Genes, Genomes and Variation

Mentors: Student: Praduman Goyal

<p>The project aims to deliver a responsive web-based analytics dashboard, integrated to an in-house catalogue of circRNAs identified from multiple species with the functionalities like searching on the basis of genome coordinates and host gene names, a visual representation of inferred circRNA structure, comparing isoforms across different samples that would be linked to Ensembl genome browser.</p>

Mentors: Student: Harshit Gupta-1

<p>Homology refers to the shared ancestry between a pair of structures, organisms or genes, in different taxa. Currently, homology types are decided on the basis of phylogenetic trees. They are later checked, for quality-control measures, by a whole genome-alignment score. The aim of this project is to use the methods of Deep Learning to predict the homology calls and check the homologies predicted by the above methods.</p>

Mentors: Student: Srijan Verma

<p>Advances in RNA sequencing technologies have revealed the complexity of our genome. Long non-coding RNAs (lncRNAs) make up the majority of the non-coding transcriptome. Understanding the significance of this RNA world is one of the most important challenges faced in biology today, and the lncRNAs within it represent a gold mine of potential new biomarkers and drug targets. Its discovery is still at a preliminary stage. To date, very few lncRNAs have been characterized in detail. However, it is clear that lncRNAs are important regulators of gene expression, and lncRNAs are thought to have a wide range of functions in cellular and developmental processes. There are many specialized lncRNA databases (like RefSeq, GENCODE, Ensembl, SGD, tair). We will use Machine Learning techniques to highlight and compare two sets of calls (of Ensembl / GENCODE and RefSeq) and determine which calls are incorrect. Goal of the Project: Implement a machine learning model (a 2nd pass filter) which will predict / validate credible calls (true positive/false positive cases) produced by RefSeq and GENCODE (or Ensembl).</p>

Mentors: Student: Tony Yang

<p>Develop an automated system that performs analyses on newly sequenced genomes.</p>

Mentors: Student: Nabil Ibtehaz

<p>In Comparative Genomics we compare an unknown gene with some other known genes, for better inference of biological properties of that unknown gene. Identification of Gene Orthology Relation is the most important task of Comparative Genomics, as they tend to preserve similar molecular and biological functions. Thus if we can establish orthology relationships between two genes, we can obtain valuable evolutionary history of the two genes. However, with advanced sequencing depth and expansion in transcriptome data, genes are no longer the proper units for interrogation in functional conservation, evolutionary events, and expressional patterns, especially in the field of alternative splicing. As the accumulation of transcriptomic data, alternative splicing is taken into account in the assignments of gene orthologs and the orthology is suggested to be further considered at transcript level. Whether gene or transcript orthology, exons are the basic units that represent the whole gene structure; however, there is not much reported study on how to build exon level orthology in a whole genome scale. Therefore, it is essential to establish a transcription oriented gene orthology algorithm.</p>