Virus-encoded histone doublets are essential and form nucleosome-like structures

Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways

(2021) Samuel Bowerman et al.   eLife

The structure of a virus-encoded nucleosome

(2021) Marco Igor Valencia-Sánchez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analysis of a Marseillevirus Transcriptome Reveals Temporal Gene Expression Profile and Host Transcriptional Shift

(2020) Rodrigo Araújo Lima Rodrigues et al.   Frontiers in Microbiology

Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2

(2020) Min Zhou et al.   EMBO JOURNAL

Old cogs, new tricks: the evolution of gene expression in a chromatin context

(2019) Paul B. Talbert et al.   NATURE REVIEWS GENETICS

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly

(2018) Kenta Okamoto et al.   VIROLOGY

The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome

(2018) Emma A Morrison et al.   eLife

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

Structure of histone-based chromatin in Archaea

(2017) Francesca Mattiroli et al.   SCIENCE

Phylogenetic analysis of the core histone doublet and DNA topo II genes of Marseilleviridae: evidence of proto-eukaryotic provenance

(2017) Albert J. Erives   Epigenetics & Chromatin

Noumeavirus replication relies on a transient remote control of the host nucleus

(2017) Elisabeth Fabre et al.   Nature Communications

Decoding the centromeric nucleosome through CENP-N

(2017) Satyakrishna Pentakota et al.   eLife

Gctf: Real-time CTF determination and correction

(2016) Kai Zhang   JOURNAL OF STRUCTURAL BIOLOGY

Advances in the molecular dynamics flexible fitting method for cryo-EM modeling

(2016) Ryan McGreevy et al.   METHODS

The SWISS-MODEL Repository—new features and functionality

(2016) Stefan Bienert et al.   NUCLEIC ACIDS RESEARCH

Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core

(2016) Yujie Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A quantitative investigation of linker histone interactions with nucleosomes and chromatin

(2016) Alison E. White et al.   Scientific Reports

Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability in Saccharomyces cerevisiae

(2015) Amelia J. Hodges et al.   GENETICS

Genome Wide Nucleosome Mapping for HSV-1 Shows Nucleosomes Are Deposited at Preferred Positions during Lytic Infection

(2015) Jaewook Oh et al.   PLoS One

Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability in Saccharomyces cerevisiae

(2015) Amelia J. Hodges et al.   GENETICS

Characterization of Size, Anisotropy, and Density Heterogeneity of Nanoparticles by Sedimentation Velocity

(2014) Borries Demeler et al.   ANALYTICAL CHEMISTRY

A Parametrically Constrained Optimization Method for Fitting Sedimentation Velocity Experiments

(2014) Gary Gorbet et al.   BIOPHYSICAL JOURNAL

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Cryo-Electron Microscopy Modeling by the Molecular Dynamics Flexible Fitting Method

(2012) Kwok-Yan Chan et al.   BIOPOLYMERS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The mechanics behind DNA sequence-dependent properties of the nucleosome

(2012) Eugene Y. D. Chua et al.   NUCLEIC ACIDS RESEARCH

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Lausannevirus, a giant amoebal virus encoding histone doublets

(2011) Vincent Thomas et al.   ENVIRONMENTAL MICROBIOLOGY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective

(2010) Nicolas Guex et al.   ELECTROPHORESIS

Crystal Structures of Nucleosome Core Particles Containing the ‘601’ Strong Positioning Sequence

(2010) Dileep Vasudevan et al.   JOURNAL OF MOLECULAR BIOLOGY

Developments in the US-SOMO Bead Modeling Suite: New Features in the Direct Residue-to-Bead Method, Improved Grid Routines, and Influence of Accessible Surface Area Screening

(2010) Emre Brookes et al.   MACROMOLECULAR BIOSCIENCE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms

(2009) M. Boyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression plasmids and production of EGFP in stably transfected Acanthamoeba

(2009) Erik Bateman   PROTEIN EXPRESSION AND PURIFICATION

Chromatin organization and virus gene expression

(2008) Paul M. Lieberman   JOURNAL OF CELLULAR PHYSIOLOGY