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Published on Jul 1, 1998 in Intelligent Systems in Molecular Biology
Patricia G. Baker11
Estimated H-index: 11
(University of Manchester),
Andy Brass39
Estimated H-index: 39
(University of Manchester)
+ 3 AuthorsRobert Stevens23
Estimated H-index: 23
(University of Manchester)
Summary: TAMBIS (Transparent Access to Multiple Bioinformatics Information Sources) is an application that allows biologists to ask rich and complex questions over a range of bioinformatics resources. It is based on a model of the knowledge of the concepts and their relationships in molecular biology and bioinformatics. Availability: TAMBIS is available as an applet from http: // tambis Supplementary Information: A full user manual, tutorial and videos can ...
458 Citations Source Cite
Published on Jul 29, 2016in Briefings in Bioinformatics 6.30
Seonwoo Min4
Estimated H-index: 4
(Seoul National University),
Byunghan Lee6
Estimated H-index: 6
(Seoul National University),
Sungroh Yoon18
Estimated H-index: 18
(Seoul National University)
In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examp...
123 Citations Source Cite
Published on Jun 21, 2010 in High Performance Distributed Computing
Fábio Coutinho2
Estimated H-index: 2
(Federal University of Rio de Janeiro),
Eduardo S. Ogasawara15
Estimated H-index: 15
(Federal University of Rio de Janeiro)
+ 4 AuthorsMarta Mattoso23
Estimated H-index: 23
(Federal University of Rio de Janeiro)
Large scale bioinformatics experiments are usually composed by a set of data flows generated by a chain of activities (programs or services) that may be modeled as scientific workflows. Current Scientific Workflow Management Systems (SWfMS) are used to orchestrate these workflows to control and monitor the whole execution. It is very common in bioinformatics experiments to process very large datasets. In this way, data parallelism is a common approach used to increase performance a...
19 Citations Source Cite
Published on Jul 1, 2014in Briefings in Bioinformatics 6.30
Quan Zou34
Estimated H-index: 34
Xubin Li2
Estimated H-index: 2
+ 3 AuthorsKe Chen3
Estimated H-index: 3
Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-base...
119 Citations Source Cite
Published on Sep 1, 2009 in International Conference on Parallel Processing
Simone Leo7
Estimated H-index: 7
Federico Santoni24
Estimated H-index: 24
Gianluigi Zanetti20
Estimated H-index: 20
Bioinformatics applications currently require both processing of huge amounts of data and heavy computation. Fulfilling these requirements calls for simple ways to implement parallel computing. MapReduce is a general-purpose parallelization model that seems particularly well-suited to this task and for which an open source implementation (Hadoop) is available. Here we report on its application to three relevant algorithms: BLAST, GSEA and GRAMMAR. The first is characterized by relatively ...
43 Citations Source Cite
Published on Jan 8, 2003 in International Conference on Database Theory
Jinyan Li33
Estimated H-index: 33
See-Kiong Ng24
Estimated H-index: 24
Limsoon Wong46
Estimated H-index: 46
Informatics has helped launch molecular biology into the genomic era. It appears certain that informatics will remain a major contributor to molecular biology in the post-genome era.We discuss here data integration and datamining in bioinformatics, as well as the role that database theory played in these topics. We also describe LIMS as a third key topic in bioinformatics where advances in database system and theory can be very relevant.
16 Citations Source Cite
Published on Jul 1, 2014in Bioinformatics 5.48
Manja Marz17
Estimated H-index: 17
(University of Jena),
Niko Beerenwinkel37
Estimated H-index: 37
(Swiss Institute of Bioinformatics)
+ 8 AuthorsArmin Töpfer7
Estimated H-index: 7
(Swiss Institute of Bioinformatics)
Motivation: Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of4200 talks held at ISMB 2013, the largest international bioinformatics conference, only one presentation explicitly dealt with viruses. In contrast to many broad, established and wellorganized...
15 Citations Source Cite
Published on Jul 1, 2012in Nucleic Acids Research 11.56
Panu Artimo3
Estimated H-index: 3
(Swiss Institute of Bioinformatics),
Manohar Jonnalagedda1
Estimated H-index: 1
(Swiss Institute of Bioinformatics)
+ 18 AuthorsHeinz Stockinger13
Estimated H-index: 13
(Swiss Institute of Bioinformatics)
ExPASy ( has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. ...
588 Citations Source Cite
Published on Aug 19, 2000 in Intelligent Systems in Molecular Biology
Robin McEntire3
Estimated H-index: 3
Peter Karp1
Estimated H-index: 1
+ 13 AuthorsThodoros Topaloglou10
Estimated H-index: 10
Ontologies are specifications of the concepts in a given field, and of the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among th...
32 Citations
Published on Jan 1, 2016in Briefings in Bioinformatics 6.30
Anna C. Greene7
Estimated H-index: 7
Kristine A. Giffin1
Estimated H-index: 1
+ 1 AuthorsJason H. Moore61
Estimated H-index: 61
(Dartmouth College)
Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet t...
11 Citations Source Cite