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What makes  Bio-informatics interesting?

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What makes  Bio-informatics interesting?

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Bioinformatics is interesting because it has the potential to create a genomics and biology revolution.

Here is a schematic explainer on bioinformatics:

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An introduction to basic tools for bioinformatics that you can use locally on your own computer. By David Francis, Ohio State University. Delivered live at the Tomato Disease Workshop 2010. For more information, please visit http://www.extension.org/pages/32521/bioinformatics-101-video.

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Bioinformatics is the science of collecting and analysing complex biological data such as genetic codes.

Here is a video about the introduction to Bioinformatics:

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What is Bioinformatics and Computational Biology?

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Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

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The link below is a presentation by Dr.Todd.A.Gibson from the university of Chicago,outlining the role of maths in Bioinformatics.

http://rce.csuchico.edu/sites/default/files/online/the_role_of_mathematics_stats_and_computer_science_in_bioinformatics_reduced.pdf

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The following article illustrates the contribution of mathematics in making bioinformatics education comprehensible.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771232/

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Molecular and personalized medicine gives a lot of challenges which can be solved only by using bioinformatics.

How will it help in molecular medicine?

The completion of the human genome means that we can search for the genes directly associated with different diseases and begin to understand the molecular basis of these diseases more clearly. This new knowledge of the molecular mechanisms of disease will enable better treatments, cures and even preventative tests to be developed.

How will it help in personalized medicine?

Potentially life saving drugs never make it to the marketplace. Today, doctors have to use trial and error to find the best drug to treat a particular patient as those with the same clinical symptoms can show a wide range of responses to the same treatment. In the future,with personalized medicine coming into play, doctors will be able to analyse a patient's genetic profile and prescribe the best available drug therapy and dosage from the beginning which can prove helpful in many life-or-death situations also.

Does it help in preventive medicine?

Keeping in mind the adage "Prevention is better than cure" with the help of bioinformatics one can follow this to the best possible extent.

With the specific details of the genetic mechanisms o diseases being unravelled, the development of diagnostic tests to measure a persons susceptibility to different diseases may become a distinct reality. Preventative actions such as change of lifestyle or having treatment at the earliest possible stages when they are more likely to be successful, could result in huge advances in our struggle to conquer disease.

With the specific details of the genetic mechanisms of diseases being unravelled, the development of diagnostic tests to measure a persons susceptibility to different diseases may become a distinct reality. Preventative actions such as change of lifestyle or having treatment at the earliest possible stages when they are more likely to be successful, could result in huge advances in our struggle to conquer disease.

In what way it help in drug development?

Using computational tools to identify and validate new drug targets, more specific medicines that act on the cause, not merely the symptoms, of the disease can be developed. These highly specific drugs promise to have fewer side effects than many of today's medicines.

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Powerpoint Presentations

1) http://www.powershow.com/view1/24a535-ZDc1Z/Computational_Statistics_with_Application_to_Bioinformatics_powerpoint_ppt_presentation 2) http://www.powershow.com/view1/233fd6-ZDc1Z/Bayesian_Statistics_for_Bioinformatics_powerpoint_ppt_presentation Books and Journals 1) http://chagall.med.cornell.edu/BioinfoCourse/PDFs/Lecture3/bioinformatics_tutorial.pdf 2) https://cran.r-project.org/doc/contrib/Seefeld_StatsRBio.pdf 3) http://iase-web.org/documents/papers/icots7/5D2_ARHI.pdf Videos 1) www.youtube.com/watch?v=p_REiNh2DWw 2) www.youtube.com/watch?v=YL8Lys3t-hQ

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Stochastic processes

In probability theory, a stochastic process, or often random process, is a collection of random variables, representing the evolution of some system of random values over time.

Phylogenetic tree estimation

A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities—their phylogeny—based upon similarities and differences in their physical or genetic characteristics.

Bayesian Statistics

Bayesian statistics is a system for describing epistemological uncertainty using the mathematical language of probability. In the 'Bayesian paradigm,' degrees of belief in states of nature are specified; these are non-negative, and the total belief in all states of nature is fixed to be one.

PAM Substitution Matrix

A PAM matrix is a matrix where each column and row represents one of the twenty standard amino acids. In bioinformatics, PAM matrices are regularly used as substitution matrices to score sequence alignment for proteins.

Markov Model

In probability theory, a Markov model is  used to model randomly changing systems where it is assumed that future states depend only on the present state and not on the sequence of events that preceded it.Generally, this assumption enables reasoning and computation with the model that would otherwise be intractable.

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We conclude that BioInformatics serves humanity best in the area of medicine as it can be studied right from the molecular level(molecular medicine) and hence, personalized diagnosis and treatment can be given

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Preventative medicine

With the specific details of the genetic mechanisms of diseases being unravelled, the development of diagnostic tests to measure a persons susceptibility to different diseases may become a distinct reality. Preventative actions such as change of lifestyle or having treatment at the earliest possible stages when they are more likely to be successful, could result in huge advances in our struggle to conquer disease.

Alternative energy sources

Scientists are studying the genome of the microbe Chlorobium tepidum which has an unusual capacity for generating energy from light.

Antibiotic resistance

Scientists have been examining the genome of Enterococcus faecalis -a leading cause of bacterial infection among hospital patients. They have discovered a virulence region made up of a number of antibiotic-resistant genes that may contribute to the bacterium's transformation from a harmless gut bacteria to a menacing invader. The discovery of the region, known as a pathogenicity island, could provide useful markers for detecting pathogenic strains and help to establish controls to prevent the spread of infection in wards.

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Gene therapy

In the not too distant future, the potential for using genes themselves to treat disease may become a reality. Gene therapy is the approach used to treat, cure or even prevent disease by changing the expression of a persons genes. Currently, this field is in its infantile stage with clinical trials for many different types of cancer and other diseases ongoing.

Waste cleanup

Deinococcus radiodurans is known as the world's toughest bacteria and it is the most radiation resistant organism known. Scientists are interested in this organism because of its potential usefulness in cleaning up waste sites that contain radiation and toxic chemicals.

Personalised medicine

Clinical medicine will become more personalised with the development of the field of pharmacogenomics. This is the study of how an individual's genetic inheritance affects the body's response to drugs. At present, some drugs fail to make it to the market because a small percentage of the clinical patient population show adverse affects to a drug due to sequence variants in their DNA.

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Evolutionary studies-The sequencing of genomes from all three domains of life, eukaryota, bacteria and archaea means that evolutionary studies can be performed in a quest to determine the tree of life and the last universal common ancestor.

Comparative Studies

Analysing and comparing the genetic material of different species is an important method for studying the functions of genes, the mechanisms of inherited diseases and species evolution. Bioinformatics tools can be used to make comparisons between the numbers, locations and biochemical functions of genes in different organisms.

Molecular medicine

The human genome will have profound effects on the fields of biomedical research and clinical medicine. Every disease has a genetic component. This may be inherited (as is the case with an estimated 3000-4000 hereditary disease including Cystic Fibrosis and Huntingtons disease) or a result of the body's response to an environmental stress which causes alterations in the genome (eg. cancers, heart disease, diabetes.).

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Genetic code: The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells

Mathematical Knot: A mathematician's knot differs from the regular in that the ends are joined together so that it cannot be undone.In mathematical language, a knot is an embedding of a circle in 3-dimensional space.

Composite knot:A knot that can be expressed as the composition of two nontrivial knots is called a composite knot.

Linking number: This is a topological property that determines the degree of supercoiling. It defi nes the number of times a strand of DNA winds in the right - handed direction around the helix axis when the axis is constrained to lie in a plane

Supercoiling: Supercoiling is an abstract mathematical property representing the sum of twist and writhe. The twist is the number of helical turns in the DNA and the writhe is the number of times the double helix crosses over on itself (these are the supercoils)

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Sequencers: an apparatus for determining the sequence of amino acids or other monomers in a biological polymer.

Gene expression: Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA.

Phylogenetic tree:A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities—their phylogeny—based upon similarities and differences in their physical or genetic characteristics.

Context-free grammar:In formal language theory, a context-free grammar (CFG) is a formal grammar in which every production rule is of the form V → w

where V is a single nonterminal symbol, and w is a string of terminals and/or nonterminals (w can be empty). A formal grammar is considered "context free" when its production rules can be applied regardless of the context of a nonterminal.

Terminal and non-terminal symbols: In computer science, terminal and non-terminal symbols are the lexical elements used in specifying the production rules constituting a formal grammar. Terminal symbols are the elementary symbols of the language defined by a formal grammar.

Percent identity: Percent identity refers to a quantitative measurement of the similarity between two sequences (DNA, amino acid or otherwise)

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The journal article was taken from the book "Mathematics of Bioinformatics" by Matthew He and Sergey Petoukhov and published by Wiley Publications or the Wiley series of Bioinformatics

The image explainer of Biological networks was taken from https://imdevsoftware.files.wordpress.com/2013/04/bionetwork1.png

The image illustrating concept of Mendel's law was taken from

http://media.web.britannica.com/eb-media/75/775-004-F3BAFB88.gif

The links mentioned below feature videos explaining the application of discrete mathematics in bioinformatics.

www.youtube.com/watch?v=hSld-Cf-3oQ

https://www.youtube.com/watch?v=immUv5c8ieU

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Questionnaire for Survey on this Research Topic

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Questionnaire for Survey on this Research Topic

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The intended target audience is the general public and for university students pursuing Bio Technology and related fields.

Do you think that the field of Bio Informatics is relevant today?

What are the roles of Mathematics,Statistics and Computing in Bioinformatics?

Do you think Bio Informatics will directly affect you in your day-to-day activities?

Will advances in Bio Informatics result in a big difference/impact in your current lifestyle?

Do you think that Bio Informatics will be an effective tool for Disease Diagnosis?

Will Bio Informatics be used to enhance human abilities(like physical and mental strength) in your opinion?

Do you think that the Human Genome Project is a very useful undertaking?

Will you approve getting your DNA sequenced(from privacy and medical points of view)?

Do you believe that Bio Informatics is the way forward for human progress?

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Here is the logo and schematic of what the project is about:

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Here are other images and schematics depicting the Human Genome Project:

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A video explainer of the Human Genome Project, a direct result of applying BioInformatics:

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PROJECT CAMELOT :  SECRETS BEHIND THE HUMAN GENOME PROJECT

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A PRELIMINARY INVESTIGATION INTO THE CLAIMS OF CYNTHIA MARIE BREWER Cynthia Marie Brewer claims her DNA was taken and used as the original fully sequenced DNA for the Human Genome Project against her will. From there on her story, if she is to be believed, has tentacles in nearly every aspect of human endeavor on the planet.

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The journal articles were taken from Brandeis University and the other journal was published in the Indian Journal of Computer Science and Engineering by Khalid Raza.

The image schematic showing the flow of data mining in bioinformatics were taken from BioInformatics Institute of India: http://image.slidesharecdn.com/bioinformatics-090429002240-phpapp02/95/bioinformatics-36-638.jpg?cb=1427754692

The video explaining genome annotation was taken from

http://www.youtube.com/watch?v=on4TMnuYTaU

The video explaining sequence analysis was taken from http://www.youtube.com/watch?v=Z72nvSUtEng

The video explainer of the Human Genome Project was taken from http://www.youtube.com/watch?v=ifMkMsq3pGs

The poster of the Human Genome Project was taken at

http://www.abpischools.org.uk/page/modules/hgenome/index.cfm

The schematic logo of the Human Genome Project was taken from http://www.knowledgene.com/Image61.gif

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Biological systems ranging from food webs in ecology to biochemical interactions in molecular biology can be modeled and analyzed as networks. Biological networks are abstract representations of biological systems which capture many of their essential characteristics.

Here is an example:-

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Mathematics has a fundamental role in describing the complexities of biological structures, patterns, and processes. Mathematical analysis of structures of molecular systems has essential meaning for bioinformatics, biomathematics, and biotechnology.

For eg, the concept of Mendel's law of inheritance:-

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Arvind, what is the importance of mathematics in bioinformatics?

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What are biological networks?

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We use a protocol called BLAST(Basic Local Alignment Search Tool).It is an algorithm that finds regions of local similarity between biological sequences and calculates the statistical significance of matches.

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Srikanth, How do you compare primary biological sequence information?

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In genetics, shotgun sequencing, also known as shotgun cloning, is a method used for sequencing long DNA strands. It is named by analogy with the rapidly expanding, quasi-random firing pattern of a shotgun

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Srikanth, so what is this shotgun sequencing?

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What methods do you use for your estimations?

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We use probability theory, stochastic and random processes,shotgun sequencing and BLAST (Basic Local Alignment Search Tool),which is a widely used method for assessing which nucleic acid or protein sequences in a large database have

significant similarity to a given query sequence

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Hey Srikanth, how is statistics related to Bioinformatics?

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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.

Here is a video explainer:

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Dr. Rob Edwards describes some of the problems, challenges, and approches in genome annotation, with a particular emphasis on how the Fellowship for the Interpretation of Genomes (FIG) developed subsystems using the SEED database available at http://www.theseed.org/

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What is genome annotation?

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Mathematics and biological data have a synergistic relationship. Biological information creates interesting problems, mathematical theory and methods provide models for understanding them, and biology validates the mathematical models.

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Sequence analysis consists of finding which part of the biological sequences are alike and which part differs during medical analysis and genome mapping processes.

Here is a video explainer:

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National Human Genome Research Institute

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Biological Sequence Analysis I - Andy Baxevanis (2014)

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March 5, 2014 - Current Topics in Genome Analysis 2014 A lecture series covering contemporary areas in genomics and bioinformatics. More: http://www.genome.gov/COURSE2014

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Why did you choose the topic of Mathematics in BioInformatics?

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What is sequence analysis?

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Bioinformatics involves the analysis of biological data. Many chance mechanisms are involved in the creation of these data, most importantly the many random processes inherent in biological evolution and the randomness inherent in any sampling process

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My article is about the aspects of mathematics in biology

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Applications of data mining to bioinformatics include gene finding, protein function domain detection, function motif detection, protein function inference, disease diagnosis, disease prognosis, disease treatment optimization, protein and gene interaction network reconstruction, data cleansing, and protein sub-cellular location prediction.

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Hey Arvind, what is your article about?

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Hey Bharat, what is the application of data mining in bioinformatics?

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My articles:-

www.ohio.edu/people/just/TALKS/Wyatt.ppt

http://www.ibis.org.ir/files/site1/books/mathematics_of_bioinformatics.pdf

Introduction: Bioinformatics is conceptualising biology in terms of molecules (in the sense of physical chemistry) and applying "informatics techniques" (derived from disciplines such as applied maths, computer science and statistics) to understand and organise the information associated with these molecules, on a large scale. In short, bioinformatics is a management information system for molecular biology and has many practical applicationsMath can be used to understand life from the molecular to the biosphere level - the origin and evolution of organisms, - the nature of the genomic blueprints - the universal genetic code - ecological relationships.Math helps us look for trends, patterns and relationships that may or may not be obvious to scientists.Math allows us to describe the dimensions of genes, sizes of organelles, cells organs and whole organisms cells, organs and whole organisms

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Hey Bharat, what is your article about?

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This article highlights some of the basic concepts of bioinformatics and data mining.

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My articles:

http://www.statru.org/wp-content/uploads/2012/04/01_Statistical-Methods-in-Bioinformatics.pdf

Introduction:

The significance of any genetic or biological implication based on dna sequencing depends on its accuracy. The statistical evaluation of accuracy requires a probabilistic model of measurement error.Here, we describe two statistical models of sequence assembly from shotgun sequencing respectively for the cases of haploid and diploid genome. The first model allows us to convert quality scores into probabilities. it combines quality scores of base calling and the power of alignment to improve sequencing accuracy. Specifically, we represent probabilistic errors by logistical models that takes quality scores and other genomic features as covariates. since the true sequence is unknown , an Em algorithm is used to deal with missing data. The second model describes the case in which Dna reads are from one diploid genome. The statistical model consists of sequencing errors, compositional information and haplotype memberships of dna fragment. Consequently, optimal haplotype sequences can be inferred by maximising the probability among all configurations conditional on the given assembly. In the meantime, this probability, together with the coverage information, provides an assessment of the confidence for the reconstruction.

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My articles:-

Introduction to Bioinformatics to Computer Scientists

http://www.cs.indiana.edu/~predrag/files/cohen_2004.pdf

Data Mining for Computer Scientists

http://arxiv.org/ftp/arxiv/papers/1205/1205.1125.pdf

Introduction:-

What is bioinformatics

Bioinformatics is the application of computer technology to the management of biological information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied to gene-based drug discovery and development. The need for Bioinformatics capabilities has been precipitated by the explosion of publicly available genomic information resulting from the Human Genome Project.

The goal of this project – determination of the sequence of the entire human genome (approximately three billion base pairs) – will be reached by the year 2020. The science of Bioinformatics, which is the melding of molecular biology with computer science, is essential to the use of genomic information in understanding human diseases and in the identification of new molecular targets for drug discovery.

In recognition of this, many universities, government institutions and pharmaceutical firms have formed bioinformatics groups, consisting of computational biologists and bioinformatics computer scientists. Such groups will be key to unraveling the mass of information generated by large scale sequencing efforts underway in laboratories around the world.