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Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…

Genomics · Quantitative Biology 2011-02-14 Gergely J Szöllősi , Vincent Daubin

In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of…

Populations and Evolution · Quantitative Biology 2021-03-23 Benjamin M Moran , Cheyenne Payne , Quinn Langdon , Daniel L Powell , Yaniv Brandvain , Molly Schumer

In recent years, machine learning has seen an increasing presencein a large variety of fields, especially in health care and bioinformatics.More specifically, the field where machine learning algorithms have found most applications is…

Neural and Evolutionary Computing · Computer Science 2020-08-21 Mekaal Swerhun , Jasmine Foley , Brandon Massop , Vijay Mago

Honey bees have been domesticated by humans for several thousand years and mainly provide honey and pollination, which is fundamental for plant reproduction. Nowadays, the work of beekeepers is constrained by external factors that stress…

Hardware Architecture · Computer Science 2020-10-29 Hugo Hadjur , Doreid Ammar , Laurent Lefèvre

Over the past several years, DNA sequencing has emerged as one of the driving forces in life-sciences, paving the way for affordable and accurate whole genome sequencing. As genomes represent the entirety of an organism's hereditary…

Cryptography and Security · Computer Science 2015-02-17 Emiliano De Cristofaro

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

Populations and Evolution · Quantitative Biology 2018-08-28 R. A. L. Elworth , H. A. Ogilvie , J. Zhu , L. Nakhleh

By 2050, the global population will exceed 9 billion, demanding a 70% increase in food production. Animal proteins alone may not suffice and contribute to global warming. Alternative proteins such as legumes, algae, and insects are being…

The current rate of species extinction is rapidly approaching unprecedented highs and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change and ecological collapse. The field of…

Populations and Evolution · Quantitative Biology 2022-10-12 João C Teixeira , Christian D Huber

Nutrigenomics is an emerging field that explores the intricate interaction between genes and diet. This study aimed to develop a comprehensive database to help clinicians and patients understand the connections between genetic disorders,…

Quantitative Methods · Quantitative Biology 2025-06-25 Fahmida Hai , Shriya Samudrala , Ijeoma Ezengwa , Rubayat Khan , Saif Nirzhor , Don Roosan

Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…

Quantitative Methods · Quantitative Biology 2024-11-04 Liang He , Peiran Jin , Yaosen Min , Shufang Xie , Lijun Wu , Tao Qin , Xiaozhuan Liang , Kaiyuan Gao , Yuliang Jiang , Tie-Yan Liu

Agriculture faces a growing challenge with wildlife wreaking havoc on crops, threatening sustainability. The project employs advanced object detection, the system utilizes the Mobile Net SSD model for real-time animal classification. The…

Computer Vision and Pattern Recognition · Computer Science 2024-07-02 Balaji VS , Mahi AR , Anirudh Ganapathy PS , Manju M

Recent years have witnessed major advances in the ability of computerized systems to track the positions of animals as they move through large and unconstrained environments. These systems have so far been a great boon in the fields of…

Neurons and Cognition · Quantitative Biology 2022-05-27 Brenna Knaebe , Claudia C. Weiss , Jan Zimmermann , Benjamin Y. Hayden

Manual observation and monitoring of individual cows for disease detection present significant challenges in large-scale farming operations, as the process is labor-intensive, time-consuming, and prone to reduced accuracy. The reliance on…

Machine Learning · Computer Science 2026-01-09 Rupsa Rani Mishra , D. Chandrasekhar Rao , Ajaya Kumar Tripathy

In response to the increasing global demand for food, feed, fiber, and fuel, digital agriculture is rapidly evolving to meet these demands while reducing environmental impact. This evolution involves incorporating data science, machine…

Computers and Society · Computer Science 2023-12-07 Ribana Roscher , Lukas Roth , Cyrill Stachniss , Achim Walter

Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…

Computational Engineering, Finance, and Science · Computer Science 2014-09-24 Bassam AlKindy , Jean-François Couchot , Christophe Guyeux , Arnaud Mouly , Michel Salomon , Jacques M. Bahi

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…

Molecular Networks · Quantitative Biology 2024-08-15 Rohan Shawn Sunil , Shan Chun Lim , Manoj Itharajula , Marek Mutwil

Diagnostic tests that can detect pre-clinical or sub-clinical infection, are one of the most powerful tools in our armoury of weapons to control infectious diseases. Considerable effort has been paid to improving diagnostic testing for…

Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…

Biomolecules · Quantitative Biology 2024-09-17 Boqiao Lai

Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…

Genomics · Quantitative Biology 2015-02-02 Keith R. Bradnam , Joseph N. Fass , Anton Alexandrov , Paul Baranay , Michael Bechner , İnanç Birol , Sébastien Boisvert , Jarrod A. Chapman , Guillaume Chapuis , Rayan Chikhi , Hamidreza Chitsaz , Wen-Chi Chou , Jacques Corbeil , Cristian Del Fabbro , T. Roderick Docking , Richard Durbin , Dent Earl , Scott Emrich , Pavel Fedotov , Nuno A. Fonseca , Ganeshkumar Ganapathy , Richard A. Gibbs , Sante Gnerre , Élénie Godzaridis , Steve Goldstein , Matthias Haimel , Giles Hall , David Haussler , Joseph B. Hiatt , Isaac Y. Ho , Jason Howard , Martin Hunt , Shaun D. Jackman , David B Jaffe , Erich Jarvis , Huaiyang Jiang , Sergey Kazakov , Paul J. Kersey , Jacob O. Kitzman , James R. Knight , Sergey Koren , Tak-Wah Lam , Dominique Lavenier , François Laviolette , Yingrui Li , Zhenyu Li , Binghang Liu , Yue Liu , Ruibang Luo , Iain MacCallum , Matthew D MacManes , Nicolas Maillet , Sergey Melnikov , Bruno Miguel Vieira , Delphine Naquin , Zemin Ning , Thomas D. Otto , Benedict Paten , Octávio S. Paulo , Adam M. Phillippy , Francisco Pina-Martins , Michael Place , Dariusz Przybylski , Xiang Qin , Carson Qu , Filipe J Ribeiro , Stephen Richards , Daniel S. Rokhsar , J. Graham Ruby , Simone Scalabrin , Michael C. Schatz , David C. Schwartz , Alexey Sergushichev , Ted Sharpe , Timothy I. Shaw , Jay Shendure , Yujian Shi , Jared T. Simpson , Henry Song , Fedor Tsarev , Francesco Vezzi , Riccardo Vicedomini , Jun Wang , Kim C. Worley , Shuangye Yin , Siu-Ming Yiu , Jianying Yuan , Guojie Zhang , Hao Zhang , Shiguo Zhou , Ian F. Korf

Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…

Biomolecules · Quantitative Biology 2021-09-29 Leonardo V. Castorina , Rokas Petrenas , Kartic Subr , Christopher W. Wood