An integrated approach to the prediction of domain-domain interactions.

abstract：BACKGROUND:Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta-analysis framework is also n...

journal_title：BMC bioinformatics

authors： Di Narzo AF,Cheng H,Lu J,Hao K

更新日期：2014-11-28 00:00:00

abstract：:Transcript quantification is a long-standing problem in genomics and estimating the relative abundance of alternatively-spliced isoforms from the same transcript is an important special case. Both problems have recently been illuminated by high-throughput RNA sequencing experiments which are quickly generating large a...

journal_title：BMC bioinformatics

authors： Kakaradov B,Xiong HY,Lee LJ,Jojic N,Frey BJ

更新日期：2012-04-19 00:00:00

abstract：BACKGROUND:Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D model...

journal_title：BMC bioinformatics

authors： Antczak M,Kasprzak M,Lukasiak P,Blazewicz J

更新日期：2016-09-17 00:00:00

abstract：BACKGROUND:RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high performance computing environment. RESULTS:Developed as a tool by the Bioinformatics Shared Resource Group (BISR) at...

journal_title：BMC bioinformatics

authors： Gadepalli VS,Ozer HG,Yilmaz AS,Pietrzak M,Webb A

更新日期：2019-12-20 00:00:00

abstract：BACKGROUND:Many methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify "sufficiently large". RESULTS:Using the multispecies coalescent model, we report a general an...

journal_title：BMC bioinformatics

authors： Uricchio LH,Warnow T,Rosenberg NA

更新日期：2016-11-11 00:00:00

abstract：BACKGROUND:It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool wh...

journal_title：BMC bioinformatics

authors： David MP,Lapid CM,Daria VR

更新日期：2008-04-28 00:00:00

abstract：BACKGROUND:A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. Howeve...

journal_title：BMC bioinformatics

authors： Guerra-Assunção JA,Enright AJ

更新日期：2010-03-16 00:00:00

abstract：BACKGROUND:Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is ne...

journal_title：BMC bioinformatics

authors： Fang L,Hu J,Wang D,Wang K

更新日期：2018-05-23 00:00:00

abstract：BACKGROUND:Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. RESULTS:We developed a...

journal_title：BMC bioinformatics

authors： Condon DE,Tran PV,Lien YC,Schug J,Georgieff MK,Simmons RA,Won KJ

更新日期：2018-02-05 00:00:00

abstract：BACKGROUND:DNA methylation of CpG dinucleotides is an essential epigenetic modification that plays a key role in transcription. Widely used DNA enrichment-based methods offer high coverage for measuring methylated CpG dinucleotides, with the lowest cost per CpG covered genome-wide. However, these methods measure the DN...

journal_title：BMC bioinformatics

authors： Xu J,Liu S,Yin P,Bulun S,Dai Y

更新日期：2018-12-22 00:00:00

abstract：BACKGROUND:Identification of transcription factors (TFs) responsible for modulation of differentially expressed genes is a key step in deducing gene regulatory pathways. Most current methods identify TFs by searching for presence of DNA binding motifs in the promoter regions of co-regulated genes. However, this strateg...

journal_title：BMC bioinformatics

authors： Roy S,Heinrich K,Phan V,Berry MW,Homayouni R

更新日期：2011-10-18 00:00:00

abstract：BACKGROUND:Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning models using gene expression data from patients' primary tumor tissues to predict whether a patient wi...

journal_title：BMC bioinformatics

authors： Clayton EA,Pujol TA,McDonald JF,Qiu P

更新日期：2020-09-30 00:00:00

abstract：BACKGROUND:With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the followin...

journal_title：BMC bioinformatics

authors： Lin J

更新日期：2009-02-03 00:00:00

abstract：BACKGROUND:Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. RESULTS:We present a data structure called a history graph that offers a practical ba...

journal_title：BMC bioinformatics

authors： Paten B,Zerbino DR,Hickey G,Haussler D

更新日期：2014-06-19 00:00:00

abstract：BACKGROUND:Computer-aided segmentation and border detection in dermoscopic images is one of the core components of diagnostic procedures and therapeutic interventions for skin cancer. Automated assessment tools for dermoscopy images have become an important research field mainly because of inter- and intra-observer var...

journal_title：BMC bioinformatics

authors： Kockara S,Mete M,Chen B,Aydin K

更新日期：2010-10-07 00:00:00

abstract：BACKGROUND:A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for ...

journal_title：BMC bioinformatics

authors： Bertolazzi P,Guerra C,Liuzzi G

更新日期：2010-09-29 00:00:00

abstract：BACKGROUND:Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discrimin...

journal_title：BMC bioinformatics

authors： Garrow AG,Agnew A,Westhead DR

更新日期：2005-03-15 00:00:00

abstract：BACKGROUND:Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences s...

journal_title：BMC bioinformatics

authors： Arenas M,Posada D

更新日期：2007-11-20 00:00:00

abstract：BACKGROUND:Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and specificities in cancer molecular pattern recognition. In fact, high-dimensional and heterogeneous tu...

journal_title：BMC bioinformatics

authors： Han H,Li XL

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-prot...

journal_title：BMC bioinformatics

authors： Chen J,Aronow BJ,Jegga AG

更新日期：2009-02-27 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

authors： Clarke TH,Brinkac LM,Inman JM,Sutton G,Fouts DE

更新日期：2018-06-27 00:00:00

abstract：BACKGROUND:Multiple co-inertia analysis (mCIA) is a multivariate analysis method that can assess relationships and trends in multiple datasets. Recently it has been used for integrative analysis of multiple high-dimensional -omics datasets. However, its estimated loading vectors are non-sparse, which presents challenge...

journal_title：BMC bioinformatics

authors： Min EJ,Long Q

更新日期：2020-04-15 00:00:00

abstract：BACKGROUND:Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area is assigned to each spot and the sum of the pixel intensities in that area, the so-called volume, is ...

journal_title：BMC bioinformatics

authors： Brauner JM,Groemer TW,Stroebel A,Grosse-Holz S,Oberstein T,Wiltfang J,Kornhuber J,Maler JM

更新日期：2014-06-11 00:00:00

abstract：BACKGROUND:In real-time PCR, it is necessary to consider the efficiency of amplification (EA) of amplicons in order to determine initial target levels properly. EAs can be deduced from standard curves, but these involve extra effort and cost and may yield invalid EAs. Alternatively, EA can be extracted from individual ...

journal_title：BMC bioinformatics

authors： Batsch A,Noetel A,Fork C,Urban A,Lazic D,Lucas T,Pietsch J,Lazar A,Schömig E,Gründemann D

更新日期：2008-02-12 00:00:00

abstract：BACKGROUND:Many practical tasks in biomedicine require accessing specific types of information in scientific literature; e.g. information about the results or conclusions of the study in question. Several schemes have been developed to characterize such information in scientific journal articles. For example, a simple ...

journal_title：BMC bioinformatics

authors： Guo Y,Korhonen A,Liakata M,Silins I,Hogberg J,Stenius U

更新日期：2011-03-08 00:00:00

abstract：BACKGROUND:Discovering patterns from gene expression levels is regarded as a classification problem when tissue classes of the samples are given and solved as a discrete-data problem by discretizing the expression levels of each gene into intervals maximizing the interdependence between that gene and the class labels. ...

journal_title：BMC bioinformatics

authors： Wu GP,Chan KC,Wong AK

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:It is possible to predict whether a tuberculosis (TB) patient will fail to respond to specific antibiotics by sequencing the genome of the infecting Mycobacterium tuberculosis (Mtb) and observing whether the pathogen carries specific mutations at drug-resistance sites. This advancement has led to the collati...

journal_title：BMC bioinformatics

authors： Ngo TM,Teo YY

更新日期：2019-02-08 00:00:00

abstract：BACKGROUND:Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by ...

journal_title：BMC bioinformatics

authors： Memarian N,Jessulat M,Alirezaie J,Mir-Rashed N,Xu J,Zareie M,Smith M,Golshani A

更新日期：2007-04-04 00:00:00

abstract：BACKGROUND:A drug-drug interaction (DDI) occurs when one drug influences the level or activity of another drug. The increasing volume of the scientific literature overwhelms health care professionals trying to be kept up-to-date with all published studies on DDI. METHODS:This paper describes a hybrid linguistic approa...

journal_title：BMC bioinformatics

authors： Segura-Bedmar I,Martínez P,de Pablo-Sánchez C

更新日期：2011-03-29 00:00:00

abstract：BACKGROUND:GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Previous studies suggested that G...

journal_title：BMC bioinformatics

authors： Machnicka MA,Kaminska KH,Dunin-Horkawicz S,Bujnicki JM

更新日期：2015-10-23 00:00:00