Deep learning to predict the lab-of-origin of engineered DNA

Methods for interpreting and understanding deep neural networks

(2018) Grégoire Montavon et al.   DIGITAL SIGNAL PROCESSING

A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology

(2018) Arturo Casini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mastering the game of Go without human knowledge

(2017) David Silver et al.   NATURE

Genetic Design via Combinatorial Constraint Specification

(2017) Swapnil P. Bhatia et al.   ACS Synthetic Biology

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Rewriting yeast central carbon metabolism for industrial isoprenoid production

(2016) Adam L. Meadows et al.   NATURE

DNA writers attract investors

(2016) Justin Petrone   NATURE BIOTECHNOLOGY

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

The Genome Project-Write

(2016) J. D. Boeke et al.   SCIENCE

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

Human-level control through deep reinforcement learning

(2015) Volodymyr Mnih et al.   NATURE

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

Interactive assembly algorithms for molecular cloning

(2014) Evan Appleton et al.   NATURE METHODS

Realizing the potential of synthetic biology

(2014) George M. Church et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Total Synthesis of a Functional Designer Eukaryotic Chromosome

(2014) N. Annaluru et al.   SCIENCE

Genome-scale engineering for systems and synthetic biology

(2013) K. M. Esvelt et al.   Molecular Systems Biology

Computational design of ligand-binding proteins with high affinity and selectivity

(2013) Christine E. Tinberg et al.   NATURE

Addgene provides an open forum for plasmid sharing

(2012) Melanie Herscovitch et al.   NATURE BIOTECHNOLOGY

Specification and Simulation of Synthetic Multicelled Behaviors

(2012) Seunghee S. Jang et al.   ACS Synthetic Biology

An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications

(2012) Jacob Beal et al.   ACS Synthetic Biology

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

(2011) Lesia Bilitchenko et al.   PLoS One

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

(2011) D. A. Rasko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

In the light of directed evolution: Pathways of adaptive protein evolution

(2009) J. D. Bloom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

UpGene: Application of a Web-Based DNA Codon Optimization Algorithm

(2004) Wentao Gao et al.   BIOTECHNOLOGY PROGRESS