MPAgenomics: an R package for multi-patient analysis of genomic markers.

abstract：BACKGROUND:Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ranking of docked poses using a scoring function, for which many methods have been developed. There is ...

journal_title：BMC bioinformatics

authors： Moal IH,Torchala M,Bates PA,Fernández-Recio J

更新日期：2013-10-01 00:00:00

abstract：BACKGROUND:For the development of genome assembly tools, some comprehensive and efficiently computable validation measures are required to assess the quality of the assembly. The mostly used N50 measure summarizes the assembly results by the length of the scaffold (or contig) overlapping the midpoint of the length-orde...

journal_title：BMC bioinformatics

authors： Mäkinen V,Salmela L,Ylinen J

更新日期：2012-10-03 00:00:00

abstract：BACKGROUND:To identify and prioritize the influential hub genes in a gene-set or biological pathway, most analyses rely on calculation of marginal effects or tests of statistical significance. These procedures may be inappropriate since hub nodes are common connection points and therefore may interact with other nodes ...

journal_title：BMC bioinformatics

authors： Chang HC,Chu CP,Lin SJ,Hsiao CK

更新日期：2020-03-12 00:00:00

abstract：BACKGROUND:Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. RESULTS:PubFocus w...

journal_title：BMC bioinformatics

authors： Plikus MV,Zhang Z,Chuong CM

更新日期：2006-10-02 00:00:00

abstract：BACKGROUND:Genes occurring co-localized in multiple genomes can be strong indicators for either functional constraints on the genome organization or remnant ancestral gene order. The computational detection of these patterns, which are usually referred to as gene clusters, has become increasingly sensitive over the pas...

journal_title：BMC bioinformatics

authors： Jahn K,Winter S,Stoye J,Böcker S

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further proc...

journal_title：BMC bioinformatics

authors： Choo KH,Tan TW,Ranganathan S

更新日期：2005-10-13 00:00:00

abstract：BACKGROUND:Differences in cell-type composition across subjects and conditions often carry biological significance. Recent advancements in single cell sequencing technologies enable cell-types to be identified at the single cell level, and as a result, cell-type composition of tissues can now be studied in exquisite de...

journal_title：BMC bioinformatics

authors： Cao Y,Lin Y,Ormerod JT,Yang P,Yang JYH,Lo KK

更新日期：2019-12-24 00:00:00

abstract：BACKGROUND:Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discreti...

journal_title：BMC bioinformatics

authors： Li Y,Liu L,Bai X,Cai H,Ji W,Guo D,Zhu Y

更新日期：2010-10-19 00:00:00

abstract：BACKGROUND:For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significant...

journal_title：BMC bioinformatics

authors： Lee M,Jeong CS,Kim D

更新日期：2007-12-03 00:00:00

abstract：BACKGROUND:Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in prote...

journal_title：BMC bioinformatics

authors： Shlomi T,Segal D,Ruppin E,Sharan R

更新日期：2006-04-10 00:00:00

abstract：BACKGROUND:It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enou...

journal_title：BMC bioinformatics

authors： Meyer F,Kurtz S,Beckstette M

更新日期：2013-07-17 00:00:00

abstract：BACKGROUND:We present a model for tagging gene and protein mentions from text using the probabilistic sequence tagging framework of conditional random fields (CRFs). Conditional random fields model the probability P(t/o) of a tag sequence given an observation sequence directly, and have previously been employed success...

journal_title：BMC bioinformatics

authors： McDonald R,Pereira F

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Genome-wide transcriptional profiling of patient blood samples offers a powerful tool to investigate underlying disease mechanisms and personalized treatment decisions. Most studies are based on analysis of total peripheral blood mononuclear cells (PBMCs), a mixed population. In this case, accuracy is inhere...

journal_title：BMC bioinformatics

authors： Bolen CR,Uduman M,Kleinstein SH

更新日期：2011-06-24 00:00:00

abstract：BACKGROUND:Quantitative polymerase chain reaction (qPCR) is the technique of choice for quantifying gene expression. While the technique itself is well established, approaches for the analysis of qPCR data continue to improve. RESULTS:Here we expand on the common base method to develop procedures for testing linear re...

journal_title：BMC bioinformatics

authors： Ganger MT,Dietz GD,Headley P,Ewing SJ

更新日期：2020-09-29 00:00:00

abstract：BACKGROUND:In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniq...

journal_title：BMC bioinformatics

authors： Bhattacharya S,Bhattacharyya C,Chandra NR

更新日期：2006-12-18 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:Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoin...

journal_title：BMC bioinformatics

authors： Pluskal T,Castillo S,Villar-Briones A,Oresic M

更新日期：2010-07-23 00:00:00

abstract：BACKGROUND:Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene regulatory, and metabolic pathways. Among these, metabolic networks are probably the most studied, as t...

journal_title：BMC bioinformatics

authors： Manipur I,Granata I,Maddalena L,Guarracino MR

更新日期：2020-08-21 00:00:00

abstract：BACKGROUND:Membrane transport proteins (transporters) play an essential role in every living cell by transporting hydrophilic molecules across the hydrophobic membranes. While the sequences of many membrane proteins are known, their structure and function is still not well characterized and understood, owing to the imm...

journal_title：BMC bioinformatics

authors： Alballa M,Butler G

更新日期：2020-04-23 00:00:00

abstract：BACKGROUND:Improvements in technology have been accompanied by the generation of large amounts of complex data. This same technology must be harnessed effectively if the knowledge stored within the data is to be retrieved. Storing data in ontologies aids its management; ontologies serve as controlled vocabularies that ...

journal_title：BMC bioinformatics

authors： Dadzie AS,Burger A

更新日期：2005-03-24 00:00:00

abstract：BACKGROUND:The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the simila...

journal_title：BMC bioinformatics

authors： Zhang M,Yang L,Ren J,Ahlgren NA,Fuhrman JA,Sun F

更新日期：2017-03-14 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:Microarray experiments, as well as other genomic analyses, often result in large gene sets containing up to several hundred genes. The biological significance of such sets of genes is, usually, not readily apparent. Identification of the functions of the genes in the set can help highlight features of intere...

journal_title：BMC bioinformatics

authors： Lee JS,Katari G,Sachidanandam R

更新日期：2005-07-25 00:00:00

abstract：BACKGROUND:Metabolome analysis with GC/MS has meanwhile been established as one of the "omics" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other rele...

journal_title：BMC bioinformatics

authors： Thielen B,Heinen S,Schomburg D

更新日期：2009-07-22 00:00:00

abstract：BACKGROUND:Conservation and variation scores are used when evaluating sites in a multiple sequence alignment, in order to identify residues critical for structure or function. A variety of scores are available today but it is not clear how different scores relate to each other. RESULTS:We applied 25 conservation and v...

journal_title：BMC bioinformatics

authors： Johansson F,Toh H

更新日期：2010-07-21 00:00:00

abstract：BACKGROUND:Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and a...

journal_title：BMC bioinformatics

authors： Signorelli M,Vinciotti V,Wit EC

更新日期：2016-09-05 00:00:00

abstract：BACKGROUND:Scaffolding is an important step in genome assembly that orders and orients the contigs produced by assemblers. However, repetitive regions in contigs usually prevent scaffolding from producing accurate results. How to solve the problem of repetitive regions has received a great deal of attention. In the pas...

journal_title：BMC bioinformatics

authors： Luo J,Lyu M,Chen R,Zhang X,Luo H,Yan C

更新日期：2019-10-30 00:00:00

abstract：BACKGROUND:Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary...

journal_title：BMC bioinformatics

authors： Solares EA,Tao Y,Long AD,Gaut BS

更新日期：2021-01-06 00:00:00

abstract：BACKGROUND:Identification of the recombination hot/cold spots is critical for understanding the mechanism of recombination as well as the genome evolution process. However, experimental identification of recombination spots is both time-consuming and costly. Developing an accurate and automated method for reliably and ...

journal_title：BMC bioinformatics

authors： Li L,Yu S,Xiao W,Li Y,Huang L,Zheng X,Zhou S,Yang H

更新日期：2014-11-20 00:00:00

abstract：BACKGROUND:Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematica...

journal_title：BMC bioinformatics

authors： Chain B,Bowen H,Hammond J,Posch W,Rasaiyaah J,Tsang J,Noursadeghi M

更新日期：2010-06-24 00:00:00