BIO401 Wikipedia Bioinformatics 2.7.2012

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Bioinformatics 1

Bioinformatics

Map of the human X chromosome (from the NCBI

website). Assembly of the human genome is one of the

greatest achievements of bioinformatics.

Bioinformaticsi/ba.onfrmtks/ is the application of

computer science and information technology to the field of

biology and medicine. Bioinformatics deals with algorithms,

databases and information systems, web technologies,

artificial intelligence and soft computing, information and

computation theory, software engineering, data mining, image

processing, modeling and simulation, signal processing,

discrete mathematics, control and system theory, circuit

theory, and statistics, for generating new knowledge of

biology and medicine, and improving & discovering new

models of computation (e.g. DNA computing, neural

computing, evolutionary computing, immuno-computing,

swarm-computing, cellular-computing).

Commonly used software tools and technologies in this field

include Java, XML, Perl, C, C++, Python, R, SQL, CUDA

and MATLAB.

Introduction

Bioinformatics was applied in the creation and maintenance of a database to store biological information at the

beginning of the "genomic revolution", such as nucleotide sequences and amino acid sequences. Development of this

type of database involved not only design issues but the development of complex interfaces whereby researchers

could both access existing data as well as submit new or revised data.

In order to study how normal cellular activities are altered in different disease states, the biological data must be

combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such

that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide

and amino acid sequences, protein domains, and protein structures[1]

. The actual process of analyzing and

interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and

computational biology include:

the development and implementation of tools that enable efficient access to, and use and management of, various

types of information.

the development of new algorithms (mathematical formulas) and statistics with which to assess relationships

among members of large data sets, such as methods to locate a gene within a sequence, predict protein structure

and/or function, and cluster protein sequences into families of related sequences.

The primary goal of bioinformatics is to increase the understanding of biological processes. What sets it apart from

other approaches, however, is its focus on developing and applying computationally intensive techniques (e.g.,

pattern recognition, data mining, machine learning algorithms, and visualization) to achieve this goal. Major research

efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein

structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions,

genome-wide association studies and the modeling of evolution.

Interestingly, the term bioinformatics was coined before the "genomic revolution". Paulien Hogeweg and Ben

Hesper introduced the term in 1978 to refer to "the study of information processes in biotic systems". [2][3], a

definition that placed bioinformatics as a field parallel to biophysics or biochemistry (e.g. biochemistry is the study
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Bioinformatics 2

of chemical processes in biological systems)[4]

. However, its primary use since at least the late 1980s has been to

describe the application of computer science and information sciences to the analysis of biological data, particularly

in those areas of genomics involving large-scale DNA sequencing.

Bioinformatics now entails the creation and advancement of databases, algorithms, computational and statistical

techniques and theory to solve formal and practical problems arising from the management and analysis of biological

data.Over the past few decades rapid developments in genomic and other molecular research technologies and

developments in information technologies have combined to produce a tremendous amount of information related to

molecular biology. It is the name given to these mathematical and computing approaches used to glean

understanding of biological processes.

Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different

DNA and protein sequences to compare them and creating and viewing 3-D models of protein structures.

There are two fundamental ways of modelling a Biological system (e.g. living cell) both coming under Bioinformatic

approaches.

Static Sequences Proteins, Nucleic acids and Peptides

Structures Proteins, Nucleic acids, Ligands (including metabolites and drugs) and Peptides

Interaction data among the above entities including microarray data and Networks of proteins, metabolites

Dynamic

Systems Biology comes under this category including reaction fluxes and variable concentrations of

metabolites

Multi-Agent Based modelling approaches capturing cellular events such as signalling, transcription and

reaction dynamics

A broad sub-category under bioinformatics is structural bioinformatics.

Major research areas

Sequence analysis

Since the Phage -X174 was sequenced in 1977,[5]

the DNA sequences of thousands of organisms have been

decoded and stored in databases. This sequence information is analyzed to determine genes that encode polypeptides

(proteins), RNA genes, regulatory sequences, structural motifs, and repetitive sequences. A comparison of genes

within a species or between different species can show similarities between protein functions, or relations between

species (the use of molecular systematics to construct phylogenetic trees). With the growing amount ofdata, it long

ago became impractical to analyze DNA sequences manually. Today, computer programs such as BLAST are useddaily to search sequences from more than 260 000 organisms, containing over 190 billion nucleotides.

[6]These

programs can compensate for mutations (exchanged, deleted or inserted bases) in the DNA sequence, to identify

sequences that are related, but not identical. A variant of this sequence alignment is used in the sequencing process

itself. The so-called shotgun sequencing technique (which was used, for example, by The Institute for Genomic

Research to sequence the first bacterial genome,Haemophilus influenzae)[7]

does not produce entire chromosomes,

but instead generates the sequences of many thousands of small DNA fragments (ranging from 35 to 900 nucleotides

long, depending on the sequencing technology). The ends of these fragments overlap and, when aligned properly by

a genome assembly program, can be used to reconstruct the complete genome. Shotgun sequencing yields sequence

data quickly, but the task of assembling the fragments can be quite complicated for larger genomes. For a genome as

large as the human genome, it may take many days of CPU time on large-memory, multiprocessor computers toassemble the fragments, and the resulting assembly will usually contain numerous gaps that have to be filled in later.
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Shotgun sequencing is the method of choice for virtually all genomes sequenced today, and genome assembly

algorithms are a critical area of bioinformatics research.

Another aspect of bioinformatics in sequence analysis is annotation, which involves computational gene finding to

search for protein-coding genes, RNA genes, and other functional sequences within a genome. Not all of the

nucleotides within a genome are part of genes. Within the genome of higher organisms, large parts of the DNA do

not serve any obvious purpose. This so-called junk DNA may, however, contain unrecognized functional elements.Bioinformatics helps to bridge the gap between genome and proteome projects for example, in the use of DNA

sequences for protein identification.

Genome annotation

In the context of genomics, annotation is the process of marking the genes and other biological features in a DNA

sequence. The first genome annotation software system was designed in 1995 by Dr. Owen White, who was part of

the team at The Institute for Genomic Research that sequenced and analyzed the first genome of a free-living

organism to be decoded, the bacteriumHaemophilus influenzae. Dr. White built a software system to find the genes

(places in the DNA sequence that encode a protein), the transfer RNA, and other features, and to make initial

assignments of function to those genes. Most current genome annotation systems work similarly, but the programs

available for analysis of genomic DNA are constantly changing and improving.

Computational evolutionary biology

Evolutionary biology is the study of the origin and descent of species, as well as their change over time. Informatics

has assisted evolutionary biologists in several key ways; it has enabled researchers to:

trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through

physical taxonomy or physiological observations alone,

more recently, compare entire genomes, which permits the study of more complex evolutionary events, such as

gene duplication, horizontal gene transfer, and the prediction of factors important in bacterial speciation, build complex computational models of populations to predict the outcome of the system over time

track and share information on an increasingly large number of species and organisms

Future work endeavours to reconstruct the now more complex tree of life.

The area of research within computer science that uses genetic algorithms is sometimes confused with computational

evolutionary biology, but the two areas are not necessarily related.

Literature analysis

The growth in the number of published literature makes it virtually impossible to read every paper, resulting in

disjointed subfields of research. Literature analysis aims to employ computational and statistical linguistics to mine

this growing library of text resources. For example:

abbreviation recognition - identify the long-form and abbreviation of biological terms,

named entity recognition - recognizing biological terms such as gene names

protein-protein interaction - identify which proteins interact with which proteins from text

The area of research draws from statistics and computational linguistics.
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Analysis of gene expression

The expression of many genes can be determined by measuring mRNA levels with multiple techniques including

microarrays, expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression (SAGE) tag

sequencing, massively parallel signature sequencing (MPSS), RNA-Seq, also known as "Whole Transcriptome

Shotgun Sequencing" (WTSS), or various applications of multiplexed in-situ hybridization. All of these techniques

are extremely noise-prone and/or subject to bias in the biological measurement, and a major research area incomputational biology involves developing statistical tools to separate signal from noise in high-throughput gene

expression studies. Such studies are often used to determine the genes implicated in a disorder: one might compare

microarray data from cancerous epithelial cells to data from non-cancerous cells to determine the transcripts that are

up-regulated and down-regulated in a particular population of cancer cells.

Analysis of regulation

Regulation is the complex orchestration of events starting with an extracellular signal such as a hormone and leading

to an increase or decrease in the activity of one or more proteins. Bioinformatics techniques have been applied to

explore various steps in this process. For example, promoter analysis involves the identification and study of

sequence motifs in the DNA surrounding the coding region of a gene. These motifs influence the extent to which that

region is transcribed into mRNA. Expression data can be used to infer gene regulation: one might compare

microarray data from a wide variety of states of an organism to form hypotheses about the genes involved in each

state. In a single-cell organism, one might compare stages of the cell cycle, along with various stress conditions (heat

shock, starvation, etc.). One can then apply clustering algorithms to that expression data to determine which genes

are co-expressed. For example, the upstream regions (promoters) of co-expressed genes can be searched for

over-represented regulatory elements.

Analysis of protein expression

Protein microarrays and high throughput (HT) mass spectrometry (MS) can provide a snapshot of the proteins

present in a biological sample. Bioinformatics is very much involved in making sense of protein microarray and HT

MS data; the former approach faces similar problems as with microarrays targeted at mRNA, the latter involves the

problem of matching large amounts of mass data against predicted masses from protein sequence databases, and the

complicated statistical analysis of samples where multiple, but incomplete peptides from each protein are detected.

Analysis of mutations in cancer

In cancer, the genomes of affected cells are rearranged in complex or even unpredictable ways. Massive sequencing

efforts are used to identify previously unknown point mutations in a variety of genes in cancer. Bioinformaticians

continue to produce specialized automated systems to manage the sheer volume of sequence data produced, and they

create new algorithms and software to compare the sequencing results to the growing collection of human genomesequences and germline polymorphisms. New physical detection technologies are employed, such as oligonucleotide

microarrays to identify chromosomal gains and losses (called comparative genomic hybridization), and

single-nucleotide polymorphism arrays to detect known point mutations. These detection methods simultaneously

measure several hundred thousand sites throughout the genome, and when used in high-throughput to measure

thousands of samples, generate terabytes of data per experiment. Again the massive amounts and new types of data

generate new opportunities for bioinformaticians. The data is often found to contain considerable variability, or

noise, and thus Hidden Markov model and change-point analysis methods are being developed to infer real copy

number changes.

Another type of data that requires novel informatics development is the analysis of lesions found to be recurrent

among many tumors.
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Comparative genomics

The core of comparative genome analysis is the establishment of the correspondence between genes (orthology

analysis) or other genomic features in different organisms. It is these intergenomic maps that make it possible to

trace the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary events

acting at various organizational levels shape genome evolution. At the lowest level, point mutations affect individual

nucleotides. At a higher level, large chromosomal segments undergo duplication, lateral transfer, inversion,transposition, deletion and insertion. Ultimately, whole genomes are involved in processes of hybridization,

polyploidization and endosymbiosis, often leading to rapid speciation. The complexity of genome evolution poses

many exciting challenges to developers of mathematical models and algorithms, who have recourse to a spectra of

algorithmic, statistical and mathematical techniques, ranging from exact, heuristics, fixed parameter and

approximation algorithms for problems based on parsimony models to Markov Chain Monte Carlo algorithms for

Bayesian analysis of problems based on probabilistic models.

Many of these studies are based on the homology detection and protein families computation.

Modeling biological systems

Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of

metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks)

to both analyze and visualize the complex connections of these cellular processes. Artificial life or virtual evolution

attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.

High-throughput image analysis

Computational technologies are used to accelerate or fully automate the processing, quantification and analysis of

large amounts of high-information-content biomedical imagery. Modern image analysis systems augment an

observer's ability to make measurements from a large or complex set of images, by improving accuracy, objectivity,

or speed. A fully developed analysis system may completely replace the observer. Although these systems are notunique to biomedical imagery, biomedical imaging is becoming more important for both diagnostics and research.

Some examples are:

high-throughput and high-fidelity quantification and sub-cellular localization (high-content screening,

cytohistopathology, Bioimage informatics)

morphometrics

clinical image analysis and visualization

determining the real-time air-flow patterns in breathing lungs of living animals

quantifying occlusion size in real-time imagery from the development of and recovery during arterial injury

making behavioral observations from extended video recordings of laboratory animals

infrared measurements for metabolic activity determination

inferring clone overlaps in DNA mapping, e.g. the Sulston score

Structural Bioinformatic Approaches

Prediction of protein structure

Protein structure prediction is another important application of bioinformatics. The amino acid sequence of a protein,

the so-called primary structure, can be easily determined from the sequence on the gene that codes for it. In the vast

majority of cases, this primary structure uniquely determines a structure in its native environment. (Of course, there

are exceptions, such as the bovine spongiform encephalopathy a.k.a. Mad Cow Disease prion.) Knowledge of

this structure is vital in understanding the function of the protein. For lack of better terms, structural information is

usually classified as one of secondary, tertiary and quaternary structure. A viable general solution to such
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Bioinformatics 6

predictions remains an open problem. As of now, most efforts have been directed towards heuristics that work most

of the time.

One of the key ideas in bioinformatics is the notion of homology. In the genomic branch of bioinformatics,

homology is used to predict the function of a gene: if the sequence of gene A, whose function is known, is

homologous to the sequence of geneB, whose function is unknown, one could infer that B may share A's function. In

the structural branch of bioinformatics, homology is used to determine which parts of a protein are important instructure formation and interaction with other proteins. In a technique called homology modeling, this information is

used to predict the structure of a protein once the structure of a homologous protein is known. This currently remains

the only way to predict protein structures reliably.

One example of this is the similar protein homology between hemoglobin in humans and the hemoglobin in legumes

(leghemoglobin). Both serve the same purpose of transporting oxygen in the organism. Though both of these

proteins have completely different amino acid sequences, their protein structures are virtually identical, which

reflects their near identical purposes.

Other techniques for predicting protein structure include protein threading and de novo (from scratch) physics-based

modeling.

See also: structural motif and structural domain.

Molecular Interaction

Efficient software is available today for studying interactions among proteins, ligands and peptides. Types of

interactions most often encountered in the field include Proteinligand (including drug), proteinprotein and

proteinpeptide.

Molecular dynamic simulation of movement of atoms about rotatable bonds is the fundamental principle behind

computational algorithms, termed docking algorithms for studying molecular interactions.

See also: proteinprotein interaction prediction.

Docking algorithms

In the last two decades, tens of thousands of protein three-dimensional structures have been determined by X-ray

crystallography and Protein nuclear magnetic resonance spectroscopy (protein NMR). One central question for the

biological scientist is whether it is practical to predict possible proteinprotein interactions only based on these 3D

shapes, without doing proteinprotein interaction experiments. A variety of methods have been developed to tackle

the Proteinprotein docking problem, though it seems that there is still much work to be done in this field.

Software and tools

Software tools for bioinformatics range from simple command-line tools, to more complex graphical programs and

standalone web-services available from various bioinformatics companies or public institutions.

Open source bioinformatics software

Many free and open source software tools have existed and continued to grow since the 1980s.[8]

The combination of

a continued need for new algorithms for the analysis of emerging types of biological readouts, the potential for

innovative in silico experiments, and freely available open code bases have helped to create opportunities for all

research groups to contribute to both bioinformatics and the range of open source software available, regardless of

their funding arrangements. The open source tools often act as incubators of ideas, or community-supported plug-ins

in commercial applications. They may also provide de facto standards and shared object models for assisting with

the challenge of bioinformation integration.
http://en.wikipedia.org/w/index.php?title=De_factohttp://en.wikipedia.org/w/index.php?title=Plug-in_%28computing%29http://en.wikipedia.org/w/index.php?title=Open_codehttp://en.wikipedia.org/w/index.php?title=In_silicohttp://en.wikipedia.org/w/index.php?title=Algorithmhttp://en.wikipedia.org/w/index.php?title=Free_and_open_source_softwarehttp://en.wikipedia.org/w/index.php?title=List_of_bioinformatics_companieshttp://en.wikipedia.org/w/index.php?title=Softwarehttp://en.wikipedia.org/w/index.php?title=Protein%E2%80%93protein_dockinghttp://en.wikipedia.org/w/index.php?title=Protein%E2%80%93protein_interactionhttp://en.wikipedia.org/w/index.php?title=Protein_nuclear_magnetic_resonance_spectroscopyhttp://en.wikipedia.org/w/index.php?title=X-ray_crystallographyhttp://en.wikipedia.org/w/index.php?title=X-ray_crystallographyhttp://en.wikipedia.org/w/index.php?title=Protein%E2%80%93protein_interaction_predictionhttp://en.wikipedia.org/w/index.php?title=Structural_domainhttp://en.wikipedia.org/w/index.php?title=Structural_motifhttp://en.wikipedia.org/w/index.php?title=Leghemoglobinhttp://en.wikipedia.org/w/index.php?title=Homology_%28biology%29


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The range of open source software packages includes titles such as Bioconductor, BioPerl, Biopython, BioJava,

BioRuby, Bioclipse, EMBOSS, Taverna workbench, and UGENE. In order to maintain this tradition and create

further opportunities, the non-profit Open Bioinformatics Foundation[8]

have supported the annual Bioinformatics

Open Source Conference (BOSC) since 2000.[8]

Web services in bioinformaticsSOAP and REST-based interfaces have been developed for a wide variety of bioinformatics applications allowing an

application running on one computer in one part of the world to use algorithms, data and computing resources on

servers in other parts of the world. The main advantages derive from the fact that end users do not have to deal with

software and database maintenance overheads.

Basic bioinformatics services are classified by the EBI into three categories: SSS (Sequence Search Services), MSA

(Multiple Sequence Alignment) and BSA (Biological Sequence Analysis). The availability of these service-oriented

bioinformatics resources demonstrate the applicability of web based bioinformatics solutions, and range from a

collection of standalone tools with a common data format under a single, standalone or web-based interface, to

integrative, distributed and extensible bioinformatics workflow management systems.

References

[1] Attwood T.K., Gisel A., Eriksson N-E. and Bongcam-Rudloff E. (2011). "Concepts, Historical Milestones and the Central Place of

Bioinformatics in Modern Biology: A European Perspective" (http://www.intechopen. com/articles/show/title/

concepts-historical-milestones-and-the-central-place-of-bioinformatics-in-modern-biology-a-european-). Bioinformatics - Trends and

Methodologies. InTech. . Retrieved 8 Jan 2012.

[2] Hogeweg, P. (1978). "Simulating the growth of cellular forms". Simulation31 (3): 9096. doi:10.1177/003754977803100305.

[3] Hogeweg, P. (2011). Searls, David B.. ed. "The Roots of Bioinformatics in Theoretical Biology".PLoS Computational Biology7 (3):

e1002021. Bibcode 2011PLSCB...7E0020H. doi:10.1371/journal.pcbi.1002021. PMC 3068925. PMID 21483479.

[4] Hogeweg, P. (2011). Searls, David B.. ed. "The Roots of Bioinformatics in Theoretical Biology".PLoS Computational Biology7 (3):

e1002021. Bibcode 2011PLSCB...7E0020H. doi:10.1371/journal.pcbi.1002021. PMC 3068925. PMID 21483479.

[5] Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (February 1977). "Nucleotidesequence of bacteriophage phi X174 DNA".Nature265 (5596): 68795. doi:10.1038/265687a0. PMID 870828.

[6] Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (January 2008). "GenBank".Nucleic Acids Res.36 (Database issue):

D2530. doi:10.1093/nar/gkm929. PMC 2238942. PMID 18073190.

[7] Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM (July

1995). "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd". Science269 (5223): 496512.

doi:10.1126/science.7542800. PMID 7542800.

[8] "Open Bioinformatics Foundation: About us" (http://www.open-bio. org/wiki/Main_Page). Official website. Open Bioinformatics

Foundation. . Retrieved 10 May 2011.

Further reading

Achuthsankar S Nair Computational Biology & Bioinformatics A gentle Overview (http:/

/

print.achuth.googlepages.com/BINFTutorialV5.0CSI07.pdf), Communications of Computer Society of India, January 2007

Aluru, Srinivas, ed.Handbook of Computational Molecular Biology. Chapman & Hall/Crc, 2006. ISBN

1584884061 (Chapman & Hall/Crc Computer and Information Science Series)

Baldi, P and Brunak, S,Bioinformatics: The Machine Learning Approach, 2nd edition. MIT Press, 2001. ISBN

0-262-02506-X

Barnes, M.R. and Gray, I.C., eds.,Bioinformatics for Geneticists, first edition. Wiley, 2003. ISBN 0-470-84394-2

Baxevanis, A.D. and Ouellette, B.F.F., eds.,Bioinformatics: A Practical Guide to the Analysis of Genes and

Proteins, third edition. Wiley, 2005. ISBN 0-471-47878-4

Baxevanis, A.D., Petsko, G.A., Stein, L.D., and Stormo, G.D., eds., Current Protocols in Bioinformatics. Wiley,

2007. ISBN 0-471-25093-7 Claverie, J.M. and C. Notredame,Bioinformatics for Dummies. Wiley, 2003. ISBN 0-7645-1696-5
http://en.wikipedia.org/w/index.php?title=Current_Protocolshttp://print.achuth.googlepages.com/BINFTutorialV5.0CSI07.pdfhttp://print.achuth.googlepages.com/BINFTutorialV5.0CSI07.pdfhttp://en.wikipedia.org/w/index.php?title=Open_Bioinformatics_Foundationhttp://en.wikipedia.org/w/index.php?title=Open_Bioinformatics_Foundationhttp://www.open-bio.org/wiki/Main_Pagehttp://www.intechopen.com/articles/show/title/concepts-historical-milestones-and-the-central-place-of-bioinformatics-in-modern-biology-a-european-http://www.intechopen.com/articles/show/title/concepts-historical-milestones-and-the-central-place-of-bioinformatics-in-modern-biology-a-european-http://en.wikipedia.org/w/index.php?title=Bioinformatics_workflow_management_systemshttp://en.wikipedia.org/w/index.php?title=Service-orientationhttp://en.wikipedia.org/w/index.php?title=Bioinformatics%23Sequence_analysishttp://en.wikipedia.org/w/index.php?title=Multiple_sequence_alignmenthttp://en.wikipedia.org/w/index.php?title=Sequence_alignment_softwarehttp://en.wikipedia.org/w/index.php?title=European_Bioinformatics_Institutehttp://en.wikipedia.org/w/index.php?title=RESThttp://en.wikipedia.org/w/index.php?title=SOAPhttp://en.wikipedia.org/w/index.php?title=Open_Bioinformatics_Foundationhttp://en.wikipedia.org/w/index.php?title=UGENEhttp://en.wikipedia.org/w/index.php?title=Taverna_workbenchhttp://en.wikipedia.org/w/index.php?title=EMBOSShttp://en.wikipedia.org/w/index.php?title=Bioclipsehttp://en.wikipedia.org/w/index.php?title=BioRubyhttp://en.wikipedia.org/w/index.php?title=BioJavahttp://en.wikipedia.org/w/index.php?title=Biopythonhttp://en.wikipedia.org/w/index.php?title=BioPerlhttp://en.wikipedia.org/w/index.php?title=Bioconductorhttp://en.wikipedia.org/w/index.php?title=List_of_open_source_bioinformatics_software


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Bioinformatics 8

Cristianini, N. and Hahn, M.Introduction to Computational Genomics (http://www.computational-genomics.

net/), Cambridge University Press, 2006. (ISBN 9780521671910 | ISBN 0521671914)

Durbin, R., S. Eddy, A. Krogh and G. Mitchison,Biological sequence analysis. Cambridge University Press,

1998. ISBN 0-521-62971-3

Gilbert, D.Bioinformatics software resources (http://bib.oxfordjournals.org/cgi/content/abstract/5/3/300).

Briefings in Bioinformatics, Briefings in Bioinformatics, 2004 5(3):300304.

Keedwell, E.,Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques to Bioinformatics

Problems. Wiley, 2005. ISBN 0-470-02175-6

Kohane, et al.Microarrays for an Integrative Genomics. The MIT Press, 2002. ISBN 0-262-11271-X

Lund, O. et al.Immunological Bioinformatics. The MIT Press, 2005. ISBN 0-262-12280-4

Michael S. Waterman,Introduction to Computational Biology: Sequences, Maps and Genomes. CRC Press, 1995.

ISBN 0-412-99391-0

Mount, David W.Bioinformatics: Sequence and Genome Analysis Spring Harbor Press, May 2002. ISBN

0-87969-608-7

Pachter, Lior and Sturmfels, Bernd. "Algebraic Statistics for Computational Biology" Cambridge University

Press, 2005. ISBN 0-521-85700-7 Pevzner, Pavel A. Computational Molecular Biology: An Algorithmic Approach The MIT Press, 2000. ISBN

0-262-16197-4

Soinov, L. Bioinformatics and Pattern Recognition Come Together (http://jprr. org/index.php/jprr/article/

view/8/5) Journal of Pattern Recognition Research ( JPRR (http://www.jprr.org)), Vol 1 (1) 2006 p. 3741

Tisdall, James. "Beginning Perl for Bioinformatics" O'Reilly, 2001. ISBN 0-596-00080-4

Dedicated issue ofPhilosophical Transactions B on Bioinformatics freely available (http://publishing.

royalsociety.org/bioinformatics)

Catalyzing Inquiry at the Interface of Computing and Biology (2005) CSTB report (http://www.nap.edu/

catalog/11480.html)

Calculating the Secrets of Life: Contributions of the Mathematical Sciences and computing to Molecular Biology(1995) (http://www.nap.edu/catalog/2121.html)

Foundations of Computational and Systems Biology MIT Course (http://ocw.mit.edu/OcwWeb/Biology/

7-91JSpring2004/LectureNotes/index.htm)

Computational Biology: Genomes, Networks, Evolution Free MIT Course (http://compbio.mit.edu/6.047/)

Algorithms for Computational Biology Free MIT Course (http://ocw.mit.edu/OcwWeb/

Electrical-Engineering-and-Computer-Science/6-096Spring-2005/CourseHome/index.htm)

Zhang, Z., Cheung, K.H. and Townsend, J.P. Bringing Web 2.0 to bioinformatics, Briefing in Bioinformatics. In

press (http://www.ncbi.nlm.nih.gov/pubmed/18842678)

External links Bioinformatics Organization (http://bioinformatics.org/)

EMBnet (http://www.embnet.org/)

Open Bioinformatics Foundation (http://www.open-bio.org/)

The Center for Modeling Immunity to Enteric Pathogens (MIEP) (http://www.modelingimmunity.org)
http://www.modelingimmunity.org/http://www.open-bio.org/http://www.embnet.org/http://bioinformatics.org/http://www.ncbi.nlm.nih.gov/pubmed/18842678http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-Science/6-096Spring-2005/CourseHome/index.htmhttp://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-Science/6-096Spring-2005/CourseHome/index.htmhttp://compbio.mit.edu/6.047/http://ocw.mit.edu/OcwWeb/Biology/7-91JSpring2004/LectureNotes/index.htmhttp://ocw.mit.edu/OcwWeb/Biology/7-91JSpring2004/LectureNotes/index.htmhttp://www.nap.edu/catalog/2121.htmlhttp://www.nap.edu/catalog/11480.htmlhttp://www.nap.edu/catalog/11480.htmlhttp://publishing.royalsociety.org/bioinformaticshttp://publishing.royalsociety.org/bioinformaticshttp://www.jprr.org/http://jprr.org/index.php/jprr/article/view/8/5http://jprr.org/index.php/jprr/article/view/8/5http://en.wikipedia.org/w/index.php?title=Bernd_Sturmfelshttp://bib.oxfordjournals.org/cgi/content/abstract/5/3/300http://www.computational-genomics.net/http://www.computational-genomics.net/


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