eggNOG v4.0: nested orthology inference across 3686 organisms

Sean Powell, Damian Szklarczyk, Kalliopi Trachana, +9

Nucleic Acids Research

Comparative GenomicsGeneticsGenomicsEggnog V4.0Phylogenetics +18

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Sean Powell, Damian Szklarczyk, Kalliopi Trachana, +10

Nucleic Acids Research

Comparative GenomicsGeneticsZoological TaxonomyGenomicsPhylogenetic Analysis +20

Cell Fate Decision as High-Dimensional Critical State Transition

Mitra Mojtahedi, Alexander Skupin, Joseph Zhou, +6

PLoS Biology

EngineeringTrajectory AnalysisCell Fate DecisionSingle Cell SequencingGene Expression Configuration +15

Ancient animal microRNAs and the evolution of tissue identity

Foteini Christodoulou, Florian Raible, Raju Tomer, +7

Nature

GeneticsAncient Animal MicrornasMorphogenesisMicrorna DetectionSmall Rna +3

Orthology prediction methods: A quality assessment using curated protein families

Kalliopi Trachana, Tomas Larsson, Sean Powell, +4

BioEssays

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

Rhishikesh Bargaje, Kalliopi Trachana, Martin N. Shelton, +7

Proceedings of the National Academy of Sciences

State TransitionCell DifferentiationCell SpecializationCellular PhysiologyDirected Differentiation +15

Acquisition of a bacterial RumA‐type tRNA(uracil‐54, C5)‐methyltransferase by Archaea through an ancient horizontal gene transfer

Jaunius Urbonavičius, Sylvie Auxilien, Hélène Walbott, +4

Molecular Microbiology

Phylostratigraphic analysis of tumor and developmental transcriptomes reveals relationship between oncogenesis, phylogenesis and ontogenesis

Joseph Zhou, Luis Cisneros, Theo Knijnenburg, +3

Convergent Science Physical Oncology

Tumor BiologyEmbryologyAtavism TransitionPhylostratigraphic AnalysisTumor Heterogeneity +16

Gene socialization: gene order, GC content and gene silencing in Salmonella

Nikolas Papanikolaou, Kalliopi Trachana, Vasilis J. Promponas, +1

BMC Genomics

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation

Kalliopi Trachana, Tomas Larsson, Sean Powell, +3

PLoS ONE

Comparative GenomicsGeneticsTaxonomyBenchmark SetGenomics +21