Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu)

Bioactive 3D Structure of Phenylalanine Ammonia-Lyase Reveal Key Insights into Ligand Binding Dynamics

(2018) Zsofia Bata et al.   BIOPHYSICAL JOURNAL

Update on natural food pigments - A mini-review on carotenoids, anthocyanins, and betalains

(2018) Delia B. Rodriguez-Amaya   FOOD RESEARCH INTERNATIONAL

Extrapolation of significant genes and transcriptional regulatory networks involved in Zea mays in response in UV-B stress

(2018) Saurabh Gupta et al.   Genes & Genomics

The C–S–A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice

(2018) Xingming Sun et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants

(2018) Jae-Hyeon Oh et al.   3 Biotech

Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants

(2018) Jae-Hyeon Oh et al.   3 Biotech

Deciphering genome-wide WRKY gene family of Triticum aestivum L. and their functional role in response to Abiotic stress

(2018) Saurabh Gupta et al.   Genes & Genomics

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of miRNAs and Tasi-RNAs in Zea mays in response to phosphate deficiency

(2017) Saurabh Gupta et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Origin of rice (Oryza sativa L.) domestication genes

(2017) Peter Civáň et al.   GENETIC RESOURCES AND CROP EVOLUTION

Genomic variation associated with local adaptation of weedy rice during de-domestication

(2017) Jie Qiu et al.   Nature Communications

Anthocyanidins and anthocyanins: colored pigments as food, pharmaceutical ingredients, and the potential health benefits

(2017) Hock Eng Khoo et al.   Food & Nutrition Research

Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency

(2017) Saurabh Gupta et al.   Frontiers in Plant Science

Whole genome sequencing of Oryza sativa L. cv. Seeragasamba identifies a new fragrance allele in rice

(2017) Ganigara Bindusree et al.   PLoS One

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

Genetic and Evolutionary Analysis of Purple Leaf Sheath in Rice

(2016) Han-shiuan Chin et al.   Rice

WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants

(2016) Ujjal J. Phukan et al.   Frontiers in Plant Science

Identification of Novel Abiotic Stress Proteins in Triticum aestivum Through Functional Annotation of Hypothetical Proteins

(2016) Saurabh Gupta et al.   Interdisciplinary Sciences-Computational Life Sciences

Regulation of the Flavonoid Biosynthesis Pathway Genes in Purple and Black Grains of Hordeum vulgare

(2016) Olesya Yu. Shoeva et al.   PLoS One

Regulation of MYB and bHLH Transcription Factors: A Glance at the Protein Level

(2015) Marie Pireyre et al.   Molecular Plant

MYB Transcription Factors as Regulators of Phenylpropanoid Metabolism in Plants

(2015) Jingying Liu et al.   Molecular Plant

Molecular and Biochemical Analysis of Chalcone Synthase from Freesia hybrid in Flavonoid Biosynthetic Pathway

(2015) Wei Sun et al.   PLoS One

Whole-Genome Resequencing and Transcriptomic Analysis to Identify Genes Involved in Leaf-Color Diversity in Ornamental Rice Plants

(2015) Chang-Kug Kim et al.   PLoS One

An overview of global rice production, supply, trade, and consumption

(2014) Sumithra Muthayya et al.   Annals of the New York Academy of Sciences

Genetic dissection of black grain rice by the development of a near isogenic line

(2014) Hiroaki Maeda et al.   BREEDING SCIENCE

Identification of the flavonoid 3′-hydroxylase and flavonoid 3′,5′-hydroxylase genes from Antarctic moss and their regulation during abiotic stress

(2014) Shenghao Liu et al.   GENE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

The role ofBh4in parallel evolution of hull colour in domesticated and weedy rice

(2013) C. C. Vigueira et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The genetic constitutions of complementary genes Pp and Pb determine the purple color variation in pericarps with cyanidin-3-O-glucoside depositions in black rice

(2013) Md Mominur Rahman et al.   JOURNAL OF PLANT BIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

MYB transcription factor genes as regulators for plant responses: an overview

(2013) Supriya Ambawat et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Genome-wide DNA polymorphisms in eliteindicarice inbreds discovered by whole-genome sequencing

(2012) Gopala K. Subbaiyan et al.   PLANT BIOTECHNOLOGY JOURNAL

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

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

NAC transcription factors in plant abiotic stress responses

(2011) Kazuo Nakashima et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Identification and characterization of seed-specific transcription factors regulating anthocyanin biosynthesis in black rice

(2011) C.-K Kim et al.   JOURNAL OF APPLIED GENETICS

Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication

(2011) B.-F. Zhu et al.   PLANT PHYSIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Coexpression Analysis Identifies Rice Starch Regulator1, a Rice AP2/EREBP Family Transcription Factor, as a Novel Rice Starch Biosynthesis Regulator

(2010) F.-F. Fu et al.   PLANT PHYSIOLOGY

Genome-Wide Classification and Evolutionary Analysis of the bHLH Family of Transcription Factors in Arabidopsis, Poplar, Rice, Moss, and Algae

(2010) L. Carretero-Paulet et al.   PLANT PHYSIOLOGY

Plant molecular stress responses face climate change

(2010) Ishita Ahuja et al.   TRENDS IN PLANT SCIENCE

Genetic perspectives on crop domestication

(2010) Briana L. Gross et al.   TRENDS IN PLANT SCIENCE

Q-TARO: QTL Annotation Rice Online Database

(2010) Jun-ichi Yonemaru et al.   Rice

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

SNP deserts of Asian cultivated rice: genomic regions under domestication

(2009) L. WANG et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences

(2008) Javier Terol et al.   BMC GENOMICS