Abstract:
BACKGROUND:The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA interference, the prior state of the art. New methods for analyzing the data and evaluating results are needed. RESULTS:We offer BAGEL (Bayesian Analysis of Gene EssentiaLity), a supervised learning method for analyzing gene knockout screens. Coupled with gold-standard reference sets of essential and nonessential genes, BAGEL offers significantly greater sensitivity than current methods, while computational optimizations reduce runtime by an order of magnitude. CONCLUSIONS:Using BAGEL, we identify ~2000 fitness genes in pooled library knockout screens in human cell lines at 5 % FDR, a major advance over competing platforms. BAGEL shows high sensitivity and specificity even across screens performed by different labs using different libraries and reagents.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Hart T,Moffat Jdoi
10.1186/s12859-016-1015-8subject
Has Abstractpub_date
2016-04-16 00:00:00pages
164issn
1471-2105pii
10.1186/s12859-016-1015-8journal_volume
17pub_type
杂志文章abstract:BACKGROUND:Biological resources are essential tools for biomedical research. Their availability is promoted through on-line catalogues. Common Access to Biological Resources and Information (CABRI) is a service for distribution of biological resources and related data collected by 28 European culture collections. Linki...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-S4-S23
更新日期:2005-12-01 00:00:00
abstract:BACKGROUND:In template-based modeling when using a single template, inter-atomic distances of an unknown protein structure are assumed to be distributed by Gaussian probability density functions, whose center peaks are located at the distances between corresponding atoms in the template structure. The width of the Gaus...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0526-z
更新日期:2015-03-21 00:00:00
abstract:BACKGROUND:The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologist...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-264
更新日期:2008-06-05 00:00:00
abstract:BACKGROUND:Analysis of expression quantitative trait loci (eQTL) aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-269
更新日期:2011-06-30 00:00:00
abstract:BACKGROUND:Human breast cancer resistance protein (BCRP) is an ATP-binding cassette (ABC) efflux transporter that confers multidrug resistance in cancers and also plays an important role in the absorption, distribution and elimination of drugs. Prediction as to if drugs or new molecular entities are BCRP substrates sho...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-130
更新日期:2013-04-15 00:00:00
abstract:BACKGROUND:In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-318
更新日期:2006-06-23 00:00:00
abstract:BACKGROUND:Antibacterial peptides are important components of the innate immune system, used by the host to protect itself from different types of pathogenic bacteria. Over the last few decades, the search for new drugs and drug targets has prompted an interest in these antibacterial peptides. We analyzed 486 antibacte...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-263
更新日期:2007-07-23 00:00:00
abstract:BACKGROUND:One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metabolic phenotype which typically means having a high yield/productivity. This challenge is not only du...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-499
更新日期:2008-11-27 00:00:00
abstract:BACKGROUND:Frequent pattern mining analysis applied on microarray dataset appears to be a promising strategy for identifying relationships between gene expression levels. Unfortunately, too many itemsets (co-expressed genes) are identified by this analysis method since it does not consider the importance of each gene w...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-230
更新日期:2013-07-21 00:00:00
abstract:BACKGROUND:Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3073-1
更新日期:2019-12-02 00:00:00
abstract:BACKGROUND:Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs oft...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-102
更新日期:2007-03-26 00:00:00
abstract:BACKGROUND:Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-203
更新日期:2012-08-16 00:00:00
abstract:BACKGROUND:Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structu...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1616-x
更新日期:2017-04-11 00:00:00
abstract:BACKGROUND:The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-104
更新日期:2013-03-22 00:00:00
abstract:BACKGROUND:In real-time PCR data analysis, the cycle threshold (CT) method is currently the gold standard. This method is based on an assumption of equal PCR efficiency in all reactions, and precision may suffer if this condition is not met. Nonlinear regression analysis (NLR) or curve fitting has therefore been sugges...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-107
更新日期:2006-03-03 00:00:00
abstract:BACKGROUND:To further our understanding of immunopeptidomics, improved tools are needed to identify peptides presented by major histocompatibility complex class I (MHC-I). Many existing tools are limited by their reliance upon chemical affinity data, which is less biologically relevant than sampling by mass spectrometr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2561-z
更新日期:2019-01-05 00:00:00
abstract:BACKGROUND:Systematic mutagenesis studies have shown that only a few interface residues termed hot spots contribute significantly to the binding free energy of protein-protein interactions. Therefore, hot spots prediction becomes increasingly important for well understanding the essence of proteins interactions and hel...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-311
更新日期:2011-07-29 00:00:00
abstract:BACKGROUND:Protein function is closely intertwined with protein structure. Discovery of meaningful structure-function relationships is of utmost importance in protein biochemistry and has led to creation of high-quality, manually curated classification databases, such as the gold-standard SCOP (Structural Classificatio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S2-S1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated comp...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1270-8
更新日期:2016-09-29 00:00:00
abstract:BACKGROUND:New "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-100
更新日期:2010-02-22 00:00:00
abstract:BACKGROUND:Selecting a parsimonious set of informative genes to build highly generalized performance classifier is the most important task for the analysis of tumor microarray expression data. Many existing gene pair evaluation methods cannot highlight diverse patterns of gene pairs only used one strategy of vertical c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0893-0
更新日期:2016-01-20 00:00:00
abstract:BACKGROUND:Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2-5% of the genes encode for peptidases, irrespectively of the organism source. The basic peptidase function is "protein digestion" and this can be potentially dangerous in living organisms w...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S1-S3
更新日期:2007-03-08 00:00:00
abstract:BACKGROUND:Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introd...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-256
更新日期:2013-08-22 00:00:00
abstract:BACKGROUND:Interpretation of gene expression microarray data in the light of external information on both columns and rows (experimental variables and gene annotations) facilitates the extraction of pertinent information hidden in these complex data. Biologists classically interpret genes of interest after retrieving f...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-178
更新日期:2013-06-06 00:00:00
abstract:BACKGROUND:Identifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phe...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2210-6
更新日期:2018-06-11 00:00:00
abstract:BACKGROUND:Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-0887-y
更新日期:2016-01-20 00:00:00
abstract:BACKGROUND:Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune sup...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S6-S9
更新日期:2010-10-07 00:00:00
abstract:BACKGROUND:Periodogram analysis of time-series is widespread in biology. A new challenge for analyzing the microarray time series data is to identify genes that are periodically expressed. Such challenge occurs due to the fact that the observed time series usually exhibit non-idealities, such as noise, short length, an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-137
更新日期:2007-04-24 00:00:00
abstract:BACKGROUND:Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-217
更新日期:2009-07-15 00:00:00
abstract:BACKGROUND:Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) representing a major drawback for the use of the clustering methods. Usually the MVs are not treated,...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-114
更新日期:2004-08-23 00:00:00