Determining gene expression on a single pair of microarrays.

abstract：BACKGROUND:An approach to molecular classification based on the comparative expression of protein pairs is presented. The method overcomes some of the present limitations in using peptide intensity data for class prediction for problems such as the detection of a disease, disease prognosis, or for predicting treatment ...

journal_title：BMC bioinformatics

authors： Kaur P,Schlatzer D,Cooke K,Chance MR

更新日期：2012-08-07 00:00:00

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:Abundant information about gene products is stored in online searchable databases such as annotation or literature. To efficiently obtain and digest such information, there is a pressing need for automated information-summarization and functional-similarity clustering of genes. RESULTS:We have developed a n...

journal_title：BMC bioinformatics

authors： Chiang JH,Shin JW,Liu HH,Chin CL

更新日期：2006-08-29 00:00:00

abstract：BACKGROUND:A new algorithm has been developed for generating conservation profiles that reflect the evolutionary history of the subfamily associated with a query sequence. It is based on n-gram patterns (NP{n,m}) which are sets of n residues and m wildcards in windows of size n+m. The generation of conservation profile...

journal_title：BMC bioinformatics

authors： Vries JK,Liu X

更新日期：2008-01-30 00:00:00

abstract：BACKGROUND:A recently proposed method for estimating qPCR amplification efficiency E analyzes fluorescence intensity ratios from pairs of points deemed to lie in the exponential growth region on the amplification curves for all reactions in a dilution series. This method suffers from a serious problem: The resulting ra...

journal_title：BMC bioinformatics

authors： Tellinghuisen J

更新日期：2020-07-08 00:00:00

abstract：BACKGROUND:The identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. In this paper, a new method is presented for the identification of exonic regions in DNA sequences. This method is based on th...

journal_title：BMC bioinformatics

authors： Abbasi O,Rostami A,Karimian G

更新日期：2011-11-03 00:00:00

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 rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function i...

journal_title：BMC bioinformatics

authors： Bray T,Chan P,Bougouffa S,Greaves R,Doig AJ,Warwicker J

更新日期：2009-11-18 00:00:00

abstract：BACKGROUND:The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the breeding progress. Laserscanning is a highly accurate and high resolution technique to acquire the 3D sh...

journal_title：BMC bioinformatics

authors： Heeren B,Paulus S,Goldbach H,Kuhlmann H,Mahlein AK,Rumpf M,Wirth B

更新日期：2020-07-29 00:00:00

abstract：BACKGROUND:Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles are challenging, because they comprise reads not only from the grafted human cancer but also from t...

journal_title：BMC bioinformatics

authors： Kluin RJC,Kemper K,Kuilman T,de Ruiter JR,Iyer V,Forment JV,Cornelissen-Steijger P,de Rink I,Ter Brugge P,Song JY,Klarenbeek S,McDermott U,Jonkers J,Velds A,Adams DJ,Peeper DS,Krijgsman O

更新日期：2018-10-04 00:00:00

abstract：BACKGROUND:The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as fl...

journal_title：BMC bioinformatics

authors： Negre V,Grunau C

更新日期：2004-05-07 00:00:00

abstract：BACKGROUND:Endometrial cancers (ECs) are one of the most common types of malignant tumor in females. Substantial efforts had been made to identify significantly mutated genes (SMGs) in ECs and use them as biomarkers for the classification of histological subtypes and the prediction of clinical outcomes. However, the im...

journal_title：BMC bioinformatics

authors： Liu K,He L,Liu Z,Xu J,Liu Y,Kuang Q,Wen Z,Li M

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Me...

journal_title：BMC bioinformatics

authors： Tan YD,Fornage M,Xu H

更新日期：2008-03-06 00:00:00

abstract：BACKGROUND:Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared data science infrastructures like Boag is needed to efficiently process and parse data co...

journal_title：BMC bioinformatics

authors： Bagheri H,Muppirala U,Masonbrink RE,Severin AJ,Rajan H

更新日期：2019-08-22 00:00:00

abstract：BACKGROUND:Chemical named entities represent an important facet of biomedical text. RESULTS:We have developed a system to use character-based n-grams, Maximum Entropy Markov Models and rescoring to recognise chemical names and other such entities, and to make confidence estimates for the extracted entities. An adjusta...

journal_title：BMC bioinformatics

authors： Corbett P,Copestake A

更新日期：2008-11-19 00:00:00

abstract：BACKGROUND:Many methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify "sufficiently large". RESULTS:Using the multispecies coalescent model, we report a general an...

journal_title：BMC bioinformatics

authors： Uricchio LH,Warnow T,Rosenberg NA

更新日期：2016-11-11 00:00:00

abstract：BACKGROUND:Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes. RESULTS:We pres...

journal_title：BMC bioinformatics

authors： Kharchenko P,Chen L,Freund Y,Vitkup D,Church GM

更新日期：2006-03-29 00:00:00

abstract：BACKGROUND:The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootst...

journal_title：BMC bioinformatics

authors： Cai B,Yang X,Tuskan GA,Cheng ZM

更新日期：2011-03-18 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:Cancer progression is caused by the sequential accumulation of mutations, but not all orders of accumulation are equally likely. When the fixation of some mutations depends on the presence of previous ones, identifying restrictions in the order of accumulation of mutations can lead to the discovery of therap...

journal_title：BMC bioinformatics

authors： Diaz-Uriarte R

更新日期：2015-02-12 00:00:00

abstract：BACKGROUND:Normalization in real-time qRT-PCR is necessary to compensate for experimental variation. A popular normalization strategy employs reference gene(s), which may introduce additional variability into normalized expression levels due to innate variation (between tissues, individuals, etc). To minimize this inna...

journal_title：BMC bioinformatics

authors： Chervoneva I,Li Y,Schulz S,Croker S,Wilson C,Waldman SA,Hyslop T

更新日期：2010-05-14 00:00:00

abstract：BACKGROUND:Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describing known gene transcripts through the development of numerous databases. Nevertheless, owing to the...

journal_title：BMC bioinformatics

authors： de la Grange P,Dutertre M,Correa M,Auboeuf D

更新日期：2007-06-04 00:00:00

abstract：BACKGROUND:Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed. A number of prediction algorithms have been developed based on amino acid compositions or on the N-terminal characteristics (signal peptides) of proteins. Ho...

journal_title：BMC bioinformatics

authors： Sarda D,Chua GH,Li KB,Krishnan A

更新日期：2005-06-17 00:00:00

abstract：BACKGROUND:The median of k≥3 genomes was originally defined to find a compromise genome indicative of a common ancestor. However, in gene order comparisons, the usual definitions based on minimizing the sum of distances to the input genomes lead to degenerate medians reflecting only one of the input genomes. "Near-medi...

journal_title：BMC bioinformatics

authors： Larlee CA,Brandts A,Sankoff D

更新日期：2016-12-15 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:Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have been developed for predicting aggregation propensity and identifying aggregation-prone regions in pro...

journal_title：BMC bioinformatics

authors： Fang Y,Gao S,Tai D,Middaugh CR,Fang J

更新日期：2013-10-28 00:00:00

abstract：BACKGROUND:Histopathology image analysis is a gold standard for cancer recognition and diagnosis. Automatic analysis of histopathology images can help pathologists diagnose tumor and cancer subtypes, alleviating the workload of pathologists. There are two basic types of tasks in digital histopathology image analysis: i...

journal_title：BMC bioinformatics

authors： Xu Y,Jia Z,Wang LB,Ai Y,Zhang F,Lai M,Chang EI

更新日期：2017-05-26 00:00:00

abstract：BACKGROUND:Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembled onto a single support - ty...

journal_title：BMC bioinformatics

authors： Nguyen HN,Paveau V,Cauchois C,Kervrann C

更新日期：2018-04-19 00:00:00

abstract：BACKGROUND:Antibiotics are the widely prescribed drugs for children and most likely to be related with adverse reactions. Record on adverse reactions and allergies from antibiotics considerably affect the prescription choices. We consider this a biomedical decision-making problem and explore hidden knowledge in survey ...

journal_title：BMC bioinformatics

authors： Yildirim P,Majnarić L,Ekmekci O,Holzinger A

更新日期：2014-01-01 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