Related papers: Is there any sense in antisense editing?
Changes in gene expression occurring during differentiation of human monocytes into dendritic cells were studied at the RNA and protein levels. These studies showed the induction of several gene classes corresponding to various biological…
Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae.…
microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study non- model organisms. However, when the reference transcriptome used to calculate differential expression is incomplete, significant error in…
Motivated by applications in DNA storage, we study a setting in which strings are affected by tandem-duplication errors. In particular, we look at two settings: disjoint tandem-duplication errors, and equal-length tandem-duplication errors.…
Recent experiments [J. van Mameren et al. PNAS 106, 18231 (2009)] provide a detailed spatial picture of overstretched DNA, showing that under certain conditions the two strands of the double helix separate at about 65 pN. It was proposed…
Studies using assays to quantify the expression of thousands of genes on tens to thousands of cell samples have been carried out for over 20 years. Such assays are based on microarrays, DNA sequencing or other molecular technologies. All…
Commonsense reasoning is intuitive for humans but has been a long-term challenge for artificial intelligence (AI). Recent advancements in pretrained language models have shown promising results on several commonsense benchmark datasets.…
Both short interfering RNAs (siRNAs) and microRNAs (miRNAs) mediate the repression of specific sequences of mRNA through the RNA interference pathway. In the last years several experiments have supported the hypothesis that siRNAs and…
With the widespread adoption of large language models (LLMs), understanding their personality representation mechanisms has become critical. As a novel paradigm in Personality Editing, most existing methods employ neuron-editing to locate…
This paper presents a new approach in understanding how deep neural networks (DNNs) work by applying homomorphic signal processing techniques. Focusing on the task of multi-pitch estimation (MPE), this paper demonstrates the equivalence…
Over the past few years, microRNAs (miRNAs) have emerged as a new prominent class of gene regulatory factors that negatively regulate expression of approximately one-third of the genes in animal genomes at post-transcriptional level.…
The last decade of machine learning has seen drastic increases in scale and capabilities. Deep neural networks (DNNs) are increasingly being deployed in the real world. However, they are difficult to analyze, raising concerns about using…
The ability to explain decisions made by AI systems is highly sought after, especially in domains where human lives are at stake such as medicine or autonomous vehicles. While it is often possible to approximate the input-output relations…
Editing model parameters directly in Transformers makes updating open-source transformer-based models possible without re-training (Meng et al., 2023). However, these editing methods have only been evaluated on statements about encyclopedic…
We revisit some aspects of D-brane theory from the point of view of anomalies. When the boundary condition on a worldsheet boson is flipped from Neumann to Dirichlet, worldsheet supersymmetry requires also reversing the sign of the boundary…
According to the `ceRNA hypothesis', microRNAs (miRNAs) may act as mediators of an effective positive interaction between long coding or non-coding RNA molecules, carrying significant potential implications for a variety of biological…
Deep learning as represented by the artificial deep neural networks (DNNs) has achieved great success in many important areas that deal with text, images, videos, graphs, and so on. However, the black-box nature of DNNs has become one of…
Full-duplex systems require very strong self-interference cancellation in order to operate correctly and a significant part of the self-interference signal is due to non-linear effects created by various transceiver impairments. As such,…