Welcome

Our main research interest is in understanding the structure and function of genomes, especially those of medical or agricultural importance. The core strength of our research is in developing novel algorithms and computational systems for large-scale biological sequence analysis, including leading algorithms for de novo genome assembly, variant detection, and related –omics assays. Using these advances we have contributed to the de novo genome assemblies of dozens of species; probed the sequence variations related to autism, cancer, and other human diseases; mapped the transcriptional and epigenetic profiles of tomatoes, corn, and other important plant species; and explored the role of microbes in different environments. In response to the deluge of biological sequence data we are now facing, we have also been at the forefront of distributed and parallel computing in genomics, and have pioneered the use of cloud computing and Hadoop/MapReduce as an enabling platform to address the big data challenges we are all facing.

Looking forward, we see ourselves at the intersection of biotechnology and algorithmics, developing systems for probing the structure and function of genomes using the best technologies possible. Our expertise spans from low level computer architecture, through sequencing, de novo assembly, variant identification, transcriptome & other -omics data and up to machine learning approaches to build predictive models of diseases and treatment response. In addition to ongoing projects in autism & other human diseases, and developmental plant biology, last summer I was granted an NSF CAREER award to research new approaches for analyzing single molecule sequencing, especially for genome and transcriptome analysis of crop species. Another recent thrust has been to develop algorithms for single cell analysis, especially to use copy number variations within individual tumor cells to examine how cancer progresses. Altogether, we intend to develop powerful new methods for analyzing large collections of genomes to address questions of disease, development, and evolution.

Recent News
» Whole genome assemblies of 3 divergent strains of rice used to discover their novel genes
Dec 3, 2014
» Lecture Notes from the Advanced Sequencing Course
Nov 22, 2014
» SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips
Nov 14, 2014
» The contribution of de novo coding mutations to autism spectrum disorder
Oct 29, 2014
» Reducing INDEL calling errors in whole-genome and exome sequencing data
Oct 27, 2014
(past news)

Upcoming Events

» Plant and Animal Genome XXIII (PAG)
San Diego CA. Jan 10 - 14, 2015
» Advances in Genome Biology and Technology (AGBT)
Marco Island FL. Feb 25 - 28, 2015
» Future of Long Read Assembly
University of Minnesota. St. Paul, MN, April 9-10, 2015
» The Biology of Genomes
CSHL, Cold Spring Harbor NY. May 5 - 9, 2015
» NYU Genomics and Systems Biology Symposium
CSHL. May 22, 2015
» Probabilistic Modeling in Genomics
CSHL. Oct 14-17, 2015
» Genome Informatics
CSHL. Oct 28-31, 2015
~~ 2016 ~~

» Biological Data Science
CSHL. Oct 26-29, 2016
(presentation archive)



Michael Schatz
Cold Spring Harbor Laboratory
One Bungtown Road
Koch Building 1119
Cold Spring Harbor, NY 11724

Tel: (516) 367-5218
Cel: (703) 966-1987
Fax: (516) 367-8380
E-mail: mschatz <at> cshl.edu
Twitter: @mike_schatz