A Sort-Seq Approach to the Development of Single Fluorescent Protein Biosensors

Low-N protein engineering with data-efficient deep learning

(2021) Surojit Biswas et al.   NATURE METHODS

A highly responsive pyruvate sensor reveals pathway-regulatory role of the mitochondrial pyruvate carrier MPC

(2020) Robinson Arce-Molina et al.   eLife

Deep Dive into Machine Learning Models for Protein Engineering

(2020) Yuting Xu et al.   Journal of Chemical Information and Modeling

Hyperparameters and tuning strategies for random forest

(2019) Philipp Probst et al.   Wiley Interdisciplinary Reviews-Data Mining and Knowledge Discovery

Machine learning-assisted directed protein evolution with combinatorial libraries

(2019) Zachary Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics

(2019) Claire N. Bedbrook et al.   NATURE METHODS

Unified rational protein engineering with sequence-based deep representation learning

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

Targeted insertional mutagenesis libraries for deep domain insertion profiling

(2019) Willow Coyote-Maestas et al.   NUCLEIC ACIDS RESEARCH

Learned protein embeddings for machine learning

(2018) Kevin K Yang et al.   BIOINFORMATICS

Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks

(2018) Eric C. Greenwald et al.   CHEMICAL REVIEWS

Live-cell imaging of cell signaling using genetically encoded fluorescent reporters

(2017) Qiang Ni et al.   FEBS Journal

ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

(2017) Marvin N. Wright et al.   Journal of Statistical Software

A platform for functional assessment of large variant libraries in mammalian cells

(2017) Kenneth A. Matreyek et al.   NUCLEIC ACIDS RESEARCH

Deciphering the molecular mechanism responsible for GCaMP6m's Ca2+-dependent change in fluorescence

(2017) Lauren M. Barnett et al.   PLoS One

EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors

(2017) Andrea Martella et al.   ACS Synthetic Biology

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Sort-seq under the hood: implications of design choices on large-scale characterization of sequence-function relations

(2016) Neil Peterman et al.   BMC GENOMICS

Exploring cells with targeted biosensors

(2016) Diana Pendin et al.   JOURNAL OF GENERAL PHYSIOLOGY

Rapid construction of metabolite biosensors using domain-insertion profiling

(2016) Dana C. Nadler et al.   Nature Communications

Molecular Spies for Bioimaging—Fluorescent Protein-Based Probes

(2015) Atsushi Miyawaki et al.   MOLECULAR CELL

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

(2014) Eilon Sharon et al.   GENOME RESEARCH

Quantitative analysis of mammalian translation initiation sites by FACS-seq

(2014) W. L. Noderer et al.   Molecular Systems Biology

Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity

(2014) Neil Peterman et al.   NUCLEIC ACIDS RESEARCH

An optimized fluorescent probe for visualizing glutamate neurotransmission

(2013) Jonathan S Marvin et al.   NATURE METHODS

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement

(2013) Yingxiao Chen et al.   Protein & Cell

Quantitative Imaging with Fluorescent Biosensors

(2012) Sakiko Okumoto et al.   Annual Review of Plant Biology

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Optical sensors for monitoring dynamic changes of intracellular metabolite levels in mammalian cells

(2011) Bi-Huei Hou et al.   Nature Protocols

A genetically encoded, high-signal-to-noise maltose sensor

(2011) Jonathan S. Marvin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

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

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators

(2009) Lin Tian et al.   NATURE METHODS

Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design

(2008) Jasper Akerboom et al.   JOURNAL OF BIOLOGICAL CHEMISTRY