Opportunities and methods for studying alternative splicing in cancer with RNA-Seq

H Feng, Z Qin, X Zhang - Cancer letters, 2013 - Elsevier
The biogenesis, development and metastases of cancer are associated with many variations
in the transcriptome. Alternative splicing of genes is a major post-transcriptional regulation …

Integrated genome browser: visual analytics platform for genomics

NH Freese, DC Norris, AE Loraine - Bioinformatics, 2016 - academic.oup.com
Motivation: Genome browsers that support fast navigation through vast datasets and provide
interactive visual analytics functions can help scientists achieve deeper insight into …

Role of tertiary lymphoid structures (TLS) in anti-tumor immunity: potential tumor-induced cytokines/chemokines that regulate TLS formation in epithelial-derived …

EM Pimenta, BJ Barnes - Cancers, 2014 - mdpi.com
Following the successes of monoclonal antibody immunotherapies (trastuzumab
(Herceptin®) and rituximab (Rituxan®)) and the first approved cancer vaccine …

[HTML][HTML] The PRKCI and SOX2 oncogenes are coamplified and cooperate to activate Hedgehog signaling in lung squamous cell carcinoma

V Justilien, MP Walsh, SA Ali, EA Thompson… - Cancer cell, 2014 - cell.com
We report that two oncogenes coamplified on chromosome 3q26, PRKCI and SOX2,
cooperate to drive a stem-like phenotype in lung squamous cell carcinoma (LSCC). Protein …

Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers

D Albanese, M Filosi, R Visintainer… - …, 2013 - academic.oup.com
We introduce a novel implementation in ANSI C of the MINE family of algorithms for
computing maximal information-based measures of dependence between two variables in …

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer

E Sebestyén, M Zawisza, E Eyras - Nucleic acids research, 2015 - academic.oup.com
The determination of the alternative splicing isoforms expressed in cancer is fundamental for
the development of tumor-specific molecular targets for prognosis and therapy, but it is …

[HTML][HTML] Validation of a next-generation sequencing assay for clinical molecular oncology

CE Cottrell, H Al-Kateb, AJ Bredemeyer… - The Journal of molecular …, 2014 - Elsevier
Currently, oncology testing includes molecular studies and cytogenetic analysis to detect
genetic aberrations of clinical significance. Next-generation sequencing (NGS) allows rapid …

Protein kinase Cι drives a NOTCH3-dependent stem-like phenotype in mutant KRAS lung adenocarcinoma

SA Ali, V Justilien, L Jamieson, NR Murray, AP Fields - Cancer cell, 2016 - cell.com
We report that the protein kinase Cι (PKCι) oncogene controls expression of NOTCH3, a key
driver of stemness, in KRAS-mediated lung adenocarcinoma (LADC). PKCι activates …

Genome-wide analysis of microRNA and mRNA expression signatures in cancer

M Li, S Fu, H Xiao - Acta Pharmacologica Sinica, 2015 - nature.com
Cancer is an extremely diverse and complex disease that results from various genetic and
epigenetic changes such as DNA copy-number variations, mutations, and aberrant mRNA …

[HTML][HTML] Use of blood-based biomarkers for early diagnosis and surveillance of colorectal cancer

GAP Ganepola, J Nizin, JR Rutledge… - World journal of …, 2014 - ncbi.nlm.nih.gov
Early screening for colorectal cancer (CRC) holds the key to combat and control the
increasing global burden of CRC morbidity and mortality. However, the current available …