A MATLAB tool for pathway enrichment using a topology-based pathway regulation score.

abstract：BACKGROUND:Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, th...

journal_title：BMC bioinformatics

authors： Sheikhizadeh Anari S,de Ridder D,Schranz ME,Smit S

更新日期：2018-09-26 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. Most proteins perform their functions by interacting with other proteins, so predicting PPIs acc...

journal_title：BMC bioinformatics

authors： Liu L,Zhu X,Ma Y,Piao H,Yang Y,Hao X,Fu Y,Wang L,Peng J

更新日期：2020-12-16 00:00:00

abstract：BACKGROUND:Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error that affect measurement of expression using Agilent arrays and to compare Agilent's Feature Extraction ...

journal_title：BMC bioinformatics

authors： Zahurak M,Parmigiani G,Yu W,Scharpf RB,Berman D,Schaeffer E,Shabbeer S,Cope L

更新日期：2007-05-01 00:00:00

abstract：:Following publication of the original article [1], the author reported that there are several errors in the original article. ...

journal_title：BMC bioinformatics

authors： Ranjard L,Wong TKF,Rodrigo AG

更新日期：2020-01-22 00:00:00

abstract：BACKGROUND:Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis ...

journal_title：BMC bioinformatics

authors： Yu G

更新日期：2010-10-12 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:Computational discovery of transcription factor binding sites (TFBS) is a challenging but important problem of bioinformatics. In this study, improvement of a Gibbs sampling based technique for TFBS discovery is attempted through an approach that is widely known, but which has never been investigated before:...

journal_title：BMC bioinformatics

authors： Shida K

更新日期：2006-11-04 00:00:00

abstract：BACKGROUND:Antibacterial peptides are important components of the innate immune system, used by the host to protect itself from different types of pathogenic bacteria. Over the last few decades, the search for new drugs and drug targets has prompted an interest in these antibacterial peptides. We analyzed 486 antibacte...

journal_title：BMC bioinformatics

authors： Lata S,Sharma BK,Raghava GP

更新日期：2007-07-23 00:00:00

abstract：BACKGROUND:Most human genes produce several transcripts with different exon contents by using alternative promoters, alternative polyadenylation sites and alternative splice sites. Much effort has been devoted to describing known gene transcripts through the development of numerous databases. Nevertheless, owing to the...

journal_title：BMC bioinformatics

authors： de la Grange P,Dutertre M,Correa M,Auboeuf D

更新日期：2007-06-04 00:00:00

abstract：BACKGROUND:Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features. In this work, we analyze t...

journal_title：BMC bioinformatics

authors： Lopes Ide O,Schliep A,de Carvalho AC

更新日期：2014-05-02 00:00:00

abstract：BACKGROUND:Post-transcriptional regulation is a complex mechanism that plays a central role in defining multiple cellular identities starting from a common genome. Modifications in the length of 3'UTRs have been found to play an important role in this context, since alternative 3' UTRs could lead to differences for exa...

journal_title：BMC bioinformatics

authors： Grassi E,Mariella E,Lembo A,Molineris I,Provero P

更新日期：2016-10-18 00:00:00

abstract：BACKGROUND:Feed-forward loops (FFLs), consisting of miRNAs, transcription factors (TFs) and their common target genes, have been validated to be important for the initialization and development of complex diseases, including cancer. Esophageal Carcinoma (ESCA) and Stomach Adenocarcinoma (STAD) are two types of malignan...

journal_title：BMC bioinformatics

authors： Qin G,Yang L,Ma Y,Liu J,Huo Q

更新日期：2019-12-30 00:00:00

abstract：BACKGROUND:Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as p...

journal_title：BMC bioinformatics

authors： Nagar A,Hahsler M

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics...

journal_title：BMC bioinformatics

authors： Leung E,Huang A,Cadag E,Montana A,Soliman JL,Zhou CL

更新日期：2016-01-20 00:00:00

abstract：BACKGROUND:Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area is assigned to each spot and the sum of the pixel intensities in that area, the so-called volume, is ...

journal_title：BMC bioinformatics

authors： Brauner JM,Groemer TW,Stroebel A,Grosse-Holz S,Oberstein T,Wiltfang J,Kornhuber J,Maler JM

更新日期：2014-06-11 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:We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so ...

journal_title：BMC bioinformatics

authors： Saunders NF,Brinkworth RI,Huber T,Kemp BE,Kobe B

更新日期：2008-05-26 00:00:00

abstract：BACKGROUND:It is possible to predict whether a tuberculosis (TB) patient will fail to respond to specific antibiotics by sequencing the genome of the infecting Mycobacterium tuberculosis (Mtb) and observing whether the pathogen carries specific mutations at drug-resistance sites. This advancement has led to the collati...

journal_title：BMC bioinformatics

authors： Ngo TM,Teo YY

更新日期：2019-02-08 00:00:00

abstract：BACKGROUND:Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entiti...

journal_title：BMC bioinformatics

authors： Henriques R,Ferreira FL,Madeira SC

更新日期：2017-02-02 00:00:00

abstract：BACKGROUND:RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high performance computing environment. RESULTS:Developed as a tool by the Bioinformatics Shared Resource Group (BISR) at...

journal_title：BMC bioinformatics

authors： Gadepalli VS,Ozer HG,Yilmaz AS,Pietrzak M,Webb A

更新日期：2019-12-20 00:00:00

abstract：BACKGROUND:The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, in The Cancer Genome Atlas, collects protein expressions in human cancers and it is a reference reso...

journal_title：BMC bioinformatics

authors： Sardina DS,Micale G,Ferro A,Pulvirenti A,Giugno R

更新日期：2018-07-09 00:00:00

abstract：BACKGROUND:Ontologies are widely used to represent knowledge in biomedicine. Systematic approaches for detecting errors and disagreements are needed for large ontologies with hundreds or thousands of terms and semantic relationships. A recent approach of defining terms using logical definitions is now increasingly bein...

journal_title：BMC bioinformatics

authors： Köhler S,Bauer S,Mungall CJ,Carletti G,Smith CL,Schofield P,Gkoutos GV,Robinson PN

更新日期：2011-10-27 00:00:00

abstract：BACKGROUND:Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene...

journal_title：BMC bioinformatics

authors： Noureen M,Tada I,Kawashima T,Arita M

更新日期：2019-12-27 00:00:00

abstract：BACKGROUND:Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions....

journal_title：BMC bioinformatics

authors： Bayerlová M,Jung K,Kramer F,Klemm F,Bleckmann A,Beißbarth T

更新日期：2015-10-22 00:00:00

abstract：BACKGROUND:The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to retrieve relevant data as quickly as possible. RESULTS:In this paper, we present TPMS (Tree Pattern-...

journal_title：BMC bioinformatics

authors： Bigot T,Daubin V,Lassalle F,Perrière G

更新日期：2013-03-27 00:00:00

abstract：BACKGROUND:In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein structure prediction methods. It is also observed that for almost all globular proteins, the quality of co...

journal_title：BMC bioinformatics

authors： Adhikari B,Nowotny J,Bhattacharya D,Hou J,Cheng J

更新日期：2016-12-07 00:00:00

abstract：BACKGROUND:Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-prot...

journal_title：BMC bioinformatics

authors： Chen J,Aronow BJ,Jegga AG

更新日期：2009-02-27 00:00:00

abstract：BACKGROUND:Copy number variants (CNVs) have been demonstrated to occur at a high frequency and are now widely believed to make a significant contribution to the phenotypic variation in human populations. Array-based comparative genomic hybridization (array-CGH) and newly developed read-depth approach through ultrahigh ...

journal_title：BMC bioinformatics

authors： Zhang ZD,Gerstein MB

更新日期：2010-10-31 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:In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences. As the number of software packages increases, it becomes more important to identify the tools with ...

journal_title：BMC bioinformatics

authors： Quest D,Dempsey K,Shafiullah M,Bastola D,Ali H

更新日期：2008-08-12 00:00:00