Tentative Term Presentation Topics:

1)  Comparative genomics and applications      
2)  Metagenomics and comparative metagenomics
3)  Gene regulatory networks and modules
4)  Computational approaches for functional genomics  
5)  RNA secondary structure prediction
6)  Small RNAs, microRNAs and other noncoding RNAs   
7)  Protein secondary structure determination   
8)  Protein tertiary structure determination (or protein folding), 
    especially recent breakthroughs including AlphaFold/RoseTTAFold/ESMFold
    Kenny Thai, 5/28 talk 1
9)  Protein-protein (or protein-drug) interactions   
10) Peptide sequencing/identification by mass spec
11) Molecular dyanmics modeling and simulation  
    Nina Phatak, 6/2 talk 1
12) SNPs and haplotype inference  
13) Genome-wide association studies (GWAS)   
14) Disease gene prioritization based on networks of genes and diseases
15) Genetic drug discovery and combinatorial chemistry  
16) Drug repositioning and repurposing with applications in COVID-19
17) Representation, simulation, and inference of gene networks and pathways
18) Next generation resequencing (NGS) technologies (DNA-Seq, RNA-Seq, 
    ChIP-Seq, DNase-Seq, ATAC-Seq, SHAPE-Seq, CLIP-Seq, etc) on Illumina/Solexa, 
    454, SOLiD, SMRT, Nanopore, etc. platforms and their data analysis; 
    multiple non-overlapping talks are possible
19) Genome assembly from NGS short reads, de Bruijn graphs
20) Transcriptome assembly and abundance quantification
21) Computational challenges in epigenomics    
22) Computational prediction of chromosomal structures using Hi-C, ChIA-PET, etc
23) Spatial (or 4D) genomics
23) Single-cell spatial transcriptomics
25) Integration of multi-omics data
26) The ENCODE project and its key findings/datasets
    Neda Farahmandi, 5/26 talk 1
27) Analysis of medical (such as CT, MRI, X-ray, etc.) images
28) Genomics and human health, immunotherapy, etc.
29) Evolution of viruses (e.g., SARS-CoV-2)
30) Foundation models in biology and medicine such as AlphaGenome,
    Evo 2, scGPA, Geneformer, DNABERT, RNABERT, etc.
31) A deeper treatment of some topic covered in class such as the complexity 
    of PDP, gene/exon prediction, sequence assembly, phylogenies, etc;
    multiple non-overlapping talks are possible
32) An interesting extension/observation/revision on some technical
    result discussed in class or the textbooks
33) A comparison between combinatorial and statistical approaches for
    solving the same problem   
34) Other interesting topics that I have missed in the above, e.g.
    applications of well-known data structures, algorithmic techniques and
    ML/DL models such as suffix trees/arrays, BW/FM transformations, etc.
    in computational biology;
    multiple non-overlapping talks are possible


Each topic will be presented by a student. Ideally, a presentation should 
begin with (1) the biological background, (2) an overview of computational 
problems, (3) a survey of algorithmic approaches for solving the problems, 
and then (4) some discussion of one or two of the approaches in more depth. 
Every student should prepare to read 3 to 5 papers, speak for about 22 minutes 
and answer questions for about 3 minutes at the end of the presentation. 

The presentations will take place from Thursday May 21 to Thursday June 4
during the regular lecture hours. We can accommodate three speakers in 
a lecture. Please let me know your preferred presentation topic and date ASAP. 
Remember that the earlier you choose, the more choices you will have :-) 

Note that you are supposed to create your own slides for the presentation, but 
if you have to borrow some material from somewhere (e.g., figures, tables, or 
sometimes entire slides), you must cite the sources (including AI) explicitly.