PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm.

abstract：BACKGROUND:Urokinase, its receptor and the integrins are functionally associated and involved in regulation of cell signaling, migration, adhesion and proliferation. No structural information is available on this potential multimolecular complex. However, the tri-dimensional structure of urokinase, urokinase receptor a...

journal_title：BMC bioinformatics

authors： Degryse B,Fernandez-Recio J,Citro V,Blasi F,Cubellis MV

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appea...

journal_title：BMC bioinformatics

authors： Tatusov RL,Fedorova ND,Jackson JD,Jacobs AR,Kiryutin B,Koonin EV,Krylov DM,Mazumder R,Mekhedov SL,Nikolskaya AN,Rao BS,Smirnov S,Sverdlov AV,Vasudevan S,Wolf YI,Yin JJ,Natale DA

更新日期：2003-09-11 00:00:00

abstract：BACKGROUND:Infectious disease modeling and computational power have evolved such that large-scale agent-based models (ABMs) have become feasible. However, the increasing hardware complexity requires adapted software designs to achieve the full potential of current high-performance workstations. RESULTS:We have found l...

journal_title：BMC bioinformatics

authors： Willem L,Stijven S,Tijskens E,Beutels P,Hens N,Broeckhove J

更新日期：2015-06-02 00:00:00

abstract：BACKGROUND:The explosive growth of biological data provides opportunities for new statistical and comparative analyses of large information sets, such as alignments comprising tens of thousands of sequences. In such studies, sequence annotations frequently play an essential role, and reliable results depend on metadata...

journal_title：BMC bioinformatics

authors： Miotto O,Tan TW,Brusic V

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:The improvements of high throughput technologies have produced large amounts of multi-omics experiments datasets. Initial analysis of these data has revealed many concurrent gene alterations within single dataset or/and among multiple omics datasets. Although powerful bioinformatics pipelines have been devel...

journal_title：BMC bioinformatics

authors： Chen D,Zhang F,Zhao Q,Xu J

更新日期：2019-11-08 00:00:00

abstract：BACKGROUND:Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicted protein models in perspective is one of the key components of successful protein structure predict...

journal_title：BMC bioinformatics

authors： Jing X,Dong Q

更新日期：2017-05-25 00:00:00

abstract：BACKGROUND:Identification of transcription factors (TFs) responsible for modulation of differentially expressed genes is a key step in deducing gene regulatory pathways. Most current methods identify TFs by searching for presence of DNA binding motifs in the promoter regions of co-regulated genes. However, this strateg...

journal_title：BMC bioinformatics

authors： Roy S,Heinrich K,Phan V,Berry MW,Homayouni R

更新日期：2011-10-18 00:00:00

abstract：BACKGROUND:Quantitative polymerase chain reaction (qPCR) is the technique of choice for quantifying gene expression. While the technique itself is well established, approaches for the analysis of qPCR data continue to improve. RESULTS:Here we expand on the common base method to develop procedures for testing linear re...

journal_title：BMC bioinformatics

authors： Ganger MT,Dietz GD,Headley P,Ewing SJ

更新日期：2020-09-29 00:00:00

abstract：BACKGROUND:The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS) which can also be isolated and characterized. Each DIS corr...

journal_title：BMC bioinformatics

authors： Agoston V,Cemazar M,Kaján L,Pongor S

更新日期：2005-01-27 00:00:00

abstract：BACKGROUND:Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. RESULTS:MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic ma...

journal_title：BMC bioinformatics

authors： Grimonprez Q,Celisse A,Blanck S,Cheok M,Figeac M,Marot G

更新日期：2014-12-14 00:00:00

abstract：BACKGROUND:DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS:Here, we describe a method to detect copy number varia...

journal_title：BMC bioinformatics

authors： Xie C,Tammi MT

更新日期：2009-03-06 00:00:00

abstract：BACKGROUND:The reconstruction of reliable graphical models from observational data is important in bioinformatics and other computational fields applying network reconstruction methods to large, yet finite datasets. The main network reconstruction approaches are either based on Bayesian scores, which enable the ranking...

journal_title：BMC bioinformatics

authors： Affeldt S,Verny L,Isambert H

更新日期：2016-01-20 00:00:00

abstract：BACKGROUND:Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures ca...

journal_title：BMC bioinformatics

authors： Schreiner E,Trabuco LG,Freddolino PL,Schulten K

更新日期：2011-05-23 00:00:00

abstract：BACKGROUND:Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to...

journal_title：BMC bioinformatics

authors： Clarke TH,Brinkac LM,Inman JM,Sutton G,Fouts DE

更新日期：2018-06-27 00:00:00

abstract：BACKGROUND:Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods could yield valuable insight into cell biology and mechanisms of human disease. However, it is currently not clear how to control ...

journal_title：BMC bioinformatics

authors： Nilsson R,Björkegren J,Tegnér J

更新日期：2009-01-29 00:00:00

abstract：BACKGROUND:For the development of genome assembly tools, some comprehensive and efficiently computable validation measures are required to assess the quality of the assembly. The mostly used N50 measure summarizes the assembly results by the length of the scaffold (or contig) overlapping the midpoint of the length-orde...

journal_title：BMC bioinformatics

authors： Mäkinen V,Salmela L,Ylinen J

更新日期：2012-10-03 00:00:00

abstract：BACKGROUND:As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective. RESULTS:We reconstruct...

journal_title：BMC bioinformatics

authors： Zhang Y,Li S,Skogerbø G,Zhang Z,Zhu X,Zhang Z,Sun S,Lu H,Shi B,Chen R

更新日期：2006-05-09 00:00:00

abstract：BACKGROUND:Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mec...

journal_title：BMC bioinformatics

authors： Rousseau M,Fraser J,Ferraiuolo MA,Dostie J,Blanchette M

更新日期：2011-10-25 00:00:00

abstract：BACKGROUND:Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA's 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within biotechnological applications, is lacking the feature of incor...

journal_title：BMC bioinformatics

authors： Kleinkauf R,Houwaart T,Backofen R,Mann M

更新日期：2015-11-18 00:00:00

abstract：BACKGROUND:A fundamental fact in biology states that genes do not operate in isolation, and yet, methods that infer regulatory networks for single cell gene expression data have been slow to emerge. With single cell sequencing methods now becoming accessible, general network inference algorithms that were initially dev...

journal_title：BMC bioinformatics

authors： Chen S,Mar JC

更新日期：2018-06-19 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：BACKGROUND:Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to...

journal_title：BMC bioinformatics

authors： Casneuf T,Van de Peer Y,Huber W

更新日期：2007-11-26 00:00:00

abstract：BACKGROUND:Text mining tools have gained popularity to process the vast amount of available research articles in the biomedical literature. It is crucial that such tools extract information with a sufficient level of detail to be applicable in real life scenarios. Studies of mining non-causal molecular relations attrib...

journal_title：BMC bioinformatics

authors： Van Landeghem S,Björne J,Abeel T,De Baets B,Salakoski T,Van de Peer Y

更新日期：2012-06-26 00:00:00

abstract：BACKGROUND:The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutat...

journal_title：BMC bioinformatics

authors： Santos J,Monteagudo Á

更新日期：2017-03-27 00:00:00

abstract：BACKGROUND:With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the followin...

journal_title：BMC bioinformatics

authors： Lin J

更新日期：2009-02-03 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 specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for model...

journal_title：BMC bioinformatics

authors： Angarica VE,Pérez AG,Vasconcelos AT,Collado-Vides J,Contreras-Moreira B

更新日期：2008-10-16 00:00:00

abstract：BACKGROUND:To infer gene regulatory networks from time series gene profiles, two important tasks that are related to biological systems must be undertaken. One task is to determine a valid network structure that has topological properties that can influence the network dynamics profoundly. The other task is to optimize...

journal_title：BMC bioinformatics

authors： Hsiao YT,Lee WP

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The BioCreative text mining evaluation investigated the application of text mining methods to the task of automatically extracting information from text in biomedical research articles. We participated in Task 2 of the evaluation. For this task, we built a system to automatically annotate a given protein wit...

journal_title：BMC bioinformatics

authors： Ray S,Craven M

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be ...

journal_title：BMC bioinformatics

authors： Andrieu O,Fiston AS,Anxolabéhère D,Quesneville H

更新日期：2004-07-13 00:00:00