Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins.

abstract：BACKGROUND:Prognosis is of critical interest in breast cancer research. Biomedical studies suggest that genomic measurements may have independent predictive power for prognosis. Gene profiling studies have been conducted to search for predictive genomic measurements. Genes have the inherent pathway structure, where pat...

journal_title：BMC bioinformatics

authors： Ma S,Kosorok MR

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:InterPro is a collection of protein signatures for the classification and automated annotation of proteins. Interproscan is a software tool that scans protein sequences against Interpro member databases using a variety of profile-based, hidden markov model and positional specific score matrix methods. It not...

journal_title：BMC bioinformatics

authors： Kelly RJ,Vincent DE,Friedberg I

更新日期：2010-12-21 00:00:00

abstract：BACKGROUND:The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software t...

journal_title：BMC bioinformatics

authors： Xi L,Fondufe-Mittendorf Y,Xia L,Flatow J,Widom J,Wang JP

更新日期：2010-06-24 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: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:Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, t...

journal_title：BMC bioinformatics

authors： Ranjbar MR,Di Poto C,Wang Y,Ressom HW

更新日期：2015-08-19 00:00:00

abstract：BACKGROUND:The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in identifying putative biomarkers of disease from high-dimensional proteomic mass spectral data. In pa...

journal_title：BMC bioinformatics

authors： Lustgarten JL,Visweswaran S,Bowser RP,Hogan WR,Gopalakrishnan V

更新日期：2009-09-17 00:00:00

abstract：BACKGROUND:Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to ...

journal_title：BMC bioinformatics

authors： Lindsay J,Salooti H,Măndoiu I,Zelikovsky A

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Prioritizing genes according to their associations with a cancer allows researchers to explore genes in more informed ways. By far, Gene-centric or network-centric gene prioritization methods are predominated. Genes and their protein products carry out cellular processes in the context of functional modules....

journal_title：BMC bioinformatics

authors： Su L,Liu G,Bai T,Meng X,Ma Q

更新日期：2018-06-05 00:00:00

abstract：:Selected reaction monitoring (SRM)-based proteomics approaches enable highly sensitive and reproducible assays for profiling of thousands of peptides in one experiment. The development of such assays involves the determination of retention time, detectability and fragmentation properties of peptides, followed by an op...

journal_title：BMC bioinformatics

authors： Nahnsen S,Kohlbacher O

更新日期：2012-01-01 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:One of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models. Because profiles are built from sequence alignments, the sequences included in the alignment and the method used to align them will be important to th...

journal_title：BMC bioinformatics

authors： Scheeff ED,Bourne PE

更新日期：2006-09-14 00:00:00

abstract：BACKGROUND:Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to uncover their functions. RESULTS:We present a computational pipeline for detecting novel lncRNAs fro...

journal_title：BMC bioinformatics

authors： Sun L,Zhang Z,Bailey TL,Perkins AC,Tallack MR,Xu Z,Liu H

更新日期：2012-12-13 00:00:00

abstract：BACKGROUND:With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceabilit...

journal_title：BMC bioinformatics

authors： Thallinger GG,Baumgartner K,Pirklbauer M,Uray M,Pauritsch E,Mehes G,Buck CR,Zatloukal K,Trajanoski Z

更新日期：2007-03-07 00:00:00

abstract：BACKGROUND:Routine application of gene expression microarray technology is rapidly producing large amounts of data that necessitate new approaches of analysis. The analysis of a specific microarray experiment profits enormously from cross-comparing to other experiments. This process is generally performed by numerical ...

journal_title：BMC bioinformatics

authors： Finocchiaro G,Mancuso F,Muller H

更新日期：2005-12-01 00:00:00

abstract：BACKGROUND:Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carboh...

journal_title：BMC bioinformatics

authors： Ranzinger R,Herget S,Wetter T,von der Lieth CW

更新日期：2008-09-19 00:00:00

abstract：BACKGROUND:Schizophrenia, bipolar disorder, and major depression are devastating mental diseases, each with distinctive yet overlapping epidemiologic characteristics. Microarray and proteomics data have revealed genes which expressed abnormally in patients. Several single nucleotide polymorphisms (SNPs) and mutations a...

journal_title：BMC bioinformatics

authors： Lee SA,Tsao TT,Yang KC,Lin H,Kuo YL,Hsu CH,Lee WK,Huang KC,Kao CY

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Antibacterial peptides are important components of the innate immune system, used by the host to protect itself from different types of pathogenic bacteria. Over the last few decades, the search for new drugs and drug targets has prompted an interest in these antibacterial peptides. We analyzed 486 antibacte...

journal_title：BMC bioinformatics

authors： Lata S,Sharma BK,Raghava GP

更新日期：2007-07-23 00:00:00

abstract：BACKGROUND:As whole-genome sequencing is becoming a routine technique, it is important to identify a cost-effective depth of sequencing for such studies. However, the relationship between sequencing depth and biological results from the aspects of whole-genome coverage, variant discovery power and the quality of varian...

journal_title：BMC bioinformatics

authors： Jiang Y,Jiang Y,Wang S,Zhang Q,Ding X

更新日期：2019-11-08 00:00:00

abstract：BACKGROUND:Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effective prevention and control measures for blood pressure diseases. Traditional blood pressure measure...

journal_title：BMC bioinformatics

authors： Zhang B,Ren H,Huang G,Cheng Y,Hu C

更新日期：2019-02-28 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:Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between proteins from the same species (related to protein function, expression or subcellular localization, fo...

journal_title：BMC bioinformatics

authors： Pasamontes A,Garcia-Vallve S

更新日期：2006-05-18 00:00:00

abstract：BACKGROUND:Several studies demonstrated the feasibility of predicting bacterial antibiotic resistance phenotypes from whole-genome sequences, the prediction process usually amounting to detecting the presence of genes involved in antibiotic resistance mechanisms, or of specific mutations, previously identified from a t...

journal_title：BMC bioinformatics

authors： Mahé P,Tournoud M

更新日期：2018-10-17 00:00:00

abstract：BACKGROUND:Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entiti...

journal_title：BMC bioinformatics

authors： Henriques R,Ferreira FL,Madeira SC

更新日期：2017-02-02 00:00:00

abstract：BACKGROUNDS:Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to the data platforms. However, rapid progress of the NGS applications and processing methods urgentl...

journal_title：BMC bioinformatics

authors： Joo T,Choi JH,Lee JH,Park SE,Jeon Y,Jung SH,Woo HG

更新日期：2019-02-20 00:00:00

abstract：BACKGROUND:Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactio...

journal_title：BMC bioinformatics

authors： Oda K,Kim JD,Ohta T,Okanohara D,Matsuzaki T,Tateisi Y,Tsujii J

更新日期：2008-04-11 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:Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever ...

journal_title：BMC bioinformatics

authors： Sturm M,Bertsch A,Gröpl C,Hildebrandt A,Hussong R,Lange E,Pfeifer N,Schulz-Trieglaff O,Zerck A,Reinert K,Kohlbacher O

更新日期：2008-03-26 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:In the last decade, there have been many applications of formal language theory in bioinformatics such as RNA structure prediction and detection of patterns in DNA. However, in the field of proteomics, the size of the protein alphabet and the complexity of relationship between amino acids have mainly limited...

journal_title：BMC bioinformatics

authors： Dyrka W,Nebel JC

更新日期：2009-10-08 00:00:00