Related papers: Embed-Search-Align: DNA Sequence Alignment using T…

Since Bahdanau et al. [1] first introduced attention for neural machine translation, most sequence-to-sequence models made use of attention mechanisms [2, 3, 4]. While they produce soft-alignment matrices that could be interpreted as…

The most common gene regulation mechanism is when a transcription factor protein binds to a regulatory sequence to increase or decrease RNA transcription. However, transcription factors face two main challenges when searching for these…

Fine-tuning Pre-trained protein language models (PLMs) has emerged as a prominent strategy for enhancing downstream prediction tasks, often outperforming traditional supervised learning approaches. As a widely applied powerful technique in…

How DNA-binding proteins locate specific genomic targets remains a central challenge in molecular biology. Traditional protein-centric approaches, which rely on wet-lab experiments and visualization techniques, often lack genome-wide…

The exponential growth of DNA sequencing data has outpaced traditional heuristic-based methods, which struggle to scale effectively. Efficient computational approaches are urgently needed to support large-scale similarity search, a…

Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…

Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…

The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…

RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…

The video action segmentation task is regularly explored under weaker forms of supervision, such as transcript supervision, where a list of actions is easier to obtain than dense frame-wise labels. In this formulation, the task presents…

Network alignment, in general, seeks to discover the hidden underlying correspondence between nodes across two (or more) networks when given their network structure. However, most existing network alignment methods have added assumptions of…

We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e., DNA…

Many studies have been conducted to improve the efficiency of Transformer from quadric to linear. Among them, the low-rank-based methods aim to learn the projection matrices to compress the sequence length. However, the projection matrices…

Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…

DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…

Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…

We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…

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…

In recent years, aligning a sequence to a pangenome has become a central problem in genomics and pangenomics. A fast and accurate solution to this problem can serve as a toolkit to many crucial tasks such as read-correction, Multiple…

Microbiome sample representation to input into LLMs is essential for downstream tasks such as phenotype prediction and environmental classification. While prior studies have explored embedding-based representations of each microbiome…