Programmable protein circuit design

Computation-guided optimization of split protein systems

(2021) Taylor B. Dolberg et al.   Nature Chemical Biology

Phase separation provides a mechanism to reduce noise in cells

(2020) A. Klosin et al.   SCIENCE

Rewiring of endogenous signaling pathways to genomic targets for therapeutic cell reprogramming

(2020) Krzysztof Krawczyk et al.   Nature Communications

Constraints on the expansion of paralogous protein families

(2020) Conor J. McClune et al.   CURRENT BIOLOGY

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

(2020) Kathy Y. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo design of protein logic gates

(2020) Zibo Chen et al.   SCIENCE

Systematically optimized BCMA/CS1 bispecific CAR-T cells robustly control heterogeneous multiple myeloma

(2020) Eugenia Zah et al.   Nature Communications

Engineering CAR-T Cells for Next-Generation Cancer Therapy

(2020) Mihe Hong et al.   CANCER CELL

On the cutting edge: protease-based methods for sensing and controlling cell biology

(2020) H. Kay Chung et al.   NATURE METHODS

Phosphoregulated orthogonal signal transduction in mammalian cells

(2020) Leo Scheller et al.   Nature Communications

Point-of-care CRISPR/Cas nucleic acid detection: Recent advances, challenges and opportunities

(2020) Jeanne E. van Dongen et al.   BIOSENSORS & BIOELECTRONICS

Designed protein logic to target cells with precise combinations of surface antigens

(2020) Marc J. Lajoie et al.   SCIENCE

Tunable multiphase dynamics of arginine and lysine liquid condensates

(2020) Rachel S. Fisher et al.   Nature Communications

Protease circuits for processing biological information

(2020) Brandon Alexander Holt et al.   Nature Communications

Conditional Recruitment to a DNA-Bound CRISPR–Cas Complex Using a Colocalization-Dependent Protein Switch

(2020) Robin L. Kirkpatrick et al.   ACS Synthetic Biology

Precise T cell recognition programs designed by transcriptionally linking multiple receptors

(2020) Jasper Z. Williams et al.   SCIENCE

Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes

(2019) Christopher D. Reinkemeier et al.   SCIENCE

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly

(2019) Damien Woods et al.   NATURE

Rewiring bacterial two-component systems by modular DNA-binding domain swapping

(2019) Sebastian R. Schmidl et al.   Nature Chemical Biology

Molecular digital data storage using DNA

(2019) Luis Ceze et al.   NATURE REVIEWS GENETICS

Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies

(2019) Caleb J. Bashor et al.   SCIENCE

A compact synthetic pathway rewires cancer signaling to therapeutic effector release

(2019) Hokyung K. Chung et al.   SCIENCE

Controlling Matter at the Molecular Scale with DNA Circuits

(2019) Dominic Scalise et al.   Annual Review of Biomedical Engineering

A universal biomolecular integral feedback controller for robust perfect adaptation

(2019) Stephanie K. Aoki et al.   NATURE

Modular and tunable biological feedback control using a de novo protein switch

(2019) Andrew H. Ng et al.   NATURE

De novo design of bioactive protein switches

(2019) Robert A. Langan et al.   NATURE

Dynamic Control of Peptide Strand Displacement Reaction Using Functional Biomolecular Domain for Biosensing

(2019) Yifan Dai et al.   ACS Sensors

Multi-input chemical control of protein dimerization for programming graded cellular responses

(2019) Glenna Wink Foight et al.   NATURE BIOTECHNOLOGY

Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space

(2019) Conor J. McClune et al.   NATURE

Programmable biomolecular switches for rewiring flux in Escherichia coli

(2019) Cong Gao et al.   Nature Communications

Artificial signaling in mammalian cells enabled by prokaryotic two-component system

(2019) Alain Mazé et al.   Nature Chemical Biology

Universal Chimeric Antigen Receptors for Multiplexed and Logical Control of T Cell Responses

(2018) Jang Hwan Cho et al.   CELL

A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo

(2018) Suping Li et al.   NATURE BIOTECHNOLOGY

Generalized extracellular molecule sensor platform for programming cellular behavior

(2018) Leo Scheller et al.   Nature Chemical Biology

Designing cell function: assembly of synthetic gene circuits for cell biology applications

(2018) Mingqi Xie et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils

(2018) Mike C. Groth et al.   Chemical Science

Engineering modular intracellular protein sensor-actuator devices

(2018) Velia Siciliano et al.   Nature Communications

Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks

(2018) Kevin M. Cherry et al.   NATURE

Programmable protein circuits in living cells

(2018) Xiaojing J. Gao et al.   SCIENCE

Controllable protein phase separation and modular recruitment to form responsive membraneless organelles

(2018) Benjamin S. Schuster et al.   Nature Communications

Protease-Activatable Scaffold Proteins as Versatile Molecular Hubs in Synthetic Signaling Networks

(2018) Stijn J. A. Aper et al.   ACS Synthetic Biology

Engineering Epigenetic Regulation Using Synthetic Read-Write Modules

(2018) Minhee Park et al.   CELL

Dynamic control of endogenous metabolism with combinatorial logic circuits

(2018) Felix Moser et al.   Molecular Systems Biology

Programmable design of orthogonal protein heterodimers

(2018) Zibo Chen et al.   NATURE

Polarized displacement by transcription activator-like effectors for regulatory circuits

(2018) Tina Lebar et al.   Nature Chemical Biology

Design of fast proteolysis-based signaling and logic circuits in mammalian cells

(2018) Tina Fink et al.   Nature Chemical Biology

Ultrahigh specificity in a network of computationally designed protein-interaction pairs

(2018) Ravit Netzer et al.   Nature Communications

Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits

(2017) Omer Karin et al.   Molecular Systems Biology

Massively parallel de novo protein design for targeted therapeutics

(2017) Aaron Chevalier et al.   NATURE

Gigadalton-scale shape-programmable DNA assemblies

(2017) Klaus F. Wagenbauer et al.   NATURE

Enzyme-free nucleic acid dynamical systems

(2017) Niranjan Srinivas et al.   SCIENCE

A cargo-sorting DNA robot

(2017) Anupama J. Thubagere et al.   SCIENCE

Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system

(2017) Nathan H. Kipniss et al.   Nature Communications

Multiplexing Engineered Receptors for Multiparametric Evaluation of Environmental Ligands

(2017) Rachel M. Hartfield et al.   ACS Synthetic Biology

Ultrasensitive Scaffold-Dependent Protease Sensors with Large Dynamic Range

(2017) Viktor Stein et al.   ACS Synthetic Biology

Synthekines are surrogate cytokine and growth factor agonists that compel signaling through non-natural receptor dimers

(2017) Ignacio Moraga et al.   eLife

Tracing neuronal circuits in transgenic animals by transneuronal control of transcription (TRACT)

(2017) Ting-hao Huang et al.   eLife

Nanobody Technology: A Versatile Toolkit for Microscopic Imaging, Protein–Protein Interaction Analysis, and Protein Function Exploration

(2017) Els Beghein et al.   Frontiers in Immunology

Design of Tunable Oscillatory Dynamics in a Synthetic NF-κB Signaling Circuit

(2017) Zhi-Bo Zhang et al.   Cell Systems

Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits

(2016) Kole T. Roybal et al.   CELL

Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors

(2016) Leonardo Morsut et al.   CELL

Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors

(2016) Kole T. Roybal et al.   CELL

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

Tandem CAR T cells targeting HER2 and IL13Rα2 mitigate tumor antigen escape

(2016) Meenakshi Hegde et al.   JOURNAL OF CLINICAL INVESTIGATION

Dual CD19 and CD123 targeting prevents antigen-loss relapses after CD19-directed immunotherapies

(2016) Marco Ruella et al.   JOURNAL OF CLINICAL INVESTIGATION

Rewiring human cellular input–output using modular extracellular sensors

(2016) Kelly A Schwarz et al.   Nature Chemical Biology

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Post-translational control of genetic circuits usingPotyvirusproteases

(2016) Jesus Fernandez-Rodriguez et al.   NUCLEIC ACIDS RESEARCH

Engineering dynamical control of cell fate switching using synthetic phospho-regulons

(2016) Russell M. Gordley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity

(2016) S. E. Boyken et al.   SCIENCE

Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology

(2016) Barbara Jusiak et al.   TRENDS IN BIOTECHNOLOGY

Rewiring MAP kinases in Saccharomyces cerevisiae to regulate novel targets through ubiquitination

(2016) Benjamin Groves et al.   eLife

T Cells Expressing CD19/CD20 Bispecific Chimeric Antigen Receptors Prevent Antigen Escape by Malignant B Cells

(2016) E. Zah et al.   Cancer Immunology Research

Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates

(2015) Christopher D. Aakre et al.   CELL

Advances in synthetic dynamic circuits design: using novel synthetic parts to engineer new generations of gene oscillations

(2015) Steven William Sowa et al.   CURRENT OPINION IN BIOTECHNOLOGY

DNA sense-and-respond protein modules for mammalian cells

(2015) Shimyn Slomovic et al.   NATURE METHODS

Simple synthetic protein scaffolds can create adjustable artificial MAPK circuits in yeast and mammalian cells

(2015) Jihoon Ryu et al.   Science Signaling

Simple synthetic protein scaffolds can create adjustable artificial MAPK circuits in yeast and mammalian cells

(2015) Jihoon Ryu et al.   Science Signaling

Paradoxical Signaling by a Secreted Molecule Leads to Homeostasis of Cell Levels

(2014) Yuval Hart et al.   CELL

Toehold Switches: De-Novo-Designed Regulators of Gene Expression

(2014) Alexander A. Green et al.   CELL

Chemical Biology Strategies for Posttranslational Control of Protein Function

(2014) Rishi Rakhit et al.   CHEMISTRY & BIOLOGY

mRNA-based therapeutics — developing a new class of drugs

(2014) Ugur Sahin et al.   NATURE REVIEWS DRUG DISCOVERY

A brief history of synthetic biology

(2014) D. Ewen Cameron et al.   NATURE REVIEWS MICROBIOLOGY

Protease-based synthetic sensing and signal amplification

(2014) Viktor Stein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transplantation of prokaryotic two-component signaling pathways into mammalian cells

(2014) J. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

Ultrasensitivity part I: Michaelian responses and zero-order ultrasensitivity

(2014) James E. Ferrell et al.   TRENDS IN BIOCHEMICAL SCIENCES

Ultrasensitivity part II: multisite phosphorylation, stoichiometric inhibitors, and positive feedback

(2014) James E. Ferrell et al.   TRENDS IN BIOCHEMICAL SCIENCES

Ultrasensitivity part III: cascades, bistable switches, and oscillators

(2014) James E. Ferrell et al.   TRENDS IN BIOCHEMICAL SCIENCES

Modular Extracellular Sensor Architecture for Engineering Mammalian Cell-based Devices

(2014) Nichole M. Daringer et al.   ACS Synthetic Biology

Design and Implementation of a Biomolecular Concentration Tracker

(2014) Victoria Hsiao et al.   ACS Synthetic Biology

Programmable chemical controllers made from DNA

(2013) Yuan-Jyue Chen et al.   Nature Nanotechnology

PD-1- and CTLA-4-Based Inhibitory Chimeric Antigen Receptors (iCARs) Divert Off-Target Immunotherapy Responses

(2013) V. D. Fedorov et al.   Science Translational Medicine

Evolution of Two-Component Signal Transduction Systems

(2012) Emily J. Capra et al.   Annual Review of Microbiology

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

(2012) Ping Wei et al.   NATURE

Complex shapes self-assembled from single-stranded DNA tiles

(2012) Bryan Wei et al.   NATURE

Biomolecular computing systems: principles, progress and potential

(2012) Yaakov Benenson   NATURE REVIEWS GENETICS

Targeted DNA Methylation Using an Artificially Bisected M.HhaI Fused to Zinc Fingers

(2012) Brian Chaikind 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

Engineering robust control of two-component system phosphotransfer using modular scaffolds

(2012) W. R. Whitaker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology

(2012) Jordan M. Fletcher et al.   ACS Synthetic Biology

Studying G protein-coupled receptor activation using split-tobacco etch virus assays

(2011) Minou S. Djannatian et al.   ANALYTICAL BIOCHEMISTRY

Tunable Signal Processing in Synthetic MAP Kinase Cascades

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

Neural network computation with DNA strand displacement cascades

(2011) Lulu Qian et al.   NATURE

Dynamic DNA nanotechnology using strand-displacement reactions

(2011) David Yu Zhang et al.   Nature Chemistry

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

(2011) Z. Xie et al.   SCIENCE

Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information

(2011) M. C. Good et al.   SCIENCE

De novo design of orthogonal peptide pairs forming parallel coiled-coil heterodimers

(2010) Helena Gradišar et al.   JOURNAL OF PEPTIDE SCIENCE

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

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

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation

(2009) Lea Goentoro et al.   MOLECULAR CELL

Protein sequestration generates a flexible ultrasensitive response in a genetic network

(2009) Nicolas E Buchler et al.   Molecular Systems Biology

Synthetic protein scaffolds provide modular control over metabolic flux

(2009) John E Dueber et al.   NATURE BIOTECHNOLOGY

Modularity of MAP kinases allows deformation of their signalling pathways

(2009) Areez Mody et al.   NATURE CELL BIOLOGY

Analysis of transient phosphorylation-dependent protein-protein interactions in living mammalian cells using split-TEV

(2008) Michael C Wehr et al.   BMC BIOTECHNOLOGY

Rewiring the Specificity of Two-Component Signal Transduction Systems

(2008) Jeffrey M. Skerker et al.   CELL

DARPins: A new generation of protein therapeutics

(2008) Michael T. Stumpp et al.   DRUG DISCOVERY TODAY

Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics

(2008) C. J. Bashor et al.   SCIENCE