Phytoplankton pangenome reveals extensive prokaryotic horizontal gene transfer of diverse functions

Genome analysis of the rice coral Montipora capitata

(2019) Alexander Shumaker et al.   Scientific Reports

Evolutionary dynamics of the chromatophore genome in three photosynthetic Paulinella species

(2019) Duckhyun Lhee et al.   Scientific Reports

Analysis of an improved Cyanophora paradoxa genome assembly

(2019) Dana C Price et al.   DNA RESEARCH

The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

(2019) Alessandro W Rossoni et al.   eLife

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Biological uptake and reversible scavenging of zinc in the global ocean

(2018) Thomas Weber et al.   SCIENCE

Polyamines in Microalgae: Something Borrowed, Something New

(2018) Hung-Yun Lin et al.   Marine Drugs

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

(2017) Thomas Mock et al.   NATURE

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Functional horizontal gene transfer from bacteria to eukaryotes

(2017) Filip Husnik et al.   NATURE REVIEWS MICROBIOLOGY

Extensive horizontal gene transfers between plant pathogenic fungi

(2016) Huan Qiu et al.   BMC BIOLOGY

Erratum to: On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1

(2016) Feifei Xu et al.   BMC BIOLOGY

A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule

(2016) Chuan Ku et al.   BMC BIOLOGY

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore ofPaulinella chromatophora

(2016) Eva C. M. Nowack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides

(2016) William G. Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transfer of DNA from Bacteria to Eukaryotes

(2016) Benoît Lacroix et al.   mBio

Endosymbiosis and Eukaryotic Cell Evolution

(2015) John M. Archibald   CURRENT BIOLOGY

Codon optimization, promoter and expression system selection that achieved high-level production of Yarrowia lipolytica lipase in Pichia pastoris

(2015) Wen-Jing Zhou et al.   ENZYME AND MICROBIAL TECHNOLOGY

Endosymbiotic origin and differential loss of eukaryotic genes

(2015) Chuan Ku et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

(2015) Chuan Ku et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Saccharina genomes provide novel insight into kelp biology

(2015) Naihao Ye et al.   Nature Communications

Inferring Horizontal Gene Transfer

(2015) Matt Ravenhall et al.   PLoS Computational Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Horizontal gene transfer in eukaryotes: The weak-link model

(2013) Jinling Huang   BIOESSAYS

Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution

(2013) Gerald Schönknecht et al.   BIOESSAYS

Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis

(2013) Filip Husnik et al.   CELL

Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea

(2013) Huan Qiu et al.   CURRENT BIOLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Transporter Classification Database

(2013) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Interdomain lateral gene transfer of an essential ferrochelatase gene in human parasitic nematodes

(2013) B. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ANALYSIS OFALEXANDRIUM TAMARENSE(DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE1

(2012) Cheong Xin Chan et al.   JOURNAL OF PHYCOLOGY

Recurrent Horizontal Transfer of Bacterial Toxin Genes to Eukaryotes

(2012) Y. Moran et al.   MOLECULAR BIOLOGY AND EVOLUTION

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms

(2009) A. Moustafa et al.   SCIENCE

Acquisition of prokaryotic genes by fungal genomes

(2009) Marina Marcet-Houben et al.   TRENDS IN GENETICS

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)

(2008) Pere Puigbò et al.   BMC BIOINFORMATICS

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE