Local search for the generalized tree alignment problem.

abstract：BACKGROUND:Recent years have seen an increased amount of natural language processing (NLP) work on full text biomedical journal publications. Much of this work is done with Open Access journal articles. Such work assumes that Open Access articles are representative of biomedical publications in general and that methods...

journal_title：BMC bioinformatics

authors： Verspoor K,Cohen KB,Hunter L

更新日期：2009-06-15 00:00:00

abstract：BACKGROUND:For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significant...

journal_title：BMC bioinformatics

authors： Lee M,Jeong CS,Kim D

更新日期：2007-12-03 00:00:00

abstract：BACKGROUND:Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range o...

journal_title：BMC bioinformatics

authors： Iacoangeli A,Al Khleifat A,Sproviero W,Shatunov A,Jones AR,Morgan SL,Pittman A,Dobson RJ,Newhouse SJ,Al-Chalabi A

更新日期：2019-04-27 00:00:00

abstract：BACKGROUND:High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false negative rates. A number of researchers have recently presented methods for integrating direct and indirect data for predicting interacti...

journal_title：BMC bioinformatics

authors： Qi Y,Klein-Seetharaman J,Bar-Joseph Z

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000). RESULTS:We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to...

journal_title：BMC bioinformatics

authors： Karwath A,King RD

更新日期：2002-04-23 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: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:Antibacterial peptides are one of the effecter molecules of innate immune system. Over the last few decades several antibacterial peptides have successfully approved as drug by FDA, which has prompted an interest in these antibacterial peptides. In our recent study we analyzed 999 antibacterial peptides, whi...

journal_title：BMC bioinformatics

authors： Lata S,Mishra NK,Raghava GP

更新日期：2010-01-18 00:00:00

abstract：BACKGROUND:The continuous flow of EST data remains one of the richest sources for discoveries in modern biology. The first step in EST data mining is usually associated with EST clustering, the process of grouping of original fragments according to their annotation, similarity to known genomic DNA or each other. Cluste...

journal_title：BMC bioinformatics

authors： Ptitsyn A,Hide W

更新日期：2005-07-15 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: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:RNA-seq is a powerful tool for measuring transcriptomes, especially for identifying differentially expressed genes or transcripts (DEGs) between sample groups. A number of methods have been developed for this task, and several evaluation studies have also been reported. However, those evaluations so far have...

journal_title：BMC bioinformatics

authors： Tang M,Sun J,Shimizu K,Kadota K

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:The increasing availability of Electronic Health Record (EHR) data and specifically free-text patient notes presents opportunities for phenotype extraction. Text-mining methods in particular can help disease modeling by mapping named-entities mentions to terminologies and clustering semantically related term...

journal_title：BMC bioinformatics

authors： Cohen R,Elhadad M,Elhadad N

更新日期：2013-01-16 00:00:00

abstract：BACKGROUND:Light microscopy is of central importance in cell biology. The recent introduction of automated high content screening has expanded this technology towards automation of experiments and performing large scale perturbation assays. Nevertheless, evaluation of microscopy data continues to be a bottleneck in man...

journal_title：BMC bioinformatics

authors： Misselwitz B,Strittmatter G,Periaswamy B,Schlumberger MC,Rout S,Horvath P,Kozak K,Hardt WD

更新日期：2010-01-14 00:00:00

abstract：BACKGROUND:Heart disease (HD) is one of the most common diseases nowadays, and an early diagnosis of such a disease is a crucial task for many health care providers to prevent their patients for such a disease and to save lives. In this paper, a comparative analysis of different classifiers was performed for the classi...

journal_title：BMC bioinformatics

authors： Almustafa KM

更新日期：2020-07-02 00:00:00

abstract：BACKGROUND:Microarray data discretization is a basic preprocess for many algorithms of gene regulatory network inference. Some common discretization methods in informatics are used to discretize microarray data. Selection of the discretization method is often arbitrary and no systematic comparison of different discreti...

journal_title：BMC bioinformatics

authors： Li Y,Liu L,Bai X,Cai H,Ji W,Guo D,Zhu Y

更新日期：2010-10-19 00:00:00

abstract：BACKGROUND:The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression data remains a challenge. RESULTS:We introduce a new general-purpose analytic method called Mechanistic Bayesian Networks (MBNs) that allows for the ...

journal_title：BMC bioinformatics

authors： Shah A,Tenzen T,McMahon AP,Woolf PJ

更新日期：2009-12-18 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: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:Different human responses to the same vaccine were frequently observed. For example, independent studies identified overlapping but different transcriptomic gene expression profiles in Yellow Fever vaccine 17D (YF-17D) immunized human subjects. Different experimental and analysis conditions were likely contr...

journal_title：BMC bioinformatics

authors： Ong E,Sun P,Berke K,Zheng J,Wu G,He Y

更新日期：2019-12-23 00:00:00

abstract：BACKGROUND:Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as "molecular switches" in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and...

journal_title：BMC bioinformatics

authors： Sarkar A,Kumar S,Sundar D

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the m...

journal_title：BMC bioinformatics

authors： McQuisten KA,Peek AS

更新日期：2007-06-07 00:00:00

abstract：BACKGROUND:Despite the widespread use of high throughput expression platforms and the availability of a desktop implementation of Gene Set Enrichment Analysis (GSEA) that enables non-experts to perform gene set based analyses, the availability of the necessary precompiled gene sets is rare for species other than human....

journal_title：BMC bioinformatics

authors： Powell JA

更新日期：2014-05-17 00:00:00

abstract：:Advances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher sys...

journal_title：BMC bioinformatics

authors： Yang JY,Dunker A,Liu JS,Qin X,Arabnia HR,Yang W,Niemierko A,Chen Z,Luo Z,Wang L,Liu Y,Xu D,Deng Y,Tong W,Yang M

更新日期：2014-01-01 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:Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regu...

journal_title：BMC bioinformatics

authors： Li L,Che D,Wang X,Zhang P,Rahman SU,Zhao J,Yu J,Tao S,Lu H,Liao M

更新日期：2019-03-04 00:00:00

abstract：BACKGROUND:Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites. RESULTS:We propose to identify and group similar profiles using tw...

journal_title：BMC bioinformatics

authors： Kielbasa SM,Gonze D,Herzel H

更新日期：2005-09-28 00:00:00

abstract：BACKGROUND:Viral infection by dengue virus is a major public health problem in tropical countries. Early diagnosis and detection are increasingly based on quantitative reverse transcriptase real-time polymerase chain reaction (RT-qPCR) directed against genomic regions conserved between different isolates. Genetic varia...

journal_title：BMC bioinformatics

authors： Vanneste K,Garlant L,Broeders S,Van Gucht S,Roosens NH

更新日期：2018-09-04 00:00:00

abstract：BACKGROUND:Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of pot...

journal_title：BMC bioinformatics

authors： Che D,Guo S,Jiang Q,Chen L

更新日期：2020-07-14 00:00:00

abstract：BACKGROUND:Protein function in eukaryotic cells is often controlled in a cell cycle-dependent manner. Therefore, the correct assignment of cellular phenotypes to cell cycle phases is a crucial task in cell biology research. Nuclear proteins whose localization varies during the cell cycle are valuable and frequently use...

journal_title：BMC bioinformatics

authors： Schönenberger F,Deutzmann A,Ferrando-May E,Merhof D

更新日期：2015-05-29 00:00:00