Phylogenetic detection of conserved gene clusters in microbial genomes.

abstract：BACKGROUND:Identification of causal SNPs in most genome wide association studies relies on approaches that consider each SNP individually. However, there is a strong correlation structure among SNPs that needs to be taken into account. Hence, increasingly modern computationally expensive regression methods are employed...

journal_title：BMC bioinformatics

authors： Zuber V,Duarte Silva AP,Strimmer K

更新日期：2012-10-31 00:00:00

abstract：BACKGROUND:The main goal of the whole transcriptome analysis is to correctly identify all expressed transcripts within a specific cell/tissue--at a particular stage and condition--to determine their structures and to measure their abundances. RNA-seq data promise to allow identification and quantification of transcript...

journal_title：BMC bioinformatics

authors： Angelini C,De Canditiis D,De Feis I

更新日期：2014-05-09 00:00:00

abstract：BACKGROUND:Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions. RESULTS:Here, we weighted edges of a human protein interaction network and a transcriptional r...

journal_title：BMC bioinformatics

authors： Chen L,Wang H,Zhang L,Li W,Wang Q,Shang Y,He Y,He W,Li X,Tai J,Li X

更新日期：2010-07-22 00:00:00

abstract：BACKGROUND:The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where seq...

journal_title：BMC bioinformatics

authors： Konopka BM,Marciniak M,Dyrka W

更新日期：2017-07-17 00:00:00

abstract：BACKGROUND:Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compound...

journal_title：BMC bioinformatics

authors： Le Guilloux V,Schmidtke P,Tuffery P

更新日期：2009-06-02 00:00:00

abstract：BACKGROUND:Throughout the metazoan lineage, typically gonadal expressed Piwi proteins and their guiding piRNAs (~26-32nt in length) form a protective mechanism of RNA interference directed against the propagation of transposable elements (TEs). Most piRNAs are generated from genomic piRNA clusters. Annotation of experi...

journal_title：BMC bioinformatics

authors： Rosenkranz D,Zischler H

更新日期：2012-01-10 00:00:00

abstract：:Advances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher sys...

journal_title：BMC bioinformatics

authors： Yang JY,Dunker A,Liu JS,Qin X,Arabnia HR,Yang W,Niemierko A,Chen Z,Luo Z,Wang L,Liu Y,Xu D,Deng Y,Tong W,Yang M

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number...

journal_title：BMC bioinformatics

authors： Sonnhammer EL,Hollich V

更新日期：2005-04-27 00:00:00

abstract：BACKGROUND:Amplified fragment length polymorphism (AFLP) is a PCR-based technique that involves restriction of genomic DNA followed by ligation of adaptors to the fragments generated and selective PCR amplification of a subset of these fragments. The amplified fragments are separated on a sequencing gel and visualized ...

journal_title：BMC bioinformatics

authors： Hong Y,Chuah A

更新日期：2003-02-25 00:00:00

abstract：BACKGROUND:Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mec...

journal_title：BMC bioinformatics

authors： Rousseau M,Fraser J,Ferraiuolo MA,Dostie J,Blanchette M

更新日期：2011-10-25 00:00:00

abstract：BACKGROUND:Prostate carcinoma is among the most common types of cancer affecting hundreds of thousands people every year. Once the metastatic form of prostate carcinoma is documented, the majority of patients die from their tumors as opposed to other causes. The key to successful treatment is in the earliest possible d...

journal_title：BMC bioinformatics

authors： Ptitsyn A

更新日期：2009-10-08 00:00:00

abstract：BACKGROUND:Sparse principal component analysis (PCA) is a popular tool for dimensionality reduction, pattern recognition, and visualization of high dimensional data. It has been recognized that complex biological mechanisms occur through concerted relationships of multiple genes working in networks that are often repre...

journal_title：BMC bioinformatics

authors： Li Z,Safo SE,Long Q

更新日期：2017-07-11 00:00:00

abstract：BACKGROUND:Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelian diseases, the implication of such events in multi-genic disorders is yet to be well understood. We...

journal_title：BMC bioinformatics

authors： Churbanov A,Vorechovský I,Hicks C

更新日期：2010-01-12 00:00:00

abstract：BACKGROUND:Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to ac...

journal_title：BMC bioinformatics

authors： Lemaitre C,Barré A,Citti C,Tardy F,Thiaucourt F,Sirand-Pugnet P,Thébault P

更新日期：2011-11-24 00:00:00

abstract：BACKGROUND:Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of pot...

journal_title：BMC bioinformatics

authors： Che D,Guo S,Jiang Q,Chen L

更新日期：2020-07-14 00:00:00

abstract：BACKGROUND:Parametric feature selection methods for machine learning and association studies based on genetic data are not robust with respect to outliers or influential observations. While rank-based, distribution-free statistics offer a robust alternative to parametric methods, their practical utility can be limited,...

journal_title：BMC bioinformatics

authors： Lin J,Sibley A,Shterev I,Nixon A,Innocenti F,Chan C,Owzar K

更新日期：2019-06-13 00:00:00

abstract：BACKGROUND:Recently, revealing the function of proteins with protein-protein interaction (PPI) networks is regarded as one of important issues in bioinformatics. With the development of experimental methods such as the yeast two-hybrid method, the data of protein interaction have been increasing extremely. Many databas...

journal_title：BMC bioinformatics

authors： Monji H,Koizumi S,Ozaki T,Ohkawa T

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Cancer is caused through a multistep process, in which a succession of genetic changes, each conferring a competitive advantage for growth and proliferation, leads to the progressive conversion of normal human cells into malignant cancer cells. Interrogation of cancer genomes holds the promise of understandi...

journal_title：BMC bioinformatics

authors： Sanchez-Garcia F,Akavia UD,Mozes E,Pe'er D

更新日期：2010-04-14 00:00:00

abstract：BACKGROUND:Many biases and spurious effects are inherent in RNA-seq technology, resulting in a non-uniform distribution of sequencing read counts for each base position in a gene. Therefore, a base-level strategy is required to model the non-uniformity. Also, the properties of sequencing read counts can be leveraged to...

journal_title：BMC bioinformatics

authors： Cai G,Liang S,Zheng X,Xiao F

更新日期：2017-08-09 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved miRNAs. Plants and invertebrates employ their miRNA in defense against viruses by targeting and degrad...

journal_title：BMC bioinformatics

authors： Carl JW Jr,Trgovcich J,Hannenhalli S

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research. However, current mainstream variant caller tools have a serious pro...

journal_title：BMC bioinformatics

authors： Xiao A,Wu Z,Dong S

更新日期：2019-02-14 00:00:00

abstract：BACKGROUND:The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics...

journal_title：BMC bioinformatics

authors： Widmer C,Toussaint NC,Altun Y,Rätsch G

更新日期：2010-10-26 00:00:00

abstract：BACKGROUND:Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been...

journal_title：BMC bioinformatics

authors： Kang JB,Siranosian BA,Moss EL,Banaei N,Andermann TM,Bhatt AS

更新日期：2019-12-02 00:00:00

abstract：BACKGROUND:Drug resistance testing is mandatory in antiretroviral therapy in human immunodeficiency virus (HIV) infected patients for successful treatment. The emergence of resistances against antiretroviral agents remains the major obstacle in inhibition of viral replication and thus to control infection. Due to the h...

journal_title：BMC bioinformatics

authors： Riemenschneider M,Hummel T,Heider D

更新日期：2016-08-22 00:00:00

abstract：BACKGROUND:Observed co-expression of a group of genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led to the hypothesis that promoters of co-expressed genes should share common regulatory motifs, which forms the basis for numerous computational tools that search for th...

journal_title：BMC bioinformatics

authors： Meng G,Mosig A,Vingron M

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic seq...

journal_title：BMC bioinformatics

authors： Zamani N,Sundström G,Meadows JR,Höppner MP,Dainat J,Lantz H,Haas BJ,Grabherr MG

更新日期：2014-06-30 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:Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning models using gene expression data from patients' primary tumor tissues to predict whether a patient wi...

journal_title：BMC bioinformatics

authors： Clayton EA,Pujol TA,McDonald JF,Qiu P

更新日期：2020-09-30 00:00:00

abstract：BACKGROUND:To infer gene regulatory networks from time series gene profiles, two important tasks that are related to biological systems must be undertaken. One task is to determine a valid network structure that has topological properties that can influence the network dynamics profoundly. The other task is to optimize...

journal_title：BMC bioinformatics

authors： Hsiao YT,Lee WP

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-absence data, we evaluate species co-occurrences that help elucidate relationships among organisms and ...

journal_title：BMC bioinformatics

authors： Chung NC,Miasojedow B,Startek M,Gambin A

更新日期：2019-12-24 00:00:00