Automated multiplex genome-scale engineering in yeast

A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae

(2016) Shuobo Shi et al.   METABOLIC ENGINEERING

Rapid prototyping of microbial cell factories via genome-scale engineering

(2015) Tong Si et al.   BIOTECHNOLOGY ADVANCES

Experimental evolution of the model eukaryote Saccharomyces cerevisiae yields insight into the molecular mechanisms underlying adaptation

(2015) Karin Voordeckers et al.   CURRENT OPINION IN MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Utilizing an endogenous pathway for 1-butanol production in Saccharomyces cerevisiae

(2014) Tong Si et al.   METABOLIC ENGINEERING

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

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

(2013) Luke A. Gilbert et al.   CELL

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

(2013) Dokyun Na et al.   NATURE BIOTECHNOLOGY

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

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Yeast Reveal a "Druggable" Rsp5/Nedd4 Network that Ameliorates  -Synuclein Toxicity in Neurons

(2013) D. F. Tardiff et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Yeast Oligo-Mediated Genome Engineering (YOGE)

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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries

(2012) Kuk-Ki Hong et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol

(2012) Karla Martínez-Gómez et al.   Microbial Cell Factories

Strategy for directing combinatorial genome engineering in Escherichia coli

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

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

An evolutionary strategy for isobutanol production strain development in Escherichia coli

(2011) Kevin M. Smith et al.   METABOLIC ENGINEERING

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome-wide identification of Saccharomyces cerevisiae genes required for tolerance to acetic acid

(2010) Nuno P Mira et al.   Microbial Cell Factories

Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides

(2010) Joseph R Warner et al.   NATURE BIOTECHNOLOGY

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Yeast Surface Display of Trifunctional Minicellulosomes for Simultaneous Saccharification and Fermentation of Cellulose to Ethanol

(2009) F. Wen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Transcriptional regulation of nonfermentable carbon utilization in budding yeast

(2009) Bernard Turcotte et al.   FEMS YEAST RESEARCH

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds

(2009) Cheuk Hei Ho et al.   NATURE BIOTECHNOLOGY

Genome engineering

(2009) Peter A Carr et al.   NATURE BIOTECHNOLOGY

An optimized microplate assay system for quantitative evaluation of plant cell wall-degrading enzyme activity of fungal culture extracts

(2008) Brian C. King et al.   BIOTECHNOLOGY AND BIOENGINEERING

Progress in Metabolic Engineering of Saccharomyces cerevisiae

(2008) E. Nevoigt   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Normalization of full-length enriched cDNA

(2008) Ekaterina A. Bogdanova et al.   Molecular BioSystems

A comprehensive strategy enabling high-resolution functional analysis of the yeast genome

(2008) David K Breslow et al.   NATURE METHODS

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

(2008) Zengyi Shao et al.   NUCLEIC ACIDS RESEARCH