Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics.

abstract：BACKGROUND:The goal of class prediction studies is to develop rules to accurately predict the class membership of new samples. The rules are derived using the values of the variables available for each subject: the main characteristic of high-dimensional data is that the number of variables greatly exceeds the number o...

journal_title：BMC bioinformatics

authors： Blagus R,Lusa L

更新日期：2010-10-20 00:00:00

abstract：BACKGROUND:Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on c...

journal_title：BMC bioinformatics

authors： He X,Sarma MS,Ling X,Chee B,Zhai C,Schatz B

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results...

journal_title：BMC bioinformatics

authors： Gautier L,Møller M,Friis-Hansen L,Knudsen S

更新日期：2004-08-14 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:Mixed models have a long and fruitful history in statistics. They are pertinent to genomics problems because they are highly versatile, accommodating a wide variety of situations within the same theoretical and algorithmic framework. RESULTS:Qxpak is a package for versatile statistical genomics, specificall...

journal_title：BMC bioinformatics

authors： Pérez-Enciso M,Misztal I

更新日期：2011-05-25 00:00:00

abstract：BACKGROUND:Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models requires the distinction between non-specific crystal packing contacts and biologically relevant interactions. This has been investiga...

journal_title：BMC bioinformatics

authors： Zhu H,Domingues FS,Sommer I,Lengauer T

更新日期：2006-01-19 00:00:00

abstract：BACKGROUND:Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a 'molecular picture' of the cell state. On the other hand, the genomic responses to a pharmacological or hormonal stimulus are dynamic molecular processes, where t...

journal_title：BMC bioinformatics

authors： Mutarelli M,Cicatiello L,Ferraro L,Grober OM,Ravo M,Facchiano AM,Angelini C,Weisz A

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:Inference of sequence homology is inherently an evolutionary question, dependent upon evolutionary divergence. However, the insertion and deletion penalties in the most widely used methods for inferring homology by sequence alignment, including BLAST and profile hidden Markov models (profile HMMs), are not b...

journal_title：BMC bioinformatics

authors： Rivas E,Eddy SR

更新日期：2015-12-10 00:00:00

abstract：BACKGROUND:Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microarrays does not capture all alternative splicing events. Moreover, for many species genomic data is be...

journal_title：BMC bioinformatics

authors： Sinha R,Hiller M,Pudimat R,Gausmann U,Platzer M,Backofen R

更新日期：2008-11-12 00:00:00

abstract：BACKGROUND:In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene express...

journal_title：BMC bioinformatics

authors： Acharya S,Cui L,Pan Y

更新日期：2020-12-30 00:00:00

abstract：BACKGROUND:Integrative network methods are commonly used for interpretation of high-throughput experimental biological data: transcriptomics, proteomics, metabolomics and others. One of the common approaches is finding a connected subnetwork of a global interaction network that best encompasses significant individual c...

journal_title：BMC bioinformatics

authors： Alexeev N,Isomurodov J,Sukhov V,Korotkevich G,Sergushichev A

更新日期：2020-11-18 00:00:00

abstract：BACKGROUND:Cryo-electron microscopy (Cryo-EM) is widely used in the determination of the three-dimensional (3D) structures of macromolecules. Particle picking from 2D micrographs remains a challenging early step in the Cryo-EM pipeline due to the diversity of particle shapes and the extremely low signal-to-noise ratio ...

journal_title：BMC bioinformatics

authors： Al-Azzawi A,Ouadou A,Max H,Duan Y,Tanner JJ,Cheng J

更新日期：2020-11-09 00:00:00

abstract：BACKGROUND:Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. The higher the quality of a reference genome assembly the more accurate the downstream analysis will be. During the last few years, major efforts have been made towards improving the qua...

journal_title：BMC bioinformatics

authors： Yuan Y,Bayer PE,Scheben A,Chan CK,Edwards D

更新日期：2017-06-30 00:00:00

abstract：BACKGROUND:The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another using the substitution, insertion, deletion and transposition operations. Lowrance and Wagner have ...

journal_title：BMC bioinformatics

authors： Zhao C,Sahni S

更新日期：2020-12-09 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:Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objectiv...

journal_title：BMC bioinformatics

authors： Zuyderduyn SD,Jones SJ

更新日期：2003-10-28 00:00:00

abstract：BACKGROUND:Current malaria diagnosis relies primarily on microscopic examination of Giemsa-stained thick and thin blood films. This method requires vigorously trained technicians to efficiently detect and classify the malaria parasite species such as Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) for an appropria...

journal_title：BMC bioinformatics

authors： Kaewkamnerd S,Uthaipibull C,Intarapanich A,Pannarut M,Chaotheing S,Tongsima S

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Numerous tools have been developed to predict the fitness effects (i.e., neutral, deleterious, or beneficial) of genetic variants on corresponding proteins. However, prediction in terms of whether a variant causes the variant bearing protein to lose the original function or gain new function is also needed f...

journal_title：BMC bioinformatics

authors： Liu M,Watson LT,Zhang L

更新日期：2015-10-30 00:00:00

abstract：BACKGROUND:In this short article, we discuss a simple method for assessing sample size requirements in microarray experiments. RESULTS:Our method starts with the output from a permutation-based analysis for a set of pilot data, e.g. from the SAM package. Then for a given hypothesized mean difference and various sample...

journal_title：BMC bioinformatics

authors： Tibshirani R

更新日期：2006-03-02 00:00:00

abstract：BACKGROUND:Linkage disequilibrium (LD)-the non-random association of alleles at different loci-defines population-specific haplotypes which vary by genomic ancestry. Assessment of allelic frequencies and LD patterns from a variety of ancestral populations enables researchers to better understand population histories as...

journal_title：BMC bioinformatics

authors： Alexander TA,Machiela MJ

更新日期：2020-01-10 00:00:00

abstract：BACKGROUND:Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data managemen...

journal_title：BMC bioinformatics

authors： Suhr M,Lehmann C,Bauer CR,Bender T,Knopp C,Freckmann L,Öst Hansen B,Henke C,Aschenbrandt G,Kühlborn LK,Rheinländer S,Weber L,Marzec B,Hellkamp M,Wieder P,Sax U,Kusch H,Nussbeck SY

更新日期：2020-12-17 00:00:00

abstract：BACKGROUND:Interpretation of gene expression microarray data in the light of external information on both columns and rows (experimental variables and gene annotations) facilitates the extraction of pertinent information hidden in these complex data. Biologists classically interpret genes of interest after retrieving f...

journal_title：BMC bioinformatics

authors： Baty F,Rüdiger J,Miglino N,Kern L,Borger P,Brutsche M

更新日期：2013-06-06 00:00:00

abstract：BACKGROUND:A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal gen...

journal_title：BMC bioinformatics

authors： Khan A,Liu Q,Wang K

更新日期：2018-12-28 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:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...

journal_title：BMC bioinformatics

authors： Bui VK,Wei C

更新日期：2020-10-20 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:Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientifi...

journal_title：BMC bioinformatics

authors： Durrant JD,Amaro RE

更新日期：2014-05-23 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: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:Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcriptome data with pathway based interpretation. Over the years, the amount of omics data has become hu...

journal_title：BMC bioinformatics

authors： Kim I,Choi S,Kim S

更新日期：2018-02-19 00:00:00