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Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions.
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Enzyme Nomenclature · 1992
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Interactions among strategies associated with bacterial infection: pathogenicity, epidemicity, and antibiotic resistance
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Catabolite activator protein: Dna binding and transcription activation
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Vfdb: a reference database for bacterial virulence factors
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Influence of human genome polymorphism on gene expression
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Micrornas preferentially target the genes with high transcriptional regulation complexity
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An earth-system perspective of the global nitrogen cycle
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Atp synthase and the actions of inhibitors utilized to study its roles in human health, disease, and other scientific areas
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Global trends in emerging infectious diseases
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Patric: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species
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Classification of metagenomic sequences: methods and challenges
Sharmila S Mande, Monzoorul Haque Mohammed, and Tarini Shankar Ghosh · 2012
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Metagenomic microbial community profiling using unique clade-specific marker genes
Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, and Curtis Huttenhower · 2012
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The comprehensive antibiotic resistance database
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Analysis tool web services from the embl-ebi
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Redundancy of the genetic code enables translational pausing
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Card 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
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Tackling drug-resistant infections globally: final report and recommendations
Jim O’Neill · 2016
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Args-oap: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured arg-database
Ying Yang, Xiaotao Jiang, Benli Chai, Liping Ma, Bing Li, Anni Zhang, James R Cole, James M Tiedje, and Tong Zhang · 2016
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In defense of the triplet loss for person re-identification
Alexander Hermans, Lucas Beyer, and Bastian Leibe · 2017
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Duplication-correcting codes for data storage in the dna of living organisms
Siddharth Jain, Farzad Farnoud Hassanzadeh, Moshe Schwartz, and Jehoshua Bruck · 2017
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Ilya Loshchilov and Frank Hutter · 2017
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Bert: Pre-training of deep bidirectional transformers for language understanding
Diverse virus-encoded crispr-cas systems include streamlined genome editors
Basem Al-Shayeb, Petr Skopintsev, Katarzyna M Soczek, Elizabeth C Stahl, Zheng Li, Evan Groover, Dylan Smock, Amy R Eggers, Patrick Pausch, Brady F Cress, et al · 2022
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Horizontal gene transfer and adaptive evolution in bacteria
Brian J Arnold, I-Ting Huang, and William P Hanage · 2022
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Vibe: a hierarchical bert model to identify eukaryotic viruses using metagenome sequencing data
Ho-Jin Gwak and Mina Rho · 2022
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Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter
A Hoarfrost, A Aptekmann, G Farfañuk, and Y Bromberg · 2022
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Metagenomic discovery of novel crispr-cas13 systems
Yanping Hu, Yangcan Chen, Jing Xu, Xinge Wang, Shengqiu Luo, Bangwei Mao, Qi Zhou, and Wei Li · 2022
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Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova · 2018
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Deep learning models for bacteria taxonomic classification of metagenomic data
Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Giosue’ Lo Bosco, Giovanni Renda, Riccardo Rizzo, Salvatore Gaglio, and Alfonso Urso · 2018
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Using regulondb, the escherichia coli k-12 gene regulatory transcriptional network database
Heladia Salgado, Irma Martínez-Flores, Víctor H Bustamante, Kevin Alquicira-Hernández, Jair S García-Sotelo, Delfino García-Alonso, and Julio Collado-Vides · 2018
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Cnn-mgp: convolutional neural networks for metagenomics gene prediction
Amani Al-Ajlan and Achraf El Allali · 2019
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The biocyc collection of microbial genomes and metabolic pathways
Peter D Karp, Richard Billington, Ron Caspi, Carol A Fulcher, Mario Latendresse, Anamika Kothari, Ingrid M Keseler, Markus Krummenacker, Peter E Midford, Quang Ong, et al · 2019
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Ncycdb: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes
Qichao Tu, Lu Lin, Lei Cheng, Ye Deng, and Zhili He · 2019
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annonex2embl: automatic preparation of annotated dna sequences for bulk submissions to ena
Michael Gruenstaeudl · 2020
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Supervised contrastive learning
Prannay Khosla, Piotr Teterwak, Chen Wang, Aaron Sarna, Yonglong Tian, Phillip Isola, Aaron Maschinot, Ce Liu, and Dilip Krishnan · 2020
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Multimodal deep learning applied to classify healthy and disease states of human microbiome
Seung Jae Lee and Mina Rho · 2022
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Language models of protein sequences at the scale of evolution enable accurate structure prediction
Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Nikita Smetanin, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, et al · 2022
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Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation
Sijia Liu, Christina D Moon, Nan Zheng, Sharon Huws, Shengguo Zhao, and Jiaqi Wang · 2022
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Machine learning-aided engineering of hydrolases for pet depolymerization
Hongyuan Lu, Daniel J Diaz, Natalie J Czarnecki, Congzhi Zhu, Wantae Kim, Raghav Shroff, Daniel J Acosta, Bradley R Alexander, Hannah O Cole, Yan Zhang, et al · 2022
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Machine learning and deep learning applications in metagenomic taxonomy and functional annotation
Alban Mathieu, Mickael Leclercq, Melissa Sanabria, Olivier Perin, and Arnaud Droit · 2022
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Virtifier: a deep learning-based identifier for viral sequences from metagenomes
Yan Miao, Fu Liu, Tao Hou, and Yun Liu · 2022
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Deciphering microbial gene function using natural language processing
Danielle Miller, Adi Stern, and David Burstein · 2022
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Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution
Meng Yang, Lichao Huang, Haiping Huang, Hui Tang, Nan Zhang, Huanming Yang, Jihong Wu, and Feng Mu · 2022
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Genslms: Genome-scale language models reveal sars-cov-2 evolutionary dynamics
Maxim Zvyagin, Alexander Brace, Kyle Hippe, Yuntian Deng, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, et al · 2022
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Nucleic Acids Research
Uniprot: the universal protein knowledgebase in 2023 · 2023
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Long-read metagenomics paves the way toward a complete microbial tree of life
Mads Albertsen · 2023
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The nucleotide transformer: Building and evaluating robust foundation models for human genomics
Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza-Revilla, Nicolas Lopez Carranza, Adam Henryk Grzywaczewski, Francesco Oteri, Christian Dallago, Evan Trop, Bernardo P de Almeida, Hassan Sirelkhatim, et al · 2023
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Evolutionary-scale prediction of atomic-level protein structure with a language model
Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Nikita Smetanin, Robert Verkuil, Ori Kabeli, Yaniv Shmueli, et al · 2023
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Hyenadna: Long-range genomic sequence modeling at single nucleotide resolution
Eric Nguyen, Michael Poli, Marjan Faizi, Armin Thomas, Callum Birch-Sykes, Michael Wornow, Aman Patel, Clayton Rabideau, Stefano Massaroli, Yoshua Bengio, et al · 2023
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Unraveling the functional dark matter through global metagenomics
Georgios A Pavlopoulos, Fotis A Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N Ivanova, et al · 2023
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Metatransformer: deep metagenomic sequencing read classification using self-attention models
Alexander Wichmann, Etienne Buschong, André Müller, Daniel Jünger, Andreas Hildebrandt, Thomas Hankeln, and Bertil Schmidt · 2023
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Dnabert-2: Efficient foundation model and benchmark for multi-species genome
Zhihan Zhou, Yanrong Ji, Weijian Li, Pratik Dutta, Ramana Davuluri, and Han Liu · 2023
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