GlycomeDB - integration of open-access carbohydrate structure databases.

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:Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the reproducibility of identified biomarkers across tissues and experiments is still a challenge for this...

journal_title：BMC bioinformatics

authors： Zhang X,Gao L,Liu ZP,Chen L

更新日期：2015-03-18 00:00:00

abstract：BACKGROUND:Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. In order to fully capture the intrinsic value and knowledge expressed within them, we need to take advantage of their inner structure, which implicitly co...

journal_title：BMC bioinformatics

authors： Groza T,Hunter J,Zankl A

更新日期：2012-10-15 00:00:00

abstract：BACKGROUND:Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc). Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and...

journal_title：BMC bioinformatics

authors： Liu Q,Crammer K,Pereira FC,Roos DS

更新日期：2008-10-14 00:00:00

abstract：BACKGROUND:High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key for drawing meaningful and accurate conclusions from the massive and complex datasets generat...

journal_title：BMC bioinformatics

authors： Bullard JH,Purdom E,Hansen KD,Dudoit S

更新日期：2010-02-18 00:00:00

abstract：BACKGROUND:Reproducibility of results can have a significant impact on the acceptance of new technologies in gene expression analysis. With the recent introduction of the so-called next-generation sequencing (NGS) technology and established microarrays, one is able to choose between two completely different platforms f...

journal_title：BMC bioinformatics

authors： Stiglic G,Bajgot M,Kokol P

更新日期：2010-04-08 00:00:00

abstract：BACKGROUND:Cartilage damage is a crucial feature involved in several pathological conditions characterized by joint disorders, such as osteoarthritis and rheumatoid arthritis. Accumulated evidences showed that Wnt/β-catenin pathway plays a role in the pathogenesis of cartilage damage. In addition, it is experimentally ...

journal_title：BMC bioinformatics

authors： Zhou W,He X,Chen Z,Fan D,Wang Y,Feng H,Zhang G,Lu A,Xiao L

更新日期：2019-07-31 00:00:00

abstract：BACKGROUND:Expression quantitative trait loci (eQTL) mapping is often used to identify genetic loci and candidate genes correlated with traits. Although usually a group of genes affect complex traits, genes in most eQTL mapping methods are considered as independent. Recently, some eQTL mapping methods have accounted fo...

journal_title：BMC bioinformatics

authors： Wang Y,Richard R,Pan Y

更新日期：2016-12-13 00:00:00

abstract：BACKGROUND:Biologists often conduct multiple but different cDNA microarray studies that all target the same biological system or pathway. Within each study, replicate slides within repeated identical experiments are often produced. Pooling information across studies can help more accurately identify true target genes. ...

journal_title：BMC bioinformatics

authors： Conlon EM,Song JJ,Liu JS

更新日期：2006-05-05 00:00:00

abstract：BACKGROUND:Scaffold proteins are known for being crucial regulators of various cellular functions by assembling multiple proteins involved in signaling and metabolic pathways. Identification of scaffold proteins and the study of their molecular mechanisms can open a new aspect of cellular systemic regulation and the re...

journal_title：BMC bioinformatics

authors： Oh K,Yi GS

更新日期：2016-07-28 00:00:00

abstract：UNLABELLED: BACKGROUND:Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing...

journal_title：BMC bioinformatics

authors： Antoniw J,Beacham AM,Baldwin TK,Urban M,Rudd JJ,Hammond-Kosack KE

更新日期：2011-11-15 00:00:00

abstract：BACKGROUND:Single amino acid repeats make up a significant proportion in all of the proteomes that have currently been determined. They have been shown to be functionally and medically significant, and are associated with cancers and neuro-degenerative diseases such as Huntington's Chorea, where a poly-glutamine repeat...

journal_title：BMC bioinformatics

authors： Depledge DP,Dalby AR

更新日期：2005-08-03 00:00:00

abstract：BACKGROUND:Schizophrenia, bipolar disorder, and major depression are devastating mental diseases, each with distinctive yet overlapping epidemiologic characteristics. Microarray and proteomics data have revealed genes which expressed abnormally in patients. Several single nucleotide polymorphisms (SNPs) and mutations a...

journal_title：BMC bioinformatics

authors： Lee SA,Tsao TT,Yang KC,Lin H,Kuo YL,Hsu CH,Lee WK,Huang KC,Kao CY

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The...

journal_title：BMC bioinformatics

authors： Varón A,Wheeler WC

更新日期：2013-02-26 00:00:00

abstract：BACKGROUND:Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis methods if meaningful biological conclusions are to be drawn. For example, a range of traditional s...

journal_title：BMC bioinformatics

authors： Ibrahim M,Jassim S,Cawthorne MA,Langlands K

更新日期：2014-11-04 00:00:00

abstract：BACKGROUND:Cellular functions are coordinately carried out by groups of genes forming functional modules. Identifying such modules in the transcriptional regulatory network (TRN) of organisms is important for understanding the structure and function of these fundamental cellular networks and essential for the emerging ...

journal_title：BMC bioinformatics

authors： Ma HW,Buer J,Zeng AP

更新日期：2004-12-16 00:00:00

abstract：BACKGROUND:Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences followi...

journal_title：BMC bioinformatics

authors： Frank RL,Mane A,Ercal F

更新日期：2006-09-06 00:00:00

abstract：BACKGROUND:RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence o...

journal_title：BMC bioinformatics

authors： Li B,Dewey CN

更新日期：2011-08-04 00:00:00

abstract：BACKGROUND:Biomedical processes can provide essential information about the (mal-) functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attribute...

journal_title：BMC bioinformatics

authors： Andrade AQ,Blondé W,Hastings J,Schulz S

更新日期：2012-08-28 00:00:00

abstract：BACKGROUND:Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e., spun coat, large microfiber, and medium microfiber). Our analysis of the acquired terabyte-sized c...

journal_title：BMC bioinformatics

authors： Bajcsy P,Yoon S,Florczyk SJ,Hotaling NA,Simon M,Szczypinski PM,Schaub NJ,Simon CG Jr,Brady M,Sriram RD

更新日期：2017-11-28 00:00:00

abstract：BACKGROUND:Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presen...

journal_title：BMC bioinformatics

authors： Wenskovitch JE Jr,Harris LA,Tapia JJ,Faeder JR,Marai GE

更新日期：2014-09-25 00:00:00

abstract：BACKGROUND:Whole exome sequencing (WES) has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder. This approach is a revolution in medical genetics history, impacting both fundamental research, and diagnostic methods leading to personalized medicine. A plethora of effic...

journal_title：BMC bioinformatics

authors： Coutant S,Cabot C,Lefebvre A,Léonard M,Prieur-Gaston E,Campion D,Lecroq T,Dauchel H

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various existing methods measure similarity between two profiles and, hence, the likelihood that the two prote...

journal_title：BMC bioinformatics

authors： Cokus S,Mizutani S,Pellegrini M

更新日期：2007-05-22 00:00:00

abstract：BACKGROUND:Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. Howeve...

journal_title：BMC bioinformatics

authors： Rueda AJV,Monzon AM,Ardanaz SM,Iglesias LE,Parisi G

更新日期：2018-01-30 00:00:00

abstract：BACKGROUND:The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files design...

journal_title：BMC bioinformatics

authors： Stoneberg Holt SD,Holt JA

更新日期：2004-10-29 00:00:00

abstract：BACKGROUND:Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs from possible false positive hits. As a consequence, some BLAST hits are discar...

journal_title：BMC bioinformatics

authors： Fokkens L,Botelho SM,Boekhorst J,Snel B

更新日期：2010-02-12 00:00:00

abstract：BACKGROUND:The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have...

journal_title：BMC bioinformatics

authors： Veuthey AL,Bridge A,Gobeill J,Ruch P,McEntyre JR,Bougueleret L,Xenarios I

更新日期：2013-03-22 00:00:00

abstract：BACKGROUND:Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methylation, especially N6-methyladenosine, has become one of the most researched topics in epigenetics. ...

journal_title：BMC bioinformatics

authors： Wu X,Wei Z,Chen K,Zhang Q,Su J,Liu H,Zhang L,Meng J

更新日期：2019-05-02 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

abstract：BACKGROUND:Many readers will sympathize with the following story. You are viewing a gene sequence in Entrez, and you want to find whether it contains a particular sequence motif. You reach for the browser's "find in page" button, but those darn spaces every 10 bp get in the way. And what if the motif is on the opposite...

journal_title：BMC bioinformatics

authors： Hu Z,Frith M,Niu T,Weng Z

更新日期：2003-01-04 00:00:00