Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants

Extensive intraspecific gene order and gene structural variations in upland cotton cultivars

(2019) Zhaoen Yang et al.   Nature Communications

Diverse modes of clonal evolution in HBV-related hepatocellular carcinoma revealed by single-cell genome sequencing

(2018) Meng Duan et al.   CELL RESEARCH

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Natural variation and dosage of the HEI10 meiotic E3 ligase controlArabidopsiscrossover recombination

(2017) Piotr A. Ziolkowski et al.   GENES & DEVELOPMENT

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

De novo assembly of a haplotype-resolved human genome

(2015) Hongzhi Cao et al.   NATURE BIOTECHNOLOGY

Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation

(2015) Björn Reinius et al.   NATURE REVIEWS GENETICS

Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize

(2015) Xiang Li et al.   Nature Communications

Methods to isolate a large amount of generative cells, sperm cells and vegetative nuclei from tomato pollen for “omics” analysis

(2015) Yunlong Lu et al.   Frontiers in Plant Science

Extending reference assembly models

(2015) Deanna M Church et al.   GENOME BIOLOGY

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

(2015) Yong Hou et al.   GigaScience

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

(2014) Margret R. Hoehe et al.   Nature Communications

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Sequencing of isolated sperm cells for direct haplotyping of a human genome

(2013) E. F. Kirkness et al.   GENOME RESEARCH

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

BLAST: a more efficient report with usability improvements

(2013) Grzegorz M. Boratyn et al.   NUCLEIC ACIDS RESEARCH

The genome of the pear (Pyrus bretschneideri Rehd.)

(2012) J. Wu et al.   GENOME RESEARCH

HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data

(2012) Derek Aguiar et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The draft genome of sweet orange (Citrus sinensis)

(2012) Qiang Xu et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Monoallelic gene expression and its mechanisms

(2011) Yoshiaki Tarutani et al.   CURRENT OPINION IN PLANT BIOLOGY

Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis

(2011) P. Lu et al.   GENOME RESEARCH

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae

(2010) Kui Lin-Wang et al.   BMC PLANT BIOLOGY

Utility testing of an apple skin color MdMYB1 marker in two progenies

(2010) Yanmin Zhu et al.   MOLECULAR BREEDING

Whole-genome molecular haplotyping of single cells

(2010) H Christina Fan et al.   NATURE BIOTECHNOLOGY

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

Anther culture for haploid and doubled haploid production

(2010) Maria Antonietta Germanà   PLANT CELL TISSUE AND ORGAN CULTURE

Allelic Variation in the Perennial Ryegrass FLOWERING LOCUS T Gene Is Associated with Changes in Flowering Time across a Range of Populations

(2010) L. Skot et al.   PLANT PHYSIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

High-resolution mapping of meiotic crossovers and non-crossovers in yeast

(2008) Eugenio Mancera et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A procedure for highly specific, sensitive, and unbiased whole-genome amplification

(2008) X. Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA