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: cran: CGE
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/CGE
Computing General Equilibrium
8 versions
Latest release: over 4 years ago
1 dependent package
233 downloads last month
Papers Mentioning CGE 55
10.1186/s12866-019-1598-0
Characterization of Salmonella Dublin isolated from bovine and human hostsCited by: 35
Author(s): Narayan Paudyal, Hang Pan, Mohammed Elbediwi, Xiao Hua Zhou, Xianqi Peng, Xiaoliang Li, Weihuan Fang, Min Yue
Software Mentions: 15
Published: almost 5 years ago
10.3389/fmicb.2018.02077
Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the ChaosCited by: 237
Author(s): Alba Pérez-Cataluña, Nuria Salas-Massó, Ana L. Diéguez, Sabela Balboa, Alberto Lema, Jesús L. Romalde, María José Figueras
Software Mentions: 5
Published: about 6 years ago
10.1093/database/baz136
The COMPARE Data HubsCited by: 23
Author(s): Clara Amid, Nima Pakseresht, Nicole C. Silvester, Suran Jayathilaka, Ole Lund, Lukasz D. Dynovski, Bálint Ármin Pataki, Dávid Visontai, Basil Britto Xavier, Blaise T. F. Alako, Ariane Belka, Jose Luis Bellod Cisneros, Matthew Cotten, George B. Haringhuizen, Peter W. Harrison, Dirk W. Höper, Sam Holt, Camilla Hundahl, Abdulrahman Hussein, Rolf Sommer Kaas, Xin Liu, Rasko Leinonen, Surbhi Malhotra-Kumar, David F. Nieuwenhuijse, Nadim Rahman, Carolina dos S. Ribeiro, Jeffrey Edward Skiby, Dennis Schmitz, József Stéger, János M. Szalai-Gindl, Martin Christen Frølund Thomsen, Simone M. Cacciò, István Csabai, Annelies Kroneman, Marion Koopmans, Frank Møller Aarestrup, Guy Cochrane
Software Mentions: 4
Published: over 5 years ago
10.1186/s42522-020-0010-1
Typing methods based on whole genome sequencing dataCited by: 72
Author(s): Laura Uelze, Josephine Grützke, Maria Blettner, Jens A. Hammerl, Katharina Juraschek, Carlus Deneke, Simon H. Tausch, Burkhard Malorny
Software Mentions: 3
Published: over 4 years ago
10.3390/microorganisms9040707
Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated InfectionsCited by: 2
Author(s): J Christopher Noone, Fabienne Antunes Ferreira, Hege Vangstein Aamot
Software Mentions: 3
Published: over 3 years ago
10.1128/mSphere.00344-16
Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei with either Increased Virulence or Fluoroquinolone ResistanceCited by: 40
Author(s): Varvara K. Kozyreva, Guillaume Jospin, Alexander L. Greninger, James Watt, Jonathan A. Eisen, Vishnu Chaturvedi
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0239924
Clinical and molecular characteristics of carbapenem non-susceptible Escherichia coli: A nationwide survey from OmanCited by: 16
Author(s): Hissa Al-Farsi, Angela Camporeale, Karolina Ininbergs, Saleh Al-Azri, Zakariya Al-Muharrmi, Amina Al-Jardani, Christian G. Giske
Software Mentions: 3
Published: almost 4 years ago
10.3389/fmicb.2020.00549
Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial ResistanceCited by: 45
Author(s): Ashley Cooper, Andrew Low, Adam Koziol, Matthew C. Thomas, Daniel Leclair, Sandeep Tamber, Alex Wong, Burton W. Blais, Catherine D. Carrillo
Software Mentions: 3
Published: over 4 years ago
10.3389/fnbot.2016.00006
Design of Spiking Central Pattern Generators for Multiple Locomotion Gaits in Hexapod Robots by Christiansen Grammar EvolutionCited by: 20
Author(s): Andrés Espinal, Horacio Rostro-González, Martín Carpio, Erick Israel Guerra-Hernandez, Manuel Ornelas-Rodríguez, Marco Aurelio Sotelo-Figueroa
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pone.0157718
A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and SurveillanceCited by: 132
Author(s): Martin Christen Frølund Thomsen, Johanne Ahrenfeldt, Jose Luis Bellod Cisneros, Vanessa Isabell Jurtz, Mette Voldby Larsen, Henrik Hasman, Frank Møller Aarestrup, Ole Lund
Software Mentions: 3
Published: about 8 years ago
10.3389/fpubh.2019.00066
Clustering of Vibrio parahaemolyticus Isolates Using MLST and Whole-Genome Phylogenetics and Protein Motif FingerprintingCited by: 6
Author(s): Kelsey J. Jesser, Willy Valdivia-Granda, Jessica Jones, Rachel T. Noble
Software Mentions: 2
Published: over 5 years ago
10.3390/ijerph18168276
A Comprehensive Review on Types, Methods and Different Regions Related to Water–Energy–Food NexusCited by: 12
Author(s): Zeyang Bian, Dan Liŭ
Software Mentions: 2
Published: about 3 years ago
10.1038/s41598-019-56763-7
Meta-analysis of Pandemic Escherichia coli ST131 Plasmidome Proves Restricted Plasmid-clade AssociationsCited by: 36
Author(s): Kira Kondratyeva, Mali Salmon‐Divon, Shiri Navon-Venezia
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0169324
Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in ThailandCited by: 62
Author(s): Achiraya Siriphap, Pimlapas Leekitcharoenphon, Rolf Sommer Kaas, Chonchanok Theethakaew, Frank Møller Aarestrup, Orasa Sutheinkul, René S. Hendriksen
Software Mentions: 2
Published: over 7 years ago
10.3389/fmicb.2020.01134
Phenotypic Variation and Carbapenem Resistance Potential in OXA-499-Producing Acinetobacter pittiiCited by: 5
Author(s): Linyue Zhang, Ying Fu, Xinhong Han, Qingye Xu, Shanshan Weng, Biyong Yan, Lilin Liu, Xiaoting Hua, Yan Chen, Yunsong Yu
Software Mentions: 2
Published: over 4 years ago
10.1128/MRA.00990-18
Draft Genome Sequence of Salmonella enterica subsp. enterica Serotype Typhimurium Sequence Type 313, Isolated from IndiaCited by: 0
Author(s): Sohan Rodney Bangera, Shashikiran Umakanth, Asish K. Mukhopadhyay, Pimlapas Leekitcharoenphon, Goutam Chowdhury, René S. Hendriksen, Mamatha Ballal
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2020.622663
Whole-Genome Phylogenetic Analysis Reveals a Wide Diversity of Non-O157 STEC Isolated From Ground Beef and Cattle FecesCited by: 6
Author(s): Sebastián Gutiérrez, Leonela Díaz, Angélica Reyes-Jara, Xihua Yang, Jianghong Meng, Narjol González-Escalona, Mauricio Toro
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2019.02469
Genomic Characterization of Prevalent mcr-1, mcr-4, and mcr-5 Escherichia coli Within Swine Enteric Colibacillosis in SpainCited by: 29
Author(s): Isidro García-Meniño, Dafne Díaz-Jiménez, Vanesa García, María de Toro, Saskia-Camille Flament-Simon, Jorge Blanco, Azucena Mora
Software Mentions: 1
Published: almost 5 years ago
10.3389/fmicb.2020.609280
Variable Release of Lipoteichoic Acid From Staphylococcus aureus Bloodstream Isolates Relates to Distinct Clinical Phenotypes, Strain Background, and Antibiotic ExposureCited by: 1
Author(s): Marquerita Algorri, Peter Jorth, Annie Wong-Beringer
Software Mentions: 1
Published: over 3 years ago
10.3389/fmicb.2018.01880
Colistin Resistance Mediated by mcr-1 in ESBL-Producing, Multidrug Resistant Salmonella Infantis in Broiler Chicken Industry, Italy (2016–2017)Cited by: 39
Author(s): Virginia Carfora, Patricia Alba, Pimlapas Leekitcharoenphon, Daniele Ballarò, Gessica Cordaro, P. Di Matteo, Valentina Donati, Angela Ianzano, Manuela Iurescia, Fiorentino Stravino, Tania Tagliaferri, Antonio Battisti, Alessia Franco
Software Mentions: 1
Published: about 6 years ago
10.3389/fmicb.2020.604067
Characterization of the Complete Nucleotide Sequences of mcr-1-Encoding Plasmids From Enterobacterales Isolates in Retailed Raw Meat Products From the Czech RepublicCited by: 17
Author(s): Markéta Zelendová, Costas C. Papagiannitsis, Adam Valček, Matej Medvecký, Ibrahim Bitar, Jaroslav Hrabák, Tereza Gelbíčová, Alžběta Baráková, Iva Kutilová, Renata Karpíšková, Monika Dolejská
Software Mentions: 1
Published: over 3 years ago
10.3389/fmicb.2019.01657
Commonality of Multidrug-Resistant Klebsiella pneumoniae ST348 Isolates in Horses and Humans in PortugalCited by: 10
Author(s): Filipa Trigo da Roza, Natacha Couto, C. Carneiro, Eva Cunha, Teresa da Silva Rosa, Mariana Magalhães, Luís Tavares, Ângela Novais, Luı́sa Peixe, John W. A. Rossen, L. P. Lamas, Manuela Oliveira
Software Mentions: 1
Published: about 5 years ago
10.3389/fmicb.2020.629189
Genomic Investigation of Virulence Potential in Shiga Toxin Escherichia coli (STEC) Strains From a Semi-Hard Raw Milk CheeseCited by: 4
Author(s): Claudia Cortimiglia, Maria Francesca Borney, Daniela Bassi, Pier Sandro Cocconcelli
Software Mentions: 1
Published: over 3 years ago
10.3389/fmicb.2019.02119
Antibiotic-Induced, Increased Conjugative Transfer Is Common to Diverse Naturally Occurring ESBL Plasmids in Escherichia coliCited by: 48
Author(s): Gang Liu, Karolina Bogaj, Valeria Bortolaia, John Elmerdahl Olsen, Line Elnif Thomsen
Software Mentions: 1
Published: about 5 years ago
10.3389/fmicb.2021.656223
Antimicrobial Resistance Glides in the Sky—Free-Living Birds as a Reservoir of Resistant Escherichia coli With Zoonotic PotentialCited by: 31
Author(s): Magdalena Skarżyńska, Magdalena Zaja C, Arkadiusz Bomba, Łukasz Bocian, W. Kozdruń, Marcin Polak, Jarosław Wia Cek, Dariusz Wasyl
Software Mentions: 1
Published: over 3 years ago
10.1186/s13099-016-0119-z
Genome sequence of OXA-23 producing Acinetobacter baumannii IHIT7853, a carbapenem-resistant strain from a cat belonging to international clone IC1Cited by: 22
Author(s): Christa Ewers, Peter Klotz, Sandra Scheufen, Ursula Leidner, Stephan Göttig, Torsten Semmler
Software Mentions: 1
Published: about 8 years ago
10.1128/JCM.00422-16
Phenotypic H-Antigen Typing by Mass Spectrometry Combined with Genetic Typing of H Antigens, O Antigens, and Toxins by Whole-Genome Sequencing Enhances Identification of Escherichia coli IsolatesCited by: 4
Author(s): Keding Cheng, Huixia Chui, Larissa Domish, Angela Sloan, Drexler Hernandez, Stuart McCorrister, Alyssia Robinson, Matthew Walker, Lorea Peterson, Miles R. Majcher, Sam Ratnam, David Haldane, Sadjia Békal, John Wylie, Linda Chui, Shaun Tyler, Bingying Xu, Aleisha Reimer, Céline Nadon, J. David Knox, Gehua Wang
Software Mentions: 1
Published: about 8 years ago
10.1128/JCM.01269-20
<i>In Silico</i> Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing DataCited by: 141
Author(s): Anna Maria Malberg Tetzschner, James R. Johnson, Brian Johnston, Ole Lund, Flemming Scheutz
Software Mentions: 1
Published: almost 4 years ago
10.1038/srep15587
High-throughput genotyping of CRISPR/Cas9-mediated mutants using fluorescent PCR-capillary gel electrophoresisCited by: 73
Author(s): Muhammad Khairul Ramlee, Tingdong Yan, Alice Cheung, Charles Chuah, Shang Li
Software Mentions: 1
Published: almost 9 years ago
10.1038/srep19437
Gel electrophoresis in a polyvinylalcohol coated fused silica capillary for purity assessment of modified and secondary-structured oligo- and polyribonucleotidesCited by: 8
Author(s): Martyna Barciszewska, Agnieszka Sucha, Sandra Bałabańska, Marcin K. Chmielewski
Software Mentions: 1
Published: over 8 years ago
10.1038/s41598-020-65632-7
Complete genome sequence of a methicillin-resistant Staphylococcus lugdunensis strain and characteristics of its staphylococcal cassette chromosome mecCited by: 7
Author(s): Rie Shibuya, Yuki Uehara, Tadashi Baba, Kuniko Teruya, Kazuhito Satou, Takashi Hirano, Teruo Kirikae, Kazumasa Hiramatsu
Software Mentions: 1
Published: over 4 years ago
10.1155/2014/148479
CGE Simulation Analysis on the Labor Transfer, Agricultural Technical Progress, and Economic Development in ChongqingCited by: 1
Author(s): Heng Wang, Maosheng Ran
Software Mentions: 1
Published: over 10 years ago
10.1128/mSphere.00517-17
<i>In Situ</i> Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio choleraeCited by: 12
Author(s): Yasmin Begum, Hanna Rydberg, Kaisa Thorell, Young-Keun Kwak, Lei Sun, Enrique Joffré, Firdausi Qadri, Åsa Sjöling
Software Mentions: 1
Published: over 6 years ago
10.1186/s13568-018-0646-8
Genetic characterization of extraintestinal Escherichia coli isolates from chicken, cow and swineCited by: 11
Author(s): Li Chen, Leyi Wang, Afrah Kamal Yassin, Jilei Zhang, Jicheng Gong, Kezong Qi, Roman R. Ganta, Yuanyuan Zhang, Yi Yang, Xiangan Han, Chengming Wang
Software Mentions: 1
Published: about 6 years ago
10.1038/s41396-018-0200-3
Dissemination and persistence of extended-spectrum cephalosporin-resistance encoding IncI1-blaCTXM-1 plasmid among Escherichia coli in pigsCited by: 47
Author(s): Sam Abraham, Roy N. Kirkwood, Tanya Laird, Sugiyono Saputra, Tahlia Mitchell, Mandeep Singh, Benjamin Linn, Rebecca Abraham, Stanley Pang, David M. Gordon, Darren J. Trott, Mark O’Dea
Software Mentions: 1
Published: over 6 years ago
10.7150/jgen.58823
Genetic Diversity of Clinical Bordetella Pertussis ST2 Strains in comparison with Vaccine Reference Strains of IndiaCited by: 1
Author(s): Neetu Sharma, Shalini Anandan, Naveen Kumar Devanga Ragupathi, Dhiviya Prabaa Muthuirulandi Sethuvel, Karthick Vasudevan, Dhirendra Kumar, Sushil K. Gupta, Lucky Sangal, Balaji Veeraraghavan
Software Mentions: 1
Published: over 3 years ago
10.3390/ijerph18030937
Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates from Jurong Lake, Singapore with Whole-Genome-SequencingCited by: 13
Author(s): Zhong Yang, Siyao Guo, Kelyn Lee Ghee Seow, Glendon Ong Hong Ming, Jørgen Schlundt
Software Mentions: 1
Published: over 3 years ago
10.3390/ijms22179381
Antimicrobial Resistance and Whole-Genome Characterisation of High-Level Ciprofloxacin-Resistant Salmonella Enterica Serovar Kentucky ST 198 Strains Isolated from Human in PolandCited by: 4
Author(s): Tomasz Wołkowicz, Katarzyna Zacharczuk, Rafał Gierczyński, Magdalena Nowakowska, Katarzyna Piekarska
Software Mentions: 1
Published: about 3 years ago
10.1128/mSphere.00337-18
<i>Escherichia coli</i> Sequence Type 410 Is Causing New International High-Risk ClonesCited by: 154
Author(s): Louise Roer, Søren Overballe‐Petersen, Frank Hansen, Kristian Schønning, Mikala Wang, Bent Røder, Dennis Schrøder Hansen, Ulrik Stenz Justesen, Leif Percival Andersen, David Fulgsang-Damgaard, Katie L. Hopkins, Neil Woodford, Linda Falgenhauer, Trinad Chakraborty, Ørjan Samuelsen, Karin Sjöström, Thor Bech Johannesen, Kim Lee Ng, Jens Nielsen, Steen Ethelberg, Marc Stegger, Anette M. Hammerum, Henrik Hasman
Software Mentions: 1
Published: about 6 years ago
10.1099/acmi.0.000061
Shiga toxin-producing Escherichia coli O26:H11 associated with a cluster of haemolytic uraemic syndrome cases in South Africa, 2017Cited by: 6
Author(s): Anthony M. Smith, Nomsa P. Tau, John Bosco Kalule, Mark P. Nicol, Mignon McCulloch, Charlene Jacobs, Kerrigan McCarthy, Arshad Ismail, Mushal Allam, Jackie Kleynhans
Software Mentions: 1
Published: almost 5 years ago
10.3390/ani11082388
Diversity of Non-O157 Shiga Toxin-Producing Escherichia coli Isolated from Cattle from Central and Southern ChileCited by: 3
Author(s): Leonela Díaz, Sebastián Gutiérrez, Andrea I. Moreno Switt, Luis Pablo Hervé, Christopher Hamilton‐West, Nora Lía Padola, Paola Navarrete, Angélica Reyes-Jara, Jianghong Meng, Narjol González-Escalona, Mauricio Toro
Software Mentions: 1
Published: about 3 years ago
10.3390/antibiotics10030244
High Risk Clone: A Proposal of Criteria Adapted to the One Health Context with Application to Enterotoxigenic Escherichia coli in the Pig PopulationCited by: 9
Author(s): Maud de Lagarde, Ghyslaine Vanier, Julie Arsenault, John M. Fairbrother
Software Mentions: 1
Published: over 3 years ago
10.1186/s13756-021-00930-x
Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environmentsCited by: 49
Author(s): Mabel Kamweli Aworh, J. K. P. Kwaga, René S. Hendriksen, Emmanuel C. Okolocha, Siddhartha Thakur
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-018-5100-4
Comparative genome analysis provides deep insights into Aeromonas hydrophila taxonomy and virulence-related factorsCited by: 23
Author(s): Furqan Awan, Yuhao Dong, Lan Jin, Nannan Wang, Muhammad Mushtaq, Lu Chen, Yongjie Liu
Software Mentions: 1
Published: almost 6 years ago
10.3390/pathogens10080966
Detection and Characterization of Clinical Bordetella trematum Isolates from Chronic WoundsCited by: 4
Author(s): Christian Buechler, Claudio Neidhöfer, Thorsten Hornung, Marcel Neuenhoff, Marijo Parčina
Software Mentions: 1
Published: about 3 years ago
10.1371/currents.outbreaks.1bb3e36e74bd5779bc43ac3a8dae52e6
Laboratory Investigation of Salmonella enterica serovar Poona Outbreak in California: Comparison of Pulsed-Field Gel Electrophoresis (PFGE) and Whole Genome Sequencing (WGS) ResultsCited by: 13
Author(s): Varvara K. Kozyreva, John Crandall, Ashley Sabol, Alyssa Poe, Peng Zhang, Jeniffer Concepción-Acevedo, Morgan N Schroeder, Darlene Wagner, Jeffrey Higa, Eija Trees, Vishnu Chaturvedi
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0210735
Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, BoliviaCited by: 31
Author(s): Jessica Guzman-Otazo, Lucia Gonzales-Silès, Violeta Poma, Johan Bengtsson‐Palme, Kaisa Thorell, Carl-Fredrik Flach, Volga Iñiguez, Åsa Sjöling
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0176938
Genotypic and phenotypic characterization of multidrug resistant Salmonella Typhimurium and Salmonella Kentucky strains recovered from chicken carcassesCited by: 15
Author(s): Rizwana Tasmin, Nur A. Hasan, Christopher J. Grim, Ar’Quette Grant, Seon Young Choi, Mohammad Samiul Alam, Rebecca Bell, Christopher Cavanaugh, Kannan V. Balan, Uma S. Babu, Salina Parveen
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0178623
The genetic diversity of commensal Escherichia coli strains isolated from non-antimicrobial treated pigs varies according to age groupCited by: 33
Author(s): Shahana Ahmed, John Elmerdahl Olsen, Ana Herrero-Fresno
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0169445
Genetic Attributes of E. coli Isolates from Chlorinated Drinking WaterCited by: 13
Author(s): Michaela D. J. Blyton, David M. Gordon
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0144884
Energy Structure and Energy Security under Climate Mitigation Scenarios in ChinaCited by: 14
Author(s): Kousuke Matsumoto
Software Mentions: 1
Published: almost 9 years ago
10.1186/1747-1028-5-17
A software solution for recording circadian oscillator features in time-lapse live cell microscopyCited by: 21
Author(s): Daniel Sage, Michaël Unser, Patrick Salmon, Charna Dibner
Software Mentions: 1
Published: over 14 years ago
10.3389/fmicb.2019.02132
Emergence and Characterization of a Novel IncP-6 Plasmid Harboring blaKPC–2 and qnrS2 Genes in Aeromonas taiwanensis IsolatesCited by: 16
Author(s): Xinjun Hu, Yu X, Yibing Shang, Hao Xu, Lan-Ping Guo, Yile Liang, Yixin Kang, Li Song, Jifeng Sun, Yue Feng, Yimin Mao, Beiwen Zheng
Software Mentions: 1
Published: about 5 years ago
10.3389/fmicb.2019.00901
Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, TanzaniaCited by: 13
Author(s): Yaovi Mahuton Gildas Hounmanou, Pimlapas Leekitcharoenphon, René S. Hendriksen, Victorien Dougnon, Robinson H. Mdegela, John Elmerdahl Olsen, Anders Dalsgaard
Software Mentions: 1
Published: over 5 years ago
10.3389/fmicb.2017.00263
A Novel pAA Virulence Plasmid Encoding Toxins and Two Distinct Variants of the Fimbriae of Enteroaggregative Escherichia coliCited by: 16
Author(s): Rie Jønsson, Carsten Struve, Erik J. Boll, Nadia Boisen, Katrine Grimstrup Joensen, Camilla Adler Sørensen, Bo Jensen, Flemming Scheutz, Håvard Jenssen, Karen A. Krogfelt
Software Mentions: 1
Published: over 7 years ago