Yen Chun Chen

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.

Large cross-phase modulations at the few-photon level

We demonstrate an efficient cross-phase modulation (XPM) based on a closed-loop double-Λ system. The property of the double-Λ medium can be controlled by changing the phases of the applied optical fields. This phase-dependent XPM scheme can achieve large phase modulations at low-light intensities without requiring cavities or tightly focusing laser beams. With this scheme, we observe a π-level phase shift with two pulses, both consisting of eight photons in cold rubidium atoms. Such a novel scheme provides a simple route to generate strong interactions between photons and may have potential applications in all-optical quantum signal processing.

Low-light-level four-wave mixing by quantum interference

We observed electromagnetically induced transparency-based four-wave mixing (FWM) in the pulsed regime at low light levels. The FWM conversion efficiency of

Microstructural investigation of stress-assisted α″-α' phase transformation in cold-rolled Ti-7.5Mo alloy.

3.8(9)%

Electromagnetically-induced-transparency-based cross-phase-modulation at attojoule levels

was observed in a four-level system of cold

Study of solids by use of nonthermalized positrons.

{}^{87}mathrm{Rb}

Workability of spray-formed 7075 Al alloy reinforced with SiCp at elevated temperatures

atoms using a driving laser pulse with a peak intensity of

Effect of cold rolling on structure and tensile properties of cast Ti–7.5Mo alloy

ensuremath{approx}80

Effects of post-aging cooling condition on structure and tensile properties of aged Ti–7.5Mo alloy

ensuremath{mu}mathrm{W}/{mathrm{cm}}^{2}