Model-driven discovery of underground metabolic functions inEscherichia coli

Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency?

(2014) Dan S Tawfik   CURRENT OPINION IN CHEMICAL BIOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

Determination of the Structure of the Catabolic N-Succinylornithine Transaminase (AstC) from Escherichia coli

(2013) Janet Newman et al.   PLoS One

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

(2012) Jeffrey D Orth et al.   BMC Systems Biology

Current challenges in genome annotation through structural biology and bioinformatics

(2012) Nicholas Furnham et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Mechanism for Regulation of the Putrescine Utilization Pathway by the Transcription Factor PuuR in Escherichia coli K-12

(2012) N. Nemoto et al.   JOURNAL OF BACTERIOLOGY

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective

(2010) Olga Khersonsky and Dan S. Tawfik   Annual Review of Biochemistry

Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, L-1,2-Propanediol

(2010) D.-H. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily

(2010) B. van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Amplification and Adaptive Evolution in Bacteria

(2009) Dan I. Andersson et al.   Annual Review of Genetics

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology