WiChR, a highly potassium-selective channelrhodopsin for low-light one- and two-photon inhibition of excitable cells

Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine

(2022) Koichiro E. Kishi et al.   CELL

Emerging Diversity of Channelrhodopsins and Their Structure-Function Relationships

(2022) Elena G. Govorunova et al.   Frontiers in Cellular Neuroscience

Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles

(2022) Anna Cho et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Differential ion dehydration energetics explains selectivity in the non-canonical lysosomal K+ channel TMEM175

(2022) SeCheol Oh et al.   eLife

Kalium channelrhodopsins are natural light-gated potassium channels that mediate optogenetic inhibition

(2022) Elena G. Govorunova et al.   NATURE NEUROSCIENCE

Cryo-EM structures of the channelrhodopsin ChRmine in lipid nanodiscs

(2022) Kyle Tucker et al.   Nature Communications

Biophysical characterization of light-gated ion channels using planar automated patch clamp

(2022) Elena G. Govorunova et al.   Frontiers in Molecular Neuroscience

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Efficient optogenetic silencing of neurotransmitter release with a mosquito rhodopsin

(2021) Mathias Mahn et al.   NEURON

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic Distribution

(2021) Elena G. Govorunova et al.   mBio

Modeling Transposition of the Great Arteries with Patient-Specific Induced Pluripotent Stem Cells

(2021) Imelda Ontoria-Oviedo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses

(2020) Andrey Rozenberg et al.   CURRENT BIOLOGY

Engineered Passive Potassium Conductance in the KR2 Sodium Pump

(2019) Arend Vogt et al.   BIOPHYSICAL JOURNAL

High-performance calcium sensors for imaging activity in neuronal populations and microcompartments

(2019) Hod Dana et al.   NATURE METHODS

Taxon-rich Multigene Phylogenetic Analyses Resolve the Phylogenetic Relationship Among Deep-branching Stramenopiles

(2019) Rabindra Thakur et al.   PROTIST

Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

(2018) Guy Leonard et al.   Open Biology

Temperature Rise under Two-Photon Optogenetic Brain Stimulation

(2018) Alexis Picot et al.   Cell Reports

High-efficiency optogenetic silencing with soma-targeted anion-conducting channelrhodopsins

(2018) Mathias Mahn et al.   Nature Communications

Potassium channel-based optogenetic silencing

(2018) Yinth Andrea Bernal Sierra et al.   Nature Communications

Cardiac Electrophysiological Effects of Light-Activated Chloride Channels

(2018) Ramona A. Kopton et al.   Frontiers in Physiology

Multiplexed temporally focused light shaping for high-resolution multi-cell targeting

(2018) Nicolò Accanto et al.   Optica

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacteriorhodopsin-like channelrhodopsins: Alternative mechanism for control of cation conductance

(2017) Oleg A. Sineshchekov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improvements to the APBS biomolecular solvation software suite

(2017) Elizabeth Jurrus et al.   PROTEIN SCIENCE

Pseudophyllomitus vesiculosus (Larsen and Patterson 1990) Lee, 2002, a Poorly Studied Phagotrophic Biflagellate is the First Characterized Member of Stramenopile Environmental Clade MAST-6

(2017) Takashi Shiratori et al.   PROTIST

Recent advances in patterned photostimulation for optogenetics

(2017) Emiliano Ronzitti et al.   Journal of Optics

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Structurally Distinct Cation Channelrhodopsins from Cryptophyte Algae

(2016) Elena G. Govorunova et al.   BIOPHYSICAL JOURNAL

Complex evolution of two types of cardiolipin synthase in the eukaryotic lineage stramenopiles

(2016) Fumiya Noguchi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Biophysical constraints of optogenetic inhibition at presynaptic terminals

(2016) Mathias Mahn et al.   NATURE NEUROSCIENCE

Dowser++, a new method of hydrating protein structures

(2016) A. Morozenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Three-dimensional spatiotemporal focusing of holographic patterns

(2016) Oscar Hernandez et al.   Nature Communications

pKa Values in Proteins Determined by Electrostatics Applied to Molecular Dynamics Trajectories

(2015) Tim Meyer et al.   Journal of Chemical Theory and Computation

Engineering of a light-gated potassium channel

(2015) C. Cosentino et al.   SCIENCE

Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics

(2013) Jasper Akerboom et al.   Frontiers in Molecular Neuroscience

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Crystal structure of the channelrhodopsin light-gated cation channel

(2012) Hideaki E. Kato et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

An Expanded Palette of Genetically Encoded Ca2+ Indicators

(2011) Y. Zhao et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing

(2010) Harald Janovjak et al.   NATURE NEUROSCIENCE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Holographic photolysis of caged neurotransmitters

(2008) Christoph Lutz et al.   NATURE METHODS