Hit integration for identifying optimal spaced seeds.

abstract：BACKGROUND:Recent studies have shown that N6-methyladenosine (m6A) plays a critical role in numbers of biological processes and complex human diseases. However, the regulatory mechanisms of most methylation sites remain uncharted. Thus, in-depth study of the epi-transcriptomic patterns of m6A may provide insights into ...

journal_title：BMC bioinformatics

authors： Zhang L,Chen S,Zhu J,Meng J,Liu H

更新日期：2020-10-09 00:00:00

abstract：BACKGROUND:Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. RESULTS:In this wor...

journal_title：BMC bioinformatics

authors： Arkun Y

更新日期：2019-11-28 00:00:00

abstract：BACKGROUND:De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, sequencing errors and repeated subsequences render the identification of the true underlying sequence dif...

journal_title：BMC bioinformatics

authors： Steyaert A,Audenaert P,Fostier J

更新日期：2020-09-14 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:Comparison of metabolic networks is typically performed based on the organisms' enzyme contents. This approach disregards functional replacements as well as orthologies that are misannotated. Direct comparison of the structure of metabolic networks can circumvent these problems. RESULTS:Metabolic networks a...

journal_title：BMC bioinformatics

authors： Forst CV,Flamm C,Hofacker IL,Stadler PF

更新日期：2006-02-14 00:00:00

abstract：BACKGROUND:Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the defa...

journal_title：BMC bioinformatics

authors： Ong E,Xie J,Ni Z,Liu Q,Sarntivijai S,Lin Y,Cooper D,Terryn R,Stathias V,Chung C,Schürer S,He Y

更新日期：2017-12-21 00:00:00

abstract：BACKGROUND:Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance...

journal_title：BMC bioinformatics

authors： Giri AV,Anishetty S,Gautam P

更新日期：2004-09-09 00:00:00

abstract：BACKGROUND:A common feature of microarray experiments is the occurrence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative backgro...

journal_title：BMC bioinformatics

authors： Tom BD,Gilks WR,Brooke-Powell ET,Ajioka JW

更新日期：2005-09-26 00:00:00

abstract：BACKGROUND:Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips need...

journal_title：BMC bioinformatics

authors： Page GP,Edwards JW,Gadbury GL,Yelisetti P,Wang J,Trivedi P,Allison DB

更新日期：2006-02-22 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:miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight in order to gain insig...

journal_title：BMC bioinformatics

authors： Licursi V,Conte F,Fiscon G,Paci P

更新日期：2019-11-04 00:00:00

abstract：BACKGROUND:The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. However, an alignment is often difficult to obtain without prior structural information. Thus the need for tools to automate this process. RESUL...

journal_title：BMC bioinformatics

authors： Anwar M,Nguyen T,Turcotte M

更新日期：2006-05-05 00:00:00

abstract：BACKGROUND:Genome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context. RESU...

journal_title：BMC bioinformatics

authors： Konietzny SG,Dietz L,McHardy AC

更新日期：2011-05-09 00:00:00

abstract：BACKGROUND:Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and m...

journal_title：BMC bioinformatics

authors： Rios D,McLaren WM,Chen Y,Birney E,Stabenau A,Flicek P,Cunningham F

更新日期：2010-05-11 00:00:00

abstract：BACKGROUND:Drug discovery is the process through which potential new medicines are identified. High-throughput screening and computer-aided drug discovery/design are the two main drug discovery methods for now, which have successfully discovered a series of drugs. However, development of new drugs is still an extremely...

journal_title：BMC bioinformatics

authors： Sang S,Yang Z,Wang L,Liu X,Lin H,Wang J

更新日期：2018-05-30 00:00:00

abstract：BACKGROUND:Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene express...

journal_title：BMC bioinformatics

authors： Zhang SD,Gant TW

更新日期：2008-06-02 00:00:00

abstract：BACKGROUND:The recent explosion in biological and other real-world network data has created the need for improved tools for large network analyses. In addition to well established global network properties, several new mathematical techniques for analyzing local structural properties of large networks have been develop...

journal_title：BMC bioinformatics

authors： Milenković T,Lai J,Przulj N

更新日期：2008-01-30 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:Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction h...

journal_title：BMC bioinformatics

authors： Su EC,Chiu HS,Lo A,Hwang JK,Sung TY,Hsu WL

更新日期：2007-09-08 00:00:00

abstract：BACKGROUND:Infections are often associated to comorbidity that increases the risk of medical conditions which can lead to further morbidity and mortality. SARS is a threat which is similar to MERS virus, but the comorbidity is the key aspect to underline their different impacts. One UK doctor says "I'd rather have HIV ...

journal_title：BMC bioinformatics

authors： Moni MA,Liò P

更新日期：2014-10-24 00:00:00

abstract：BACKGROUND:One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The ...

journal_title：BMC bioinformatics

authors： Gdanetz K,Benucci GMN,Vande Pol N,Bonito G

更新日期：2017-12-06 00:00:00

abstract：BACKGROUND:Pattern recognition receptors of the immune system have key roles in the regulation of pathways after the recognition of microbial- and danger-associated molecular patterns in vertebrates. Members of NOD-like receptor (NLR) family typically function intracellularly. The NOD-like receptor family CARD domain c...

journal_title：BMC bioinformatics

authors： Mótyán JA,Bagossi P,Benkő S,Tőzsér J

更新日期：2013-09-17 00:00:00

abstract：BACKGROUND:This paper presents a novel approach for Generative Anatomy Modeling Language (GAML). This approach automatically detects the geometric partitions in 3D anatomy that in turn speeds up integrated non-linear optimization model in GAML for 3D anatomy modeling with constraints (e.g. joints). This integrated non-...

journal_title：BMC bioinformatics

authors： Demirel D,Cetinsaya B,Halic T,Kockara S,Ahmadi S

更新日期：2019-03-14 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: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:In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functional antibody sequences to their sourcing germline gene segments is vital not only for understanding...

journal_title：BMC bioinformatics

authors： Wang X,Wu D,Zheng S,Sun J,Tao L,Li Y,Cao Z

更新日期：2008-12-12 00:00:00

abstract：BACKGROUND:MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes ba...

journal_title：BMC bioinformatics

authors： González JR,Carrasco JL,Armengol L,Villatoro S,Jover L,Yasui Y,Estivill X

更新日期：2008-06-04 00:00:00

abstract：BACKGROUND:In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the test and reference sample DNA levels. This ratio may be influenced by systematic measurement effect...

journal_title：BMC bioinformatics

authors： Khojasteh M,Lam WL,Ward RK,MacAulay C

更新日期：2005-11-18 00:00:00

abstract：BACKGROUND:The BioCreative text mining evaluation investigated the application of text mining methods to the task of automatically extracting information from text in biomedical research articles. We participated in Task 2 of the evaluation. For this task, we built a system to automatically annotate a given protein wit...

journal_title：BMC bioinformatics

authors： Ray S,Craven M

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Bioluminescent proteins (BLPs) widely exist in many living organisms. As BLPs are featured by the capability of emitting lights, they can be served as biomarkers and easily detected in biomedical research, such as gene expression analysis and signal transduction pathways. Therefore, accurate identification o...

journal_title：BMC bioinformatics

authors： Zhang J,Chai H,Yang G,Ma Z

更新日期：2017-06-05 00:00:00