Synthetic biology in mammalian cells: next generation research tools and therapeutics

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

A LOV2 Domain-Based Optogenetic Tool to Control Protein Degradation and Cellular Function

(2013) Christian Renicke et al.   CHEMISTRY & BIOLOGY

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

Protein Scaffold-Activated Protein Trans-Splicing in Mammalian Cells

(2013) Daniel F. Selgrade et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Generation of tumor-targeted human T lymphocytes from induced pluripotent stem cells for cancer therapy

(2013) Maria Themeli et al.   NATURE BIOTECHNOLOGY

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

Locus-specific editing of histone modifications at endogenous enhancers

(2013) Eric M Mendenhall et al.   NATURE BIOTECHNOLOGY

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

Optogenetic protein clustering and signaling activation in mammalian cells

(2013) Lukasz J Bugaj et al.   NATURE METHODS

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

Precise and reliable gene expression via standard transcription and translation initiation elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

Rapid, modular and reliable construction of complex mammalian gene circuits

(2013) Patrick Guye et al.   NUCLEIC ACIDS RESEARCH

Two- and three-input TALE-based AND logic computation in embryonic stem cells

(2013) Florian Lienert et al.   NUCLEIC ACIDS RESEARCH

Multi-chromatic control of mammalian gene expression and signaling

(2013) Konrad Müller et al.   NUCLEIC ACIDS RESEARCH

Dynamically Reshaping Signaling Networks to Program Cell Fate via Genetic Controllers

(2013) K. E. Galloway et al.   SCIENCE

Lentiviral Hematopoietic Stem Cell Gene Therapy in Patients with Wiskott-Aldrich Syndrome

(2013) A. Aiuti et al.   SCIENCE

Lentiviral Hematopoietic Stem Cell Gene Therapy Benefits Metachromatic Leukodystrophy

(2013) A. Biffi et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

In Vivo-Directed Evolution of a New Adeno-Associated Virus for Therapeutic Outer Retinal Gene Delivery from the Vitreous

(2013) D. Dalkara et al.   Science Translational Medicine

Synthetic Generation of Influenza Vaccine Viruses for Rapid Response to Pandemics

(2013) P. R. Dormitzer et al.   Science Translational Medicine

RNA: The new revolution in nucleic acid vaccines

(2013) Andrew J. Geall et al.   SEMINARS IN IMMUNOLOGY

A tale of two specificities: bispecific antibodies for therapeutic and diagnostic applications

(2013) Hannah Byrne et al.   TRENDS IN BIOTECHNOLOGY

Ultraviolet-B-mediated induction of protein–protein interactions in mammalian cells

(2013) Remco P. Crefcoeur et al.   Nature Communications

Reverse Engineering Validation using a Benchmark Synthetic Gene Circuit in Human Cells

(2013) Taek Kang et al.   ACS Synthetic Biology

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

Optogenetic control of cell function using engineered photoreceptors

(2012) Gopal P. Pathak et al.   BIOLOGY OF THE CELL

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Synthetic biology advancing clinical applications

(2012) Marc Folcher et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Efficacy and long-term safety of alipogene tiparvovec (AAV1-LPLS447X) gene therapy for lipoprotein lipase deficiency: an open-label trial

(2012) D Gaudet et al.   GENE THERAPY

Synthetic memory circuits for tracking human cell fate

(2012) D. R. Burrill et al.   GENES & DEVELOPMENT

Light-Inducible Spatiotemporal Control of Gene Activation by Customizable Zinc Finger Transcription Factors

(2012) Lauren R. Polstein et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells

(2012) Ping Wei et al.   NATURE

Disentangling nestedness from models of ecological complexity

(2012) Alex James et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Combinatorial antigen recognition with balanced signaling promotes selective tumor eradication by engineered T cells

(2012) Christopher C Kloss et al.   NATURE BIOTECHNOLOGY

Rapid hierarchical assembly of medium-size DNA cassettes

(2012) Jonathan Leo Schmid-Burgk et al.   NUCLEIC ACIDS RESEARCH

Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells

(2012) Maarten Holkers et al.   NUCLEIC ACIDS RESEARCH

A tunable zinc finger-based framework for Boolean logic computation in mammalian cells

(2012) Jason J. Lohmueller et al.   NUCLEIC ACIDS RESEARCH

Engineering synthetic TAL effectors with orthogonal target sites

(2012) Abhishek Garg et al.   NUCLEIC ACIDS RESEARCH

Stable Gene Targeting in Human Cells Using Single-Strand Oligonucleotides with Modified Bases

(2012) Xavier Rios et al.   PLoS One

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair

(2012) G. T. Kapp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pharmaceutically controlled designer circuit for the treatment of the metabolic syndrome

(2012) H. Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Synthetic Biology Approach to Understanding Cellular Information Processing

(2012) Katherine A. Riccione et al.   ACS Synthetic Biology

Functional analysis of transcription factor binding sites in human promoters

(2012) Troy W Whitfield et al.   GENOME BIOLOGY

Safety and persistence of adoptively transferred autologous CD19-targeted T cells in patients with relapsed or chemotherapy refractory B-cell leukemias

(2011) R. J. Brentjens et al.   BLOOD

Tunable Signal Processing in Synthetic MAP Kinase Cascades

(2011) Ellen C. O'Shaughnessy et al.   CELL

A Class of Human Proteins that Deliver Functional Proteins into Mammalian Cells In Vitro and In Vivo

(2011) James J. Cronican et al.   CHEMISTRY & BIOLOGY

Engineering Biological Systems with Synthetic RNA Molecules

(2011) Joe C. Liang et al.   MOLECULAR CELL

Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template

(2011) L. Bleris et al.   Molecular Systems Biology

Engineering Dendritic Cells to Enhance Cancer Immunotherapy

(2011) Jeanette E Boudreau et al.   MOLECULAR THERAPY

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

(2011) Jessica S. Dymond et al.   NATURE

Small-molecule displacement of a cryptic degron causes conditional protein degradation

(2011) Kimberly M Bonger et al.   Nature Chemical Biology

A Resource of Cre Driver Lines for Genetic Targeting of GABAergic Neurons in Cerebral Cortex

(2011) Hiroki Taniguchi et al.   NEURON

Assembly of custom TALE-type DNA binding domains by modular cloning

(2011) Robert Morbitzer et al.   NUCLEIC ACIDS RESEARCH

A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice

(2011) H. Ye et al.   SCIENCE

Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells

(2011) Z. Xie et al.   SCIENCE

Cell penetrating elastin-like polypeptides for therapeutic peptide delivery

(2010) Gene L. Bidwell et al.   ADVANCED DRUG DELIVERY REVIEWS

Photomodulation of Protein Trans-Splicing Through Backbone Photocaging of the DnaE Split Intein

(2010) Luis Berrade et al.   CHEMBIOCHEM

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS

A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering

(2010) Aaron W. Reinke et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A tunable dual-promoter integrator for targeting of cancer cells

(2010) Lior Nissim et al.   Molecular Systems Biology

Targeted Delivery of RNAi Therapeutics With Endogenous and Exogenous Ligand-Based Mechanisms

(2010) Akin Akinc et al.   MOLECULAR THERAPY

Live attenuated influenza virus vaccines by computer-aided rational design

(2010) Steffen Mueller et al.   NATURE BIOTECHNOLOGY

Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells

(2010) Eirini P Papapetrou et al.   NATURE BIOTECHNOLOGY

Self-sufficient control of urate homeostasis in mice by a synthetic circuit

(2010) Christian Kemmer et al.   NATURE BIOTECHNOLOGY

Chemical synthesis of the mouse mitochondrial genome

(2010) Daniel G Gibson et al.   NATURE METHODS

Rationally designed logic integration of regulatory signals in mammalian cells

(2010) Madeleine Leisner et al.   Nature Nanotechnology

Directed molecular evolution of DREADDs: a generic approach to creating next-generation RASSLs

(2010) Shuyun Dong et al.   Nature Protocols

Synthetic biology: applications come of age

(2010) Ahmad S. Khalil et al.   NATURE REVIEWS GENETICS

Designing customized cell signalling circuits

(2010) Wendell A. Lim   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An engineered mammalian band-pass network

(2010) D. Greber et al.   NUCLEIC ACIDS RESEARCH

Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems

(2010) Y. Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors

(2010) R. Morbitzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic design of strong promoters

(2010) M. R. Schlabach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anti-glycophorin single-chain Fv fusion to low-affinity mutant erythropoietin improves red blood cell-lineage specificity

(2010) N. D. Taylor et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins

(2010) S. J. Culler et al.   SCIENCE

Effective Gene Silencing by Multilayered siRNA-Coated Gold Nanoparticles

(2010) Seung Koo Lee et al.   Small

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Functional Protein Delivery into Neurons Using Polymeric Nanoparticles

(2009) Linda Hasadsri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A tunable synthetic mammalian oscillator

(2009) Marcel Tigges et al.   NATURE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Genome engineering

(2009) Peter A Carr et al.   NATURE BIOTECHNOLOGY

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Split-Cre Complementation Indicates Coincident Activity of Different Genes In Vivo

(2009) Johannes Hirrlinger et al.   PLoS One

An engineered substance P variant for receptor-mediated delivery of synthetic antibodies into tumor cells

(2009) S. S. Rizk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

Antibody–cytokine fusion proteins: applications in cancer therapy

(2008) Elizabeth Ortiz-Sánchez et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Enhancement of Cell Type Specificity by Quantitative Modulation of a Chimeric Ligand

(2008) Pablo Cironi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rapid “Open-Source” Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification

(2008) Morgan L. Maeder et al.   MOLECULAR CELL

Efficient In Vivo Delivery of siRNA to the Liver by Conjugation of α-Tocopherol

(2008) Kazutaka Nishina et al.   MOLECULAR THERAPY

Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases

(2008) Elena E Perez et al.   NATURE BIOTECHNOLOGY

A combinatorial library of lipid-like materials for delivery of RNAi therapeutics

(2008) Akin Akinc et al.   NATURE BIOTECHNOLOGY

Global Protein Stability Profiling in Mammalian Cells

(2008) H.-C. S. Yen et al.   SCIENCE

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

(2008) J. R. Coleman et al.   SCIENCE

Higher-Order Cellular Information Processing with Synthetic RNA Devices

(2008) M. N. Win et al.   SCIENCE