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Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…

Populations and Evolution · Quantitative Biology 2024-03-26 Mingyang Zhou , Zichao Yan , Elliot Layne , Nikolay Malkin , Dinghuai Zhang , Moksh Jain , Mathieu Blanchette , Yoshua Bengio

A quantitative understanding of the dynamics of bee colonies is important to support global efforts to improve bee health and enhance pollination services. Traditional approaches focus either on theoretical models or data-centred…

Biological Physics · Physics 2022-11-07 Karina Arias-Calluari , Theotime Colin , Tanya Latty , Mary Myerscough , Eduardo G. Altmann

Gene Regulatory Networks (GRNs) are intricate biological systems that control gene expression and regulation in response to environmental and developmental cues. Advances in computational biology, coupled with high throughput sequencing…

Machine Learning · Computer Science 2025-04-18 Akshata Hegde , Tom Nguyen , Jianlin Cheng

Emerging technologies, such as Blockchain and the Internet of Things (IoT), have had an immense role in propelling the agricultural industry towards the fourth agricultural revolution. Blockchain and IoT can greatly improve the…

Computers and Society · Computer Science 2022-12-08 David Cuellar , Zechariah Johnson

It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research…

Neural and Evolutionary Computing · Computer Science 2023-01-18 Jose Guadalupe Hernandez , Alexander Lalejini , Emily Dolson

With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…

Genomics · Quantitative Biology 2014-03-05 Dongying Wu , Guillaume Jospin , Jonathan A. Eisen

Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions-including those that have yet to be…

In an era of rapid climate change and its adverse effects on food production, technological intervention to monitor pollinator conservation is of paramount importance for environmental monitoring and conservation for global food security.…

Computer Vision and Pattern Recognition · Computer Science 2024-05-27 Ajay John Alex , Chloe M. Barnes , Pedro Machado , Isibor Ihianle , Gábor Markó , Martin Bencsik , Jordan J. Bird

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one from each of three putative centers of dog domestication,…

Big streams of Earth images from satellites or other platforms (e.g., drones and mobile phones) are becoming increasingly available at low or no cost and with enhanced spatial and temporal resolution. This thesis recognizes the…

Machine Learning · Computer Science 2022-11-24 Vasileios Sitokonstantinou

This paper provides a global picture about the deployment of networked processing services for genomic data sets. Many current research make an extensive use genomic data, which are massive and rapidly increasing over time. They are…

Distributed, Parallel, and Cluster Computing · Computer Science 2018-09-27 Gianluca Reali , Mauro Femminella , Emilia Nunzi , Dario Valocchi

Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…

Molecular Networks · Quantitative Biology 2008-02-14 Arend Hintze , Christoph Adami

Protein family design emerges as a promising alternative by combining the advantages of de novo protein design and mutation-based directed evolution.In this paper, we propose ProfileBFN, the Profile Bayesian Flow Networks, for specifically…

Biomolecules · Quantitative Biology 2025-02-25 Jingjing Gong , Yu Pei , Siyu Long , Yuxuan Song , Zhe Zhang , Wenhao Huang , Ziyao Cao , Shuyi Zhang , Hao Zhou , Wei-Ying Ma

It was reported that buffalo is a low susceptibility species resisting to prion diseases, which are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species. In molecular structures, TSE…

Biological Physics · Physics 2016-03-31 Jiapu Zhang , Feng Wang , Subhojyoti Chatterjee

Selected applications of novel techniques in Agricultural Biotechnology, Health Food formulations and Medical Biotechnology are being reviewed with the aim of unraveling future developments and policy changes that are likely to open new…

Other Quantitative Biology · Quantitative Biology 2007-05-23 I. C. Baianu , P. R. Lozano , V. I. Prisecaru , H. C. Lin

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…

Cryptography and Security · Computer Science 2015-03-19 Pierre Baldi , Roberta Baronio , Emiliano De Cristofaro , Paolo Gasti , Gene Tsudik

This survey investigates the transformative potential of various YOLO variants, from YOLOv1 to the state-of-the-art YOLOv10, in the context of agricultural advancements. The primary objective is to elucidate how these cutting-edge object…

Computer Vision and Pattern Recognition · Computer Science 2024-06-17 Mujadded Al Rabbani Alif , Muhammad Hussain

Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule…

Machine Learning · Computer Science 2026-03-10 Zihao Li , Zhichen Zeng , Xiao Lin , Feihao Fang , Yanru Qu , Zhe Xu , Zhining Liu , Xuying Ning , Tianxin Wei , Ge Liu , Hanghang Tong , Jingrui He

Feeding a larger and wealthier global population without transgressing ecological limits is increasingly challenging, as rising food demand (especially for animal products) intensifies pressure on ecosystems, accelerates deforestation, and…

Theoretical Economics · Economics 2025-10-17 Moretti Elia , Loreau Michel , Benzaquen Michael

Deep learning is catalyzing a scientific revolution fueled by big data, accessible toolkits, and powerful computational resources, impacting many fields including protein structural modeling. Protein structural modeling, such as predicting…

Biomolecules · Quantitative Biology 2020-07-17 Wenhao Gao , Sai Pooja Mahajan , Jeremias Sulam , Jeffrey J. Gray