Ecosyste.ms: Papers

10.1186/s12864-015-2324-4

Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout
Cited by: 10
Author(s): Henrique César Pereira Figueiredo, Siomar C. Soares, Felipe Luiz Pereira, Fernanda Alves Dorella, Alex F. Carvalho, Júnia Pacheco Teixeira, Vasco Azevedo, Carlos Augusto Gomes Leal
Software Mentions: 6
Published: almost 9 years ago

10.1111/1751-7915.12006

Tips and tricks for the assembly of aCorynebacterium pseudotuberculosisgenome using a semiconductor sequencer
Cited by: 12
Author(s): Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Siomar de Castro Soares, Anderson Santos, Síntia Almeida, Luís Carlos Guimarães, Flávia Figueira, Eudes Guilherme Vieria Barbosa, Andreas Tauch, Vasco Azevedo, Artur M. S. Silva
Software Mentions: 4
Published: almost 12 years ago

10.1093/bib/bby042

Microbial genomic island discovery, visualization and analysis
Cited by: 59
Author(s): Claire Bertelli, Keith E Tilley, Fiona S. L. Brinkman
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1000349

Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin
Cited by: 63
Author(s): Jesse D. Bloom, Matthew Glassman
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pcbi.1006828

Scalable nonlinear programming framework for parameter estimation in dynamic biological system models
Cited by: 15
Author(s): Sungho Shin, Ophelia S. Venturelli, Ví­ctor M. Zavala
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-15-737

Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt
Cited by: 143
Author(s): Egon A. Ozer, Jonathan P. Allen, Alan R. Hauser
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0022201

A Computational-Experimental Approach Identifies Mutations That Enhance Surface Expression of an Oseltamivir-Resistant Influenza Neuraminidase
Cited by: 50
Author(s): Jesse D. Bloom, Jagannath S. Nayak, David Baltimore
Software Mentions: 3
Published: about 13 years ago

10.1128/genomeA.00038-16

Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated from the Abscess of a Goat in California
Cited by: 0
Author(s): Larissa Maranhão Dias, Jorianne Thyeska Castro Alves, Adonney Allan de Oliveira Veras, Rafael Azevedo Baraúna, Pablo Henrique Caracciolo Gomes de Sá, Sharon J. Spier, Judy M. Edman, Luís Carlos Guimarães, Flávia Souza Rocha, Rommel Thiago Jucá Ramos, Vasco Azevedo, Artur M. S. Silva, Adriana Ribeiro Carneiro
Software Mentions: 3
Published: over 8 years ago

10.3390/pathogens3010036

Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches
Cited by: 55
Author(s): Dongsheng Che, Mohammad Shabbir Hasan, Bernard Chen
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0152515

Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum
Cited by: 29
Author(s): Daniel Castillo, Rói Hammershaimb Christiansen, Inger Dalsgaard, Lone Madsen, Romilio T. Espejo, Mathias Middelboe
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0030848

PIPS: Pathogenicity Island Prediction Software
Cited by: 68
Author(s): Siomar C. Soares, Vinícius Augusto Carvalho de Abreu, Rommel Thiago Jucá Ramos, Louise Cerdeira, Artur M. S. Silva, Jan Baumbach, Eva Trost, Andreas Tauch, Raphael Hirata, Ana Luíza Mattos‐Guaraldi, Anderson Miyoshi, Vasco Azevedo
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0030938

SPPS: A Sequence-Based Method for Predicting Probability of Protein-Protein Interaction Partners
Cited by: 22
Author(s): Xinyi Liu, Bin Liu, Zhimin Huang, Ting Shi, Yingyi Chen, Jian Zhang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0053818

The Pan-Genome of the Animal Pathogen Corynebacterium pseudotuberculosis Reveals Differences in Genome Plasticity between the Biovar ovis and equi Strains
Cited by: 91
Author(s): Siomar C. Soares, Artur M. S. Silva, Eva Trost, Jochen Blom, Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Amjad Ali, Anderson Santos, Anne C. Pinto, Carlos Diniz, Eudes Guilherme Vieria Barbosa, Fernanda Alves Dorella, Flávia Figueira Aburjaile, Flávia Souza Rocha, Karina K F Nascimento, Luís Carlos Guimarães, Síntia Almeida, Syed Shah Hassan, Syeda Marriam Bakhtiar, Ulisses de Pádua Pereira, Vinícius Augusto Carvalho de Abreu, Maria Paula Cruz Schneider, Anderson Miyoshi, Andreas Tauch, Vasco Azevedo
Software Mentions: 2
Published: over 11 years ago

10.1016/j.csbj.2016.05.001

Computational methods for predicting genomic islands in microbial genomes
Cited by: 49
Author(s): Bingxin Lu, Hon Wai Leong
Software Mentions: 2
Published: over 8 years ago

10.5936/csbj.201303013

PROGRESSION OF ‘OMICS’ METHODOLOGIES FOR UNDERSTANDING THE PATHOGENICITY OF CORYNEBACTERIUM PSEUDOTUBERCULOSIS: THE BRAZILIAN EXPERIENCE
Cited by: 13
Author(s): Fernanda Alves Dorella, Alfonso Gala-García, Anne Cybelle Pinto, Boutros Sarrouh, Camila Azevedo Antunes, Débora da Silva Freitas Ribeiro, Flávia Figueira Aburjaile, Karina Fiaux, Luís Carlos Guimarães, Núbia Seyffert, Rachid A. El-Aouar, Renata Silva, Syed Shah Hassan, Thiago Luiz de Paula Castro, Wanderson S. Marques, Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Pablo de Sá, Anderson Miyoshi, Vasco Azevedo, Artur M. S. Silva
Software Mentions: 2
Published: over 11 years ago

10.3892/etm.2014.1728

Expression of hypoxia-inducible factor-1α, endothelin-1 and adrenomedullin in newborn rats with hypoxia-induced pulmonary hypertension
Cited by: 17
Author(s): Le Wang, Ying Zhou, Mingxia Li, Yan-Ping Zhu
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2016.01946

Intraclonal Genome Stability of the Metallo-β-lactamase SPM-1-producing Pseudomonas aeruginosa ST277, an Endemic Clone Disseminated in Brazilian Hospitals
Cited by: 32
Author(s): Ana Paula Barbosa do Nascimento, Mauro Freitas Ortiz, Willames M. B. S. Martins, Guilherme Loss de Morais, Lorena Cristina Corrêa Fehlberg, Luiz Gonzaga Paula de Almeida, Luciane Prioli Ciapina, Ana Cristina Gales, Ana Tereza Ribeiro de Vasconcelos
Software Mentions: 2
Published: almost 8 years ago

10.1128/genomeA.00586-13

Draft Genome Sequence of Pseudomonas plecoglossicida Strain NB2011, the Causative Agent of White Nodules in Large Yellow Croaker ( <i>Larimichthys crocea</i> )
Cited by: 23
Author(s): Zhijuan Mao, Meifang Li, Jigang Chen
Software Mentions: 2
Published: about 11 years ago

10.1128/genomeA.00176-16

Whole-Genome Sequence of Corynebacterium pseudotuberculosis 262 Biovar equi Isolated from Cow Milk
Cited by: 3
Author(s): Carlos Araújo, Larissa Maranhão Dias, Adonney Allan de Oliveira Veras, Jorianne Thyeska Castro Alves, Ana Lídia Queiroz Cavalcante, Christopher G. Dowson, Vasco Azevedo, Rommel Thiago Jucá Ramos, Artur M. S. Silva, Adriana Ribeiro Carneiro
Software Mentions: 2
Published: over 8 years ago

10.1186/s13012-018-0838-2

Testing implementation facilitation of a primary care-based collaborative care clinical program using a hybrid type III interrupted time series design: a study protocol
Cited by: 8
Author(s): Amanda M. Midboe, Steve Martino, Sarah L. Krein, Janet C. Frank, Jacob T. Painter, Michael J. Chandler, Allison Schroeder, Brenda T. Fenton, Lara Troszak, Taryn Erhardt, Robert D. Kerns, William C. Becker
Software Mentions: 2
Published: almost 6 years ago

10.1120/jacmp.v1i2.2645

Guide to clinical use of electronic portal imaging
Cited by: 24
Author(s): Michael Herman, Jon J. Kruse, C.R. Hagness
Software Mentions: 2
Published: over 24 years ago

10.1002/acm2.12301

Development of clinically relevant QA procedures for the BrainLab ExacTrac imaging system
Cited by: 1
Author(s): Ileana Iftimia, Per H. Halvorsen
Software Mentions: 2
Published: over 6 years ago

10.1002/acm2.12289

An evaluation of the stability of image quality parameters of Elekta X-ray volume imager and iViewGT imaging systems
Cited by: 3
Author(s): Dennis N. Stanley, Karl Rasmussen, Neil Kirby, Nikos Papanikolaou, Alonso N. Gutiérrez
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-1065

Label-free proteomic analysis to confirm the predicted proteome of Corynebacterium pseudotuberculosis under nitrosative stress mediated by nitric oxide
Cited by: 19
Author(s): Wanderson M. Silva, Rodrigo Dias de Oliveira Carvalho, Siomar C. Soares, Isabela Fs Bastos, Edson Luiz Folador, Gustavo H. M. F. Souza, Yves Le Loir, Anderson Miyoshi, Artur M. S. Silva, Vasco Azevedo
Software Mentions: 2
Published: almost 10 years ago

10.3390/s21051703

Noise-Resilient Acoustic Low Energy Beacon for Proximity-Based Indoor Positioning Systems
Cited by: 1
Author(s): Teodoro Aguilera, Fernando J. Aranda, Felipe Parralejo, Juan Diego Gutiérrez, José A. Moreno, F. Álvarez
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-16-S5-S7

Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology
Cited by: 10
Author(s): Luís Carlos Guimarães, Siomar de Castro Soares, Eva Trost, Jochen Blom, Rommel Thiago Jucá Ramos, Artur M. S. Silva, Debmalya Barh, Vasco Azevedo
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-16-S5-S9

An integrated structural proteomics approach along the druggable genome of Corynebacterium pseudotuberculosis species for putative druggable targets
Cited by: 24
Author(s): Leandro Radusky, Syed Shah Hassan, Esteban Lanzarotti, Sandeep Tiwari, Syed Babar Jamal, Ali Javed, Amjad Ali, Rafaela Salgado Ferreira, Debmalya Barh, Artur M. S. Silva, Adrián Turjanski, Vasco Azevedo
Software Mentions: 2
Published: over 9 years ago

10.1186/s12866-017-0925-6

A shift in the virulence potential of Corynebacterium pseudotuberculosis biovar ovis after passage in a murine host demonstrated through comparative proteomics
Cited by: 16
Author(s): Wanderson M. Silva, Fernanda Alves Dorella, Siomar C. Soares, Gustavo H. M. F. Souza, Thiago Luiz de Paula Castro, Núbia Seyffert, Henrique César Pereira Figueiredo, Anderson Miyoshi, Yves Le Loir, Artur M. S. Silva, Vasco Azevedo
Software Mentions: 2
Published: over 7 years ago

10.1186/s12891-015-0641-z

The Psychological Inflexibility in Pain Scale (PIPS) – validation, factor structure and comparison to the Chronic Pain Acceptance Questionnaire (CPAQ) and other validated measures in German chronic back pain patients
Cited by: 19
Author(s): Antonia Barke, Jenny Riecke, Winfried Rief, Julia Anna Glombiewski
Software Mentions: 2
Published: about 9 years ago

10.1155/2015/139580

Pan-Genome Analysis of Human Gastric Pathogen<i>H. pylori</i>: Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets
Cited by: 38
Author(s): Amjad Ali, Anam Naz, Siomar C. Soares, Marriam Bakhtiar, Sandeep Tiwari, Syed Shah Hassan, Fazal Hanan, Rommel Thiago Jucá Ramos, Ulisses de Pádua Pereira, Debmalya Barh, Henrique César Pereira Figueiredo, David W. Ussery, Anderson Miyoshi, Artur M. S. Silva, Vasco Azevedo
Software Mentions: 2
Published: over 9 years ago

10.1016/j.ymeth.2011.08.014

Computational approaches to selecting and optimising targets for structural biology
Cited by: 7
Author(s): Ian M. Overton, Geoffrey J. Barton
Software Mentions: 2
Published: about 13 years ago

10.1186/s13567-014-0106-7

Fine-tuned characterization of Staphylococcus aureus Newbould 305, a strain associated with mild and chronic mastitis in bovines
Cited by: 30
Author(s): Vincent Péton, Damien Bouchard, Síntia Almeida, Lucie Rault, Hélène Falentin, Julien Jardin, Gwénaël Jan, David Hernández, Patrice François, Jacques Schrenzel, Vasco Azevedo, Anderson Miyoshi, Nadejda Berkova, Sergine Even, Yves Le Loir
Software Mentions: 2
Published: almost 10 years ago