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Bioinformatics: Tools and applications

Published on Jan 1, 2009
· DOI :10.1007/978-0-387-92738-1
A. David Edwards DSc FMedSci94
Estimated H-index: 94
(University of Queensland),
Jason E. Stajich48
Estimated H-index: 48
(University of California, Berkeley),
David Hansen13
Estimated H-index: 13
(Commonwealth Scientific and Industrial Research Organisation)
Biology has progressed tremendously in the last decade due in part to the increased automation in the generation of data from sequences to genotypes to phenotypes. Biology is now very much an information science and bioinformatics provides the means to connect biological data to hypotheses. Bioinformatics: Tools and Applications provides up-to-date descriptions of the various areas of applied bioinformatics, from the analysis of sequence, literature, and functional data to the function and evolution of organisms. The ability to process and interpret large volumes of data is essential with the application of new high throughput DNA sequencers providing an overload of sequence data. Initial chapters provide an introduction to the analysis of DNA and protein sequences, from motif detection to gene prediction and annotation, with specific chapters on DNA and protein databases as well as data visualization. Additional chapters focus on gene expression analysis from the perspective of traditional microarrays and more recent sequence based approaches, followed by an introduction to the evolving field of phenomics, with specific chapters detailing advances in plant and microbial phenome analysis and a chapter dealing with the important issue of standards for functional genomics. Further chapters present the area of literature databases and associated mining tools which are becoming increasingly essential to interpret the vast volume of published biological information, while the final chapters present bioinformatics purely from a developers point of view, describing the various data and databases as well as common programming languages used for bioinformatics applications. These chapters provide an introduction and motivation to further avenues for implementation. Together, this volume aims to provide a resource for biology students wanting a greater understanding of the encroaching area of bioinformatics, as well as computer scientists who are interested learning more about the field of applied bioinformatics.
  • References (688)
  • Citations (13)
Published on Jan 1, 2014
Zhipeng Luo1
Estimated H-index: 1
57 Citations
Published on Jan 1, 2011
Stasys Jukna14
Estimated H-index: 14
(Goethe University Frankfurt)
Let X 1,…,X n be random variables, and X=c 1 X 1+⋯+c n X n . Linearity of expectation states that $$\mathrm{E} [X] = c_1 \mathrm{E} [X_1] + \cdots + c_n \mathrm{E} [X_n].$$ The power of this principle comes from there being no restrictions on the dependence or independence of the X i ’s. In applications we often use the fact that there must be a point in the probability space for which X≥E[X] and a point for which X≤E[X]. This principle (known as the pigeonhole property of the expectation) is us...
1 Citations Source Cite
Published on Dec 1, 2009in Current protocols in human genetics
Maureen J. Donlin15
Estimated H-index: 15
(Saint Louis University)
133 Citations Source Cite
Published on Aug 3, 2009
Christoph Wierling18
Estimated H-index: 18
Edda Klipp42
Estimated H-index: 42
Wolfram Liebermeister14
Estimated H-index: 14
564 Citations
Published on Dec 31, 2008in Protein Science 2.41
Toshimasa Yamazaki22
Estimated H-index: 22
Andrew P. Hinck23
Estimated H-index: 23
+ 8 AuthorsPeter J. Domaille31
Estimated H-index: 31
(Wilmington University)
The three-dimensional solution structure of the HIV-1 protease homodimer, MW 22.2 kDa, complexed to a potent, cyclic urea-based inhibitor, DMP323, is reported. This is the first solution structure of an HIV protease/inhibitor complex that has been elucidated. Multidimensional heteronuclear NMR spectra were used to assemble more than 4,200 distance and angle constraints. Using the constraints, together with a hybrid distance geometry/simulated annealing protocol, an ensemble of 28 NMR structures ...
59 Citations Source Cite
Published on Nov 1, 2008in Genome Research 10.10
Li Heng49
Estimated H-index: 49
(Wellcome Trust Sanger Institute),
Jue Ruan18
Estimated H-index: 18
(Chinese Academy of Sciences),
Richard Durbin103
Estimated H-index: 103
(Wellcome Trust Sanger Institute)
New sequencing technologies promise a new era in the use of DNA sequence. However, some of these technologies produce very short reads, typically of a few tens of base pairs, and to use these reads effectively requires new algorithms and software. In particular, there is a major issue in efficiently aligning short reads to a reference genome and handling ambiguity or lack of accuracy in this alignment. Here we introduce the concept ofmapping quality ,a measure of the confidence that a read actua...
2,207 Citations Source Cite
Published on Nov 1, 2008in Nature 41.58
David R. Bentley38
Estimated H-index: 38
Shankar Balasubramanian64
Estimated H-index: 64
+ 191 AuthorsHelen R. Bignell1
Estimated H-index: 1
DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of ...
2,580 Citations Source Cite
Published on Oct 15, 2008in Bioinformatics 5.48
Hui Jiang22
Estimated H-index: 22
(Stanford University),
Wing Hung Wong76
Estimated H-index: 76
(Stanford University)
Summary: SeqMap is a tool for mapping large amount of short sequences to the genome. It is designed for finding all the places in a reference genome where each sequence may come from. This task is essential to the analysis of data from ultra high-throughput sequencing machines. With a carefully designed index-filtering algorithm and an efficient implementation, SeqMap can map tens of millions of short sequences to a genome of several billions of nucleotides. Multiple substitutions and insertions...
309 Citations Source Cite
Published on Oct 1, 2008in BMC Bioinformatics 2.21
Fabio De Bona6
Estimated H-index: 6
(Max Planck Society),
Stephan Ossowski35
Estimated H-index: 35
(Max Planck Society)
+ 1 AuthorsGunnar Rätsch54
Estimated H-index: 54
(Max Planck Society)
A fishing reel consists of a crank which can be folded, when the reel is not in use for fishing. The crank consists of a hub which supports a lateral operating lever. The hub consists of two parts which are joined one on the other for relative pivoting around a shaft arranged perpendicularly to the hub and in a plane which contains the lever. These parts are held against relative pivoting by a sliding bolt which can be moved in directions along the lever. A spring tends to keep a profiled part o...
127 Citations Source Cite
Published on Aug 15, 2008in Science 41.06
Marc Sultan24
Estimated H-index: 24
(Max Planck Society),
Marcel H. Schulz18
Estimated H-index: 18
(Max Planck Society)
+ 13 AuthorsDmitri Parkhomchuk10
Estimated H-index: 10
(Max Planck Society)
The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. We used shotgun sequencing of transcripts to generate randomly distributed reads. Of these, 50% mapped to unique genomic locations, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to nonannotated genomic regions. On the basis o...
991 Citations Source Cite
Cited By13
Published on Jun 20, 2018 in International Symposium on Distributed Computing
Noé Vázquez1
Estimated H-index: 1
(University of Vigo)
The main objective of this work is the design and implementation of a reduced set of automated pipelines able to integrate a wide range of existing bioinformatics applications and libraries with the goal of delivering an easy-to-use resource, which can be further used to provide different answers to complex biological questions mainly related with nucleotide and amino acid sequences.
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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. Bones41
Estimated H-index: 41
(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...
23 Citations Source Cite
Published on Jan 1, 2015
Hifzur Rahman9
Estimated H-index: 9
(Tamil Nadu Agricultural University),
Valarmathi Ramanathan2
Estimated H-index: 2
(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...
2 Citations Source Cite
Published on Jan 1, 2015
Estimated H-index: 1
Estimated H-index: 1
+ 6 AuthorsWidayanti1
Estimated H-index: 1
Pseudomonas stutzeri caused an outbreak of freshwater fish in Luwuk Banggai (tilapia and catfish), Bali (tilapia), Jambi (tilapia and catfish) and Tanjung Pinang (catfish). The study was purposed to comprehensively identify special phenotypic and genotypic characteristics of P. stutzeri isolated from several areas in Indonesia, including its morphometric and biochemical characteristics and molecular variation. Bacteria were isolated from internal organs (kidney, ulcer and eye) of fish. They were...
1 Citations
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 Jan 1, 2014in BMC Genomics 3.73
Qifeng Ma1
Estimated H-index: 1
(Northwest A&F University),
Man Wu8
Estimated H-index: 8
(Civil Aviation Authority of Singapore)
+ 5 AuthorsShuxun Yu13
Estimated H-index: 13
(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 ...
20 Citations Source Cite
Published on Aug 1, 2013
Hasniliati Hassan1
Estimated H-index: 1
Zulkifli Abd. Majid5
Estimated H-index: 5
+ 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 Aug 1, 2013in Expert Systems With Applications 3.77
Daniela Xavier2
Estimated H-index: 2
(Complutense University of Madrid),
Federico Morán18
Estimated H-index: 18
(Complutense University of Madrid)
+ 1 AuthorsGonzalo Pajares-Martinsanz25
Estimated H-index: 25
(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 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 Feb 29, 2012
Hee-Jin Lee3
Estimated H-index: 3
Jong C. Park11
Estimated H-index: 11
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