Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

Alexander Sczyrba, Peter Hofmann, Peter Belmann, +64

Nature Methods

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Robert A. Edwards, Alejandro A. Vega, Holly M. Norman, +111

Nature Microbiology

BiologyViral EvolutionPhylogeneticsNatural SciencesVirus Phylogeny +8

Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

Terry Disz, Sajia Akhter, Daniel Cuevas, +5

BMC Bioinformatics

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome

Lance Boling, Daniel Cuevas, Juris A. Grasis, +9

Gut Microbes

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

Genivaldo Gueiros Z. Silva, Daniel Cuevas, Bas E. Dutilh, +1

PeerJ

EngineeringNon-negative Least SquaresAlignment-free ModelGenomicsSequence Alignment +18

From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

Daniel Cuevas, Janaka N. Edirisinghe, Chris Henry, +3

Frontiers in Microbiology

EngineeringMolecular BiologyMetabolic NetworksMetabolic ModelMicrobiological Studies +20

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Alexander Sczyrba, Peter Hofmann, Peter Belmann, +64

EngineeringGeneticsMetagenome InterpretationBenchmark MetagenomesGenomics +18

Prophage genomics reveals patterns in phage genome organization and replication

Han Suh Kang, Katelyn McNair, Daniel Cuevas, +3

Phispy AlgorithmGeneticsConserved Genome AlignmentsBacteriophageGenomic Mechanism +19

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Robert A. Edwards, Alejandro A. Vega, Holly S. Norman, +109

Dna SequencesHuman Gut ViromeMicrobial VirusMicrobial EvolutionAncient Evolution +18

PMAnalyzer: a new web interface for bacterial growth curve analysis

Daniel Cuevas, Robert A. Edwards

Bioinformatics