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Seed Lab

Work in our lab is centered on approaches to identify interesting genes and pathway connections using automated methods for analysis of function. We have amassed a collection of high efficiency expression plasmids that encompass a large fraction of the human genome, which allows us to comprehensively explore the contributions of each gene product individually. We have also created simple systems for the rapid generation of homozygous mutant embryonic stem cells, and, by extension, convenient methods for the creation of homozygous mutant mouse embryonic fibroblasts. Together these approaches provide a powerful and relatively simple system for rigorously evaluating the proposed roles of individual gene products for signaling in vivo.

A fraction of the lab is also engaged in the development of new therapeutic entities to treat human diseases. This effort is multidisciplinary and includes the development of technologies to address and correct acquired disorders as well as the creation of new biologicals and chemically modified hybrid biologicals. The majority of this effort is aimed at new approaches to treat tumors and metabolic conditions.

Team

Linda Chun
Assistant in Molecular Biology
John Darga
Lab Manager
Sandip Datta
Research Scientist
Nitya Jain
Assistant Immunologist, MGH Pediatrics
Naifang Lu
Research Lab Manager
Drew Phelan
Research Technician 1
Prabhat Singhal
Research Associate
Huajun Wang
Bioinformatics Specialist II
Guoling Zhou
Research Team Leader II
Isin Dalkilic-Liddle
Biogen Idec
Danfeng Dong
Robin Ketteler
University College, London, UK
Hwijin Kim
Young Bae Kim
Assistant Professor in Biology/Natural Sciences at North Shore Community College, Danvers, MA
Vidya Kunjathoor
Research Investigator, Novartis
Stefan Lichtenthaler
Group Leader, University of Munich
Laryssa Manigat
University of Virginia- student
Soon-Young Na
College of Life Science, S. Korea
Rasma Niedra
Winfried Pickl
Associate Professor, Institute of Immunology, University of Vienna Medical School, Austria
Felipe Pimentel-Muinos
Professor, University of Salamanca
Shahrooz Rabizadeh
Adjunct Assistant Professor, Department of Bioengineering, UCLA
Felix Randow
Group Leader, MRC Cambridge
Sasa Rodoja
Principal Investigator, Center for Cancer and Immunology Research (CCIR), Children's National Medical Center
Athanasia Spandidos
Research Collaborator, University of Athens, Greece
Ming-Hsiang Sung
Adrian Ting
Associate Professor, Clinical Immunology, The Mount Sinai Hospital
Xiaowei Wang
Assistant Professor of Cancer Biology, Washington University
Qiang Xie
SUNY Downstate Medical Center, NY
Yi Yang
Research Investigator, Novartis
Haisheng Zhou

Research

Director, Center for Computational and Integrative Biology

Brian Seed is a Professor of Genetics at Harvard and Director of the Center for Computational and Integrative Biology at the Massachusetts General Hospital (MGH). He obtained his B.S. and Ph.D. degrees from the California Institute of Technology. Prof. Seed is the author of a number of publications on genetics and molecular biology with an emphasis on the development of methods and technology. His early efforts to develop of genetic selections for transiently expressed genes led to the identification of cDNAs encoding the majority of the then-recognized lineage antigens of the immune system. In addition he has made several contributions to the understanding of the mechanisms of T cell activation. His work on immunoglobulin fusion proteins led to the identification of several co-receptors and ligands and laid the basis for the development of several therapeutic fusion proteins. He co-founded several biotech companies including Connetics, Edge Biosystems, Phylos, Egret Pharma (Shanghai) Ltd. and Theracos, Inc. and has served on the advisory boards for Hoechst/Aventis, Medigene A.G., St. Jude Children’s Research Hospital, Phylos and New Leaf Ventures.

Brian Seed’s page at Harvard Biophysics

Brian Seed’s page at Harvard-MIT HST

Resources

Web Resources

Parallel Biological Systems

This research program is centered at the Massachusetts General Hospital, Harvard Medical School, with bioinformatics participation from the Boston University Biomedical Engineering Department and the Genetics Department at Harvard Medical School. The investigators in the program are working to identify and characterize gene networks activated by pro-inflammatory, metabolic, and pathogen stresses that affect the cardiovascular system and the lungs.

Software

MGH-PGA BASE Plug-in Suite
A number of plug-ins written for the BioArray Software Environment provide it with a greatly expanded ability to analyze microarray expression data.|

MGH-PGA Proteomic Tools
Our database is based on NCBI’s protein database, with additional information about the DNA coding sequences. It allows identification of the DNA coding sequences by searching for peptide sequences. You may also upload a protein file and get the corresponding DNA coding sequences, as well as primers designed for PCR.|

OligoPicker
OligoPicker selects up to five oligo probes for each of the DNA sequences you provide for microarray printing. OligoPicker picks specific oligos by skipping regions with contiguous bases common in other sequences. In addition, oligo specificity is double-checked by BLAST.|

Oligo List Builder for Synthetic Genes

PrimerBank
PrimerBank is a public resource for PCR primers. These primers are designed for gene-expression detection or quantification (real-time PCR). PrimerBank contains about 180,000 primers covering most known human and mouse genes.|

Web Edit
This program can facilitate the assembly of new plasmid sequences by turning map sequences into raw DNA fragments.

Web Map
This program creates flexibly formatted sequence maps from a variety of inputs, including GenBank pages formatted as either text or html. The maps are hyperlinked to GenBank resources and present expository information through popup windows. A very large number of style options are available to display SNPs, open reading frames, and restriction enzyme cleavage sites.

Materials

Over the years, the Seed laboratory has provided research materials upon requests as a professional courtesy. These materials include recombinant DNAs, cell lines, and mice. To request plasmids or materials, send your request with a complete mailing address via email or fax to Brian Seed. The request should contain the following assertion: The materials received are for research use only and will not be used for commercial purposes without the prior written consent of Massachusetts General Hospital. Please avoid phone requests; they have a tendency to get lost.

Below are selected sequences of highly-demanded DNA plasmids and their related protocols. The Webmap software listed above may assist you in mapping the plasmid sequences.

Recombinant DNA Plasmids

Names of vectors using SupF system for selection: pCDM and pPACEBV
Names of vectors using Amp resistance for selection: pCDNA3, pRX, pPEAK

Protocols

Panning (method for expression cloning)
High-efficiency transformation in E. coli
DEAE dextran transfection
Propagation of suppressor tRNA plasmids

IgFusionProteins

Peak13CD5Lnegl

RIP

RX
humanRIP
murineRIP

HIV

Peak10-Syngp160mn