Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms

Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures

(2023) Hassan Badrane et al.   Nature Communications

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

(2022) Josh L. Espinoza et al.   BMC BIOINFORMATICS

Selective constraints on global plankton dispersal

(2021) Ben A. Ward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unification of functional annotation descriptions using text mining

(2021) Pedro Queirós et al.   BIOLOGICAL CHEMISTRY

Thoughts on the evolution and ecological niche of diatoms

(2021) Michael J. Behrenfeld et al.   ECOLOGICAL MONOGRAPHS

Population bottlenecks strongly affect the evolutionary dynamics of antibiotic persistence

(2021) Etthel M Windels et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach

(2021) Josh L. Espinoza et al.   PLoS Computational Biology

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality

(2021) Erika P. Santoro et al.   Science Advances

A High-Throughput Assay for Quantifying Phenotypic Traits of Microalgae

(2021) Phoebe A. Argyle et al.   Frontiers in Microbiology

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

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Applications of weighted association networks applied to compositional data in biology

(2020) Josh L. Espinoza et al.   ENVIRONMENTAL MICROBIOLOGY

Multiple global change stressor effects on phytoplankton nutrient acquisition in a future ocean

(2020) Dedmer B. Van de Waal et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Trehalose and (iso)floridoside production under desiccation stress in red alga Porphyra umbilicalis and the genes involved in their synthesis 1

(2020) Yuanyu Cao et al.   JOURNAL OF PHYCOLOGY

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

(2020) Jacob L. Steenwyk et al.   PLOS BIOLOGY

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

(2019) Elena Bushmanova et al.   GigaScience

Responses of Marine Diatom Skeletonema marinoi to Nutrient Deficiency: Programmed Cell Death

(2019) Hualong Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom

(2019) Sarah R. Smith et al.   Nature Communications

Fitness change in relation to mutation number in spontaneous mutation accumulation lines of Chlamydomonas reinhardtii

(2017) Susanne A. Kraemer et al.   EVOLUTION

Clonal expansion behind a marine diatom bloom

(2017) Maria Valeria Ruggiero et al.   ISME Journal

The Impact of Population Bottlenecks on Microbial Adaptation

(2017) Joshua S. LeClair et al.   JOURNAL OF STATISTICAL PHYSICS

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

(2017) Thomas Mock et al.   NATURE

Adaptive benefits from small mutation supplies in an antibiotic resistance enzyme

(2017) Merijn L. M. Salverda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

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

The physiology and genetics of CO 2 concentrating mechanisms in model diatoms

(2016) Brian M Hopkinson et al.   CURRENT OPINION IN PLANT BIOLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into global diatom distribution and diversity in the world’s ocean

(2016) Shruti Malviya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping energy transfer channels in fucoxanthin–chlorophyll protein complex

(2015) Andrius Gelzinis et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Key genes as stress indicators in the ubiquitous diatom Skeletonema marinoi

(2015) Chiara Lauritano et al.   BMC GENOMICS

The nature of the CO2-concentrating mechanisms in a marine diatom,Thalassiosira pseudonana

(2015) Romain Clement et al.   NEW PHYTOLOGIST

Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression

(2015) Gwenn M. M. Hennon et al.   Nature Climate Change

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Fitness Is Strongly Influenced by Rare Mutations of Large Effect in a Microbial Mutation Accumulation Experiment

(2014) K. Heilbron et al.   GENETICS

Extensive cross-environment fitness variation lies along few axes of genetic variation in the model alga,Chlamydomonas reinhardtii

(2014) Jacob W. Malcom et al.   NEW PHYTOLOGIST

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

The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella

(2011) Andrew J Alverson et al.   BMC EVOLUTIONARY BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Spontaneous Mutation Accumulation Studies in Evolutionary Genetics

(2009) Daniel L. Halligan et al.   Annual Review of Ecology Evolution and Systematics

Deciphering diatom biochemical pathways via whole-cell proteomics

(2009) BL Nunn et al.   AQUATIC MICROBIAL ECOLOGY

The Properties of Adaptive Walks in Evolving Populations of Fungus

(2009) Sijmen E. Schoustra et al.   PLOS BIOLOGY

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation

(2008) A. E. Allen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA