Oct 9, 2006: Genome Assembly after the Human Genome
Filed in: Colloquium
Dr. Mihai Pop, University of Maryland at College Park
The success of the human genome project is in no small part due to computer programs, called assemblers, that were used to reconstruct the three billion letters representing our genetic make-up from the small pieces of DNA (usually shorter than one thousand letters) produced by automated sequencing machines. While the human genome is now complete, numerous other genomes remain to be sequenced, providing new challenges to genome assembly algorithms. I will describe some of our recent results and ongoing research projects in the area of genome assembly and provide an overview of the modular assembly package AMOS developed within our group.
Dr. Mihai Pop did his undergraduate studies at the Politechnica University in Bucharest, Romania. He then joined the graduate program in Computer Science at Johns Hopkins University where he obtained his Ph.D. in 2000. His thesis work concentrated on multi-dimensional data-structures and computer graphics applications. Soon after graduation he commenced a career in bioinformatics at The Institute for Genomic Research (TIGR). At TIGR Dr. Pop developed an expertise in genome sequence assembly and was actively involved in many genome projects, including several organisms of great importance to human health, such as Bacillus anthracis, Streptococcus pneumoniae, and Trypanosoma cruzi. He is also the author of several open-source software packages: the scaffolding package Bambus, and the modular genome assembly and analysis package AMOS. Currently, Dr. Pop is an Assistant Professor in Computer Science at the University of Maryland and is affiliated with the Center for Bioinformatics and Computational Biology at the University of Maryland Institute for Advanced Computer Studies.
Abstract
The success of the human genome project is in no small part due to computer programs, called assemblers, that were used to reconstruct the three billion letters representing our genetic make-up from the small pieces of DNA (usually shorter than one thousand letters) produced by automated sequencing machines. While the human genome is now complete, numerous other genomes remain to be sequenced, providing new challenges to genome assembly algorithms. I will describe some of our recent results and ongoing research projects in the area of genome assembly and provide an overview of the modular assembly package AMOS developed within our group.
Bio
Dr. Mihai Pop did his undergraduate studies at the Politechnica University in Bucharest, Romania. He then joined the graduate program in Computer Science at Johns Hopkins University where he obtained his Ph.D. in 2000. His thesis work concentrated on multi-dimensional data-structures and computer graphics applications. Soon after graduation he commenced a career in bioinformatics at The Institute for Genomic Research (TIGR). At TIGR Dr. Pop developed an expertise in genome sequence assembly and was actively involved in many genome projects, including several organisms of great importance to human health, such as Bacillus anthracis, Streptococcus pneumoniae, and Trypanosoma cruzi. He is also the author of several open-source software packages: the scaffolding package Bambus, and the modular genome assembly and analysis package AMOS. Currently, Dr. Pop is an Assistant Professor in Computer Science at the University of Maryland and is affiliated with the Center for Bioinformatics and Computational Biology at the University of Maryland Institute for Advanced Computer Studies.