments (such as the growth of a particular mutant strain in a particular medium) has the potential to allow researchers to devote resources to experiments with higher expected numbers of 'hits'. RESULTS: We use decision trees to predict phenotypes associated with Saccharomyces cerevisiae genes on the basis of Gene Ontology (GO) functional annotations from the Saccharomyces Genome Database (SGD) and other phenotypic annotations from the Yeast Phenotype Catalog at the Munich Information Center for Protein Sequences (MIPS). We assess the methodology in three ways: (1) we use cross-validation on the phenotypic annotations listed in MIPS, and show ROC curves indicating the tradeoff between true-positive rate and false-positive rate; (2) we do a literature-search for 100 of the predicted gene-phenotype associations that are not listed in MIPS, and find evidence for 43 of them; (3) we use deletion strains to experimentally assess 61 predicted gene-phenotype associations not listed in MIPS; significantly more of these deletion strains show abnormal growth than would be expected by chance.

Algorithms↗
PubMed2004

Identifying periodically expressed transcripts in microarray time series data.

MOTIVATION: Microarray experiments are now routinely used to collect large-scale time series data, for example to monitor gene expression during the cell cycle. Statistical analysis of this data poses many challenges, one being that it is hard to identify correctly the subset of genes with a clear periodic signature. This has lead to a controversial argument with regard to the suitability of both available methods and current microarray data. METHODS: We introduce two simple but efficient statistical methods for signal detection and gene selection in gene expression time series data. First, we suggest the average periodogram as an exploratory device for graphical assessment of the presence of periodic transcripts in the data. Second, we describe an exact statistical test to identify periodically expressed genes that allows one to distinguish periodic from purely random processes. This identification method is based on the so-called g-statistic and uses the false discovery rate approach to multiple testing. RESULTS: Using simulated data it is shown that the suggested method is capable of identifying cell-cycle-activated genes in a gene expression data set even if the number of the cyclic genes is very small and regardless the presence of a dominant non-periodic component in the data. Subsequently, we re-examine 12 large microarray time series data sets (in part controversially discussed) from yeast, human fibroblast, human HeLa and bacterial cells. Based on the statistical analysis it is found that a majority of these data sets contained little or no statistical significant evidence for genes with periodic variation linked to cell cycle regulation. On the other hand, for the remaining data the method extends the catalog of previously known cell-cycle-specific transcripts by identifying additional periodic genes not found by other methods. The problem of distinguishing periodicity due to generic cell cycle activity and to artifacts from synchronization is also discussed. AVAILABILITY: The approach has been implemented in the R package GeneTS available from http://www.stat.uni-muenchen.de/~strimmer/software.html under the terms of the GNU General Public License.

Algorithms↗
PubMed2004

STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces.

UNLABELLED: Amino acid contacts in terms of atomic interactions are essential factors to be considered in the analysis of the structure of a protein and its complexes. Consequently, molecular biologists do require specific tools for the identification and visualization of all such contacts. Graphical contacts (GC) and interface forming residue graphical contacts (IFRgc) presented here, calculate atomic contacts among amino acids based on a table of predefined pairs of the atom types and their distances, and then display them using number of different forms. The inventory of currently listed contact types by GC and IFRgc include hydrogen bonds (in nine different flavors), hydrophobic interactions, charge-charge interactions, aromatic stacking and disulfide bonds. Such extensive catalog of the interactions, representing the forces that govern protein folding, stability and binding, is the key feature of these two applications. GC and IFRgc are part of STING Millennium Suite. AVAILABILITY: http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org//SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS (Options: Graphical Contacts and IFR Graphical Contacts).

Algorithms↗
PubMed2004

Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data.

UNLABELLED: We have developed a web-based system (Pathway Miner) for visualizing gene expression profiles in the context of biological pathways. Pathway Miner catalogs genes based on their role in metabolic, cellular and regulatory pathways. A Fisher exact test is provided as an option to rank pathways. The genes are mapped onto pathways and gene product association networks are extracted for genes that co-occur in pathways. The networks can be filtered for analysis based on user-selected options. AVAILABILITY: Pathway Miner is a freely available web accessible tool at http://www.biorag.org/pathway.html

Algorithms↗
PubMed2004

Predicting protein functions with message passing algorithms.

MOTIVATION: In the last few years, a growing interest in biology has been shifting toward the problem of optimal information extraction from the huge amount of data generated via large-scale and high-throughput techniques. One of the most relevant issues has recently emerged that of correctly and reliably predicting the functions of a given protein with that of functions exploiting information coming from the whole network of proteins physically interacting with the functionally undetermined one. In the present work, we will refer to an 'observed' protein as the one present in the protein-protein interaction networks published in the literature. METHODS: The method proposed in this paper is based on a message passing algorithm known as Belief Propagation, which accepts the network of protein's physical interactions and a catalog of known protein's functions as input, and returns the probabilities for each unclassified protein of having one chosen function. The implementation of the algorithm allows for fast online analysis, and can easily be generalized into more complex graph topologies taking into account hypergraphs, i.e. complexes of more than two interacting proteins. RESULTS: Benchmarks of our method are the two Saccharomyces cerevisiae protein-protein interaction networks and the Database of Interacting Proteins. The validity of our approach is successfully tested against other available techniques. CONTACT: leone@isiosf.isi.it SUPPLEMENTARY INFORMATION: http://isiosf.isi.it/~pagnani

Algorithms↗
PubMed2005

PACdb: PolyA Cleavage Site and 3'-UTR Database.

UNLABELLED: The PolyA Cleavage Site and 3'-UTR Database (PACdb) is a web-accessible database that catalogs putative 3'-processing sites and 3'-UTR sequences for multiple organisms. Sites have been identified primarily via expressed sequence tag-genome alignments, enabling delineation of both the specificities and heterogeneity of 3'-processing events. AVAILABILITY: By web browser or CGI: PACdb: http://harlequin.jax.org/pacdb/; AtPACdb: http://harlequin.jax.org/atpacdb/. SUPPLEMENTARY INFORMATION: Available online at http://harlequin.jax.org/pacdb/supplemental.php.

3' Untranslated Regions↗
PubMed2005

ChemDB: a public database of small molecules and related chemoinformatics resources.

MOTIVATION: The development of chemoinformatics has been hampered by the lack of large, publicly available, comprehensive repositories of molecules, in particular of small molecules. Small molecules play a fundamental role in organic chemistry and biology. They can be used as combinatorial building blocks for chemical synthesis, as molecular probes in chemical genomics and systems biology, and for the screening and discovery of new drugs and other useful compounds. RESULTS: We describe ChemDB, a public database of small molecules available on the Web. ChemDB is built using the digital catalogs of over a hundred vendors and other public sources and is annotated with information derived from these sources as well as from computational methods, such as predicted solubility and three-dimensional structure. It supports multiple molecular formats and is periodically updated, automatically whenever possible. The current version of the database contains approximately 4.1 million commercially available compounds and 8.2 million counting isomers. The database includes a user-friendly graphical interface, chemical reactions capabilities, as well as unique search capabilities. AVAILABILITY: Database and datasets are available on http://cdb.ics.uci.edu.

Access to Information↗
PubMed2006

A scalable method for integration and functional analysis of multiple microarray datasets.

MOTIVATION: The diverse microarray datasets that have become available over the past several years represent a rich opportunity and challenge for biological data mining. Many supervised and unsupervised methods have been developed for the analysis of individual microarray datasets. However, integrated analysis of multiple datasets can provide a broader insight into genetic regulation of specific biological pathways under a variety of conditions. RESULTS: To aid in the analysis of such large compendia of microarray experiments, we present Microarray Experiment Functional Integration Technology (MEFIT), a scalable Bayesian framework for predicting functional relationships from integrated microarray datasets. Furthermore, MEFIT predicts these functional relationships within the context of specific biological processes. All results are provided in the context of one or more specific biological functions, which can be provided by a biologist or drawn automatically from catalogs such as the Gene Ontology (GO). Using MEFIT, we integrated 40 Saccharomyces cerevisiae microarray datasets spanning 712 unique conditions. In tests based on 110 biological functions drawn from the GO biological process ontology, MEFIT provided a 5% or greater performance increase for 54 functions, with a 5% or more decrease in performance in only two functions.

Algorithms↗
PubMed2002

Individual factors in nasal chemesthesis.

Population variability in nasal irritant (chemesthesic) sensitivity has been postulated by both clinicians and epidemiologists studying indoor and ambient air pollution. Among experimentalists, however, limited attention has been paid to variance in this trait. Candidate susceptibility markers include age, gender, presence or absence of nasal allergies or olfactory dysfunction, cognitive bias and self-reported pollutant reactivity. For most of these markers, conflicting data exist. This review distinguishes between functional subcomponents of nasal irritant sensitivity (sensory acuity versus physiologic reactivity), catalogs psychophysical and physiological methods for their study and examines the current evidence for variation in this trait. In general, interindividual variability has been an under-studied phenomenon.

Air Pollutants↗