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
    Tejas Machkar, 5/27, talk 2
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  
    Fatima Nawmi, 5/22, talk 1
9)  Protein-protein (or protein-drug) interactions   
10) Peptide sequencing/identification by mass spec
    Yourae Shin, 5/22, talk 2
11) Molecular dyanmics modeling and simulation  
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  
    Ahmad Mersaghian, 5/27, talk 1
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
    Kwok Ho Hanson, ?
19) Genome assembly from NGS short reads, de Bruijn graphs
    Krishna Priya K M, 6/3, talk 3
20) Transcriptome assembly and abundance quantification
21) Computational challenges in epigenomics    
22) Computational prediction of chromosomal structures using Hi-C, ChIA-PET, etc
    Jinli Zhang, 5/27, talk 3
23) Single cell technologies (sequencing, gene expression, etc) and data analysis
24) Spatial (or 4D) genomics
25) Integration of multi-omics data
    Pratyay Dutta, 5/22, talk 3
26) The ENCODE project and its key findings/data
27) Analysis of medical (such as CT, MRI, X-ray, etc.) images
    Brian Chen, 5/29, talk 3
28) Genomics and human health, immunotherapy, etc.
29) Evolution of viruses (e.g., SARS-CoV-2)
    Alvin Hoang, 5/29, talk 1
30) A deeper treatment of some topic covered in class such as the complexity 
    of PDP, gene/exon prediction, sequence assembly, phylogenies, etc.   
    G M Shahariar (Phylogenetic Species Tree Estimation from Gene Trees), 6/3, talk 1
31) An interesting extension/observation/revision on some technical
    result discussed in class or the textbooks
    Sunny Atalig (Distance measures in comp biol and their complexity?), 6/3, talk 2
32) A comparison between combinatorial and statistical approaches for
    solving the same problem   
33) 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, LLMs, etc.
    in computational biology;
    multiple non-overlapping talks are possible
    Zabir Al Nazi (Genomic sequence modeling with Transformers and 
       Genomic Language Models (gLMs), 5/29, talk 2
    Niki Nezakati (Generative Models for DNA Sequence Design), date?


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 20 minutes 
and answer questions for about 3 minutes at the end of the presentation. 

The presentations will take place from Tuesday May 20 to Thursday June 5
during the regular lecture hours and end on Thursday June 12 at 11:30 - 12:30pm
during the scheduled final exam slot. We can accommodate three speakers in 
a lecture and at most two speakers in the final exam slot. 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 explicitly.