Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album

Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism

(2018) Karolina Heyduk et al.   AMERICAN JOURNAL OF BOTANY

Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

(2018) Hengfu Yin et al.   BMC GENOMICS

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

(2017) Xiaohan Yang et al.   Nature Communications

Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

(2017) Kathleen Greenham et al.   eLife

MetaCycle: an integrated R package to evaluate periodicity in large scale data

(2016) Gang Wu et al.   BIOINFORMATICS

CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data

(2016) Guangyong Zheng et al.   BMC BIOINFORMATICS

Phylogenetic relationships between Sedum L. and related genera (Crassulaceae) based on ITS rDNA sequence comparisons

(2016) Vyacheslav Yu. Nikulin et al.   FLORA

Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae)

(2016) Karolina Heyduk et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought

(2016) Marieke Dubois et al.   PLANT CELL AND ENVIRONMENT

The ALMT Family of Organic Acid Transporters in Plants and Their Involvement in Detoxification and Nutrient Security

(2016) Tripti Sharma et al.   Frontiers in Plant Science

The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution

(2016) Guo-Qiang Zhang et al.   Scientific Reports

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The glucose 6-phosphate shunt around the Calvin–Benson cycle

(2015) Thomas D. Sharkey et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb

(2015) Liang Yan et al.   Molecular Plant

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world

(2015) Xiaohan Yang et al.   NEW PHYTOLOGIST

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Photosynthesis and water use by two Sedum species in green roof substrate

(2014) O. Starry et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Engineering crassulacean acid metabolism to improve water-use efficiency

(2014) Anne M. Borland et al.   TRENDS IN PLANT SCIENCE

Characterization of the Plastidic Phosphate Translocators in the Inducible Crassulacean Acid Metabolism PlantMesembryanthemum crystallinum

(2013) Shin KORE-EDA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comparison of photosynthesis and antioxidative protection in Sedum album and Sedum stoloniferum (Crassulaceae) under water stress

(2012) G. Habibi et al.   PHOTOSYNTHETICA

Engineering starch accumulation by manipulation of phosphate metabolism of starch

(2012) Sean E. Weise et al.   PLANT BIOTECHNOLOGY JOURNAL

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information

(2011) Xiujun Zhang et al.   BIOINFORMATICS

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

(2011) Sergei A. Filichkin et al.   PLoS One

Evolution along the crassulacean acid metabolism continuum

(2010) Katia Silvera et al.   FUNCTIONAL PLANT BIOLOGY

JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets

(2010) Michael E. Hughes et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Time of day shapes Arabidopsis drought transcriptomes

(2010) Olivia Wilkins et al.   PLANT JOURNAL

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)

(2008) John C. Cushman et al.   JOURNAL OF EXPERIMENTAL BOTANY

Isolation and Characterization of Mutants of Common Ice Plant Deficient in Crassulacean Acid Metabolism

(2008) J. C. Cushman et al.   PLANT PHYSIOLOGY

Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules

(2008) Todd P. Michael et al.   PLoS Genetics

A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth

(2008) Todd P Michael et al.   PLOS BIOLOGY

Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development

(2008) Michael F Covington et al.   GENOME BIOLOGY

Conserved Daily Transcriptional Programs in Carica papaya

(2008) Anna Zdepski et al.   Tropical Plant Biology

Drought tolerance improvement in crop plants: An integrated view from breeding to genomics

(2007) Luigi Cattivelli et al.   FIELD CROPS RESEARCH