Introduction to Computational Biology

Question 1

the development and application of data-analytical and theoretical methods, mathematical modeling, and computational simulation techniques to the study of biological, behavioral, and social systems (Pevsner, 2015)

Answer 1

Computational Biology

Question 2

▪ is a broad term, which covers all efforts of scientific investigations on or related to biology that involves mathematics and computation (Jianget. al., 2013)

Answer 2

Computational Biology

Question 3

▪ an emerging discipline that draws upon the strengths of computer sciences, mathematics, and information technology to determine and analyze genetic information (Singh, 2015)

Answer 3

Bioinformatics

Question 4

▪ research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral, or health data, including those to acquire, store, organize, analyze, or visualize such data (Pevsner, 2015)

Answer 4

Bioinformatics

Question 5

one-by-one cleavage of N-terminal amino acid residues with phenylisothiocyanate

Answer 5

Edman sequencing

Question 6

first protein to be sequenced

Answer 6

Insulin

Question 7

the first bioinformatician

pioneered the application of computational methods

Developed the3-letter and 1-letter amino acid code

Answer 7

Margaret Dayhoff

Question 8

‘a complete computer program for the IBM 7090’ designed to determine protein primary structure

Answer 8

COMPROTEIN

Question 9

first-ever biological sequence database

Answer 9

Atlas of Protein Sequence and Structure

Question 10

▪ Coined the term ‘Paleogenetics’
▪ hypothesized that orthologous proteins evolved through divergence from a common ancestor

Answer 10

Emile Zuckerkandl & Linus Pauling

Question 11

▪ developed the first dynamic programming algorithm for pairwise protein sequence alignments

Answer 11

Saul B. Needleman & Christian D. Wunsch

Question 12

became the basis for the first published MSA algorithm

Answer 12

Needleman–Wunsch algorithm

Question 13

developed the first truly practical approach to MSA

Answer 13

Da-Fei Feng & Russell F. Doolitle

Question 14

became the basis for the now popular CLUSTALMSA software

Answer 14

Feng–Doolittle algorithm

Question 15

what sequencing is this: radioactive reagents

Answer 15

Maxam–Gilbert sequencing

Question 16

‘plus and minus’ DNA sequencing; first to rely on primed synthesis with DNA polymerase

Answer 16

Sanger Sequencing

Question 17

first sequence analysis software to include additional characters
▪ search + contigs assembly + annotate and manipulate sequence file

Answer 17

Staden Package

Question 18

The least number of changes as the main mechanism driving evolutionary change

Usually, for protein sequence
based phylogeny

Answer 18

Maximum Parsimony

Question 19

Who proposed Maximum Parsimony

Answer 19

Walter M. Fitch

Question 20

finding the evolutionary tree that yields the highest probability of evolving

Usually, for nucleic acid sequence-based phylogeny

Answer 20

Maximum Likelihood

Question 21

Who proposed Maximum Likelihood

Answer 21

Joseph Felsenstein

Question 22

promoted the freedom to run, copy, distribute, study, change and improve the software

Answer 22

Richard Stallman

Question 23

first complete genome that was sequenced

Answer 23

Haemophilus influenzae

Question 24

turning point of the genomic era

Answer 24

Human Genome Project

Question 25

Human Genome Project from Public

Answer 25

National Institute of Health

Question 26

Human Genome Project from Private

Answer 26

Celera Genomics

Question 27

first 3D structure experimentally determined

Answer 27

Myoglobin

Question 28

▪ Effect of lowering the cost of massively
parallel sequencing technologies
▪ New repositories being made for model
organisms

Answer 28

‘Biological Big Data’

Question 29

▪ Started with the ‘454 pyrosequencing
technology’
▪ Availability of a multitude of platforms

Answer 29

Second-generation sequencing or NGS

Question 30

Central dogma of genomics

Answer 30

Genome -> Transcriptome -> Proteome -> Cellular phenotyppe

Question 31

A main culture in bioinformatics that do not require knowledge of programming and are immediately accessible

Answer 31

Web-based or Graphical User Interface (GUI)

Question 32

2 main culture of bioinformatics

Answer 32

1. Web-based or Graphical User Interface (GUI)
2. Command Line (often Linux)

Question 33

A main culture in bioinformatics that has high‐throughput approaches that is more appropriate for analyzing large‐scale datasets

Answer 33

Command Line (often Linux)

Question 34

(1) A workflow should be well documented.
(2) Information should be well organized.
(3) Data should be made available to others.
(4) Metadata can be equally as crucial as data.
(5) Databases that are used should be documented.
(6) Software should be documented