arXiv subjects

Yang Liao

Publications and source records attributed to Yang Liao.

22 records · Page 2Linked to original sources

arXiv2014

Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures

There is a critical need for standard approaches to assess, report, and compare the technical performance of genome-scale differential gene expression experiments. We assess technical performance with a proposed "standard" dashboard of metrics derived from analysis of external spike-in RNA control ratio mixtures. These control ratio mixtures with defined abundance ratios enable assessment of diagnostic performance of differentially expressed transcript lists, limit of detection of ratio (LODR) estimates, and expression ratio variability and measurement bias. The performance metrics suite is applicable to analysis of a typical experiment, and here we also apply these metrics to evaluate technical performance among laboratories. An interlaboratory study using identical samples shared amongst 12 laboratories with three different measurement processes demonstrated generally consistent diagnostic power across 11 laboratories. Ratio measurement variability and bias were also comparable amongst laboratories for the same measurement process. Different biases were observed for measurement processes using different mRNA enrichment protocols.

q-bio.GN↗

arXiv2014

Fabrication of an integrated high-quality-factor (high-Q) optofluidic sensor by femtosecond laser micromachining

We report on fabrication of a microtoroid resonator of a high-quality factor (i. e., Q-factor of ~3.24x10^6 measured under the critical coupling condition) integrated in a microfluidic channel using femtosecond laser three-dimensional (3D) micromachining. Coupling of light into and out of the microresonator has been realized with a fiber taper that is reliably assembled with the microtoroid. The assembly of the fiber to the microtoroid is achieved by welding the fiber taper onto the sidewall of the microtoroid using CO_2 laser irradiation. The integrated microresonator maintains a high Q-factor of 3.21x10^5 as measured in air, which should still be sufficient for many sensing applications. We test the functionality of the integrated optofluidic sensor by performing bulk refractive index sensing of purified water doped with tiny amount of salt. It is shown that a detection limit of ~1.2x10^-4 refractive index unit can be achieved. Our result showcases the capability of integration of high-Q microresonators with complex microfluidic systems using femtosecond laser 3D micromachining.

physics.optics↗

arXiv2013

featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.

q-bio.GN↗

arXiv2012

Femtosecond laser nanostructuring in glass with sub-50nm feature sizes

We report on controllable production of nanostructures embedded in a porous glass substrate by femtosecond laser direct writing. We show that a hollow nano-void with a lateral size of ~40 nm and an axial size of ~1500 nm can be achieved by manipulating the peak intensity and polarization of the writing laser beam. Our finding enables direct construction of 3D nanofluidics inside glass.

physics.optics↗