Kris Gunsalus

Kris Gunsalus

Assistant Professor of Biology
Ph.D. 1997 (Section of Genetics and Development), Cornell University; B.A. 1984 (Chemistry and Biology), Cornell University.

Office Address:
New York University
Center for Genomics and Systems Biology
Department of Biology
1009 Silver Center
100 Washington Square East
New York, NY 10003-6688

Email:
Phone: (212) 998-8236
Fax: (212) 995-4015
List of Publications from Pubmed

Research

With the advent of the "post-genomics era" a major new challenge has arisen in how to extract meaningful biology from large heterogeneous data sets. Our laboratory is interested in the analysis of diverse functional genomics data to identify groups of genes that work in specific cellular and developmental processes, focusing primarily on C. elegans. For example, we have used an integrative approach to characterize gene networks that function in C. elegans early embryogenesis, based on data from different kinds of functional genomics projects such as protein-protein interactions, gene expression profiles, and phenotypic maps (Fig. 1).


Figure 1. C. elegans gene networks in early embryogenesis. (a) A composite view of around 30,000 functional linkages between 661 C. elegans genes with phenotypes in the early embryo, based on protein-protein interactions (Int), phenotypic similarity based on a signature of 45 early embryonic phenotypic characters (Ph), and gene co-expression in a compendium of gene expression data (Tr). (b) When the network is filtered for high-confidence functional links between genes (supported by two or more types of functional genomic data, e.g. phenotypic correlation and protein-protein interaction), a modular organization of molecular machinery is revealed, in which groups of highly interconnected genes are linked to each other via a small number of functional interactions. Adapted from Gunsalus et al., Nature 2005.

We are using this kind of approach both to help interpret large-scale datasets and to generate testable hypotheses on gene function. We are applying these analyses in different systems in collaboration with other NYU Biology faculty, including C. elegans early embryogenesis (with Dr. Fabio Piano), C. elegans microRNA-target relationships (with Dr. Piano and Dr. Nikolaus Rajewsky) and C. elegans gonadogenesis (with Dr. Jane Hubbard).

As part of these projects we develop web-based tools and graphical interfaces to provide the research community at large with enhanced access to and mining capabilities for functional genomic data. To facilitate a systems-level view of gene networks, we have developed a web-based network visualization tool called "N-Browse" (http://www.gnetbrowse.org) that allows researchers to browse gene neighborhoods and functional relationships in a modular way based on these integrated data. We have also developed a web-accessible database of RNA interference (RNAi) phenotypes in C. elegans, "RNAiDB" (http://www.rnai.org), which we use both to distribute data from large-scale RNAi studies and as an online notebook for ongoing high-content phenotypic analysis. In conjunction with this work, we are developing strategies to make phenotypic data more amenable to computational analysis and are developing tools to mine these data.

Web Resources:

Job Opportunity:

An experienced Programmer/Software Engineer with expertise in Java and familiarity with relational databases is needed to join a growing team in the Gunsalus lab. The position is for lead developer of an open-source web-based network visualization tool for navigating biological interaction data, N-Browse (www.gnetbrowse.org). Development tasks will involve Java programming (incl. JSP, Swing) with database and server infrastructure design/implementation. Some familiarity with molecular biology/bioinformatics is a plus but not required. The work environment is a friendly and dynamic university research center operating on an open-lab model that combines experimental and computational approaches to functional genomics/systems biology. NYU's Center for Comparative Functional Genomics is located in state-of-the-art space on Washington Square in Greenwich Village. Salary will be commensurate with experience. Contact Dr. Kris Gunsalus (kcg1-at-nyu.edu) with a letter of intent, resume, and three references. NYU is an equal opportunity employer.

Areas of Research/Interest

Genome informatics and functional genomics of C. elegans.

Fellowships/Honors

National Academies Education Fellow in the Life Sciences, NSF ADVANCE Fellows Award, W.M. Keck Foundation Fellowship in Biology

Publications