SitesIdentify: a protein functional site prediction tool.

abstract：BACKGROUND:Current network-based microarray analysis uses the information of interactions among concerned genes/gene products, but still considers each gene expression individually. We propose an organized knowledge-supervised approach - Integrative eXpression Profiling (IXP), to improve microarray classification accur...

journal_title：BMC bioinformatics

authors： Wu X,Huang H,Sonachalam M,Reinhard S,Shen J,Pandey R,Chen JY

更新日期：2012-03-13 00:00:00

abstract：BACKGROUND:The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can h...

journal_title：BMC bioinformatics

authors： Zampieri G,Tran DV,Donini M,Navarin N,Aiolli F,Sperduti A,Valle G

更新日期：2018-01-25 00:00:00

abstract：BACKGROUND:Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides...

journal_title：BMC bioinformatics

authors： Haskins WE,Petritis K,Zhang J

更新日期：2011-03-15 00:00:00

abstract：BACKGROUND:Ubiquitylation plays an important role in regulating protein functions. Recently, experimental methods were developed toward effective identification of ubiquitylation sites. To efficiently explore more undiscovered ubiquitylation sites, this study aims to develop an accurate sequence-based prediction method...

journal_title：BMC bioinformatics

authors： Tung CW,Ho SY

更新日期：2008-07-15 00:00:00

abstract：BACKGROUND:Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, th...

journal_title：BMC bioinformatics

authors： Sheikhizadeh Anari S,de Ridder D,Schranz ME,Smit S

更新日期：2018-09-26 00:00:00

abstract：BACKGROUND:Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC) molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as...

journal_title：BMC bioinformatics

authors： Peters B,Sette A

更新日期：2005-05-31 00:00:00

abstract：BACKGROUND:The rapid pace of bioscience research makes it very challenging to track relevant articles in one's area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year. Thus it is not surprising to se...

journal_title：BMC bioinformatics

authors： Srinivasan P,Zhang XN,Bouten R,Chang C

更新日期：2015-06-20 00:00:00

abstract：BACKGROUND:Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biologi...

journal_title：BMC bioinformatics

authors： Pinoli P,Chicco D,Masseroli M

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of pot...

journal_title：BMC bioinformatics

authors： Che D,Guo S,Jiang Q,Chen L

更新日期：2020-07-14 00:00:00

abstract：BACKGROUND:Viral infection by dengue virus is a major public health problem in tropical countries. Early diagnosis and detection are increasingly based on quantitative reverse transcriptase real-time polymerase chain reaction (RT-qPCR) directed against genomic regions conserved between different isolates. Genetic varia...

journal_title：BMC bioinformatics

authors： Vanneste K,Garlant L,Broeders S,Van Gucht S,Roosens NH

更新日期：2018-09-04 00:00:00

abstract：BACKGROUND:A standard procedure in many areas of bioinformatics is to use a multiple sequence alignment (MSA) as the basis for various types of homology-based inference. Applications include 3D structure modelling, protein functional annotation, prediction of molecular interactions, etc. These applications, however sop...

journal_title：BMC bioinformatics

authors： Vanhoutreve R,Kress A,Legrand B,Gass H,Poch O,Thompson JD

更新日期：2016-07-07 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:Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional natur...

journal_title：BMC bioinformatics

authors： Arakawa K,Tamaki S,Kono N,Kido N,Ikegami K,Ogawa R,Tomita M

更新日期：2009-01-23 00:00:00

abstract：BACKGROUND:High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino ac...

journal_title：BMC bioinformatics

authors： Pan C,Park BH,McDonald WH,Carey PA,Banfield JF,VerBerkmoes NC,Hettich RL,Samatova NF

更新日期：2010-03-05 00:00:00

abstract：BACKGROUND:Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major c...

journal_title：BMC bioinformatics

authors： Yue Y,Huang H,Qi Z,Dou HM,Liu XY,Han TF,Chen Y,Song XJ,Zhang YH,Tu J

更新日期：2020-07-28 00:00:00

abstract：BACKGROUND:In many research areas it is necessary to find differences between treatment groups with several variables. For example, studies of microarray data seek to find a significant difference in location parameters from zero or one for ratios thereof for each variable. However, in some studies a significant deviat...

journal_title：BMC bioinformatics

authors： Frömke C,Hothorn LA,Kropf S

更新日期：2008-01-27 00:00:00

abstract：BACKGROUND:High-throughput sequencing can identify numerous potential genomic targets for microbial strain typing, but identification of the most informative combinations requires the use of computational screening tools. This paper describes novel software-- Automated Selection of Typing Target Subsets (AuSeTTS)--that...

journal_title：BMC bioinformatics

authors： O'Sullivan MV,Sintchenko V,Gilbert GL

更新日期：2013-05-01 00:00:00

abstract：BACKGROUND:Transcriptome sequencing is a powerful tool for measuring gene expression, but as well as some other technologies, various artifacts and biases affect the quantification. In order to correct some of them, several normalization approaches have emerged, differing both in the statistical strategy employed and i...

journal_title：BMC bioinformatics

authors： Filloux C,Cédric M,Romain P,Lionel F,Christophe K,Dominique R,Abderrahman M,Daniel P

更新日期：2014-06-14 00:00:00

abstract：BACKGROUND:Gene expression patterns of olfactory receptors (ORs) are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD) to house OR gene exp...

journal_title：BMC bioinformatics

authors： Liu N,Crasto CJ,Ma M

更新日期：2007-06-30 00:00:00

abstract：BACKGROUND:Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles are challenging, because they comprise reads not only from the grafted human cancer but also from t...

journal_title：BMC bioinformatics

authors： Kluin RJC,Kemper K,Kuilman T,de Ruiter JR,Iyer V,Forment JV,Cornelissen-Steijger P,de Rink I,Ter Brugge P,Song JY,Klarenbeek S,McDermott U,Jonkers J,Velds A,Adams DJ,Peeper DS,Krijgsman O

更新日期：2018-10-04 00:00:00

abstract：BACKGROUND:The efficiency of lymph nodes depends on tissue structure and organization, which allow the coordination of lymphocyte traffic. Despite their essential role, our understanding of lymph node specific mechanisms is still incomplete and currently a topic of intense research. RESULTS:In this paper, we present a...

journal_title：BMC bioinformatics

authors： Baldazzi V,Paci P,Bernaschi M,Castiglione F

更新日期：2009-11-25 00:00:00

abstract：BACKGROUND:One of the important goals in the post-genomic era is to determine the regulatory elements within the non-coding DNA of a given organism's genome. The identification of functional cis-regulatory modules has proven difficult since the component factor binding sites are small and the rules governing their arra...

journal_title：BMC bioinformatics

authors： Emberly E,Rajewsky N,Siggia ED

更新日期：2003-11-20 00:00:00

abstract：BACKGROUND:Aptamers are nucleic acids selected for their ability to bind to molecules of interest and may provide the basis for a whole new class of medicines. If the aptamer is simply a dsDNA molecule with a ssDNA overhang (a "sticky" end) then the segment of ssDNA that complements that overhang provides a known bindi...

journal_title：BMC bioinformatics

authors： Thomson K,Amin I,Morales E,Winters-Hilt S

更新日期：2007-11-01 00:00:00

abstract：BACKGROUND:The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain i...

journal_title：BMC bioinformatics

authors： Lee H,Deng M,Sun F,Chen T

更新日期：2006-05-25 00:00:00

abstract：BACKGROUND:With the development of sequencing technologies, more and more sequence variants are available for investigation. Different classes of variants in the human genome have been identified, including single nucleotide substitutions, insertion and deletion, and large structural variations such as duplications and...

journal_title：BMC bioinformatics

authors： Liu M,Watson LT,Zhang L

更新日期：2014-01-09 00:00:00

abstract：BACKGROUND:The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000). RESULTS:We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to...

journal_title：BMC bioinformatics

authors： Karwath A,King RD

更新日期：2002-04-23 00:00:00

abstract：BACKGROUND:Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. RESULTS:In this wor...

journal_title：BMC bioinformatics

authors： Arkun Y

更新日期：2019-11-28 00:00:00

abstract：BACKGROUND:In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach. RESULTS:We developed ImproViser...

journal_title：BMC bioinformatics

authors： Videm P,Gunasekaran D,Schröder B,Mayer B,Biniossek ML,Schilling O

更新日期：2014-06-19 00:00:00

abstract：BACKGROUND:Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams. RESULTS:Our primary contribution is a local sliding-...

journal_title：BMC bioinformatics

authors： Sarkar A,Soueidan H,Nikolski M

更新日期：2011-10-05 00:00:00

abstract：BACKGROUND:Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting m...

journal_title：BMC bioinformatics

authors： Mei S,Fei W,Zhou S

更新日期：2011-02-02 00:00:00