George M. Church

Publications

• Predispositional Genome Sequencing in Healthy Adults: Design, Participant Characteristics, and Early Outcomes of the PeopleSeq Consortium
  Genome Medicine. Feb, 2019  |   Pubmed ID: 30808425
• REST and Neural Gene Network Dysregulation in IPSC Models of Alzheimer's Disease
  Cell Reports. Jan, 2019  |   Pubmed ID: 30699343
• Significant Abundance of Cis Configurations of Coding Variants in Diploid Human Genomes
  Nucleic Acids Research. Jan, 2019  |   Pubmed ID: 30698752
• Crystal Structure of the Redβ C-terminal Domain in Complex with λ Exonuclease Reveals an Unexpected Homology with λ Orf and an Interaction with Escherichia Coli Single Stranded DNA Binding Protein
  Nucleic Acids Research. Feb, 2019  |   Pubmed ID: 30624736
• CRISPR-C: Circularization of Genes and Chromosome by CRISPR in Human Cells
  Nucleic Acids Research. Dec, 2018  |   Pubmed ID: 30551175
• Characterizing Posttranslational Modifications in Prokaryotic Metabolism Using a Multiscale Workflow
  Proceedings of the National Academy of Sciences of the United States of America. 10, 2018  |   Pubmed ID: 30301795
• Establishing a Cell-Free Vibrio Natriegens Expression System
  ACS Synthetic Biology. Oct, 2018  |   Pubmed ID: 30160938
• Developmental Barcoding of Whole Mouse Via Homing CRISPR
  Science (New York, N.Y.). 08, 2018  |   Pubmed ID: 30093604
• Inter-homologue Repair in Fertilized Human Eggs?
  Nature. 08, 2018  |   Pubmed ID: 30089924
• Biosensor Libraries Harness Large Classes of Binding Domains for Construction of Allosteric Transcriptional Regulators
  Nature Communications. Aug, 2018  |   Pubmed ID: 30082754
• An Enhanced CRISPR Repressor for Targeted Mammalian Gene Regulation
  Nature Methods. Aug, 2018  |   Pubmed ID: 30013045
• Directed Differentiation of Human Induced Pluripotent Stem Cells into Mature Kidney Podocytes and Establishment of a Glomerulus Chip
  Nature Protocols. Jul, 2018  |   Pubmed ID: 29995874
• Enhanced Bacterial Immunity and Mammalian Genome Editing Via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks
  Molecular Cell. Jul, 2018  |   Pubmed ID: 29979968
• Characterizing Protein Kinase Substrate Specificity Using the Proteomic Peptide Library (ProPeL) Approach
  Current Protocols in Chemical Biology. 06, 2018  |   Pubmed ID: 29927115
• Current CRISPR Gene Drive Systems Are Likely to Be Highly Invasive in Wild Populations
  ELife. Jun, 2018  |   Pubmed ID: 29916367
• High-throughput Creation and Functional Profiling of DNA Sequence Variant Libraries Using CRISPR-Cas9 in Yeast
  Nature Biotechnology. Jul, 2018  |   Pubmed ID: 29786095
• Codon Usage of Highly Expressed Genes Affects Proteome-wide Translation Efficiency
  Proceedings of the National Academy of Sciences of the United States of America. 05, 2018  |   Pubmed ID: 29735666
• High-resolution Mapping of DNA Polymerase Fidelity Using Nucleotide Imbalances and Next-generation Sequencing
  Nucleic Acids Research. Jul, 2018  |   Pubmed ID: 29718339
• Simultaneous Discovery of Cell-Free DNA and the Nucleosome Ladder
  Genetics. May, 2018  |   Pubmed ID: 29716984
• An Integrated Genome-wide CRISPRa Approach to Functionalize LncRNAs in Drug Resistance
  Cell. Apr, 2018  |   Pubmed ID: 29677511
• Enabling Multiplexed Testing of Pooled Donor Cells Through Whole-genome Sequencing
  Genome Medicine. 04, 2018  |   Pubmed ID: 29673390
• Response to "Unexpected Mutations After CRISPR-Cas9 Editing in Vivo"
  Nature Methods. Apr, 2018  |   Pubmed ID: 29600989
• Precise Cas9 Targeting Enables Genomic Mutation Prevention
  Proceedings of the National Academy of Sciences of the United States of America. 04, 2018  |   Pubmed ID: 29555762
• Adaptive Evolution of Genomically Recoded
  Proceedings of the National Academy of Sciences of the United States of America. 03, 2018  |   Pubmed ID: 29440500
• Spontaneous CRISPR Loci Generation in Vivo by Non-canonical Spacer Integration
  Nature Microbiology. Mar, 2018  |   Pubmed ID: 29379209
• From Designing the Molecules of Life to Designing Life: Future Applications Derived from Advances in DNA Technologies
  Angewandte Chemie (International Ed. in English). Apr, 2018  |   Pubmed ID: 29316123
• Engineering Posttranslational Proofreading to Discriminate Nonstandard Amino Acids
  Proceedings of the National Academy of Sciences of the United States of America. 01, 2018  |   Pubmed ID: 29301968
• The Future of Multiplexed Eukaryotic Genome Engineering
  ACS Chemical Biology. 02, 2018  |   Pubmed ID: 29241002
• Efficient in Situ Barcode Sequencing Using Padlock Probe-based BaristaSeq
  Nucleic Acids Research. Feb, 2018  |   Pubmed ID: 29190363
• Heterologous Erythromycin Production Across Strain and Plasmid Construction
  Biotechnology Progress. Jan, 2018  |   Pubmed ID: 28960932
• A CRISPR-Cas9-based Gene Drive Platform for Genetic Interaction Analysis in Candida Albicans
  Nature Microbiology. Oct, 2017  |   Pubmed ID: 29062088
• Mature Induced-pluripotent-stem-cell-derived Human Podocytes Reconstitute Kidney Glomerular-capillary-wall Function on a Chip
  Nature Biomedical Engineering. 2017  |   Pubmed ID: 29038743
• DNA Sequencing at 40: Past, Present and Future
  Nature. 10, 2017  |   Pubmed ID: 29019985
• Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues
  Nano Letters. 10, 2017  |   Pubmed ID: 28933153
• A Systematic Comparison of Error Correction Enzymes by Next-generation Sequencing
  Nucleic Acids Research. Sep, 2017  |   Pubmed ID: 28911123
• Beyond Editing to Writing Large Genomes
  Nature Reviews. Genetics. 12, 2017  |   Pubmed ID: 28852223
• Imaging of Isolated Extracellular Vesicles Using Fluorescence Microscopy
  Methods in Molecular Biology (Clifton, N.J.). 2017  |   Pubmed ID: 28828661
• Extracellular Vesicle Isolation and Analysis by Western Blotting
  Methods in Molecular Biology (Clifton, N.J.). 2017  |   Pubmed ID: 28828654
• Inactivation of Porcine Endogenous Retrovirus in Pigs Using CRISPR-Cas9
  Science (New York, N.Y.). 09, 2017  |   Pubmed ID: 28798043
• Rates, Distribution and Implications of Postzygotic Mosaic Mutations in Autism Spectrum Disorder
  Nature Neuroscience. 09, 2017  |   Pubmed ID: 28714951
• Dissecting Limiting Factors of the Protein Synthesis Using Recombinant Elements (PURE) System
  Translation (Austin, Tex.). 2017  |   Pubmed ID: 28702280
• CRISPR-Cas Encoding of a Digital Movie into the Genomes of a Population of Living Bacteria
  Nature. 07, 2017  |   Pubmed ID: 28700573
• The Promise of Organ and Tissue Preservation to Transform Medicine
  Nature Biotechnology. 06, 2017  |   Pubmed ID: 28591112
• Scalable Device for Automated Microbial Electroporation in a Digital Microfluidic Platform
  ACS Synthetic Biology. 09, 2017  |   Pubmed ID: 28569062
• Millstone: Software for Multiplex Microbial Genome Analysis and Engineering
  Genome Biology. 05, 2017  |   Pubmed ID: 28545559
• Optimizing Complex Phenotypes Through Model-guided Multiplex Genome Engineering
  Genome Biology. 05, 2017  |   Pubmed ID: 28545477
• Addressing the Ethical Issues Raised by Synthetic Human Entities with Embryo-like Features
  ELife. 03, 2017  |   Pubmed ID: 28494856
• Nucleotide-time Alignment for Molecular Recorders
  PLoS Computational Biology. May, 2017  |   Pubmed ID: 28459860
• Evolutionary Dynamics of CRISPR Gene Drives
  Science Advances. Apr, 2017  |   Pubmed ID: 28435878
• An Unbiased Index to Quantify Participant's Phenotypic Contribution to an Open-access Cohort
  Scientific Reports. 04, 2017  |   Pubmed ID: 28387241
• Cogenerating Synthetic Parts Toward a Self-Replicating System
  ACS Synthetic Biology. 07, 2017  |   Pubmed ID: 28330337
• Programmable Transcriptional Repression in Mycobacteria Using an Orthogonal CRISPR Interference Platform
  Nature Microbiology. Feb, 2017  |   Pubmed ID: 28165460
• SgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity
  ACS Synthetic Biology. 05, 2017  |   Pubmed ID: 28146356
• Cushing's Syndrome Mutant PKA Exhibits Altered Substrate Specificity
  FEBS Letters. 02, 2017  |   Pubmed ID: 28100013
• Efficient, Footprint-free Human IPSC Genome Editing by Consolidation of Cas9/CRISPR and PiggyBac Technologies
  Nature Protocols. Jan, 2017  |   Pubmed ID: 27929521
• Rapidly Evolving Homing CRISPR Barcodes
  Nature Methods. 02, 2017  |   Pubmed ID: 27918539
• An Ethnically Relevant Consensus Korean Reference Genome is a Step Towards Personal Reference Genomes
  Nature Communications. 11, 2016  |   Pubmed ID: 27882922
• Complete Mitochondrial Genomes of Living and Extinct Pigeons Revise the Timing of the Columbiform Radiation
  BMC Evolutionary Biology. 10, 2016  |   Pubmed ID: 27782796
• Design and Characterization of a Nanopore-coupled Polymerase for Single-molecule DNA Sequencing by Synthesis on an Electrode Array
  Proceedings of the National Academy of Sciences of the United States of America. 11, 2016  |   Pubmed ID: 27729524
• The Whole Genome Sequences and Experimentally Phased Haplotypes of over 100 Personal Genomes
  GigaScience. Oct, 2016  |   Pubmed ID: 27724973
• Emergent Rules for Codon Choice Elucidated by Editing Rare Arginine Codons in Escherichia Coli
  Proceedings of the National Academy of Sciences of the United States of America. 09, 2016  |   Pubmed ID: 27601680
• A Multifunctional AAV-CRISPR-Cas9 and Its Host Response
  Nature Methods. 10, 2016  |   Pubmed ID: 27595405
• CRISPR-Cas9 System: Opportunities and Concerns
  Clinical Chemistry. 10, 2016  |   Pubmed ID: 27551006
• Design, Synthesis, and Testing Toward a 57-codon Genome
  Science (New York, N.Y.). Aug, 2016  |   Pubmed ID: 27540174
• Nanoscale Imaging of RNA with Expansion Microscopy
  Nature Methods. 08, 2016  |   Pubmed ID: 27376770
• Molecular Recordings by Directed CRISPR Spacer Acquisition
  Science (New York, N.Y.). Jul, 2016  |   Pubmed ID: 27284167
• Extensive Sequencing of Seven Human Genomes to Characterize Benchmark Reference Materials
  Scientific Data. Jun, 2016  |   Pubmed ID: 27271295
• Characterization of Cas9-Guide RNA Orthologs
  Cold Spring Harbor Protocols. 05, 2016  |   Pubmed ID: 27140923
• Characterizing Cas9 Protospacer-Adjacent Motifs with High-Throughput Sequencing of Library Depletion Experiments
  Cold Spring Harbor Protocols. 05, 2016  |   Pubmed ID: 27140916
• Real-time Single-molecule Electronic DNA Sequencing by Synthesis Using Polymer-tagged Nucleotides on a Nanopore Array
  Proceedings of the National Academy of Sciences of the United States of America. May, 2016  |   Pubmed ID: 27091962
• Performance of Optimized Noncanonical Amino Acid Mutagenesis Systems in the Absence of Release Factor 1
  Molecular BioSystems. 05, 2016  |   Pubmed ID: 27027374
• Biosensor-based Engineering of Biosynthetic Pathways
  Current Opinion in Biotechnology. 12, 2016  |   Pubmed ID: 26998575
• Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
  PloS One. 2016  |   Pubmed ID: 26821252
• In Vivo Gene Editing in Dystrophic Mouse Muscle and Muscle Stem Cells
  Science (New York, N.Y.). Jan, 2016  |   Pubmed ID: 26721686
• Engineering an Allosteric Transcription Factor to Respond to New Ligands
  Nature Methods. Feb, 2016  |   Pubmed ID: 26689263
• Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia Coli
  ACS Synthetic Biology. Feb, 2016  |   Pubmed ID: 26544153
• Precision Chemistry for Precision Medicine
  ACS Central Science. Mar, 2015  |   Pubmed ID: 27162939
• Crispr-mediated Gene Targeting of Human Induced Pluripotent Stem Cells
  Current Protocols in Stem Cell Biology. 2015  |   Pubmed ID: 26949444
• A General Strategy to Construct Small Molecule Biosensors in Eukaryotes
  ELife. Dec, 2015  |   Pubmed ID: 26714111
• Bioart
  Trends in Biotechnology. Dec, 2015  |   Pubmed ID: 26617334
• Safeguarding CRISPR-Cas9 Gene Drives in Yeast
  Nature Biotechnology. Dec, 2015  |   Pubmed ID: 26571100
• Neutralizing Antibodies Against West Nile Virus Identified Directly from Human B Cells by Single-cell Analysis and Next Generation Sequencing
  Integrative Biology : Quantitative Biosciences from Nano to Macro. Dec, 2015  |   Pubmed ID: 26481611
• A National Network of Neurotechnology Centers for the BRAIN Initiative
  Neuron. Nov, 2015  |   Pubmed ID: 26481036
• BIOSAFETY. Safeguarding Gene Drive Experiments in the Laboratory
  Science (New York, N.Y.). Aug, 2015  |   Pubmed ID: 26229113
• Puzzle Imaging: Using Large-Scale Dimensionality Reduction Algorithms for Localization
  PloS One. 2015  |   Pubmed ID: 26192446
• Unraveling CRISPR-Cas9 Genome Engineering Parameters Via a Library-on-library Approach
  Nature Methods. Sep, 2015  |   Pubmed ID: 26167643
• Synthetic Biosensors for Precise Gene Control and Real-time Monitoring of Metabolites
  Nucleic Acids Research. Sep, 2015  |   Pubmed ID: 26152303
• Genome and Transcriptome of Clostridium Phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels
  PloS One. 2015  |   Pubmed ID: 26035711
• Highly Efficient Cas9-mediated Transcriptional Programming
  Nature Methods. Apr, 2015  |   Pubmed ID: 25730490
• Fluorescent in Situ Sequencing (FISSEQ) of RNA for Gene Expression Profiling in Intact Cells and Tissues
  Nature Protocols. Mar, 2015  |   Pubmed ID: 25675209
• Biocontainment of Genetically Modified Organisms by Synthetic Protein Design
  Nature. Feb, 2015  |   Pubmed ID: 25607366
• Insights into the Evolution of Longevity from the Bowhead Whale Genome
  Cell Reports. Jan, 2015  |   Pubmed ID: 25565328
• Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68
  Genome Announcements. Jan, 2015  |   Pubmed ID: 25555735
• Accurate Whole Genome Sequencing As the Ultimate Genetic Test
  Clinical Chemistry. Jan, 2015  |   Pubmed ID: 25479756
• Multi-kilobase Homozygous Targeted Gene Replacement in Human Induced Pluripotent Stem Cells
  Nucleic Acids Research. Feb, 2015  |   Pubmed ID: 25414332
• Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-derived Oligonucleotides
  ACS Synthetic Biology. Jan, 2015  |   Pubmed ID: 24856730
• Spatial Information in Large-scale Neural Recordings
  Frontiers in Computational Neuroscience. 2014  |   Pubmed ID: 25653613
• Evolution-guided Optimization of Biosynthetic Pathways
  Proceedings of the National Academy of Sciences of the United States of America. Dec, 2014  |   Pubmed ID: 25453111
• Multiple Haplotype-resolved Genomes Reveal Population Patterns of Gene and Protein Diplotypes
  Nature Communications. Nov, 2014  |   Pubmed ID: 25424553
• Rapid Neurogenesis Through Transcriptional Activation in Human Stem Cells
  Molecular Systems Biology. Nov, 2014  |   Pubmed ID: 25403753
• Genome Editing in Human Stem Cells
  Methods in Enzymology. 2014  |   Pubmed ID: 25398338
• Engineering Allostery
  Trends in Genetics : TIG. Dec, 2014  |   Pubmed ID: 25306102
• Multiplex Single-molecule Interaction Profiling of DNA-barcoded Proteins
  Nature. Nov, 2014  |   Pubmed ID: 25252978
• Improved Cell-free RNA and Protein Synthesis System
  PloS One. 2014  |   Pubmed ID: 25180701
• The Naked Mole Rat Genome Resource: Facilitating Analyses of Cancer and Longevity-related Adaptations
  Bioinformatics (Oxford, England). Dec, 2014  |   Pubmed ID: 25172923
• Concerning RNA-guided Gene Drives for the Alteration of Wild Populations
  ELife. 07, 2014  |   Pubmed ID: 25035423
• Genome Editing Assessment Using CRISPR Genome Analyzer (CRISPR-GA)
  Bioinformatics (Oxford, England). Oct, 2014  |   Pubmed ID: 24990609
• CRISPR/Cas9-Directed Genome Editing of Cultured Cells
  Current Protocols in Molecular Biology. Jul, 2014  |   Pubmed ID: 24984853
• CRISPR/Cas9-mediated Phage Resistance is Not Impeded by the DNA Modifications of Phage T4
  PloS One. 2014  |   Pubmed ID: 24886988
• CHOPCHOP: a CRISPR/Cas9 and TALEN Web Tool for Genome Editing
  Nucleic Acids Research. Jul, 2014  |   Pubmed ID: 24861617
• Modeling the Mitochondrial Cardiomyopathy of Barth Syndrome with Induced Pluripotent Stem Cell and Heart-on-chip Technologies
  Nature Medicine. Jun, 2014  |   Pubmed ID: 24813252
• Fungal Lysis by a Soil Bacterium Fermenting Cellulose
  Environmental Microbiology. May, 2014  |   Pubmed ID: 24798076
• Large-scale De Novo DNA Synthesis: Technologies and Applications
  Nature Methods. May, 2014  |   Pubmed ID: 24781323
• Syntrophic Exchange in Synthetic Microbial Communities
  Proceedings of the National Academy of Sciences of the United States of America. May, 2014  |   Pubmed ID: 24778240
• Harvard Personal Genome Project: Lessons from Participatory Public Research
  Genome Medicine. Feb, 2014  |   Pubmed ID: 24713084
• High-resolution Antibody Dynamics of Vaccine-induced Immune Responses
  Proceedings of the National Academy of Sciences of the United States of America. Apr, 2014  |   Pubmed ID: 24639495
• Realizing the Potential of Synthetic Biology
  Nature Reviews. Molecular Cell Biology. 04, 2014  |   Pubmed ID: 24622617
• Raw Data: Access to Inaccuracy--response
  Science (New York, N.Y.). Feb, 2014  |   Pubmed ID: 24578564
• Highly Multiplexed Subcellular RNA Sequencing in Situ
  Science (New York, N.Y.). Mar, 2014  |   Pubmed ID: 24578530
• Recoding the Genetic Code with Selenocysteine
  Angewandte Chemie (International Ed. in English). Jan, 2014  |   Pubmed ID: 24511637
• Information Access. Raw Personal Data: Providing Access
  Science (New York, N.Y.). Jan, 2014  |   Pubmed ID: 24458627
• Rational Optimization of TolC As a Powerful Dual Selectable Marker for Genome Engineering
  Nucleic Acids Research. Apr, 2014  |   Pubmed ID: 24452804
• Integrating B Cell Lineage Information into Statistical Tests for Detecting Selection in Ig Sequences
  Journal of Immunology (Baltimore, Md. : 1950). Feb, 2014  |   Pubmed ID: 24376267
• The Role of Replicates for Error Mitigation in Next-generation Sequencing
  Nature Reviews. Genetics. 01, 2014  |   Pubmed ID: 24322726
• Natural Reassignment of CUU and CUA Sense Codons to Alanine in Ashbya Mitochondria
  Nucleic Acids Research. Jan, 2014  |   Pubmed ID: 24049072
• Next-generation Carrier Screening
  Genetics in Medicine : Official Journal of the American College of Medical Genetics. Feb, 2014  |   Pubmed ID: 23765052
• The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies
  PLoS Pathogens. 2013  |   Pubmed ID: 24278016
• BRAIN: Innovative Neurotechnologies for Imaging and Therapeutics
  Dialogues in Clinical Neuroscience. Sep, 2013  |   Pubmed ID: 24174897
• Deciphering the Functions and Regulation of Brain-enriched A-to-I RNA Editing
  Nature Neuroscience. Nov, 2013  |   Pubmed ID: 24165678
• Yeast Oligo-mediated Genome Engineering (YOGE)
  ACS Synthetic Biology. Dec, 2013  |   Pubmed ID: 24160921
• Genomically Recoded Organisms Expand Biological Functions
  Science (New York, N.Y.). Oct, 2013  |   Pubmed ID: 24136966
• Cas9 As a Versatile Tool for Engineering Biology
  Nature Methods. Oct, 2013  |   Pubmed ID: 24076990
• Orthogonal Cas9 Proteins for RNA-guided Gene Regulation and Editing
  Nature Methods. Nov, 2013  |   Pubmed ID: 24076762
• Mutants of Cre Recombinase with Improved Accuracy
  Nature Communications. 2013  |   Pubmed ID: 24056590
• Heritable Custom Genomic Modifications in Caenorhabditis Elegans Via a CRISPR-Cas9 System
  Genetics. Nov, 2013  |   Pubmed ID: 23979579
• Multiplex and Homologous Recombination-mediated Genome Editing in Arabidopsis and Nicotiana Benthamiana Using Guide RNA and Cas9
  Nature Biotechnology. Aug, 2013  |   Pubmed ID: 23929339
• Composability of Regulatory Sequences Controlling Transcription and Translation in Escherichia Coli
  Proceedings of the National Academy of Sciences of the United States of America. Aug, 2013  |   Pubmed ID: 23924614
• CAS9 Transcriptional Activators for Target Specificity Screening and Paired Nickases for Cooperative Genome Engineering
  Nature Biotechnology. Sep, 2013  |   Pubmed ID: 23907171
• Optical Control of Mammalian Endogenous Transcription and Epigenetic States
  Nature. Aug, 2013  |   Pubmed ID: 23877069
• Quantification of MicroRNA Expression with Next-generation Sequencing
  Current Protocols in Molecular Biology. Jul, 2013  |   Pubmed ID: 23821442
• Heritable Genome Editing in C. Elegans Via a CRISPR-Cas9 System
  Nature Methods. Aug, 2013  |   Pubmed ID: 23817069
• In Vitro Integration of Ribosomal RNA Synthesis, Ribosome Assembly, and Translation
  Molecular Systems Biology. Jun, 2013  |   Pubmed ID: 23799452
• Nanotools for Neuroscience and Brain Activity Mapping
  ACS Nano. Mar, 2013  |   Pubmed ID: 23514423
• Barcoding Cells Using Cell-surface Programmable DNA-binding Domains
  Nature Methods. May, 2013  |   Pubmed ID: 23503053
• PhIP-Seq Characterization of Autoantibodies from Patients with Multiple Sclerosis, Type 1 Diabetes and Rheumatoid Arthritis
  Journal of Autoimmunity. Jun, 2013  |   Pubmed ID: 23497938
• Neuroscience. The Brain Activity Map
  Science (New York, N.Y.). Mar, 2013  |   Pubmed ID: 23470729
• Genome Engineering in Saccharomyces Cerevisiae Using CRISPR-Cas Systems
  Nucleic Acids Research. Apr, 2013  |   Pubmed ID: 23460208
• Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective
  PLoS Computational Biology. 2013  |   Pubmed ID: 23341769
• Reading and Writing Omes
  Molecular Systems Biology. 2013  |   Pubmed ID: 23340848
• An Analysis and Validation Pipeline for Large-scale RNAi-based Screens
  Scientific Reports. 2013  |   Pubmed ID: 23326633
• RNA-guided Human Genome Engineering Via Cas9
  Science (New York, N.Y.). Feb, 2013  |   Pubmed ID: 23287722
• Gene Assembly from Chip-Synthesized Oligonucleotides
  Current Protocols in Chemical Biology. Mar, 2012  |   Pubmed ID: 25077042
• Using Bacteria to Determine Protein Kinase Specificity and Predict Target Substrates
  PloS One. 2012  |   Pubmed ID: 23300758
• Submicrometre Geometrically Encoded Fluorescent Barcodes Self-assembled from DNA
  Nature Chemistry. Oct, 2012  |   Pubmed ID: 23000997
• Improving Lambda Red Genome Engineering in Escherichia Coli Via Rational Removal of Endogenous Nucleases
  PloS One. 2012  |   Pubmed ID: 22957093
• Next-generation Digital Information Storage in DNA
  Science (New York, N.Y.). Sep, 2012  |   Pubmed ID: 22903519
• How Accurate Can Genetic Predictions Be?
  BMC Genomics. Jul, 2012  |   Pubmed ID: 22827772
• A Public Resource Facilitating Clinical Use of Genomes
  Proceedings of the National Academy of Sciences of the United States of America. Jul, 2012  |   Pubmed ID: 22797899
• Accurate Whole-genome Sequencing and Haplotyping from 10 to 20 Human Cells
  Nature. Jul, 2012  |   Pubmed ID: 22785314
• Iterative Capped Assembly: Rapid and Scalable Synthesis of Repeat-module DNA Such As TAL Effectors from Individual Monomers
  Nucleic Acids Research. Aug, 2012  |   Pubmed ID: 22740649
• Multiplexed in Vivo His-tagging of Enzyme Pathways for in Vitro Single-pot Multienzyme Catalysis
  ACS Synthetic Biology. Feb, 2012  |   Pubmed ID: 22737598
• The Brain Activity Map Project and the Challenge of Functional Connectomics
  Neuron. Jun, 2012  |   Pubmed ID: 22726828
• A BioBrick Compatible Strategy for Genetic Modification of Plants
  Journal of Biological Engineering. 2012  |   Pubmed ID: 22716313
• Enhanced Multiplex Genome Engineering Through Co-operative Oligonucleotide Co-selection
  Nucleic Acids Research. Sep, 2012  |   Pubmed ID: 22638574
• Stable Gene Targeting in Human Cells Using Single-strand Oligonucleotides with Modified Bases
  PloS One. 2012  |   Pubmed ID: 22615794
• Systematic Identification of Edited MicroRNAs in the Human Brain
  Genome Research. Aug, 2012  |   Pubmed ID: 22499667
• Genome-scale Promoter Engineering by Coselection MAGE
  Nature Methods. Jun, 2012  |   Pubmed ID: 22484848
• High-throughput Multiplex Sequencing of MiRNA
  Current Protocols in Human Genetics. Apr, 2012  |   Pubmed ID: 22470142
• Back to the Future: from Genome to Metabolome
  Human Mutation. May, 2012  |   Pubmed ID: 22431014
• Genomic Analysis of the Hydrocarbon-producing, Cellulolytic, Endophytic Fungus Ascocoryne Sarcoides
  PLoS Genetics. 2012  |   Pubmed ID: 22396667
• A Logic-gated Nanorobot for Targeted Transport of Molecular Payloads
  Science (New York, N.Y.). Feb, 2012  |   Pubmed ID: 22344439
• RNA Sequencing Reveals Differential Expression of Mitochondrial and Oxidation Reduction Genes in the Long-lived Naked Mole-rat when Compared to Mice
  PloS One. 2011  |   Pubmed ID: 22073188
• The Three-dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation
  Molecular Cell. Oct, 2011  |   Pubmed ID: 22017872
• Panel Discussion: Can There Be a Biomarker for Sleepiness?
  Journal of Clinical Sleep Medicine : JCSM : Official Publication of the American Academy of Sleep Medicine. Oct, 2011  |   Pubmed ID: 22003333
• New Technologies for Integrating Genomic, Environmental and Trait Data
  Journal of Clinical Sleep Medicine : JCSM : Official Publication of the American Academy of Sleep Medicine. Oct, 2011  |   Pubmed ID: 22003332
• Phased Whole-genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence
  PLoS Genetics. Sep, 2011  |   Pubmed ID: 21935354
• Precise Manipulation of Chromosomes in Vivo Enables Genome-wide Codon Replacement
  Science (New York, N.Y.). Jul, 2011  |   Pubmed ID: 21764749
• Barcoding Bias in High-throughput Multiplex Sequencing of MiRNA
  Genome Research. Sep, 2011  |   Pubmed ID: 21750102
• Multiplexed Genome Engineering and Genotyping Methods Applications for Synthetic Biology and Metabolic Engineering
  Methods in Enzymology. 2011  |   Pubmed ID: 21601688
• Proteome-wide Systems Analysis of a Cellulosic Biofuel-producing Microbe
  Molecular Systems Biology. Jan, 2011  |   Pubmed ID: 21245846
• Research, Collaboration, and Open Science Using Web 2.0
  Journal of Microbiology & Biology Education. 2010  |   Pubmed ID: 23653712
• The Human Microbiome Harbors a Diverse Reservoir of Antibiotic Resistance Genes
  Virulence. Jul-Aug, 2010  |   Pubmed ID: 21178459
• Scalable Gene Synthesis by Selective Amplification of DNA Pools from High-fidelity Microchips
  Nature Biotechnology. Dec, 2010  |   Pubmed ID: 21113165
• Collection and Motif-based Prediction of Phosphorylation Sites in Human Viruses
  Science Signaling. Aug, 2010  |   Pubmed ID: 20807955
• Reprogramming of T Cells from Human Peripheral Blood
  Cell Stem Cell. Jul, 2010  |   Pubmed ID: 20621044
• A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing
  PLoS Genetics. May, 2010  |   Pubmed ID: 20531933
• A Functional Metagenomic Approach for Expanding the Synthetic Biology Toolbox for Biomass Conversion
  Molecular Systems Biology. Apr, 2010  |   Pubmed ID: 20393580
• Extensive Phosphorylation with Overlapping Specificity by Mycobacterium Tuberculosis Serine/threonine Protein Kinases
  Proceedings of the National Academy of Sciences of the United States of America. Apr, 2010  |   Pubmed ID: 20368441
• Generation of Functional Human Hepatic Endoderm from Human Induced Pluripotent Stem Cells
  Hepatology (Baltimore, Md.). Jan, 2010  |   Pubmed ID: 19877180
• A Robust Approach to Identifying Tissue-specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells
  PLoS Genetics. Nov, 2009  |   Pubmed ID: 19911041
• Targeted Gene Inactivation in Clostridium Phytofermentans Shows That Cellulose Degradation Requires the Family 9 Hydrolase Cphy3367
  Molecular Microbiology. Dec, 2009  |   Pubmed ID: 19775243
• Evidence for Large Diversity in the Human Transcriptome Created by Alu RNA Editing
  Nucleic Acids Research. Nov, 2009  |   Pubmed ID: 19740767
• Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora
  Science (New York, N.Y.). Aug, 2009  |   Pubmed ID: 19713526
• Large-scale Identification of Genetic Design Strategies Using Local Search
  Molecular Systems Biology. 2009  |   Pubmed ID: 19690565
• Programming Cells by Multiplex Genome Engineering and Accelerated Evolution
  Nature. Aug, 2009  |   Pubmed ID: 19633652
• The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of Health-Centers for Disease Control and Prevention Multidisciplinary Workshop
  Genetics in Medicine : Official Journal of the American College of Medical Genetics. Aug, 2009  |   Pubmed ID: 19617843
• A Highly Annotated Whole-genome Sequence of a Korean Individual
  Nature. Aug, 2009  |   Pubmed ID: 19587683
• Rapid Prototyping of 3D DNA-origami Shapes with CaDNAno
  Nucleic Acids Research. Aug, 2009  |   Pubmed ID: 19531737
• Multiplex Padlock Targeted Sequencing Reveals Human Hypermutable CpG Variations
  Genome Research. Sep, 2009  |   Pubmed ID: 19525355
• Genome-wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing
  Science (New York, N.Y.). May, 2009  |   Pubmed ID: 19478186
• Targeted and Genome-scale Strategies Reveal Gene-body Methylation Signatures in Human Cells
  Nature Biotechnology. Apr, 2009  |   Pubmed ID: 19329998
• Meta-analysis of Age-related Gene Expression Profiles Identifies Common Signatures of Aging
  Bioinformatics (Oxford, England). Apr, 2009  |   Pubmed ID: 19189975
• The Human Ageing Genomic Resources: Online Databases and Tools for Biogerontologists
  Aging Cell. Feb, 2009  |   Pubmed ID: 18986374
• Predicting Protein Post-translational Modifications Using Meta-analysis of Proteome Scale Data Sets
  Molecular & Cellular Proteomics : MCP. Feb, 2009  |   Pubmed ID: 18974045
• Efficient MicroRNA Capture and Bar-coding Via Enzymatic Oligonucleotide Adenylation
  Nature Methods. Sep, 2008  |   Pubmed ID: 19160512
• Model-driven Analysis of Experimentally Determined Growth Phenotypes for 465 Yeast Gene Deletion Mutants Under 16 Different Conditions
  Genome Biology. 2008  |   Pubmed ID: 18808699
• Hippocrates Revisited? Old Ideals and New Realities
  Genomic Medicine. Jan, 2008  |   Pubmed ID: 18716915
• Bacteria Subsisting on Antibiotics
  Science (New York, N.Y.). Apr, 2008  |   Pubmed ID: 18388292
• Gene Synthesis by Circular Assembly Amplification
  Nature Methods. Jan, 2008  |   Pubmed ID: 18037891
• Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
  PLoS Genetics. Dec, 2007  |   Pubmed ID: 18159947
• Multiplex Amplification of Large Sets of Human Exons
  Nature Methods. Nov, 2007  |   Pubmed ID: 17934468
• A Proposal to Sequence Genomes of Unique Interest for Research on Aging
  The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences. Jun, 2007  |   Pubmed ID: 17595413
• Chromosomal Periodicity of Evolutionarily Conserved Gene Pairs
  Proceedings of the National Academy of Sciences of the United States of America. Jun, 2007  |   Pubmed ID: 17563360
• Analyses of Human-chimpanzee Orthologous Gene Pairs to Explore Evolutionary Hypotheses of Aging
  Mechanisms of Ageing and Development. May-Jun, 2007  |   Pubmed ID: 17459455
• An Analysis of the Relationship Between Metabolism, Developmental Schedules, and Longevity Using Phylogenetic Independent Contrasts
  The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences. Feb, 2007  |   Pubmed ID: 17339640
• Polony DNA Sequencing
  Current Protocols in Molecular Biology. Nov, 2006  |   Pubmed ID: 18265387
• Relationships Between P63 Binding, DNA Sequence, Transcription Activity, and Biological Function in Human Cells
  Molecular Cell. Nov, 2006  |   Pubmed ID: 17188034
• The Transition Between Transcriptional Initiation and Elongation in E. Coli is Highly Variable and Often Rate Limiting
  Molecular Cell. Dec, 2006  |   Pubmed ID: 17157257
• Global Gene Expression of Prochlorococcus Ecotypes in Response to Changes in Nitrogen Availability
  Molecular Systems Biology. 2006  |   Pubmed ID: 17016519
• Mammalian Ultraconserved Elements Are Strongly Depleted Among Segmental Duplications and Copy Number Variants
  Nature Genetics. Oct, 2006  |   Pubmed ID: 16998490
• Identifying Regulatory Mechanisms Using Individual Variation Reveals Key Role for Chromatin Modification
  Proceedings of the National Academy of Sciences of the United States of America. Sep, 2006  |   Pubmed ID: 16968785
• Towards Synthesis of a Minimal Cell
  Molecular Systems Biology. 2006  |   Pubmed ID: 16924266
• Sequencing Genomes from Single Cells by Polymerase Cloning
  Nature Biotechnology. Jun, 2006  |   Pubmed ID: 16732271
• Identifying Metabolic Enzymes with Multiple Types of Association Evidence
  BMC Bioinformatics. Mar, 2006  |   Pubmed ID: 16571130
• Long-range Polony Haplotyping of Individual Human Chromosome Molecules
  Nature Genetics. Mar, 2006  |   Pubmed ID: 16493423
• An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes
  PLoS Genetics. Feb, 2006  |   Pubmed ID: 16482229
• MapQuant: Open-source Software for Large-scale Protein Quantification
  Proteomics. Mar, 2006  |   Pubmed ID: 16470651
• Genomes for All
  Scientific American. Jan, 2006  |   Pubmed ID: 16468433
• Cells Discover Fire: Employing Reactive Oxygen Species in Development and Consequences for Aging
  Experimental Gerontology. Jan, 2006  |   Pubmed ID: 16226003
• From Systems Biology to Synthetic Biology
  Molecular Systems Biology. 2005  |   Pubmed ID: 16729067
• Expression Dynamics of a Cellular Metabolic Network
  Molecular Systems Biology. 2005  |   Pubmed ID: 16729051
• Genomic Analysis of LexA Binding Reveals the Permissive Nature of the Escherichia Coli Genome and Identifies Unconventional Target Sites
  Genes & Development. Nov, 2005  |   Pubmed ID: 16264194
• A Network of Transcriptionally Coordinated Functional Modules in Saccharomyces Cerevisiae
  Genome Research. Sep, 2005  |   Pubmed ID: 16109970
• Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome
  Science (New York, N.Y.). Sep, 2005  |   Pubmed ID: 16081699
• Genomes Optimize Reproduction: Aging As a Consequence of the Developmental Program
  Physiology (Bethesda, Md.). Aug, 2005  |   Pubmed ID: 16024513
• Molecular Weight Assessment of Proteins in Total Proteome Profiles Using 1D-PAGE and LC/MS/MS
  Proteome Science. Jun, 2005  |   Pubmed ID: 15941491
• Discovering Functional Transcription-factor Combinations in the Human Cell Cycle
  Genome Research. Jun, 2005  |   Pubmed ID: 15930495
• Preferred Analysis Methods for Affymetrix GeneChips Revealed by a Wholly Defined Control Dataset
  Genome Biology. 2005  |   Pubmed ID: 15693945
• Modular Epistasis in Yeast Metabolism
  Nature Genetics. Jan, 2005  |   Pubmed ID: 15592468
• Estimating and Improving Protein Interaction Error Rates
  Proceedings. IEEE Computational Systems Bioinformatics Conference. 2004  |   Pubmed ID: 16448015
• The Complete Genome and Proteome of Mycoplasma Mobile
  Genome Research. Aug, 2004  |   Pubmed ID: 15289470
• Filling Gaps in a Metabolic Network Using Expression Information
  Bioinformatics (Oxford, England). Aug, 2004  |   Pubmed ID: 15262797
• Preferred in Vivo Ubiquitination Sites
  Bioinformatics (Oxford, England). Dec, 2004  |   Pubmed ID: 15256413
• Prediction of Similarly Acting Cis-regulatory Modules by Subsequence Profiling and Comparative Genomics in Drosophila Melanogaster and D.pseudoobscura
  Bioinformatics (Oxford, England). Nov, 2004  |   Pubmed ID: 15145800
• Advanced Sequencing Technologies: Methods and Goals
  Nature Reviews. Genetics. May, 2004  |   Pubmed ID: 15143316
• Mathematical Models of Diffusion-constrained Polymerase Chain Reactions: Basis of High-throughput Nucleic Acid Assays and Simple Self-organizing Systems
  Journal of Theoretical Biology. May, 2004  |   Pubmed ID: 15064081
• A Motif Co-occurrence Approach for Genome-wide Prediction of Transcription-factor-binding Sites in Escherichia Coli
  Genome Research. Feb, 2004  |   Pubmed ID: 14762058
• Identification of Many MicroRNAs That Copurify with Polyribosomes in Mammalian Neurons
  Proceedings of the National Academy of Sciences of the United States of America. Jan, 2004  |   Pubmed ID: 14691248
• YMGV: a Cross-species Expression Data Mining Tool
  Nucleic Acids Research. Jan, 2004  |   Pubmed ID: 14681424
• The Amino-acid Mutational Spectrum of Human Genetic Disease
  Genome Biology. 2003  |   Pubmed ID: 14611658
• Parallel Competition Analysis of Saccharomyces Cerevisiae Strains Differing by a Single Base Using Polymerase Colonies
  Nucleic Acids Research. Aug, 2003  |   Pubmed ID: 12888536
• Digital Genotyping and Haplotyping with Polymerase Colonies
  Proceedings of the National Academy of Sciences of the United States of America. May, 2003  |   Pubmed ID: 12730373
• Global RNA Half-life Analysis in Escherichia Coli Reveals Positional Patterns of Transcript Degradation
  Genome Research. Feb, 2003  |   Pubmed ID: 12566399
• A Microarray-based Antibiotic Screen Identifies a Regulatory Role for Supercoiling in the Osmotic Stress Response of Escherichia Coli
  Genome Research. Feb, 2003  |   Pubmed ID: 12566398
• Genome-wide Co-occurrence of Promoter Elements Reveals a Cis-regulatory Cassette of RRNA Transcription Motifs in Saccharomyces Cerevisiae
  Genome Research. Nov, 2002  |   Pubmed ID: 12421759
• Analysis of Optimality in Natural and Perturbed Metabolic Networks
  Proceedings of the National Academy of Sciences of the United States of America. Nov, 2002  |   Pubmed ID: 12415116
• Escherichia Coli Gene Expression Responsive to Levels of the Response Regulator EvgA
  Journal of Bacteriology. Nov, 2002  |   Pubmed ID: 12399493
• Computational Discovery of Sense-antisense Transcription in the Human and Mouse Genomes
  Genome Biology. Aug, 2002  |   Pubmed ID: 12225583
• Genome-scale Metabolic Model of Helicobacter Pylori 26695
  Journal of Bacteriology. Aug, 2002  |   Pubmed ID: 12142428
• Computation-based Discovery of Related Transcriptional Regulatory Modules and Motifs Using an Experimentally Validated Combinatorial Model
  Genome Research. Jul, 2002  |   Pubmed ID: 12097338
• Measuring Absolute Expression with Microarrays with a Calibrated Reference Sample and an Extended Signal Intensity Range
  Proceedings of the National Academy of Sciences of the United States of America. May, 2002  |   Pubmed ID: 12032321
• Discrimination Between Paralogs Using Microarray Analysis: Application to the Yap1p and Yap2p Transcriptional Networks
  Molecular Biology of the Cell. May, 2002  |   Pubmed ID: 12006656
• Nucleotides of Transcription Factor Binding Sites Exert Interdependent Effects on the Binding Affinities of Transcription Factors
  Nucleic Acids Research. Mar, 2002  |   Pubmed ID: 11861919
• Exploring the DNA-binding Specificities of Zinc Fingers with DNA Microarrays
  Proceedings of the National Academy of Sciences of the United States of America. Jun, 2001  |   Pubmed ID: 11404456
• Predicting Regulons and Their Cis-regulatory Motifs by Comparative Genomics
  Nucleic Acids Research. Nov, 2000  |   Pubmed ID: 11071941