Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing

Single-cell RNA sequencing resolves molecular relationships among individual plant cells

(2019) Kook Hui Ryu et al.   PLANT PHYSIOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing

(2018) Bo Wang et al.   GENOME RESEARCH

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

(2018) Manuel Tardaguila et al.   GENOME RESEARCH

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

(2018) Simon Ardui et al.   NUCLEIC ACIDS RESEARCH

Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing

(2018) David E. Cook et al.   PLANT PHYSIOLOGY

HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads

(2017) Serghei Mangul et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Transcriptome Profiling in Human Diseases: New Advances and Perspectives

(2017) Amelia Casamassimi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome

(2017) Xiaoxian Liu et al.   Molecular Ecology Resources

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

DNA sequencing at 40: past, present and future

(2017) Jay Shendure et al.   NATURE

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

(2017) Hélène Badouin et al.   NATURE

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings

(2017) Fu-Yuan Zhu et al.   PLANT JOURNAL

Advances in single-cell RNA sequencing and its applications in cancer research

(2017) Sibo Zhu et al.   Oncotarget

Transcriptomics technologies

(2017) Rohan Lowe et al.   PLoS Computational Biology

Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

(2017) Bing Cheng et al.   GigaScience

Advancements in Next-Generation Sequencing

(2016) Shawn E. Levy et al.   Annual Review of Genomics and Human Genetics

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

High Throughput Sequencing: An Overview of Sequencing Chemistry

(2016) Sheetal Ambardar et al.   INDIAN JOURNAL OF MICROBIOLOGY

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing

(2016) Benjamin Deonovic et al.   NUCLEIC ACIDS RESEARCH

Rare variant phasing and haplotypic expression from RNA sequencing with phASER

(2016) Stephane E. Castel et al.   Nature Communications

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

The Epigenomic Landscape of Prokaryotes

(2016) Matthew J. Blow et al.   PLoS Genetics

Identifying fusion transcripts using next generation sequencing

(2016) Shailesh Kumar et al.   Wiley Interdisciplinary Reviews-RNA

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

(2015) Alison C Testa et al.   BMC GENOMICS

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing

(2015) Jason L. Weirather et al.   NUCLEIC ACIDS RESEARCH

Leveraging transcript quantification for fast computation of alternative splicing profiles

(2015) Gael P. Alamancos et al.   RNA

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Next-generation sequencing technologies: breaking the sound barrier of human genetics

(2014) E. M. Bahassi et al.   MUTAGENESIS

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FuseFISH: Robust Detection of Transcribed Gene Fusions in Single Cells

(2014) Stefan Semrau et al.   Cell Reports

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors

(2013) Andreas R. Gruber et al.   Wiley Interdisciplinary Reviews-RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

(2012) Mark F Rogers et al.   GENOME BIOLOGY

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Next-generation sequencing technologies for gene expression profiling in plants

(2011) M. Jain   Briefings in Functional Genomics

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing

(2011) Y. Shen et al.   GENOME RESEARCH

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

Sequencing technology does not eliminate biological variability

(2011) Kasper D Hansen et al.   NATURE BIOTECHNOLOGY

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Applications of New Sequencing Technologies for Transcriptome Analysis

(2009) Olena Morozova et al.   Annual Review of Genomics and Human Genetics

Swift: primary data analysis for the Illumina Solexa sequencing platform

(2009) Nava Whiteford et al.   BIOINFORMATICS

How to get genomes at one ten-thousandth the cost

(2008) Jeffery A Schloss   NATURE BIOTECHNOLOGY

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

(2008) Yingjia Shen et al.   NUCLEIC ACIDS RESEARCH