Tapping the Promise of Genomics in Species with Complex, Nonmodel Genomes

Genome and gene duplications and gene expression divergence: a view from plants

(2012) Yupeng Wang et al.   Annals of the New York Academy of Sciences

RNA-Seq Analysis of Developing Nasturtium Seeds (Tropaeolum majus): Identification and Characterization of an Additional Galactosyltransferase Involved in Xyloglucan Biosynthesis

(2012) Jacob K. Jensen et al.   Molecular Plant

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Test driving genome assemblers

(2012) Wei Fan et al.   NATURE BIOTECHNOLOGY

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

DNA sequencing with nanopores

(2012) Grégory F Schneider et al.   NATURE BIOTECHNOLOGY

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

De novo genome assembly: what every biologist should know

(2012) Monya Baker   NATURE METHODS

Advances in plant genome sequencing

(2012) John P. Hamilton et al.   PLANT JOURNAL

Integration of deep transcript and targeted metabolite profiles for eight cultivars of opium poppy

(2012) Isabel Desgagné-Penix et al.   PLANT MOLECULAR BIOLOGY

Deep EST profiling of developing fenugreek endosperm to investigate galactomannan biosynthesis and its regulation

(2012) Yan Wang et al.   PLANT MOLECULAR BIOLOGY

Transcriptional and Metabolic Analysis of Senescence Induced by Preventing Pollination in Maize

(2012) R. S. Sekhon et al.   PLANT PHYSIOLOGY

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

(2012) Candice N. Hansey et al.   PLoS One

Fatty Acid Composition of Developing Sea Buckthorn (Hippophae rhamnoides L.) Berry and the Transcriptome of the Mature Seed

(2012) Tahira Fatima et al.   PLoS One

Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence

(2012) Kimberly J. Felcher et al.   PLoS One

De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosynthesis of Active Metabolites

(2012) Miao He et al.   PLoS One

Pyrosequencing of the Camptotheca acuminata transcriptome reveals putative genes involved in camptothecin biosynthesis and transport

(2011) Yongzhen Sun et al.   BMC GENOMICS

Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)

(2011) Prabin Bajgain et al.   BMC GENOMICS

Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress

(2011) John P Délano-Frier et al.   BMC GENOMICS

Single nucleotide polymorphism discovery in elite north american potato germplasm

(2011) John P Hamilton et al.   BMC GENOMICS

Transcriptome Analysis of Sarracenia, an Insectivorous Plant

(2011) A. Srivastava et al.   DNA RESEARCH

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients

(2011) Hua Wenping et al.   GENOMICS

A Stereoselective Hydroxylation Step of Alkaloid Biosynthesis by a Unique Cytochrome P450 inCatharanthus roseus

(2011) Lesley-Ann Giddings et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

Unlocking the Barley Genome by Chromosomal and Comparative Genomics

(2011) Klaus F.X. Mayer et al.   PLANT CELL

454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng

(2011) S. Chen et al.   PLANT CELL REPORTS

Comparative deep transcriptional profiling of four developing oilseeds

(2011) Manuel A. Troncoso-Ponce et al.   PLANT JOURNAL

The Switchgrass Genome: Tools and Strategies

(2011) Michael D. Casler et al.   Plant Genome

The draft genome and transcriptome of Cannabis sativa

(2011) Harm van Bakel et al.   GENOME BIOLOGY

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

THE EFFECT OF COLCHICINE ON ROOT MITOSES IN ALLIUM

(2010) ALBERT LEVAN   HEREDITAS

Haploid plants produced by centromere-mediated genome elimination

(2010) Maruthachalam Ravi et al.   NATURE

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Transcriptome Analysis ofTaxus cuspidataNeedles Based on 454 Pyrosequencing

(2010) Qiong Wu et al.   PLANTA MEDICA

A distinct DGAT with sn-3 acetyltransferase activity that synthesizes unusual, reduced-viscosity oils in Euonymus and transgenic seeds

(2010) T. P. Durrett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genetic Map of Artemisia annua L. Identifies Loci Affecting Yield of the Antimalarial Drug Artemisinin

(2010) I. A. Graham et al.   SCIENCE

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

(2009) Richard G. F. Visser et al.   AMERICAN JOURNAL OF POTATO RESEARCH

De novo sequencing of plant genomes using second-generation technologies

(2009) M. Imelfort et al.   BRIEFINGS IN BIOINFORMATICS

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The Genetic Architecture of Maize Flowering Time

(2009) E. S. Buckler et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski et al.   GENOME RESEARCH

The age of the grasses and clusters of origins of C4photosynthesis

(2008) ALBERTO VICENTINI et al.   GLOBAL CHANGE BIOLOGY

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Chromosome elimination and in vivo haploid production induced by Stock 6-derived inducer line in maize (Zea mays L.)

(2008) Zili Zhang et al.   PLANT CELL REPORTS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE