Directed Evolution: Methodologies and Applications

Deep diversification of an AAV capsid protein by machine learning

(2021) Drew H. Bryant et al.   NATURE BIOTECHNOLOGY

Efficient Lewis acid catalysis of an abiological reaction in a de novo protein scaffold

(2021) Sophie Basler et al.   Nature Chemistry

Low-N protein engineering with data-efficient deep learning

(2021) Surojit Biswas et al.   NATURE METHODS

Directed evolution for high functional production and stability of a challenging G protein-coupled receptor

(2021) Yann Waltenspühl et al.   Scientific Reports

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors

(2020) Chao Li et al.   NATURE BIOTECHNOLOGY

Directed Evolution of the Stringency of the LuxR Vibrio fischeri Quorum Sensor without OFF-State Selection

(2020) Yuki Kimura et al.   ACS Synthetic Biology

Transcription Factor Engineering for High-Throughput Strain Evolution and Organic Acid Bioproduction: A Review

(2020) Jia-Wei Li et al.   Frontiers in Bioengineering and Biotechnology

A Simple and Direct Assay for Monitoring Fatty Acid Synthase Activity and Product-Specificity by High-Resolution Mass Spectrometry

(2020) Magdalena Topolska et al.   Biomolecules

Expanding the enzyme universe with genetically encoded unnatural amino acids

(2020) Ivana Drienovská et al.   Nature Catalysis

Engineering new catalytic activities in enzymes

(2020) Kai Chen et al.   Nature Catalysis

Multidimensional engineering of Saccharomyces cerevisiae for efficient synthesis of medium-chain fatty acids

(2020) Zhiwei Zhu et al.   Nature Catalysis

“Development and application of analytical detection techniques for droplet-based microfluidics”-A review

(2020) Wen-wen Liu et al.   ANALYTICA CHIMICA ACTA

A mass spectrometry-based high-throughput screening method for engineering fatty acid synthases with improved production of medium-chain fatty acids

(2020) Pu Xue et al.   BIOTECHNOLOGY AND BIOENGINEERING

Engineering Cytochrome P450s for Enantioselective Cyclopropenation of Internal Alkynes

(2020) Kai Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Engineered Artificial Carboligases Facilitate Regioselective Preparation of Enantioenriched Aldol Adducts

(2020) Duncan S. Macdonald et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enzymatic Primary Amination of Benzylic and Allylic C(sp3)–H Bonds

(2020) Zhi-Jun Jia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In vivo evolutionary engineering of riboswitch with high-threshold for N-acetylneuraminic acid production

(2020) Qingxiao Pang et al.   METABOLIC ENGINEERING

Automated Continuous Evolution of Proteins in Vivo

(2020) Ziwei Zhong et al.   ACS Synthetic Biology

High-Efficiency Secretion and Directed Evolution of Chitinase BcChiA1 in Bacillus subtilis for the Conversion of Chitinaceous Wastes Into Chitooligosaccharides

(2020) Sijia Wang et al.   Frontiers in Bioengineering and Biotechnology

An enzymatic platform for the highy enantioselective and stereodivergent construction of cyclopropyl‐δ‐lactones

(2020) Rudi Fasan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

A protein-independent fluorescent RNA aptamer reporter system for plant genetic engineering

(2020) Jiuyuan Bai et al.   Nature Communications

Development of Novel Riboswitches for Synthetic Biology in the Green Alga Chlamydomonas

(2020) Payam Mehrshahi et al.   ACS Synthetic Biology

In vivo–directed evolution of adeno-associated virus in the primate retina

(2020) Leah C. Byrne et al.   JCI Insight

Production, Processing, and Characterization of synthetic AAV Gene Therapy Vectors

(2020) Jihad El Andari et al.   Biotechnology Journal

Insights from the comparison of genomic variants from two influenza B viruses grown in the presence of human antibodies in cell culture

(2020) Ewan P. Plant et al.   PLoS One

Unlocking nature’s biosynthetic potential by directed genome evolution

(2020) Mingfeng Cao et al.   CURRENT OPINION IN BIOTECHNOLOGY

In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9

(2020) Beatriz Álvarez et al.   Nature Communications

A Biocatalytic Platform for Synthesis of Chiral α-Trifluoromethylated Organoborons

(2019) Xiongyi Huang et al.   ACS Central Science

Viruses and Evolution – Viruses First? A Personal Perspective

(2019) Karin Moelling et al.   Frontiers in Microbiology

Adeno-associated virus vector as a platform for gene therapy delivery

(2019) Dan Wang et al.   NATURE REVIEWS DRUG DISCOVERY

Biocatalytic strategy for highly diastereo- and enantioselective synthesis of 2,3-dihydrobenzofuran based tricyclic scaffolds

(2019) Rudi Fasan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Combining directed evolution of pathway enzymes and dynamic pathway regulation using a quorum-sensing circuit to improve the production of 4-hydroxyphenylacetic acid in Escherichia coli

(2019) Yu-Ping Shen et al.   Biotechnology for Biofuels

Directed Evolution of a Cytochrome P450 Carbene Transferase for Selective Functionalization of Cyclic Compounds

(2019) Oliver F. Brandenberg et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Stereodivergent Protein Engineering of a Lipase To Access All Possible Stereoisomers of Chiral Esters with Two Stereocenters

(2019) Jian Xu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In vivo continuous evolution of metabolic pathways for chemical production

(2019) Zheng Lin Tan et al.   Microbial Cell Factories

Design and evolution of an enzyme with a non-canonical organocatalytic mechanism

(2019) Ashleigh J. Burke et al.   NATURE

Next-level riboswitch development—implementation of Capture-SELEX facilitates identification of a new synthetic riboswitch

(2019) Adrien Boussebayle et al.   NUCLEIC ACIDS RESEARCH

Machine learning-assisted directed protein evolution with combinatorial libraries

(2019) Zachary Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biosystems design by directed evolution

(2019) Yajie Wang et al.   AICHE JOURNAL

Site-Selective Functionalization of (sp3)C-H Bonds Catayzed by Artificial Metalloenzymes Containing an Iridium-Porphyrin Cofactor

(2019) Yang Gu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enantiodivergent α-Amino C–H Fluoroalkylation Catalyzed by Engineered Cytochrome P450s

(2019) Juner Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Continuous evolution of base editors with expanded target compatibility and improved activity

(2019) Benjamin W. Thuronyi et al.   NATURE BIOTECHNOLOGY

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks

(2019) Jia Zheng et al.   SCIENCE

Golden Mutagenesis: An efficient multi-site-saturation mutagenesis approach by Golden Gate cloning with automated primer design

(2019) Pascal Püllmann et al.   Scientific Reports

Beyond the Ligand: Extracellular and Transcellular G Protein–Coupled Receptor Complexes in Physiology and Pharmacology

(2019) Henry A. Dunn et al.   PHARMACOLOGICAL REVIEWS

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

(2019) Andrea Cossarizza et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Aptamers: A Review of Their Chemical Properties and Modifications for Therapeutic Application

(2019) Adachi et al.   MOLECULES

An enzymatic platform for the asymmetric amination of primary, secondary and tertiary C(sp3)–H bonds

(2019) Yang Yang et al.   Nature Chemistry

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

Towards a fully automated algorithm driven platform for biosystems design

(2019) Mohammad HamediRad et al.   Nature Communications

Genome shuffling enhances stress tolerance of Zymomonas mobilis to two inhibitors

(2019) Weiting Wang et al.   Biotechnology for Biofuels

Protein engineers turned evolutionists—the quest for the optimal starting point

(2019) Devin L Trudeau et al.   CURRENT OPINION IN BIOTECHNOLOGY

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

(2019) Troy E. Sandberg et al.   METABOLIC ENGINEERING

Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor

(2019) Haiqi Chen et al.   NATURE BIOTECHNOLOGY

Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping

(2019) Jiazhang Lian et al.   Nature Communications

Stereodivergent Evolution of Artificial Enzymes for the Michael Reaction

(2018) Xavier Garrabou et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Myoglobin-Catalyzed C−H Functionalization of Unprotected Indoles

(2018) David A. Vargas et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Directed Evolution of an Artificial Imine Reductase

(2018) Martina Hestericová et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Directed Evolution of Protein Catalysts

(2018) Cathleen Zeymer et al.   Annual Review of Biochemistry

DeepSol: a deep learning framework for sequence-based protein solubility prediction

(2018) Sameer Khurana et al.   BIOINFORMATICS

mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion

(2018) Emmi Jokinen et al.   BIOINFORMATICS

RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization

(2018) Mohammad HamediRad et al.   BIOTECHNOLOGY AND BIOENGINEERING

Mapping the Evolutionary Potential of RNA Viruses

(2018) Patrick T. Dolan et al.   Cell Host & Microbe

Advances in analytical tools for high throughput strain engineering

(2018) Esteban Marcellin et al.   CURRENT OPINION IN BIOTECHNOLOGY

A statistical model for improved membrane protein expression using sequence-derived features

(2018) Shyam M. Saladi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

First investigations for the characterization of glucosamine-6-phosphate synthase by capillary electrophoresis

(2018) Miriam Beneito-Cambra et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

A Noncanonical Proximal Heme Ligand Affords an Efficient Peroxidase in a Globin Fold

(2018) Moritz Pott et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo

(2018) Christopher L. Moore et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Directed evolution of the 3-hydroxypropionic acid production pathway by engineering aldehyde dehydrogenase using a synthetic selection device

(2018) Joo Yeon Seok et al.   METABOLIC ENGINEERING

CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9

(2018) Tadas Jakočiūnas et al.   METABOLIC ENGINEERING

G Protein-Coupled Receptors as Targets for Approved Drugs: How Many Targets and How Many Drugs?

(2018) Krishna Sriram et al.   MOLECULAR PHARMACOLOGY

Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision

(2018) Zehua Bao et al.   NATURE BIOTECHNOLOGY

High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast

(2018) Xiaoge Guo et al.   NATURE BIOTECHNOLOGY

Multiplexed precision genome editing with trackable genomic barcodes in yeast

(2018) Kevin R Roy et al.   NATURE BIOTECHNOLOGY

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

(2018) Brandon G Wong et al.   NATURE BIOTECHNOLOGY

A highly specific SpCas9 variant is identified by in vivo screening in yeast

(2018) Antonio Casini et al.   NATURE BIOTECHNOLOGY

Directed evolution of a synthetic phylogeny of programmable Trp repressors

(2018) Jared W. Ellefson et al.   Nature Chemical Biology

Evolving artificial metalloenzymes via random mutagenesis

(2018) Hao Yang et al.   Nature Chemistry

CRISPR off-target analysis in genetically engineered rats and mice

(2018) Keith R. Anderson et al.   NATURE METHODS

High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis

(2018) Derek M Mason et al.   NUCLEIC ACIDS RESEARCH

Bispecific antibodies for cancer therapy: A review

(2018) Anuradha Krishnamurthy et al.   PHARMACOLOGY & THERAPEUTICS

Laboratory evolution of virus-like nucleocapsids from nonviral protein cages

(2018) Naohiro Terasaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catalytic iron-carbene intermediate revealed in a cytochromeccarbene transferase

(2018) Russell D. Lewis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance

(2018) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enzymatic construction of highly strained carbocycles

(2018) Kai Chen et al.   SCIENCE

Heterozygous diploid and interspecies SCRaMbLEing

(2018) Michael J. Shen et al.   Nature Communications

L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast

(2018) Lena Hochrein et al.   Nature Communications

A cell-penetrating artificial metalloenzyme regulates a gene switch in a designer mammalian cell

(2018) Yasunori Okamoto et al.   Nature Communications

The CRISPR tool kit for genome editing and beyond

(2018) Mazhar Adli   Nature Communications

Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome

(2018) B. A. Blount et al.   Nature Communications

Precise control of SCRaMbLE in synthetic haploid and diploid yeast

(2018) Bin Jia et al.   Nature Communications

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window

(2018) Shakked O. Halperin et al.   NATURE

Continuous directed evolution of proteins with improved soluble expression

(2018) Tina Wang et al.   Nature Chemical Biology

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

Directed evolution of CRISPR-Cas9 to increase its specificity

(2018) Jungjoon K. Lee et al.   Nature Communications

Machine-Learning-Guided Mutagenesis for Directed Evolution of Fluorescent Proteins

(2018) Yutaka Saito et al.   ACS Synthetic Biology

Engineering Riboswitches in Vivo Using Dual Genetic Selection and Fluorescence-Activated Cell Sorting

(2018) Katharine Page et al.   ACS Synthetic Biology

Retroelement-based genome editing and evolution

(2018) Anna J. Simon et al.   ACS Synthetic Biology

Directed Evolution of a Designer Enzyme Featuring an Unnatural Catalytic Amino Acid

(2018) Clemens Mayer et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Directed Evolution Empowered Redesign of Natural Proteins for the Sustainable Production of Chemicals and Pharmaceuticals

(2018) Uwe T. Bornscheuer et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds

(2018) Arjun Ravikumar et al.   CELL

An Adaptable Platform for Directed Evolution in Human Cells

(2018) Chet M. Berman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enzymatic assembly of carbon–carbon bonds via iron-catalysed sp3 C–H functionalization

(2018) Ruijie K. Zhang et al.   NATURE

Evolution of a highly active and enantiospecific metalloenzyme from short peptides

(2018) Sabine Studer et al.   SCIENCE

Screening of inhibitors of angiotensin-converting enzyme (ACE) employing high performance liquid chromatography-electrospray ionization triple quadrupole mass spectrometry (HPLC-ESI-QqQ-MS)

(2017) Syed Ghulam Musharraf et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

Learning epistatic interactions from sequence-activity data to predict enantioselectivity

(2017) Julian Zaugg et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

(2017) Tong Si et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling

(2017) Troy J. Comi et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

A directed evolution approach to select for novel Adeno-associated virus capsids on an HIV-1 producer T cell line

(2017) Dawn P. Wooley et al.   JOURNAL OF VIROLOGICAL METHODS

Therapeutic T cell engineering

(2017) Michel Sadelain et al.   NATURE

Site-selective and stereoselective functionalization of non-activated tertiary C–H bonds

(2017) Kuangbiao Liao et al.   NATURE

Enhanced proofreading governs CRISPR–Cas9 targeting accuracy

(2017) Janice S. Chen et al.   NATURE

Genetically programmed chiral organoborane synthesis

(2017) S. B. Jennifer Kan et al.   NATURE

Evolution of a designed protein assembly encapsulating its own RNA genome

(2017) Gabriel L. Butterfield et al.   NATURE

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Evolution of a split RNA polymerase as a versatile biosensor platform

(2017) Jinyue Pu et al.   Nature Chemical Biology

Continuous directed evolution of aminoacyl-tRNA synthetases

(2017) David I Bryson et al.   Nature Chemical Biology

Enantioselective, intermolecular benzylic C–H amination catalysed by an engineered iron-haem enzyme

(2017) Christopher K. Prier et al.   Nature Chemistry

CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations

(2017) Cem Kuscu et al.   NATURE METHODS

Compartmentalized partnered replication for the directed evolution of genetic parts and circuits

(2017) Zhanar Abil et al.   Nature Protocols

Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system

(2017) Jiazhang Lian et al.   Nature Communications

Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes

(2017) Hoang Long Pham et al.   Nature Communications

Automated multiplex genome-scale engineering in yeast

(2017) Tong Si et al.   Nature Communications

Phage-assisted continuous evolution of proteases with altered substrate specificity

(2017) Michael S. Packer et al.   Nature Communications

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

(2017) Claire N. Bedbrook et al.   PLoS Computational Biology

Biosensor-Enabled Directed Evolution to Improve Muconic Acid Production in Saccharomyces cerevisiae

(2017) John M. Leavitt et al.   Biotechnology Journal

Beyond Iron: Iridium-Containing P450 Enzymes for Selective Cyclopropanations of Structurally Diverse Alkenes

(2017) Hanna M. Key et al.   ACS Central Science

Artificial Metalloenzymes Based on the Biotin–Streptavidin Technology: Challenges and Opportunities

(2016) Tillmann Heinisch et al.   ACCOUNTS OF CHEMICAL RESEARCH

Highly Sensitive Raman Spectroscopy with Low Laser Power for Fast In-Line Reaction and Multiphase Flow Monitoring

(2016) Frank Braun et al.   ANALYTICAL CHEMISTRY

Asymmetric Enzymatic Synthesis of Allylic Amines: A Sigmatropic Rearrangement Strategy

(2016) Christopher K. Prier et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genetic Optimization of Metalloenzymes: Enhancing Enzymes for Non-Natural Reactions

(2016) Todd K. Hyster et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Gram-Scale Synthesis of Chiral Cyclopropane-Containing Drugs and Drug Precursors with Engineered Myoglobin Catalysts Featuring Complementary Stereoselectivity

(2016) Priyanka Bajaj et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Identification of gene knockdown targets conferring enhanced isobutanol and 1-butanol tolerance to Saccharomyces cerevisiae using a tunable RNAi screening approach

(2016) Nathan Crook et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Recent advances on halohydrin dehalogenases—from enzyme identification to novel biocatalytic applications

(2016) Anett Schallmey et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

Mechanisms of viral mutation

(2016) Rafael Sanjuán et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Novel GM1 ganglioside-like peptide mimics prevent the association of cholera toxin to human intestinal epithelial in vitro

(2016) Robert K Yu et al.   GLYCOBIOLOGY

Fast Knoevenagel Condensations Catalyzed by an Artificial Schiff-Base-Forming Enzyme

(2016) Xavier Garrabou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Signal preprocessing, multivariate analysis and software tools for MA(LDI)-TOF mass spectrometry imaging for biological applications

(2016) Pere Ràfols et al.   MASS SPECTROMETRY REVIEWS

Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance

(2016) Ahmed H. Badran et al.   NATURE

Abiological catalysis by artificial haem proteins containing noble metals in place of iron

(2016) Hanna M. Key et al.   NATURE

Directed evolution of artificial metalloenzymes for in vivo metathesis

(2016) Markus Jeschek et al.   NATURE

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering

(2016) Andrew D Garst et al.   NATURE BIOTECHNOLOGY

Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase

(2016) Richard Obexer et al.   Nature Chemistry

Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells

(2016) Yunqing Ma et al.   NATURE METHODS

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

(2016) Gaelen T Hess et al.   NATURE METHODS

Library design and screening protocol for artificial metalloenzymes based on the biotin-streptavidin technology

(2016) Hendrik Mallin et al.   Nature Protocols

A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

(2016) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated droplet sorting

(2016) Richard Obexer et al.   PROTEIN ENGINEERING DESIGN & SELECTION

An artificial metalloenzyme with the kinetics of native enzymes

(2016) P. Dydio et al.   SCIENCE

Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life

(2016) S. B. Jennifer Kan et al.   SCIENCE

An enantioselective artificial Suzukiase based on the biotin–streptavidin technology

(2016) Anamitra Chatterjee et al.   Chemical Science

Iridium(iii)-bis(imidazolinyl)phenyl catalysts for enantioselective C–H functionalization with ethyl diazoacetate

(2016) N. Mace Weldy et al.   Chemical Science

In vivo continuous evolution of genes and pathways in yeast

(2016) Nathan Crook et al.   Nature Communications

Highly Stereoselective Biocatalytic Synthesis of Key Cyclopropane Intermediate to Ticagrelor

(2016) Kari E. Hernandez et al.   ACS Catalysis

Semisupervised Gaussian Process for Automated Enzyme Search

(2016) Joseph Mellor et al.   ACS Synthetic Biology

Yeast Pathway Kit: A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation

(2016) Filipa Pereira et al.   ACS Synthetic Biology

CRMAGE: CRISPR Optimized MAGE Recombineering

(2016) Carlotta Ronda et al.   Scientific Reports

Electrochemical droplet-based microfluidics using chip-based carbon paste electrodes for high-throughput analysis in pharmaceutical applications

(2015) Akkapol Suea-Ngam et al.   ANALYTICA CHIMICA ACTA

A Promiscuous De Novo Retro-Aldolase Catalyzes Asymmetric Michael Additions via Schiff Base Intermediates

(2015) Xavier Garrabou et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution

(2015) Hans Renata et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Evolution of Orbitrap Mass Spectrometry Instrumentation

(2015) Shannon Eliuk et al.   Annual Review of Analytical Chemistry

Myoglobin-catalyzed intermolecular carbene N–H insertion with arylamine substrates

(2015) Gopeekrishnan Sreenilayam et al.   CHEMICAL COMMUNICATIONS

High throughput screening of enzyme activity with mass spectrometry imaging

(2015) Tristan de Rond et al.   CURRENT OPINION IN BIOTECHNOLOGY

Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment

(2015) Leslie P Silva et al.   CURRENT OPINION IN BIOTECHNOLOGY

Adeno-associated virus serotypes for gene therapeutics

(2015) Leszek Lisowski et al.   CURRENT OPINION IN PHARMACOLOGY

Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing

(2015) Yifan Li et al.   METABOLIC ENGINEERING

Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration

(2015) Chiam Yu Ng et al.   METABOLIC ENGINEERING

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Multiplexed tracking of combinatorial genomic mutations in engineered cell populations

(2015) Ramsey I Zeitoun et al.   NATURE BIOTECHNOLOGY

Continuous directed evolution of DNA-binding proteins to improve TALEN specificity

(2015) Basil P Hubbard et al.   NATURE METHODS

Methods for the directed evolution of proteins

(2015) Michael S. Packer et al.   NATURE REVIEWS GENETICS

Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation

(2015) Antonia A. Dominguez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A deep learning framework for modeling structural features of RNA-binding protein targets

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects

(2015) Rebecca M. Lennen et al.   NUCLEIC ACIDS RESEARCH

Exploring the potential impact of an expanded genetic code on protein function

(2015) Han Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rationally engineered Cas9 nucleases with improved specificity

(2015) I. M. Slaymaker et al.   SCIENCE

α-Enolase–binding peptide enhances drug delivery efficiency and therapeutic efficacy against colorectal cancer

(2015) Chien-Hsun Wu et al.   Science Translational Medicine

Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis

(2015) Douglas B. Kell et al.   TRENDS IN BIOTECHNOLOGY

Intermolecular carbene S–H insertion catalysed by engineered myoglobin-based catalysts

(2015) Vikas Tyagi et al.   Chemical Science

Engineering a dirhodium artificial metalloenzyme for selective olefin cyclopropanation

(2015) Poonam Srivastava et al.   Nature Communications

Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics

(2015) Pierre-Yves Colin et al.   Nature Communications

Enzymatic C(sp3)-H Amination: P450-Catalyzed Conversion of Carbonazidates into Oxazolidinones

(2015) Ritesh Singh et al.   ACS Catalysis

Enantioselective Enzyme-Catalyzed Aziridination Enabled by Active-Site Evolution of a Cytochrome P450

(2015) Christopher C. Farwell et al.   ACS Central Science

Structure Based Thermostability Prediction Models for Protein Single Point Mutations with Machine Learning Tools

(2015) Lei Jia et al.   PLoS One

Improved Cyclopropanation Activity of Histidine-Ligated Cytochrome P450 Enables the Enantioselective Formal Synthesis of Levomilnacipran

(2014) Z. Jane Wang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Highly Diastereoselective and Enantioselective Olefin Cyclopropanation Using Engineered Myoglobin-Based Catalysts

(2014) Melanie Bordeaux et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Elevated Catalytic Activity of Ruthenium(II)-Porphyrin-Catalyzed Carbene/Nitrene Transfer and Insertion Reactions with N-Heterocyclic Carbene Ligands

(2014) Ka-Ho Chan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genome Engineering with Targetable Nucleases

(2014) Dana Carroll   Annual Review of Biochemistry

Directed evolution of a cellodextrin transporter for improved biofuel production under anaerobic conditions inSaccharomyces cerevisiae

(2014) Jiazhang Lian et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae

(2014) Han Xiao et al.   Biotechnology for Biofuels

NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation

(2014) Manuel Giollo et al.   BMC GENOMICS

The enduring utility of continuous culturing in experimental evolution

(2014) David Gresham et al.   GENOMICS

High Throughput Screening and Selection Methods for Directed Enzyme Evolution

(2014) Han Xiao et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

An experimental framework for improved selection of binding proteins using SNAP display

(2014) Gillian Houlihan et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Enzyme-Controlled Nitrogen-Atom Transfer Enables Regiodivergent C–H Amination

(2014) Todd K. Hyster et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution

(2014) Grigory S. Filonov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enantioselective Imidation of Sulfides via Enzyme-Catalyzed Intermolecular Nitrogen-Atom Transfer

(2014) Christopher C. Farwell et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Neutralizing the Detrimental Effect of Glutathione on Precious Metal Catalysts

(2014) Yvonne M. Wilson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fourier transform ion cyclotron resonance (FT ICR) mass spectrometry: Theory and simulations

(2014) Eugene N. Nikolaev et al.   MASS SPECTROMETRY REVIEWS

Employing a combinatorial expression approach to characterize xylose utilization in Saccharomyces cerevisiae

(2014) Luke N. Latimer et al.   METABOLIC ENGINEERING

Negative selection and stringency modulation in phage-assisted continuous evolution

(2014) Jacob C Carlson et al.   Nature Chemical Biology

Principles of genetic circuit design

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

Cryptic genetic variation: evolution's hidden substrate

(2014) Annalise B. Paaby et al.   NATURE REVIEWS GENETICS

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase

(2014) N. Preiswerk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution-guided optimization of biosynthetic pathways

(2014) Srivatsan Raman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent evolution of a bifunctionalde novoprotein

(2014) Betsy A. Smith et al.   PROTEIN SCIENCE

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

(2014) F. Farzadfard et al.   SCIENCE

Changing the peptide specificity of a human T-cell receptor by directed evolution

(2014) Sheena N. Smith et al.   Nature Communications

A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations

(2014) Bryan C. Dickinson et al.   Nature Communications

P450-Catalyzed Intramolecular sp3 C–H Amination with Arylsulfonyl Azide Substrates

(2014) Ritesh Singh et al.   ACS Catalysis

RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering

(2014) Tong Si et al.   ACS Synthetic Biology

Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae

(2014) Zehua Bao et al.   ACS Synthetic Biology

Computational Enzyme Design

(2013) Gert Kiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Directed evolution of a highly efficient cellobiose utilizing pathway in an industrialSaccharomyces cerevisiaestrain

(2013) Yongbo Yuan et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome replication engineering assisted continuous evolution (GREACE) to improve microbial tolerance for biofuels production

(2013) Guodong Luan et al.   Biotechnology for Biofuels

Directed evolution of an E. coli inner membrane transporter for improved efflux of biofuel molecules

(2013) Jee Foo et al.   Biotechnology for Biofuels

Chromosomal evolution of Escherichia coli for the efficient production of lycopene

(2013) Yun-Yan Chen et al.   BMC BIOTECHNOLOGY

A General Method for Artificial Metalloenzyme Formation through Strain-Promoted Azide-Alkyne Cycloaddition

(2013) Hao Yang et al.   CHEMBIOCHEM

Combinatorial Peptide Libraries: Mining for Cell-Binding Peptides

(2013) Bethany Powell Gray et al.   CHEMICAL REVIEWS

Enzymatic reactions on immobilised substrates

(2013) Christopher J. Gray et al.   CHEMICAL SOCIETY REVIEWS

De novo enzymes by computational design

(2013) Hajo Kries et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Reporter-based screening and selection of enzymes

(2013) Teunke van Rossum et al.   FEBS Journal

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs

(2013) Eynat Dellus-Gur et al.   JOURNAL OF MOLECULAR BIOLOGY

Enantioselective Synthesis of Cyclobutanes via Sequential Rh-catalyzed Bicyclobutanation/Cu-catalyzed Homoconjugate Addition

(2013) Robert Panish et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Dual Anchoring Strategy for the Localization and Activation of Artificial Metalloenzymes Based on the Biotin–Streptavidin Technology

(2013) Jeremy M. Zimbron et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A multifunctional microfluidic droplet-array chip for analysis by electrospray ionization mass spectrometry

(2013) Yuan Su et al.   LAB ON A CHIP

Directed evolution of a cellobiose utilization pathway in Saccharomyces cerevisiae by simultaneously engineering multiple proteins

(2013) Dawn T Eriksen et al.   Microbial Cell Factories

Building synthetic gene circuits from combinatorial libraries: screening and selection strategies

(2013) Yolanda Schaerli et al.   Molecular BioSystems

Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody

(2013) Aaron M. Ring et al.   NATURE

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

Directed evolution of genetic parts and circuits by compartmentalized partnered replication

(2013) Jared W Ellefson et al.   NATURE BIOTECHNOLOGY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

A serine-substituted P450 catalyzes highly efficient carbene transfer to olefins in vivo

(2013) Pedro S Coelho et al.   Nature Chemical Biology

Evolution of a designed retro-aldolase leads to complete active site remodeling

(2013) Lars Giger et al.   Nature Chemical Biology

Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry

(2013) Peter Nemes et al.   Nature Protocols

Targeted Drug Delivery Systems Mediated by a Novel Peptide in Breast Cancer Therapy and Imaging

(2013) Ruei-Min Lu et al.   PLoS One

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution

(2013) B. C. Dickinson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries

(2013) L. Yi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

Cytochrome P450-catalyzed insertion of carbenoids into N–H bonds

(2013) Z. Jane Wang et al.   Chemical Science

Artificial Metalloenzymes and Metallopeptide Catalysts for Organic Synthesis

(2013) Jared C. Lewis   ACS Catalysis

Enhancing Tolerance to Short-Chain Alcohols by Engineering the Escherichia coli AcrB Efflux Pump to Secrete the Non-native Substrate n-Butanol

(2013) Michael A. Fisher et al.   ACS Synthetic Biology

Yeast Oligo-Mediated Genome Engineering (YOGE)

(2013) James E. DiCarlo et al.   ACS Synthetic Biology

Acoustic deposition with NIMS as a high-throughput enzyme activity assay

(2012) Matthew Greving et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Combinatorial Design of a Highly Efficient Xylose-Utilizing Pathway in Saccharomyces cerevisiae for the Production of Cellulosic Biofuels

(2012) Byoungjin Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhanced enantioselectivity of a carboxyl esterase from Rhodobacter sphaeroides by directed evolution

(2012) Jingbo Ma et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Improved ethanol production by a xylose-fermenting recombinant yeast strain constructed through a modified genome shuffling method

(2012) Wei Zhang et al.   Biotechnology for Biofuels

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Engineering multicellular traits in synthetic microbial populations

(2012) John S Chuang   CURRENT OPINION IN CHEMICAL BIOLOGY

Directed evolution of novel adeno-associated viruses for therapeutic gene delivery

(2012) M A Bartel et al.   GENE THERAPY

dRTP and dPTP a complementary nucleotide couple for the Sequence Saturation Mutagenesis (SeSaM) method

(2012) Anna Joëlle Ruff et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch

(2012) Joshua K. Michener et al.   METABOLIC ENGINEERING

In vitro selection of proteins with desired characteristics using mRNA-display

(2012) C. Alexander Valencia et al.   METHODS

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

(2012) Christopher B Eiben et al.   NATURE BIOTECHNOLOGY

Genome-scale promoter engineering by coselection MAGE

(2012) Harris H Wang et al.   NATURE METHODS

Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection

(2012) Peter A. Carr et al.   NUCLEIC ACIDS RESEARCH

Customized optimization of metabolic pathways by combinatorial transcriptional engineering

(2012) Jing Du et al.   NUCLEIC ACIDS RESEARCH

Olefin Cyclopropanation Catalyzed by Iridium(III) Porphyrin Complexes

(2012) Bernie J. Anding et al.   ORGANOMETALLICS

PROTS-RF: A Robust Model for Predicting Mutation-Induced Protein Stability Changes

(2012) Yunqi Li et al.   PLoS One

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

(2012) O. Khersonsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Olefin Cyclopropanation via Carbene Transfer Catalyzed by Engineered Cytochrome P450 Enzymes

(2012) P. S. Coelho et al.   SCIENCE

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

(2012) A. N.-S. Mak et al.   SCIENCE

Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

(2012) D. Deng et al.   SCIENCE

Biotinylated Rh(III) Complexes in Engineered Streptavidin for Accelerated Asymmetric C-H Activation

(2012) T. K. Hyster et al.   SCIENCE

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

(2012) Eva Chovancova et al.   PLoS Computational Biology

The Saccharomyces cerevisiae SCRaMbLE system and genome minimization

(2012) Jessica Dymond et al.   Bioengineered

OsO4⋅Streptavidin: A Tunable Hybrid Catalyst for the Enantioselective cis-Dihydroxylation of Olefins

(2011) Valentin Köhler et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Artificial Transfer Hydrogenases for the Enantioselective Reduction of Cyclic Imines

(2011) Marc Dürrenberger et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Saccharomyces cerevisiae Genome Shuffling through Recursive Population Mating Leads to Improved Tolerance to Spent Sulfite Liquor

(2011) Dominic Pinel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

(2011) Yves Dehouck et al.   BMC BIOINFORMATICS

SeSaM-Tv-II Generates a Protein Sequence Space that is Unobtainable by epPCR

(2011) Hemanshu Mundhada et al.   CHEMBIOCHEM

SNAP Dendrimers: Multivalent Protein Display on Dendrimer-Like DNA for Directed Evolution

(2011) Miriam Kaltenbach et al.   CHEMBIOCHEM

Artificial metalloenzymes for olefin metathesis based on the biotin-(strept)avidin technology

(2011) Cheikh Lo et al.   CHEMICAL COMMUNICATIONS

Synthetic inter-species cooperation of host and virus for targeted genetic evolution

(2011) Dokyun Na et al.   JOURNAL OF BIOTECHNOLOGY

Directed evolution of a thermophilic endoglucanase (Cel5A) into highly active Cel5A variants with an expanded temperature profile

(2011) Chaoning Liang et al.   JOURNAL OF BIOTECHNOLOGY

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery

(2011) Roman A. Laskowski et al.   Journal of Chemical Information and Modeling

Evolution of Three Human GPCRs for Higher Expression and Stability

(2011) Igor Dodevski et al.   JOURNAL OF MOLECULAR BIOLOGY

New insights into riboswitch regulation mechanisms

(2011) Laurène Bastet et al.   MOLECULAR MICROBIOLOGY

A system for the continuous directed evolution of biomolecules

(2011) Kevin M. Esvelt et al.   NATURE

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

(2011) Eric J. Hayden et al.   NATURE

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

(2011) Jessica S. Dymond et al.   NATURE

Predicting mutation outcome from early stochastic variation in genetic interaction partners

(2011) Alejandro Burga et al.   NATURE

OmniChange: The Sequence Independent Method for Simultaneous Site-Saturation of Five Codons

(2011) Alexander Dennig et al.   PLoS One

A general strategy for the evolution of bond-forming enzymes using yeast display

(2011) I. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequential Establishment of Stripe Patterns in an Expanding Cell Population

(2011) C. Liu et al.   SCIENCE

Silver-Catalyzed C-C Bond Formation Between Methane and Ethyl Diazoacetate in Supercritical CO2

(2011) A. Caballero et al.   SCIENCE

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

(2011) Farren J. Isaacs et al.   SCIENCE

High-Throughput Screening of Small Molecule Libraries using SAMDI Mass Spectrometry

(2011) Zachary A. Gurard-Levin et al.   ACS Combinatorial Science

Retroviral Display in Gene Therapy, Protein Engineering, and Vaccine Development

(2010) Johannes H. Urban et al.   ACS Chemical Biology

Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions

(2010) Manfred T. Reetz   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Improved galactose fermentation of Saccharomyces cerevisiae through inverse metabolic engineering

(2010) Ki-Sung Lee et al.   BIOTECHNOLOGY AND BIOENGINEERING

Improved product-per-glucose yields in P450-dependent propane biotransformations using engineered Escherichia coli

(2010) Rudi Fasan et al.   BIOTECHNOLOGY AND BIOENGINEERING

Screening of cellulases for biofuel production: Online monitoring of the enzymatic hydrolysis of insoluble cellulose using high-throughput scattered light detection

(2010) Gernot Jäger et al.   Biotechnology Journal

Screening for enzyme activity in turbid suspensions with scattered light

(2010) Robert Huber et al.   BIOTECHNOLOGY PROGRESS

Predicting changes in protein thermostability brought about by single- or multi-site mutations

(2010) Jian Tian et al.   BMC BIOINFORMATICS

Natural Diversity to Guide Focused Directed Evolution

(2010) Helge Jochens et al.   CHEMBIOCHEM

High-Throughput Screening of Enzymes by Retroviral Display Using Droplet-Based Microfluidics

(2010) Lucia Granieri et al.   CHEMISTRY & BIOLOGY

Protein-based hybrid catalysts—design and evolution

(2010) Valentin Köhler et al.   CURRENT OPINION IN BIOTECHNOLOGY

The renaissance of continuous culture in the post-genomics age

(2010) Alan T. Bull   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Directed Evolution of an Enhanced and Highly Efficient FokI Cleavage Domain for Zinc Finger Nucleases

(2010) Jing Guo et al.   JOURNAL OF MOLECULAR BIOLOGY

Glycan Array on Aluminum Oxide-Coated Glass Slides through Phosphonate Chemistry

(2010) Shih-Huang Chang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Iterative Saturation Mutagenesis Accelerates Laboratory Evolution of Enzyme Stereoselectivity: Rigorous Comparison with Traditional Methods

(2010) Manfred T. Reetz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rapid and label-free screening of enzyme inhibitors using segmented flow electrospray ionization mass spectrometry

(2010) Jian Pei et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides

(2010) Joseph R Warner et al.   NATURE BIOTECHNOLOGY

A nucleoside kinase as a dual selector for genetic switches and circuits

(2010) Yohei Tashiro et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Development of an In Vitro Compartmentalization Screen for High-Throughput Directed Evolution of [FeFe] Hydrogenases

(2010) James A. Stapleton et al.   PLoS One

Induced allostery in the directed evolution of an enantioselective Baeyer-Villiger monooxygenase

(2010) S. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrahigh-throughput screening in drop-based microfluidics for directed evolution

(2010) J. J. Agresti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation

(2010) Aaron Klug   QUARTERLY REVIEWS OF BIOPHYSICS

Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture

(2010) C. K. Savile et al.   SCIENCE

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

(2010) J. B. Siegel et al.   SCIENCE

Analysis of Samples Stored as Individual Plugs in a Capillary by Electrospray Ionization Mass Spectrometry

(2009) Jian Pei et al.   ANALYTICAL CHEMISTRY

Coupling Microdroplet Microreactors with Mass Spectrometry: Reading the Contents of Single Droplets Online

(2009) Luis M. Fidalgo et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genome Shuffling in Clostridium diolis DSM 15410 for Improved 1,3-Propanediol Production

(2009) B. Otte et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Aptamers and riboswitches: perspectives in biotechnology

(2009) Julia E. Weigand et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

Fluorophore Binding Aptamers as a Tool for RNA Visualization

(2009) Katja Eydeler et al.   BIOPHYSICAL JOURNAL

Genome shuffling: Progress and applications for phenotype improvement

(2009) Jixian Gong et al.   BIOTECHNOLOGY ADVANCES

An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol

(2009) Huanting Liu et al.   BMC BIOTECHNOLOGY

Ultrahigh-Throughput FACS-Based Screening for Directed Enzyme Evolution

(2009) Guangyu Yang et al.   CHEMBIOCHEM

A pH-responsive riboregulator

(2009) Gal Nechooshtan et al.   GENES & DEVELOPMENT

Development of a liquid chromatography-based screening methodology for proteolytic enzyme activity

(2009) Nils Helge Schebb et al.   JOURNAL OF CHROMATOGRAPHY A

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

(2009) Martina Pavlova et al.   Nature Chemical Biology

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

HotSpot Wizard: a web server for identification of hot spots in protein engineering

(2009) A. Pavelka et al.   NUCLEIC ACIDS RESEARCH

SITEHOUND-web: a server for ligand binding site identification in protein structures

(2009) M. Hernandez et al.   NUCLEIC ACIDS RESEARCH

A Novel Peptide Enhances Therapeutic Efficacy of Liposomal Anti-Cancer Drugs in Mice Models of Human Lung Cancer

(2009) De-Kuan Chang et al.   PLoS One

Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes

(2009) Carola Engler et al.   PLoS One

Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways

(2009) Jiayuan Quan et al.   PLoS One

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

Antigenic Fingerprinting of H5N1 Avian Influenza Using Convalescent Sera and Monoclonal Antibodies Reveals Potential Vaccine and Diagnostic Targets

(2009) Surender Khurana et al.   PLOS MEDICINE

Artificial Metalloenzymes for Asymmetric Allylic Alkylation on the Basis of the Biotin–Avidin Technology

(2008) Julien Pierron et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

X-Ray Structure and Designed Evolution of an Artificial Transfer Hydrogenase

(2008) Marc Creus et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Protein Design by Directed Evolution

(2008) Christian Jäckel et al.   Annual Review of Biophysics

A Robust Protein Host for Anchoring Chelating Ligands and Organocatalysts

(2008) Manfred T. Reetz et al.   CHEMBIOCHEM

Constructing and Analyzing the Fitness Landscape of an Experimental Evolutionary Process

(2008) Manfred T. Reetz et al.   CHEMBIOCHEM

A Novel Genetic Selection System for Improved Enantioselectivity ofBacillus subtilis Lipase A

(2008) Ykelien L. Boersma et al.   CHEMBIOCHEM

Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions

(2008) Manfred T. Reetz et al.   CHEMICAL COMMUNICATIONS

Directed Evolution of a Lysosomal Enzyme with Enhanced Activity at Neutral pH by Mammalian Cell-Surface Display

(2008) Kai-Chuan Chen et al.   CHEMISTRY & BIOLOGY

Evolutionary History of a Specialized P450 Propane Monooxygenase

(2008) Rudi Fasan et al.   JOURNAL OF MOLECULAR BIOLOGY

Artificial Metalloenzyme for Enantioselective Sulfoxidation Based on Vanadyl-Loaded Streptavidin

(2008) Anca Pordea et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

AraC Regulatory Protein Mutants with Altered Effector Specificity

(2008) Shuang-Yan Tang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Hepatocellular carcinoma cell-specific peptide ligand for targeted drug delivery

(2008) A. Lo et al.   MOLECULAR CANCER THERAPEUTICS

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

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

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Catalytic C–H functionalization by metal carbenoid and nitrenoid insertion

(2008) Huw M. L. Davies et al.   NATURE

Directed enzyme evolution via small and effective neutral drift libraries

(2008) Rinkoo D Gupta et al.   NATURE METHODS

Rates of evolutionary change in viruses: patterns and determinants

(2008) Siobain Duffy et al.   NATURE REVIEWS GENETICS

Catalytic C−H Insertions Using Iron(III) Porphyrin Complexes

(2008) Harun M. Mbuvi et al.   ORGANOMETALLICS

Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity

(2008) C. A. Sarkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Digital screening methodology for the directed evolution of transglycosidases

(2008) F. M.T. Kone et al.   PROTEIN ENGINEERING DESIGN & SELECTION

A high-throughput microtiter plate-based screening method for the detection of full-length recombinant proteins

(2008) Matthias Mack et al.   PROTEIN EXPRESSION AND PURIFICATION

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

A novel megaprimed and ligase-free, PCR-based, site-directed mutagenesis method

(2007) Wen-Chi Tseng et al.   ANALYTICAL BIOCHEMISTRY

Transversion-enriched sequence saturation mutagenesis (SeSaM-Tv+): A random mutagenesis method with consecutive nucleotide exchanges that complements the bias of error-prone PCR

(2007) Tuck Seng Wong et al.   Biotechnology Journal

Asymmetric catalytic cyclopropanation reactions in water

(2007) Irène Nicolas et al.   COORDINATION CHEMISTRY REVIEWS