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Bioinformatics : Tools and Applications
Published on Jan 1, 2009
· DOI :10.1007/978-0-387-92738-1
David Edwards59
Estimated H-index: 59
(University of Queensland),
Jason E. Stajich47
Estimated H-index: 47
(University of California, Berkeley),
David Hansen12
Estimated H-index: 12
(Commonwealth Scientific and Industrial Research Organisation)
Abstract
DNA Sequence Databases.- Sequence Comparison Tools.- Genome Browsers.- Predicting Non-coding RNA Transcripts.- Gene Prediction Methods.- Gene Annotation Methods.- Regulatory Motif Analysis.- Molecular Marker Discovery and Genetic Map Visualisation.- Sequence Based Gene Expression Analysis.- Protein Sequence Databases.- Protein Structure Prediction.- Classification of Information About Proteins.- High-Throughput Plant Phenotyping - Data Acquisition, Transformation, and Analysis.- Phenome Analysis of Microorganisms.- Standards for Functional Genomics.- Literature Databases.- Advanced Literature-Mining Tools.- Data and Databases.- Programming Languages.
  • References (687)
  • Cited By (13)
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References687
Published on Jan 1, 2004 in The Web Conference
Dan Brickley12
Estimated H-index: 12
,
Ramanathan V. Guha20
Estimated H-index: 20
1,133 Citations
Published on Dec 28, 2001in Cell 31.40
Victor R. Ambros56
Estimated H-index: 56
(Dartmouth College)
Animal genomes contain an abundance of small genes that produce regulatory RNAs of about 22 nucleotides in length. These microRNAs are diverse in sequence and expression patterns, and are evolutionarily widespread, suggesting that they may participate in a wide range of genetic regulatory pathways.
1,123 Citations Source Cite
Published on Sep 28, 1995in Nature 41.58
Adams2
Estimated H-index: 2
(J. Craig Venter Institute),
Anthony R. Kerlavage19
Estimated H-index: 19
(J. Craig Venter Institute)
+ 7 AuthorsOwen White58
Estimated H-index: 58
(J. Craig Venter Institute)
In an effort to identify new genes and analyse their expression patterns, 174,472 partial complementary DNA sequences (expressed sequence tags (ESTs)), totalling more than 52 million nucleotides of human DNA sequence, have been generated from 300 cDNA libraries constructed from 37 distinct organs and tissues. These ESTs have been combined with an additional 118,406 ESTs from the database dbEST, for a total of 83 million nucleotides, and treated as a shotgun sequence assembly project. The assembl...
897 Citations
Published on Jan 1, 1992
Nicky J. Mulder1
Estimated H-index: 1
,
Rolf Apweiler48
Estimated H-index: 48
+ 37 AuthorsLaurent Cerutti1
Estimated H-index: 1
1,298 Citations
Published on Jan 1, 2000in Nucleic Acids Research 11.56
Michael Ashburner70
Estimated H-index: 70
,
Catherine A. Ball33
Estimated H-index: 33
+ 17 AuthorsJanan T. Eppig44
Estimated H-index: 44
5,826 Citations
Published on Jan 1, 2000in Methods of Molecular Biology
William R. Pearson45
Estimated H-index: 45
(University of Virginia)
537 Citations Source Cite
Published on Jan 1, 1999in Cold Spring Harbor Monograph Archive
Kazimierz T. Tycowski14
Estimated H-index: 14
,
Nikolay G. Kolev12
Estimated H-index: 12
+ 2 AuthorsJoan A. Steitz91
Estimated H-index: 91
Small r ibo n ucleo p roteins (RNPs)—defined as tight complexes of one or more proteins with a short RNA molecule (usually 60–300 nucleotides)—inhabit every compartment of eukaryotic cells. Those that reside in the nucleus, the s mall n uclear RNPs (snRNPs), can themselves be divided into two families. There are snRNPs of the nucleoplasm, whose major business is the generation of messenger RNAs for export to the cytoplasm. A different set of snRNPs, called snoRNPs, reside in the cell nucleolus, ...
2,959 Citations Source Cite
Published on Jan 1, 2007in Advances in Experimental Medicine and Biology 1.76
John A. Calarco10
Estimated H-index: 10
,
Arneet L. Saltzman7
Estimated H-index: 7
+ 1 AuthorsBenjamin J. Blencowe64
Estimated H-index: 64
During the past ∼20 years, studies on alternative splicing (AS) have largely been directed at the identification and characterization of factors and mechanisms responsible for the control of splice site selection, using model substrates and on a case by case basis. These studies have provided a wealth of information on the factors and interactions that control formation of the spliceosome. However, relatively little is known about the global regulatory properties of AS. Important questions that ...
30 Citations
Published on Mar 1, 2005in Journal of Plant Biotechnology
Jennifer C Mortimer1
Estimated H-index: 1
,
Jacqueline Batley41
Estimated H-index: 41
+ 2 AuthorsDavid Edwards59
Estimated H-index: 59
We have mined each of the five A. thaliana chromosomes for the presence of simple sequence repeats (SSRs) and developed custom perl scripts to examine their distribution and abundance in relation to genomic position, local G/C content and location within and around transcribed sequences. The distribution of repeats and G/C content with respect to genomic regions (exons, UTRs, introns, intergenic regions and proximity to expressed genes) are shown. SSRs show a non-random distribution across the g...
14 Citations
Published on Jan 1, 2007in Methods of Molecular Biology
Jonathan Crabtree35
Estimated H-index: 35
,
Samuel V. Angiuoli30
Estimated H-index: 30
+ 1 AuthorsOwen White58
Estimated H-index: 58
49 Citations Source Cite
Cited By13
Published on Jan 1, 2015
Hifzur Rahman3
Estimated H-index: 3
(Tamil Nadu Agricultural University),
Valarmathi Ramanathan1
Estimated H-index: 1
(Tamil Nadu Agricultural University)
+ 6 AuthorsRaveendran Muthurajan12
Estimated H-index: 12
(Tamil Nadu Agricultural University)
To meet the challenges of global food security in the changing climatic scenario, it would be most imperative to enhance crop productivity under resource competence. It is estimated that approximately 70 % of reduction in crop yield is due to the direct impact of abiotic stresses such as drought, salinity, and extreme temperatures. In the present context, one of the major challenges is large-scale screening of crop performance as a consequence of its genetic makeup. The development of advanced b...
1 Citations Source Cite
Published on Jan 1, 2014
Mark L. Crowe (University of Adelaide), Timothy J. March7
Estimated H-index: 7
(University of Adelaide),
Joanne Tilbrook7
Estimated H-index: 7
(University of Adelaide)
Over the last decade, biological sciences have been revolutionised by the adoption of high-throughput omics technologies, and many of the discoveries that have underpinned this revolution have now been adopted for use in plant phenotyping. The field of whole-plant phenomics resulting from this combines robotics, image capture and high-performance computational analysis and provides plant scientists with the ability to characterise dozens of phenotypes on thousands of plants daily.
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Published on Aug 1, 2013in Expert Systems With Applications 3.77
Daniela Xavier2
Estimated H-index: 2
(Complutense University of Madrid),
Federico Morán15
Estimated H-index: 15
(Complutense University of Madrid)
+ 1 AuthorsGonzalo Pajares24
Estimated H-index: 24
(Complutense University of Madrid)
Finding the genes that exist within a DNA sequence and assigning them biological features and functions is one of the biggest challenges of Genomics. This task, called annotation, has to be as accurate and reliable as possible, because this information will be applied in other researches. Ideally, each sequence should be annotated and validated by a human expert, who has the knowledge to infer the most appropriate annotation. Nevertheless, the huge amount of genomic data produced by the new sequ...
4 Citations Source Cite
Published on Jan 1, 2011in BMC Bioinformatics 2.21
Amin Zia7
Estimated H-index: 7
(University of Toronto),
Alan M. Moses29
Estimated H-index: 29
(University of Toronto)
Background Genetic variations contribute to normal phenotypic differences as well as diseases, and new sequencing technologies are greatly increasing the capacity to identify these variations. Given the large number of variations now being discovered, computational methods to prioritize the functional importance of genetic variations are of growing interest. Thus far, the focus of computational tools has been mainly on the prediction of the effects of amino acid changing single nucleotide polymo...
23 Citations Source Cite
Published on Jan 17, 2011in Aquatic Toxicology 3.88
Rebekka Henke1
Estimated H-index: 1
(University of Jena),
Matthias Eberius3
Estimated H-index: 3
,
Klaus-J. Appenroth18
Estimated H-index: 18
(University of Jena)
Abstract Fronds of the duckweed Lemna minor L. clone St form colonies of different sizes on the basis of stipes connecting mother and daughter fronds for some time after the development of daughter fronds. All the metals (AsO 4 3− , AsO 2 − , Cd 2+ , CrO 4 2− , Co 2+ , Cu 2+ , Ni 2+ , Hg 2+ , Tl + and Zn 2+ ) and one non-metal (SeO 4 2− , SeO 3 2− ) tested here induced frond abscission, thus decreasing the colony size on the basis of a novel mechanism of abscission described recently. Concentrat...
14 Citations Source Cite
Published on Aug 1, 2013
Hasniliati Hassan1
Estimated H-index: 1
,
Zulkifli Abd. Majid4
Estimated H-index: 4
+ 1 AuthorsAzlina Ibrahim1
Estimated H-index: 1
From time to time, researchers always try to improve algorithm for DNA fragment assembly that using de Bruijn graph. A de Bruijn graph is one of graph theoretical approach that based on short words (k-mers) that is ideal for high coverage, very short read (25-50bp) data sets. Therefore, the content of this paper proposed the development of DNA fragment assembly by using one of method that applied de Bruijn graph to construct complete a sequence, called Idury Waterman and Pevzner method. The algo...
2 Citations Source Cite
Published on Jan 29, 2013in Holos
Neyvan Renato Rodrigues Silva1
Estimated H-index: 1
Experimentos bem sucedidos e amplamente conhecidos, como o Projeto Genoma Humano, confirmam a potencialidade da bioinformatica como novo ramo cientifico, os quais antes seriam inviaveis sem o desenvolvimento de tecnologias para o sequenciamento e analise dos dados obtidos. Nesse preâmbulo, esse trabalho tem como principal objetivo apresentar uma proposta de capacitacao dos alunos do IFRN atraves da proposta de um curso de extensao apresentando ferramentas introdutorias de biologia computacional....
1 Citations Source Cite
Published on Jan 1, 2014in BMC Genomics 3.73
Qifeng Ma1
Estimated H-index: 1
(Northwest A&F University),
Man Wu7
Estimated H-index: 7
(Civil Aviation Authority of Singapore)
+ 5 AuthorsShuxun Yu9
Estimated H-index: 9
(Northwest A&F University)
Background The cotton (Gossypium spp.) fiber cell is an important unicellular model for studying cell differentiation. There is evidence suggesting that phosphorylation is a critical post-translational modification involved in regulation of a wide range of cell activities. Nevertheless, the sites of phosphorylation in G. hirsutum and their regulatory roles in fiber cell initiation are largely unknown. In this study, we employed a mass spectrometry-based phosphoproteomics to conduct a global and ...
16 Citations Source Cite
Published on Feb 29, 2012
Hee-Jin Lee3
Estimated H-index: 3
,
Jong C. Park10
Estimated H-index: 10
In this paper, we discuss the structure of biological knowledge discovery system based on text mining and automatic inference. Given a set of biology documents, the system produces a new hypothesis in an integrated manner. The text mining module of the system first extracts the `event` information of predefined types from the documents. The inference module then produces a new hypothesis based on the extracted results. Such an integrated system can use information more up-to-date and diverse tha...
2 Citations Source Cite
Published on Feb 1, 2015in Journal of Experimental Botany 5.35
Pankaj Barah7
Estimated H-index: 7
(Norwegian University of Science and Technology),
Atle M. Bones40
Estimated H-index: 40
(Norwegian University of Science and Technology)
The biggest challenge for modern biology is to integrate multidisciplinary approaches towards understanding the organizational and functional complexity of biological systems at different hierarchies, starting from the subcellular molecular mechanisms (microscopic) to the functional interactions of ecological communities (macroscopic). The plant–insect interaction is a good model for this purpose with the availability of an enormous amount of information at the molecular and the ecosystem levels...
21 Citations Source Cite
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