Talk:National Center for Genome Resources

Jeffrey Blanchard Assistant Professor

Phone: 413-577-2130 Fax: 413-545-1578 Email: blanchard@microbio.umass.edu Mailing address

Ph.D.: Botany, University of Georgia

Lab Group Home Page

Microbial cellular and community networks; influence of environmental change on the evolution of molecular processes; systems biology; bioinformatics We use systems-level approaches to understand bacterial stress response networks related to host-pathogen interactions and the influence of global climate change on populations of marine cyanobacteria and communities of bacteria. Our research program is characterized by a synergistic integration of computation, experiment and theory and we welcome new people from different academic disciplines. There are three fundamental aspects of our research; (1) Effectively utilize genomic data from different sources to discover functions for genes and proteins. (2) Uncover rules governing and constraining biological systems. (3) Enable predictive models of biological systems that incorporate biochemical and genetic data. Here are some of our project areas for systems research.

The effects of global climate change on populations of marine cyanobacteria

Global climate change is an international problem that already is impacting the evolutionary trajectory of our planet's biota. In spite of the widely appreciated magnitude of this problem, we still have a limited ability to estimate current and long-term biological effects. As the most numerically dominant species in the ocean, Prochlorococcus has become a central object of study for understanding carbon fixation by photosynthetic organisms. Prochlorococcus is very unusual for a free living organism in that it show signs of reductive genome evolution that are typically found in organelles, endosymbionts and pathogens (see Blanchard et al. 2000) and now has a minimal transcriptional regulator network for sensing environmental change. The long-term goal of our research is to integrate large-scale “genomic” data sets into probabilistic models that allow inferences and decisions regarding the trajectory of photosynthetic organisms in a changing global climate. Towards this goal we are working on;

• Integrating genome sequence and expression microarray data into models that allow us to identify process and subnetworks subject to different selective pressures related to changes in ocean chemistry. • Developing and applying statistical methods to identify regulatory motifs and their relative binding strength in sequence data using a combination of microarray and sequence data (In collaboration with Erin Conlon).

Stress response networks in enteric bacteria (In collaboration with Pablo Pomposiello)

Signals initiated by diverse factors involved in host pathogen interactions, including antibiotics and nitric oxide, are funneled by three dissimilar sensor transcriptional regulators (SoxR, MarR and RamR) to three homologous transcriptional activators (SoxS, MarA and RamA) to regulate a similar but not completely overlapping set of genes coding for key metabolic control points and defense mechanisms. This unusual regulatory circuit design was assembled fairly recently in the ancestor of Escherichia, Salmonella and Klebsiella and soxS, marA and ramA are derived from duplications events that occurred around this time. Because, these transcriptional activators historically bound the same set of genes we are using comparative experimental and computational approaches for determining the regulatory network structure and creating models that describe the response of the bacteria to host and other environmental factors.

Microbial environmental and community genomics

Most microbes are currently impossible to grow in the laboratory. New approaches are being developed to sequence genomes of microbes straight from environmental samples obviating the need to first culture microbes. One spectacular application of this evolving technology was to a microbial community in the Sargasso Sea (Venter et al. 2004). The published data set included at least 1800 bacterial species many which have not been previously described. Fortunately for us there is also a lot of sequence data on marine cyanobacteria, particularly Prochlorococcus marinus. We have developed a new method for separating genomes from cocultures of bacteria (in collaboration with Derek Lovely) and are applying the methods to the Sargasso Sea and other environmental sequencing data sets. We are also interested in developing methods that utilize variation in DNA sequences to understand microbial population dynamics and methods for building a conceptual model of the interactions among various members of these communities. Selected Publications Blanchard JL (2004) Bioinformatics and Systems Biology, rapidly evolving tools for interpreting plant response to global change. Field Crops Research. 90:117-131.

De Visser AJM, Hermisson J, Wagner, GP, Ancel LW, Bagheri-Chaichian H, Blanchard JL, Chao L, Cheverud JM, Elena SF, Fontana W, Gibson G, Hansen TF, Krakauer D, Lewontin RC, Ofria C, Rice SH, von Dassow G, Wagner A, Whitlock MC (2003) Perspective: Evolution and detection of genetic robustness. Evolution. 57:1959-1972.

Kuffner RM, Gonzales M, Steadman P, Wlodek DK, Jankowitz RJ, Boinoff JR, Montoya AL, Peterson TF, Bulmore DL, Blanchard JL (2002) PathDB. Nucleic Acids Research Database Issue.

Brinkman FSL, Blanchard JL, Greberg H, Wan I, De Koning A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BF, Keeling P, Hancock REW, Rose AM, SJM Jones (2002) Plant-like genes in Chlamydia species reflect Chlamydia's ancestral relationship with cyanobacteria and the chloroplast. Genome Research. 12 :1159-67

Blanchard JL, Lynch M (2000) Why do organellar genes end up in the nucleus? Trends in Genetics. 16 :315-320.

De Visser AJM, Zeyl CW, Gerrish PJ, Blanchard JL, Lenski RE (1999) Diminishing returns from mutation supply rate in asexual populations. Science. 283 :404-406.

Lynch M, Blanchard JL, Houle D, Kibota T, Schultz S, Vassileva L, Willis J (1999) Spontaneous deleterious mutation. Evolution. 53 :645-663.

Blanchard JL, Hicks JS (1999) The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage. Journal of Eukaryotic Microbiology. 46 :367-375.

Mailing Address Jeffrey Blanchard Department of Microbiology 203 Morrill Science Center IVN University of Massachusetts 639 North Pleasant Street Amherst, MA 01003

Department of Microbiology 203 Morrill Science Center IVN University of Massachusetts 639 North Pleasant Street Amherst, MA 01003

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NCGR :: About NCGR

"We are what we repeatedly do. Excellence, then, is not an act, but a habit. " -- Aristotle

STRATEGIC INTENT NCGR is a nonprofit life sciences research institute.

Our mission is to translate research at intersections between bioscience, computing and mathematics into improvements in infectious disease, global health, and nutrition.

Our objectives are improved diagnosis, control and cure of infectious disease, and better nutrition and food safety.

Our approach is the development of innovative computational solutions using: Integrated informatics, Inferential statistics, and Complex Networks Analysis. RESEARCH TOPICS Through our research programs, NCGR develops technologies that help scientists comprehend biological data. People around the world can benefit from our research programs through improved food crops, a cleaner environment, and better medical treatments.

Scientists who use our programs or collaborate with us choose NCGR because we provide unique opportunities for understanding data.

GENETIC VARIABILITY

The Center's research programs focus on understanding the dynamics of infectious diseases and genetic variability on human health by using our expertise in biological research and information technologies. NCGR's core interests include expertise in simulation modeling, population genetics, quantitative genetics, biological networks, and information systems integration.

BIOINFORMATICS

The Bioinformatics Program at NCGR is devoted to the development of computer software products that provide scientists with resources for addressing issues of biological importance. Some of the projects currently under development within the Bioinformatics Program include The Arabidopsis Information Resource (TAIR) and the Model Plants Initiative (MPI).

COMPUTATIONAL SYSTEMS BIOLOGY

Computational Systems Biology focuses on the bioinformatic application and development of computational techniques from a systems biology perspective. This paradigm involves the use of computers and associated databases and algorithms to build explanatory and predictive models for biological systems from the molecular to the ecosystem level.

BIOLOGICAL PATHWAY RECONSTRUCTION

In living cells, biological pathways are integrated to form intricate regulatory networks that respond and adapt to changing environments. We have learned basic statistical properties that explain the robustness and resistance to random perturbation of individual components of networks, but the underlying principles of network evolution and extensibility have not been revealed.

With the accelerated accumulation of various molecular data, we can start to address these questions. One particular example of a regulatory network is the apoptotic machinery that is fundamental to the development, maintenance, and survival of multi-cellular organisms. We are dissecting the building blocks of this regulatory network from genomics to proteomics to further understand its cellular regulation.

GENE EXPRESSION INTERPRETATION

A cell has thousands of genes. At any instance, some of these genes are used to produce proteins while others lie quiescent. As a cell grows, metabolizes, or responds to stimuli, different genes are used to make proteins in different proportions. By studying the process of cell growth scientists observe the conditions that foster the selection of genes.

Data generated from gene expression arrays allow scientists to measure gene regulation. Research at NCGR on gene expression focuses on many areas: developing a gene expression data management system with the incorporation, compatibility, exchangeability, and comparability of expression data from many different technologies into an integrated database; understanding the functions of hypothetical proteins; analyzing gene expression data using heterogeneous, synthesized, and distributed biological databases and resources; finding gene regulatory networks based on knowledge discovery and multistage optimization; and using molecular expression to diagnose diseases.

FROM GENOTYPE TO PHENOTYPE

To enable predictive system level models we need to better understand phenomenon related to cellular interactions including robustness, buffering, canalization and epistasis. The focus of NCGR's research is the "middle layer" of cellular networks that influences the translation of genotypes with relevant environmental parameters into phenotypes. Our goal is to encapsulate data related to the fundamental cellular building blocks of genes, proteins and metabolites into models that predict change in phenotypic tratis in response to environmental and genetic changes.

EVOLUTION OF RECOMBINATION

Virtually all organisms exchange their DNA with other organisms. This process, broadly known as recombination, occurs during the production of gametes, in a process known as meiosis, in plants and animals. This is of particular interest to scientists since uncontrolled cellular replication is the hallmark of cancer. NCGR research focuses on a bioinformatic reconstruction of the biochemical pathways involved in yeast DNA repair, meiosis, and replication, and links them to a theoretical population genetic understanding of the evolution of recombination and meiosis. By understanding how these pathways evolved and how they function, we are better able to understand the genes that are responsible for the body's response to DNA damage and its natural suppression of cancer. Conversely, the elucidation of these pathways yields answers on the evolution of the process of meiosis itself.

DATA INTEGRATION

NCGR'S Integrated System, ISYS™, is the result of our research into data and system integration. It is a software platform allowing integration of many tools that manage and analyze biological data. It provides an intuitive environment for investigators to explore data and detect relationships that they might not otherwise see. ISYS's strength is that it provides a way for tools that may have been developed completely separately from each other or ISYS to share data and operate interactively.

ANNUAL REPORT

The Annual Report is neither an offer to sell, nor a solicitation of an offer, on behalf of the National Center for Genome Resources (NCGR) or any associated organizations or companies. It is a formal declaration of our organization's financial performance in the preceding year and it expresses the scope of our mission and management philosophy.

NCGR Annual Report for 2003 (pdf)

Note: Free software to view & print PDF files is available at the Adobe Reader download page.

OUR HISTORY

With support from Senator Pete Domenici, NCGR was founded in 1994 as an independent non-profit institute for discovery-driven research in computational biology, medicine, and bioinformatics. The Center's mandate was to share and analyze genomic data and develop the Genome Sequence Data Base (GSDB) from technology transfer research on the human genome occurring at Los Alamos National Laboratory.

R&D CLUSTER - THE TECHNOLOGY RESEARCH CORRIDOR COLLABORATIVE

The New Mexico Technology Research Corridor Collaborative (TRC) is comprised of a variety of organizations across the various regions of New Mexico. Members range from research universities and institutes to national laboratories and technology accelerators. All have one thing in common: an interest in promoting technology and acting as a resource for both public and private sector entities. Utilizing the combined strength of member organizations, the individual efforts of each of the TRC member are combined and amplified, resulting in benefits to the community, research institutions, entrepreneurs, industry and investors.

LOCAL EVENTS

Santa Fe Institute Lectures and Colloquia (Santa Fe)

University of New Mexico Biology Departmental and Brown Bag Seminar Schedule (Albuquerque)

University of New Mexico Computer Science Colloquium Schedules (Albuquerque)

NCGR :: Management & Board of Directors

"It is not always what we know or analyzed before we make a decision that makes it a great decision. It is what we do after we make the decision to implement and execute it that makes it a good decision."--William Pollard

MANAGEMENT

Miguel Rios, Jr., Ph.D. Chairman of the Board, joined NCGR in 2001. Dr. Rios has served as a member of NCGR's Board of Directors since 1995.

Stephen F. Kingsmore, M.B., C.h.B., B.A.O. President & CEO, joined NCGR in 2004. Dr. Kingsmore has served as a member of NCGR's Board of Directors since 2004. ( email, bio )

Susan M. Baxter, Ph.D. Chief Operating Officer, joined NCGR in 2004. ( email, bio )

William D. Beavis, Ph.D. Chief Scientific Officer, joined NCGR in 1998. Dr. Beavis has served as a member of NCGR's Board of Directors since 2001. ( email, bio )

Damian D. Gessler, Ph.D. Program Lead, joined NCGR in 1999. ( email, bio )

Vickie Hall Director of Software Engineering, joined NCGR in 2003. ( email, bio )

John Utsey Systems Manager, joined NCGR in 1998. ( email )

BOARD OF DIRECTORS Donald Armstrong, M.D. Consultant, Infectious Disease Service Memorial Sloan-Kettering Cancer Center Professor of Medicine Cornell University Medical College

William D. Beavis, Ph.D. Chief Scientific Officer NCGR

Michael A. Grantham private investor

Stephen F. Kingsmore, M.B., C.h.B., B.A.O. President & CEO NCGR

Mary F. Lipscomb, M.D. Professor and Chair, Department of Pathology Associate Dean, Office of Research University of New Mexico School of Medicine

C. Rick Lyons, M.D., Ph.D. Director of Biodefense Associate Professor of Medicine Hematology & Oncology Infection and Inflammation Program University of New Mexico

Thomas J. Meyer, Ph.D. Associate Director, Strategic Research Los Alamos National Laboratories

Marvin Miller Executive Chairman Onconova Therapeutics

Sandra Panem, Ph.D. Partner Cross Atlantic Partners

Miguel Rios Jr., Ph.D. President & CEO ORION International Technology

Van Romero, Ph.D. Vice President for Research New Mexico Tech

Gloria E. Sarto M.D., Ph.D. Director, UW Center for Women's Health Meritor Hospital

Waneta Tuttle, Ph.D., M.B.A. President & CEO Exagen Diagnostics

© NCGR. National Center for Genome Resources Contact NCGR |   Site Feedback  |  Top of Page - Relocated from SW pers profile of CEO --Bob Burton 16:53, 25 Jun 2005 (EDT) NCGR's vision and mission are discussed in detail at http://www.uctv.tv/library-popup.asp?showID=9870, a 30 minute talk show, entitled "Behind the White Coat", originally shown on UCTV.