Deep protein representations enable recombinant protein expression prediction

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

(2021) Alexander Rives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent Advances in Recombinant Protein Production by Bacillus subtilis

(2020) Kang Zhang et al.   Annual Review of Food Science and Technology

Insight into the protein solubility driving forces with neural attention

(2020) Daniele Raimondi et al.   PLoS Computational Biology

Solubility-Weighted Index: fast and accurate prediction of protein solubility

(2020) Bikash K Bhandari et al.   BIOINFORMATICS

Codon optimization with deep learning to enhance protein expression

(2020) Hongguang Fu et al.   Scientific Reports

SoluProt: Prediction of Soluble Protein Expression in Escherichia coli

(2020) Jiri Hon et al.   BIOINFORMATICS

New tools for recombinant protein production in Escherichia coli : A 5-year update

(2019) Germán L. Rosano et al.   PROTEIN SCIENCE

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

DeepSol: a deep learning framework for sequence-based protein solubility prediction

(2018) Sameer Khurana et al.   BIOINFORMATICS

Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli

(2018) Guillaume Cambray et al.   NATURE BIOTECHNOLOGY

Deep learning

(2015) Yann LeCun et al.   NATURE

ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli

(2014) F. Agostini et al.   BIOINFORMATICS

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility

(2013) C. Mirabello et al.   BIOINFORMATICS

PROSO II - a new method for protein solubility prediction

(2012) Pawel Smialowski et al.   FEBS Journal

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE