Abstract:
BACKGROUND:Cancer is caused through a multistep process, in which a succession of genetic changes, each conferring a competitive advantage for growth and proliferation, leads to the progressive conversion of normal human cells into malignant cancer cells. Interrogation of cancer genomes holds the promise of understanding this process, thus revolutionizing cancer research and treatment. As datasets measuring copy number aberrations in tumors accumulate, a major challenge has become to distinguish between those mutations that drive the cancer versus those passenger mutations that have no effect. RESULTS:We present JISTIC, a tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer. JISTIC is an improvement over the widely used GISTIC algorithm. We compared the performance of JISTIC versus GISTIC on a dataset of glioblastoma copy number variation, JISTIC finds 173 significant regions, whereas GISTIC only finds 103 significant regions. Importantly, the additional regions detected by JISTIC are enriched for oncogenes and genes involved in cell-cycle and proliferation. CONCLUSIONS:JISTIC is an easy-to-install platform independent implementation of GISTIC that outperforms the original algorithm detecting more relevant candidate genes and regions. The software and documentation are freely available and can be found at: http://www.c2b2.columbia.edu/danapeerlab/html/software.html.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Sanchez-Garcia F,Akavia UD,Mozes E,Pe'er Ddoi
10.1186/1471-2105-11-189subject
Has Abstractpub_date
2010-04-14 00:00:00pages
189issn
1471-2105pii
1471-2105-11-189journal_volume
11pub_type
杂志文章abstract:BACKGROUND:Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S9-S9
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector intensity readings, each uniquely addressed along dimensions of time (e.g., retention time of chemic...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S9-S15
更新日期:2008-08-12 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of endogenous regulatory small RNAs which play an important role in posttranscriptional regulations by targeting mRNAs for cleavage or translational repression. The base-pairing between the 5'-end of miRNA and the target mRNA 3'-UTRs is essential for the miRNA:mRNA recognition....
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-432
更新日期:2007-11-08 00:00:00
abstract:BACKGROUND:Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data. RESULTS:We ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-S9-S2
更新日期:2010-10-28 00:00:00
abstract:BACKGROUND:The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatures of phenotypes such as clinical outcome has not been attained in almost any disease area. Here, w...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3427-8
更新日期:2020-03-20 00:00:00
abstract::Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughp...
journal_title:BMC bioinformatics
pub_type: 杂志文章,评审
doi:10.1186/1471-2105-13-S16-S4
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Feed-forward loops (FFLs), consisting of miRNAs, transcription factors (TFs) and their common target genes, have been validated to be important for the initialization and development of complex diseases, including cancer. Esophageal Carcinoma (ESCA) and Stomach Adenocarcinoma (STAD) are two types of malignan...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3230-6
更新日期:2019-12-30 00:00:00
abstract:BACKGROUND:Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelian diseases, the implication of such events in multi-genic disorders is yet to be well understood. We...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-22
更新日期:2010-01-12 00:00:00
abstract:BACKGROUND:The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootst...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-79
更新日期:2011-03-18 00:00:00
abstract:BACKGROUND:Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptio...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-439
更新日期:2006-10-10 00:00:00
abstract:BACKGROUND:Non-coding RNAs gain more attention as their diverse roles in many cellular processes are discovered. At the same time, the need for efficient computational prediction of ncRNAs increases with the pace of sequencing technology. Existing tools are based on various approaches and techniques, but none of them p...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-491
更新日期:2010-09-29 00:00:00
abstract:BACKGROUND:In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm. The classification task is performed by a multi-classifier system where each classifier (Linear or Radial Basis function Support Vector Machines) is trained using feat...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-45
更新日期:2008-01-24 00:00:00
abstract:BACKGROUND:The Acel_2062 protein from Acidothermus cellulolyticus is a protein of unknown function. Initial sequence analysis predicted that it was a metallopeptidase from the presence of a motif conserved amongst the Asp-zincins, which are peptidases that contain a single, catalytic zinc ion ligated by the histidines ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-1
更新日期:2014-01-03 00:00:00
abstract:BACKGROUND:Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain datab...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-4-16
更新日期:2003-05-06 00:00:00
abstract:BACKGROUND:Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc). Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-433
更新日期:2008-10-14 00:00:00
abstract:BACKGROUND:Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed. A number of prediction algorithms have been developed based on amino acid compositions or on the N-terminal characteristics (signal peptides) of proteins. Ho...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-152
更新日期:2005-06-17 00:00:00
abstract:BACKGROUND:Bioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information extraction (IE) systems that incorporate natural language processing (NLP) techniques have thus been developed for use in the biomedical fi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-325
更新日期:2007-09-01 00:00:00
abstract:BACKGROUND:A recently proposed method for estimating qPCR amplification efficiency E analyzes fluorescence intensity ratios from pairs of points deemed to lie in the exponential growth region on the amplification curves for all reactions in a dilution series. This method suffers from a serious problem: The resulting ra...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03604-4
更新日期:2020-07-08 00:00:00
abstract:BACKGROUND:Clustering techniques are routinely used in gene expression data analysis to organize the massive data. Clustering techniques arrange a large number of genes or assays into a few clusters while maximizing the intra-cluster similarity and inter-cluster separation. While clustering of genes facilitates learnin...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-40
更新日期:2009-01-30 00:00:00
abstract:BACKGROUND:Ensemble predictors such as the random forest are known to have superior accuracy but their black-box predictions are difficult to interpret. In contrast, a generalized linear model (GLM) is very interpretable especially when forward feature selection is used to construct the model. However, forward feature ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-5
更新日期:2013-01-16 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:In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of microarrays where N = 1 in each condition. In this paper, we demonstrate the effectiveness of a new al...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-489
更新日期:2008-11-21 00:00:00
abstract:BACKGROUND:Somatic copy number alternation (SCNA) is a common feature of the cancer genome and is associated with cancer etiology and prognosis. The allele-specific SCNA analysis of a tumor sample aims to identify the allele-specific copy numbers of both alleles, adjusting for the ploidy and the tumor purity. Next gene...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2412-y
更新日期:2018-11-14 00:00:00
abstract:BACKGROUND:Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and relate...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2413-x
更新日期:2018-11-30 00:00:00
abstract:UNLABELLED: BACKGROUND:Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-447
更新日期:2011-11-15 00:00:00
abstract:BACKGROUND:Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs that attract great attention because of their role in regulation of...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0836-1
更新日期:2015-12-10 00:00:00
abstract:BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03777-y
更新日期:2020-10-20 00:00:00
abstract:BACKGROUND:Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2250-y
更新日期:2018-06-27 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:Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for th...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-161
更新日期:2006-03-20 00:00:00