Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria

Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria

(2016) Ding He et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells

(2016) Iain C. Macaulay et al.   Cell Reports

WHAMM Directs the Arp2/3 Complex to the ER for Autophagosome Biogenesis through an Actin Comet Tail Mechanism

(2015) David J. Kast et al.   CURRENT BIOLOGY

Evolutionary Origins of Rhizarian Parasites

(2015) Roberto Sierra et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista

(2015) Thomas Cavalier-Smith et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Single-cell transcriptomics for microbial eukaryotes

(2014) Martin Kolisko et al.   CURRENT BIOLOGY

Rhizaria

(2014) Fabien Burki et al.   CURRENT BIOLOGY

Evolution and Classification of Myosins, a Paneukaryotic Whole-Genome Approach

(2014) Arnau Sebé-Pedrós et al.   Genome Biology and Evolution

The contribution of αβ-tubulin curvature to microtubule dynamics

(2014) Gary J. Brouhard et al.   JOURNAL OF CELL BIOLOGY

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

The Neomuran Revolution and Phagotrophic Origin of Eukaryotes and Cilia in the Light of Intracellular Coevolution and a Revised Tree of Life

(2014) T. Cavalier-Smith   Cold Spring Harbor Perspectives in Biology

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

(2013) Gershon Celniker et al.   ISRAEL JOURNAL OF CHEMISTRY

Molecular Evidence for β-tubulin Neofunctionalization in Retaria (Foraminifera and Radiolarians)

(2013) Yubo Hou et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships

(2013) Torsten H. Struck   PLoS One

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Pseudopod Growth and Evolution during Cell Movement Is Controlled through SCAR/WAVE Dephosphorylation

(2012) Seiji Ura et al.   CURRENT BIOLOGY

The Ras protein superfamily: Evolutionary tree and role of conserved amino acids

(2012) Ana Maria Rojas et al.   JOURNAL OF CELL BIOLOGY

Deep relationships of Rhizaria revealed by phylogenomics: A farewell to Haeckel’s Radiolaria

(2012) Roberto Sierra et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins

(2012) F. Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

(2012) Andre J. Aberer et al.   SYSTEMATIC BIOLOGY

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

The evolution of the cytoskeleton

(2011) Bill Wickstead et al.   JOURNAL OF CELL BIOLOGY

Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny

(2011) Anders K. Krabberød et al.   PLoS One

A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases

(2011) Carla A. Cummins et al.   SYSTEMATIC BIOLOGY

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Radiolaria: achievements and unresolved issues: taxonomy and cytology

(2011) Noritoshi Suzuki et al.   Plankton & Benthos Research

Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists

(2010) Fabien Burki et al.   BMC EVOLUTIONARY BIOLOGY

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Research note: Amorphochlora amoebiformis gen. et comb. nov. (Chlorarachniophyceae)

(2010) Ken-ichiro Ishida et al.   PHYCOLOGICAL RESEARCH

The Shape of Motile Cells

(2009) Alex Mogilner et al.   CURRENT BIOLOGY

The structural basis of actin filament branching by the Arp2/3 complex

(2008) Isabelle Rouiller et al.   JOURNAL OF CELL BIOLOGY

Megaphylogeny, Cell Body Plans, Adaptive Zones: Causes and Timing of Eukaryote Basal Radiations

(2008) THOMAS CAVALIER-SMITH   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Filopodia: molecular architecture and cellular functions

(2008) Pieta K. Mattila et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pseudopodial features and feeding behavior of living nassellarians Eucyrtidium hexagonatum Haeckel, Pterocorys zancleus (Müler) and Dictyocodon prometheus Haeckel

(2008) Kazuhiro Sugiyama et al.   PALEONTOLOGICAL RESEARCH

Phylogeny of Novel Naked Filose and Reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea Revised

(2008) David Bass et al.   PROTIST

X-Ray Scattering Study of Activated Arp2/3 Complex with Bound Actin-WCA

(2008) Malgorzata Boczkowska et al.   STRUCTURE