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1,971 Newest Publications in bioinformatics
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Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
15-05-2013 | Danni Yu; Wolfgang Huber; Olga Vitek, Bioinformatics, 2013
Motivation: RNA-seq experiments produce digital counts of reads that are affected by both biological and technical variation. To distinguish the systematic changes in expression between conditions from noise, the counts are frequently modeled by the Negative Binomial distribution. However, ...
CistromeFinder for ChIP-seq and DNase-seq data reuse
15-05-2013 | Hanfei Sun; Bo Qin; Tao Liu; Qixuan Wang; Jing Liu; Juan Wang; Xueqiu Lin; Yulin Yang; Len Taing; Prakash K. Rao; My ..., Bioinformatics, 2013
Summary: Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing have greatly accelerated the understanding of transcriptional and epigenetic regulation, although data reuse for the community of experimental biologists has been challenging. We ...
Network predicting drug’s anatomical therapeutic chemical code
15-05-2013 | Yong-Cui Wang; Shi-Long Chen; Nai-Yang Deng; Yong Wang, Bioinformatics, 2013
Motivation: Discovering drug’s Anatomical Therapeutic Chemical (ATC) classification rules at molecular level is of vital importance to understand a vast majority of drugs action. However, few studies attempt to annotate drug’s potential ATC-codes by computational approaches. Results: Here, ...
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
15-05-2013 | Jon Ison; Matúš Kalaš; Inge Jonassen; Dan Bolser; Mahmut Uludag; Hamish McWilliam; James Malone; Rodrigo Lopez; Stev ..., Bioinformatics, 2013
Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations ...
Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements
15-05-2013 | Tarmo Äijö; Kirsi Granberg; Harri Lähdesmäki, Bioinformatics, 2013
Motivation: Signaling networks mediate responses to different stimuli using a multitude of feed-forward, feedback and cross-talk mechanisms, and malfunctions in these mechanisms have an important role in various diseases. To understand a disease and to help discover novel therapeutic ...
SRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets
15-05-2013 | Vincent Navratil; Clément Pontoizeau; Elise Billoir; Benjamin J. Blaise, Bioinformatics, 2013
Motivation: Supervised multivariate statistical analyses are often required to analyze the high-density spectral information in metabolic datasets acquired from complex mixtures in metabolic phenotyping studies. Here we present an implementation of the SRV—Statistical Recoupling of ...
EPSILON: an eQTL prioritization framework using similarity measures derived from local networks
15-05-2013 | Lieven P. C. Verbeke; Lore Cloots; Piet Demeester; Jan Fostier; Kathleen Marchal, Bioinformatics, 2013
Motivation: When genomic data are associated with gene expression data, the resulting expression quantitative trait loci (eQTL) will likely span multiple genes. eQTL prioritization techniques can be used to select the most likely causal gene affecting the expression of a target gene from a ...
PHISTO: pathogen–host interaction search tool
15-05-2013 | Saliha Durmuş Tekir; Tunahan Çakır; Emre Ardıç; Ali Semih Sayılırbaş; Gökhan Konuk; Mithat Konuk; Hasret Sarıyer; Az ..., Bioinformatics, 2013
Summary: Knowledge of pathogen–host protein interactions is required to better understand infection mechanisms. The pathogen–host interaction search tool (PHISTO) is a web-accessible platform that provides relevant information about pathogen–host interactions (PHIs). It enables access to the ...
BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences
15-05-2013 | Ergude Bao; Tao Jiang; Thomas Girke, Bioinformatics, 2013
Motivation: De novo transcriptome assemblies of RNA-Seq data are important for genomics applications of unsequenced organisms. Owing to the complexity and often incomplete representation of transcripts in sequencing libraries, the assembly of high-quality transcriptomes can be challenging. ...
Density-based hierarchical clustering of pyro-sequences on a large scale—the case of fungal ITS1
15-05-2013 | Marco Pagni; Hélène Niculita-Hirzel; Loïc Pellissier; Anne Dubuis; Ioannis Xenarios; Antoine Guisan; Ian R. Sanders; ..., Bioinformatics, 2013
Motivation: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, ...
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