9 Future Challenges for Bioinformatics Adapted from an article by: E. Birney, C. Burge, and J. Fickett, Genome Technology, issue 17, Jan. 2002

9 Future Challenges for Bioinformatics #1: Precise model of transcription initiation and termination: ability to predict where, when, and at what rate transcription will occur

Endo16 Regulatory Network

9 Future Challenges for Bioinformatics #2: Precise model of RNA splicing: ability to predict the splicing pattern of any primary transcript in any tissue

9 Future Challenges for Bioinformatics #3: Precise model of signal transduction pathways: ability to predict cellular responses to external stimuli

EGF Recepter Signaling Pathway

9 Future Challenges for Bioinformatics #4: Precise model for the following binding interactions: protein-DNA protein-RNA protein-protein RNA-RNA

Zinc Finger – DNA Binding

9 Future Challenges for Bioinformatics #5: Accurate ab initio RNA structure prediction

SARS s2m RNA

9 Future Challenges for Bioinformatics #6: Accurate ab initio protein structure prediction

Structure of β-amylase

9 Future Challenges for Bioinformatics #7: Rational design of small molecule inhibitors of proteins

Fasciculin Docked with AChE

9 Future Challenges for Bioinformatics #8: Development of gene ontologies: systematic ways to describe and predict the functions of any gene or protein

9 Future Challenges for Bioinformatics #9: Precise model of evolution: understanding exactly how biological sequences evolve

HERV-K Retrovirus Insertions

Other Challenges Development: how do cells specialize? Speciation: what is the mechanism? Disease models: diagnosis, prognosis, treatment Drug design: discovery, validation, development Individualized medicine

Relevant Math. & Comp. Sci. Probability and statistics Combinatorics Information theory Mathematical modeling Algorithm design and analysis Databases Machine learning Text mining, natural language processing Image processing User interfaces