Considering scores between unrelated proteins in the search database improves profile comparison.

abstract：BACKGROUND:One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metabolic phenotype which typically means having a high yield/productivity. This challenge is not only du...

journal_title：BMC bioinformatics

authors： Rocha M,Maia P,Mendes R,Pinto JP,Ferreira EC,Nielsen J,Patil KR,Rocha I

更新日期：2008-11-27 00:00:00

abstract：BACKGROUND:Hierarchical Multi-Label Classification is a classification task where the classes to be predicted are hierarchically organized. Each instance can be assigned to classes belonging to more than one path in the hierarchy. This scenario is typically found in protein function prediction, considering that each pr...

journal_title：BMC bioinformatics

authors： Cerri R,Barros RC,P L F de Carvalho AC,Jin Y

更新日期：2016-09-15 00:00:00

abstract：BACKGROUND:Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint ...

journal_title：BMC bioinformatics

authors： Bozdag S,Close TJ,Lonardi S

更新日期：2009-07-15 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:The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research. We present a novel method called MergeAlign which constructs consensus MSAs fro...

journal_title：BMC bioinformatics

authors： Collingridge PW,Kelly S

更新日期：2012-05-30 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:To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides inf...

journal_title：BMC bioinformatics

authors： Oh SJ,Joung JG,Chang JH,Zhang BT

更新日期：2006-06-06 00:00:00

abstract：BACKGROUND:We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism ...

journal_title：BMC bioinformatics

authors： Nath N,Mitchell JB

更新日期：2012-04-24 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:New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bio...

journal_title：BMC bioinformatics

authors： Hajibabaei M,Singer GA

更新日期：2009-11-10 00:00:00

abstract：BACKGROUND:Traditional algorithms for hidden Markov model decoding seek to maximize either the probability of a state path or the number of positions of a sequence assigned to the correct state. These algorithms provide only a single answer and in practice do not produce good results. RESULTS:We explore an alternative...

journal_title：BMC bioinformatics

authors： Brown DG,Golod D

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes. Transcription factors control the expression of their downstream target genes by interacting ...

journal_title：BMC bioinformatics

authors： Wang K,Nishida H

更新日期：2015-04-10 00:00:00

abstract：BACKGROUND:Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data analysis, little attention has been paid to uncertainty in the results obtained. RESULTS:We present an R/Bioconductor port of a fast novel algorithm for...

journal_title：BMC bioinformatics

authors： Savage RS,Heller K,Xu Y,Ghahramani Z,Truman WM,Grant M,Denby KJ,Wild DL

更新日期：2009-08-06 00:00:00

abstract：BACKGROUND:We aim to solve the problem of determining word senses for ambiguous biomedical terms with minimal human effort. METHODS:We build a fully automated system for Word Sense Disambiguation by designing a system that does not require manually-constructed external resources or manually-labeled training examples e...

journal_title：BMC bioinformatics

authors： Duan W,Song M,Yates A

更新日期：2009-03-19 00:00:00

abstract：BACKGROUND:The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multi...

journal_title：BMC bioinformatics

authors： Tebel K,Boldt V,Steininger A,Port M,Ebert G,Ullmann R

更新日期：2017-01-06 00:00:00

abstract：BACKGROUND:Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidences to enhance the quality of predicted complexes. However, it is still a challenge to integrate diffe...

journal_title：BMC bioinformatics

authors： Xu B,Li K,Zheng W,Liu X,Zhang Y,Zhao Z,He Z

更新日期：2018-12-20 00:00:00

abstract：BACKGROUND:The goal of metabolomics analyses is a comprehensive and systematic understanding of all metabolites in biological samples. Many useful platforms have been developed to achieve this goal. Gas chromatography coupled to mass spectrometry (GC/MS) is a well-established analytical method in metabolomics study, an...

journal_title：BMC bioinformatics

authors： Tsugawa H,Tsujimoto Y,Arita M,Bamba T,Fukusaki E

更新日期：2011-05-04 00:00:00

abstract：BACKGROUND:Multidimensional protein identification technology (MudPIT)-based shot-gun proteomics has been proven to be an effective platform for functional proteomics. In particular, the various sample preparation methods and bioinformatics tools can be integrated to improve the proteomics platform for applications lik...

journal_title：BMC bioinformatics

authors： Zhang Y,Liu S,Dai SY,Yuan JS

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserved synteny, or synteny blocks, must be precisely identified and quantified, as a prerequisite to bet...

journal_title：BMC bioinformatics

authors： Lucas JM,Muffato M,Roest Crollius H

更新日期：2014-08-08 00:00:00

abstract：BACKGROUND:DNA methylation is an important heritable epigenetic mark that plays a crucial role in transcriptional regulation and the pathogenesis of various human disorders. The commonly used DNA methylation measurement approaches, e.g., Illumina Infinium HumanMethylation-27 and -450 BeadChip arrays (27 K and 450 K arr...

journal_title：BMC bioinformatics

authors： Yu F,Xu C,Deng HW,Shen H

更新日期：2020-12-01 00:00:00

abstract：BACKGROUND:The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. RESULTS:In order to improve accessibil...

journal_title：BMC bioinformatics

authors： Deng M,Brägelmann J,Schultze JL,Perner S

更新日期：2016-02-06 00:00:00

abstract：BACKGROUND:As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease development or therapeutic intervention would assist in drug development, design of therapy, and target ide...

journal_title：BMC bioinformatics

authors： Bidaut G,Suhre K,Claverie JM,Ochs MF

更新日期：2006-02-28 00:00:00

abstract：:We developed a new computational technique called Step-Level Differential Response (SLDR) to identify genetic regulatory relationships. Our technique takes advantages of functional genomics data for the same species under different perturbation conditions, therefore complementary to current popular computational techn...

journal_title：BMC bioinformatics

authors： Yue Z,Wan P,Huang H,Xie Z,Chen JY

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Population stratification is a systematic difference in allele frequencies between subpopulations. This can lead to spurious association findings in the case-control genome wide association studies (GWASs) used to identify single nucleotide polymorphisms (SNPs) associated with disease-linked phenotypes. Meth...

journal_title：BMC bioinformatics

authors： Hajiloo M,Sapkota Y,Mackey JR,Robson P,Greiner R,Damaraju S

更新日期：2013-02-22 00:00:00

abstract：BACKGROUND:The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caeno...

journal_title：BMC bioinformatics

authors： Blei DM,Franks K,Jordan MI,Mian IS

更新日期：2006-05-08 00:00:00

abstract：BACKGROUND:Knowledge of when and in which cells each gene is expressed across multicellular organisms is critical in understanding both gene function and regulation of cell type diversity. However, methods for measuring expression typically involve a trade-off between imaging-based methods, which give the precise locat...

journal_title：BMC bioinformatics

authors： Burdick JT,Murray JI

更新日期：2013-06-22 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hu...

journal_title：BMC bioinformatics

authors： Huang TH,Fan B,Rothschild MF,Hu ZL,Li K,Zhao SH

更新日期：2007-09-17 00:00:00

abstract：BACKGROUND:Differential co-expression (DCX) signifies change in degree of co-expression of a set of genes among different biological conditions. It has been used to identify differential co-expression networks or interactomes. Many algorithms have been developed for single-factor differential co-expression analysis and...

journal_title：BMC bioinformatics

authors： Liany H,Rajapakse JC,Karuturi RKM

更新日期：2017-12-28 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:Recently, mass spectrometry data have been mined using a genetic algorithm to produce discriminatory models that distinguish healthy individuals from those with cancer. This algorithm is the basis for claims of 100% sensitivity and specificity in two related publicly available datasets. To date, no detailed ...

journal_title：BMC bioinformatics

authors： Jeffries NO

更新日期：2004-11-19 00:00:00