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High-throughput experimental technologies often identify dozens to hundreds of genes related to, or changed in, a biological or pathological process. From these genes one wants to identify biological pathways that may be involved and diseases that may be implicated. Here, we report a web server, KOBAS 2.0, which annotates an input set of genes with putative(More)
Deep sequencing now provides detailed snapshots of ribosome occupancy on mRNAs. We leverage these data to parameterize a computational model of translation, keeping track of every ribosome, tRNA, and mRNA molecule in a yeast cell. We determine the parameter regimes in which fast initiation or high codon bias in a transgene increases protein yield and infer(More)
The desert-dwelling sandfish (Scincus scincus) moves within dry sand, a material that displays solid and fluidlike behavior. High-speed x-ray imaging shows that below the surface, the lizard no longer uses limbs for propulsion but generates thrust to overcome drag by propagating an undulatory traveling wave down the body. Although viscous hydrodynamics can(More)
We integrate biological experiment, empirical theory, numerical simulation and a physical model to reveal principles of undulatory locomotion in granular media. High-speed X-ray imaging of the sandfish lizard, Scincus scincus, in 3 mm glass particles shows that it swims within the medium without using its limbs by propagating a single-period travelling(More)
Combining geometric mechanics theory, laboratory robotic experiment, and numerical simulation, we study the locomotion in granular media of the simplest noninertial swimmer, the Purcell three-link swimmer. Using granular resistive force laws as inputs, the theory relates translation and rotation of the body to shape changes (movements of the links). This(More)
The sandfish lizard (Scincus scincus) swims within granular media (sand) using axial body undulations to propel itself without the use of limbs. In previous work we predicted average swimming speed by developing a numerical simulation that incorporated experimentally measured biological kinematics into a multibody sandfish model. The model was coupled to an(More)
Lexical chains provide a representation of the lexical cohesion structure of a text. In this paper , we propose two lexical chain based cohesion models to incorporate lexical cohesion into document-level statistical machine translation: 1) a count cohesion model that rewards a hypothesis whenever a chain word occurs in the hypothesis, 2) and a probability(More)
  • Yang Ding
  • 2015
Codes in rank metric have a wide range of applications. To construct such codes with better list-decoding performance explicitly, it is of interest to investigate the listdecodability of random rank metric codes. It is shown that if n/m = b is a constant, then for every rank metric code in Fm×n q with rate R and list-decoding radius ρ must(More)
Experimental studies of translation have found that short genes tend to exhibit greater densities of ribosomes than long genes in eukaryotic species. It remains an open question whether the elevated ribosome density on short genes is due to faster initiation or slower elongation dynamics. Here, we address this question computationally using 5'-mRNA folding(More)
Laboratory experiments and numerical simulation reveal that a submerged intruder dragged horizontally at a constant velocity within a granular medium experiences a lift force whose sign and magnitude depend on the intruder shape. Comparing the stress on a flat plate at varied inclination angle with the local surface stress on the intruders at regions with(More)