A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity

(2019) Lachezar A. Nikolov et al.   NEW PHYTOLOGIST

Employing a biochemical protecting group for a sustainable indigo dyeing strategy

(2018) Tammy M Hsu et al.   Nature Chemical Biology

Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

(2018) Lei Zhang et al.   Horticulture Research

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Diglycosidic indole alkaloid derivatives from an aqueous extract of Isatis indigotica roots

(2017) Ling-Jie Meng et al.   JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads

(2017) Jonas Korlach et al.   GigaScience

Comparative paleogenomics of crucifers: ancestral genomic blocks revisited

(2016) Martin A Lysak et al.   CURRENT OPINION IN PLANT BIOLOGY

Isovitexin Exerts Anti-Inflammatory and Anti-Oxidant Activities on Lipopolysaccharide-Induced Acute Lung Injury by Inhibiting MAPK and NF-κB and Activating HO-1/Nrf2 Pathways

(2016) Hongming Lv et al.   International Journal of Biological Sciences

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Antiviral glycosidic bisindole alkaloids from the roots ofIsatis indigotica

(2015) Yu-Feng Liu et al.   JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH

Daucosterol inhibits cancer cell proliferation by inducing autophagy through reactive oxygen species-dependent manner

(2015) Chuanke Zhao et al.   LIFE SCIENCES

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

Genome-guided investigation of plant natural product biosynthesis

(2015) Franziska Kellner et al.   PLANT JOURNAL

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Indole alkaloids from the roots of Isatis indigotica and their inhibitory effects on nitric oxide production

(2014) Liguo Yang et al.   FITOTERAPIA

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

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

Genomic Signatures of Specialized Metabolism in Plants

(2014) L. Chae et al.   SCIENCE

Genome sequence of mungbean and insights into evolution within Vigna species

(2014) Yang Jae Kang et al.   Nature Communications

Research Progress of Chinese Herbal Medicine Radix isatidis (Banlangen)

(2013) Wei Zhou et al.   AMERICAN JOURNAL OF CHINESE MEDICINE

Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling

(2013) Junfeng Chen et al.   BMC GENOMICS

Antioxidant and anti-inflammatory activities of Radix Isatidis polysaccharide in murine alveolar macrophages

(2013) Zhaojiang Du et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Deciphering the Diploid Ancestral Genome of the MesohexaploidBrassica rapa

(2013) Feng Cheng et al.   PLANT CELL

Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model

(2012) M Eric Schranz et al.   CURRENT OPINION IN PLANT BIOLOGY

Alkaloids from the Root of Isatis indigotica

(2012) Minghua Chen et al.   JOURNAL OF NATURAL PRODUCTS

Among Plant Lignans, Pinoresinol Has the Strongest Antiinflammatory Properties in Human Intestinal Caco-2 Cells

(2012) Alexandrine During et al.   JOURNAL OF NUTRITION

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Indole alkaloids from the roots of Isatis ingigotica and their antiherpes simplex virus type 2 (HSV-2) activity in vitro

(2010) Dong-Dong Sun et al.   CHEMISTRY OF NATURAL COMPOUNDS

Novel indole C-glycosides from Isatis indigotica and their potential cytotoxic activity

(2010) Yixuan Wu et al.   FITOTERAPIA

Altering the regioselectivity of cytochrome P450 BM-3 by saturation mutagenesis for the biosynthesis of indirubin

(2010) Sheng Hu et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

Isolation and characterization of a gene encoding cinnamoyl-CoA reductase from Isatis indigotica Fort.

(2010) Yongsheng Hu et al.   MOLECULAR BIOLOGY REPORTS

Cabbage family affairs: the evolutionary history of Brassicaceae

(2010) Andreas Franzke et al.   TRENDS IN PLANT SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales

(2009) Michael S. Barker et al.   Genome Biology and Evolution

Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)

(2009) Marieke Louwers et al.   Nature Protocols

A comprehensive metabolite profiling of Isatis tinctoria leaf extracts

(2009) Tobias Mohn et al.   PHYTOCHEMISTRY

Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited

(2008) Mark A. Beilstein et al.   AMERICAN JOURNAL OF BOTANY

Dietary lariciresinol attenuates mammary tumor growth and reduces blood vessel density in human MCF‐7 breast cancer xenografts and carcinogen‐induced mammary tumors in rats

(2008) Niina M. Saarinen et al.   INTERNATIONAL JOURNAL OF CANCER

Qualitative and quantitative analysis of flavonoids in the leaves of Isatis indigatica Fort. by ultra-performance liquid chromatography with PDA and electrospray ionization tandem mass spectrometry detection

(2008) Xiangyu Deng et al.   JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS

Chromosomal Phylogeny and Karyotype Evolution in x=7 Crucifer Species (Brassicaceae)

(2008) T. Mandakova et al.   PLANT CELL

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

(2008) K. Hanada et al.   PLANT PHYSIOLOGY

Alpha-tryptophan synthase of Isatis tinctoria: gene cloning and expression

(2008) M. Salvini et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

A Role for Gene Duplication and Natural Variation of Gene Expression in the Evolution of Metabolism

(2008) Daniel J. Kliebenstein   PLoS One

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY