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: gdtools

https://packages.ecosyste.ms/registries/pypi.org/packages/gdtools

GeneDock command-line client for interacting with GeneDock platform
1 version
Latest release: over 7 years ago
78 downloads last month

Papers Mentioning gdtools 18

Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes
Cited by: 22
Author(s): Pavla Debeljak, Ève Toulza, Sara Beier, Stéphane Blain, Ingrid Obernosterer
Software Mentions: 12
Published: over 5 years ago

10.1111/eva.13200

Evolution of honey resistance in experimental populations of bacteria depends on the type of honey and has no major side effects for antibiotic susceptibility
Cited by: 5
Author(s): Anna M. Bischofberger, Katia R. Pfrunder‐Cardozo, Michael Baumgärtner, Alex R. Hall
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-15-1039

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq
Cited by: 200
Author(s): Jeffrey E. Barrick, Geoffrey Colburn, Daniel E. Deatherage, Charles C. Traverse, Matthew D Strand, Jordan J Borges, David B. Knoester, Aaron Reba, Austin G. Meyer
Software Mentions: 4
Published: almost 11 years ago

10.15252/msb.202010189

Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion
Cited by: 15
Author(s): D. Konstantinidis, Filipa Pereira, Eva Maria Geissen, Kristina Grkovska, Eleni Kafkia, Paula Jouhten, Yong-Kyu Kim, Saravanan Devendran, Michael Zimmermann, Kiran Raosaheb Patil
Software Mentions: 3
Published: over 3 years ago

10.1093/gbe/evx104

Structured Populations of Sulfolobus acidocaldarius with Susceptibility to Mobile Genetic Elements
Cited by: 17
Author(s): R. Anderson, Angela Kouris, Christopher H. Seward, Kate M. Campbell, Rachel J. Whitaker
Software Mentions: 3
Published: over 7 years ago

10.3389/fbioe.2020.00129

Differential Contribution of the Parental Genomes to a S. cerevisiae × S. uvarum Hybrid, Inferred by Phenomic, Genomic, and Transcriptomic Analyses, at Different Industrial Stress Conditions
Cited by: 14
Author(s): María Lairón-Peris, Laura Pérez‐Través, Sara Muñiz-Calvo, José Manuel Guillamón, José María Heras, Eladio Barrio, Amparo Querol
Software Mentions: 3
Published: over 4 years ago

10.1128/mSystems.00202-19

Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence
Cited by: 12
Author(s): Muyoung Lee, Naina Adren Pinto, Chan Yeong Kim, Sunmo Yang, Roshan D’Souza, Dongeun Yong, Insuk Lee
Software Mentions: 3
Published: about 5 years ago

10.1002/ece3.5322

Disadvantages and benefits of evolved unicellularity versus multicellularity in budding yeast
Cited by: 23
Author(s): Jennie J. Kuzdzal‐Fick, Lin Chen, Gábor Balázsi
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2014.00468

Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq
Cited by: 74
Author(s): Daniel E. Deatherage, Charles C. Traverse, Lindsey N. Wolf, Jeffrey E. Barrick
Software Mentions: 3
Published: almost 10 years ago

10.1534/g3.120.401124

<i>Escherichia coli</i> with a Tunable Point Mutation Rate for Evolution Experiments
Cited by: 3
Author(s): Nicholas Sherer, Thomas E. Kuhlman
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.47088

Rapid decline of bacterial drug-resistance in an antibiotic-free environment through phenotypic reversion
Cited by: 47
Author(s): Anett Dunai, Réka Spohn, Zoltán Farkas, Viktória Lázár, Ádám Györkei, Gábor Apjok, Gábor Boross, Balázs Szappanos, Gábor Grézal, Anikó Faragó, László Bodai, Balázs Papp, Csaba Pál
Software Mentions: 2
Published: over 5 years ago

10.1186/s12862-017-0950-y

A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations
Cited by: 38
Author(s): Marie Marchal, Felix Goldschmidt, Selina N. Derksen-Müller, Sven Panke, Martin Ackermann, David R. Johnson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pbio.3001093

Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics
Cited by: 29
Author(s): Lucas A. Meirelles, Elena K. Perry, Megan Bergkessel, Dianne K. Newman
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pbio.3000579

Photosensing and quorum sensing are integrated to control Pseudomonas aeruginosa collective behaviors
Cited by: 39
Author(s): Sampriti Mukherjee, Matthew Jemielita, Vasiliki Stergioula, Mikhail Tikhonov, Bonnie L. Bassler
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0140489

Acinetobacter baumannii Repeatedly Evolves a Hypermutator Phenotype in Response to Tigecycline That Effectively Surveys Evolutionary Trajectories to Resistance
Cited by: 49
Author(s): Troy G. Hammerstrom, Kathryn Beabout, Thomas P. Clements, Gerda Saxer, Yousif Shamoo
Software Mentions: 2
Published: about 9 years ago

10.1093/g3journal/jkab192

The genetic basis of differential autodiploidization in evolving yeast populations
Cited by: 7
Author(s): Sudipta Tung, Christopher W Bakerlee, Angela M Phillips, Alex N Nguyen Ba, Michael M. Desai
Software Mentions: 2
Published: over 3 years ago

10.1128/mBio.03341-19

Obesity-Related Microenvironment Promotes Emergence of Virulent Influenza Virus Strains
Cited by: 82
Author(s): Rebekah Honce, Erik A. Karlsson, Nicholas Wohlgemuth, Leonardo Estrada, Victoria A. Meliopoulos, Jiangwei Yao, Stacey Schultz‐Cherry
Software Mentions: 2
Published: over 4 years ago

10.3390/antibiotics9040165

Advanced Resistance Studies Identify Two Discrete Mechanisms in Staphylococcus aureus to Overcome Antibacterial Compounds that Target Biotin Protein Ligase
Cited by: 3
Author(s): Andrew Hayes, Jiulia Satiaputra, Louise M. Sternicki, Ashleigh S. Paparella, Zikai Feng, Kwang J. Lee, Beatriz Blanco-Rodriguez, William Tieu, Bart A. Eijkelkamp, Keith E. Shearwin, Tara L. Pukala, Andrew D. Abell, Grant W. Booker, Steven W. Polyak
Software Mentions: 2
Published: over 4 years ago