Related papers: TROM: A Testing-based Method for Finding Transcrip…
Spatial transcriptomics is a technology that captures gene expression levels at different spatial locations, widely used in tumor microenvironment analysis and molecular profiling of histopathology, providing valuable insights into…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
Recent multilingual pretrained language models (mPLMs) have been shown to encode strong language-specific signals, which are not explicitly provided during pretraining. It remains an open question whether it is feasible to employ mPLMs to…
RNA-seq allows detection and precise quantification of transcripts, provides comprehensive understanding of exon/intron boundaries, aids discovery of alternatively spliced isoforms and fusion transcripts along with measurement of…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
In most of the recent immunological literature the differences across antigen receptor populations are examined via non-parametric statistical measures of species overlap and diversity borrowed from ecological studies. While this approach…
Analyses of high-throughput genomic data often lead to ranked lists of genomic loci. How to characterize concordant signals between two rank lists is a common problem with many applications. One example is measuring the reproducibility…
Response-adaptive randomization (RAR) has been studied extensively in conventional, single-stage clinical trials, where it has been shown to yield ethical and statistical benefits, especially in trials with many treatment arms. However, RAR…
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…
Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However,…
Genomic aberrations, such as somatic copy number alterations, are frequently observed in tumor tissue. Recurrent aberrations, occurring in the same region across multiple subjects, are of interest because they may highlight genes associated…
The Coronal Multichannel Polarimeter (CoMP) routinely performs coronal polarimetric measurements using the Fe XIII 10747 $\AA$ and 10798 $\AA$ lines, which are sensitive to the coronal magnetic field. However, inverting such polarimetric…
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…
Multimodal Large Language Models (MLLMs) exhibit promising advancements across various tasks, yet they still encounter significant trustworthiness issues. Prior studies apply Split Conformal Prediction (SCP) in language modeling to…
Much of the natural variation for a complex trait can be explained by variation in DNA sequence levels. As part of sequence variation, gene-gene interaction has been ubiquitously observed in nature, where its role in shaping the development…
For a nonlinear dynamical system that depends on parameters, the paper introduces a novel tensorial reduced-order model (TROM). The reduced model is projection-based, and for systems with no parameters involved, it resembles proper…
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples…
Measuring gene expression simultaneously in both hosts and symbionts offers a powerful approach to explore the biology underlying species interactions. Such dual or simultaneous RNAseq approaches have primarily been used to gain insight…