Chia-Jung Chang (張家榮) & Wu-Lung R

clumpfrustratedBiotechnology

Oct 2, 2013 (3 years and 11 months ago)

91 views

A Whirlwind Tour of Bioinformatics

Kun
-
Mao Chao (
趙坤茂
)

National Taiwan University

http://www.csie.ntu.edu.tw/~kmchao/

2

About this course


Course: Introduction to Biomedical Informatics


Spring semester, 2012


9:10
-

12:10 Monday, 101 CSIE Building.


3 credits


Web site
:
http://www.csie.ntu.edu.tw/~kmchao/bioinformatics12spr


Instructor:
Kun
-
Mao Chao

(
趙坤茂
)


Teaching assistant: Chia
-
Jung Chang (
張家榮
) & Wu
-
Lung R. Yang (
楊伍隆
)

3

TA: Chia
-
Jung Chang (
張家榮
⤠☠
Wu
-
Lung R. Yang (
楊伍隆


Chia
-
Jung

Wu
-
Lung

4

Coursework


Homework assignments and Class participation
(10%)


Two midterm exams (70%; 35% each):


Midterm #1: April 9, 2012 (tentative)


Midterm #2: May 21, 2012 (tentative)


Oral presentation of selected papers/projects
(20%)

5

The Best? The Cheapest?

The Best

Entrance

The Cheapest

6

Bio
-
X? X
-
Informatics?

Bio
-
X

Bioinformatics

X
-
Informatics

Source: NIH, Bioinformatics Journal, NPS

7

Interdisciplinary Pioneers

Leonardo da Vinci

Isaac Newton

Archimedes of Syracuse

Source: Wikipedia

8

Amphibia, Triphibia

Source: Wikipedia, xplanes

9



Band Alignment

(Joint work with W. Pearson and W. Miller, 1992)

Seq. 1

Seq. 2

10

Alignment in an Arbitrary Region

(Joint work with R. C. Hardison and W. Miller, 1993)

11

Aligning Very Similar Sequences


(Joint work with J. Zhang, J. Ostell and Webb Miller, 1997)

12

Generalized Global Alignment


(Joint work with X. Huang, 2003)

13

Tag SNPs & Haplotype Inference


(Joint work with Y.
-
T. Huang
et al
., 2006)

Yao
-
Ting Huang

Ting Chen

Kui Zhang

Chia
-
Jung Chang

Kun
-
Mao Chao

14

Sequence Comparison: Theory and Methods


(Joint work with L. Zhang, 2009)




15

Bioinformatics for Biologists

Edited by Pavel Pevzner and Ron Shamir

Cambridge University Press, 2011

16

Bioinformatics for Biologists

Edited by Pavel Pevzner and Ron Shamir

17

Bioinformatics for Biologists

Edited by Pavel Pevzner and Ron Shamir

18

Central Dogma of Molecular Biology

Source: http://www.ncbi.nlm.nih.gov

19

From Genes to Proteins

Source: http://www.ornl.gov

20

Double Helix

Source: http://www.nature.com

21

A Brief History of Genetics


1859 Charles Darwin published “The Origin of Species.”


1865 Genes are particular factors. [Gregor Mendel]


1869 Discovery of nucleic acid [Friedrich Miescher]


1903 Chromosomes are hereditary units. [Walter Sutton]


1910 Genes lie on chromosomes. [Thomas Hunt Morgan]


1913 Chromosomes are linear arrays of genes. [Alfred Sturtevant]


1931 Recombination occurs by crossing over. [Harriet Creighton and
Barbara McClintock]

22

A Brief History of Genetics (cont’d)


1944 DNA is the genetic material. [Oswald Avery, Colin McLeod and
Maclyn McCarty]


1953 DNA is a double helix. [James Watson and Francis Crick]


1961
-
1967 Genetic code is triplet. [Marshall Nirenberg, Har Gobind
Khorana, Sydney Brenner & Francis Crick]


1977 DNA was sequenced for the first time. [Fred Sanger, Walter
Gilbert, and Allan Maxam]


21th Century: Many genomes completely sequenced


MIT Open Courseware:

Biology

7.012 Introduction to Biology

23

Milestones of Bioinformatics


1962 Pauling's theory of molecular evolution


1965
Margaret Dayhoff's

Atlas of Protein Sequences


1970
Needleman
-
Wunsch

algorithm


1977 DNA sequencing and software to analyze it
(
Staden
)


1981
Smith
-
Waterman algorithm

developed


1981 The concept of a sequence motif (
Doolittle
)


1982 GenBank Release 3 made public


1982 Phage lambda genome sequenced

24

Multiple Nobel Laureates

25

Milestones of Bioinformatics (cont’d)


1983 Sequence database searching algorithm (
Wilbur
-
Lipman
)


1985
FASTP/FASTN
: fast sequence similarity searching


1988
National Center for Biotechnology Information

(NCBI) created at NIH/NLM


1990
BLAST
: fast sequence similarity searching


1991 EST: expressed sequence tag sequencing


1993
Sanger Centre
, Hinxton, UK


1994
EMBL European Bioinformatics Institute
, Hinxton,
UK

26

Milestones of Bioinformatics (cont’d)


1995 First
bacterial genomes

completely sequenced


1996
Yeast genome completely sequenced


1997
PSI
-
BLAST


1998
Worm (multicellular) genome completely
sequenced



1999 Fly genome completely sequenced

27

Milestones of Bioinformatics (cont’d)


Human Genome Project

(1990
-
2003)


Mouse 2002


Rat 2004


Chimpanzee 2005


Completed Genomes

28

Chimpanzee Genome

29

The Primate Family Tree

Source: Nature

30

orz’s Sequence Evolution


orz (kid)


OTZ (adult)


Orz (big head)


Crz (motorcycle driver)


on_

(soldier)


or2

(bottom up)


oΩ (back high)


STO (the other way around)


Oroz (me)


the origin?


their evolutionary
relationships?


their putative
functional
relationships?


31

Topics


Sequencing and genotyping technologies


Molecular sequence analysis


Recognition of genes and regulatory elements


Comparative genomics


Gene expression


Molecular structural biology


Biological networks


Systems biology


Computational proteomics


Molecular evolution


Phylogenetic trees


Population genetics


Medical informatics

32

Bioinformatics Centers


National Center for Biotechnology
Information (NCBI, NIH)
:


http://www.ncbi.nlm.nih.gov/


European Bioinformatics Institute (EBI)
:


http://www.ebi.ac.uk/


DNA Data Bank of Japan (DDBJ)
:


http://www.ddbj.nig.ac.jp/index
-
e.html


UCSC

Genome Browser Home


RCSB
Protein Data Bank

33

Bioinformatics Departments


Computational Biology and Bioinformatics, USC


Bioinformatics and Systems Biology, UCSD


The Broad Institute of MIT and Harvard


Computational and Genomic Biology, UC Berkeley


Biomedical Informatics Research, Stanford University


Comparative Genomics and Bioinformatics, Penn State


Penn Center for Bioinformatics


Max Planck Institute for Molecular Genetics


Bioinformatics and Computational Biology, Iowa State

34

Bioinformatics Journals


Bioinformatics


Journal of Computational Biology


Genome Research


Nature


Nucleic Acid Research


PLoS Computational Biology


Science

35

Nature & Science


36

Bioinformatics Conferences


The Annual International Conference on
Research in Computational Molecular Biology
(RECOMB)


The Symposium on Intelligent Systems for
Molecular Biology (ISMB)


The European Conferences on Computational
Biology (ECCB)

37

Bioinformatics Books

38

Bioinformatics Community


The International Society for Computational Biology (
ISCB
)


Senior Scientist Accomplishment Award

39

10 Steps to Success in Bioinformatics

by Webb Miller

1.
Become a biologist.

2.
Value your number of citations above your
number of publications.

3.
Collaborate, and do it with great collaborators.

4.
Do not expect a warm welcome from everyone.

5.
Be a good collaborator.

6.
Distribute and maintain software and/or run
web servers that you personally continue to use.

40

10 Steps to Success in Bioinformatics

by Webb Miller

7.
Alternate between working on specific datasets
and writing general
-
purpose software.

8.
Write some of your own software.

9.
Don't give up.

10.
Be excited about your work.