NIPM Seminar - Genome Assembly and Comparison: Algorithmic Challenges and Applications in Psychiatric Disorders


Mar. 11, 2016, 1pm to 2pm

Office/Remote Location

Auditorium, Room 197


The Nevada Institute of Personalized Medicine and the School of Life Sciences invites you to attend a seminar with Dr. Pham from Salk Institute.

Dr. Pham studies the molecular and cellular mechanisms of schizophrenia, autism spectrum disorder, and bipolar disorder via the induced pluripotent stem cell (iPSC) approach and deep sequencing data (whole genome and transcriptome sequencing). Also understanding the cellular and molecular mechanisms that gives rise to the disease is therefore a crucial step in developing new drug targets and treatments.

Abstract: The rapid development of algorithms and sequencing technologies opens new opportunities for biological studies and medical applications, but at the same time yields many computational challenges. Assembling complex genomes into full-length chromosomes arguably is among the most challenging problems in bioinformatics. In the first part of the talk, I will cover important de Bruijn and breakpoint graph-based algorithms for single cell genome assembly and comparative genomics, including three new variations of de Bruijn graphs that have been used in modern single cell assemblers (SPAdes), and the recent developments of Ragout2: a rearrangement-based algorithm for finishing mammalian genomes. The availability of Ragout2 paves the way to potentially complete thousands of draft assemblies in the G10K project. In the second part of the talk, I will discuss the application of transcriptome and genome analysis in iPSC models to study psychiatric diseases, including bipolar and schizophrenia disorders, and demonstrate its potential in developing new therapies and drugs. Finally, I will present BioTuring, a cloud-based platform that combines in-memory/parallel computing, bioinformatics algorithms, deep learning, and natural language processing to allow biologists interact in real-time with transcriptome data using ordinary English. BioTuring will open a new and efficient way to explore high-throughput sequencing data and will help to bridge the gap between computer science and biology.

Admission Information

This event is free and open to the public.

Contact Information

Leslie Rafalovich

External Sponsor

Nevada Institute of Personalized Medicine / School of Life Sciences