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Topics in Computational Biology (COSI 230a) Pengyu Hong 09/02/2005 Background As high-throughput methods for biological data generation become more prominent and the amount and complexity of the data increase, computational methods have become essential to biological research in this post-genome age. Background High-throughput methods … Transcriptional profiling cDNA arrays Simultaneously monitor the transcriptional activities of tens of thousands of genes. Oligonucleotide arrays • Functions of gene • Relationships between gene-products • …… • New drugs • Personalized medicine • …… Background High-throughput methods … Transcriptional profiling High-Content Screening 104 images in one experiment Background High-throughput methods … Transcriptional profiling High-Content Screening Statistical Machine Learning Score histogram of phenotype images Score histogram of wildtype images Background High-throughput methods … Transcriptional profiling High-Content Screening …… Publications PubMed: 15+ million bibliographic citations and abstracts Background In turn, biological problems are motivating innovations in computational sciences, such as computer science, information science, mathematics, and statistics. Background Complex biological systems need novel computational methods … Stimuli S1 K S2 S3 P1 K2 1 Signal transduction networks K3 P3 Transcriptional regulatory networks Cellular phenotypes P2 K4 K5 Gene group 3 Gene group 1 Gene group 2 Gene group 4 Background Complex biological systems need novel computational methods … Stimuli S1 K S2 S3 P1 K2 Spatial 1 Signal transduction networks K3 P3 Transcriptional regulatory networks Cellular phenotypes P2 K4 Temporal K5 Gene group 3 Gene group 1 Gene group 2 Gene group 4 Background Large scale data needs novel information systems Local Data Local Data SOAP APIs Functions Functions UBIC2 Unit A Remote biological databases LocusLink RGD HGNC MGI UCSC …… UBIC2 Unit B Ubiquitous bio-information computing (UBIC2) • Integrate heterogeneous data Background Novel Human-computer interfaces (e.g., visualization, multimodal interaction techniques, and context-aware learning functions.) are needed to help biologists efficiently navigate through the complicated landscape of biomedical information and effectively manipulate various computational tools. • Collect information while surfing the Internet. • Manage multimedia biological information (text, PDF, images, sequences, etc.) GeneNotes • Functional based literature search (about to release this year). Background There is high demand for scientists who are capable of bridging these disciplines. Trend Shallow biology + Shallow computing Shallow biology + Deep computing or Deep biology + shallow computing Deep biology + Deep computing Background High demand for interdisciplinary scientists who are capable of speaking multiple “languages”. Design experiment s Analyze data Generate biologically meaningful computational results. Carry out experiment s Generate informative experimental data. Background High demand for interdisciplinary scientists who are capable of speaking multiple “languages”. Design experiment s Analyze data Generate biologically meaningful computational results. Carry out experiment s Generate informative experimental data. Background High demand for interdisciplinary scientists who are capable of speaking multiple “languages”. Goal: Customize cDNA arrays to measure the temporal transcriptional profiles of a set of genes Design experiment s Analyze data Carry out experiments Genes besides those of interest? Computational tools? How to choose time point for sampling? Background High demand for interdisciplinary scientists who are capable of speaking multiple “languages”. Design experiment s Analyze data Goal: Use a 384 well plate to test the effects of various treatments on cells. Carry out experiments Duplicates? Treatment arrangement? Base line? Goal Create an environment Transcends traditional departmental boundaries Facilitates communications between researchers from life sciences and computational sciences. Goal Learn knowledge (bio + comp) specific to a set of problems. • Regulatory motif finding • Microarray data analysis • Biomedical literature mining • Signal transduction network modeling • Cis-regulatory network discovery • …… Goal Acquire skills Initiate interdisciplinary collaborations (choose research partners) Establish long-term win-win collaborations. Key: Seek first to understand, then to be understood. (Stephen R. Covey) Main Themes Presentation Term Project Main Themes Presentation Materials: Your own work or other people’s published results Your own work: This is a good opportunity for you to attract collaborators. Published papers: Suggest to choose one and search for related ones. 60 Minutes followed by questions and discussions Written report after presentation Main Themes Presentation Materials: Your own work or other people’s published results 60 minutes presentation followed by questions and discussions Written report after presentation Main Themes Presentation Materials: Your own work or other people’s published results 60 minutes presentations followed by questions and discussions Written report after presentation Background of the research Motivation for the research Approach Results Criticisms and/or suggestions for improvement. Main Themes Term project Decide by mid-term Due on 12/22 mid-night. Evaluation Grading will be based on class participation and on the project. Evaluation Grading will be based on class participation and on the project. Teamwork is strongly encouraged !!! Indicate the contribution of each individual. Questions? Prepare your presentation. Choose a right project. …… Me at: Office hour Tue & Fri 4:30-5:30pm. Office Volen 135 Email: [email protected]. Please fill the form and return it to me now. Thanks