LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network.

abstract：BACKGROUND:Phenotype prediction problems are usually considered ill-posed, as the amount of samples is very limited with respect to the scrutinized genetic probes. This fact complicates the sampling of the defective genetic pathways due to the high number of possible discriminatory genetic networks involved. In this re...

journal_title：BMC bioinformatics

authors： Cernea A,Fernández-Martínez JL,deAndrés-Galiana EJ,Fernández-Ovies FJ,Alvarez-Machancoses O,Fernández-Muñiz Z,Saligan LN,Sonis ST

更新日期：2020-03-11 00:00:00

abstract：BACKGROUND:The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics...

journal_title：BMC bioinformatics

authors： Widmer C,Toussaint NC,Altun Y,Rätsch G

更新日期：2010-10-26 00:00:00

abstract：BACKGROUND:Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to illustrate the role of mechanisms such as copy number variation (CNV) or epigene...

journal_title：BMC bioinformatics

authors： Delatola EI,Lebarbier E,Mary-Huard T,Radvanyi F,Robin S,Wong J

更新日期：2017-07-11 00:00:00

abstract：BACKGROUND:The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible...

journal_title：BMC bioinformatics

authors： Sloat N,Liu JW,Schroeder SJ

更新日期：2017-11-21 00:00:00

abstract：BACKGROUND:Throughout the metazoan lineage, typically gonadal expressed Piwi proteins and their guiding piRNAs (~26-32nt in length) form a protective mechanism of RNA interference directed against the propagation of transposable elements (TEs). Most piRNAs are generated from genomic piRNA clusters. Annotation of experi...

journal_title：BMC bioinformatics

authors： Rosenkranz D,Zischler H

更新日期：2012-01-10 00:00:00

abstract：BACKGROUND:Recent increases in the number of deposited membrane protein crystal structures necessitate the use of automated computational tools to position them within the lipid bilayer. Identifying the correct orientation allows us to study the complex relationship between sequence, structure and the lipid environment...

journal_title：BMC bioinformatics

authors： Nugent T,Jones DT

更新日期：2013-09-18 00:00:00

abstract：BACKGROUND:In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare gene functional similarities at the molecular level. The existing gene similarity measures, however...

journal_title：BMC bioinformatics

authors： Peng J,Wang Y,Chen J

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly ass...

journal_title：BMC bioinformatics

authors： Gai X,Perin JC,Murphy K,O'Hara R,D'arcy M,Wenocur A,Xie HM,Rappaport EF,Shaikh TH,White PS

更新日期：2010-02-04 00:00:00

abstract：BACKGROUND:We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how thi...

journal_title：BMC bioinformatics

authors： Evans SN,Hower V,Pachter L

更新日期：2010-08-18 00:00:00

abstract：BACKGROUND:Many proteins contain conserved sequence patterns (motifs) that contribute to their functionality. The process of experimentally identifying and validating novel protein motifs can be difficult, expensive, and time consuming. A means for helping to identify in advance the possible function of a novel motif i...

journal_title：BMC bioinformatics

authors： Bristow F,He R,Van Domselaar G

更新日期：2011-09-26 00:00:00

abstract：BACKGROUND:As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease development or therapeutic intervention would assist in drug development, design of therapy, and target ide...

journal_title：BMC bioinformatics

authors： Bidaut G,Suhre K,Claverie JM,Ochs MF

更新日期：2006-02-28 00:00:00

abstract：BACKGROUND:Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings i...

journal_title：BMC bioinformatics

authors： Camacho C,Coulouris G,Avagyan V,Ma N,Papadopoulos J,Bealer K,Madden TL

更新日期：2009-12-15 00:00:00

abstract：BACKGROUND:Current malaria diagnosis relies primarily on microscopic examination of Giemsa-stained thick and thin blood films. This method requires vigorously trained technicians to efficiently detect and classify the malaria parasite species such as Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) for an appropria...

journal_title：BMC bioinformatics

authors： Kaewkamnerd S,Uthaipibull C,Intarapanich A,Pannarut M,Chaotheing S,Tongsima S

更新日期：2012-01-01 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

authors： Ammari M,McCarthy FM,Nanduri B,Pinchuk LM

更新日期：2010-10-07 00:00:00

abstract：BACKGROUND:Heritability of a phenotypic or molecular trait measures the proportion of variance that is attributable to genotypic variance. It is an important concept in breeding and genetics. Few methods are available for calculating heritability for traits derived from high-throughput sequencing. RESULTS:We propose s...

journal_title：BMC bioinformatics

authors： Rudra P,Shi WJ,Vestal B,Russell PH,Odell A,Dowell RD,Radcliffe RA,Saba LM,Kechris K

更新日期：2017-03-02 00:00:00

abstract：BACKGROUND:It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software ...

journal_title：BMC bioinformatics

authors： Zi Z,Zheng Y,Rundell AE,Klipp E

更新日期：2008-08-15 00:00:00

abstract：BACKGROUND:Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compound...

journal_title：BMC bioinformatics

authors： Le Guilloux V,Schmidtke P,Tuffery P

更新日期：2009-06-02 00:00:00

abstract：BACKGROUND:Inference of sequence homology is inherently an evolutionary question, dependent upon evolutionary divergence. However, the insertion and deletion penalties in the most widely used methods for inferring homology by sequence alignment, including BLAST and profile hidden Markov models (profile HMMs), are not b...

journal_title：BMC bioinformatics

authors： Rivas E,Eddy SR

更新日期：2015-12-10 00:00:00

abstract：BACKGROUND:In microarray data analysis, factors such as data quality, biological variation, and the increasingly multi-layered nature of more complex biological systems complicates the modelling of regulatory networks that can represent and capture the interactions among genes. We believe that the use of multiple datas...

journal_title：BMC bioinformatics

authors： Anvar SY,'t Hoen PA,Tucker A

更新日期：2010-01-15 00:00:00

abstract：BACKGROUND:Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecting specific pathway structures. However, our understanding is rather limited to the relationship bet...

journal_title：BMC bioinformatics

authors： You ZH,Yin Z,Han K,Huang DS,Zhou X

更新日期：2010-06-24 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

authors： Reid RW,Fodor AA

更新日期：2008-11-21 00:00:00

abstract：BACKGROUND:One approach to improving the personalized treatment of cancer is to understand the cellular signaling transduction pathways that cause cancer at the level of the individual patient. In this study, we used unsupervised deep learning to learn the hierarchical structure within cancer gene expression data. Deep...

journal_title：BMC bioinformatics

authors： Young JD,Cai C,Lu X

更新日期：2017-10-03 00:00:00

abstract：BACKGROUND:Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regu...

journal_title：BMC bioinformatics

authors： Li L,Che D,Wang X,Zhang P,Rahman SU,Zhao J,Yu J,Tao S,Lu H,Liao M

更新日期：2019-03-04 00:00:00

abstract：BACKGROUND:Supervised learning and many stochastic methods for predicting protein-protein interactions require both negative and positive interactions in the training data set. Unlike positive interactions, negative interactions cannot be readily obtained from interaction data, so these must be generated. In protein-pr...

journal_title：BMC bioinformatics

authors： Kim J,Huang DS,Han K

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:The increasing availability of Electronic Health Record (EHR) data and specifically free-text patient notes presents opportunities for phenotype extraction. Text-mining methods in particular can help disease modeling by mapping named-entities mentions to terminologies and clustering semantically related term...

journal_title：BMC bioinformatics

authors： Cohen R,Elhadad M,Elhadad N

更新日期：2013-01-16 00:00:00

abstract：BACKGROUND:The low success rate and high cost of drug discovery requires the development of new paradigms to identify molecules of therapeutic value. The Anatomical Therapeutic Chemical (ATC) Code System is a World Health Organization (WHO) proposed classification that assigns multi-level codes to compounds based on th...

journal_title：BMC bioinformatics

authors： Olson T,Singh R

更新日期：2017-06-07 00:00:00

abstract：BACKGROUND:Microarray technology has become very popular for globally evaluating gene expression in biological samples. However, non-linear variation associated with the technology can make data interpretation unreliable. Therefore, methods to correct this kind of technical variation are critical. Here we consider a me...

journal_title：BMC bioinformatics

authors： Pelz CR,Kulesz-Martin M,Bagby G,Sears RC

更新日期：2008-12-04 00:00:00

abstract：BACKGROUND:Although protein-protein interaction networks determined with high-throughput methods are incomplete, they are commonly used to infer the topology of the complete interactome. These partial networks often show a scale-free behavior with only a few proteins having many and the majority having only a few conne...

journal_title：BMC bioinformatics

authors： Friedel CC,Zimmer R

更新日期：2006-11-30 00:00:00

abstract：BACKGROUND:Deep mutational scanning is a technique to estimate the impacts of mutations on a gene by using deep sequencing to count mutations in a library of variants before and after imposing a functional selection. The impacts of mutations must be inferred from changes in their counts after selection. RESULTS:I desc...

journal_title：BMC bioinformatics

authors： Bloom JD

更新日期：2015-05-20 00:00:00

abstract：BACKGROUND:Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling ...

journal_title：BMC bioinformatics

authors： Chelaru F,Corrada Bravo H

更新日期：2015-01-01 00:00:00