Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

Synthetic multistability in mammalian cells

(2022) Ronghui Zhu et al.   SCIENCE

Modular design of synthetic receptors for programmed gene regulation in cell therapies

(2022) Iowis Zhu et al.   CELL

Evolution of binding preferences among whole-genome duplicated transcription factors

(2022) Tamar Gera et al.   eLife

Multidimensional control of therapeutic human cell function with synthetic gene circuits

(2022) Hui-Shan Li et al.   SCIENCE

Memorizing environmental signals through feedback and feedforward loops

(2021) Yanfei Jiang et al.   CURRENT OPINION IN CELL BIOLOGY

The COMET toolkit for composing customizable genetic programs in mammalian cells

(2020) Patrick S. Donahue et al.   Nature Communications

The second decade of synthetic biology: 2010–2020

(2020) Fankang Meng et al.   Nature Communications

Synthetic biology 2020–2030: six commercially-available products that are changing our world

(2020) Christopher A. Voigt   Nature Communications

Engineering Robust Production Microbes for Large-Scale Cultivation

(2019) Maren Wehrs et al.   TRENDS IN MICROBIOLOGY

A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation

(2019) Rajaraman Gopalakrishnan et al.   NUCLEIC ACIDS RESEARCH

Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies

(2019) Caleb J. Bashor et al.   SCIENCE

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

Gene networks that compensate for crosstalk with crosstalk

(2019) Isaak E. Müller et al.   Nature Communications

Understanding Biological Regulation Through Synthetic Biology

(2018) Caleb J. Bashor et al.   Annual Review of Biophysics

Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER

(2018) Brandon G Wong et al.   NATURE BIOTECHNOLOGY

Burden-driven feedback control of gene expression

(2018) Francesca Ceroni et al.   NATURE METHODS

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

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

Programming gene and engineered-cell therapies with synthetic biology

(2018) Tasuku Kitada et al.   SCIENCE

Diverse genetic error modes constrain large-scale bio-based production

(2018) Peter Rugbjerg et al.   Nature Communications

Intrinsic cooperativity potentiates parallel cis-regulatory evolution

(2018) Trevor R Sorrells et al.   eLife

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Engineering Epigenetic Regulation Using Synthetic Read-Write Modules

(2018) Minhee Park et al.   CELL

Spt6 Is Required for the Fidelity of Promoter Selection

(2018) Stephen M. Doris et al.   MOLECULAR CELL

Programmable design of orthogonal protein heterodimers

(2018) Zibo Chen et al.   NATURE

Evolution of weak cooperative interactions for biological specificity

(2018) Ang Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic circuit characterization and debugging using RNA‐seq

(2017) Thomas E Gorochowski et al.   Molecular Systems Biology

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation

(2017) David T Riglar et al.   NATURE BIOTECHNOLOGY

Information Integration and Energy Expenditure in Gene Regulation

(2016) Javier Estrada et al.   CELL

Overloaded and stressed: whole-cell considerations for bacterial synthetic biology

(2016) Olivier Borkowski et al.   CURRENT OPINION IN MICROBIOLOGY

Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability

(2016) Kevin R. Gillinder et al.   NUCLEIC ACIDS RESEARCH

Intrinsic limits to gene regulation by global crosstalk

(2016) Tamar Friedlander et al.   Nature Communications

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Intersecting transcription networks constrain gene regulatory evolution

(2015) Trevor R. Sorrells et al.   NATURE

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

Systems strategies for developing industrial microbial strains

(2015) Sang Yup Lee et al.   NATURE BIOTECHNOLOGY

Quantifying cellular capacity identifies gene expression designs with reduced burden

(2015) Francesca Ceroni et al.   NATURE METHODS

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly

(2015) Michael E. Lee et al.   ACS Synthetic Biology

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation

(2014) Albert J. Keung et al.   CELL

Principles of genetic circuit design

(2014) Jennifer A N Brophy et al.   NATURE METHODS

A brief history of synthetic biology

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

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

Transcription factors: specific DNA binding and specific gene regulation

(2014) Anne-Laure Todeschini et al.   TRENDS IN GENETICS

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

(2013) Klara Stefflova et al.   CELL

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Cell-Based Therapeutics: The Next Pillar of Medicine

(2013) M. A. Fischbach et al.   Science Translational Medicine

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

(2012) Ahmad S. Khalil et al.   CELL

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

(2012) A. J. Stewart et al.   GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

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

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

ChIP-Seq: technical considerations for obtaining high-quality data

(2011) Benjamin L Kidder et al.   NATURE IMMUNOLOGY

Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection

(2011) Vikram Pattanayak et al.   NATURE METHODS

Synthetic Biology: Integrated Gene Circuits

(2011) N. Nandagopal et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Engineering Static and Dynamic Control of Synthetic Pathways

(2010) William J. Holtz et al.   CELL

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites

(2010) Savina A. Jaeger et al.   GENOMICS

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The pedestrian watchmaker: Genetic clocks from engineered oscillators

(2009) Natalie A. Cookson et al.   FEBS LETTERS

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

The second wave of synthetic biology: from modules to systems

(2009) Priscilla E. M. Purnick et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

The enhanceosome

(2008) Daniel Panne   CURRENT OPINION IN STRUCTURAL BIOLOGY

Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae

(2008) Gregory I. Lang et al.   GENETICS

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

Evolution of Eukaryotic Transcription Circuits

(2008) B. B. Tuch et al.   SCIENCE

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY