Random forest versus logistic regression: a large-scale benchmark experiment.

abstract：BACKGROUND:Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presen...

journal_title：BMC bioinformatics

authors： Wenskovitch JE Jr,Harris LA,Tapia JJ,Faeder JR,Marai GE

更新日期：2014-09-25 00:00:00

abstract：BACKGROUND:As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease development or therapeutic intervention would assist in drug development, design of therapy, and target ide...

journal_title：BMC bioinformatics

authors： Bidaut G,Suhre K,Claverie JM,Ochs MF

更新日期：2006-02-28 00:00:00

abstract：BACKGROUND:Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and a...

journal_title：BMC bioinformatics

authors： Signorelli M,Vinciotti V,Wit EC

更新日期：2016-09-05 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hu...

journal_title：BMC bioinformatics

authors： Huang TH,Fan B,Rothschild MF,Hu ZL,Li K,Zhao SH

更新日期：2007-09-17 00:00:00

abstract：BACKGROUND:Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright ...

journal_title：BMC bioinformatics

authors： Prlić A,Martinez MA,Dimitropoulos D,Beran B,Yukich BT,Rose PW,Bourne PE,Fink JL

更新日期：2010-04-29 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysa...

journal_title：BMC bioinformatics

authors： Kim JG,Park D,Kim BC,Cho SW,Kim YT,Park YJ,Cho HJ,Park H,Kim KB,Yoon KO,Park SJ,Lee BM,Bhak J

更新日期：2008-01-24 00:00:00

abstract：BACKGROUND:Intrinsically Disordered Proteins (IDPs) lack an ordered three-dimensional structure and are enriched in various biological processes. The Molecular Recognition Features (MoRFs) are functional regions within IDPs that undergo a disorder-to-order transition on binding to a partner protein. Identifying MoRFs i...

journal_title：BMC bioinformatics

authors： Sharma R,Kumar S,Tsunoda T,Patil A,Sharma A

更新日期：2016-12-22 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:A massive amount of proteomic data is generated on a daily basis, nonetheless annotating all sequences is costly and often unfeasible. As a countermeasure, machine learning methods have been used to automatically annotate new protein functions. More specifically, many studies have investigated hierarchical m...

journal_title：BMC bioinformatics

authors： Nakano FK,Lietaert M,Vens C

更新日期：2019-09-23 00:00:00

abstract：BACKGROUND:Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. The higher the quality of a reference genome assembly the more accurate the downstream analysis will be. During the last few years, major efforts have been made towards improving the qua...

journal_title：BMC bioinformatics

authors： Yuan Y,Bayer PE,Scheben A,Chan CK,Edwards D

更新日期：2017-06-30 00:00:00

abstract：BACKGROUND:Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or ...

journal_title：BMC bioinformatics

authors： You FM,Huo N,Gu YQ,Luo MC,Ma Y,Hane D,Lazo GR,Dvorak J,Anderson OD

更新日期：2008-05-29 00:00:00

abstract：BACKGROUND:A professional recognition mechanism is required to encourage expedited publishing of an adequate volume of 'fit-for-use' biodiversity data. As a component of such a recognition mechanism, we propose the development of the Data Usage Index (DUI) to demonstrate to data publishers that their efforts of creatin...

journal_title：BMC bioinformatics

authors： Ingwersen P,Chavan V

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as fl...

journal_title：BMC bioinformatics

authors： Negre V,Grunau C

更新日期：2004-05-07 00:00:00

abstract：BACKGROUND:Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus ...

journal_title：BMC bioinformatics

authors： Kasprzak JM,Czerwoniec A,Bujnicki JM

更新日期：2012-06-28 00:00:00

abstract：BACKGROUND:Text mining tools have gained popularity to process the vast amount of available research articles in the biomedical literature. It is crucial that such tools extract information with a sufficient level of detail to be applicable in real life scenarios. Studies of mining non-causal molecular relations attrib...

journal_title：BMC bioinformatics

authors： Van Landeghem S,Björne J,Abeel T,De Baets B,Salakoski T,Van de Peer Y

更新日期：2012-06-26 00:00:00

abstract：BACKGROUND:An important application of high dimensional gene expression measurements is the risk prediction and the interpretation of the variables in the resulting survival models. A major problem in this context is the typically large number of genes compared to the number of observations (individuals). Feature selec...

journal_title：BMC bioinformatics

authors： Kammers K,Lang M,Hengstler JG,Schmidt M,Rahnenführer J

更新日期：2011-12-16 00:00:00

abstract：BACKGROUND:Failure on Highly Active Anti-Retroviral Treatment is often accompanied with development of antiviral resistance to one or more drugs included in the treatment. In general, the virus is more likely to develop resistance to drugs with a lower genetic barrier. Previously, we developed a method to reverse engin...

journal_title：BMC bioinformatics

authors： Theys K,Deforche K,Beheydt G,Moreau Y,van Laethem K,Lemey P,Camacho RJ,Rhee SY,Shafer RW,Van Wijngaerden E,Vandamme AM

更新日期：2010-08-03 00:00:00

abstract：BACKGROUND:RNA-seq is a powerful tool for measuring transcriptomes, especially for identifying differentially expressed genes or transcripts (DEGs) between sample groups. A number of methods have been developed for this task, and several evaluation studies have also been reported. However, those evaluations so far have...

journal_title：BMC bioinformatics

authors： Tang M,Sun J,Shimizu K,Kadota K

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:High throughput DNA/RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine ...

journal_title：BMC bioinformatics

authors： Chanumolu SK,Albahrani M,Otu HH

更新日期：2019-08-15 00:00:00

abstract：BACKGROUND:SNP genotyping microarrays have revolutionized the study of complex disease. The current range of commercially available genotyping products contain extensive catalogues of low frequency and rare variants. Existing SNP calling algorithms have difficulty dealing with these low frequency variants, as the under...

journal_title：BMC bioinformatics

authors： Liu R,Dai Z,Yeager M,Irizarry RA,Ritchie ME

更新日期：2014-05-23 00:00:00

abstract：BACKGROUND:T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large proportion of the human population. The presence of clusters of promiscuous T-cell epitopes, immunolo...

journal_title：BMC bioinformatics

authors： Zhang GL,Khan AM,Srinivasan KN,Heiny A,Lee K,Kwoh CK,August JT,Brusic V

更新日期：2008-01-01 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:Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene e...

journal_title：BMC bioinformatics

authors： Müller HG,Chiou JM,Leng X

更新日期：2008-01-28 00:00:00

abstract：BACKGROUND:A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of ...

journal_title：BMC bioinformatics

authors： Alachiotis N,Berger S,Flouri T,Pissis SP,Stamatakis A

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Human breast cancer resistance protein (BCRP) is an ATP-binding cassette (ABC) efflux transporter that confers multidrug resistance in cancers and also plays an important role in the absorption, distribution and elimination of drugs. Prediction as to if drugs or new molecular entities are BCRP substrates sho...

journal_title：BMC bioinformatics

authors： Hazai E,Hazai I,Ragueneau-Majlessi I,Chung SP,Bikadi Z,Mao Q

更新日期：2013-04-15 00:00:00

abstract：BACKGROUND:Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data analysis, little attention has been paid to uncertainty in the results obtained. RESULTS:We present an R/Bioconductor port of a fast novel algorithm for...

journal_title：BMC bioinformatics

authors： Savage RS,Heller K,Xu Y,Ghahramani Z,Truman WM,Grant M,Denby KJ,Wild DL

更新日期：2009-08-06 00:00:00

abstract：BACKGROUND:The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function i...

journal_title：BMC bioinformatics

authors： Bray T,Chan P,Bougouffa S,Greaves R,Doig AJ,Warwicker J

更新日期：2009-11-18 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

abstract：BACKGROUND:Because common complex diseases are affected by multiple genes and environmental factors, it is essential to investigate gene-gene and/or gene-environment interactions to understand genetic architecture of complex diseases. After the great success of large scale genome-wide association (GWA) studies using th...

journal_title：BMC bioinformatics

authors： Oh S,Lee J,Kwon MS,Weir B,Ha K,Park T

更新日期：2012-06-11 00:00:00

abstract：BACKGROUND:The most common method of identifying groups of functionally related genes in microarray data is to apply a clustering algorithm. However, it is impossible to determine which clustering algorithm is most appropriate to apply, and it is difficult to verify the results of any algorithm due to the lack of a gol...

journal_title：BMC bioinformatics

authors： Hibbs MA,Dirksen NC,Li K,Troyanskaya OG

更新日期：2005-05-12 00:00:00