Incorporating biological information in sparse principal component analysis with application to genomic data.

abstract：BACKGROUND:Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecting specific pathway structures. However, our understanding is rather limited to the relationship bet...

journal_title：BMC bioinformatics

authors： You ZH,Yin Z,Han K,Huang DS,Zhou X

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the databas...

journal_title：BMC bioinformatics

authors： Shimizu K,Nuida K,Arai H,Mitsunari S,Attrapadung N,Hamada M,Tsuda K,Hirokawa T,Sakuma J,Hanaoka G,Asai K

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Time course microarray profiles examine the expression of genes over a time domain. They are necessary in order to determine the complete set of genes that are dynamically expressed under given conditions, and to determine the interaction between these genes. Because of cost and resource issues, most time se...

journal_title：BMC bioinformatics

authors： Sinha A,Markatou M

更新日期：2011-01-11 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: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:Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as si...

journal_title：BMC bioinformatics

authors： Alexopoulou D,Andreopoulos B,Dietze H,Doms A,Gandon F,Hakenberg J,Khelif K,Schroeder M,Wächter T

更新日期：2009-01-21 00:00:00

abstract：:We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists work...

journal_title：BMC bioinformatics

authors： Ranganathan S,Gribskov M,Tan TW

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data managemen...

journal_title：BMC bioinformatics

authors： Suhr M,Lehmann C,Bauer CR,Bender T,Knopp C,Freckmann L,Öst Hansen B,Henke C,Aschenbrandt G,Kühlborn LK,Rheinländer S,Weber L,Marzec B,Hellkamp M,Wieder P,Sax U,Kusch H,Nussbeck SY

更新日期：2020-12-17 00:00:00

abstract：BACKGROUND:The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and ass...

journal_title：BMC bioinformatics

authors： Meehan TF,Masci AM,Abdulla A,Cowell LG,Blake JA,Mungall CJ,Diehl AD

更新日期：2011-01-05 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:Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to...

journal_title：BMC bioinformatics

authors： Clarke TH,Brinkac LM,Inman JM,Sutton G,Fouts DE

更新日期：2018-06-27 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:Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever ...

journal_title：BMC bioinformatics

authors： Sturm M,Bertsch A,Gröpl C,Hildebrandt A,Hussong R,Lange E,Pfeifer N,Schulz-Trieglaff O,Zerck A,Reinert K,Kohlbacher O

更新日期：2008-03-26 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:Although protein-protein interaction networks determined with high-throughput methods are incomplete, they are commonly used to infer the topology of the complete interactome. These partial networks often show a scale-free behavior with only a few proteins having many and the majority having only a few conne...

journal_title：BMC bioinformatics

authors： Friedel CC,Zimmer R

更新日期：2006-11-30 00:00:00

abstract：BACKGROUND:We present the algorithm PFClust (Parameter Free Clustering), which is able automatically to cluster data and identify a suitable number of clusters to group them into without requiring any parameters to be specified by the user. The algorithm partitions a dataset into a number of clusters that share some co...

journal_title：BMC bioinformatics

authors： Mavridis L,Nath N,Mitchell JB

更新日期：2013-07-03 00:00:00

abstract：BACKGROUND:Quadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions. Recent discoveries confirmed their importance in biomedicine and led to an intensified examination of their properties. So far, the study of these motifs has focused mainly on the sequence and the...

journal_title：BMC bioinformatics

authors： Zok T,Popenda M,Szachniuk M

更新日期：2020-01-31 00:00:00

abstract：BACKGROUND:A large number of experimental studies show that the mutation and regulation of long non-coding RNAs (lncRNAs) are associated with various human diseases. Accurate prediction of lncRNA-disease associations can provide a new perspective for the diagnosis and treatment of diseases. The main function of many ln...

journal_title：BMC bioinformatics

authors： Zhang Y,Ye F,Xiong D,Gao X

更新日期：2020-09-03 00:00:00

abstract：BACKGROUND:Since proteins perform their functions by interacting with one another and with other biomolecules, reconstructing a map of the protein-protein interactions of a cell, experimentally or computationally, is an important first step toward understanding cellular function and machinery of a proteome. Solely deri...

journal_title：BMC bioinformatics

authors： Wu X,Zhu L,Guo J,Fu C,Zhou H,Dong D,Li Z,Zhang DY,Lin K

更新日期：2006-12-18 00:00:00

abstract：BACKGROUND:Targeted resequencing offers a cost-effective alternative to whole-genome and whole-exome sequencing when investigating regions known to be associated with a trait or disease. There are a number of approaches to targeted resequencing, including microfluidic PCR amplification, which may be enhanced by multipl...

journal_title：BMC bioinformatics

authors： Wingo TS,Kotlar A,Cutler DJ

更新日期：2017-01-05 00:00:00

abstract：BACKGROUND:Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major c...

journal_title：BMC bioinformatics

authors： Yue Y,Huang H,Qi Z,Dou HM,Liu XY,Han TF,Chen Y,Song XJ,Zhang YH,Tu J

更新日期：2020-07-28 00:00:00

abstract：BACKGROUND:Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. RESULTS:We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams includin...

journal_title：BMC bioinformatics

authors： Heberle H,Meirelles GV,da Silva FR,Telles GP,Minghim R

更新日期：2015-05-22 00:00:00

abstract：BACKGROUND:In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the...

journal_title：BMC bioinformatics

authors： Thompson JD,Muller A,Waterhouse A,Procter J,Barton GJ,Plewniak F,Poch O

更新日期：2006-06-23 00:00:00

abstract：BACKGROUND:Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objectiv...

journal_title：BMC bioinformatics

authors： Zuyderduyn SD,Jones SJ

更新日期：2003-10-28 00:00:00

abstract：BACKGROUND:Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functi...

journal_title：BMC bioinformatics

authors： Tchagang AB,Gawronski A,Bérubé H,Phan S,Famili F,Pan Y

更新日期：2010-05-06 00:00:00

abstract：BACKGROUND:The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. RESULTS:In order to improve accessibil...

journal_title：BMC bioinformatics

authors： Deng M,Brägelmann J,Schultze JL,Perner S

更新日期：2016-02-06 00:00:00

abstract：BACKGROUND:Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biologi...

journal_title：BMC bioinformatics

authors： Pinoli P,Chicco D,Masseroli M

更新日期：2015-01-01 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:Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has beco...

journal_title：BMC bioinformatics

authors： Zare F,Dow M,Monteleone N,Hosny A,Nabavi S

更新日期：2017-05-31 00:00:00

abstract：BACKGROUND:The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further proc...

journal_title：BMC bioinformatics

authors： Choo KH,Tan TW,Ranganathan S

更新日期：2005-10-13 00:00:00