Fregene: simulation of realistic sequence-level data in populations and ascertained samples.

abstract：BACKGROUND:Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenom...

journal_title：BMC bioinformatics

authors： Techa-Angkoon P,Sun Y,Lei J

更新日期：2017-10-16 00:00:00

abstract：BACKGROUND:S-glutathionylation is the formation of disulfide bonds between the tripeptide glutathione and cysteine residues of the protein, protecting them from irreversible oxidation and in some cases causing change in their functions. Regulatory glutathionylation of proteins is a controllable and reversible process a...

journal_title：BMC bioinformatics

authors： Anashkina AA,Poluektov YM,Dmitriev VA,Kuznetsov EN,Mitkevich VA,Makarov AA,Petrushanko IY

更新日期：2020-09-14 00:00:00

abstract：BACKGROUND:The family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins. They help maintain and regulate the potassium ion-based component of the membrane potential and are thus central to many critical physiological processes. VKCDB (Voltage-gated potassium [K] Channel Dat...

journal_title：BMC bioinformatics

authors： Li B,Gallin WJ

更新日期：2004-01-09 00:00:00

abstract：BACKGROUND:Recently, revealing the function of proteins with protein-protein interaction (PPI) networks is regarded as one of important issues in bioinformatics. With the development of experimental methods such as the yeast two-hybrid method, the data of protein interaction have been increasing extremely. Many databas...

journal_title：BMC bioinformatics

authors： Monji H,Koizumi S,Ozaki T,Ohkawa T

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2-5% of the genes encode for peptidases, irrespectively of the organism source. The basic peptidase function is "protein digestion" and this can be potentially dangerous in living organisms w...

journal_title：BMC bioinformatics

authors： Bartoli L,Calabrese R,Fariselli P,Mita DG,Casadio R

更新日期：2007-03-08 00:00:00

abstract：BACKGROUND:An important mechanism of endocrine activity is chemicals entering target cells via transport proteins and then interacting with hormone receptors such as the estrogen receptor (ER). α-Fetoprotein (AFP) is a major transport protein in rodent serum that can bind and sequester estrogens, thus preventing entry ...

journal_title：BMC bioinformatics

authors： Shen J,Zhang W,Fang H,Perkins R,Tong W,Hong H

更新日期：2013-01-01 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:We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples ...

journal_title：BMC bioinformatics

authors： Seoighe C,Korir PK

更新日期：2011-10-05 00:00:00

abstract：BACKGROUND:Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how the organism regulates its transcriptomic profile, enabling cells to survive in hostile environmen...

journal_title：BMC bioinformatics

authors： Staunton PM,Miranda-CasoLuengo AA,Loftus BJ,Gormley IC

更新日期：2019-09-10 00:00:00

abstract：BACKGROUND:Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabolic networks are constructed from the genome sequence of an organism, and the graphs can be used to s...

journal_title：BMC bioinformatics

authors： Weber Zendrera A,Sokolovska N,Soula HA

更新日期：2019-10-15 00:00:00

abstract：BACKGROUND:There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage, environmental condition, or disease state. Accurate analysis of microarray expression data and des...

journal_title：BMC bioinformatics

authors： Kahn AB,Ryan MC,Liu H,Zeeberg BR,Jamison DC,Weinstein JN

更新日期：2007-03-05 00:00:00

abstract：:DNA methylation exhibits different patterns in different cancers. DNA methylation rates at different genomic loci appear to be highly correlated in some samples but not in others. We call such phenomena conditional concordant relationships (CCRs). In this study, we explored DNA methylation patterns in 12 common cancer...

journal_title：BMC bioinformatics

authors： Qiu P,Zhang L

更新日期：2012-01-01 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:The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear ...

journal_title：BMC bioinformatics

authors： Lemieux S

更新日期：2006-08-25 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：BACKGROUND:Zebrafish is a widely used model organism for studying heart development and cardiac-related pathogenesis. With the ability of surviving without a functional circulation at larval stages, strong genetic similarity between zebrafish and mammals, prolific reproduction and optically transparent embryos, zebrafi...

journal_title：BMC bioinformatics

authors： Kang CP,Tu HC,Fu TF,Wu JM,Chu PH,Chang DT

更新日期：2018-05-09 00:00:00

abstract：BACKGROUND:A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Si...

journal_title：BMC bioinformatics

authors： Alanko J,Cunial F,Belazzougui D,Mäkinen V

更新日期：2017-03-14 00:00:00

abstract：BACKGROUND:Prioritizing disease genes is trying to identify potential disease causing genes for a given phenotype, which can be applied to reveal the inherited basis of human diseases and facilitate drug development. Our motivation is inspired by label propagation algorithm and the false positive protein-protein intera...

journal_title：BMC bioinformatics

authors： Zhang Y,Liu J,Liu X,Fan X,Hong Y,Wang Y,Huang Y,Xie M

更新日期：2018-02-08 00:00:00

abstract：BACKGROUND:Orthologs inference is the starting point of most comparative genomics studies, and a plethora of methods have been designed in the last decade to address this challenging task. In this paper we focus on the problems of deciding consistency with a species tree (known or not) of a partial set of orthology/par...

journal_title：BMC bioinformatics

authors： Jones M,Paul C,Scornavacca C

更新日期：2016-11-11 00:00:00

abstract：BACKGROUND:In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the...

journal_title：BMC bioinformatics

authors： Thompson JD,Muller A,Waterhouse A,Procter J,Barton GJ,Plewniak F,Poch O

更新日期：2006-06-23 00:00:00

abstract：BACKGROUND:Event sequences where different types of events often occur close together arise, e.g., when studying potential transcription factor binding sites (TFBS, events) of certain transcription factors (TF, types) in a DNA sequence. These events tend to occur in bursts: in some genomic regions there are more genes ...

journal_title：BMC bioinformatics

authors： Haiminen N,Mannila H,Terzi E

更新日期：2008-08-08 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：BACKGROUND:The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical value. RESULTS:We trained models using 217 high-quality morphologies of rat somatosensory neocortex interneurons reconstructed by a single...

journal_title：BMC bioinformatics

authors： Mihaljević B,Larrañaga P,Benavides-Piccione R,Hill S,DeFelipe J,Bielza C

更新日期：2018-12-17 00:00:00

abstract：BACKGROUND:Continuous enzyme kinetic assays are often used in high-throughput applications, as they allow rapid acquisition of large amounts of kinetic data and increased confidence compared to discontinuous assays. However, data analysis is often rate-limiting in high-throughput enzyme assays, as manual inspection and...

journal_title：BMC bioinformatics

authors： Olp MD,Kalous KS,Smith BC

更新日期：2020-05-14 00:00:00

abstract：BACKGROUND:The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the genome is divided into tiling windows and windowed read-count data is generated for the entire geno...

journal_title：BMC bioinformatics

authors： Wang W,Sun W,Wang W,Szatkiewicz J

更新日期：2018-03-01 00:00:00

abstract：BACKGROUND:XHMM is a widely used tool for copy-number variant (CNV) discovery from whole exome sequencing data but can require hours to days to run for large cohorts. A more scalable implementation would reduce the need for specialized computational resources and enable increased exploration of the configuration parame...

journal_title：BMC bioinformatics

authors： Linderman MD,Chia D,Wallace F,Nothaft FA

更新日期：2019-10-11 00:00:00

abstract：BACKGROUND:Computational gene finding algorithms have proven their robustness in identifying genes in complete genomes. However, metagenomic sequencing has presented new challenges due to the incomplete and fragmented nature of the data. During the last few years, attempts have been made to extract complete and incompl...

journal_title：BMC bioinformatics

authors： El Allali A,Rose JR

更新日期：2013-01-01 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:Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential ...

journal_title：BMC bioinformatics

authors： Li X,Fu Y,Wang X,Qiu W

更新日期：2018-05-18 00:00:00

abstract：BACKGROUND:Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area is assigned to each spot and the sum of the pixel intensities in that area, the so-called volume, is ...

journal_title：BMC bioinformatics

authors： Brauner JM,Groemer TW,Stroebel A,Grosse-Holz S,Oberstein T,Wiltfang J,Kornhuber J,Maler JM

更新日期：2014-06-11 00:00:00