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)
[TA's office hours: 2:00pm - 4:00pm Mondays]

 

Prerequisites: Background in biology and informatics is welcome but not required for taking this course.

 

Classmates: I  II  III  IV  V  VI

　

Coursework: Grades

    Homework assignments and Class participation (10%)

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

        1. Midterm #1: April 9, 2012 (tentative) Scoreboard

        2. Midterm #2: May 21, 2012 (tentative) Scoreboard

    Oral presentation of selected papers/projects (20%)

 

Topics:

Supporting materials:

    A Whirlwind Tour of Bioinformatics [2/20/2012]  Survey

    Selected Videos [3/3/2012]

    Next-Generation Sequencing by Dr. Stuart M. Brown (NYU) [3/5/2012]

      -- Genome Reconstruction (pdf, ppt) by Phillip E. C. Compeau and Pavel A. Pevzner [3/19/2012; 3/26/2012]
(For ppt, read Sec. 2, Sec. 3, Sec. 4, Sec. 8, Sec. 9)

      -- Eulerian Tours by Christos H. Papadimitriou & Umesh Vazirani [3/19/2012; 3/26/2012]
(Exchange 10 and 01 of the left figure on Page 4)

    Sequence Alignment [3/5/2012; 3/12/2012]

      -- Global Alignment [3/5/2012]

      -- Local Alignment [3/12/2012]

      -- Various Scoring Schemes [3/12/2012]

      -- An affine-gap-penalty example [3/19/2012]

      -- Scoring scheme examples [3/19/2012]

    Space-Saving Strategies [3/19/2012]

      -- Space-Saving Strategies (pdf) [3/19/2012]

    Multiple Sequence Alignment [3/26/2012; 4/16/2012]

      -- Multiple Sequence Alignment (pdf) [3/26/2012; 4/16/2012]

    Homology Search Tools [4/16/2012; 4/23/2012] [See also PH.ppt (pp. 16-24)]

      -- Homology Search Tools (pdf) [4/16/2012; 4/23/2012]

    Pattern Identification in a Haplotype Block (ppt, pdf) [4/23/2012; 4/30/2012]

    Haplotype Inference (ppt, pdf) [4/30/2012] (Some other ways of formulation, 5/1/2012)

    R, Ensembl, Galaxy, ... [5/7/2012 by Chia-Jung Chang]

    Connectivity Map [5/14/2012 by Roger Yang]

　

Homework assignments:

　

Class presentations:

1.      The expected number of team members: 1~8;

2.      Each member is required to present in turn (about 6-7 minutes each);

3.      Revised slides should be sent to me within one week after the presentation. Please compress your figures.

4.      Questions in class are always welcome.

　

Selected papers for presentation:

5/28/2012

  1. Fast and accurate short read alignment with Burrows-Wheeler transform
    Li H, Durbin R. Bioinformatics. 2009 Jul 15;25(14):1754-60.
    吳彥緯  沈國曄  陳伊瑋  廖婉馨  魏銘良
    Slides
    　
  2. PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
    Yangho Chen, Tade Souaiaia and Ting Chen   Bioinformatics, 2009
    王柏易  蔡博倫  蔡誠軒  翁健庭  王舜玄  黃子容  何恩
    Slides
    　
  3. Protein multiple sequence alignment by hybrid bio-inspired algorithms
    Vincenzo Cutello, Giuseppe Nicosia,* Mario Pavone, and Igor Prizzi  Nucleic Acids Res. 2011 March
    陳子筠  黃任鋒  張庭耀  蘇宏麒
    Slides
    　
  4. Waiting for the Revolution
    Eliot Marshall  Science 4 February 2011: Vol. 331 no. 6017 pp. 526-529
    鄭柏暐  李允傑  林偉博  莊明儒
    Slides
    　
  5. Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants
    Alon Keinan and Andrew G. Clark  Science 11 May 2012: Vol. 336 no. 6082 pp. 740-743
    王淳毅  柯彥圻  林培鈞
    Slides: PDF Keynote
    　

6/4/2012

  1. Will Computers Crash Genomics?
    Elizabeth Pennisi   Science 11 February 2011: 666-668.
    吳宜瑾  何宜靜  林芳伃  魏裕明  范剛瑋  陳柏融
    Slides
    　
  2. On the Future of Genomic Data
    Scott D. Kahn   Science 11 February 2011: 728-729.
    徐國翔  邵祈諭  楊竣宇  邱璽安  謝宗潛  邱相茹  林易徵
    Slides
    　
  3. Integrating Genomes
    D. R. Zerbino, B. Paten, and D. Haussler  Science 13 April 2012: 179-182.
    何秉聖
    Slides
    　
  4. Big data: The future of biocuration
    Doug Howe et al.  Nature. 2008 September 4; 455(7209): 47–50.
    馬雲鵬
    　
  5. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead*, Cole Trapnell, Mihai Pop and Steven L Salzberg Genome Biology 2009, 10:R25
    林恩羽  陳翰平  宋曉亞
    Slides
    　
  6. Repetitive DNA and next-generation sequencing: computational challenges and solutions
    Todd J. Treangen and Steven L. Salzberg, Nature Reviews Genetics 13, 36-46 (January 2012)
    黃建龍  黃元鴻
    Slides: PDF  PPT
    　
  7. DNA sequencing: Read with quantum mechanics
    Thomas Thundat  Nature Nanotechnology 5, 246 - 247 (2010)
    楊偉杰
    Slides
    　
  8. DNA nanotechnology: Geometric sorting boards
    David W. Grainger  Nature Nanotechnology 4, 543 - 544 (2009)
    李宗翰
    Slides
    　
  9. SapoFitness: A Mobile Health Application for Dietary Evaluation
    Bruno M. Silva, Ivo M. Lopes, Joel J. P. C. Rodrigues, and Pradeep Ray  2011 IEEE 13th International Conference on e-Health Networking, Applications and Services
    陳仕偉
    Slides
    　
  10. From patients to partners: participant-centric initiatives in biomedical research
    Jane Kaye et al.  Nature Reviews Genetics 13, 371-376 (May 2012)
    韓政廷
    Slides: PDF  PPT

6/11/2012

  1. A reference ontology for biomedical informatics: the Foundational Model of Anatomy
    C Rosse, JLV Mejino - Journal of Biomedical Informatics, 2003
    陳禹恆  許自程  何泓毅  張翔竣  許逸堯  任立容  陳郁文  潘建豪
    Slides
    　
  2. Biomedical informatics for proteomics
    Mark S. Boguski & Martin W. McIntosh  Nature 422, 233-237 (13 March 2003)
    蘇鈺惠  計佩岑  施光偉  蕭雅茵  葉欣綺  葉衍陞  陳雲濤  鍾宇彥
    Slides
    　
  3. GIGA: a simple, efficient algorithm for gene tree inference in the genomic age
    Thomas PD. BMC Bioinformatics. 2010 Jun 9;11:312
    沈子琪 柯依庭
    　
  4. Electronic Health Records in Ambulatory Care — A National Survey of Physicians
    Catherine M. DesRoches, Dr.P.H., Eric G. Campbell, Ph.D., Sowmya R. Rao, Ph.D., Karen Donelan, Sc.D., Timothy G. Ferris, M.D., M.P.H., Ashish Jha, M.D., M.P.H., Rainu Kaushal, M.D., M.P.H., Douglas E. Levy, Ph.D., Sara Rosenbaum, J.D., Alexandra E. Shields, Ph.D., and David Blumenthal, M.D., M.P.P. N    Engl J Med 2008; 359:50-60.
    陳玟妤  周鈺翔  許茗鈜  章偉恩  郭泰源  陳柏安  魏逸昕  賴志豪
    Slides
    　
  5. Multidimensional Optimality of Microbial Metabolism
    Robert Schuetz, Nicola Zamboni, Mattia Zampieri, Matthias Heinemann, Uwe Sauer  Science 4 May 2012: Vol. 336 no. 6081 pp. 601-604
    黃信博  廖堃吉  張至安  林建棋  郭明宏
    Slides
References (Recommended, but not required):
1. “Bioinformatics for Biologists,” edited by Pavel Pevzner and Ron Shamir, Cambridge University Press, UK.
2. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, by Dan Gusfield (1997)
3. Biological Sequence Analysis, by Richard Durbin et al. (1998)
4. Computational Molecular Biology: An Algorithmic Approach, by Pavel Pevzner (2000)
5. An Introduction to Bioinformatics Algorithms, by Neil C. Jones and Pavel Pevzner (2004)
6. Chao, K.-M. and Zhang, L. (2009) “Sequence Comparison: Theory and Methods,” Springer. (210 pages; ISBN 978-1848003194)
7. Related journal and conference papers
　
Useful links:
  1. NCBI    
    2. NCBI Education
  2. Molecular Biology for Computer Scientists by Lawrence Hunter
  3.  Developing Bioinformatics Computer Skills by Cynthia Gibas & Per Jambeck
  4. Sense from Sequences: Stephen F. Altschul on Bettering BLAST , July/August 2000 (A story about BLAST)
  5. Initial sequencing and analysis of the human genome (15 February 2001 Nature 409, 860 - 921 (2001)
  6.  The Sequence of the Human Genome (Science 2001 February 16; 291: 1304-1351)
  7. An evaluation of the draft human genome sequence (Nature Genetics 29, 88 - 91 (01 Sep 2001) Letters)
  8.  Initial sequencing and comparative analysis of the mouse genome (Nature 420, 520 - 562 (2002))
  9. The UCSC Genome Browser
  10. The Chimpanzee Genome (Nature; Sept. 1, 2005)
    11. The Chimpanzee Sequencing and Analysis Consortium25, "Initial sequence of the chimpanzee genome and comparison with the human genome," Nature 437, 69-87 (1 September 2005) | doi: 10.1038/nature04072
  11. The HapMap Project (Nature; Oct. 27, 2005)
    Please visit:
    http://www.nature.com/nature/journal/v437/n7063/index.html
    　
    and in particular the following research articles:
    http://www.nature.com/nature/journal/v437/n7063/index.html#Article
Bibliography links: