GOPET: a tool for automated predictions of Gene Ontology terms.

abstract：BACKGROUND:Antibodies revolutionized cancer treatment over the past decades. Despite their successfully application, there are still challenges to overcome to improve efficacy, such as the heterogeneous distribution of antibodies within tumors. Tumor microenvironment features, such as the distribution of tumor and othe...

journal_title：BMC bioinformatics

authors： Cartaxo AL,Almeida J,Gualda EJ,Marsal M,Loza-Alvarez P,Brito C,Isidro IA

更新日期：2020-11-17 00:00:00

abstract：BACKGROUND:As molecular biology is creating an increasing amount of sequence and structure data, the multitude of software to analyze this data is also rising. Most of the programs are made for a specific task, hence the user often needs to combine multiple programs in order to reach a goal. This can make the data proc...

journal_title：BMC bioinformatics

authors： Kunzmann P,Hamacher K

更新日期：2018-10-01 00:00:00

abstract：BACKGROUND:Cryo-electron microscopy (Cryo-EM) is widely used in the determination of the three-dimensional (3D) structures of macromolecules. Particle picking from 2D micrographs remains a challenging early step in the Cryo-EM pipeline due to the diversity of particle shapes and the extremely low signal-to-noise ratio ...

journal_title：BMC bioinformatics

authors： Al-Azzawi A,Ouadou A,Max H,Duan Y,Tanner JJ,Cheng J

更新日期：2020-11-09 00:00:00

abstract：BACKGROUND:Metabolomics experiments using Mass Spectrometry (MS) technology measure the mass to charge ratio (m/z) and intensity of ionised molecules in crude extracts of complex biological samples to generate high dimensional metabolite 'fingerprint' or metabolite 'profile' data. High resolution MS instruments perform...

journal_title：BMC bioinformatics

authors： Draper J,Enot DP,Parker D,Beckmann M,Snowdon S,Lin W,Zubair H

更新日期：2009-07-21 00:00:00

abstract：BACKGROUND:Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings i...

journal_title：BMC bioinformatics

authors： Camacho C,Coulouris G,Avagyan V,Ma N,Papadopoulos J,Bealer K,Madden TL

更新日期：2009-12-15 00:00:00

abstract：BACKGROUND:Ensemble predictors such as the random forest are known to have superior accuracy but their black-box predictions are difficult to interpret. In contrast, a generalized linear model (GLM) is very interpretable especially when forward feature selection is used to construct the model. However, forward feature ...

journal_title：BMC bioinformatics

authors： Song L,Langfelder P,Horvath S

更新日期：2013-01-16 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:Positron Emission Tomography (PET) is increasingly utilized in radiomics studies for treatment evaluation purposes. Nevertheless, lesion volume identification in PET images is a critical and still challenging step in the process of radiomics, due to the low spatial resolution and high noise level of PET imag...

journal_title：BMC bioinformatics

authors： Stefano A,Comelli A,Bravatà V,Barone S,Daskalovski I,Savoca G,Sabini MG,Ippolito M,Russo G

更新日期：2020-09-16 00:00:00

abstract：BACKGROUND:Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathol...

journal_title：BMC bioinformatics

authors： Corradi L,Mirisola V,Porro I,Torterolo L,Fato M,Romano P,Pfeffer U

更新日期：2009-10-15 00:00:00

abstract：BACKGROUND:Event sequences where different types of events often occur close together arise, e.g., when studying potential transcription factor binding sites (TFBS, events) of certain transcription factors (TF, types) in a DNA sequence. These events tend to occur in bursts: in some genomic regions there are more genes ...

journal_title：BMC bioinformatics

authors： Haiminen N,Mannila H,Terzi E

更新日期：2008-08-08 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:Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. RESULTS:We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Wa...

journal_title：BMC bioinformatics

authors： Hughes T,Hyun Y,Liberles DA

更新日期：2004-04-29 00:00:00

abstract：BACKGROUND:Great strides have been made in the effective treatment of HIV-1 with the development of second-generation protease inhibitors (PIs) that are effective against historically multi-PI-resistant HIV-1 variants. Nevertheless, mutation patterns that confer decreasing susceptibility to available PIs continue to ar...

journal_title：BMC bioinformatics

authors： Doherty KM,Nakka P,King BM,Rhee SY,Holmes SP,Shafer RW,Radhakrishnan ML

更新日期：2011-12-15 00:00:00

abstract：BACKGROUND:The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for...

journal_title：BMC bioinformatics

authors： Needhamsen M,Ewing E,Lund H,Gomez-Cabrero D,Harris RA,Kular L,Jagodic M

更新日期：2017-11-15 00:00:00

abstract：BACKGROUND:Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to illustrate the role of mechanisms such as copy number variation (CNV) or epigene...

journal_title：BMC bioinformatics

authors： Delatola EI,Lebarbier E,Mary-Huard T,Radvanyi F,Robin S,Wong J

更新日期：2017-07-11 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:To identify and prioritize the influential hub genes in a gene-set or biological pathway, most analyses rely on calculation of marginal effects or tests of statistical significance. These procedures may be inappropriate since hub nodes are common connection points and therefore may interact with other nodes ...

journal_title：BMC bioinformatics

authors： Chang HC,Chu CP,Lin SJ,Hsiao CK

更新日期：2020-03-12 00:00:00

abstract：BACKGROUND:Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functionally diverse proteins from a single gene. The emergence of next-generation sequencing technologies, e...

journal_title：BMC bioinformatics

authors： Zhang F,Deng CK,Wang M,Deng B,Barber R,Huang G

更新日期：2020-12-03 00:00:00

abstract：BACKGROUND:Most known eukaryotic genomes contain mobile copied elements called transposable elements. In some species, these elements account for the majority of the genome sequence. They have been subject to many mutations and other genomic events (copies, deletions, captures) during transposition. The identification ...

journal_title：BMC bioinformatics

authors： Tempel S,Rousseau C,Tahi F,Nicolas J

更新日期：2010-09-22 00:00:00

abstract：:Identifying segments in the genome of different individuals that are identical-by-descent (IBD) is a fundamental element of genetics. IBD data is used for numerous applications including demographic inference, heritability estimation, and mapping disease loci. Simultaneous detection of IBD over multiple haplotypes has...

journal_title：BMC bioinformatics

authors： Park DS,Baran Y,Hormozdiari F,Eng C,Torgerson DG,Burchard EG,Zaitlen N

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstrom...

journal_title：BMC bioinformatics

authors： Carugo O

更新日期：2018-02-23 00:00:00

abstract：:Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic networks has been considered in the past, the computational complexity of the existing solutions has so far lim...

journal_title：BMC bioinformatics

authors： Ay F,Dang M,Kahveci T

更新日期：2012-03-21 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:Biological data that are well-organized by an ontology, such as Gene Ontology, enables high-throughput availability of the semantic web. It can also be used to facilitate high throughput classification of biomedical information. However, to our knowledge, no evaluation has been published on automating classi...

journal_title：BMC bioinformatics

authors： Chen JL,Liu Y,Sam LT,Li J,Lussier YA

更新日期：2007-05-09 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: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:Recent studies in computational primary protein sequence analysis have leveraged the power of unlabeled data. For example, predictive models based on string kernels trained on sequences known to belong to particular folds or superfamilies, the so-called labeled data set, can attain significantly improved acc...

journal_title：BMC bioinformatics

authors： Kuksa P,Huang PH,Pavlovic V

更新日期：2009-04-29 00:00:00

abstract：BACKGROUND:Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2-5% of the genes encode for peptidases, irrespectively of the organism source. The basic peptidase function is "protein digestion" and this can be potentially dangerous in living organisms w...

journal_title：BMC bioinformatics

authors： Bartoli L,Calabrese R,Fariselli P,Mita DG,Casadio R

更新日期：2007-03-08 00:00:00

abstract：BACKGROUND:While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of the interactions underlying immune processes. Tools to explore the immune network are critical for ...

journal_title：BMC bioinformatics

authors： Atallah MB,Tandon V,Hiam KJ,Boyce H,Hori M,Atallah W,Spitzer MH,Engleman E,Mallick P

更新日期：2020-08-10 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