SIMAT: GC-SIM-MS data analysis tool.

abstract：BACKGROUND:The immune system is multifaceted, structured by diverse components that interconnect using multilayered dynamic cellular processes. Genomic technologies provide a means for investigating, at the molecular level, the adaptations of the immune system in host defense and its dysregulation in pathological condi...

journal_title：BMC bioinformatics

authors： Liu H,Liu J,Toups M,Soos T,Arendt C

更新日期：2016-04-18 00:00:00

abstract：BACKGROUND:Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in terms of the phylogenic tree. In a similar way it has been argued that biological networks also induce correlations among sets of interacting...

journal_title：BMC bioinformatics

authors： Kelly WP,Stumpf MP

更新日期：2010-09-20 00:00:00

abstract：BACKGROUND:Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of ...

journal_title：BMC bioinformatics

authors： Cumbo F,Fiscon G,Ceri S,Masseroli M,Weitschek E

更新日期：2017-01-03 00:00:00

abstract：BACKGROUND:Profile-based comparison of multiple sequence alignments is a powerful methodology for the detection remote protein sequence similarity, which is essential for the inference and analysis of protein structure, function, and evolution. Accurate estimation of statistical significance of detected profile similar...

journal_title：BMC bioinformatics

authors： Sadreyev RI,Wang Y,Grishin NV

更新日期：2009-12-04 00:00:00

abstract：BACKGROUND:Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; http://egenbio.lsu.edu) to begin to address this....

journal_title：BMC bioinformatics

authors： Nahum LA,Reynolds MT,Wang ZO,Faith JJ,Jonna R,Jiang ZJ,Meyer TJ,Pollock DD

更新日期：2006-09-06 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:Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides...

journal_title：BMC bioinformatics

authors： Haskins WE,Petritis K,Zhang J

更新日期：2011-03-15 00:00:00

abstract：BACKGROUND:Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows conve...

journal_title：BMC bioinformatics

authors： Bray MA,Carpenter AE

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:In real-time PCR, it is necessary to consider the efficiency of amplification (EA) of amplicons in order to determine initial target levels properly. EAs can be deduced from standard curves, but these involve extra effort and cost and may yield invalid EAs. Alternatively, EA can be extracted from individual ...

journal_title：BMC bioinformatics

authors： Batsch A,Noetel A,Fork C,Urban A,Lazic D,Lucas T,Pietsch J,Lazar A,Schömig E,Gründemann D

更新日期：2008-02-12 00:00:00

abstract：BACKGROUND:Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked ...

journal_title：BMC bioinformatics

authors： Bielejec F,Lemey P,Carvalho LM,Baele G,Rambaut A,Suchard MA

更新日期：2014-05-07 00:00:00

abstract：BACKGROUND:It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enou...

journal_title：BMC bioinformatics

authors： Meyer F,Kurtz S,Beckstette M

更新日期：2013-07-17 00:00:00

abstract：BACKGROUND:To further our understanding of immunopeptidomics, improved tools are needed to identify peptides presented by major histocompatibility complex class I (MHC-I). Many existing tools are limited by their reliance upon chemical affinity data, which is less biologically relevant than sampling by mass spectrometr...

journal_title：BMC bioinformatics

authors： Boehm KM,Bhinder B,Raja VJ,Dephoure N,Elemento O

更新日期：2019-01-05 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: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:A standard procedure in many areas of bioinformatics is to use a multiple sequence alignment (MSA) as the basis for various types of homology-based inference. Applications include 3D structure modelling, protein functional annotation, prediction of molecular interactions, etc. These applications, however sop...

journal_title：BMC bioinformatics

authors： Vanhoutreve R,Kress A,Legrand B,Gass H,Poch O,Thompson JD

更新日期：2016-07-07 00:00:00

abstract：BACKGROUND:The improvements in genomics methods coupled with readily accessible high-throughput sequencing have contributed to our understanding of microbial species, metagenomes, infectious diseases and more. To maximize the impact of these genomics studies, it is important that data from biological samples will becom...

journal_title：BMC bioinformatics

authors： Quiñones M,Liou DT,Shyu C,Kim W,Vujkovic-Cvijin I,Belkaid Y,Hurt DE

更新日期：2020-09-03 00:00:00

abstract：BACKGROUND:The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine...

journal_title：BMC bioinformatics

authors： Bujnicki JM,Feder M,Radlinska M,Rychlewski L

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:Current microRNA (miRNA) research in progress has engendered rapid accumulation of expression data evolving from microarray experiments. Such experiments are generally performed over different tissues belonging to a specific species of metazoan. For disease diagnosis, microarray probes are also prepared with...

journal_title：BMC bioinformatics

authors： Bandyopadhyay S,Bhattacharyya M

更新日期：2009-05-28 00:00:00

abstract：BACKGROUND:The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical value. RESULTS:We trained models using 217 high-quality morphologies of rat somatosensory neocortex interneurons reconstructed by a single...

journal_title：BMC bioinformatics

authors： Mihaljević B,Larrañaga P,Benavides-Piccione R,Hill S,DeFelipe J,Bielza C

更新日期：2018-12-17 00:00:00

abstract：:Following last year's computational vaccinology workshop in Shanghai, China, the third ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2013) was held in Barcelona, Spain. ICoVax 2013 provided an international platform for the attendees to showcase their research and discuss problems and solutions in the ...

journal_title：BMC bioinformatics

authors： De Groot AS,De Groot P,He Y

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and ass...

journal_title：BMC bioinformatics

authors： Meehan TF,Masci AM,Abdulla A,Cowell LG,Blake JA,Mungall CJ,Diehl AD

更新日期：2011-01-05 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:To understand biology and differences among various tissues or cell types, one typically searches for molecular features that display characteristic abundance patterns. Several specificity metrics have been introduced to identify tissue-specific molecular features, but these either require an equal number of...

journal_title：BMC bioinformatics

authors： Everaert C,Volders PJ,Morlion A,Thas O,Mestdagh P

更新日期：2020-02-17 00:00:00

abstract：BACKGROUND:A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the de...

journal_title：BMC bioinformatics

authors： Cao Y,Liu S,Zhang L,Qin J,Wang J,Tang K

更新日期：2006-01-14 00:00:00

abstract：BACKGROUND:Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as "molecular switches" in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and...

journal_title：BMC bioinformatics

authors： Sarkar A,Kumar S,Sundar D

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Periodogram analysis of time-series is widespread in biology. A new challenge for analyzing the microarray time series data is to identify genes that are periodically expressed. Such challenge occurs due to the fact that the observed time series usually exhibit non-idealities, such as noise, short length, an...

journal_title：BMC bioinformatics

authors： Liew AW,Xian J,Wu S,Smith D,Yan H

更新日期：2007-04-24 00:00:00

abstract：BACKGROUND:Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational and systems biology is to go beyond identification towards an explana...

journal_title：BMC bioinformatics

authors： Samal A,Singh S,Giri V,Krishna S,Raghuram N,Jain S

更新日期：2006-03-08 00:00:00

abstract：BACKGROUND:Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical literature. In this paper, we present the Cancer Genetics (CG) and Pathway Curation (PC) tasks, two even...

journal_title：BMC bioinformatics

authors： Pyysalo S,Ohta T,Rak R,Rowley A,Chun HW,Jung SJ,Choi SP,Tsujii J,Ananiadou S

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated great success in prioritizing candidate genes for human diseases. However, most of these methods rely ...

journal_title：BMC bioinformatics

authors： Zhang W,Sun F,Jiang R

更新日期：2011-02-15 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