A unifying model of genome evolution under parsimony.

abstract：BACKGROUND:Classification and naming is a key step in the analysis, understanding and adequate management of living organisms. However, where to set limits between groups can be puzzling especially in clonal organisms. Within the Mycobacterium tuberculosis complex (MTC), the etiological agent of tuberculosis (TB), expe...

journal_title：BMC bioinformatics

authors： Borile C,Labarre M,Franz S,Sola C,Refrégier G

更新日期：2011-06-02 00:00:00

abstract：BACKGROUND:G-protein-coupled receptors (GPCRs) play a key role in diverse physiological processes and are the targets of almost two-thirds of the marketed drugs. The 3 D structures of GPCRs are largely unavailable; however, a large number of GPCR primary sequences are known. To facilitate the identification and charact...

journal_title：BMC bioinformatics

authors： Peng ZL,Yang JY,Chen X

更新日期：2010-08-09 00:00:00

abstract：BACKGROUND:Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogeny. Changes between homologous characters are typically modell...

journal_title：BMC bioinformatics

authors： Maiolo M,Zhang X,Gil M,Anisimova M

更新日期：2018-09-21 00:00:00

abstract：BACKGROUND:In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD) represents one such effort to make these data broadl...

journal_title：BMC bioinformatics

authors： Hummel J,Niemann M,Wienkoop S,Schulze W,Steinhauser D,Selbig J,Walther D,Weckwerth W

更新日期：2007-06-23 00:00:00

abstract：BACKGROUND:Leishmaniasis is a virulent parasitic infection that causes a worldwide disease burden. Most treatments have toxic side-effects and efficacy has decreased due to the emergence of resistant strains. The outlook is worsened by the absence of promising drug targets for this disease. We have taken a computationa...

journal_title：BMC bioinformatics

authors： Flórez AF,Park D,Bhak J,Kim BC,Kuchinsky A,Morris JH,Espinosa J,Muskus C

更新日期：2010-09-27 00:00:00

abstract：BACKGROUND:Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various existing methods measure similarity between two profiles and, hence, the likelihood that the two prote...

journal_title：BMC bioinformatics

authors： Cokus S,Mizutani S,Pellegrini M

更新日期：2007-05-22 00:00:00

abstract：BACKGROUND:Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial speci...

journal_title：BMC bioinformatics

authors： Seitzer P,Huynh TA,Facciotti MT

更新日期：2013-01-16 00:00:00

abstract：BACKGROUND:When constructing new biomarker or gene signature scores for time-to-event outcomes, the underlying aims are to develop a discrimination model that helps to predict whether patients have a poor or good prognosis and to identify the most influential variables for this task. In practice, this is often done fit...

journal_title：BMC bioinformatics

authors： Mayr A,Hofner B,Schmid M

更新日期：2016-07-22 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

authors： Kang JB,Siranosian BA,Moss EL,Banaei N,Andermann TM,Bhatt AS

更新日期：2019-12-02 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:Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have been developed for predicting aggregation propensity and identifying aggregation-prone regions in pro...

journal_title：BMC bioinformatics

authors： Fang Y,Gao S,Tai D,Middaugh CR,Fang J

更新日期：2013-10-28 00:00:00

abstract：BACKGROUND:Two important challenges in the analysis of molecular biology information are data (multi-omic information) integration and the detection of patterns across large scale molecular networks and sequences. They are are actually coupled beause the integration of omic information may provide better means to detec...

journal_title：BMC bioinformatics

authors： Bardozzo F,Lió P,Tagliaferri R

更新日期：2018-07-09 00:00:00

abstract：BACKGROUND:Phosphorylated histone H2AX, also known as γH2AX, forms μm-sized nuclear foci at the sites of DNA double-strand breaks (DSBs) induced by ionizing radiation and other agents. Due to their specificity and sensitivity, γH2AX immunoassays have become the gold standard for studying DSB induction and repair. One o...

journal_title：BMC bioinformatics

authors： Memmel S,Sisario D,Zimmermann H,Sauer M,Sukhorukov VL,Djuzenova CS,Flentje M

更新日期：2020-01-28 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:Polychromatic flow cytometry is a popular technique that has wide usage in the medical sciences, especially for studying phenotypic properties of cells. The high-dimensionality of data generated by flow cytometry usually makes it difficult to visualize. The naive solution of simply plotting two-dimensional g...

journal_title：BMC bioinformatics

authors： Raj S,Hussain F,Husein Z,Torosdagli N,Turgut D,Deo N,Pattanaik S,Chang CJ,Jha SK

更新日期：2017-06-07 00:00:00

abstract：BACKGROUND:Different human responses to the same vaccine were frequently observed. For example, independent studies identified overlapping but different transcriptomic gene expression profiles in Yellow Fever vaccine 17D (YF-17D) immunized human subjects. Different experimental and analysis conditions were likely contr...

journal_title：BMC bioinformatics

authors： Ong E,Sun P,Berke K,Zheng J,Wu G,He Y

更新日期：2019-12-23 00:00:00

abstract：BACKGROUND:With the advent of high-throughput proteomic experiments such as arrays of purified proteins comes the need to analyse sets of proteins as an ensemble, as opposed to the traditional one-protein-at-a-time approach. Although there are several publicly available tools that facilitate the analysis of protein set...

journal_title：BMC bioinformatics

authors： Wolting C,McGlade CJ,Tritchler D

更新日期：2006-07-12 00:00:00

abstract：BACKGROUND:Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn. For example, a range of traditional s...

journal_title：BMC bioinformatics

authors： Ibrahim M,Jassim S,Cawthorne MA,Langlands K

更新日期：2014-11-04 00:00:00

abstract：BACKGROUND:In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein-small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (MC) and REMC sampling methods, these methods use multi-objective optimization Pareto front informatio...

journal_title：BMC bioinformatics

authors： Wang H,Liu H,Cai L,Wang C,Lv Q

更新日期：2017-07-10 00:00:00

abstract：BACKGROUND:Biochemically detailed stoichiometric matrices have now been reconstructed for various bacteria, yeast, and for the human cardiac mitochondrion based on genomic and proteomic data. These networks have been manually curated based on legacy data and elementally and charge balanced. Comparative analysis of thes...

journal_title：BMC bioinformatics

authors： Becker SA,Price ND,Palsson BØ

更新日期：2006-03-06 00:00:00

abstract：BACKGROUND:The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-rea...

journal_title：BMC bioinformatics

authors： Donaldson I,Martin J,de Bruijn B,Wolting C,Lay V,Tuekam B,Zhang S,Baskin B,Bader GD,Michalickova K,Pawson T,Hogue CW

更新日期：2003-03-27 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:The improvements in genomics methods coupled with readily accessible high-throughput sequencing have contributed to our understanding of microbial species, metagenomes, infectious diseases and more. To maximize the impact of these genomics studies, it is important that data from biological samples will becom...

journal_title：BMC bioinformatics

authors： Quiñones M,Liou DT,Shyu C,Kim W,Vujkovic-Cvijin I,Belkaid Y,Hurt DE

更新日期：2020-09-03 00:00:00

abstract：BACKGROUND:REX1 and REX2 are protein components of the RNA editing complex (the editosome) and function as exouridylylases. The exact roles of REX1 and REX2 in the editosome are unclear and the consequences of the presence of two related proteins are not fully understood. Here, a variety of computational studies were p...

journal_title：BMC bioinformatics

authors： Mian IS,Worthey EA,Salavati R

更新日期：2006-06-16 00:00:00

abstract：BACKGROUND:Transposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting all aspects of genome function. With the dramatic reduction in cost of DNA sequencing, it is now poss...

journal_title：BMC bioinformatics

authors： Gilly A,Etcheverry M,Madoui MA,Guy J,Quadrana L,Alberti A,Martin A,Heitkam T,Engelen S,Labadie K,Le Pen J,Wincker P,Colot V,Aury JM

更新日期：2014-11-19 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

authors： Gu J,Fu H,Zhang X,Li Y

更新日期：2007-11-08 00:00:00

abstract：BACKGROUND:Many centrality measures have been proposed to mine and characterize the correlations between network topological properties and protein essentiality. However, most of them show limited prediction accuracy, and the number of common predicted essential proteins by different methods is very small. RESULTS:In ...

journal_title：BMC bioinformatics

authors： Zhang X,Xiao W,Acencio ML,Lemke N,Wang X

更新日期：2016-08-25 00:00:00

abstract：BACKGROUND:Activities of drug molecules can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle by employing the traditional experimental method. With the fact that the number of drug molecules with positive activity is rather fewer t...

journal_title：BMC bioinformatics

authors： Li GZ,Meng HH,Lu WC,Yang JY,Yang MQ

更新日期：2008-05-28 00:00:00

abstract：BACKGROUND:The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another using the substitution, insertion, deletion and transposition operations. Lowrance and Wagner have ...

journal_title：BMC bioinformatics

authors： Zhao C,Sahni S

更新日期：2020-12-09 00:00:00

abstract：BACKGROUND:Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and m...

journal_title：BMC bioinformatics

authors： Rios D,McLaren WM,Chen Y,Birney E,Stabenau A,Flicek P,Cunningham F

更新日期：2010-05-11 00:00:00