Wyss Institute for Biologically Inspired Engineering
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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
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors.
Nucleic acids research Mar, 2002 | Pubmed ID: 11861919
A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli.
Genome research Feb, 2004 | Pubmed ID: 14762058
The complete genome and proteome of Mycoplasma mobile.
Genome research Aug, 2004 | Pubmed ID: 15289470
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
The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.
Molecular cell Dec, 2006 | Pubmed ID: 17157257
The most conserved genome segments for life detection on Earth and other planets.
Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life Dec, 2008 | Pubmed ID: 18853276
Rapid prototyping of 3D DNA-origami shapes with caDNAno.
Nucleic acids research Aug, 2009 | Pubmed ID: 19531737
Programming cells by multiplex genome engineering and accelerated evolution.
Nature Aug, 2009 | Pubmed ID: 19633652
Free Factories: Unified Infrastructure for Data Intensive Web Services.
Proceedings of the USENIX ... annual Technical Conference. USENIX Technical Conference May, 2008 | Pubmed ID: 20514356
Reprogramming of T cells from human peripheral blood.
Cell stem cell Jul, 2010 | Pubmed ID: 20621044
Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription.
Nature biotechnology Feb, 2011 | Pubmed ID: 21248753
A new dawn for industrial photosynthesis.
Photosynthesis research Mar, 2011 | Pubmed ID: 21318462
Autoantigen discovery with a synthetic human peptidome.
Nature biotechnology May, 2011 | Pubmed ID: 21602805
Precise manipulation of chromosomes in vivo enables genome-wide codon replacement.
Science (New York, N.Y.) Jul, 2011 | Pubmed ID: 21764749
High-throughput multiplex sequencing of miRNA.
Current protocols in human genetics Apr, 2012 | Pubmed ID: 22470142
Genome-scale promoter engineering by coselection MAGE.
Nature methods Jun, 2012 | Pubmed ID: 22484848
Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection.
Nucleic acids research Sep, 2012 | Pubmed ID: 22638574
A BioBrick compatible strategy for genetic modification of plants.
Journal of biological engineering , 2012 | Pubmed ID: 22716313
Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis.
ACS synthetic biology Feb, 2012 | Pubmed ID: 22737598
How accurate can genetic predictions be?
BMC genomics Jul, 2012 | Pubmed ID: 22827772
Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases.
PloS one , 2012 | Pubmed ID: 22957093
Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA.
Nature chemistry Oct, 2012 | Pubmed ID: 23000997
RNA-guided human genome engineering via Cas9.
Science (New York, N.Y.) Feb, 2013 | Pubmed ID: 23287722
PhIP-Seq characterization of autoantibodies from patients with multiple sclerosis, type 1 diabetes and rheumatoid arthritis.
Journal of autoimmunity Jun, 2013 | Pubmed ID: 23497938
Barcoding cells using cell-surface programmable DNA-binding domains.
Nature methods May, 2013 | Pubmed ID: 23503053
Nanotools for neuroscience and brain activity mapping.
ACS nano Mar, 2013 | Pubmed ID: 23514423
Research, collaboration, and open science using web 2.0.
Journal of microbiology & biology education , 2010 | Pubmed ID: 23653712
Heritable genome editing in C. elegans via a CRISPR-Cas9 system.
Nature methods Aug, 2013 | Pubmed ID: 23817069
Optical control of mammalian endogenous transcription and epigenetic states.
Nature Aug, 2013 | Pubmed ID: 23877069
CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering.
Nature biotechnology Sep, 2013 | Pubmed ID: 23907171
Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9.
Nature biotechnology Aug, 2013 | Pubmed ID: 23929339
Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system.
Genetics Nov, 2013 | Pubmed ID: 23979579
Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria.
Nucleic acids research Jan, 2014 | Pubmed ID: 24049072
Cas9 as a versatile tool for engineering biology.
Nature methods Oct, 2013 | Pubmed ID: 24076990
Genomically recoded organisms expand biological functions.
Science (New York, N.Y.) Oct, 2013 | Pubmed ID: 24136966
Physical principles for scalable neural recording.
Frontiers in computational neuroscience , 2013 | Pubmed ID: 24187539
The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies.
PLoS pathogens , 2013 | Pubmed ID: 24278016
The role of replicates for error mitigation in next-generation sequencing.
Nature reviews. Genetics 01, 2014 | Pubmed ID: 24322726
Rational optimization of tolC as a powerful dual selectable marker for genome engineering.
Nucleic acids research Apr, 2014 | Pubmed ID: 24452804
Highly multiplexed subcellular RNA sequencing in situ.
Science (New York, N.Y.) Mar, 2014 | Pubmed ID: 24578530
Realizing the potential of synthetic biology.
Nature reviews. Molecular cell biology 04, 2014 | Pubmed ID: 24622617
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
Syntrophic exchange in synthetic microbial communities.
Proceedings of the National Academy of Sciences of the United States of America May, 2014 | Pubmed ID: 24778240
Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies.
Nature medicine Jun, 2014 | Pubmed ID: 24813252
Direct mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides.
ACS synthetic biology Jan, 2015 | Pubmed ID: 24856730
CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing.
Nucleic acids research Jul, 2014 | Pubmed ID: 24861617
Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA).
Bioinformatics (Oxford, England) Oct, 2014 | Pubmed ID: 24990609
Multiplex single-molecule interaction profiling of DNA-barcoded proteins.
Nature Nov, 2014 | Pubmed ID: 25252978
Engineering allostery.
Trends in genetics : TIG Dec, 2014 | Pubmed ID: 25306102
Rapid neurogenesis through transcriptional activation in human stem cells.
Molecular systems biology Nov, 2014 | Pubmed ID: 25403753
Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells.
Nucleic acids research Feb, 2015 | Pubmed ID: 25414332
Evolution-guided optimization of biosynthetic pathways.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2014 | Pubmed ID: 25453111
Biocontainment of genetically modified organisms by synthetic protein design.
Nature Feb, 2015 | Pubmed ID: 25607366
Spatial information in large-scale neural recordings.
Frontiers in computational neuroscience , 2014 | Pubmed ID: 25653613
Highly efficient Cas9-mediated transcriptional programming.
Nature methods Apr, 2015 | Pubmed ID: 25730490
Synthetic biosensors for precise gene control and real-time monitoring of metabolites.
Nucleic acids research Sep, 2015 | Pubmed ID: 26152303
Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach.
Nature methods Sep, 2015 | Pubmed ID: 26167643
Bioart.
Trends in biotechnology Dec, 2015 | Pubmed ID: 26617334
Engineering an allosteric transcription factor to respond to new ligands.
Nature methods Feb, 2016 | Pubmed ID: 26689263
Tools for the Microbiome: Nano and Beyond.
ACS nano Jan, 2016 | Pubmed ID: 26695070
A general strategy to construct small molecule biosensors in eukaryotes.
eLife Dec, 2015 | Pubmed ID: 26714111
In vivo gene editing in dystrophic mouse muscle and muscle stem cells.
Science (New York, N.Y.) Jan, 2016 | Pubmed ID: 26721686
Genetically encoded sensors enable real-time observation of metabolite production.
Proceedings of the National Academy of Sciences of the United States of America Mar, 2016 | Pubmed ID: 26858408
Multiplexed Engineering in Biology.
Trends in biotechnology Mar, 2016 | Pubmed ID: 26897356
Biosensor-based engineering of biosynthetic pathways.
Current opinion in biotechnology 12, 2016 | Pubmed ID: 26998575
Nucleic acid memory.
Nature materials Apr, 2016 | Pubmed ID: 27005909
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
Precision Chemistry for Precision Medicine.
ACS central science Mar, 2015 | Pubmed ID: 27162939
Molecular recordings by directed CRISPR spacer acquisition.
Science (New York, N.Y.) Jul, 2016 | Pubmed ID: 27284167
Design, synthesis, and testing toward a 57-codon genome.
Science (New York, N.Y.) Aug, 2016 | Pubmed ID: 27540174
CRISPR-Cas9 System: Opportunities and Concerns.
Clinical chemistry 10, 2016 | Pubmed ID: 27551006
A multifunctional AAV-CRISPR-Cas9 and its host response.
Nature methods 10, 2016 | Pubmed ID: 27595405
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
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
Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation.
BMC evolutionary biology 10, 2016 | Pubmed ID: 27782796
Rapidly evolving homing CRISPR barcodes.
Nature methods 02, 2017 | Pubmed ID: 27918539
Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies.
Nature protocols Jan, 2017 | Pubmed ID: 27929521
Cushing's syndrome mutant PKA exhibits altered substrate specificity.
FEBS letters 02, 2017 | Pubmed ID: 28100013
sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity.
ACS synthetic biology 05, 2017 | Pubmed ID: 28146356
Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform.
Nature microbiology Feb, 2017 | Pubmed ID: 28165460
An unbiased index to quantify participant's phenotypic contribution to an open-access cohort.
Scientific reports 04, 2017 | Pubmed ID: 28387241
Evolutionary dynamics of CRISPR gene drives.
Science advances Apr, 2017 | Pubmed ID: 28435878
Nucleotide-time alignment for molecular recorders.
PLoS computational biology May, 2017 | Pubmed ID: 28459860
Optimizing complex phenotypes through model-guided multiplex genome engineering.
Genome biology 05, 2017 | Pubmed ID: 28545477
Millstone: software for multiplex microbial genome analysis and engineering.
Genome biology 05, 2017 | Pubmed ID: 28545559
Scalable Device for Automated Microbial Electroporation in a Digital Microfluidic Platform.
ACS synthetic biology 09, 2017 | Pubmed ID: 28569062
CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria.
Nature 07, 2017 | Pubmed ID: 28700573
Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder.
Nature neuroscience 09, 2017 | Pubmed ID: 28714951
Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9.
Science (New York, N.Y.) 09, 2017 | Pubmed ID: 28798043
Extracellular Vesicle Isolation and Analysis by Western Blotting.
Methods in molecular biology (Clifton, N.J.) , 2017 | Pubmed ID: 28828654
Imaging of Isolated Extracellular Vesicles Using Fluorescence Microscopy.
Methods in molecular biology (Clifton, N.J.) , 2017 | Pubmed ID: 28828661
Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues.
Nano letters 10, 2017 | Pubmed ID: 28933153
Heterologous erythromycin production across strain and plasmid construction.
Biotechnology progress Jan, 2018 | Pubmed ID: 28960932
DNA sequencing at 40: past, present and future.
Nature 10, 2017 | Pubmed ID: 29019985
Mature induced-pluripotent-stem-cell-derived human podocytes reconstitute kidney glomerular-capillary-wall function on a chip.
Nature biomedical engineering , 2017 | Pubmed ID: 29038743
A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans.
Nature microbiology Oct, 2017 | Pubmed ID: 29062088
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
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
Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration.
Nature microbiology Mar, 2018 | Pubmed ID: 29379209
Adaptive evolution of genomically recoded .
Proceedings of the National Academy of Sciences of the United States of America 03, 2018 | Pubmed ID: 29440500
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
Enabling multiplexed testing of pooled donor cells through whole-genome sequencing.
Genome medicine 04, 2018 | Pubmed ID: 29673390
An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance.
Cell Apr, 2018 | Pubmed ID: 29677511
High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing.
Nucleic acids research Jul, 2018 | Pubmed ID: 29718339
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-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast.
Nature biotechnology Jul, 2018 | Pubmed ID: 29786095
Current CRISPR gene drive systems are likely to be highly invasive in wild populations.
eLife Jun, 2018 | Pubmed ID: 29916367
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
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
An enhanced CRISPR repressor for targeted mammalian gene regulation.
Nature methods Aug, 2018 | Pubmed ID: 30013045
Biosensor libraries harness large classes of binding domains for construction of allosteric transcriptional regulators.
Nature communications Aug, 2018 | Pubmed ID: 30082754
Developmental barcoding of whole mouse via homing CRISPR.
Science (New York, N.Y.) 08, 2018 | Pubmed ID: 30093604
Sathiji Nageshwaran*,1,2,
Alejandro Chavez*,1,2,3,
Nan Cher Yeo1,2,
Xiaoge Guo1,2,
Alissa Lance-Byrne1,
Angela Tung1,
James J. Collins1,4,5,6,7,
George M. Church1,2
1Wyss Institute for Biologically Inspired Engineering, Harvard University,
2Department of Genetics, Harvard Medical School,
3Department of Pathology, Massachusetts General Hospital,
4Institute for Medical Engineering & Science, Massachusetts Institute of Technology,
5Synthetic Biology Center, Massachusetts Institute of Technology,
6Department of Biological Engineering, Massachusetts Institute of Technology,
7, Broad Institute
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