Multiplexed gene synthesis in emulsions for exploring protein functional landscapes

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

A systematic comparison of error correction enzymes by next-generation sequencing

(2017) Nathan B. Lubock et al.   NUCLEIC ACIDS RESEARCH

Global analysis of protein folding using massively parallel design, synthesis, and testing

(2017) Gabriel J. Rocklin et al.   SCIENCE

Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology

(2017) Randall A. Hughes et al.   Cold Spring Harbor Perspectives in Biology

Precrec: fast and accurate precision–recall and ROC curve calculations in R

(2016) Takaya Saito et al.   BIOINFORMATICS

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

The power of multiplexed functional analysis of genetic variants

(2016) Molly Gasperini et al.   Nature Protocols

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

Decoding enhancers using massively parallel reporter assays

(2015) Fumitaka Inoue et al.   GENOMICS

Multiplex pairwise assembly of array-derived DNA oligonucleotides

(2015) Jason C. Klein et al.   NUCLEIC ACIDS RESEARCH

A Method for Multiplex Gene Synthesis Employing Error Correction Based on Expression

(2015) Timothy H.-C. Hsiau et al.   PLoS One

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

Large-scale de novo DNA synthesis: technologies and applications

(2014) Sriram Kosuri et al.   NATURE METHODS

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Discovery of Inhibitors of 4′-Phosphopantetheine Adenylyltransferase (PPAT) To Validate PPAT as a Target for Antibacterial Therapy

(2013) Boudewijn L. M. de Jonge et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

(2013) Tilo Buschmann et al.   BMC BIOINFORMATICS

DNA synthesis, assembly and applications in synthetic biology

(2012) Siying Ma et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Ribozyme-based insulator parts buffer synthetic circuits from genetic context

(2012) Chunbo Lou et al.   NATURE BIOTECHNOLOGY

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules

(2012) Jerrod J Schwartz et al.   NATURE METHODS

‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules

(2012) Hwangbeom Kim et al.   NUCLEIC ACIDS RESEARCH

Parallel on-chip gene synthesis and application to optimization of protein expression

(2011) Jiayuan Quan et al.   NATURE BIOTECHNOLOGY

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

(2010) Sriram Kosuri et al.   NATURE BIOTECHNOLOGY

High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides

(2010) Alex Y. Borovkov et al.   NUCLEIC ACIDS RESEARCH

Site-specific chromosomal integration of large synthetic constructs

(2010) Thomas E. Kuhlman et al.   NUCLEIC ACIDS RESEARCH

A synthetic three-color scaffold for monitoring genetic regulation and noise

(2010) Robert Cox et al.   Journal of Biological Engineering

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY