Beth Israel Deaconess Medical Center
(1) With Seigo Izumo: The Cardiogenomics Project is one of our two NHLBI Program for Genomics Applications (PGA). The goal of this project is to interface human genetics (including the large Framingham study) with functional genomics and model systems. (g)
Brigham and Women's Hospital (BWH) & Harvard Partners Center for Genetics and Genomics (HPCGG)
(2) With Alan Michelson: Combinatorial elements in heart and muscle enhancers can be analyzed computationally. (j)
(3) With Martha Bulyk (and Novartis Research): Genome-wide and combinatorial measures of mammalian promoter elements are being used to establish binding constants for regulatory factors. (j,t)
(4) With Richard Maas, Richard Lee: Pathological and physiological states are being measured with Affymetrix array methods and new algorithms for deconvolving the individual cell-types from potentially mixed-cell samples. (x,p,j)
(5) With Leonard Anderson, Richard Pratt and Victor Dzau: RNAs with renin-like responses are being found within cell-culture expression profiles and new motifs tested. (j)
(6) With Steve Blacklow: Development of in vitro selection systems involving modified ribosomes capable of synthesizing a variety of peptide and non-peptide drugs. (x,g)
(7) With Raju Kucherlapati: Development of novel methods for mammalian genome sequencing, genotyping and computational sequence comparisons, proteomics. (g)
(8) With Paul Allen and Scott Weiss: part of the collaboration (1) above. (g)
Children's Hospital
(9) With Stuart Orkin and Len Zon: Hematopoietic stem cells gene expression is being compared across vertebrate lineages. (g)
(10) With Richard Mulligan: Very pure populations of cycling and quiescent human and mouse hematopoietic stem cells are being compared. (x)
(11) With Zak Kohane: HST-MIT Graduate Bioinformatics training grant starting in 2002 and NCBC Center 2005 (g)
Dana-Farber Cancer Institute (DFCI)
(12) With Matthew Meyerson: We have developed algorithms to searches for new disease-associated viral and bacterial sequences within transcriptomes. (j)
(13) With Marc Vidal: We are statistically integrating transcriptome, interactome and other functional genomic data. (j)
Joslin Diabetes Center
(14) Vincent Butty & Christophe Benoist: We will apply new technology for haplotyping somatic VDJ profiling in autoimmunity and diabetes. (t)
Massachusetts General Hospital (MGH)
(15) With Brian Seed, Mason Freeman, Jack Szostak, et al.: NHLBI PGA for a National resource of oligonucleotide arrays, expressed protein domains &computational genomics. (g)
(16) With Ron Tompkins, Fred Ausubel, et al.: The Biological Response to Traumatic Injury. (g)
(17) With Gary Ruvkun: On methods to detect regulatory micro-RNAs and Mars DNA.(g,j)
Harvard Institute for Proteomics (HIP)
(18) With Josh LaBaer: We are developing homologous recombination tools for the modular expression of a full set human proteins in a variety of expression systems for studies on their in vivo and in vitro interactions. (p)
HMS Cell Biology
(19) With Frank McKeon: on epithelial stem cells the relationship with cancer. (g)
(20) With Steve Gygi: Multidimensional automated chromatography for full proteome analyses in microbial systems and the stem cell project above. (g)
HMS Biochemistry & Molecular Pharmacology (BCMP)
(21) With Tom Ellenberger, Gerhard Wagner, Steve Harrison: structural genomics of cancer-relevant proteins. (p,t)
(22) With Fritz Roth: Shared infrastructure for parallel computing & motif analysis (j,p)
(23) With Jim Hogle: Computational Biology/Biophysics training program since 1997(g)
(23) With Kevin Struhl: Chiip^2 on human & E.coli. (x,p,j)
HMS Genetics
(24) With Connie Cepko: on transcription circuits in neuronal cell-types. (j,t)
(25) With Phil Leder: on embryonic stem cells (g)
(26) Jon Seidman, Kricket Seidman: as part of project (1) above and polonies (g,p)
(27) With Ting Wu: on Homologous chromosome pairing & models of chromosome sensors. (t,p,j)
Harvard Center for Genomic Research (Cambridge campus)
(28) With Andrew Murray, Roy Kishony, Lani Wu & Steve Altschuler: on computational functional genomics (x,g,j).
Harvard Molecular & Cell Biology (Cambridge campus)
(29) With Howard Berg: We are interested in using proteomics to study the motility of pathogenic mycoplasmas. (t,j)
MIT Electric Engineering and Computer Science (EECS)
(30) With Tom Knight & Drew Endy (& DARPA consortium): We are establishing computer aided design for biological systems, bioSPICE/CAD (g) and iGEM competition.
With Joe Jacobson (MIT Media Lab) error correction for synthetic genomes with new genetic codes (x,g)
(31) With David Gifford, Rick Young and Tommi Jaakkola: Teaching MIT course 6.892 "Computational Functional Genomics" since 2000. (x)
MIT Chemical Engineering
(32) With Greg Stephanopoulos: Training program for Computational Biology graduate students in the HMS-MIT MEMP program; see (11) above. (g)
MIT/HMS Broad Inst. (previously Whitehead Center for Genome Research)
(33) With the Eric Lander, Bruce Birren, Chad Nussbaum, and others at the MIT Center for Genome Research: on mammalian & mycoplasmal genome sequence comparisons. (g,j,x)
Harvard School of Public Health (HSPH)
(34) With Wing Wong (now Stanford): co-developing software for statistical analysis of Affymetrix array RNA quantitation taking full advantage of the multiple oligonucleotides and multiple experiments (GAPS + dCHIP). (x,p)
(35) With Dyann Wirth: Her group is analyzing regulation Malarial gene expression. (x)
MIT Biological Engineering
(36)With James Sherley: Stem cells. (g)
MIT Civil Engineering
(37)With Penny Chisholm & Martin Polz and members of their groups on Ocean ecology and energy. (g,j)
Boston University Medical School & College of Engineering
(38) With Temple Smith: Database design for projects (15) & (16) above. (g)
(39) With Charles DeLisi: Solid-phase photochemistry arrays. (t)
(40) With Emelia J. Benjamin as part of collaboration (1) above. (g)
(41) With Jim Collins: E.coli synthetic inetgrase-based counter (x,t)

UCSD San Diego:
(42) With Bernard Palsson and Shankar Subramaniam: Metabolic modeling. (g,t)

Institute for Systems Biology (ISB), Seattle
(43) With Lee Hood, et al.: Integrative and Systems Biology of Yeast proposal in collaboration with UCSD above. (p)

U. Houston Chemistry
(44) With Lian Gao: Programmable synthesis of oligonucleotide arrays combining informatics, maskless micromirrors, and microfluidics. (x)

U. Delaware Chemical Engineering (soon U. NM)
(45) With Jeremy Edwards: Optimizing microbial metabolic & regulatory networks. (g,j,t)

UC. Berkeley
(46)With Jay Keasling: Synthetic Biology (p)

Institute for Cancer Research and Treatment of Turin, Italy.
(47) With Enzo Medico: Cancer growth factors, HGF, and EGF effects on RNA expression profiles. (g)

Institute of Biotechnology, Zurich Switzerland.
(48) With Uwe Sauer on flux measures and models. (x,p)

(49)Other Collaborating Institutions in the Trauma Glue grant, see item (15) above.
Loyola University Health System, Northwestern University, Stanford University, U. Alabama School of Medicine, U. Rochester Medical School, U. Colorado Health Sciences Center, U. Florida College of Medicine, U. Medicine and Dentistry of New Jersey, U. Michigan Medical School, U. Pittsburgh School of Medicine, U. Texas Medical Branch, U. Texas - Houston Health Science Center, U. Texas Southwestern Medical Center, U. Washington Academic Medical Center, Washington University in St. Louis Medicine and Health Care. (g)

(50) Collaborators in MIAME (Minimum information about a microarray experiment): Alvis Brazma1, Pascal Hingamp2, John Quackenbush3, Gavin Sherlock4, Paul Spellman5, Chris Stoeckert6, John Aach7, Wilhelm Ansorge8, Catherine A. Ball4, Helen C. Causton9, Terry Gaasterland10, Patrick Glenisson11, Frank C.P. Holstege12, Irene F. Kim4, Victor Markowitz13, John C. Matese4, Helen Parkinson1, Alan Robinson1, Ugis Sarkans1, Steffen Schulze-Kremer14, Jason Stewart15, Ronald Taylor16, Jaak Vilo1 & Martin Vingron17 1. European Bioinformatics Institute, EMBL outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. 2. Centre d'Immunologie de Marseille Luminy (CIML TAGC) & Universiti de la Miditerranie, Marseille, France. 3. The Institute for Genomic Research (TIGR), Rockville, Maryland, USA. 4. Stanford University, Palo Alto, California, USA. 5. University of California Berkeley, Berkeley, California, USA. 6. University of Pennsylvania, Philadelphia, Pennsylvania, USA. 7. Department of Genetics, Harvard Medical School, Cambridge, Massachusetts, USA. 8. European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. 9. CSC/Imperial College School of Medicine Microarray Centre, London, UK. 10. Rockefeller University, New York, New York, USA. 11. Katholieke Universiteit Leuven, Leuven, Belgium. 12. University Medical Center, Utrecht, Netherlands. 13. GeneLogic Inc, Gaithersburg, Maryland, USA. 14. RZDP German Genome Resource Center, Berlin, Germany. 15. Open Informatics, Albuquerque, New Mexico, USA. 16. Center for Computational Pharmacology, University of Colorado School of Medicine, Denver, Colorado, USA. 17. Max Plank Institute for Molecular Genetics, Berlin, Germany. (j)
(51) Claude Jacq , CNRS (t,j)
Other laboratories active in the Boston genomics and bioinformatics communities:
(52) David Altshuler, HMS Genetics and Director of Medical and Population Genetics at MIT CGR interested in pharmacogenomics and diabetes. (x)
(53) David Beier, Director of BWH Genome laboratory with a focus on mouse genetics.
(54) Jim Gusella, Director of MGH Neurogenetics
(55) David Kwiatkowski, Director of Harvard partners Genotyping Facility
(56) Cynthia Morton, Director of the BWH Cytogenetics Lab and Principal Investigator in the Developmental Genome Anatomy Project (DGAP) (p)
(57) Leonid Mirny (HST, MIT) a structural computational chemist working on DNA-protein interactions.
(58) Shamil Sunyaev, most recent addition to BWH, Asst. Prof. Medicine focused on integrating structural genomics with SNPs and population genetics. (x)