G-DOC Plus - an integrative bioinformatics platform for precision medicine.

abstract：BACKGROUND:The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the breeding progress. Laserscanning is a highly accurate and high resolution technique to acquire the 3D sh...

journal_title：BMC bioinformatics

authors： Heeren B,Paulus S,Goldbach H,Kuhlmann H,Mahlein AK,Rumpf M,Wirth B

更新日期：2020-07-29 00:00:00

abstract：BACKGROUND:Two-dimensional electrophoresis (2DE) is one of the most widely applied techniques in comparative proteomics. The basic task of 2DE is to identify differential protein expression by quantitative analysis of 2DE images. To reduce the errors of spot quantification in 2DE images, a novel brightness correction m...

journal_title：BMC bioinformatics

authors： Ou Q,Xiao J,Yu L,Wu K,Xiong B

更新日期：2020-03-19 00:00:00

abstract：BACKGROUND:XHMM is a widely used tool for copy-number variant (CNV) discovery from whole exome sequencing data but can require hours to days to run for large cohorts. A more scalable implementation would reduce the need for specialized computational resources and enable increased exploration of the configuration parame...

journal_title：BMC bioinformatics

authors： Linderman MD,Chia D,Wallace F,Nothaft FA

更新日期：2019-10-11 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:Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex...

journal_title：BMC bioinformatics

authors： Gouret P,Vitiello V,Balandraud N,Gilles A,Pontarotti P,Danchin EG

更新日期：2005-08-05 00:00:00

abstract：BACKGROUND:Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale va...

journal_title：BMC bioinformatics

authors： Aganezov S,Zban I,Aksenov V,Alexeev N,Schatz MC

更新日期：2019-12-17 00:00:00

abstract：BACKGROUND:Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an important first step toward understanding cellular function and machinery of a proteome. Solely deri...

journal_title：BMC bioinformatics

authors： Wu X,Zhu L,Guo J,Fu C,Zhou H,Dong D,Li Z,Zhang DY,Lin K

更新日期：2006-12-18 00:00:00

abstract：BACKGROUND:Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five...

journal_title：BMC bioinformatics

authors： Rangarajan A,Schedl T,Yook K,Chan J,Haenel S,Otis L,Faelten S,DePellegrin-Connelly T,Isaacson R,Skrzypek MS,Marygold SJ,Stefancsik R,Cherry JM,Sternberg PW,Müller HM

更新日期：2011-05-19 00:00:00

abstract：BACKGROUND:The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cryo-EM data analysis. Template-based particle picking by an objective function using fast local corre...

journal_title：BMC bioinformatics

authors： Wang WL,Yu Z,Castillo-Menendez LR,Sodroski J,Mao Y

更新日期：2019-04-03 00:00:00

abstract：BACKGROUND:Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. RESULTS:PubFocus w...

journal_title：BMC bioinformatics

authors： Plikus MV,Zhang Z,Chuong CM

更新日期：2006-10-02 00:00:00

abstract：BACKGROUND:DNA methylation of CpG dinucleotides is an essential epigenetic modification that plays a key role in transcription. Widely used DNA enrichment-based methods offer high coverage for measuring methylated CpG dinucleotides, with the lowest cost per CpG covered genome-wide. However, these methods measure the DN...

journal_title：BMC bioinformatics

authors： Xu J,Liu S,Yin P,Bulun S,Dai Y

更新日期：2018-12-22 00:00:00

abstract：BACKGROUND:Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on gene teams and homology teams. RESULTS:Our primary contribution is a local sliding-...

journal_title：BMC bioinformatics

authors： Sarkar A,Soueidan H,Nikolski M

更新日期：2011-10-05 00:00:00

abstract：BACKGROUND:Over the last few years transcriptome sequencing (RNA-Seq) has almost completely taken over microarrays for high-throughput studies of gene expression. Currently, the most popular use of RNA-Seq is to identify genes which are differentially expressed between two or more conditions. Despite the importance of ...

journal_title：BMC bioinformatics

authors： Rahmatallah Y,Emmert-Streib F,Glazko G

更新日期：2014-12-05 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: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:Genome-wide transcriptional profiling of patient blood samples offers a powerful tool to investigate underlying disease mechanisms and personalized treatment decisions. Most studies are based on analysis of total peripheral blood mononuclear cells (PBMCs), a mixed population. In this case, accuracy is inhere...

journal_title：BMC bioinformatics

authors： Bolen CR,Uduman M,Kleinstein SH

更新日期：2011-06-24 00:00:00

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:The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain i...

journal_title：BMC bioinformatics

authors： Lee H,Deng M,Sun F,Chen T

更新日期：2006-05-25 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:We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs. RESULTS:LAVA identifies combinations of six primer regions for basic LAM...

journal_title：BMC bioinformatics

authors： Torres C,Vitalis EA,Baker BR,Gardner SN,Torres MW,Dzenitis JM

更新日期：2011-06-16 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:Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introd...

journal_title：BMC bioinformatics

authors： Block A,Debode F,Grohmann L,Hulin J,Taverniers I,Kluga L,Barbau-Piednoir E,Broeders S,Huber I,Van den Bulcke M,Heinze P,Berben G,Busch U,Roosens N,Janssen E,Žel J,Gruden K,Morisset D

更新日期：2013-08-22 00:00:00

abstract：BACKGROUND:Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential ...

journal_title：BMC bioinformatics

authors： Li X,Fu Y,Wang X,Qiu W

更新日期：2018-05-18 00:00:00

abstract：BACKGROUND:In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare gene functional similarities at the molecular level. The existing gene similarity measures, however...

journal_title：BMC bioinformatics

authors： Peng J,Wang Y,Chen J

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions that can be approached in a new way with the nanopore detector. RESULTS:We present evidence that diff...

journal_title：BMC bioinformatics

authors： Winters-Hilt S,Morales E,Amin I,Stoyanov A

更新日期：2007-11-01 00:00:00

abstract：BACKGROUND:The Triplex cell vaccine is a cancer cellular vaccine that can prevent almost completely the mammary tumor onset in HER-2/neu transgenic mice. In a translational perspective, the activity of the Triplex vaccine was also investigated against lung metastases showing that the vaccine is an effective treatment a...

journal_title：BMC bioinformatics

authors： Pennisi M,Pappalardo F,Palladini A,Nicoletti G,Nanni P,Lollini PL,Motta S

更新日期：2010-10-15 00:00:00

abstract：BACKGROUND:Analysis of expression quantitative trait loci (eQTL) aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge o...

journal_title：BMC bioinformatics

authors： Wang W,Zhang X

更新日期：2011-06-30 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: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:Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful technique which has gained increasing attention over the last two decades. The GC × GC-MS provides much increased separation capacity, chemical selectivity and sensitivity for complex sample analysis an...

journal_title：BMC bioinformatics

authors： Kim S,Koo I,Fang A,Zhang X

更新日期：2011-06-15 00:00:00