Ecosyste.ms: Papers

10.3390/toxins12060414

Metabolic Traits of Bovine Shiga Toxin-Producing Escherichia coli (STEC) Strains with Different Colonization Properties
Cited by: 4
Author(s): Stefanie A. Barth, M. Weber, Katharina Schaufler, Christian Berens, Lutz Geue, Christian Menge
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0034846

Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics
Cited by: 152
Author(s): Lea A. I. Vaas, Johannes Sikorski, Victoria Michael, Markus Göker, Hans‐Peter Klenk
Software Mentions: 6
Published: over 12 years ago

10.3390/genes11111291

The Role of Salmonella Genomic Island 4 in Metal Tolerance of Salmonella enterica Serovar I 4,[5],12:i:- Pork Outbreak Isolate USDA15WA-1
Cited by: 13
Author(s): Bradley L. Bearson, Julian Trachsel, Daniel C. Shippy, Sathesh K Sivasankaran, B. J. Kerr, Crystal L. Loving, Brian W. Brunelle, Shelby M Curry, Nicholas K. Gabler, Shawn M. D. Bearson
Software Mentions: 6
Published: about 4 years ago

10.1155/2014/649453

Computational Approaches for Microalgal Biofuel Optimization: A Review
Cited by: 21
Author(s): Joseph Koussa, Amphun Chaiboonchoe, Kourosh Salehi‐Ashtiani
Software Mentions: 6
Published: almost 11 years ago

10.1186/s12864-019-5892-x

Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization
Cited by: 25
Author(s): Petya Berger, Ivan U. Kouzel, Michael Berger, Nadja Haarmann, Ulrich Dobrindt, Gerald B. Koudelka, Alexander Mellmann
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0235066

Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies
Cited by: 3
Author(s): Rose M. Collis, Patrick J. Biggs, Anne C. Midwinter, A. Springer Browne, David Wilkinson, Hamid Irshad, Nigel French, Gale Brightwell, Adrian L. Cookson
Software Mentions: 5
Published: over 4 years ago

10.1155/2014/914767

<i>Geodermatophilus poikilotrophi</i>sp. nov.: A Multitolerant Actinomycete Isolated from Dolomitic Marble
Cited by: 32
Author(s): María del Carmen Montero-Calasanz, Benjamin Hofner, Markus Göker, Manfred Rohde, Cathrin Spröer, Karima Hezbri, Maher Gtari, Peter Schümann, Hans‐Peter Klenk
Software Mentions: 4
Published: almost 11 years ago

10.3389/fmicb.2017.02501

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae
Cited by: 88
Author(s): María del Carmen Montero-Calasanz, Jan P. Meier‐Kolthoff, Dao‐Feng Zhang, Adnan Yaramis, Manfred Rohde, Tanja Woyke, Nikos C. Kyrpides, Peter Schümann, Wenjun Li, Markus Göker
Software Mentions: 3
Published: about 7 years ago

10.1128/mSphereDirect.00454-18

Most <i>Sinorhizobium meliloti</i> Extracytoplasmic Function Sigma Factors Control Accessory Functions
Cited by: 15
Author(s): Claus Lang, Melanie J. Barnett, Robert F. Fisher, Liane Smith, Michelle E. Diodati, Sharon R. Long
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2016.02003

Genome-Based Taxonomic Classification of Bacteroidetes
Cited by: 450
Author(s): Richard L. Hahnke, Jan P. Meier‐Kolthoff, Marina García-López, Supratim Mukherjee, Marcel Huntemann, Natalia Ivanova, Tanja Woyke, Nikos C. Kyrpides, Hans‐Peter Klenk, Markus Göker
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0171363

Two stable variants of Burkholderia pseudomallei strain MSHR5848 express broadly divergent in vitro phenotypes associated with their virulence differences
Cited by: 9
Author(s): April A. Shea, Robert C. Bernhards, Christopher K. Cote, C. J. Chase, Jeffrey W. Koehler, Christopher P. Klimko, Jason T. Ladner, David A. Rozak, Mark J. Wolcott, David P. Fetterer, Steven J. Kern, G. I. Koroleva, Sean Lovett, Gustavo Palacios, Ronald G. Toothman, Joel A. Bozue, Patricia L. Worsham, Susan L. Welkos
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0118392

Novel R Pipeline for Analyzing Biolog Phenotypic Microarray Data
Cited by: 26
Author(s): Minna Vehkala, M. A. Shubin, Thomas R. Connor, Nicholas R. Thomson, Jukka Corander
Software Mentions: 2
Published: almost 10 years ago

10.1038/s42003-021-02013-4

Ecological niche adaptation of Salmonella Typhimurium U288 is associated with altered pathogenicity and reduced zoonotic potential
Cited by: 13
Author(s): Mark Kirkwood, Prerna Vohra, Matt Bawn, Gaëtan Thilliez, Hannah Pye, Jennifer R. Tanner, Cosmin Chintoan-Uta, Priscilla Branchu, Liljana Petrovska, Timothy J. Dallman, Neil Hall, Mark P. Stevens, Robert A. Kingsley
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.00468

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria
Cited by: 1,516
Author(s): Anton Hördt, Marina García López, Jan P. Meier‐Kolthoff, Marcel Schleuning, Lisa-Maria Weinhold, Brian J. Tindall, Sabine Gronow, Nikos C. Kyrpides, Tanja Woyke, Markus Göker
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2019.00957

Variable Carbon Source Utilization, Stress Resistance, and Virulence Profiles Among Listeria monocytogenes Strains Responsible for Listeriosis Outbreaks in Switzerland
Cited by: 20
Author(s): Francis Muchaamba, Athmanya K. Eshwar, Marc J. A. Stevens, Ueli von Ah, Taurai Tasara
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.02083

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
Cited by: 1,241
Author(s): Marina García-López, Jan P. Meier‐Kolthoff, Brian J. Tindall, Sabine Gronow, Tanja Woyke, Nikos C. Kyrpides, Richard L. Hahnke, Markus Göker
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2020.01726

Evolution of Listeria monocytogenes During a Persistent Human Prosthetic Hip Joint Infection
Cited by: 6
Author(s): Francis Muchaamba, Athmanya K. Eshwar, Ueli von Ah, Marc J. A. Stevens, Taurai Tasara
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-12700-0

Co-inoculum of Beauveria brongniartii and B. bassiana shows in vitro different metabolic behaviour in comparison to single inoculums
Cited by: 15
Author(s): Loredana Canfora, Nadir Abu-Samra, Małgorzata Tartanus, B.H. Łabanowska, A. Benedetti, Flavia Pinzari, Eligio Malusà
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-17392-0

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential
Cited by: 74
Author(s): Lorena Carro, Imen Nouioui, Vartul Sangal, Jan P. Meier‐Kolthoff, Martha E. Trujillo, María del Carmen Montero-Calasanz, Nevzat Şahi̇n, Darren Smith, Kristi E Kim, Paul Peluso, Shweta Deshpande, Tanja Woyke, Nicole Shapiro, Nikos C. Kyrpides, Hans‐Peter Klenk, Markus Göker, Michael Goodfellow
Software Mentions: 2
Published: almost 7 years ago

10.4056/sigs.5179110

Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210T (= DSM 26640T = BS107T)
Cited by: 17
Author(s): Oliver Frank, Silke Pradella, Manfred Rohde, Carmen Scheuner, Hans‐Peter Klenk, Markus Göker, Joern Petersen
Software Mentions: 2
Published: over 10 years ago

10.1128/mBio.00903-19

Mice Fed an Obesogenic Western Diet, Administered Antibiotics, and Subjected to a Sterile Surgical Procedure Develop Lethal Septicemia with Multidrug-Resistant Pathobionts
Cited by: 34
Author(s): Sanjiv Hyoju, Alexander Zaborin, Robert Keskey, Anukriti Sharma, Wyatt Arnold, Fons van den Berg, Sangman Kim, Neil Gottel, Cindy Bethel, Angella Charnot-Katsikas, Jianxin Peng, Carleen M. E. M. Adriaansens, Esther Wang, Jack A. Gilbert, Olga Zaborina, John C. Alverdy
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0162276

Identifying Multiple Potential Metabolic Cycles in Time-Series from Biolog Experiments
Cited by: 3
Author(s): M. A. Shubin, Katharina Schaufler, Karsten Tedin, Minna Vehkala, Jukka Corander
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pntd.0008991

Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya
Cited by: 3
Author(s): Jessica Z. Kubicek-Sutherland, Gary Xie, Migun Shakya, Priya Dighe, Lindsey Jacobs, Hajnalka Daligault, Karen W. Davenport, Loreen R. Stromberg, Zachary R. Stromberg, Qing Cheng, Prakasha Kempaiah, John Michael Ong’echa, Vincent Otieno, Evans Raballah, Samuel B. Anyona, Collins Ouma, Patrick Chain, Douglas J Perkins, Harshini Mukundan, Benjamin H. McMahon, Norman A. Doggett
Software Mentions: 1
Published: almost 4 years ago

10.3390/cancers12113484

Evidences of a Direct Relationship between Cellular Fuel Supply and Ciliogenesis Regulated by Hypoxic VDAC1-ΔC
Cited by: 8
Author(s): Monique Meyenberg Cunha-de Padua, Lucilla Fabbri, Maeva Dufies, Sandra Lacas‐Gervais, Julie Contenti, Charles Voyton, Sofia Fazio, Marie Irondelle, Baharia Mograbi, Matthieu Rouleau, Nirvana Sadaghianloo, Amandine Rovini, Catherine Brenner, William J. Craigen, Jérôme Bourgeais, Olivier Hérault, Fréd́eric Bost, Nathalie M. Mazure
Software Mentions: 1
Published: about 4 years ago

10.1038/s41388-019-1069-y

Disruption of gap junctions attenuates acute myeloid leukemia chemoresistance induced by bone marrow mesenchymal stromal cells
Cited by: 31
Author(s): Farah Kouzi, Kazem Zibara, Jérôme Bourgeais, Frédéric Picou, Nathalie Gallay, Julie Brossaud, Hassan Dakik, Benjamin Roux, Sophie Hamard, Louis-Romée Le Nail, Rita Hleihel, Amélie Foucault, Noémie Ravalet, Florence Rouleux‐Bonnin, Fabrice Gouilleux, Frédéric Mazurier, Marie C. Béné, Haidar Akl, Emmanuel Gyan, Jorge Domenech, Marwan El-Sabban, Olivier Hérault
Software Mentions: 1
Published: about 5 years ago

10.3390/foods10010114

Potassium Lactate as a Strategy for Sodium Content Reduction without Compromising Salt-Associated Antimicrobial Activity in Salami
Cited by: 8
Author(s): Francis Muchaamba, Helena Stoffers, Ralf Blase, Ueli von Ah, Taurai Tasara
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-019-38789-z

Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil
Cited by: 32
Author(s): Lorena Carro, Jean Franco Castro, Valeria Razmilic, Imen Nouioui, Che Pan, José M. Igual, Marcel Jaspars, Michael Goodfellow, Alan T. Bull, Juan A. Asenjo, Hans Peter Klenk
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0122354

Phenotypic Profiling of Scedosporium aurantiacum, an Opportunistic Pathogen Colonizing Human Lungs
Cited by: 20
Author(s): Jashanpreet Kaur, Shu Yao Duan, Lea A. I. Vaas, Anahit Penesyan, Wieland Meyer, Ian T. Paulsen, Helena Nevalainen
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0073189

Phenotypic Variation in the Plant Pathogenic Bacterium Acidovorax citrulli
Cited by: 16
Author(s): Ram-Krishna Shrestha, Tally Rosenberg, Daria Makarovsky, Noam Eckshtain‐Levi, Einat Zelinger, June Kopelowitz, Johannes Sikorski, Saul Burdman
Software Mentions: 1
Published: over 11 years ago

10.4056/sigs.3096473

Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema
Cited by: 42
Author(s): Birte Abt, Markus Göker, Carmen Scheuner, Cliff Han, Megan Lu, Monica Misra, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan‐Fang Cheng, Roxanne Tapia, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Marcel Huntemann, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, Manfred Rohde, Stefan Spring, Sabine Gronow, John C. Detter, James Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Tanja Woyke, Hans Peter Klenk
Software Mentions: 1
Published: over 11 years ago

10.1099/mgen.0.000084

Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks
Cited by: 26
Author(s): Lauren A. Cowley, Timothy J. Dallman, Stephen Fitzgerald, Neil Irvine, Paul J. Rooney, Sean P. McAteer, Martin Day, Neil T. Perry, James L. Bono, Claire Jenkins, David L. Gally
Software Mentions: 1
Published: over 8 years ago

10.1186/1944-3277-9-2

Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy
Cited by: 379
Author(s): Jan P. Meier‐Kolthoff, Richard L. Hahnke, Jörn Petersen, Carmen Scheuner, Victoria Michael, Anne Fiebig, Christine Rohde, Manfred Rohde, Berthold Fartmann, Lynne Goodwin, Olga Chertkov, T. B. K. Reddy, Amrita Pati, Natalia Ivanova, Victor Markowitz, Nikos C. Kyrpides, Tanja Woyke, Markus Göker, Hans Peter Klenk
Software Mentions: 1
Published: about 10 years ago