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The gene set analysis (GSA) is a foundational approach for uncovering the molecular functions associated with a group of genes. Recently, LLM-powered methods have emerged to annotate gene sets with biological functions together with…
High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental…
This paper describes NCRF++, a toolkit for neural sequence labeling. NCRF++ is designed for quick implementation of different neural sequence labeling models with a CRF inference layer. It provides users with an inference for building the…
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation. However, the experimental determination of miRNA sequence and structure is both expensive and time-consuming.…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach. It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA…
We propose a new alignment-free algorithm by constructing a compact vector representation on $\mathbb{R}^{24}$ of a DNA sequence of arbitrary length. Each component of this vector is obtained from a representative sequence, the elements of…
In recent years, several machine learning approaches have been proposed to predict gene expression and epigenetic signals from the DNA sequence alone. These models are often used to deduce, and, to some extent, assess putative new…
In the post-genomic era, large-scale personal DNA sequences are produced and collected for genetic medical diagnoses and new drug discovery, which, however, simultaneously poses serious challenges to the protection of personal genomic…
There has been a growing academic interest in the recognition of nested named entities in many domains. We tackle the task with a novel local hypergraph-based method: We first propose start token candidates and generate corresponding…
RNAs are essential molecules that carry genetic information vital for life, with profound implications for drug development and biotechnology. Despite this importance, RNA research is often hindered by the vast literature available on the…
The deep Convolutional Neural Network (CNN) is the state-of-the-art solution for large-scale visual recognition. Following basic principles such as increasing the depth and constructing highway connections, researchers have manually…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
Gene mining is an important topic in the field of life sciences, but traditional machine learning methods cannot consider the regulatory relationships between genes. Deep learning methods perform poorly in small sample sizes. This study…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene…
Development of a proper names pronunciation lexicon is usually a manual effort which can not be avoided. Grapheme to phoneme (G2P) conversion modules, in literature, are usually rule based and work best for non-proper names in a particular…
Background: Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…