Bioinformatics

Open Access Bibliographic Resources and Applications

Submitted by: Priyanka Kasturia

Student ID: 202105846
Couse: MSc Biophysics (Semester 1)
Bioinformatics: An Introduction
Bioinformatics is an emerging discipline whose scope has broadened and importance increased over time. A
series of definitions is given to reflect these changes and the continuing excitement in the subject. The term
Bioinformatics was first used in 1968 and the content of a bioinformatics course was first defined in 1978. These
predate the techniques leading to the flood of biological data in which we now swim. In the mid-1990s, there
was great excitement about the subject, which generated a spectrum of strong opinions both for and against
it. On occasions, there was more money than sense spent on the area.

Bioinformatics is the discipline at the interface between biology, information science, and mathematics. This
definition broadens the subject from just the analysis of biomolecular sequences and structures to include other
types of biological data (biomolecular profiles, interactions, population and cell biology). The multi-disciplinary
nature of the subject and the role of a bioinformatician as an interpreter are implicitly acknowledged.

Open Access bibliographic resources

PubMed

PubMed is a free resource supporting the search and retrieval of biomedical and life sciences literature with
the aim of improving health–both globally and personally. The PubMed database contains more than 33 million
citations and abstracts of biomedical literature. It does not include full text journal articles; however, links to the
full text are often present when available from other sources, such as the publisher’s website or PubMed Central
(PMC). Available to the public online since 1996, PubMed was developed and is maintained by the National
Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM), located at
the National Institutes of Health (NIH). Citations in PubMed primarily stem from the biomedicine and health
fields, and related disciplines such as life sciences, behavioral sciences, chemical sciences, and bioengineering.
PubMed facilitates searching across several NLM literature resources:

MEDLINE
MEDLINE is the National Library of Medicine’s (NLM) premier bibliographic database that contains more
than 28 million references to journal articles in life sciences with a concentration on biomedicine. A distinctive
feature of MEDLINE is that the records are indexed with NLM Medical Subject Headings (MeSH).

MEDLINE is the primary component of PubMed, a literature database developed and maintained by the NLM
National Center for Biotechnology Information (NCBI). MEDLINE is the online counterpart to the MEDical

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Literature Analysis and Retrieval System (MEDLARS) that originated in 1964 (see MEDLINE history). The
majority of journals are selected for MEDLINE based on the recommendation of the Literature Selection Tech-
nical Review Committee (LSTRC), an NIH-chartered advisory committee of external experts.

Time coverage: MEDLINE includes literature published from 1966 to present, and selected coverage of lit-
erature prior to that period. For details about pre-1966 citations see OLDMEDLINE Data.

Source: Currently, citations from more than 5,200 worldwide journals in about 40 languages.

Updates: Citations are added to PubMed 7 days a week.

The majority of the publications in MEDLINE are scholarly journals; however, a small number of newspa-
pers, magazines, and newsletters considered useful to particular segments of the NLM broad user community
are also included.

A growing number of MEDLINE citations in PubMed contain a link to the free full-text of the article archived
in PubMed Central. Some MEDLINE citations also have publisher-provided links to the full-text of the article
at the journal website; exact details depend on the publisher’s access requirements.

NLM also supports access to MEDLINE data via download with documentation available at MEDLINE/PubMed
Data Documentation – additional access to various MEDLINE services is often available from medical libraries,
many public libraries, and commercial sources.

MedlinePlus is a consumer-oriented health information resource from the NLM. It contains carefully selected
links to online resources with authoritative health information on a broad range of health topics. MedlinePlus
has more information on the difference between MedlinePlus and MEDLINE. Health consumers are encouraged
to discuss search results with their health care provider.

PubMed Central (PMC)

PubMed Central (PMC) is a free full-text archive of biomedical and life sciences journal literature at the U.S.
National Institutes of Health’s National Library of Medicine (NIH/NLM). In keeping with NLM’s legislative
mandate to collect and preserve the biomedical literature, PMC serves as a digital counterpart to NLM’s ex-
tensive print journal collection.

PMC was developed and is managed by NLM’s National Center for Biotechnology Information (NCBI).

About the Content: Since its inception in 2000, PMC has grown from comprising only two journals, PNAS:
Proceedings of the National Academy of Sciences and Molecular Biology of the Cell, to an archive of articles
from thousands of journals.

Today, PMC contains more than 7 million full-text records, spanning several centuries of biomedical and
life science research (late 1700s to present).

The resulting collaborations with publishers, societies, research funders, and international organizations form
the foundation of PMC. PMC is not a publisher and does not publish journal articles itself.

Bookshelf
The final component of PubMed is citations for books and some individual chapters available on Bookshelf.
Bookshelf is a full text archive of books, reports, databases, and other documents related to biomedical, health,
and life sciences.

The Bookshelf covers a wide range of topics including molecular biology, biochemistry, cell biology, genet-
ics, microbiology, disease states from a molecular and cellular point of view, research methods, and virology.
Some of the books are online versions of previously published books, while others, such as Coffee Break, are
written and edited by NCBI staff. The Bookshelf is a complement to the Entrez PubMed repository of peer-
reviewed publication abstracts in that Bookshelf contents provide established perspectives on evolving areas of
study and a context in which many disparate individual pieces of reported research can be organized.

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BioMed Central

BioMed Central (BMC) has an evolving portfolio of some 300 peer-reviewed journals, sharing discoveries
from research communities in science, technology, engineering and medicine. In 1999 we made high quality
research open to everyone who needed to access it – and in making the open access model sustainable, we
changed the world of academic publishing.

They are committed to continual innovation in research publishing to better support the needs of our com-
munities, ensuring the integrity of the research we publish and championing the benefits of open research for all.

Their leading research journals include selective titles such as BMC Biology, BMC Medicine, Genome Biol-
ogy and Genome Medicine, academic journals such as Journal of Hematology & Oncology, Malaria Journal and
Microbiome, and the BMC series, 65 inclusive journals focused on the needs of individual research communities.
They have also partnered with leading institutions and societies to publish journals on their behalf.

BMC is part of Springer Nature, giving greater opportunities to help authors everywhere make more con-
nections with research communities across the world.

Public Library of Sciences

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 PLOS (for Public Library of Science; PLoS until 2012) is a nonprofit open-access science, technology, and
medicine publisher with a library of open-access journals and other scientific literature under an open-content
license. It launched its first journal, PLOS Biology, in October 2003 and (as of October 2015) publishes seven
journals. The organization is based in San Francisco, California, and has a European editorial office in Cam-
bridge, Great Britain. The publications are primarily funded by payments from the authors.

As a publishing company, the Public Library of Science officially launched its operation on 13 October 2003,
with the publication of a print and online scientific journal entitled PLOS Biology, and has since launched 11
more journals. One, PLOS Clinical Trials, has since been merged into PLOS ONE. Following the merger, the
company started the PLOS Hub for Clinical Trials to collect journal articles published in any PLOS journal
and relating to clinical trials; the hub was discontinued in July 2013.

The PLOS journals are what is described as ”open-access content”; all content is published under the Cre-
ative Commons ”attribution” license. The project states (quoting the Budapest Open Access Initiative) that:
”The only constraint on reproduction and distribution, and the only role for copyright in this domain, should
be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.”

Applications of Bioinformatics
From Genetics and Toxicology to Mycology and Radiobiology, there are scores of branches of Biology to
specialize in. And out of the many, Bioinformatics is one of the intriguing fields which enables you to identify,
evaluate, store, and retrieve biological information. Being an interdisciplinary field of study, it incorporates
various facets of Computer Science, Statistics, and Biology to develop software applications for understanding
the biological data like DNA sequencing, protein analysis, evolutionary genetics, etc. Not only restricted to
Medicine, but the scope of Bioinformatics is spread across Microbial Genome as well as in the field of Agriculture.

Plant Breeding and Crop Improvement

Plant genomics helps in understanding the genetic and molecular basis of all biological process which helps in
developing new cultivars with improved quality and reduced economic and environmental cost. Now-a-days the
Genome program is an important tool for the plant improvement. This genome programme helps in identifying
the key genes and their function. This genome project generates data, which includes sequence information,
markers etc. These data are then distributed to the multinational research community. The bioinformatics
tools helps in the submission of all data through ENTREZ Global Query Cross-Database Search System to
the public domain. This helps in retrieving sequence from the NCBI. Genome sequencing of several important
plants species has enabled researchers to identify ‘chromosome’ and ‘difference’ factor in sequences. This in turn
has been used to identify value traits for crop improvement. For instance, the barley stem rust resistance gene
has been identified from rice-barley comparisons and the sugarcane rust resistance gene based on maize-sorghum
comparisons.

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Modelling of Plants
Bioinformatics plays an important role in modelling of crop plants. Such computer aided studies have already
been made in field pea and several other field crops. First the plant model is conceptualized using various plant
traits and then efforts are made to develop such model by using appropriate breeding procedures. First donor
sources for these traits are identified from the available germplasm. Then efforts are made to combine these
traits in one genotype particularly in a popular variety. Such computer-based studies help in developing plant
ideotype suitable for machine picking and used in multiple cropping system.

Drug Delivery

Infectious diseases are currently the world’s major killer of children and young adults. According to WHO,
infectious diseases account for over 13 million deaths yearly. Developing countries record the most number of
deaths from infectious diseases and this was contributed to the non-availability of drugs and high cost associated
with the drugs if available. One of the main problems encountered is the development of cheap and efficient
drugs for a disease can be solved by rational drug design using Bioinformatics.

Bioinformatics is playing an important role in drug discovery, drug assessment and drug development through
its utility for prediction, analysis and interpretation in clinical and preclinical findings. Tradition approach
of drug discovery was time consuming and cumbersome practice while the bioinformatics-based approach i.e.
computer-aided drug design (CADD) has made the task rapid, cost effective and easier to handle the increasing
and voluminous demand of drugs with low risk. Bioinformatics provides a range of drugrelated databases and
algorithms which are used for drug designing and drug development.

Medicine

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Personalized Medicine
Personalized medicine is developing practice of medicine that uses particular’s genetic profile to advice decisions
made in favour to the prevention, diagnosis, and treatment of disease. Information about patient’s genetic pro-
file can help doctors to provide proper medication using the proper dose or regimen. It applied for treatment as
personalized cancer medicine, Diabetes- related disease and HIV. Personalized medicine can be defined widely
as a model of healthcare that is predictive, personalized, preventive and participatory. Translational bioinfor-
matics is a field that can help address these challenges and is defined by the American Medical Informatics
Association as “the development of storage, analytic and interpretive methods to optimize the transformation of
increasing voluminous biomedical data into proactive, predictive, preventative and participatory health. Prac-
tical application outside of long established considerations like a patient’s family history, social circumstances,
environment and behaviours are very limited so far and practically no progress has been made in the last
decade. Personalized medicine research tries to discover individual solutions based on the susceptibility profile
of each individual. It is expected that these areas will enable new approaches to diagnosis, drug development,
and individualized therapy.

Preventive Medicine
Preventive Medicine is practiced by all physicians to possess their patients healthy. It is also a unique medical
subject affiliated by the American Board of Medical Specialties (ABMS). Preventive Medicine attentions on
the health of individuals, communities, and defined populations. It is also helpful for the treatment for obesity,
blindness. The Epidemiology Division used research methods to understand the patterns and causes of health
and disease in the population and to transform this knowledge into programs designed to stop disease. The
division has a lengthy history of association in NIH-sponsored multi-site, longitudinal cohort studies, and its
faculty oversees many investigator-initiated, NIH sponsored research projects and trials. Public trust in vaccines
is a key to the success of immunization programs worldwide in the era of preventive medicine. Preventive
medicine or preventive care contains of measures engaged to prevent diseases in stand of curing and treating
their symptoms. Many different techniques such as curative and palliative medicine, and applied public health
methods.

Predictive Medicine
Predictive medicine is an area of medicine that involves expecting the probability of disease and instituting
preventive processes in order to either prevent the disease completely or considerably decrease its influence
upon the patient. Techniques and assays include New-born screening, diagnostic testing, Medical bioinformatics,
Prenatal testing, Carrier testing, Preconception testing. New-born screening is a public health program designed
to screen infants shortly after birth for a list of conditions that are treatable, but not clinically evident in the
new born period.

Molecular Medicine
Every disease has a genetic component. There are 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 (e.g. cancers, heart disease, diabetes). 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.

Waste Clean-up
In bioinformatics bacteria and microbes are helpful in cleaning waste. Deinococcus radiodurans Bacterium is
point out in the Guinness Book of World Records and this bacterium has the ability to repair damaged DNA
and small fragments from chromosomes by isolating damage segments concentrated area. This is because it has
additional copies of its genome. Genes from other bacteria have been inserted into D. radiodurans for environ-
mental clean-up. It was used to break down organic chemicals, solvents and heavy metals in radioactive waste
sites. Bioinformatics tools are important for understanding of the mechanisms of bio degradative pathways.

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Insect Resistance

Many plants have been made insect resistant by incorporating the desired genes. Bacillus thuringiensis is a
bacterial species which increases the soil fertility and protects the plants against pests. When the researchers
mapped its genome, they used its genes to incorporate into the plant to make it resistant against insects. For
example, corn, cotton and potatoes have been made insect resistant so far. By having the genes of bacteria in
the plants genome, when insects eat the plants, the bacteria enter in their bloodstream and make them starved,
ultimately they die. B.t corn is one species of food plants which have been modified by inserting bacterial genes
in it. It is effective against insects by developing resistance against them. The use of B.t genes in the plants
genome has made the agriculturists to use the insecticides in very little amount. As a result the productivity
and nutritional value of plants will also increase and will be beneficent for human health.

Biotechnology

The archaeon Archaeoglobus fulgidus and the bacterium Thermotoga maritima have potential for practical
applications in industry and government-funded environmental remediation. These microorganisms thrive in
water temperatures above the boiling point and therefore may provide the DOE, the Department of Defence,
and private companies with heat-stable enzymes suitable for use in industrial processes. Other industrially
useful microbes include, Corynebacterium glutamicum which is of high industrial interest as a research object
because it is used by the chemical industry for the biotechnological production of the amino acid lysine. The
substance is employed as a source of protein in animal nutrition.

Lysine is one of the essential amino acids in animal nutrition. Biotechnologically produced lysine is added
to feed concentrates as a source of protein, and is an alternative to soybeans or meat and bonemeal. Xan-
thomonas campestris is grown commercially to produce the exopolysac charidexanthan gum, which is used
as a viscosifying and stabilizing agent in many industries. Lactococcus lactis is one of the most important
microorganisms involved in the dairy industry, it is a nonpathogenic rod-shaped bacterium that is critical for

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manufacturing dairy products like buttermilk, yogurt and cheese. This bacterium, Lactococcus lactis is also used
to prepare pickled vegetables, beer, wine, some breads and sausages and other fermented foods. Researchers
anticipate that understanding the physiology and genetic make-up of this bacterium will prove invaluable for
food manufacturers as well as the pharmaceutical industry, which is exploring the capacity of L. lactis to serve
as a vehicle for delivering drugs.

Evolutionary Studies/Phylogenetics

The study of evolutionary relationship among individuals or group of organisms is defined as Phylogenetics.
Taxonomists find the evolutionary relationship using various anatomical methods that takes too much time. Us-
ing Bioinformatics, phylogenetic trees are constructed based on the sequence alignment using various methods.
Various algorithmic methods are developed for the construction of phylogenetic tree that are used depending
on the various evolutionary lineages.

Veterinary Science
Food production from livestock can meet demand of human population for food. For better bio-economy,
there is a need of efficient animal production and reproduction. This is achieved with better understanding of
livestock species. Current and new methods in livestock species using data from experimental or field studies
with bioinformatics are helping in understanding the systems genetics of complex traits and provide biologically
meaningful and accurate predictions. Finally, almost all of the next generations-omics tools and methods that
are used in other fields of biological sciences, can also be used in veterinary sciences.

Forensic science

Forensic science includes the study regarding identification and relatedness of individuals. It is inherently

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interdisciplinary with bioinformatics as both are dependent on computer science and statistics. This field is
based on the molecular data and many databases are being developed to store the DNA profiles of known
offenders. This field is being pushed due to technological and statistical advances in microarray, Bayesian
networks, machine learning algorithms, TFT biosensors and others. This provides the effective way of evidence
organization and inference.

Microbial genome applications

Microorganisms are ubiquitous, that is they are found everywhere. They have been found surviving and thriving
in extremes of heat, cold, radiation, salt, acidity and pressure. They are present in the environment, our bodies,
the air, food and water. Traditionally, use has been made of a variety of microbial properties in the baking,
brewing and food industries. The arrival of the complete genome sequences and their potential to provide
a greater insight into the microbial world and its capacities could have broad and far reaching implications
for environment, health, energy and industrial applications. For these reasons, in 1994, the US Department
of Energy (DOE) initiated the MGP (Microbial Genome Project) to sequence genomes of bacteria useful in
energy production, environmental cleanup, industrial processing and toxic waste reduction. By studying the
genetic material of these organisms, scientists can begin to understand these microbes at a very fundamental
level and isolate the genes that give them their unique abilities to survive under extreme conditions.

Climate Change Studies

Another Global concern is the Climate change because of loss of sea ice, accelerated sea level rise and longer
and more intense heat waves. To solve this issue, bioinformatics may help by way of sequencing microbial
genome which can reduce levels of carbon dioxide and other greenhouse gases. This plays an important role in
stabilizing the global climate change. Not much work has been done in this area in bioinformatics domain, and
more region-specific work must be conducted considering microbes of that region and their capability in CO2
reduction.

Bioenergy/Biofuels
Biofuels offer great promise in contributing to the growing global demand for alternative sources of renewable
energy. Bioinformatics is important in understanding and analysis of biofuel producing pathways. Recent
progress in algal genomics, in conjunction with other “omics” approaches, has accelerated the ability to identify
metabolic pathways and genes that are potential targets in the development of genetically engineered micro-algal
strains with optimum lipid content.

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