pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties.

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:Inferring gene regulatory network (GRN) has been an important topic in Bioinformatics. Many computational methods infer the GRN from high-throughput expression data. Due to the presence of time delays in the regulatory relationships, High-Order Dynamic Bayesian Network (HO-DBN) is a good model of GRN. Howeve...

journal_title：BMC bioinformatics

authors： Lo LY,Wong ML,Lee KH,Leung KS

更新日期：2015-11-25 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:Many models have been proposed to detect copy number alterations in chromosomal copy number profiles, but it is usually not obvious to decide which is most effective for a given data set. Furthermore, most methods have a smoothing parameter that determines the number of breakpoints and must be chosen using v...

journal_title：BMC bioinformatics

authors： Hocking TD,Schleiermacher G,Janoueix-Lerosey I,Boeva V,Cappo J,Delattre O,Bach F,Vert JP

更新日期：2013-05-22 00:00:00

abstract：BACKGROUND:Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast-evolving sequences in a gene-specific manner, identifies subsets of sequences that evolve at a r...

journal_title：BMC bioinformatics

authors： Rivera-Rivera CJ,Montoya-Burgos JI

更新日期：2019-08-13 00:00:00

abstract：BACKGROUND:In protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intu...

journal_title：BMC bioinformatics

authors： Khan T,Panday SK,Ghosh I

更新日期：2018-05-04 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

abstract：BACKGROUND:Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic seq...

journal_title：BMC bioinformatics

authors： Zamani N,Sundström G,Meadows JR,Höppner MP,Dainat J,Lantz H,Haas BJ,Grabherr MG

更新日期：2014-06-30 00:00:00

abstract：BACKGROUND:Great strides have been made in the effective treatment of HIV-1 with the development of second-generation protease inhibitors (PIs) that are effective against historically multi-PI-resistant HIV-1 variants. Nevertheless, mutation patterns that confer decreasing susceptibility to available PIs continue to ar...

journal_title：BMC bioinformatics

authors： Doherty KM,Nakka P,King BM,Rhee SY,Holmes SP,Shafer RW,Radhakrishnan ML

更新日期：2011-12-15 00:00:00

abstract：BACKGROUND:One of the main goals in cancer studies including high-throughput microRNA (miRNA) and mRNA data is to find and assess prognostic signatures capable of predicting clinical outcome. Both mRNA and miRNA expression changes in cancer diseases are described to reflect clinical characteristics like staging and pro...

journal_title：BMC bioinformatics

authors： Gade S,Porzelius C,Fälth M,Brase JC,Wuttig D,Kuner R,Binder H,Sültmann H,Beissbarth T

更新日期：2011-12-21 00:00:00

abstract：BACKGROUND:The detection of bias due to cryptic population structure is an important step in the evaluation of findings of genetic association studies. The standard method of measuring this bias in a genetic association study is to compare the observed median association test statistic to the expected median test stati...

journal_title：BMC bioinformatics

authors： Pirie A,Wood A,Lush M,Tyrer J,Pharoah PD

更新日期：2015-02-20 00:00:00

abstract：BACKGROUND:Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many...

journal_title：BMC bioinformatics

authors： Vainshtein Y,Sanchez M,Brazma A,Hentze MW,Dandekar T,Muckenthaler MU

更新日期：2010-03-01 00:00:00

abstract：BACKGROUND:Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging vari...

journal_title：BMC bioinformatics

authors： Masino AJ,Dechene ET,Dulik MC,Wilkens A,Spinner NB,Krantz ID,Pennington JW,Robinson PN,White PS

更新日期：2014-07-21 00:00:00

abstract：BACKGROUND:It is a common practice in bioinformatics to validate each group returned by a clustering algorithm through manual analysis, according to a-priori biological knowledge. This procedure helps finding functionally related patterns to propose hypotheses for their behavior and the biological processes involved. T...

journal_title：BMC bioinformatics

authors： Milone DH,Stegmayer G,López M,Kamenetzky L,Carrari F

更新日期：2014-04-10 00:00:00

abstract：BACKGROUND:Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects graphically in an intuitively understandable way. RESULTS:We present a visualization method that incorporates both emission and transi...

journal_title：BMC bioinformatics

authors： Schuster-Böckler B,Schultz J,Rahmann S

更新日期：2004-01-21 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:Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics), the study of small molecules involved in metabolic reactions, is a rapidly expanding 'omics' field. A major technique for capturing metabolite data is 1H-NMR spectroscopy and this yields ...

journal_title：BMC bioinformatics

authors： Muncey HJ,Jones R,De Iorio M,Ebbels TM

更新日期：2010-10-06 00:00:00

abstract：BACKGROUND:The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologist...

journal_title：BMC bioinformatics

authors： Yin Z,Zhou X,Bakal C,Li F,Sun Y,Perrimon N,Wong ST

更新日期：2008-06-05 00:00:00

abstract：BACKGROUND:Infections are often associated to comorbidity that increases the risk of medical conditions which can lead to further morbidity and mortality. SARS is a threat which is similar to MERS virus, but the comorbidity is the key aspect to underline their different impacts. One UK doctor says "I'd rather have HIV ...

journal_title：BMC bioinformatics

authors： Moni MA,Liò P

更新日期：2014-10-24 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: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:Many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. Independent studies exist on the analysis and sequence-based prediction of some of these so-called one-dimensional features. However, there is little expla...

journal_title：BMC bioinformatics

authors： Ahmad S,Singh YH,Paudel Y,Mori T,Sugita Y,Mizuguchi K

更新日期：2010-10-27 00:00:00

abstract：BACKGROUND:An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA binding preferences, it is a challenging problem to establish an accurate model for recognition of fun...

journal_title：BMC bioinformatics

authors： Stepanova M,Lin F,Lin VC

更新日期：2006-12-12 00:00:00

abstract：BACKGROUND:The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is req...

journal_title：BMC bioinformatics

authors： Nazarov VI,Pogorelyy MV,Komech EA,Zvyagin IV,Bolotin DA,Shugay M,Chudakov DM,Lebedev YB,Mamedov IZ

更新日期：2015-05-28 00:00:00

abstract：BACKGROUND:High-throughput sequencing has rapidly become an essential part of precision cancer medicine. But validating results obtained from analyzing and interpreting genomic data remains a rate-limiting factor. The gold standard, of course, remains manual validation by expert panels, which is not without its weaknes...

journal_title：BMC bioinformatics

authors： Bian X,Zhu B,Wang M,Hu Y,Chen Q,Nguyen C,Hicks B,Meerzaman D

更新日期：2018-11-19 00:00:00

abstract：BACKGROUND:We introduce the decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI). ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the Universal Simila...

journal_title：BMC bioinformatics

authors： Barthel D,Hirst JD,Błazewicz J,Burke EK,Krasnogor N

更新日期：2007-10-26 00:00:00

abstract：BACKGROUND:The cost efficient two-stage design is often used in genome-wide association studies (GWASs) in searching for genetic loci underlying the susceptibility for complex diseases. Replication-based analysis, which considers data from each stage separately, often suffers from loss of efficiency. Joint test that co...

journal_title：BMC bioinformatics

authors： Pan D,Li Q,Jiang N,Liu A,Yu K

更新日期：2011-01-07 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: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:DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it rema...

journal_title：BMC bioinformatics

authors： Bulla I,Aliaga B,Lacal V,Bulla J,Grunau C,Chaparro C

更新日期：2018-03-27 00:00:00