An automated framework for understanding structural variations in the binding grooves of MHC class II molecules.

abstract：BACKGROUND:Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microarrays does not capture all alternative splicing events. Moreover, for many species genomic data is be...

journal_title：BMC bioinformatics

authors： Sinha R,Hiller M,Pudimat R,Gausmann U,Platzer M,Backofen R

更新日期：2008-11-12 00:00:00

abstract：BACKGROUND:Global maritime trade plays an important role in the modern transportation industry. It brings significant economic profit along with bioinvasion risk. Species translocate and establish in a non-native area through ballast water and biofouling. Aiming at aquatic bioinvasion issue, people proposed various sug...

journal_title：BMC bioinformatics

authors： Wang S,Wang C,Wang S,Ma L

更新日期：2018-08-13 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: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:The evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don't code for proteins, yielding a need to infer evolutionary history of sequences irrespective of what kind of functional element they may encode. Thus, sequence-, as opposed to ...

journal_title：BMC bioinformatics

authors： Gao K,Miller J

更新日期：2020-02-06 00:00:00

abstract：BACKGROUND:The detection of bias due to cryptic population structure is an important step in the evaluation of findings of genetic association studies. The standard method of measuring this bias in a genetic association study is to compare the observed median association test statistic to the expected median test stati...

journal_title：BMC bioinformatics

authors： Pirie A,Wood A,Lush M,Tyrer J,Pharoah PD

更新日期：2015-02-20 00:00:00

abstract：BACKGROUND:Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs that attract great attention because of their role in regulation of...

journal_title：BMC bioinformatics

authors： Del Vecchio F,Gallo F,Di Marco A,Mastroiaco V,Caianiello P,Zazzeroni F,Alesse E,Tessitore A

更新日期：2015-12-10 00:00:00

abstract：BACKGROUND:Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by ...

journal_title：BMC bioinformatics

authors： Memarian N,Jessulat M,Alirezaie J,Mir-Rashed N,Xu J,Zareie M,Smith M,Golshani A

更新日期：2007-04-04 00:00:00

abstract：BACKGROUND:Comparison of metabolic networks is typically performed based on the organisms' enzyme contents. This approach disregards functional replacements as well as orthologies that are misannotated. Direct comparison of the structure of metabolic networks can circumvent these problems. RESULTS:Metabolic networks a...

journal_title：BMC bioinformatics

authors： Forst CV,Flamm C,Hofacker IL,Stadler PF

更新日期：2006-02-14 00:00:00

abstract：BACKGROUND:Variation in DNA copy number, due to gains and losses of chromosome segments, is common. A first step for analyzing DNA copy number data is to identify amplified or deleted regions in individuals. To locate such regions, we propose a circular binary segmentation procedure, which is based on a sequence of nes...

journal_title：BMC bioinformatics

authors： Yang TY

更新日期：2012-10-30 00:00:00

abstract：BACKGROUND:The spatial configuration of chromosomes is essential to various cellular processes, notably gene regulation, while architecture related alterations, such as translocations and gene fusions, are often cancer drivers. Thus, eliciting chromatin conformation is important, yet challenging due to compaction, dyna...

journal_title：BMC bioinformatics

authors： Segal MR,Fletez-Brant K

更新日期：2020-02-24 00:00:00

abstract：BACKGROUND:Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and relate...

journal_title：BMC bioinformatics

authors： Xiao H,Bartoszek K,Lio' P

更新日期：2018-11-30 00:00:00

abstract：BACKGROUND:Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance...

journal_title：BMC bioinformatics

authors： Giri AV,Anishetty S,Gautam P

更新日期：2004-09-09 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:The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of...

journal_title：BMC bioinformatics

authors： Li P,Dada JO,Jameson D,Spasic I,Swainston N,Carroll K,Dunn W,Khan F,Malys N,Messiha HL,Simeonidis E,Weichart D,Winder C,Wishart J,Broomhead DS,Goble CA,Gaskell SJ,Kell DB,Westerhoff HV,Mendes P,Paton NW

更新日期：2010-11-29 00:00:00

abstract：BACKGROUND:Novel sequence motifs detection is becoming increasingly essential in computational biology. However, the high computational cost greatly constrains the efficiency of most motif discovery algorithms. RESULTS:In this paper, we accelerate MEME algorithm targeted on Intel Many Integrated Core (MIC) Architectur...

journal_title：BMC bioinformatics

authors： Peng S,Cheng M,Huang K,Cui Y,Zhang Z,Guo R,Zhang X,Yang S,Liao X,Lu Y,Zou Q,Shi B

更新日期：2018-08-13 00:00:00

abstract：BACKGROUND:HIV/AIDS is a serious threat to public health. The emergence of drug resistance mutations diminishes the effectiveness of drug therapy for HIV/AIDS. Developing a computational prediction of drug resistance phenotype will enable efficient and timely selection of the best treatment regimens. RESULTS:A unified...

journal_title：BMC bioinformatics

authors： Shen C,Yu X,Harrison RW,Weber IT

更新日期：2016-08-31 00:00:00

abstract：BACKGROUND:Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptio...

journal_title：BMC bioinformatics

authors： Chevenet F,Brun C,Bañuls AL,Jacq B,Christen R

更新日期：2006-10-10 00:00:00

abstract：BACKGROUND:In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorith...

journal_title：BMC bioinformatics

authors： Yang C,He Z,Yu W

更新日期：2009-01-06 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:Dynamic programming algorithms provide exact solutions to many problems in computational biology, such as sequence alignment, RNA folding, hidden Markov models (HMMs), and scoring of phylogenetic trees. Structurally analogous algorithms compute optimal solutions, evaluate score distributions, and perform sto...

journal_title：BMC bioinformatics

authors： zu Siederdissen CH,Prohaska SJ,Stadler PF

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Several studies demonstrated the feasibility of predicting bacterial antibiotic resistance phenotypes from whole-genome sequences, the prediction process usually amounting to detecting the presence of genes involved in antibiotic resistance mechanisms, or of specific mutations, previously identified from a t...

journal_title：BMC bioinformatics

authors： Mahé P,Tournoud M

更新日期：2018-10-17 00:00:00

abstract：BACKGROUND:Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effective prevention and control measures for blood pressure diseases. Traditional blood pressure measure...

journal_title：BMC bioinformatics

authors： Zhang B,Ren H,Huang G,Cheng Y,Hu C

更新日期：2019-02-28 00:00:00

abstract：BACKGROUND:In protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intu...

journal_title：BMC bioinformatics

authors： Khan T,Panday SK,Ghosh I

更新日期：2018-05-04 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:Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error ...

journal_title：BMC bioinformatics

authors： Skums P,Dimitrova Z,Campo DS,Vaughan G,Rossi L,Forbi JC,Yokosawa J,Zelikovsky A,Khudyakov Y

更新日期：2012-06-25 00:00:00

abstract：BACKGROUND:Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune sup...

journal_title：BMC bioinformatics

authors： Ammari M,McCarthy FM,Nanduri B,Pinchuk LM

更新日期：2010-10-07 00:00:00

abstract：BACKGROUND:Interpretation of gene expression microarray data in the light of external information on both columns and rows (experimental variables and gene annotations) facilitates the extraction of pertinent information hidden in these complex data. Biologists classically interpret genes of interest after retrieving f...

journal_title：BMC bioinformatics

authors： Baty F,Rüdiger J,Miglino N,Kern L,Borger P,Brutsche M

更新日期：2013-06-06 00:00:00

abstract：BACKGROUND:The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000). RESULTS:We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to...

journal_title：BMC bioinformatics

authors： Karwath A,King RD

更新日期：2002-04-23 00:00:00

abstract：:In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a re...

journal_title：BMC bioinformatics

authors： Aganezov S Jr,Alekseyev MA

更新日期：2012-01-01 00:00:00