SensiPath: computer-aided design of sensing-enabling metabolic pathways

A novel fluorescent aptasensor based on hairpin structure of complementary strand of aptamer and nanoparticles as a signal amplification approach for ultrasensitive detection of cocaine

(2016) Ahmad Sarreshtehdar Emrani et al.   BIOSENSORS & BIOELECTRONICS

Genetically encoded sensors enable real-time observation of metabolite production

(2016) Jameson K. Rogers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways

(2016) Vincent Libis et al.   ACS Synthetic Biology

Transcription factor-based biosensors in biotechnology: current state and future prospects

(2015) Regina Mahr et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

BioSynther: a customized biosynthetic potential explorer

(2015) Weizhong Tu et al.   BIOINFORMATICS

Ultra-high frequency piezoelectric aptasensor for the label-free detection of cocaine

(2015) Miguel A.D. Neves et al.   BIOSENSORS & BIOELECTRONICS

Screening and modular design for metabolic pathway optimization

(2015) Jason T Boock et al.   CURRENT OPINION IN BIOTECHNOLOGY

Biosensor-driven adaptive laboratory evolution of l -valine production in Corynebacterium glutamicum

(2015) Regina Mahr et al.   METABOLIC ENGINEERING

Applications and advances of metabolite biosensors for metabolic engineering

(2015) Di Liu et al.   METABOLIC ENGINEERING

An enzyme-coupled biosensor enables (S)-reticuline production in yeast from glucose

(2015) William C DeLoache et al.   Nature Chemical Biology

Engineering an allosteric transcription factor to respond to new ligands

(2015) Noah D Taylor et al.   NATURE METHODS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor

(2015) Ramesh K. Jha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates

(2015) Alexis Courbet et al.   Science Translational Medicine

M-path: a compass for navigating potential metabolic pathways

(2014) Michihiro Araki et al.   BIOINFORMATICS

Retraction Note to: Retraction: Reprogramming bacteria to seek and destroy an herbicide

(2014) Joy Sinha et al.   Nature Chemical Biology

Principles of genetic circuit design

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

XTMS: pathway design in an eXTended metabolic space

(2014) Pablo Carbonell et al.   NUCLEIC ACIDS RESEARCH

Updates in Rhea—a manually curated resource of biochemical reactions

(2014) Anne Morgat et al.   NUCLEIC ACIDS RESEARCH

BRENDA in 2015: exciting developments in its 25th year of existence

(2014) Antje Chang et al.   NUCLEIC ACIDS RESEARCH

Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

(2014) P. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

(2013) Michael J Cipriano et al.   BMC GENOMICS

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

(2013) Pavel S Novichkov et al.   BMC GENOMICS

Stereo Signature Molecular Descriptor

(2013) Pablo Carbonell et al.   Journal of Chemical Information and Modeling

Retropath: Automated Pipeline for Embedded Metabolic Circuits

(2013) Pablo Carbonell et al.   ACS Synthetic Biology

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules

(2010) Aitor de las Heras et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

Reprogramming bacteria to seek and destroy an herbicide

(2010) Joy Sinha et al.   Nature Chemical Biology

Identification and Characterization of Catabolic para-Nitrophenol 4-Monooxygenase and para-Benzoquinone Reductase from Pseudomonas sp. Strain WBC-3

(2009) J.-J. Zhang et al.   JOURNAL OF BACTERIOLOGY

The University of Minnesota Biocatalysis/Biodegradation Database: improving public access

(2009) Junfeng Gao et al.   NUCLEIC ACIDS RESEARCH

AraC Regulatory Protein Mutants with Altered Effector Specificity

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

Substrate-induced gene expression (SIGEX) screening of metagenome libraries

(2008) Taku Uchiyama et al.   Nature Protocols

Bionemo: molecular information on biodegradation metabolism

(2008) G. Carbajosa et al.   NUCLEIC ACIDS RESEARCH