TOPIC-1-Introduction-to-Bioinformatics_for dummies

What does this Tony Stark pose mean for you today?

Kamusta ang bakasyon? Ano ang feeling
ng 1st day of the new semester?

Thesis 2 Plant
Physiology
Bioinformatics
Yung sila mismo nag-usap na magkakasama sa 1 sem.
Sila nalang masaya.

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Bioinformatics
SPECORE 102
Introduction to
Bioinformatics

OBJECTIVES
1 Reiterate the fundamentals of Molecular Biology
2 Retrace the history of modern biology and its advancement
3 Point out the major events that shaped modern Biology
5 Understand the applications of Systems Biology and Computational Biology
4 Discuss the study of OMICs and their importance in modern biology

Contents
From Cell
Biology to
Molecular
Biology
1 3
Modernizing
Biotechnology
and the Era of
Genetic
Engineering
2
Molecular
Research and
the OMICs
Revolution
4
Fundamentals
of Systems
Biology and
Computational
Biology

From Cell Biology to
Molecular Biology
The Fundamental
Concepts
1

Recall the fundamental concepts of cell
and molecular biology

Cell and Molecular Biology
The cell is the basic
unit of life
Cells are made up of
molecules
Biological molecules are the
molecular basis of structure
and function in living
organisms
The Central Dogma of
Molecular Biology
Innovation of laboratory
techniques enable the study
of these molecules
Applications of molecular
study enable the
advancement of life

What are the 3 main
events in history that
shaped Biology?
From Organismal Biology to Cell Biology to
Molecular Biology
1 2 3

1
Topics
DNA Extraction,
purification, and
isolation
Polymerase Chain
Reaction
Gel electrophoresis
DNA sequencing

1
Topics
Blotting techniques
Knockout technique
DNA microarray
The use of
oligonucleotides

1
Topics
CRISPR technology
RNA interference
Karyotyping
Chromatography

1
Topics
Centrifugation
Micronucleus test

The central dogma of molecular biology and correspondence with 'omics' disciplines
(Araújo, A. M., Carvalho, F., Guedes de Pinho, P., & Carvalho, M. (2021). Toxicometabolomics: Small Molecules to Answer Big Toxicological Questions. Metabolites, 11(10), 692.)

Understanding the genetic material as
a whole
Understanding human disease
Improvement and sustainability
of food
Availability of these genomic
technologies

Molecular
Research and the OMICs
Revolution
Revolutionizing
Macromolecular Biology
2

The Great Quest
Watson and Crick with their DNA model in 1953

Discoveries in DNA:
What's
New Since You Went
to High School
(for the OG)?
Joel Eissenberg, Ph.D., associate
dean for research and professor of
biochemistry and molecular
biology at Saint Louis University
School of Medicine
https://www.slu.edu/news/2016/august/Eissen
berg-genetics-essay.php

The Great Goal
Why it has been done
Understanding the structure and function of DNA hoped to he
lp revolutionize the investigation of disease pathways, assess
an individual's genetic susceptibility to specific diseases, dia
gnose genetic disorders, and formulate new drugs.

How many oncogenes code for cancer?
In chromosome 13? 21?
How many genes may potentially code
for human diseases in each chromoso
me?

The Great Goal
What has been already done
Saad, R. (2005, April). Disc
overy, development, and c
urrent applications of DN
A identity testing. In Bayl
or University Medical Cen
ter Proceedings (Vol. 18, N
o. 2, pp. 130-133). Taylor &
Francis.

The Great Goal
Saad, R. (2005, April). Discovery, development, and current applications of DNA identity
testing. In Baylor University Medical Center Proceedings (Vol. 18, No. 2, pp. 130-133).
Taylor & Francis.

The Great Goal
What has been
already done
Pogue, R. E., Cavalcanti, D. P., Shanke
r, S., Andrade, R. V., Aguiar, L. R., de C
arvalho, J. L., & Costa, F. F. (2018). Rar
e genetic diseases: update on diagno
sis, treatment and online resources
. Drug discovery today, 23(1), 187-195.

The Great Quest
Yang, H. J., Ratnapriya, R.,
Cogliati, T., Kim, J. W., & S
waroop, A. (2015). Vision f
rom next generation sequ
encing: multi-dimensiona
l genome-wide analysis f
or producing gene regulat
ory networks underlying r
etinal development, aging
and disease. Progress in r
etinal and eye research, 4
6, 1-30.

The Great Goal

Where are we
now?
https://www.uclahealth.org/u-magazine/stem-cell-therapy-holds-
promise-for-eliminating-hiv-infection

Omics Revolution
The suffix -omics is
used frequently to
describe something
big, and refers to a
field of study in life
sciences that
focuses on large-
scale data/
information to under
stand life
Yadav SP. The wholeness in suffix -omics, -omes, an
d the word om. J Biomol Tech. 2007 Dec;18(5):277. PMI
D: 18166670; PMCID: PMC2392988.

Modernizing Biotechnology
and the Era of Genetic
Engineering
From Traditional to
the Modern Era
2

Biotechnology
It is the use of living systems and
organisms to develop or make products
(Springham et al., 1999)
TRADITIONAL BIOTECHNLOGY
It is the manipulation of living organisms
and organic material to serve human
needs (Bergeron and Paul, 2004)
MODERN BIOTECHNLOGY
Biotechnology is nearly as old as civilization itself.

The most important element in the
history of biotechnology is the
process of making alcohol, or
fermentation.

Biotechnology then Biotechnology now

Based on this tree,
can you become
successful in the
biotech industry
with studying
only 1 area of Biology?

Example of Biotechnology – Selective Breeding
What feature of Casper makes it a "model organism" to study
migration of cancer cells compared to wildtype fish?
Normal zebrafish "Casper" zebrafish – made by selective breeding
(a) (b)

Look at the two chromosomes and determine which chromosome has more
than one gene involved in promoting breast cancer. Explain your answer.

• Most drugs are
developed to
combat diseases
affecting humans
– Why?
• Which disease
has the most drug
candidates? Why
does that disease
have more drug
candidates than
hepatitis C?

• Products of Modern
Biotechnology
– Example of proteins
created by gene
cloning called
recombinant proteins

Fields of Biotechnology
Manipulation of
microorganisms to
clean up waste
Microbial Biotechnology
Better plants,
better yield
Plant Biotechnology
Animals as a source of
medically valuable
proteins
Animal Biotechnology
Based on the application of the technology

Fields of Biotechnology
This text can be replaced with your own text
Resistance to pest,
conservation of diversity, and
bioprospecting
Aquatic and Ecology
Biotechnology
Processing and production of
chemicals, materials and energy
using enzymes and micro-
organisms to make products in
sectors
Industrial Biotechnology
Enhancement of
health and combat
of diseases
Medical Biotechnology

One Heck of a History
R. Hooke and A.
Leeuwenhoek
Cells and Animalcules
1635-1723
TH Morgan and F. Griffith
Fruitfly and Transform
J. Watson and F. Crick
DNA structure
C. Darwin and G. Mendel
Evolution and Genetics
1855 1809-1884 1905-1945 1950

For the Great Implication ….
Frederick Sanger
(1918 – 2013)

But with accompanied elements…
Molecular Biology
Your thoughts?

How are food and drugs produced by research get
into the market?

Fundamentals of Systems
Biology and Computational
Biology
The Interface of Computer
Science and Biology
3

Interface of Computer Science and Molecular
Biology
What in certain ways computer science be
useful in molecular biology?
5

Wet and Dry Analytical Laboratory Experiments in Biology

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.
Biology in the 21st century is being transformed from a purely
lab-based science to an information science as well.

Hunter, L. (1993). Molecular biology for computer scientists. Artificial
intelligence and molecular biology, 177, 1-46.
One of the major
challenges for computer
scientists who wish to
work in the domain of
molecular biology is
becoming conversant
with the daunting
intricacies of existing
biological knowledge
and its extensive
technical vocabulary.
Biological data has
increased dramatically
over the past century. And
it is continually increasing
due to the advancement
in Sciences. Especially in
molecular biology. There is
so much to uncover from
our genome and its
accompanying molecular
framework.
Bentley, P. J. (2001, October). Why biologists and computer scientists
should work together. In International Conference on Artificial Evolut
ion (Evolution Artificielle) (pp. 3-15). Springer, Berlin, Heidelberg.

Computational Ecology
• Numerical modeling and computer simulations can be used as
a powerful research tool to understand, and sometimes to
predict, the tendencies and peculiarities in the dynamics of
populations and ecosystems
• Applications:
– fisheries,
– forestry,
– agriculture,
– climate change and in
– evolutionary ecology
Petrovskii, S., & Petrovskaya, N. (2012). Computational ecology as
an emerging science. Interface Focus, 2(2), 241-254.

Sketch of a hypothetical food web. The nodes correspond to
the species explicitly included into the model and the edges
correspond to the trophic interactions. Each node
corresponds to an equation in the model
Buhay
Biologist

(a) Chlorophyll distribution in the Gulf of
Alaska. Orange and yellow patches
correspond to high phytoplankton
concentration, white shows where the
data are missing. (By courtesy of NASA,
from http://oceancolor.gsfc.nasa.gov/FEA
TURE/gallery.html.) (b) Different scales in
the phenomenon of plankton patchiness.

• Modeling ecosystems
Ecologists are turning to computer models to help
them make their models of ecosystem processes
concrete and to provide predictions about the future
of the ecosystem. Computer models allow rapid
testing of ecology ideas by simulation and provide
the means to run “what-if” scenarios that would be
difficult or impossible otherwise.

Hyder, K., Rossberg, A. G., Allen, J. I., Austen, M. C., Barciela, R. M., Bannister, H. J., ... & Paterson, D. M. (2015). Making modelling count-increasing the contribution of shelf-seas community and ecosys
tem models to policy development and management. Marine Policy, 61, 291-302.

• Predator-prey interactions
Predator–prey interactions are a
major evolutionary driving force,
mediating the behavior of both
predator and prey. Ideally, in
order to maximize its fitness, an
organism would maximize the
time spent foraging for food or
finding a mating partner and
reproducing. Modeling this
relationship aids in the
management and conservation
of specific environment and
organisms
Biophysical Computational Ecology

An Example of Periodic activity
generated by Predator-Prey Model
(Lotka Volterra Model)
Study of Two species Interactions using Lotka Volterra Model
http://complexnt.blogspot.com/2012/03/study-of-two-species-interactions-using.
html

• Ecosystem-scale models
Tools from computer simulation and modeling (e.g., agent-
based simulation) as well as machine learning (e.g., learning
classifier systems) are used to help biologists and others
model the ecology of the environment to assess relations
between organisms, to further understanding complex
adaptive system models that can be used by regulators to
create more appropriate environmental management
regulations

77
The Ecosystem Demography m
odel version 2 (ED2) explicitly tr
acks the dynamics of fine-scale
ecosystem structure and functi
on. Here it has been applied to t
ropical forests in Costa Rica
https://www.rc.fas.harvard.edu/case-studies/study
ing-the-ecosystem/ecosystem/

di Porcia E Brugnera, M., Meunier, F., Longo, M., Kri
shna Moorthy, S. M., De Deurwaerder, H., Schnitzer,
S. A., ... & Verbeeck, H. (2019). Modeling the impact
of liana infestation on the demography and carbon
cycle of tropical forests. Global change biology, 25(1
1), 3767-3780.
Forest demographic composition
for the two simulated sites: Gigante,
Panama (a–b–c), and Paracou,
French Guiana (d–e–f). The K–Sstat
is the test statistic of the two-
sample Kolmogorov– Smirnov test
between the observed and
simulated size distributions (with a
sampling size of 250 for each
distribution). Liana basal area in
Gigante was the only case in which
the observed and simulated
distribution did not significantly
differ

The Interface of Computer Science and Biology
Systems
Biology
Computational systems biology research distills raw data into knowledge of how cells and
organisms function, both to advance biology and enable advances in biomedicine and
bioengineering. To bridge the gap between data and biological knowledge, researchers develop
cutting-edge computational methods for data modeling and machine learning, database search
and indexing and graphics and vision.
Computational
Biology
Bioinformatics
The computational
and mathematical
analysis and
modeling of complex
biological systems.
Use of data analysis,
mathematical modeling
and computational
simulations to
understand biological
systems and relationships
Application of tools
of computation and
analysis to the capture
and interpretation of
biological data

Systems Biology
Systems Biology of Cellular Membranes: a Convergence with Biophysics

Computational Biology
Iterative computational
biology workflow. Data are
gathered by experimentation,
from the literature or from
publicly accessible databases.
Computational models
describing biological
knowledge are generated
and refined. Models are
used for in silico simulation,
re-refinement of the model
and hypothesis generation.
Findings are validated
experimentally, feeding into
new data for the next
iteration of the cycle.
Lam, S., Doran, S., Yuksel, H. H., Altay, O., Turkez, H., Nielsen,
J., ... & Mardinoglu, A. (2021). Addressing the heterogeneity i
n liver diseases using biological networks. Briefings in Bioi
nformatics, 22(2), 1751-1766.

Individual structure
and function of
each organelle and
how they influence
the integrity of
each for the cell to
work properly
https://copib.wordpress.com/2012/07/2
4/collaborative-biology-and-computati
onal-biology/

Villa, A., & Sonis, S. T. (2020). System biology. In Translational Systems Medicine and Oral Disease (pp. 9
-16). Academic Press.
This schematic diagram depicts the Systems Biology cycle. Systems
Biology is an integrative biology that requires a multidisciplinary effort
, incorporating experimental design and data generation ('wet' lab) wi
th knowledge extraction, data analysis, mathematical modelling and s
imulations ('dry' lab). These efforts are performed in a consecutive an
iterative way with each cycle improving the quality of a system model
.
Venkatesan, A. (2014). Application of semantic web technology to establish knowledge
management and discovery in the life sciences.

Figure 1: Overall View of
Applications of Systems
Biology.
Nandikolla, S. K., Shaik, M., Varali, S., & See
lam, R. (2011). Emerging trends in various fi
elds with systems biology approach. J Comp
ut Sci Syst Biol, 13.
What paved the
way for the
creation of this
subdiscipline?

Bioinformatics, a
subdiscipline of
And Computational Biology is an area of
Systems Biology

Transforming Data into Information

Bioinformatics
Related to genetics and genomics, is a scientific subdiscipline that
involves using computer technology to collect, store, analyze and
disseminate biological data and information, such as DNA and amino
acid sequences or annotations about those sequences.

Sharma, D., Singh, S., & Mittal, M. (2021). Bioinformatics and RNA: A Practice-based Approach.
CRC Press.
Buhay
Biologist

Bioinformatics
Bailet, B., Apothéloz-Perret-Gentil, L., Baričević, A., Chonova, T., Franc, A., Frigerio, J. M., ... & Kahlert, M. (2020). Diatom DNA metabarcoding for ecological assessment: Comparison among bioinforma
tics pipelines used in six European countries reveals the need for standardization. Science of the Total Environment, 745, 140948.

Bioinformatics
Sequence Alignment Analyses

Bioinformatics
Molecular Modeling Analyses

Bioinformatics
Chemical Composition and Simulated Chemical Reaction
Analyses

What are your
key takeaways
from the
discussions?

TOPIC-1-Introduction-to-Bioinformatics_for dummies

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