FANTOM: Functional and taxonomic analysis of metagenomes.

abstract：BACKGROUND:The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologist...

journal_title：BMC bioinformatics

authors： Yin Z,Zhou X,Bakal C,Li F,Sun Y,Perrimon N,Wong ST

更新日期：2008-06-05 00:00:00

abstract：BACKGROUND:Ontologies are widely used to represent knowledge in biomedicine. Systematic approaches for detecting errors and disagreements are needed for large ontologies with hundreds or thousands of terms and semantic relationships. A recent approach of defining terms using logical definitions is now increasingly bein...

journal_title：BMC bioinformatics

authors： Köhler S,Bauer S,Mungall CJ,Carletti G,Smith CL,Schofield P,Gkoutos GV,Robinson PN

更新日期：2011-10-27 00:00:00

abstract：BACKGROUND:Current taxonomic classification tools use exact string matching algorithms that are effective to tackle the data from the next generation sequencing technology. However, the unique error patterns in the third generation sequencing (TGS) technologies could reduce the accuracy of these programs. RESULTS:We d...

journal_title：BMC bioinformatics

authors： Bui VK,Wei C

更新日期：2020-10-20 00:00:00

abstract：BACKGROUND:Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new m...

journal_title：BMC bioinformatics

authors： Karain WI

更新日期：2017-11-28 00:00:00

abstract：BACKGROUND:Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipeli...

journal_title：BMC bioinformatics

authors： McTavish EJ,Pettengill J,Davis S,Rand H,Strain E,Allard M,Timme RE

更新日期：2017-03-20 00:00:00

abstract：BACKGROUND:Word sense disambiguation (WSD) attempts to solve lexical ambiguities by identifying the correct meaning of a word based on its context. WSD has been demonstrated to be an important step in knowledge-based approaches to automatic summarization. However, the correlation between the accuracy of the WSD methods...

journal_title：BMC bioinformatics

authors： Plaza L,Jimeno-Yepes AJ,Díaz A,Aronson AR

更新日期：2011-08-26 00:00:00

abstract：BACKGROUND:Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively high cost of long-read sequencing, it is unclear what coverage is ne...

journal_title：BMC bioinformatics

authors： Fang L,Hu J,Wang D,Wang K

更新日期：2018-05-23 00:00:00

abstract：BACKGROUND:Because common complex diseases are affected by multiple genes and environmental factors, it is essential to investigate gene-gene and/or gene-environment interactions to understand genetic architecture of complex diseases. After the great success of large scale genome-wide association (GWA) studies using th...

journal_title：BMC bioinformatics

authors： Oh S,Lee J,Kwon MS,Weir B,Ha K,Park T

更新日期：2012-06-11 00:00:00

abstract：:After publication of this supplement article. ...

journal_title：BMC bioinformatics

authors： Pan B,Kusko R,Xiao W,Zheng Y,Liu Z,Xiao C,Sakkiah S,Guo W,Gong P,Zhang C,Ge W,Shi L,Tong W,Hong H

更新日期：2019-05-15 00:00:00

abstract：BACKGROUND:G-protein-coupled receptors (GPCRs) play a key role in diverse physiological processes and are the targets of almost two-thirds of the marketed drugs. The 3 D structures of GPCRs are largely unavailable; however, a large number of GPCR primary sequences are known. To facilitate the identification and charact...

journal_title：BMC bioinformatics

authors： Peng ZL,Yang JY,Chen X

更新日期：2010-08-09 00:00:00

abstract：BACKGROUND:Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, their use is still limited in the bioinformatics field due to the fundamental fact that the asynchro...

journal_title：BMC bioinformatics

authors： Ito S,Yadome M,Nishiki T,Ishiduki S,Inoue H,Yamaguchi R,Miyano S

更新日期：2019-12-02 00:00:00

abstract：BACKGROUND:Population stratification is a systematic difference in allele frequencies between subpopulations. This can lead to spurious association findings in the case-control genome wide association studies (GWASs) used to identify single nucleotide polymorphisms (SNPs) associated with disease-linked phenotypes. Meth...

journal_title：BMC bioinformatics

authors： Hajiloo M,Sapkota Y,Mackey JR,Robson P,Greiner R,Damaraju S

更新日期：2013-02-22 00:00:00

abstract：BACKGROUND:A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal gen...

journal_title：BMC bioinformatics

authors： Khan A,Liu Q,Wang K

更新日期：2018-12-28 00:00:00

abstract：BACKGROUND:To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is compu...

journal_title：BMC bioinformatics

authors： Abby SS,Tannier E,Gouy M,Daubin V

更新日期：2010-06-15 00:00:00

abstract：BACKGROUND:Human breast cancer resistance protein (BCRP) is an ATP-binding cassette (ABC) efflux transporter that confers multidrug resistance in cancers and also plays an important role in the absorption, distribution and elimination of drugs. Prediction as to if drugs or new molecular entities are BCRP substrates sho...

journal_title：BMC bioinformatics

authors： Hazai E,Hazai I,Ragueneau-Majlessi I,Chung SP,Bikadi Z,Mao Q

更新日期：2013-04-15 00:00:00

abstract：BACKGROUND:The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appea...

journal_title：BMC bioinformatics

authors： Tatusov RL,Fedorova ND,Jackson JD,Jacobs AR,Kiryutin B,Koonin EV,Krylov DM,Mazumder R,Mekhedov SL,Nikolskaya AN,Rao BS,Smirnov S,Sverdlov AV,Vasudevan S,Wolf YI,Yin JJ,Natale DA

更新日期：2003-09-11 00:00:00

abstract：BACKGROUND:In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI) network is a particular biological network which...

journal_title：BMC bioinformatics

authors： Turanalp ME,Can T

更新日期：2008-06-11 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:Orthologs inference is the starting point of most comparative genomics studies, and a plethora of methods have been designed in the last decade to address this challenging task. In this paper we focus on the problems of deciding consistency with a species tree (known or not) of a partial set of orthology/par...

journal_title：BMC bioinformatics

authors： Jones M,Paul C,Scornavacca C

更新日期：2016-11-11 00:00:00

abstract：:Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughp...

journal_title：BMC bioinformatics

authors： Li YF,Radivojac P

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Chemical named entities represent an important facet of biomedical text. RESULTS:We have developed a system to use character-based n-grams, Maximum Entropy Markov Models and rescoring to recognise chemical names and other such entities, and to make confidence estimates for the extracted entities. An adjusta...

journal_title：BMC bioinformatics

authors： Corbett P,Copestake A

更新日期：2008-11-19 00:00:00

abstract：BACKGROUND:PCR has the potential to detect and precisely quantify specific DNA sequences, but it is not yet often used as a fully quantitative method. A number of data collection and processing strategies have been described for the implementation of quantitative PCR. However, they can be experimentally cumbersome, the...

journal_title：BMC bioinformatics

authors： Karlen Y,McNair A,Perseguers S,Mazza C,Mermod N

更新日期：2007-04-20 00:00:00

abstract：BACKGROUND:The cost efficient two-stage design is often used in genome-wide association studies (GWASs) in searching for genetic loci underlying the susceptibility for complex diseases. Replication-based analysis, which considers data from each stage separately, often suffers from loss of efficiency. Joint test that co...

journal_title：BMC bioinformatics

authors： Pan D,Li Q,Jiang N,Liu A,Yu K

更新日期：2011-01-07 00:00:00

abstract：BACKGROUND:The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear ...

journal_title：BMC bioinformatics

authors： Lemieux S

更新日期：2006-08-25 00:00:00

abstract：BACKGROUND:High-throughput technology allows for genome-wide measurements at different molecular levels for the same patient, e.g. single nucleotide polymorphisms (SNPs) and gene expression. Correspondingly, it might be beneficial to also integrate complementary information from different molecular levels when building...

journal_title：BMC bioinformatics

authors： Hieke S,Benner A,Schlenl RF,Schumacher M,Bullinger L,Binder H

更新日期：2016-08-30 00:00:00

abstract：BACKGROUND:The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the simila...

journal_title：BMC bioinformatics

authors： Zhang M,Yang L,Ren J,Ahlgren NA,Fuhrman JA,Sun F

更新日期：2017-03-14 00:00:00

abstract：BACKGROUND:Microbial electrosynthesis and electro fermentation are techniques that aim to optimize microbial production of chemicals and fuels by regulating the cellular redox balance via interaction with electrodes. While the concept is known for decades major knowledge gaps remain, which make it hard to evaluate its ...

journal_title：BMC bioinformatics

authors： Kracke F,Krömer JO

更新日期：2014-12-30 00:00:00

abstract：BACKGROUND:In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching techniq...

journal_title：BMC bioinformatics

authors： Bhattacharya S,Bhattacharyya C,Chandra NR

更新日期：2006-12-18 00:00:00

abstract：BACKGROUND:Continuous enzyme kinetic assays are often used in high-throughput applications, as they allow rapid acquisition of large amounts of kinetic data and increased confidence compared to discontinuous assays. However, data analysis is often rate-limiting in high-throughput enzyme assays, as manual inspection and...

journal_title：BMC bioinformatics

authors： Olp MD,Kalous KS,Smith BC

更新日期：2020-05-14 00:00:00

abstract：BACKGROUND:Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff bet...

journal_title：BMC bioinformatics

authors： Nashta-Ali D,Aliyari A,Ahmadian Moghadam A,Edrisi MA,Motahari SA,Hossein Khalaj B

更新日期：2017-02-23 00:00:00