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
» Schatz promoted to assoicate professor of quantitative biology
Sept 30, 2014
» Accurate de novo and transmitted indel detection in exome-capture data using microassembly [Press Release]
Aug 17, 2014
» Lecture notes from our undergraduate research program in bioinformatics
Aug 14, 2014
» 101 questions with a bioinformatician @ ACGT
Aug 7, 2014
» CSHL quantitative biologist Michael Schatz wins prestigious NSF Early CAREER Award
July 30, 2014
(past news)

Upcoming Events

» Beyond the Genome
Boston, MA. Oct 8 - 10, 2014
» RECOMB Comparative Genomics
CSHL, Cold Spring Harbor NY. Oct 19 - 22, 2014
» Biological Data Science
CSHL, Cold Spring Harbor, NY. Nov 5 - 8, 2014
» CSHL Advanced Sequencing Technology & Applications
CSHL, Cold Spring Harbor, NY. Nov 11 - 23, 2014
» Personal Genomes & Pharmacogenomics
CSHL, Cold Spring Harbor NY. Nov 12 - 15, 2014
» 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
(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