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23 papers · ranked by Valyu relevance

01
BbioRxiv6 Jun 2025
GeneChat: A Multi-Modal Large Language Model for Gene Function Prediction
Shashi Dhanasekar, Akash Saranathan, Pengtao Xie
Accurately predicting gene function from DNA sequences remains a fundamental challenge in genomics, particularly given the limited experimental annotation available for most genes. Existing computational approaches often formulate function prediction as a classification task over predefined categories, limiting their…
89relevance
02
BbioRxiv17 Apr 2022
Inferring functions of coding and non-coding genes using epigenomic patterns and deciphering the effect of combinatorics of transcription factors binding at promoters
Omkar Chandra, Madhu Sharma, Neetesh Pandey, Indra Prakash Jha + 3 more
The number of annotated genes in the human genome has increased tremendously, and understanding their biological role is challenging through experimental methods alone. There is a need for a computational approach to infer the function of genes, particularly for non-coding RNAs, with reliable explainability. We have…
88relevance
03
PPubMed30 Jun 2022
Editorial: Machine Learning Techniques on Gene Function Prediction Volume II Qi et al. Editorial: Machine Learning on Gene Function
Ren Qi, Arun Kumar Sangaiah, Dariusz Mrozek, Quan Zou
Predicting the function of genes is a critical problem in biology. The current generation rate of new gene sequences is too fast to discover and validate them experimentally, emphasizing the importance of machine learning. Machine learning techniques have advanced our understanding of gene function, which have been…
86relevance
04
PPubMed15 Jan 2022
Assigning protein function from domain-function associations using DomFun
Elena Rojano, Fernando M. Jabato, James R. Perkins, José Córdoba-Caballero + 5 more
'José Córdoba-Caballero' 'Federico García-Criado' 'Ian Sillitoe' 'Christine Orengo' 'Juan A. G. Ranea' 'Pedro Seoane-Zonjic'] Background Protein function prediction remains a key challenge. Domain composition affects protein function. Here we present DomFun, a Ruby gem that uses associations between protein domains and…
86relevance
05
PPubMed30 Jan 2024
GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function
Danielle Miller, Ofir Arias, David Burstein, Janet Kelso
The “Sequence” search mode allows users to submit a sequence query in FASTA format either by uploading a file or directly pasting protein sequences into the search box. If a family with sufficient similarity is found (E-value < 10−4), the web server will provide information for the best hits to the proteins provided…
86relevance
06
AarXiv22 Nov 2024
The gene function prediction challenge: Large language models and knowledge graphs to the rescue
Rohan Shawn Sunil, Shan Chun Lim, Manoj Itharajula, Marek Mutwil
Elucidating gene function is one of the ultimate goals of plant science. Despite this, only ~15% of all genes in the model plant Arabidopsis thaliana have comprehensively experimentally verified functions. While bioinformatical gene function prediction approaches can guide biologists in their experimental efforts…
85relevance
07
BbioRxiv2 May 2023
SAP: Synteny-aware gene function prediction for bacteria using protein embeddings
Aysun Urhan, Bianca-Maria Cosma, Abigail L. Manson, Thomas Abeel
Today, we know the function of only a small fraction of all known protein sequences identified. This problem is even more salient in bacteria as human-centric studies are prioritized in the field and there is much to uncover in the bacterial genetic repertoire. Conventional approaches to bacterial gene annotation are…
83relevance
08
PPubMed27 Jul 2023
Current successes and remaining challenges in protein function prediction Jeffery 10.3389/fbinf.2023.1222182
Constance J. Jeffery
In recent years, improvements in protein function prediction methods have led to increased success in annotating protein sequences. However, the functions of over 30% of protein-coding genes remain unknown for many sequenced genomes. Protein functions vary widely, from catalyzing chemical reactions to binding DNA or…
82relevance
09
BbioRxiv18 Jul 2025
Beyond protein functions: evaluating completeness, coherence, and consistency of genome-scale function annotations
Rund Tawfiq, Maxat Kulmanov, Robert Hoehndorf
Protein function annotation has traditionally followed a reductionist approach, assigning functions to individual proteins acting in isolation. This paradigm treats each annotation as an independent fact, disconnected from the broader biological system. However, proteins operate within integrated cellular networks…
81relevance
10
AarXiv2022
A Review of Deep Learning Techniques for Protein Function Prediction
Divyanshu Aggarwal, Yasha Hasija
—Deep Learning and big data have shown tremendous success in bioinformatics and computational biology in recent years; artificial intelligence methods have also significantly contributed in the task of protein function classification. This review paper analyzes the recent developments in approaches for the task of…
80relevance
11
BbioRxiv4 Sep 2026
Gene function prediction from bulk coexpression is bounded by cell-type-level signal
Alexander Adrian-Hamazaki, Paul Pavlidis
It is widely accepted in genomics that coexpression of RNA transcripts suggests a commonality of function. This intuition is explicitly leveraged in machine learning methods that predict gene function, where it is often combined with other features such as protein interactions and sequence similarity. For example…
80relevance
12
AarXiv2023
Function Prediction
Bas Stringer, Annika Jacobsen, Qingzhen Hou, Hans de Ferrante + 5 more
'Olga Ivanova' 'Katharina Waury' 'Jose Gavaldá-García' 'Sanne Abeln' 'K. Anton Feenstra'] | 11 | Function Prediction | 1 | | --- | --- | --- | | | Bas Stringer Annika Jacobsen Qingzhen Hou | | | | Hans de Ferrante Olga Ivanova Katharina Waury | | | | Jose Gavald´a-Garc´ıa Sanne Abeln K. Anton Feenstra | | | | 1…
79relevance
13
PPubMed17 May 2022
GenePlexus: a web-server for gene discovery using network-based machine learning
Christopher A Mancuso, Patrick S Bills, Douglas Krum, Jacob Newsted + 2 more
Biomedical researchers take advantage of high-throughput, high-coverage technologies to routinely generate sets of genes of interest across a wide range of biological conditions. Although these technologies have directly shed light on the molecular underpinnings of various biological processes and diseases, the list of…
79relevance
14
PPubMed1 Oct 2025
An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions
Abigail Djossou, Wend Yam D D Ouedraogo, Aida Ouangraoua, Alex Bateman
In gene prediction tool development, the choice of information and the algorithm used to process it are crucial. Gene structures are typically predicted using four types of information: signal sensors, content sensors, gene similarity, and experimental data (). The first two are considered intrinsic information, while…
77relevance
15
AarXiv12 Nov 2025
GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences
Yan, Jingquan, Yuwei Miao, Lei Yu + 4 more
Exploring how genetic sequences shape phenotypes is a fundamental challenge in biology and a key step toward scalable, hypothesis-driven experimentation. The task is complicated by the large modality gap between sequences and phenotypes, as well as the pleiotropic nature of gene–phenotype relationships. Existing…
75relevance
16
AarXiv2022
Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression
Chengyu Liu, Wei Wang
Developing models with high interpretability and even deriving formulas to quantify relationships between biological data is an emerging need. We propose here a framework for ab initio derivation of sequence motifs and linear formula using a new approach based on the interpretable neural network model called contextual…
74relevance
17
BbioRxiv17 Apr 2024
Interactive Tools for Functional Annotation of Bacterial Genomes
Morgan N. Price, Adam P. Arkin
Automated annotations of protein function are error-prone because of our lack of knowledge of protein functions. For example, it is often impossible to predict the correct substrate for an enzyme or a transporter. Furthermore, much of the knowledge that we do have about the functions of proteins is missing from the…
72relevance
18
BbioRxiv6 Oct 2025
A Convolutional Deep Learning Approach to identify DNA Sequences for Gene Prediction
Jesús Antonio Motta, Pedro David Gómez
In this work, we present a highly efficient machine learning method for identifying DNA sequences that code for genes. The learning process is based on Human Genome Build 38 (GRCh38) sequences extracted from various specialized databases. The sequences were then translated into amino acid sequences and used to build…
72relevance
19
CchemRxiv6 Mar 2022
In Silico Characterization of Essential Hypothetical Proteins from Francisella tularensis Schu S4 Strain.
Sheikh Sunzid Ahmed
Francisella tularensis Schu S4 is the causal agent of a sporadic zoonotic disease known as Tularemia, which has shown epidemic outbreaks recently in certain parts of the world. This pathogen is a potential agent of biowarfare or bioterrorism and is classified as a category A pathogen by the National Institute of…
71relevance
20
AarXiv5 Mar 2024
A genome-scale deep learning model to predict gene expression changes of genetic perturbations from multiplex biological networks
Lingmin Zhan, Yuanyuan Zhang, Yingdong Wang, Aoyi Wang + 5 more
genetic perturbations from multiplex biological networks Authors: ['Lingmin Zhan' 'Yuanyuan Zhang' 'Yingdong Wang' 'Aoyi Wang' 'Caiping Cheng' 'Jinzhong Zhao' 'Wuxia Zhang' 'P.H. Hiller L. Lia' 'Jianxin Chen'] Systematic characterization of biological effects to genetic perturbation is essential to the application of…
67relevance
21
CchemRxiv28 May 2025
Evaluation of PE5 entries on the Human Proteome Project Target List
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
67relevance
22
CchemRxiv16 Sep 2025
Beyond conventional sequence-based encoding: a generalized Machine Learning pipeline for oligonucleotide property prediction
Authors not listed
The development of RNA-based therapeutics has significantly expanded the landscape of drug discovery by enabling precise modulation of gene expression. These approaches offer the potential to target previously "undruggable" genes, overcoming limitations inherent to traditional small molecule therapies. However, the…
58relevance
23
CchemRxiv26 Sep 2024
Machine Learning Applications in Drug Discovery
Authors not listed
Integrating machine learning (ML) into drug discovery has ushered in a new era of innovation, dramatically enhancing the efficiency and precision of identifying and developing new therapeutics. This review provides a comprehensive analysis of the current applications of machine learning in drug discovery, focusing on…
51relevance

Results for gene function prediction

GeneChat: A Multi-Modal Large Language Model for Gene Function Prediction

Inferring functions of coding and non-coding genes using epigenomic patterns and deciphering the effect of combinatorics of transcription factors binding at promoters

Editorial: Machine Learning Techniques on Gene Function Prediction Volume II Qi et al. Editorial: Machine Learning on Gene Function

Assigning protein function from domain-function associations using DomFun

GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function

The gene function prediction challenge: Large language models and knowledge graphs to the rescue

SAP: Synteny-aware gene function prediction for bacteria using protein embeddings

Current successes and remaining challenges in protein function prediction Jeffery 10.3389/fbinf.2023.1222182

Beyond protein functions: evaluating completeness, coherence, and consistency of genome-scale function annotations

A Review of Deep Learning Techniques for Protein Function Prediction

Gene function prediction from bulk coexpression is bounded by cell-type-level signal

Function Prediction

GenePlexus: a web-server for gene discovery using network-based machine learning

An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions

GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences

Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression

Interactive Tools for Functional Annotation of Bacterial Genomes

A Convolutional Deep Learning Approach to identify DNA Sequences for Gene Prediction

In Silico Characterization of Essential Hypothetical Proteins from Francisella tularensis Schu S4 Strain.

A genome-scale deep learning model to predict gene expression changes of genetic perturbations from multiplex biological networks

Evaluation of PE5 entries on the Human Proteome Project Target List

Beyond conventional sequence-based encoding: a generalized Machine Learning pipeline for oligonucleotide property prediction

Machine Learning Applications in Drug Discovery

GeneChat: A Multi-Modal Large Language Model for Gene Function Prediction

Inferring functions of coding and non-coding genes using epigenomic patterns and deciphering the effect of combinatorics of transcription factors binding at promoters

Editorial: Machine Learning Techniques on Gene Function Prediction Volume II Qi et al. Editorial: Machine Learning on Gene Function

Assigning protein function from domain-function associations using DomFun

GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function

The gene function prediction challenge: Large language models and knowledge graphs to the rescue

SAP: Synteny-aware gene function prediction for bacteria using protein embeddings

Current successes and remaining challenges in protein function prediction Jeffery 10.3389/fbinf.2023.1222182

Beyond protein functions: evaluating completeness, coherence, and consistency of genome-scale function annotations

A Review of Deep Learning Techniques for Protein Function Prediction

Gene function prediction from bulk coexpression is bounded by cell-type-level signal

Function Prediction

GenePlexus: a web-server for gene discovery using network-based machine learning

An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions

GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences

Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression

Interactive Tools for Functional Annotation of Bacterial Genomes

A Convolutional Deep Learning Approach to identify DNA Sequences for Gene Prediction

In Silico Characterization of Essential Hypothetical Proteins from Francisella tularensis Schu S4 Strain.

A genome-scale deep learning model to predict gene expression changes of genetic perturbations from multiplex biological networks

Evaluation of PE5 entries on the Human Proteome Project Target List

Beyond conventional sequence-based encoding: a generalized Machine Learning pipeline for oligonucleotide property prediction

Machine Learning Applications in Drug Discovery