methCancer-gen: a DNA methylome dataset generator for user-specified cancer type based on conditional variational autoencoder.

abstract：BACKGROUND:Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profil...

journal_title：BMC bioinformatics

authors： Vilaprinyo E,Alves R,Sorribas A

更新日期：2006-04-03 00:00:00

abstract：BACKGROUND:In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very large numbers of genetic markers currently in use, it has proven difficult to develop suitable and ...

journal_title：BMC bioinformatics

authors： Long Q,Zhang Q,Ott J

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Protein sequence profile-profile alignment is an important approach to recognizing remote homologs and generating accurate pairwise alignments. It plays an important role in protein sequence database search, protein structure prediction, protein function prediction, and phylogenetic analysis. RESULTS:In thi...

journal_title：BMC bioinformatics

authors： Deng X,Cheng J

更新日期：2014-07-25 00:00:00

abstract：BACKGROUND:A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for ...

journal_title：BMC bioinformatics

authors： Bertolazzi P,Guerra C,Liuzzi G

更新日期：2010-09-29 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

abstract：BACKGROUND:Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity, solvent accessibility, and flexibility in proteins was demonstrated. Subsequently, Thornton and colleagues proposed a method for ...

journal_title：BMC bioinformatics

authors： Ponomarenko J,Bui HH,Li W,Fusseder N,Bourne PE,Sette A,Peters B

更新日期：2008-12-02 00:00:00

abstract：BACKGROUND:Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on c...

journal_title：BMC bioinformatics

authors： He X,Sarma MS,Ling X,Chee B,Zhai C,Schatz B

更新日期：2010-05-20 00:00:00

abstract：:Time course gene expression experiments are a popular means to infer co-expression. Many methods have been proposed to cluster genes or to build networks based on similarity measures of their expression dynamics. In this paper we apply a correlation based approach to network reconstruction to three datasets of time se...

journal_title：BMC bioinformatics

authors： Neretti N,Remondini D,Tatar M,Sedivy JM,Pierini M,Mazzatti D,Powell J,Franceschi C,Castellani GC

更新日期：2007-03-08 00:00:00

abstract：BACKGROUND:Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. RESULTS:A non-parametric Bayesian ap...

journal_title：BMC bioinformatics

authors： Beam AL,Motsinger-Reif A,Doyle J

更新日期：2014-11-21 00:00:00

abstract：BACKGROUND:To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides inf...

journal_title：BMC bioinformatics

authors： Oh SJ,Joung JG,Chang JH,Zhang BT

更新日期：2006-06-06 00:00:00

abstract：BACKGROUND:Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the reproducibility of identified biomarkers across tissues and experiments is still a challenge for this...

journal_title：BMC bioinformatics

authors： Zhang X,Gao L,Liu ZP,Chen L

更新日期：2015-03-18 00:00:00

abstract：BACKGROUND:Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among transcription factors (TFs) and their target genes, with a method able to handle both the high number...

journal_title：BMC bioinformatics

authors： Sauta E,Demartini A,Vitali F,Riva A,Bellazzi R

更新日期：2020-05-29 00:00:00

abstract：BACKGROUND:Improvements in protein sequence annotation and an increase in the number of annotated protein databases has fueled development of an increasing number of software tools to predict secreted proteins. Six software programs capable of high throughput and employing a wide range of prediction methods, SignalP 3....

journal_title：BMC bioinformatics

authors： Klee EW,Ellis LB

更新日期：2005-10-14 00:00:00

abstract：BACKGROUND:As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consid...

journal_title：BMC bioinformatics

authors： Kerr KF

更新日期：2007-10-03 00:00:00

abstract：BACKGROUND:We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs. RESULTS:LAVA identifies combinations of six primer regions for basic LAM...

journal_title：BMC bioinformatics

authors： Torres C,Vitalis EA,Baker BR,Gardner SN,Torres MW,Dzenitis JM

更新日期：2011-06-16 00:00:00

abstract：BACKGROUND:A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biological systems, particularly when these tools offer analysis capabilities. However, most published networ...

journal_title：BMC bioinformatics

authors： Macpherson JI,Pinney JW,Robertson DL

更新日期：2009-03-26 00:00:00

abstract：BACKGROUND:High-throughput experiments, such as with DNA microarrays, typically result in hundreds of genes potentially relevant to the process under study, rendering the interpretation of these experiments problematic. Here, we propose and evaluate an approach to find functional associations between large numbers of g...

journal_title：BMC bioinformatics

authors： Jelier R,Jenster G,Dorssers LC,Wouters BJ,Hendriksen PJ,Mons B,Delwel R,Kors JA

更新日期：2007-01-18 00:00:00

abstract：BACKGROUND:A number of software packages are available to generate DNA multiple sequence alignments (MSAs) evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts ...

journal_title：BMC bioinformatics

authors： Kedzierska AM,Casanellas M

更新日期：2012-08-28 00:00:00

abstract：BACKGROUND:The efficiency of lymph nodes depends on tissue structure and organization, which allow the coordination of lymphocyte traffic. Despite their essential role, our understanding of lymph node specific mechanisms is still incomplete and currently a topic of intense research. RESULTS:In this paper, we present a...

journal_title：BMC bioinformatics

authors： Baldazzi V,Paci P,Bernaschi M,Castiglione F

更新日期：2009-11-25 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:Microarray experiments, as well as other genomic analyses, often result in large gene sets containing up to several hundred genes. The biological significance of such sets of genes is, usually, not readily apparent. Identification of the functions of the genes in the set can help highlight features of intere...

journal_title：BMC bioinformatics

authors： Lee JS,Katari G,Sachidanandam R

更新日期：2005-07-25 00:00:00

abstract：BACKGROUND:The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing...

journal_title：BMC bioinformatics

authors： Revanna KV,Chiu CC,Bierschank E,Dong Q

更新日期：2011-08-02 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:In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overc...

journal_title：BMC bioinformatics

authors： Triplet T,Butler G

更新日期：2012-01-26 00:00:00

abstract：BACKGROUND:Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data. RESULTS:We ...

journal_title：BMC bioinformatics

authors： Chang HH,McGeachie M,Alterovitz G,Ramoni MF

更新日期：2010-10-28 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:Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional informa...

journal_title：BMC bioinformatics

authors： Peterlongo P,Noé L,Lavenier D,Nguyen VH,Kucherov G,Giraud M

更新日期：2008-12-16 00:00:00

abstract：BACKGROUND:The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research. We present a novel method called MergeAlign which constructs consensus MSAs fro...

journal_title：BMC bioinformatics

authors： Collingridge PW,Kelly S

更新日期：2012-05-30 00:00:00

abstract：BACKGROUND:The landscape of biological and biomedical research is being changed rapidly with the invention of microarrays which enables simultaneous view on the transcription levels of a huge number of genes across different experimental conditions or time points. Using microarray data sets, clustering algorithms have ...

journal_title：BMC bioinformatics

authors： Maulik U,Mukhopadhyay A,Bandyopadhyay S

更新日期：2009-01-20 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