Software for selecting the most informative sets of genomic loci for multi-target microbial typing.

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:Molecular biology (MB) is a dynamic research domain that benefits greatly from the use of modern software technology in preparing experiments, analyzing acquired data, and even performing "in-silico" analyses. As ever new findings change the face of this domain, software for MB has to be sufficiently flexibl...

journal_title：BMC bioinformatics

authors： Busch N,Wedemann G

更新日期：2009-03-27 00:00:00

abstract：BACKGROUND:Molecular data, e.g. arising from microarray technology, is often used for predicting survival probabilities of patients. For multivariate risk prediction models on such high-dimensional data, there are established techniques that combine parameter estimation and variable selection. One big challenge is to i...

journal_title：BMC bioinformatics

authors： Sariyar M,Hoffmann I,Binder H

更新日期：2014-02-26 00:00:00

abstract：BACKGROUND:Automated protein function prediction methods are the only practical approach for assigning functions to genes obtained from model organisms. Many of the previously reported function annotation methods are of limited utility for fungal protein annotation. They are often trained only to one species, are not a...

journal_title：BMC bioinformatics

authors： Jung J,Yi G,Sukno SA,Thon MR

更新日期：2010-04-29 00:00:00

abstract：BACKGROUND:Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional selection. Thus, identification of conserved gene clusters that are under functional selection pro...

journal_title：BMC bioinformatics

authors： Zheng Y,Anton BP,Roberts RJ,Kasif S

更新日期：2005-10-03 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:Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta-analysis framework is also n...

journal_title：BMC bioinformatics

authors： Di Narzo AF,Cheng H,Lu J,Hao K

更新日期：2014-11-28 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6-8 nucleotide long target sites, usually located within the mRNA 3' untranslated region. A common approach to validate and probe microRNA-mRNA interact...

journal_title：BMC bioinformatics

authors： Ryan BC,Werner TS,Howard PL,Chow RL

更新日期：2016-04-27 00:00:00

abstract：BACKGROUND:Biological resources are essential tools for biomedical research. Their availability is promoted through on-line catalogues. Common Access to Biological Resources and Information (CABRI) is a service for distribution of biological resources and related data collected by 28 European culture collections. Linki...

journal_title：BMC bioinformatics

authors： Romano P,Dawyndt P,Piersigilli F,Swings J

更新日期：2005-12-01 00:00:00

abstract：BACKGROUND:Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper ...

journal_title：BMC bioinformatics

authors： Varadi M,Guharoy M,Zsolyomi F,Tompa P

更新日期：2015-05-13 00:00:00

abstract：BACKGROUND:In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of microarrays where N = 1 in each condition. In this paper, we demonstrate the effectiveness of a new al...

journal_title：BMC bioinformatics

authors： Reid RW,Fodor AA

更新日期：2008-11-21 00:00:00

abstract：BACKGROUND:Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has beco...

journal_title：BMC bioinformatics

authors： Zare F,Dow M,Monteleone N,Hosny A,Nabavi S

更新日期：2017-05-31 00:00:00

abstract：BACKGROUND:The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common tar...

journal_title：BMC bioinformatics

authors： Hanzlik RP,Koen YM,Theertham B,Dong Y,Fang J

更新日期：2007-03-16 00:00:00

abstract：BACKGROUND:A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the de...

journal_title：BMC bioinformatics

authors： Cao Y,Liu S,Zhang L,Qin J,Wang J,Tang K

更新日期：2006-01-14 00:00:00

abstract：BACKGROUND:Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector intensity readings, each uniquely addressed along dimensions of time (e.g., retention time of chemic...

journal_title：BMC bioinformatics

authors： Chae M,Shmookler Reis RJ,Thaden JJ

更新日期：2008-08-12 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:Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biologi...

journal_title：BMC bioinformatics

authors： Pinoli P,Chicco D,Masseroli M

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:High-throughput "omics" based data analysis play emerging roles in life sciences and molecular diagnostics. This emphasizes the urgent need for user-friendly windows-based software interfaces that could process the diversity of large tab-delimited raw data files generated by these methods. Depending on the s...

journal_title：BMC bioinformatics

authors： Schwager C,Wirkner U,Abdollahi A,Huber PE

更新日期：2009-07-29 00:00:00

abstract：BACKGROUND:Predicting protein function has become increasingly demanding in the era of next generation sequencing technology. The task to assign a curator-reviewed function to every single sequence is impracticable. Bioinformatics tools, easy to use and able to provide automatic and reliable annotations at a genomic sc...

journal_title：BMC bioinformatics

authors： Falda M,Toppo S,Pescarolo A,Lavezzo E,Di Camillo B,Facchinetti A,Cilia E,Velasco R,Fontana P

更新日期：2012-03-28 00:00:00

abstract：BACKGROUND:The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using o...

journal_title：BMC bioinformatics

authors： von Grotthuss M,Plewczynski D,Ginalski K,Rychlewski L,Shakhnovich EI

更新日期：2006-02-06 00:00:00

abstract：BACKGROUND:Cancer is a complex disease which is characterized by the accumulation of genetic alterations during the patient's lifetime. With the development of the next-generation sequencing technology, multiple omics data, such as cancer genomic, epigenomic and transcriptomic data etc., can be measured from each indiv...

journal_title：BMC bioinformatics

authors： Wei PJ,Zhang D,Xia J,Zheng CH

更新日期：2016-12-23 00:00:00

abstract：BACKGROUND:The large increase in the size of patent collections has led to the need of efficient search strategies. But the development of advanced text-mining applications dedicated to patents of the biomedical field remains rare, in particular to address the needs of the pharmaceutical & biotech industry, which inten...

journal_title：BMC bioinformatics

authors： Pasche E,Gobeill J,Kreim O,Oezdemir-Zaech F,Vachon T,Lovis C,Ruch P

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effective prevention and control measures for blood pressure diseases. Traditional blood pressure measure...

journal_title：BMC bioinformatics

authors： Zhang B,Ren H,Huang G,Cheng Y,Hu C

更新日期：2019-02-28 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:Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations fo...

journal_title：BMC bioinformatics

authors： Hayashi T,Matsuzaki Y,Yanagisawa K,Ohue M,Akiyama Y

更新日期：2018-05-08 00:00:00

abstract：BACKGROUND:Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, ...

journal_title：BMC bioinformatics

authors： Thakur S,Guttman DS

更新日期：2016-06-30 00:00:00

abstract：BACKGROUND:The NTF2-like superfamily is a versatile group of protein domains sharing a common fold. The sequences of these domains are very diverse and they share no common sequence motif. These domains serve a range of different functions within the proteins in which they are found, including both catalytic and non-ca...

journal_title：BMC bioinformatics

authors： Eberhardt RY,Chang Y,Bateman A,Murzin AG,Axelrod HL,Hwang WC,Aravind L

更新日期：2013-11-19 00:00:00

abstract：BACKGROUND:This study addresses a recurrent biological problem, that is to define a formal clustering structure for a set of tissues on the basis of the relative abundance of multiple alternatively spliced isoforms mRNAs generated by the same gene. To this aim, we have used a model-based clustering approach, based on a...

journal_title：BMC bioinformatics

authors： Pelosi M,Alfò M,Martella F,Pappalardo E,Musarò A

更新日期：2015-09-15 00:00:00

abstract：BACKGROUND:Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of the site of cross-link incorporation. The difficulties are due to higher charges of fragment ions, ...

journal_title：BMC bioinformatics

authors： Jaiswal M,Crabtree N,Bauer MA,Hall R,Raney KD,Zybailov BL

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine...

journal_title：BMC bioinformatics

authors： Bujnicki JM,Feder M,Radlinska M,Rychlewski L

更新日期：2001-01-01 00:00:00