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Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression.

Cheng, Chun-Pei Kuo, I-Ying Alakus, Hakan Frazer, Kelly A Harismendy, Olivier Wang, Yi-Ching Tseng, Vincent S

Published in Bioinformatics (Oxford, England)

A rapid progression of esophageal squamous cell carcinoma (ESCC) causes a high mortality rate because of the propensity for metastasis driven by genetic and epigenetic alterations. The identification of prognostic biomarkers would help prevent or control metastatic progression. Expression analyses have been used to find such markers, but do not alw...

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.

Kinsella, Marcus Harismendy, Olivier Nakano, Masakazu Frazer, Kelly A Bafna, Vineet

Published in Bioinformatics (Oxford, England)

Paired-end whole transcriptome sequencing provides evidence for fusion transcripts. However, due to the repetitiveness of the transcriptome, many reads have multiple high-quality mappings. Previous methods to find gene fusions either ignored these reads or required additional longer single reads. This can obscure up to 30% of fusions and unnecessar...

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Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression.

Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.