相关论文: Experimental Analysis of XPCR-based protocols

When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…

Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…

Randomized experiments are the gold standard for causal inference but face significant challenges in business applications, including limited traffic allocation, the need for heterogeneous treatment effect estimation, and the complexity of…

We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…

A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…

Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…

DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…

Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in…

Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled…

Statistically resolving the underlying haplotype pair for a genotype measurement is an important intermediate step in gene mapping studies, and has received much attention recently. Consequently, a variety of methods for this problem have…

Primary human cells offer the most faithful representation of native human physiology, yet their practical utility is constrained by the difficulty of introducing exogenous genetic material. Electroporation provides a promising non-viral…

Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of…

With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical…

Filtered diode array spectrometers are routinely employed to infer the temporal evolution of spectral power from x-ray sources, but uniquely extracting spectral content from a finite set of broad, spectrally overlapping channel spectral…

DNA data storage offers a high-density, long-term alternative to traditional storage systems, addressing the exponential growth of digital data. Composite DNA extends this paradigm by leveraging mixtures of nucleotides to increase storage…

We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…

This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…

I introduce a simple permutation procedure to test conventional (non-sharp) hypotheses about the effect of a binary treatment in the presence of a finite number of large, heterogeneous clusters when the treatment effect is identified by…