The Heterogeneity Study of HeLa S3 Cells Based on Full-Length Single-Cell RNA-Seq

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The Sequence Alignment/Map format and SAMtools

Heng Li, R. Handsaker, Alec Wysoker, et al.. (2009). Bioinformatics. Cited 54,792 times. https://doi.org/10.1093/bioinformatics/btp352

Fast gapped-read alignment with Bowtie 2

Ben Langmead, S. Salzberg. (2012). Nature Methods. Cited 48,549 times. https://doi.org/10.1038/nmeth.1923

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

M. Robinson, Davis J. McCarthy, G. Smyth. (2009). Bioinformatics. Cited 36,556 times. https://doi.org/10.1093/bioinformatics/btp616

Initial sequencing and analysis of the human genome

E. Lander, L. Linton, B. Birren, et al.. (2001). Nature. Cited 23,883 times. https://doi.org/10.1038/35057062

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

Ben Langmead, C. Trapnell, Mihai Pop, et al.. (2009). Genome Biology. Cited 21,910 times. https://doi.org/10.1186/gb-2009-10-3-r25

Integrative Genomics Viewer

James T. Robinson, H. Thorvaldsdóttir, W. Winckler, et al.. (2011). Nature biotechnology. Cited 13,579 times. https://doi.org/10.1038/nbt.1754

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

C. Trapnell, Adam Roberts, L. Goff, et al.. (2012). Nature Protocols. Cited 11,688 times. https://doi.org/10.1038/nprot.2012.016

Epidemiologic classification of human papillomavirus types associated with cervical cancer.

N. Muñoz, F. Bosch, S. de Sanjosé, et al.. (2003). The New England journal of medicine. Cited 6,384 times. https://doi.org/10.1056/NEJMOA021641

GENCODE: The reference human genome annotation for The ENCODE Project

J. Harrow, A. Frankish, J. Gonzalez, et al.. (2012). Genome Research. Cited 4,426 times. https://doi.org/10.1101/gr.135350.111

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

Anoop P. Patel, I. Tirosh, John J. Trombetta, et al.. (2014). Science. Cited 4,215 times. https://doi.org/10.1126/science.1254257

The E6 oncoprotein encoded by human papillomavirus types 16 and 18 promotes the degradation of p53

M. Scheffner, B. Werness, J. Huibregtse, et al.. (1990). Cell. Cited 4,079 times. https://doi.org/10.1016/0092-8674(90)90409-8

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

S. Picelli, O. Faridani, Åsa K. Björklund, et al.. (2014). Nature Protocols. Cited 3,589 times. https://doi.org/10.1038/nprot.2014.006

A review of human carcinogens--Part B: biological agents.

V. Bouvard, R. Baan, K. Straif, et al.. (2009). The Lancet. Oncology. Cited 2,810 times. https://doi.org/10.1016/S1470-2045(09)70096-8

The contributions of hepatitis B virus and hepatitis C virus infections to cirrhosis and primary liver cancer worldwide.

J. Perz, G. Armstrong, L. Farrington, et al.. (2006). Journal of hepatology. Cited 2,664 times. https://doi.org/10.1016/J.JHEP.2006.05.013

Tumour evolution inferred by single-cell sequencing

N. Navin, J. Kendall, J. Troge, et al.. (2011). Nature. Cited 2,558 times. https://doi.org/10.1038/nature09807

Distant Metastasis Occurs Late during the Genetic Evolution of Pancreatic Cancer

S. Yachida, Siân Jones, I. Bozic, et al.. (2010). Nature. Cited 2,453 times. https://doi.org/10.1038/nature09515

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

Catherine de Martel, J. Ferlay, S. Franceschi, et al.. (2012). The Lancet. Oncology. Cited 2,260 times. https://doi.org/10.1016/S1470-2045(12)70137-7

Identification of genes periodically expressed in the human cell cycle and their expression in tumors.

M. Whitfield, G. Sherlock, A. Saldanha, et al.. (2002). Molecular biology of the cell. Cited 1,616 times. https://doi.org/10.1091/MBC.02-02-0030

The impact of translocations and gene fusions on cancer causation

F. Mitelman, B. Johansson, F. Mertens. (2007). Nature Reviews Cancer. Cited 1,374 times. https://doi.org/10.1038/nrc2091

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

A. Shalek, R. Satija, Xian Adiconis, et al.. (2013). Nature. Cited 1,180 times. https://doi.org/10.1038/nature12172

Quantitative single-cell RNA-seq with unique molecular identifiers

Saiful Islam, Amit Zeisel, S. Joost, et al.. (2013). Nature Methods. Cited 1,131 times. https://doi.org/10.1038/nmeth.2772

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

F. Buettner, K. Natarajan, F. P. Casale, et al.. (2015). Nature Biotechnology. Cited 1,127 times. https://doi.org/10.1038/nbt.3102

Stem cell gene expression programs influence clinical outcome in human leukemia

Kolja Eppert, K. Takenaka, E. Lechman, et al.. (2011). Nature Medicine. Cited 1,056 times. https://doi.org/10.1038/nm.2415

Ensembl 2014

P. Flicek, M. Amode, D. Barrell, et al.. (2013). Nucleic Acids Research. Cited 885 times. https://doi.org/10.1093/nar/gkt1196

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

Daehwan Kim, S. Salzberg. (2011). Genome Biology. Cited 786 times. https://doi.org/10.1186/gb-2011-12-8-r72

Pathogenic mechanisms in HBV- and HCV-associated hepatocellular carcinoma

A. Arzumanyan, H. M. Reis, M. Feitelson. (2013). Nature Reviews Cancer. Cited 752 times. https://doi.org/10.1038/nrc3449

WGCNA: an R package for weighted correlation network analysis

P. Langfelder, Steve Horvath. (2008). BMC Bioinformatics. Cited 717 times. https://doi.org/10.1186/1471-2105-9-559

Reactome: a knowledge base of biologic pathways and processes

Imre Vastrik, P. D’Eustachio, E. Schmidt, et al.. (2007). Genome Biology. Cited 702 times. https://doi.org/10.1186/gb-2007-8-3-r39

Why do viruses cause cancer? Highlights of the first century of human tumour virology

P. Moore, Yuan Chang. (2010). Nature Reviews Cancer. Cited 694 times. https://doi.org/10.1038/nrc2961

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

Jian-Feng Xiang, Qing-Fei Yin, Tian Chen, et al.. (2014). Cell Research. Cited 624 times. https://doi.org/10.1038/cr.2014.35

Human viral oncogenesis: a cancer hallmarks analysis.

E. Mesri, M. Feitelson, K. Munger. (2014). Cell host & microbe. Cited 598 times. https://doi.org/10.1016/j.chom.2014.02.011

Inhibition of CDK activity and PCNA-dependent DNA replication by p21 is blocked by interaction with the HPV-16 E7 oncoprotein.

J. Funk, S. Waga, J. Harry, et al.. (1997). Genes & development. Cited 565 times. https://doi.org/10.1101/GAD.11.16.2090

NCBI Viral Genomes Resource

J. R. Brister, Danso Ako-Adjei, Yīmíng Bào, et al.. (2014). Nucleic Acids Research. Cited 563 times. https://doi.org/10.1093/nar/gku1207

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

D. Ting, Ben S. Wittner, M. Ligorio, et al.. (2014). Cell reports. Cited 475 times. https://doi.org/10.1016/j.celrep.2014.08.029

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

Zheng Hu, Da Zhu, Wei Wang, et al.. (2015). Nature Genetics. Cited 465 times. https://doi.org/10.1038/ng.3178

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

G. Marinov, B. Williams, Kenneth McCue, et al.. (2014). Genome Research. Cited 460 times. https://doi.org/10.1101/gr.161034.113

Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms.

Olivia M. Padovan-Merhar, Gautham Nair, Andrew G Biaesch, et al.. (2015). Molecular cell. Cited 450 times. https://doi.org/10.1016/j.molcel.2015.03.005

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

J. Landry, P. Pyl, T. Rausch, et al.. (2013). G3: Genes|Genomes|Genetics. Cited 449 times. https://doi.org/10.1534/g3.113.005777

The search for infectious causes of human cancers: where and why.

H. zur Hausen. (2009). Virology. Cited 403 times. https://doi.org/10.1016/j.virol.2009.06.001

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

Andrew C. Adey, Joshua N. Burton, J. Kitzman, et al.. (2013). Nature. Cited 328 times. https://doi.org/10.1038/nature12064

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

H. Edgren, A. Murumagi, S. Kangaspeska, et al.. (2011). Genome Biology. Cited 325 times. https://doi.org/10.1186/gb-2011-12-1-r6

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

Hui Li, Jinglan Wang, G. Mor, et al.. (2008). Science. Cited 307 times. https://doi.org/10.1126/science.1156725

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

Natalie A. Twine, Karolina Janitz, M. Wilkins, et al.. (2011). PLoS ONE. Cited 306 times. https://doi.org/10.1371/journal.pone.0016266

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

Ka-Wei Tang, Babak Alaeimahabadi, T. Samuelsson, et al.. (2013). Nature Communications. Cited 298 times. https://doi.org/10.1038/ncomms3513

Viral-human chimeric transcript predisposes risk to liver cancer development and progression.

C. Lau, T. Sun, A. K. Ching, et al.. (2014). Cancer cell. Cited 276 times. https://doi.org/10.1016/j.ccr.2014.01.030

Intratumor Heterogeneity in Hepatocellular Carcinoma

Juliane Friemel, M. Rechsteiner, L. Frick, et al.. (2014). Clinical Cancer Research. Cited 271 times. https://doi.org/10.1158/1078-0432.CCR-14-0122

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

J. Gole, A. Gore, Andrew Richards, et al.. (2013). Nature biotechnology. Cited 230 times. https://doi.org/10.1038/nbt.2720

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

Xiaolu He, Xueming Tan, Xiang Wang, et al.. (2014). Tumor Biology. Cited 215 times. https://doi.org/10.1007/s13277-014-2526-4

Coordinating genome expression with cell size.

S. Marguerat, J. Bähler. (2012). Trends in genetics : TIG. Cited 201 times. https://doi.org/10.1016/j.tig.2012.07.003

Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences.

Qiang Xu, Christopher J. Lee. (2003). Nucleic acids research. Cited 197 times. https://doi.org/10.1093/NAR/GKG786

Abrogation of IRF-1 response by high-risk HPV E7 protein in vivo.

S. Um, Jae-Woong Rhyu, eun-joo kim, et al.. (2002). Cancer letters. Cited 132 times. https://doi.org/10.1016/S0304-3835(01)00871-0

Binding of the human E2F transcription factor to the retinoblastoma protein but not to cyclin A is abolished in HPV-16-immortalized cells.

Michele Pagano, Matthias Dürst, Silvia Joswig, et al.. (1992). Oncogene. Cited 104 times.

What's the damage? The impact of pathogens on pathways that maintain host genome integrity.

M. Weitzman, J. Weitzman. (2014). Cell host & microbe. Cited 103 times. https://doi.org/10.1016/j.chom.2014.02.010

HPV-18 E6*I protein modulates the E6-directed degradation of p53 by binding to full-length HPV-18 E6

D. Pim, L. Banks. (1999). Oncogene. Cited 98 times. https://doi.org/10.1038/sj.onc.1203134

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

D. Pervouchine, David G. Knowles, R. Guigó. (2012). Bioinformatics. Cited 93 times. https://doi.org/10.1093/bioinformatics/bts678

Prognostic Significance of the Epstein-Barr Virus, p53, Bcl-2, and Survivin in Nasopharyngeal Cancer

K. Yip, W. Shi, M. Pintilie, et al.. (2006). Clinical Cancer Research. Cited 86 times. https://doi.org/10.1158/1078-0432.CCR-06-0571

p70 Ribosomal protein S6 kinase (Rps6kb1): an update

Farnaz Bahrami-B, P. Ataie-Kachoie, M. Pourgholami, et al.. (2014). Journal of Clinical Pathology. Cited 80 times. https://doi.org/10.1136/jclinpath-2014-202560

Single-cell gene expression signatures reveal melanoma cell heterogeneity

M. Ennen, C. Keime, D. Kobi, et al.. (2014). Oncogene. Cited 79 times. https://doi.org/10.1038/onc.2014.262

Human tumour viruses and the deregulation of cell polarity in cancer

L. Banks, D. Pim, Miranda Thomas. (2012). Nature Reviews Cancer. Cited 70 times. https://doi.org/10.1038/nrc3400

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

A. McDavid, L. Dennis, P. Danaher, et al.. (2014). PLoS Computational Biology. Cited 66 times. https://doi.org/10.1101/002295

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

N. Korzeniewski, Benjamin R. Treat, S. Duensing. (2011). Molecular Cancer. Cited 66 times. https://doi.org/10.1186/1476-4598-10-61

Amplification of the integrated viral transforming genes of human papillomavirus 18 and its 5'-flanking cellular sequence located near the myc protooncogene in HeLa cells.

Pedro A. Lazo, Joseph A. DiPaolo, Nicholas C. Popescu. (1989). Cancer research. Cited 60 times.

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

O. Sakarya, Heinz Breu, M. Radovich, et al.. (2012). PLoS Computational Biology. Cited 49 times. https://doi.org/10.1371/journal.pcbi.1002464

Regulation of the Cdc25A gene by the human papillomavirus Type 16 E7 oncogene

S. Katich, K. Zerfass-Thome, I. Hoffmann. (2001). Oncogene. Cited 46 times. https://doi.org/10.1038/sj.onc.1204130

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

D. Arıoz, H. Camuzcuoğlu, H. Toy, et al.. (2009). International Journal of Gynecologic Cancer. Cited 38 times. https://doi.org/10.1111/IGC.0b013e3181af711e

Assessment of preoperative serum prolidase activity in epithelial ovarian cancer.

H. Camuzcuoğlu, D. Arıoz, H. Toy, et al.. (2009). European journal of obstetrics, gynecology, and reproductive biology. Cited 37 times. https://doi.org/10.1016/j.ejogrb.2009.07.012

Expression of deltaNp73 and TAp73alpha independently associated with radiosensitivities and prognoses in cervical squamous cell carcinoma.

Stephanie S Liu, K. Y. Chan, A. Cheung, et al.. (2006). Clinical cancer research : an official journal of the American Association for Cancer Research. Cited 33 times.

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

S. Bellanger, Chye Ling Tan, W. Nei, et al.. (2009). Journal of Virology. Cited 33 times. https://doi.org/10.1128/JVI.01162-09

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

M. Toots, Andres Männik, Gaily Kivi, et al.. (2014). PLoS ONE. Cited 31 times. https://doi.org/10.1371/journal.pone.0116151

Overview: viral agents and cancer.

N. Mueller. (1995). Environmental Health Perspectives. Cited 30 times. https://doi.org/10.2307/3432322

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

M. Filippova, W. Evans, R. Aragon, et al.. (2014). Virology. Cited 28 times. https://doi.org/10.1016/j.virol.2013.12.011

BUBR1 expression in benign oral lesions and squamous cell carcinomas: correlation with human papillomavirus.

R. Lira, F. A. Miranda, M. C. Guimarães, et al.. (2010). Oncology reports. Cited 27 times. https://doi.org/10.3892/OR_00000729

Prolidase activity disregulation in chronic pancreatitis and pancreatic cancer.

J. Pałka, A. Surażyński, E. Karna, et al.. (2002). Hepato-gastroenterology. Cited 26 times.

Human papillomavirus 18 oncoproteins E6 and E7 enhance irradiation- and chemotherapeutic agent-induced apoptosis in p53 and Rb mutated cervical cancer cell lines.

G. Kilic, M. Cardillo, M. Ozdemirli, et al.. (1999). European journal of gynaecological oncology. Cited 21 times.

Merkel cell polyomavirus and extrapulmonary small cell carcinoma

K. Hourdequin, J. Lefferts, J. Brennick, et al.. (2013). Oncology Letters. Cited 18 times. https://doi.org/10.3892/ol.2013.1483

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

Wendy Theelen, M. Reijans, G. Simons, et al.. (2009). International Journal of Cancer. Cited 17 times. https://doi.org/10.1002/ijc.24844

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

S. R. da Silva, Deilson Elgui de Oliveira. (2011). Cancer letters. Cited 13 times. https://doi.org/10.1016/j.canlet.2011.02.007

Epstein-Barr virus and nasopharyngeal cancer.

V. Schuster, T. Pukrop. (1996). The New England journal of medicine. Cited 1 times.
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