Church, George M. - Wyss Institute for Biologically Inspired Engineering & Department of Genetics, Harvard University

• The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of
• Comparison with experimental flux measurements of a pyk knockout
• DOI: 10.1126/science.1170995 , 1210 (2009);324Science
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• MODELING GENE EXPRESSION WITH DIFFERENTIAL Department of Genetics, Harvard Medical School
• Evidence for large diversity in the human transcriptome created by Alu RNA editing
• ORIGINAL ARTICLE Quantitative monitoring by polymerase colony assay of known mutations
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• nature genetics volume 26 october 2000 183 A computational analysis of whole-genome expression
• Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactions
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• Algorithms for Identifying Protein Cross-links via Tandem Mass Spectrometry
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• Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
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• Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in S. cerevisiae
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• JOURNAL OF BACTERIOLOGY, Oct. 2004, p. 69386943 Vol. 186, No. 20 0021-9193/04/$08.00 0 DOI: 10.1128/JB.186.20.69386943.2004
• NucleicAcids Research, 1995, Vol. 23, No. 7 1231-1238 Preparation of probe-modified RNA with
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• Aging Cell (2009) 8, pp6572 Doi: 10.1111/j.1474-9726.2008.00442.x 2009 The Authors 65
• Single molecule profiling of tau gene expression in Alzheimer's Chris Conrad,*,1
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• I N N O V A T I O N The Human Genome Pro-
• Global RNA Half-Life Analysis in Escherichia coli Reveals Positional Patterns of Transcript Degradation
• Molecular Cell 24, 747757, December 8, 2006 2006 Elsevier Inc. DOI 10.1016/j.molcel.2006.10.030 The Transition between Transcriptional
• Multiplex amplification of large sets of human exons Gregory J Porreca1,8, Kun Zhang1,7,8, Jin Billy Li1, Bin Xie2, Derek Austin2, Sara L Vassallo1, Emily M LeProust3,
• Multiplex Sequencing of 1.5 Mb of the Mycobacterium leprae Genome
• Digital genotyping and haplotyping with polymerase colonies
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• 5. G. An, B. D. Watson, C. C. Chiang, Plant Physiol. 81, 301 (1986); A. M. Lloyd et al., Science 234, 464 (1986); K. A. Feldmann and M. D. Marks, Mol. Gen. Genet. 208, 1
• MouseHuman Orthology Relationships in an Olfactory Receptor Gene Cluster
• nature biotechnology volume 27 number 11 november 2009 1013 and http://www.completegenomicsinc.com/technology). At annual
• doi:10.1101/gad.1355605 2005 19: 2619-2630Genes & Dev.
• Educational Initiatives and Data Analysis in the
• Computational Identification of Cis-regulatory Elements Associated with Groups of Functionally
• SAFEGUARDING BI0LOGYBy George Church
• Digital Quantitative Measurements of Gene Expression
• Electrophoresis 1997, IR, 1259-1313 Predicted versus observed E. c d i proteins 1259 Andrew J. Link'*
• Regional Focus on GM Crop Regulation
• DOI: 10.1126/science.1137325 , 1481 (2007);316Science
• Patterns and Implications of Gene Gain and Loss in the Evolution
• / www.sciencexpress.org / 5 November 2009 / Page 1/ 10.1126/science.1181498 Genome sequencing of large numbers of individuals
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• Detection Via Laser Desorption and Mass Spectrometry of Multiplex Electrophore-labeled
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• A Comprehensive Library of DNA-binding Site Matrices for 55 Proteins Applied to the Complete
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• Discovering functional transcription-factor combinations in the human cell cycle
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• Comparative Genomic Discovery of miRNAs Grad et al.
• kPROT: A Knowledge-based Scale for the Propensity of Residue Orientation in Transmembrane Segments.
• DOI: 10.1126/science.1176950 , 1128 (2009);325Science
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• ARTICLE doi:10.1038/nature09805 Somatic coding mutations in human
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• A highly annotated whole-genome sequence of a Korean individual
• Self-assembly of DNA into nanoscale three-dimensional shapes
• he dawning of a new decade is an appropriate time to reflect on the tremendous progress that has been
• RAPID COMMUNICATION Generation of Functional Human Hepatic Endoderm
• Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human
• 10.1101/gr.092213.109Access the most recent version at doi: 2009 19: 1606-1615 originally published online June 12, 2009Genome Res.
• ASTROBIOLGY The Most Conserved Genome Segments for Life
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• Analyses of humanchimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging
• NATURE BIOTECHNOLOGY VOLUME 24 NUMBER 2 FEBRUARY 2006 139 A DNA flu vaccine in practice
• Synthetic biology projects in vitro Anthony C. Forster1,3
• Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy
• Sequencing genomes from single cells by polymerase Kun Zhang1, Adam C Martiny2, Nikos B Reppas1, Kerrie W Barry3, Joel Malek4, Sallie W Chisholm2 &
• RESEARCH ARTICLE MapQuant: Open-source software for large-scale
• 20:252-259, 2005. doi:10.1152/physiol.00010.2005Physiology Joo Pedro de Magalhes and George M. Church
• doi:10.1101/gr.3847105 2005 15: 1298-1306; originally published online Aug 18, 2005;Genome Res.
• bGal (Cappel), mouse anti-CD2 (Serotec), mouse anti-Flag (Sigma), rat anti-SmoC (ref. 15), and mouse anti-SmoN (ref. 30). For in vitro kinase assay, purified recombinant
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• The Complete Genome and Proteome of Mycoplasma mobile
• The resounding success of the Human Genome Project (HGP) is largely the result of early investments in the
• Catic A, et al. Preferred in vivo ubiquitination sites
• BIOINFORMATICS Vol. 20 Suppl. 1 2004, pages i178i185
• Identification of many microRNAs that copurify with polyribosomes in mammalian neurons
• Journal of Theoretical Biology 228 (2004) 3146 Mathematical models of diffusion-constrained polymerase chain
• 7. L. A. Tonkin et al., EMBO J. 21, 6025 (2002). 8. M. Higuchi et al., Cell 75, 1361 (1993).
• Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the pre-implantation uterus
• Molecular Microbiology (2003) 48(3), 699712 2003 Blackwell Publishing Ltd
• On the complete determination of biological systems
• A Microarray-Based Antibiotic Screen Identifies a Regulatory Role for Supercoiling in the Osmotic
• JOURNAL OF BACTERIOLOGY, Nov. 2002, p. 62256234 Vol. 184, No. 22 0021-9193/02/$04.00 0 DOI: 10.1128/JB.184.22.62256234.2002
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• Computation-Based Discovery of Related Transcriptional Regulatory Modules and Motifs
• JOURNAL OF BACTERIOLOGY, Aug. 2002, p. 000 Vol. 184, No. 16 0021-9193/02/$04.00 0 DOI: 10.1128/JB.184.16.000000.2002
• Measuring absolute expression with microarrays with a calibrated reference sample and an
• Computational Identification of Transcription Factor Binding Sites via a Transcription-factor-centric
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• Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx
• Alignment and Structure Prediction of Divergent Protein Families: Periplasmic and Outer Membrane
• Vol. 175, No. 11JOURNAL OF BACTERIOLOGY, June 1993, p. 3303-3316 0021-9193/93/113303-14$02.00/0
• [14] DIRECT TRANSFER ELECTROPHORESIS 187 which usually takes less than an hour. The database should be monitored
• J. Mol. Riol. (1991) 222, 1085-1108 Complementary Recognition in Condensed DNA: Accelerated
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• Cell, Vol. 18, 1209-l 215, December 1979, Copyright 0 1979 by MIT Pleiotropic Mutations within Two Yeast Mitochondrial
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• J. Mol. Biol. (1978) 123, 607-630 Crystal Structure of Yeast Phenylalanine Transfer RNA
• 800 EXTINCTION IN DEFORMED COPPER SINGLE CRYSTALS FREUND, A. (1973). PhD Thesis, Technische Universit/it
• Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems
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• Photocleavable fluorescent nucleotides for DNA sequencing on a chip constructed by site-specific
• Wavelength-Controlled Orthogonal Photolysis of Protecting Aurelien Blanc and Christian G. Bochet*,
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• Glue Microarray Database System Using Struts Technology
• Basic Local Alignment Search Tool Jonathan M. Urbach
• The variable and conserved interfaces of modeled olfactory receptor proteins
• Abstract Olfactory receptors (ORs) constitute the largest multigene family in multicellular organisms. Their evolu-
• The olfactory receptor gene superfamily: data mining, classification, and nomenclature
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• Primate Evolution of an Olfactory Receptor Cluster: Diversification by Gene Conversion and Recent Emergence of Pseudogenes
• Developed by Doug Selinger (selinger@fas.harvard.edu) Thesis Advisor: George M. Church, Ph.D.
• Systematic Management and Analysis of Yeast Gene Expression Data
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• A sequence-oriented comparison of gene expression measurements across different hybridization-based
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• Localization to the Proteasome Is Sufficient for Degradation* Received for publication, March 17, 2004
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• Running Title: LXR Regulated Genes in As4.1 cells Identification of a Novel Set of Genes Regulated by a Unique LXR-Mediated
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• Genome-wide Co-occurrence of Promoter Elements Reveals a cis-Regulatory Cassette of rRNA
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• DEFG0202ER63445, PI = Professor George M. Church June 28, 2011 PROPOSAL FOR DEVELOPMENT OF ENHANCED INVIVO AND EXVIVO SYNTHETIC BIOLOGY METHODS