COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

abstract：BACKGROUND:Expression profiles obtained from multiple perturbation experiments are increasingly used to reconstruct transcriptional regulatory networks, from well studied, simple organisms up to higher eukaryotes. Admittedly, a key ingredient in developing a reconstruction method is its ability to integrate heterogeneo...

journal_title：BMC bioinformatics

authors： Veber P,Guziolowski C,Le Borgne M,Radulescu O,Siegel A

更新日期：2008-05-06 00:00:00

abstract：BACKGROUND:To interpret microarray experiments, several ontological analysis tools have been developed. However, current tools are limited to specific organisms. RESULTS:We developed a bioinformatics system to assign the probe set sequences of any organism to a hierarchical functional classification modelled on KEGG o...

journal_title：BMC bioinformatics

authors： Goffard N,Weiller G

更新日期：2007-03-12 00:00:00

abstract：BACKGROUND:The rapid pace of bioscience research makes it very challenging to track relevant articles in one's area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year. Thus it is not surprising to se...

journal_title：BMC bioinformatics

authors： Srinivasan P,Zhang XN,Bouten R,Chang C

更新日期：2015-06-20 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved miRNAs. Plants and invertebrates employ their miRNA in defense against viruses by targeting and degrad...

journal_title：BMC bioinformatics

authors： Carl JW Jr,Trgovcich J,Hannenhalli S

更新日期：2013-01-01 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：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:HIV/AIDS is a serious threat to public health. The emergence of drug resistance mutations diminishes the effectiveness of drug therapy for HIV/AIDS. Developing a computational prediction of drug resistance phenotype will enable efficient and timely selection of the best treatment regimens. RESULTS:A unified...

journal_title：BMC bioinformatics

authors： Shen C,Yu X,Harrison RW,Weber IT

更新日期：2016-08-31 00:00:00

abstract：BACKGROUND:The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relations...

journal_title：BMC bioinformatics

authors： Gutiérrez FI,Rodriguez-Valenzuela F,Ibarra IL,Devos DP,Melo F

更新日期：2016-01-05 00:00:00

abstract：BACKGROUND:Given a set of t n-length DNA sequences, q satisfying 0 < q ≤ 1, and l and d satisfying 0 ≤ d < l < n, the quorum planted motif search (qPMS) finds l-length strings that occur in at least qt input sequences with up to d mismatches and is mainly used to locate transcription factor binding sites in DNA sequenc...

journal_title：BMC bioinformatics

authors： Yu Q,Wei D,Huo H

更新日期：2018-06-18 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:Current microRNA (miRNA) research in progress has engendered rapid accumulation of expression data evolving from microarray experiments. Such experiments are generally performed over different tissues belonging to a specific species of metazoan. For disease diagnosis, microarray probes are also prepared with...

journal_title：BMC bioinformatics

authors： Bandyopadhyay S,Bhattacharyya M

更新日期：2009-05-28 00:00:00

abstract：BACKGROUND:Analysis of gene expression data in terms of a priori-defined gene sets has recently received significant attention as this approach typically yields more compact and interpretable results than those produced by traditional methods that rely on individual genes. The set-level strategy can also be adopted wit...

journal_title：BMC bioinformatics

authors： Holec M,Kléma J,Zelezný F,Tolar J

更新日期：2012-06-25 00:00:00

abstract：BACKGROUND:New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bio...

journal_title：BMC bioinformatics

authors： Hajibabaei M,Singer GA

更新日期：2009-11-10 00:00:00

abstract：BACKGROUND:Computational gene finding algorithms have proven their robustness in identifying genes in complete genomes. However, metagenomic sequencing has presented new challenges due to the incomplete and fragmented nature of the data. During the last few years, attempts have been made to extract complete and incompl...

journal_title：BMC bioinformatics

authors： El Allali A,Rose JR

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accurately acquiring the synaptic connectivity, and they cannot effectively alleviate the burden of synaps...

journal_title：BMC bioinformatics

authors： Xiao C,Li W,Deng H,Chen X,Yang Y,Xie Q,Han H

更新日期：2018-07-13 00:00:00

abstract：BACKGROUND:The importance of biodiversity conservation has been increasing steadily due to its benefits to human beings. Recently, producing and managing biodiversity databases have become much easier because of the information technology (IT) advancement. This made the general public's participation in biodiversity co...

journal_title：BMC bioinformatics

authors： Paik IH,Lim J,Chun BS,Jin SD,Yu JP,Lee JW,Bhak J,Paek WK

更新日期：2009-12-03 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:Computer-aided segmentation and border detection in dermoscopic images is one of the core components of diagnostic procedures and therapeutic interventions for skin cancer. Automated assessment tools for dermoscopy images have become an important research field mainly because of inter- and intra-observer var...

journal_title：BMC bioinformatics

authors： Kockara S,Mete M,Chen B,Aydin K

更新日期：2010-10-07 00:00:00

abstract：BACKGROUND:An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA binding preferences, it is a challenging problem to establish an accurate model for recognition of fun...

journal_title：BMC bioinformatics

authors： Stepanova M,Lin F,Lin VC

更新日期：2006-12-12 00:00:00

abstract：BACKGROUND:Genome scale data on protein interactions are generally represented as large networks, or graphs, where hundreds or thousands of proteins are linked to one another. Since proteins tend to function in groups, or complexes, an important goal has been to reliably identify protein complexes from these graphs. Th...

journal_title：BMC bioinformatics

authors： Vlasblom J,Wodak SJ

更新日期：2009-03-30 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

abstract：BACKGROUND:Although many genomic features have been used in the prediction of protein-protein interactions (PPIs), frequently only one is used in a computational method. After realizing the limited power in the prediction using only one genomic feature, investigators are now moving toward integration. So far, there hav...

journal_title：BMC bioinformatics

authors： Sun J,Sun Y,Ding G,Liu Q,Wang C,He Y,Shi T,Li Y,Zhao Z

更新日期：2007-10-26 00:00:00

abstract：BACKGROUND:Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion dise...

journal_title：BMC bioinformatics

authors： Pellegrini M,Renda ME,Vecchio A

更新日期：2012-03-28 00:00:00

abstract：BACKGROUND:It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opp...

journal_title：BMC bioinformatics

authors： Borozan I,Wilson S,Blanchette P,Laflamme P,Watt SN,Krzyzanowski PM,Sircoulomb F,Rottapel R,Branton PE,Ferretti V

更新日期：2012-08-17 00:00:00

abstract：BACKGROUND:Identifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phe...

journal_title：BMC bioinformatics

authors： Lee JY,Fujimoto GM,Wilson R,Wiley HS,Payne SH

更新日期：2018-06-11 00:00:00

abstract：BACKGROUND:One of the important goals in the post-genomic era is to determine the regulatory elements within the non-coding DNA of a given organism's genome. The identification of functional cis-regulatory modules has proven difficult since the component factor binding sites are small and the rules governing their arra...

journal_title：BMC bioinformatics

authors： Emberly E,Rajewsky N,Siggia ED

更新日期：2003-11-20 00:00:00

abstract：BACKGROUND:Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment. Former benchmark studies revealed drawbacks of MSA methods on nucleo...

journal_title：BMC bioinformatics

authors： Wang Y,Wu H,Cai Y

更新日期：2018-12-31 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:We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of protein function. RESULTS:Explicit modeling of multilabels significantly improves the capability o...

journal_title：BMC bioinformatics

authors： Roth V,Fischer B

更新日期：2007-05-03 00:00:00

abstract：BACKGROUND:Time- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For example, drug-induced toxicities are not reported by the actual time or dose triggering the event, ...

journal_title：BMC bioinformatics

authors： Li Z,Lin J,Sibley AB,Truong T,Chua KC,Jiang Y,McCarthy J,Kroetz DL,Allen A,Owzar K

更新日期：2019-05-28 00:00:00