Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism

(2015) Zheng Hu et al.   NATURE GENETICS

Viral-Human Chimeric Transcript Predisposes Risk to Liver Cancer Development and Progression

(2014) Chi-Chiu Lau et al.   CANCER CELL

Human Viral Oncogenesis: A Cancer Hallmarks Analysis

(2014) Enrique A. Mesri et al.   Cell Host & Microbe

What’s the Damage? The Impact of Pathogens on Pathways that Maintain Host Genome Integrity

(2014) Matthew D. Weitzman et al.   Cell Host & Microbe

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

(2014) Jian-Feng Xiang et al.   CELL RESEARCH

Intratumor Heterogeneity in Hepatocellular Carcinoma

(2014) J. Friemel et al.   CLINICAL CANCER RESEARCH

p70 Ribosomal protein S6 kinase (Rps6kb1): an update

(2014) Farnaz Bahrami-B et al.   JOURNAL OF CLINICAL PATHOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

Single-cell gene expression signatures reveal melanoma cell heterogeneity

(2014) M Ennen et al.   ONCOGENE

The Transcription Map of Human Papillomavirus Type 18 during Genome Replication in U2OS Cells

(2014) Mart Toots et al.   PLoS One

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

C-Myc-activated long noncoding RNA CCAT1 promotes colon cancer cell proliferation and invasion

(2014) Xiaolu He et al.   TUMOR BIOLOGY

The small splice variant of HPV16 E6, E6⁎, reduces tumor formation in cervical carcinoma xenografts

(2014) Maria Filippova et al.   VIROLOGY

Single-Cell RNA Sequencing Identifies Extracellular Matrix Gene Expression by Pancreatic Circulating Tumor Cells

(2014) David T. Ting et al.   Cell Reports

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells

(2014) Andrew McDavid et al.   PLoS Computational Biology

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells

(2013) Jeff Gole et al.   NATURE BIOTECHNOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Merkel cell polyomavirus and extrapulmonary small cell carcinoma

(2013) KATHRYN C. HOURDEQUIN et al.   Oncology Letters

The landscape of viral expression and host gene fusion and adaptation in human cancer

(2013) Ka-Wei Tang et al.   Nature Communications

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

Intron-centric estimation of alternative splicing from RNA-seq data

(2012) D. D. Pervouchine et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Global burden of cancers attributable to infections in 2008: a review and synthetic analysis

(2012) Catherine de Martel et al.   LANCET ONCOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Coordinating genome expression with cell size

(2012) Samuel Marguerat et al.   TRENDS IN GENETICS

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

(2012) Onur Sakarya et al.   PLoS Computational Biology

HIV, EBV and KSHV: Viral cooperation in the pathogenesis of human malignancies

(2011) Suzane Ramos da Silva et al.   CANCER LETTERS

The HPV-16 E7 oncoprotein induces centriole multiplication through deregulation of Polo-like kinase 4 expression

(2011) Nina Korzeniewski et al.   Molecular Cancer

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Stem cell gene expression programs influence clinical outcome in human leukemia

(2011) Kolja Eppert et al.   NATURE MEDICINE

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

(2011) Natalie A. Twine et al.   PLoS One

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

(2011) Henrik Edgren et al.   GENOME BIOLOGY

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

Serum Prolidase Activity and Oxidative Status in Patients With Stage I Endometrial Cancer

(2010) Dagistan Tolga Arioz et al.   INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

(2010) Shinichi Yachida et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Assessment of preoperative serum prolidase activity in epithelial ovarian cancer

(2009) Hakan Camuzcuoglu et al.   European Journal of Obstetrics & Gynecology and Reproductive Biology

A new multiparameter assay to assess HPV 16/18, viral load and physical status together with gain of telomerase genes in HPV-related cancers

(2009) Wendy Theelen et al.   INTERNATIONAL JOURNAL OF CANCER

The Human Papillomavirus Type 18 E2 Protein Is a Cell Cycle-Dependent Target of the SCFSkp2 Ubiquitin Ligase

(2009) S. Bellanger et al.   JOURNAL OF VIROLOGY

A review of human carcinogens—Part B: biological agents

(2009) Véronique Bouvard et al.   LANCET ONCOLOGY

The search for infectious causes of human cancers: Where and why

(2009) Harald zur Hausen   VIROLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A Neoplastic Gene Fusion Mimics Trans-Splicing of RNAs in Normal Human Cells

(2008) H. Li et al.   SCIENCE