Analysis of Exercise-Induced Periodic Breathing Using an Autoregressive Model and the Hilbert-Huang Transform.

Evaluation of exercise-induced periodic breathing (PB) in cardiopulmonary exercise testing (CPET) is one of important diagnostic evidences to judge the prognosis of chronic heart failure cases. In this study, we propose a method for the quantitative analysis of measured ventilation signals from an exercise test. We used an autoregressive (AR) model to filter the breath-by-breath measurements of ventilation from exercise tests.

SeqEntropy: genome-wide assessment of repeats for short read sequencing.

Background: Recent studies on genome assembly from short-read sequencing data reported the limitation of this technology to reconstruct the entire genome even at very high depth coverage. We investigated the limitation from the perspective of information theory to evaluate the effect of repeats on short-read genome assembly using idealized (error-free) reads at different lengths.

Methodology/principal Findings: We define a metric H(k) to be the entropy of sequencing reads at a read length k and use the relative loss of entropy ΔH(k) to measure the impact of repeats for the reconstruction of whole-genome from sequences of length k.

EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

Motivation: High-accuracy de novo assembly of the short sequencing reads from RNA-Seq technology is very challenging. We introduce a de novo assembly algorithm, EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This algorithm uses an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data.

Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.

Background: Mitochondrial dysfunction is associated with various aging diseases. The copy number of mtDNA in human cells may therefore be a potential biomarker for diagnostics of aging. Here we propose a new computational method for the accurate assessment of mtDNA copies from whole genome sequencing data.

A gene expression profile for vascular invasion can predict the recurrence after resection of hepatocellular carcinoma: a microarray approach.

Background: Recurrence after hepatocellular carcinoma (HCC) resection is the major obstacle to improved survival. The presence of vascular invasion (VI) in pathology specimens is a well-known unfavorable prognostic factor for HCC recurrence. Though some VI-related genes have been reported, their association with recurrence-free survival is not known.

Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens.

Motivation: Differential detection on symptom-related pathogens (SRP) is critical for fast identification and accurate control against epidemic diseases. Conventional polymerase chain reaction (PCR) requires a large number of unique primers to amplify selected SRP target sequences. With multiple-use primers (mu-primers), multiple targets can be amplified and detected in one PCR experiment under standard reaction condition and reduced detection complexity.