Tentative Term Presentation Topics:

1)  Comparative genomics and applications      
    David Gonzalez and Yuwei Zhang, 5/21, talk 3
2)  Metagenomics and comparative metagenomics
3)  Gene regulatory networks and modules
    Deepak Reddy and Rahul Yenduri, 6/4, talk 3
4)  Computational approaches for functional genomics  
    Pedram Zaree and Chao Wu, 6/6, talk 1
5)  RNA secondary structure prediction
    Varun Narayanan and Nithya Thushara Krishna Pothula, 5/23, talk 3
6)  Small RNAs, microRNAs and other noncoding RNAs   
7)  Protein secondary structure determination   
    Sreekar Praneeth Marri and Venkata Ranga Sai Vishal Matcha, 5/23, talk 1 
8)  Protein tertiary structure determination (or protein folding), 
    especially recent breakthroughs including AlphaFold/RoseTTAFold  
    Chaitanya Ananda and Erfan Shayegani, 6/4, talk 1
9)  Protein-protein (or protein-drug) interactions   
    Ajay Virupaksha, 6/10, talk 5
10) Peptide sequencing/identification by mass spec
    Xinyu Zhang and Xingyan Zhou, 6/4, 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
    Ravi Theja Tangirala and Bhargavi Rengarajan, 5/23, talk 2
15) Genetic drug discovery and combinatorial chemistry  
16) Drug repositioning and repurposing with applications in COVID-19
    Neeha Gajula and Nikhil Mahendrakar, 5/28, talk 1
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
    Joseph Rodriguez and David Stratham, 6/10, talk 1
19) Genome assembly from NGS short reads, de Bruijn graphs
    Edgar Melendrez and Tyler Pastor, 5/30, talk 1
20) Transcriptome assembly and abundance quantification
    Huy Tran and Weihang Kuang, 5/28, talk 3
21) Computational challenges in epigenomics    
    Jordan Peck and Bowen Qi, 6/6, talk 3
22) Computational prediction of chromosomal structures using Hi-C, ChIA-PET, etc
23) Single cell technologies (sequencing, gene expression, etc) and data analysis
    Rohith Reddy K and Ravi Teja N, 6/6, talk 2
24) Spatial (or 4D) genomics
    Bo Huang and Jordan Chan, 5/30, talk 3
25) Integration of multi-omics data
     Fengchun Fan and Yusen Zhang, 5/21, talk 2
26) The ENCODE project and its key findings/data
    Sun Hye Baek and Viha B Raju, 6/10, talk 3
27) Analysis of medical (such as CT, MRI, X-ray, etc.) images
    Vasanthakumar Shanmugavadivel and Sruthi Suresh, 5/28, talk 2
28) Genomics and human health, immunotherapy, etc.
    Vishal Rohith Chinnam and Aswini Shilpha S S, 5/30, talk 2
29) Evolution of viruses (e.g., SARS-CoV-2)
    Akhila Gudumani and Yuktha Polepalli, 6/10, talk 2
30) A deeper treatment of some topic covered in class such as the complexity 
    of PDP, gene/exon prediction, sequence assembly, phylogenies, etc.   
31) An interesting extension/observation/revision on some technical
    result discussed in class or the textbooks
32) A comparison between combinatorial and statistical approaches for
    solving the same problem   
    Aaryan Bhagat and Sakthi Kumar Sampath Kumar, 6/10, talk 4
33) Other interesting topics that I have missed in the above, e.g.
    suffix arrays, BW/FM transformations, etc.


Each topic will be presented by a team of two students. 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 team should prepare to read 3 to 5 papers, speak for about 20 minutes 
and answer questions for about 4 minutes at the end of the presentation. 

The presentations will begin on Tuesday May 21 and end on Monday June 10.
We can accommodate three teams in a regular lecture and up to 7 teams in the
final exam slot. Please let me know your team members, selection of the topic 
and the date you'd prefer to present 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.