DF/HCC Program Affiliation

Cancer Cell Biology
Cancer Genetics

Research Abstract

We use genomic systems biology to model
regulatory and enzymatic networks in mammalian and microbial cells. We develop technologies based on DNA-arrays, mass-spectrometry, automated microfluidics, polonies, and homologous recombination genome engineering. We have used these to discover genes affectng cell proliferation, alternative RNA splicing, and new regulatory sites involved in cell-cycle control and stress responses. We have developed integrated gene expression and functional genomics databases. For additional information see http://arep.med.harvard.edu.

Publications

• de Magalhães JP, Church GM.Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging.Mech Ageing Dev 2007 Mar 25.
  17459455
• de Magalhães JP, Costa J, Church GM.An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts.J Gerontol A Biol Sci Med Sci 2007 Feb;62(2):149-60.
  17339640
• Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, Struhl K.Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells.Mol Cell 2006 Nov 17;24(4):593-602.
  17188034
• Reppas NB, Wade JT, Church GM, Struhl K.The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.Mol Cell 2006 Dec 8;24(5):747-57.
  17157257
• Forster AC, Church GM.Synthetic biology projects in vitro.Genome Res 2007 Jan;17(1):1-6.
  17151344
• Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW.Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability.Mol Syst Biol 2006;2:53.
  17016519
• Derti A, Roth FP, Church GM, Wu CT.Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants.Nat Genet 2006 Oct;38(10):1216-20.
  16998490
• Lee SI, Pe'er D, Dudley AM, Church GM, Koller D.Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification.Proc Natl Acad Sci U S A 2006 Sep 19;103(38):14062-7.
  16968785
• Forster AC, Church GM.Towards synthesis of a minimal cell.Mol Syst Biol 2006;2:45.
  16924266
• Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA.PEPPeR: A platform for experimental proteomic pattern recognition.Mol Cell Proteomics 2006 Jul 19.
  16857664
• Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Free
  16823376
• Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM.Sequencing genomes from single cells by polymerase cloning.Nat Biotechnol 2006 Jun;24(6):680-6.
  16732271
• Church GM.From systems biology to synthetic biology.Mol Syst Biol 2005;1:2005.0032.
  16729067
• Church GM.The personal genome project.Mol Syst Biol 2005;1:2005.0030.
  16729065
• Dudley AM, Janse DM, Tanay A, Shamir R, Church GM.A global view of pleiotropy and phenotypically derived gene function in yeast.Mol Syst Biol 2005;1:2005.0001.
  16729036
• Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM.Identifying metabolic enzymes with multiple types of association evidence.BMC Bioinformatics 2006;7:177.
  16571130
• Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM.Long-range polony haplotyping of individual human chromosome molecules.Nat Genet 2006 Mar;38(3):382-7.
  16493423
• de Magalhães JP, Church GM.Cells discover fire: employing reactive oxygen species in development and consequences for aging.Exp Gerontol 2006 Jan;41(1):1-10.
  16226003
• Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM.Accurate multiplex polony sequencing of an evolved bacterial genome.Science 2005 Sep 9;309(5741):1728-32.
  16081699
• Zhu Z, Shendure J, Church GM.Discovering functional transcription-factor combinations in the human cell cycle.Genome Res 2005 Jun;15(6):848-55.
  15930495
• Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church G.Accurate multiplex gene synthesis from programmable DNA microchips.Nature 2004 Dec 23;432(7020):1050-4.
  15616567
• Zhu J, Shendure J, Mitra RD, Church GM.Single molecule profiling of alternative pre-mRNA splicing.Science 2003 Aug 8;301(5634):836-8.
  12907803