Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments

Variation in the transcriptome of different ecotypes of Arabidopsis thaliana reveals signatures of oxidative stress in plant responses to spaceflight

(2019) Won-Gyu Choi et al.   AMERICAN JOURNAL OF BOTANY

HSFA2 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight

(2019) Agata Zupanska et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

(2019) Mingqi Zhou et al.   BMC GENOMICS

Spaceflight-induced alternative splicing during seedling development in Arabidopsis thaliana

(2019) Nicole S. Beisel et al.   NPJ Microgravity

An “eFP‐Seq Browser” for Visualizing and Exploring RNA‐Seq Data

(2019) Alexander Sullivan et al.   PLANT JOURNAL

RNA ‐seq analyses of Arabidopsis thaliana seedlings after exposure to blue‐light phototropic stimuli in microgravity

(2019) Joshua P. Vandenbrink et al.   AMERICAN JOURNAL OF BOTANY

RNAseq Analysis of the Response of Arabidopsis thaliana to Fractional Gravity Under Blue-Light Stimulation During Spaceflight

(2019) Raúl Herranz et al.   Frontiers in Plant Science

GeneMANIA update 2018

(2018) Max Franz et al.   NUCLEIC ACIDS RESEARCH

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

(2018) Steven Xijin Ge et al.   BMC BIOINFORMATICS

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Comparing RNA-Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight

(2018) Aparna Krishnamurthy et al.   Applications in Plant Sciences

Expression Atlas: gene and protein expression across multiple studies and organisms

(2017) Irene Papatheodorou et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces

(2017) Adrian M Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index

(2017) Takeshi Obayashi et al.   PLANT AND CELL PHYSIOLOGY

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

(2017) Jamie Waese et al.   PLANT CELL

Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight?

(2017) Anna-Lisa Paul et al.   PLoS One

The impact of space environment on gene expression in Arabidopsis thaliana seedlings

(2017) HuaSheng Li et al.   Science China-Technological Sciences

Effects of microgravity on osteoblast mitochondria: a proteomic and metabolomics profile

(2017) Anna Michaletti et al.   Scientific Reports

SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations

(2016) Cornelia M. Hooper et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery

(2016) Vivek Krishnakumar et al.   PLANT AND CELL PHYSIOLOGY

New BAR tools for mining expression data and exploringCis-elements inArabidopsis thaliana

(2016) Ryan S. Austin et al.   PLANT JOURNAL

The ROS Wheel: Refining ROS Transcriptional Footprints

(2016) Patrick Willems et al.   PLANT PHYSIOLOGY

Space, the final frontier: A critical review of recent experiments performed in microgravity

(2016) Joshua P. Vandenbrink et al.   PLANT SCIENCE

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

(2016) Nirav Merchant et al.   PLOS BIOLOGY

Transcriptional response of Arabidopsis seedlings during spaceflight reveals peroxidase and cell wall remodeling genes associated with root hair development

(2015) T. Kwon et al.   AMERICAN JOURNAL OF BOTANY

Spaceflight Induces Specific Alterations in the Proteomes of Arabidopsis

(2015) Robert J. Ferl et al.   ASTROBIOLOGY

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

Transcriptome Analysis of Oryza sativa Calli Under Microgravity

(2015) Jing Jin et al.   MICROGRAVITY SCIENCE AND TECHNOLOGY

A Whole-Genome Microarray Study ofArabidopsis thalianaSemisolid Callus Cultures Exposed to Microgravity and Nonmicrogravity Related Spaceflight Conditions for 5 Days on Board of Shenzhou 8

(2015) Svenja Fengler et al.   Biomed Research International

jvenn: an interactive Venn diagram viewer

(2014) Philippe Bardou et al.   BMC BIOINFORMATICS

Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight

(2014) Manabu Sugimoto et al.   BMC PLANT BIOLOGY

Differential protein expression profiling of Arabidopsis thaliana callus under microgravity on board the Chinese SZ-8 spacecraft

(2014) Yue Zhang et al.   PLANTA

Microgravity Induces Changes in Microsome-Associated Proteins of Arabidopsis Seedlings Grown on Board the International Space Station

(2014) Christian Mazars et al.   PLoS One

Salt stress-induced Ca2+ waves are associated with rapid, long-distance root-to-shoot signaling in plants

(2014) W.-G. Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core “DSB” response specific to clastogenic treatments

(2014) Victor Missirian et al.   Frontiers in Plant Science

German SIMBOX on Chinese mission Shenzhou-8: Europe's first bilateral cooperation utilizing China's Shenzhou programme

(2013) Peter Preu et al.   ACTA ASTRONAUTICA

Fundamental Plant Biology Enabled by The Space Shuttle

(2013) Anna-Lisa Paul et al.   AMERICAN JOURNAL OF BOTANY

Organ-specific remodeling of the Arabidopsis transcriptome in response to spaceflight

(2013) Anna-Lisa Paul et al.   BMC PLANT BIOLOGY

Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes

(2013) Melanie J. Correll et al.   PLANTA

A Cross-Platform Comparison of Affymetrix and Agilent Microarrays Reveals Discordant miRNA Expression in Lung Tumors of c-Raf Transgenic Mice

(2013) Valerio Del Vescovo et al.   PLoS One

Spaceflight Environment Induces Mitochondrial Oxidative Damage in Ocular Tissue

(2013) Xiao W. Mao et al.   RADIATION RESEARCH

Spaceflight engages heat shock protein and other molecular chaperone genes in tissue culture cells of Arabidopsis thaliana

(2012) Agata K. Zupanska et al.   AMERICAN JOURNAL OF BOTANY

Spaceflight Transcriptomes: Unique Responses to a Novel Environment

(2012) Anna-Lisa Paul et al.   ASTROBIOLOGY

Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures

(2012) Ana I Manzano et al.   BMC GENOMICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

(2011) Stephen A. Goff et al.   Frontiers in Plant Science

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Entrez Gene: gene-centered information at NCBI

(2010) D. Maglott et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Consistency Analysis of Redundant Probe Sets on Affymetrix Three-Prime Expression Arrays and Applications to Differential mRNA Processing

(2009) Xiangqin Cui et al.   PLoS One

Gene expression changes induced by space flight in single-cells of the fern Ceratopteris richardii

(2008) Mari L. Salmi et al.   PLANTA