Genome Sequencing: (see also Next-gen overview)
Azco Biotech Salem, NH 2003 (2009-present; sequencing system)
Danaher-Dover-Polonator Salem, NH 2007 (2007-present; sequencing instrument)
Complete Genomics Sunnyvale CA 2006 (2006-present; Sequencing by Ligase service)
IntelligentBioSystems (IBS) Waltham MA 2006 (2006-present; Sequencing by Polymerase on beads)
Halcyon Molecular Redwood City CA 2009 (2009-present; Mbp read-length EM sequencing)
Pacific Biosciences Menlo Park CA 2004 (2008-present; real-time single-molecule sequencing)
Helicos Biosciences Corp   Cambridge MA 2004 (2003-present; Single-molecule DNA sequencing)
Lynx - Solexa - Illumina   Hayward CA 1992; San Diego 1998 (2000-present; multiplex tags)
LightSpeed Genomics Sunnyvale CA 2007 (2007-present; high-speed DNA sequencing)
Noblegen Biosciences Boston MA 2010 (2010-present; optipore sequencing)
Genia Mountain View, CA (2011-present) nanopores
Ion Torrent Guilford, CT 2008 (2009-present; electronic sequencing)
IBM Yorktown Heights, NY 1911 (2009-present) DNA Sequencing.
NABsys Providence, RI 2005 (2010-present) SbH with nanopores.
Genapsys 2010 (2010-present) label-free nanosensor array sequencing.

Clinical and Consumer Genomic Diagnostics:
Alacris Pharmaceuticals Berlin 2008 (2008-present,F; Cancer genomics & systems biology)
Androcyte Florida 2011 (2011-present; Supercentenarians)
Good Start Genetics Cambridge 2009 (2009-present,F; Molecular Diagnostics)
Genomera San Francisco 2010 (2010-present; Crowd-sourced Health Insight)
Telome Boston MA 2010 (2010-present; Telomeres and aging)
23andme Mountain View CA 2006 (2006-present; personal genomics)
DNAdirect  MEDCO San Francisco CA 2004 (2006-2010; DNA diagnostics)
Knome, Inc. Cambridge MA 2007 (2007-present,F; Human Genome Sequencing)
Pathogenica Cambridge MA 2010 (2010-present,F; Pathogencity and Drug resistance diagnostics)
AbVitro 2010 (2010-present,F; Immunomes).

Synthetic Biology, Biofuels, Stem Cells & Pharma:
Celemics Korea 2011 (2011-present; Genome engineering.)
Genome Compiler Corp San Francisco CA 2011 (2011-present; Genome CAD)
Joule Unlimited Cambridge MA 2007 (2007-present,F; SolarFuels)
Warp Drive Biosynthetics Boston MA 2011 (2011-present,F; Natural product synthesis)
Gen9 Cambridge MA 2009 (2009-present,F; Synthetic Biology)
EnEvolv Cambridge MA 2011 (2011-present,F; genome engineering)
Essentient (Pronutria) 2011 (2011-present,F; nutritional synbio)
LS9   San Francisco CA 2005 (2006-present,F; Biologically engineered fuels)
Cellular Dynamics International (CDI) Madison WI 2006 (2009-present; iPS stem cells)
Enzymatics Beverly MA 2006 (2006-present; Large-scale, high quality enzymes)
Qteros (formerly SunEthanol) Amherst MA 2007 (2007-present; Biofuels)
Genomatica   San Diego CA 2001 (2001-present; microbial metabolic models)
PharmoRx   Wellesley MA 2005 (2005-present; secure medication)
Sigma-Aldrich St. Louis 1934 (2009-present; chemistry, cells, Board of Directors)
NEB Beverly MA 1975 (2009-present; protein synthesis)

Publishing and non-profit groups:
pgEd Boston 2006 (2013-present; personal genetics education)
Station for Natural Studies CT,MA 1989 (1989-present,F; genetics & education)
PersonalGenomes.org Boston 2004 (2004-present,F; open-access genome & trait data)
BioWeatherMap.org/about.html Boston 2009 (2009-present,F; DIYbio)
X-prize.org Playa Vista CA 1996 (2005-present; sequencing & energy)
Epstein Science Community and Epstein Foundations 1991 (2005-present; creative science community)
Edge Foundation 1988 (2005-present; science communication)
Scientific American 1845 (2008-present; editorial advisor)
Nature Publishing Group (NPG) 1869 (2005-present; senior editor, MSB)

Financial and Legal Consulting:
evalueSCIENCE 2011 (2011-present; Science and policy advising)
Guidepoint Global (2009-present; Genomics technologies)
Gerson Lehrman Group (GLG) (2007-present; Genomics technologies)
DeMatteo Monness LLC 1997 (2011-present; DNA Sequencing)
ACLU (2009; DNA diagnostics)
Supreme Court --Susman Godfrey LLP Amici Curiae Ebay & Half.com vs MercExchange LLC (2006; Intellectual Property)

Companies licensing Church lab patents or software:
Agilent Technologies 2000 (2001-present; nucleic acid nanopore sensors)
Oxford NanoPore Technologies Kidlington, UK 2005 (2008)
Affymetrix (Affymax)    Palo Alto CA 1993 (1990-2003; Oligonucleotide arrays)
Agencourt   (then Beckman Coulter) Beverly MA 2000 (2003-2006; Polony bead sequencing by ligation)
Applied Biosystems Foster City CA 1981 (2003-2006; via Agencourt, polony bead sequencing by ligation)
Pyrosequencing (also Biotage - 454   Stockholm 2000 (2001-2005; modified dNTPs for array sequencing)
Millipore Bedford,MA (1989-1990; multiplex sequencing) and 2009-present via EMD
Codon Devices (then Gen9) Cambridge MA 2005 (2005-2009,F; Constructive Biology)
Mosaic Technologies  (then Apogent, Illumina) Boston MA 1994 (1993-94 & 2000-2001; DNA diagnostics)

Past Advisory roles:
Bionanomatrix Philadelphia, PA 2008 (2009-2010; Fluorescent mapping)
Cambrian Genomics 2011 (2011-2012; nextgen DNA synthesis + synthesis)
Genizon Cantaloupe Quebec 2008 (2008-2010; In situ sequencing)
HySeq Chicago 1993 (1993; Sequencing by Hybridization)
GreenFuel Technologies Corp. Cambridge MA 2004 (2005-2006; Photosynthetic CO2 emissions capture)
Flagship Ventures   Cambridge MA 2000 (2000-2006; genomics & informatics)
Receptor Biologix   (then Symphogen San Francisco CA 2003 (2004-2007; alternative splicing)
Longenity Inc.; Boston MA 2001 (2001-2005; human aging)
Xeotron (then Invitrogen)  Houston TX 2000 Atactic (2001-2004; Light-directed DNA/RNA-microarray synthesis)
Genome Pharmaceuticals (see GPC Biotech, Alacris)     Martinsried, Germany 1998 (1998-2003; genomics for drug targets)
Caliper Technologies    (then PerkinElmer) Palo Alto CA 1995 (1994-2002; microfluidics)
CodonCode Corp.   Dedham MA 1996 (1996-2003); DNA sequencing software)
BeyondGenomics   (then BGMedicine) Cambridge MA 2001 (2000-2004; biomarkers & systems biology)
EngeneOS (leading to: Epitome, CodonDevices, Gen9) Cambridge MA 2001 (2000-2005,F; Engineered Genetic Operating Systems)
GenProfile AG Berlin, Germany 1998 (1997-2001; multiplex haplotyping)
Adeptient Los Altos, CA 2000 (2001-2002; inkjet aerosols for drug delivery and array manufacture)
First Genetic Trust Chicago, IL 2001 (2001-2002; personal genetic information access)
Sangamo (Gendaq) Richmond CA 1995 (2000-2002; Zn-finger engineering)
Genome Therapeutics (Oscient & Agencourt, previously Collaborative Research Inc.)   Waltham MA 1961 & 1993 (1984 & 1989-1994; microbial genomes)
Biogen Inc.   Cambridge, MA 1978 (1984-1985; genomic sequencing)
Gamera (then Tecan LabCD) Medford MA 1995 (1998-2000; microfluidics)
FamilyGenetix Oxford, UK (2000-2001; Genetic patient history software & services)
Bruker Daltonics Billerica, MA 1960 (1993-1997; Mass-tags)
Biorad-Sadtler Philadelphia, PA (1979-1981; DNA sequencing software)

Corporate research sponsors & collaborators not listed above:
Aventis, Rhone-Poulenc Rorer & Hoechst Marion Roussel   Paris, Frankfurt, Collegeville PA, etc. 1990 (1998-2001; computational functional genomics)
Merck KGaA (EMD) Darmstadt 1688 (2009-2012; protein synthesis)
MJ Research Inc. Waltham MA 1987 (1986-1995; Pulsed Electrophoresis & PCR)
Polytech Plastics. Cambridge MA 1982 (1982-1988; Sequencing electrotransfer devices)
Hamilton Company Reno NV 1957 (1986-1990; multisample handing syringes).
Intelligent Automation (then IBS) Cambridge MA (1992-1996; multipin array oligo synthesizer).
Eli Lilly Indianapolis IN, 1876 (1998; bioinformatics)
New England Nuclear (then NEN, Dupont/PerkinElmer) Boston MA 1956 (1982-1984; nylon membranes)

See also supporters of PersonalGenomes.org and related research.
Next Gen Sequencing Overview
Bloomberg Businessweek List of Connections