Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: DeepARG
https://packages.ecosyste.ms/registries/pypi.org/packages/DeepARG
3 versions
Latest release: about 4 years ago
59 downloads last month
Papers Mentioning DeepARG 25
10.3389/fmicb.2020.01376
Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?Cited by: 28
Author(s): Ilya B. Slizovskiy, Kingshuk Mukherjee, Christopher Dean, Christina Boucher, Noelle Noyes
Software Mentions: 8
Published: over 4 years ago
10.1038/s41598-019-50686-z
Antimicrobial Resistance Prediction for Gram-Negative Bacteria via Game Theory-Based Feature EvaluationCited by: 22
Author(s): Abu Sayed Chowdhury, Douglas R. Call, Shira L. Broschat
Software Mentions: 7
Published: about 5 years ago
10.1186/s40168-020-00993-9
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic dataCited by: 61
Author(s): Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz‐Buschart, Cédric Christian Laczny, Patrick May, Paul Wilmes
Software Mentions: 7
Published: over 3 years ago
10.1186/s40168-021-01006-z
Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genesCited by: 26
Author(s): Ishi Keenum, Robert Williams, Partha Pratim Ray, Emily Garner, Katharine F. Knowlton, Amy Pruden
Software Mentions: 6
Published: over 3 years ago
10.3389/fmicb.2020.00052
sraX: A Novel Comprehensive Resistome Analysis ToolCited by: 14
Author(s): Leonardo G. Panunzi
Software Mentions: 5
Published: over 4 years ago
10.1093/gigascience/giaa046
Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samplesCited by: 49
Author(s): Rafael R. C. Cuadrat, Maria Sorokina, Bruno de Bezerril Andrade, Tobias Goris, Alberto M. R. Dávila
Software Mentions: 5
Published: over 4 years ago
10.3390/antibiotics10040419
Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian HospitalCited by: 3
Author(s): Tiago Cabral Borelli, Gabriel Lencioni Lovate, Ana Flavia Tonelli Scaranello, Lucas F. Ribeiro, Livia S. Zaramela, Felipe Marcelo Pereira-dos-Santos, Rafael Silva‐Rocha, María‐Eugenia Guazzaroni
Software Mentions: 5
Published: over 3 years ago
10.3389/fmicb.2020.00322
Metatranscriptomics Reveals Antibiotic-Induced Resistance Gene Expression in the Murine Gut MicrobiotaCited by: 11
Author(s): Benjamin J. Korry, Damien J. Cabral, Peter Belenky
Software Mentions: 4
Published: over 4 years ago
10.1186/s40168-019-0703-9
NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomesCited by: 62
Author(s): Gustavo Arango-Argoty, Dongjuan Dai, Amy Pruden, Peter J. Vikesland, Lenwood S. Heath, Liqing Zhang
Software Mentions: 3
Published: over 5 years ago
10.1186/s40168-018-0401-z
DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic dataCited by: 394
Author(s): Gustavo Arango-Argoty, Emily Garner, Amy Pruden, Lenwood S. Heath, Peter J. Vikesland, Liqing Zhang
Software Mentions: 3
Published: almost 7 years ago
10.3389/fmicb.2020.00932
Impact of Microbiota Transplant on Resistome of Gut Microbiota in Gnotobiotic Piglets and Human SubjectsCited by: 10
Author(s): Liu Hu, Hua H. Wang
Software Mentions: 3
Published: over 4 years ago
10.3390/ijerph16244896
Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal HusbandryCited by: 10
Author(s): Na Li, Chong Liu, Zhiguo Zhang, Hongna Li, Tingting Song, Ting Liang, Binxu Li, Luyao Li, Shuo Feng, Qianqian Su, Jing Ye, Changliang Zhu
Software Mentions: 2
Published: almost 5 years ago
10.3390/antibiotics8010008
The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and TechnologiesCited by: 61
Author(s): Pavan K. Mantravadi, Karunakaran A. Kalesh, Renwick C. J. Dobson, André O. Hudson, Anutthaman Parthasarathy
Software Mentions: 2
Published: almost 6 years ago
10.3389/fmicb.2019.01722
Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease OutbreaksCited by: 20
Author(s): Baiba Vilne, Irēna Meistere, Lelde Grantiņa-Ieviņa, Juris Ķibilds
Software Mentions: 2
Published: over 5 years ago
10.1128/mSphere.00346-18
Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted RiverCited by: 11
Author(s): Aneisha M. Collins-Fairclough, Rebecca Co, Melessa C. Ellis, Laura A. Hug
Software Mentions: 2
Published: about 6 years ago
10.3389/fgene.2020.563975
Current Trends in Experimental and Computational Approaches to Combat Antimicrobial ResistanceCited by: 10
Author(s): Madangchanok Imchen, Jamseel Moopantakath, Ranjith Kumavath, Debmalya Barh, Sandeep Tiwari, Preetam Ghosh, Vasco Azevedo
Software Mentions: 1
Published: almost 4 years ago
10.3389/fmicb.2021.603967
Techniques Used for Analyzing Microplastics, Antimicrobial Resistance and Microbial Community Composition: A Mini-ReviewCited by: 16
Author(s): Simona Bartkova, Anne Kahru, Margit Heinlaan, Ott Scheler
Software Mentions: 1
Published: over 3 years ago
10.1186/s40168-021-01002-3
HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genesCited by: 40
Author(s): Yu Li, Zeling Xu, Wenkai Han, Huiluo Cao, Ramzan Umarov, Aixin Yan, Ming Fan, Huan Chen, Carlos M. Duarte, Lihua Li, Pak-Leung Ho, Xin Gao
Software Mentions: 1
Published: over 3 years ago
10.3389/fmicb.2020.01319
Antibiotic Administration Routes and Oral Exposure to Antibiotic Resistant Bacteria as Key Drivers for Gut Microbiota Disruption and Resistome in PoultryCited by: 20
Author(s): Yang Zhou, Yu Liu, Lu Zhang, Zhongliang Wu, Ying Huang, Yan He, Jun Zhong, Li J. Wang, Hafiz M. Abdullah, Hua H. Wang
Software Mentions: 1
Published: over 4 years ago
10.3390/antibiotics9050251
Antimicrobial Resistance Profiles of Adherent Invasive Escherichia coli Show Increased Resistance to β-LactamsCited by: 9
Author(s): Margarita Martínez-Medina, Francesco Strozzi, Belén Ruiz del Castillo, Natalia Serrano‐Morillas, Núria Ferrer-Bustins, Luis Martínez-Martínez
Software Mentions: 1
Published: over 4 years ago
10.1128/MRA.00003-20
Identification of Metagenome-Assembled Genomes Containing Antimicrobial Resistance Genes, Isolated from an Advanced Water Treatment FacilityCited by: 5
Author(s): Blake W. Stamps, John R. Spear
Software Mentions: 1
Published: over 4 years ago
10.1128/MRA.00279-20
Complete Genome Sequence of Escherichia coli GW-AmxH19, Isolated from Hospital Wastewater in Greifswald, GermanyCited by: 0
Author(s): Dominik Schneider, Daniela Zühlke, Tabea Petscheleit, Anja Poehlein, Katharina Riedel, Rolf Daniel
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-020-65981-3
BacEffluxPred: A two-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteinsCited by: 12
Author(s): Deeksha Pandey, Bandana Kumari, Neelja Singhal, Manish Kumar
Software Mentions: 1
Published: over 4 years ago
10.3389/fgene.2021.564186
Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility VariationCited by: 3
Author(s): Simone Marini, Marco Antônio Oliva, Ilya B. Slizovskiy, Noelle Noyes, Christina Boucher, Mattia Prosperi
Software Mentions: 1
Published: almost 4 years ago
10.3389/fmicb.2021.634511
Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and TreatmentCited by: 128
Author(s): Laura Judith Marcos-Zambrano, Kanita Karađuzović-Hadžiabdić, Tatjana Lončar-Turukalo, Piotr Przymus, Vladimir Trajkovik, Oliver Aasmets, Magali Berland, Aleksandra Gruca, Jasminka Hasic, Karel Hron, Thomas Klammsteiner, Mikhail Kolev, Leo Lahti, Marta B. Lopes, Vı́ctor Moreno, Irina Naskinova, Elin Org, Inês Paciência, Γεώργιος Παπουτσόγλου, Rajesh Shigdel, Blaž Stres, Baiba Vilne, Malik Yousef, Eftim Zdravevski, Ioannis Tsamardinos, Enrique Carrillo de Santa Pau, Marcus J. Claesson, Isabel Moreno-Indias, Jaak Truu
Software Mentions: 1
Published: over 3 years ago