Talks
Although the main approach of this course is hand-on practice, we do have short presentations during the course for specific topics such as database similarity search with Blast, molecular evolution and phylogenetics, molecular visualization and structure prediction. Most of the talks are given by students.
Introduction
- China’s NCBI – a dream? (Luo JC, CBI) [PDF]
- My View on Bioinformatics (Luo JC, CBI) [PDF]
- Bioinformatics Databases(Luo JC, CBI) [PDF]
- Genome Information Resource (Luo JC, CBI) [PDF]
Invited Lectures
- Xiao Xu (Peking University) – The genetic basis of white tigers.[PDF]
- Yang Zhong (Fudan University) – Horizontal gene tansfer: from phylogenetic prediction to experimental validation. [PDF]
Summary about ABC
- Lu P – A summary to the ABC by Li P (CAAS15F) [PDF]
UNIX and EMBOSS
BLAST and database search
- BLAST – Luo JC (CBI) [PDF] | Tian YL (CAAS06F) [PDF] | Xie C (PKU08S1) [PDF] | Bian Y (PKU08S1) [PDF] | Xu GX (PKU09S3) [PDF] | Liu H (CAAS09S3) [PDF] | Kang YJ (pku13f) [PDF] | Jiang S (pku14f) [PDF] | Kuang C (caas16f) [PDF]
- Database search – Gao G (CBI) [PDF]
- Multiple sequence alignment – Liu K (PKU07S) [PDF]
- Scoring Matrix – Yuan YX (PKU07S) [PDF]
Primer Design
Resources
- PubMed – Huang LY (CAAS07F) [PDF] | Gao YZ (CAAS09S2) [PDF] | Luo JC (CBI) [PDF]
- NCBI Databases – Li L (CAAS07F) [PDF]
- ExPASy – Gong JY (CAAS07F) [PDF] | Ren J (CAAS09S2) [PDF]
- PDB – Gao HB (CAAS07F) [PDF]
- SRS – Luo JC (CBI) [PDF] | Yan Ll (CAAS08S) [PDF] | Huang BY (CAAS07F) [PDF]
- Text Mining – Wang X (CAAS07F) [PDF]
- WebLab – wang J (CBI) [PDF]
Phylogeny
- MEGA – Hu YP (CAAS06F) [PDF]
- Phylogeny – Gao G (CBI) [PDF] | Huang BY (CAAS07F) [PDF] | Li Z (CBI) [PDF] | Shi XL (CBI) [PDF] | Zhu HW (CAAS07F) [PDF] | Li J (PKU08S) [PDF] | Yang Q (PKU08S) [PDF] | Sun TS (PKU12f) [PDF] | Jiang CK (PKU14F) [PDF] | Yang JX (PKU19S) [PDF]
Molecular modeling
- 3D modeling – Ye ZQ (CBI) [PDF] | Zhu HW (CAAS07F) [PDF] | Wang JL (CAAS08S) [PDF]
- 3D of Transcription Factors – Luo JC (CBI) [PDF]
- Swiss PDB Viewer – Mao SL (BBT20G04) [PDF] | Zhang J (CAAS08S) [PDF] | Li W (CAAS07F) [PDF]
- PyMol – Zhang WB (PKU13F) [PDF] [Map] | Zhou QF (PKU14F) [PDF] [Map] | Yi YP (CAAS15PhD) [PDF] | Wang Y (PKU16F) [PDF]
Omics data analysis
- Cucumber genome assembly – Li HB (CAAS17MS) [PDF]
Projects
- HB (Hemoglobin) – Li WQ (PKU07S) [PDF] | Li QC (CAAS08F) [PDF]
- CEA (Caecinoembrionic Antigene) – Wang Q (CAAS07F) [PDF]
- MDR (Fugu Multidrug Resistance Gene)- Xu LM (PKU08S1) [PDF]
- SBP (Squmosa promoter Binding Protein) – Guo AY (CBI) [PDF]
- LEC1 (Arabidopsis CCAAT-HAP3 TF family) – Xu LM (CBI)[PDF]
- Rice (Rice Genome Domestication) – Zhu QH (CBI) [PDF]
- CA3 (Carbonic Anhydrase��) – Hou XH (CAAS07F) [PDF]
- PhyB (Soybean phyB Gene) – Wu FQ (CAAS07F) [PDF]
- P53 ( Tumor Protein 53) – Shen Y (CAAS07F) [PDF]
- GP120 (HIV glycoprotein 120) – ma JN (CAAS08s) [PDF]
- EIN (Ethylene Insensitive Proteins) – He WR (PKU08S1) [PDF]
- NG (Neurogenin) – Liamg W (PKU08S1) [PDF]
- OPHC2 (Organophosphorus Hydrolase precursor) – Lu H (CAAS08S) [PDF]
- R-Gene (Potato R gene) – Qu D (CAAS08S) [PDF]
- PEAT1 (Protein Elicitor from Alternaria Tenuissima) – Yin FS (CAAS08S) [PDF]
- GCR2 (G protein coupled receptor in plants) – Liu BC (PKU09S2) [PDF]
- T2R (Bitter taste receptor) – Xiong MY (PKU13S) [PDF]
All the PDF file of the above talks can be downloaded freely for teaching. The copyright belongs to the original authors.