Reordering based integrative expression profiling for microarray classification.

abstract：BACKGROUND:Understanding the relationship between the protein sequence and the 3D structure is a major research area in bioinformatics. The prediction of complete protein tertiary structure based only on sequence information is still an impractical work. This paper aims at revealing the hidden knowledge of the sequence...

journal_title：BMC bioinformatics

authors： Chen B,Johnson M

更新日期：2009-10-08 00:00:00

abstract：BACKGROUND:DNA methylation of CpG dinucleotides is an essential epigenetic modification that plays a key role in transcription. Widely used DNA enrichment-based methods offer high coverage for measuring methylated CpG dinucleotides, with the lowest cost per CpG covered genome-wide. However, these methods measure the DN...

journal_title：BMC bioinformatics

authors： Xu J,Liu S,Yin P,Bulun S,Dai Y

更新日期：2018-12-22 00:00:00

abstract：BACKGROUND:Somatic copy number alternation (SCNA) is a common feature of the cancer genome and is associated with cancer etiology and prognosis. The allele-specific SCNA analysis of a tumor sample aims to identify the allele-specific copy numbers of both alleles, adjusting for the ploidy and the tumor purity. Next gene...

journal_title：BMC bioinformatics

authors： Choo-Wosoba H,Albert PS,Zhu B

更新日期：2018-11-14 00:00:00

abstract：BACKGROUND:Identification of causal SNPs in most genome wide association studies relies on approaches that consider each SNP individually. However, there is a strong correlation structure among SNPs that needs to be taken into account. Hence, increasingly modern computationally expensive regression methods are employed...

journal_title：BMC bioinformatics

authors： Zuber V,Duarte Silva AP,Strimmer K

更新日期：2012-10-31 00:00:00

abstract：BACKGROUND:SNP genotyping microarrays have revolutionized the study of complex disease. The current range of commercially available genotyping products contain extensive catalogues of low frequency and rare variants. Existing SNP calling algorithms have difficulty dealing with these low frequency variants, as the under...

journal_title：BMC bioinformatics

authors： Liu R,Dai Z,Yeager M,Irizarry RA,Ritchie ME

更新日期：2014-05-23 00:00:00

abstract：BACKGROUND:Copy number variants (CNVs) have been demonstrated to occur at a high frequency and are now widely believed to make a significant contribution to the phenotypic variation in human populations. Array-based comparative genomic hybridization (array-CGH) and newly developed read-depth approach through ultrahigh ...

journal_title：BMC bioinformatics

authors： Zhang ZD,Gerstein MB

更新日期：2010-10-31 00:00:00

abstract：:Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H)...

journal_title：BMC bioinformatics

authors： Mirhaji P,Zhu M,Vagnoni M,Bernstam EV,Zhang J,Smith JW

更新日期：2009-02-05 00:00:00

abstract：BACKGROUND:Antibacterial peptides are one of the effecter molecules of innate immune system. Over the last few decades several antibacterial peptides have successfully approved as drug by FDA, which has prompted an interest in these antibacterial peptides. In our recent study we analyzed 999 antibacterial peptides, whi...

journal_title：BMC bioinformatics

authors： Lata S,Mishra NK,Raghava GP

更新日期：2010-01-18 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:New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS:We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifica...

journal_title：BMC bioinformatics

authors： Hofmeister BT,Schmitz RJ

更新日期：2018-04-25 00:00:00

abstract：BACKGROUND:The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is d...

journal_title：BMC bioinformatics

authors： Wang L,Stein LD

更新日期：2010-11-08 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: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：:The RNA polymerase NS5B of Hepatitis C virus (HCV) is a well-characterised drug target with an active site and four allosteric binding sites. This work presents a workflow for virtual screening and its application to Drug Bank screening targeting the Hepatitis C Virus (HCV) RNA polymerase non-nucleoside binding sites....

journal_title：BMC bioinformatics

authors： Elhefnawi M,ElGamacy M,Fares M

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compound...

journal_title：BMC bioinformatics

authors： Le Guilloux V,Schmidtke P,Tuffery P

更新日期：2009-06-02 00:00:00

abstract：BACKGROUND:Abruptness of pigment patterns at the periphery of a skin lesion is one of the most important dermoscopic features for detection of malignancy. In current clinical setting, abrupt cutoff of a skin lesion determined by an examination of a dermatologist. This process is subjective, nonquantitative, and error-p...

journal_title：BMC bioinformatics

authors： Erol R,Bayraktar M,Kockara S,Kaya S,Halic T

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:In binary high-throughput screening projects where the goal is the identification of low-frequency events, beyond the obvious issue of efficiency, false positives and false negatives are a major concern. Pooling constitutes a natural solution: it reduces the number of tests, while providing critical duplicat...

journal_title：BMC bioinformatics

authors： Thierry-Mieg N

更新日期：2006-01-19 00:00:00

abstract：BACKGROUND:Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On...

journal_title：BMC bioinformatics

authors： Yuan Y,Li CT,Wilson R

更新日期：2008-06-18 00:00:00

abstract：BACKGROUND:Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathol...

journal_title：BMC bioinformatics

authors： Corradi L,Mirisola V,Porro I,Torterolo L,Fato M,Romano P,Pfeffer U

更新日期：2009-10-15 00:00:00

abstract：BACKGROUND:Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain datab...

journal_title：BMC bioinformatics

authors： Truong K,Ikura M

更新日期：2003-05-06 00:00:00

abstract：BACKGROUND:The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, in The Cancer Genome Atlas, collects protein expressions in human cancers and it is a reference reso...

journal_title：BMC bioinformatics

authors： Sardina DS,Micale G,Ferro A,Pulvirenti A,Giugno R

更新日期：2018-07-09 00:00:00

abstract：BACKGROUND:Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions. RESULTS:Here, we weighted edges of a human protein interaction network and a transcriptional r...

journal_title：BMC bioinformatics

authors： Chen L,Wang H,Zhang L,Li W,Wang Q,Shang Y,He Y,He W,Li X,Tai J,Li X

更新日期：2010-07-22 00:00:00

abstract：BACKGROUND:Parametric feature selection methods for machine learning and association studies based on genetic data are not robust with respect to outliers or influential observations. While rank-based, distribution-free statistics offer a robust alternative to parametric methods, their practical utility can be limited,...

journal_title：BMC bioinformatics

authors： Lin J,Sibley A,Shterev I,Nixon A,Innocenti F,Chan C,Owzar K

更新日期：2019-06-13 00:00:00

abstract：BACKGROUND:Compound Heterozygosity (CH) in classical genetics is the presence of two different recessive mutations at a particular gene locus. A relaxed form of CH alleles may account for an essential proportion of the missing heritability, i.e. heritability of phenotypes so far not accounted for by single genetic vari...

journal_title：BMC bioinformatics

authors： Zhong K,Karssen LC,Kayser M,Liu F

更新日期：2016-04-08 00:00:00

abstract：BACKGROUND:The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently ...

journal_title：BMC bioinformatics

authors： Shaw GT,Pao YY,Wang D

更新日期：2016-11-25 00:00:00

abstract：BACKGROUND:The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB), thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been develo...

journal_title：BMC bioinformatics

authors： Li GH,Huang JF

更新日期：2010-08-27 00:00:00

abstract：BACKGROUND:Designing small-molecule kinase inhibitors with desirable selectivity profiles is a major challenge in drug discovery. A high-throughput screen for inhibitors of a given kinase will typically yield many compounds that inhibit more than one kinase. A series of chemical modifications are usually required befor...

journal_title：BMC bioinformatics

authors： Caffrey DR,Lunney EA,Moshinsky DJ

更新日期：2008-11-25 00:00:00

abstract：BACKGROUND AND GOAL:The Random Forest (RF) algorithm for regression and classification has considerably gained popularity since its introduction in 2001. Meanwhile, it has grown to a standard classification approach competing with logistic regression in many innovation-friendly scientific fields. RESULTS:In this conte...

journal_title：BMC bioinformatics

authors： Couronné R,Probst P,Boulesteix AL

更新日期：2018-07-17 00:00:00

abstract：BACKGROUND:Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. RESULTS:Based on a homogeneity assumptio...

journal_title：BMC bioinformatics

authors： Hu GQ,Zheng X,Ju LN,Zhu H,She ZS

更新日期：2008-03-25 00:00:00

abstract：BACKGROUND:Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of seque...

journal_title：BMC bioinformatics

authors： Smith RP,Buchser WJ,Lemmon MB,Pardinas JR,Bixby JL,Lemmon VP

更新日期：2008-04-10 00:00:00