Related papers: Transcripts per million ratio: applying distributi…
In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a reference genome. The approach uses an RNN to transform kmers of the RNA-seq reads into a 2 dimensional…
The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a greater length increases the chance for reads being…
Blood-based biomarkers underpin clinical diagnosis and management, yet their interpretation relies largely on fixed population reference intervals that ignore stable, intra-patient variability. As such, population-based interpretation can…
This paper presents a statistical method for use in music transcription that can estimate score times of note onsets and offsets from polyphonic MIDI performance signals. Because performed note durations can deviate largely from…
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…
A fundamental characteristic of natural language is the high rate at which speakers produce novel expressions. Because of this novelty, a heavy-tail of rare events accounts for a significant amount of the total probability mass of…
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such…
Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between (i)…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
Background: The availability of high throughput methods for measurement of mRNA concentrations makes the reliability of conclusions drawn from the data and global quality control of samples and hybridization important issues. We address…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
The paper presents methods for evaluating the accuracy of alignments between transcriptions and audio recordings. The methods have been applied to the Spoken British National Corpus, which is an extensive and varied corpus of natural…
Despite the remarkable advances in language modeling, current mainstream decoding methods still struggle to generate texts that align with human texts across different aspects. In particular, sampling-based methods produce less-repetitive…
Summing or averaging nonlinearly field-normalized citation counts is a common but methodologically problematic practice, as it violates mathematical principles. The issue originates from the nonlinear transformation, which disrupts the…
In differential expression (DE) analysis of RNA-seq count data, it is known that genes with a larger read number are more likely to be differentially expressed. This bias has a profound effect on the subsequent Gene Ontology (GO) analysis…
Training neural samplers directly from unnormalized densities without access to target distribution samples presents a significant challenge. A critical desideratum in these settings is achieving comprehensive mode coverage, ensuring the…
Methods for global measurement of transcript abundance such as microarrays and RNA-Seq generate datasets in which the number of measured features far exceeds the number of observations. Extracting biologically meaningful and experimentally…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
The distribution of genetic polymorphisms in a population contains information about the mutation rate and the strength of natural selection at a locus. Here, we show that the Poisson Random Field (PRF) method of population-genetic…
By investigating the distribution of phrase pairs in phrase translation tables, the work in this paper describes an approach to increase the number of n-gram alignments in phrase translation tables output by a sampling-based alignment…