周次 |
課程主題 |
課程內容與指定閱讀 |
教學活動與作業 |
學習投入時數 |
1 |
Introduction |
What is bioinformatics?
The central dogma of molecular biology: DNA, mRNA, protein |
The DNA Journey
天下文化 觀念生物學1~4
Canadian Bioinformatics Workshops (all slides and video are available) |
6 |
2 |
Sequence alignment |
Why do we need sequence alignment?
Its application in structural homology and evolutionary modeling context
Dynamic programming |
SEAVIEW : Sequence alignment editor
T-Coffee documentation |
6 |
3 |
Pairwise Sequence alignment |
Global & Local alignments
Linear space algorithm
BLAST |
NCBI BLAST server
BLAST by O'Reilly Media |
6 |
4 |
Multiple Sequence alignment |
The variation of the algorithms, which one is better?
Another issue: a huge amount of data |
T-Coffee web server
PSI/TM-Coffee web server
- PSI/TM-Coffee: Floden, E. W. et al. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. Nucleic Acids Res. 44, W339–43 (2016).
- PSI-Coffee: Chang, J.-M. M., Di Tommaso, P., Taly, J.-F. F. & Notredame, C. Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. BMC Bioinformatics 13 Suppl 4, S1 (2012).
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6 |
5 |
Sequence alignment post-process |
Uncertainty and its effect on downstream analysis
How do we detect uncertainty? |
TCS web server
TCS: Chang, J.-M. M., Di Tommaso, P. & Notredame, C. TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.Mol. Biol. Evol. 31, 1625–37 (2014). |
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6 |
Phylogenetic tree 1/2 |
Probabilistic and ideal-data models
Character/parsimony-based methods |
Programs for molecular phylogeny summary by Manolo Gouy |
6 |
7 |
Phylogenetic tree 2/2 |
Distance-based methods: UPGMA, NJ
Maximum-likelihood methods: PhyML |
PHYLIP: an extensive package of programs for all platforms
PAUP: a very performing commercial package
PHYLO_WIN: a graphical interface, for unix only
MrBayes: Bayesian phylogenetic analysis
PhyML: fast maximum likelihood tree building
WWW-interface at Institut Pasteur, Paris |
6 |
8 |
Midterm |
One A4 page |
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0 |
9 |
Protein secondary structure prediction |
Neural network approach
Knowledge-based approach |
The Critical Assessment of protein Function Annotation algorithms (CAFA)
- CAFA1: Radivojac, P. et al. A large-scale evaluation of computational protein function prediction. Nat. Methods 10, 221–7 (2013).
- CAFA2: Jiang, Y. et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. arXiv preprint arXiv:1601.00891 (2016). at
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6 |
10 |
Protein functional class prediction |
Machine learning
Feature reduction |
PSLDoc: Chang, J.-M. M. et al. PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis. Proteins 72, 693–710 (2008)
PSLDoc2: Chang, J.-M. M. et al. Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations. PLoS ONE 8, e75542 (2013)
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11 |
Genomics1 |
What are genes and genomes? How does a gene express and regulate? |
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6 |
12 |
Genomics2 |
The Human Genome Project
Gene finding |
The Assemblathon |
6 |
13 |
Next Generation Sequencing |
RNA-Seq: large amounts of data
How to identify significant expressions? |
Applications of next-generation sequencing by Nature Reviews Genetics |
6 |
14 |
Comparative genomics 1 |
Genome alignment
Phylogenomics |
The Alignathon |
6 |
15 |
Comparative genomics 2 |
Single-nucleotide polymorphisms related to diseases |
HaploReg: a tool for exploring annotations of the noncoding genome at variants on haplotype blocks
ClinVar: aggregates information about genomic variation and its relationship to human health |
6 |
16 |
Final project presentation |
Rubrics/評分量尺 |
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3 |
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Extra Learning: 6 hours |
ENCODE: Encyclopedia of DNA Elements
modENCODE: model organism Encyclopedia of DNA Elements
NIH Roadmap Epigenomics
1000 Genomes
UCSC/Ensembl genome browser
WashU epi-genetics browser
RCSB Protein Data Bank (PDB)
NCBI Sequence Read Archive (SRA) |
Collected papers for Epigenome Roadmap
Epigenetics by Nature Reviews Genetics
ENCODE
modENCODE
Roadmap Epigenomics project |
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