DNA sequencing at 40: past, present and future

J Shendure, S Balasubramanian, GM Church… - Nature, 2017 - nature.com
This review commemorates the 40th anniversary of DNA sequencing, a period in which we
have already witnessed multiple technological revolutions and a growth in scale from a few …

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

FJ Sedlazeck, H Lee, CA Darby, MC Schatz - Nature Reviews Genetics, 2018 - nature.com
Several new genomics technologies have become available that offer long-read sequencing
or long-range mapping with higher throughput and higher resolution analysis than ever …

Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

A Song, J Su, H Wang, Z Zhang, X Zhang… - Nature …, 2023 - nature.com
Abstract Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important
ornamental plant with great economic, cultural, and symbolic value. However, research on …

The single-cell transcriptional landscape of mammalian organogenesis

J Cao, M Spielmann, X Qiu, X Huang, DM Ibrahim… - Nature, 2019 - nature.com
Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of
the three germ layers transform into an embryo that includes most of the major internal and …

Comprehensive single-cell transcriptional profiling of a multicellular organism

J Cao, JS Packer, V Ramani, DA Cusanovich, C Huynh… - Science, 2017 - science.org
To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile
the transcriptomes of single cells or nuclei, termed sci-RNA-seq (single-cell combinatorial …

Direct determination of diploid genome sequences

NI Weisenfeld, V Kumar, P Shah, DM Church… - Genome …, 2017 - genome.cshlp.org
Determining the genome sequence of an organism is challenging, yet fundamental to
understanding its biology. Over the past decade, thousands of human genomes have been …

Genome-wide analyses of introgression between two sympatric Asian oak species

R Fu, Y Zhu, Y Liu, Y Feng, RS Lu, Y Li, P Li… - Nature Ecology & …, 2022 - nature.com
Introgression can be an important source of new alleles for adaption under rapidly changing
environments, perhaps even more important than standing variation. Though introgression …

Advancements in next-generation sequencing

SE Levy, RM Myers - Annual review of genomics and human …, 2016 - annualreviews.org
The term next-generation sequencing is almost a decade old, but it remains the colloquial
way to describe highly parallel or high-output sequencing methods that produce data at or …

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

NH Putnam, BL O'Connell, JC Stites, BJ Rice… - Genome …, 2016 - genome.cshlp.org
Long-range and highly accurate de novo assembly from short-read data is one of the most
pressing challenges in genomics. Recently, it has been shown that read pairs generated by …

Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)

C Chen, D Xing, L Tan, H Li, G Zhou, L Huang, XS Xie - Science, 2017 - science.org
Single-cell genomics is important for biology and medicine. However, current whole-
genome amplification (WGA) methods are limited by low accuracy of copy-number variation …