bioconductor: MIRA | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0090914

How to Kill the Honey Bee Larva: Genomic Potential and Virulence Mechanisms of Paenibacillus larvae
Cited by: 88
Author(s): Marvin Djukic, Elżbieta Brzuszkiewicz, Anne Fünfhaus, Jörn Voss, Kathleen Gollnow, Lena Poppinga, Heiko Liesegang, Eva Garcia‐Gonzalez, Elke Genersch, Rolf Daniel
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0112617

Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome
Cited by: 21
Author(s): Nicolas Tchitchek, David Safronetz, Angela L. Rasmussen, Craig Martens, Kimmo Virtaneva, Stephen F. Porcella, Heinz Feldmann, Hideki Ebihara, Michael G. Katze
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0177896

Genomic abundance is not predictive of tandem repeat localization in grass genomes
Cited by: 4
Author(s): Paul Bilinski, Yonghua Han, Matthew B. Hufford, Anne Lorant, Pingdong Zhang, Matt C. Estep, Jiming Jiang, Jeffrey Ross‐Ibarra
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0067221

Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya
Cited by: 71
Author(s): Yury M. Shtarkman, Zeynep A. Koçer, Robyn Edgar, Ram Veerapaneni, Tom D’Elia, Paul F. Morris, Scott O. Rogers
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0055090

Transcriptome Analysis of Cytokinin Response in Tomato Leaves
Cited by: 33
Author(s): Xiulin Shi, S. Dutta Gupta, Ingrid Lindquist, Connor Cameron, Joann Mudge, Aaron M. Rashotte
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0083823

In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups
Cited by: 70
Author(s): Tarini Shankar Ghosh, Satarupa Sengupta, G. Balakrish Nair, Sharmila S. Mande
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0200104

First chloroplast genomics study of Phoenix dactylifera (var. Naghal and Khanezi): A comparative analysis
Cited by: 12
Author(s): Abdul Latif Khan, Sajjad Asaf, In‐Jung Lee, Ahmed Al‐Harrasi, Ahmed Al‐Rawahi
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0106116

Mycoplasma ovipneumoniae - A Primary Cause of Severe Pneumonia Epizootics in the Norwegian Muskox (Ovibos moschatus) Population
Cited by: 35
Author(s): Kjell Handeland, Torstein Tengs, Branko Kokotovic, Turid Vikøren, Roger D. Ayling, Bjarne Bergsjø, Ólöf Sigurðardóttir, Tord Bretten
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0123298

Rapid High Resolution Genotyping of Francisella tularensis by Whole Genome Sequence Comparison of Annotated Genes (“MLST+”)
Cited by: 38
Author(s): Markus Antwerpen, Karola Prior, Alexander Mellmann, Sebastian Höppner, Wolf D. Splettstoesser, Dag Harmsen
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0085480

Deep Sequencing-Based Analysis of the Cymbidium ensifolium Floral Transcriptome
Cited by: 56
Author(s): Xiaobai Li, Jianxun Luo, Tang Yan, Xinghua Lin, Feng Jin, Dehui Qin, Chongbo Sun, Min Xie
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0040592

Characterization of Pro-Inflammatory Flagellin Proteins Produced by Lactobacillus ruminis and Related Motile Lactobacilli
Cited by: 57
Author(s): Bridget A. Neville, Brian M. Forde, Marcus J. Claesson, Trevor Darby, Avril Coghlan, Ken Nally, R. Paul Ross, Paul W. O’Toole
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0174506

Phylogenetic analysis of family Neisseriaceae based on genome sequences and description of Populibacter corticis gen. nov., sp. nov., a member of the family Neisseriaceae, isolated from symptomatic bark of Populus × euramericana canker
Cited by: 19
Author(s): Yong Li, Xue Han, Sheng-qi Sang, Cai-li Lin, Xi-zhuo Wang
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0118741

Correction: GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers
Cited by: 0
Author(s):
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0030370

CAPRG: Sequence Assembling Pipeline for Next Generation Sequencing of Non-Model Organisms
Cited by: 5
Author(s): Arun K. Rawat, Mohamed O. Elasri, Kurt A. Gust, Glover Eugene George, Don Pham, Leona D. Scanlan, Chris D. Vulpe, Edward J. Perkins
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0083542

Assessment of the Geographic Origins of Pinewood Nematode Isolates via Single Nucleotide Polymorphism in Effector Genes
Cited by: 27
Author(s): Joana Figueiredo, Maria José Simões, Paula Fernanda Gomes, Cristina Barroso, Diogo Pinho, Luci Conceição, Luís Fonseca, Isabel Abrantes, Miguel Pinheiro, Conceição Egas
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0088615

Transcriptome Analysis of the Scleractinian Coral Stylophora pistillata
Cited by: 48
Author(s): Sarit Karako-Lampert, Didier Zoccola, Mali Salmon‐Divon, Mark Katzenellenbogen, Sylvie Tambutté, Anthony Bertucci, Ove Høegh-Guldberg, Emeline Deleury, Denis Allemand, Oren Levy
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0222457

Rapid evolution of Mexican H7N3 highly pathogenic avian influenza viruses in poultry
Cited by: 15
Author(s): Sungsu Youk, Donghun Lee, Helena Lage Ferreira, Claudio L. Afonso, Ángel E. Absalón, David E. Swayne, David L. Suarez, Mary J. Pantin‐Jackwood
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0087648

Diversity of Conotoxin Gene Superfamilies in the Venomous Snail, Conus victoriae
Cited by: 100
Author(s): Samuel D. Robinson, Helena Safavi-Hemami, Lachlan McIntosh, Anthony W. Purcell, Raymond S. Norton, Anthony T. Papenfuss
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0151434

Transcriptome Analysis of an Insecticide Resistant Housefly Strain: Insights about SNPs and Regulatory Elements in Cytochrome P450 Genes
Cited by: 11
Author(s): Khalid Mahmood, Dorte H. Højland, Torben Asp, Michael Kristensen
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0109952

Species-Specific Viromes in the Ancestral Holobiont Hydra
Cited by: 53
Author(s): Juris A. Grasis, Tim Lachnit, Friederike Anton-Erxleben, Yan Wei Lim, Robert Schmieder, Sebastian Fraune, Sören Franzenburg, Santiago Insua, GloriaMay Machado, Matthew Haynes, Mark Little, Robert B. Kimble, Philip Rosenstiel, Forest Rohwer, Thomas C. G. Bosch
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0232667

Adaptation to unstable coordination patterns in individual and joint actions
Cited by: 1
Author(s): Thomas Wolf, Natalie Sebanz, Günther Knoblich
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0053632

Transcriptome Exploration in Leymus chinensis under Saline-Alkaline Treatment Using 454 Pyrosequencing
Cited by: 39
Author(s): Yueru Sun, Fawei Wang, Nan Wang, Yanjun Dong, Qi Liu, Lei Zhao, Huan Chen, Weican Liu, Hai-Long Yin, Xiaomei Zhang, Yanxi Yuan, Haiyan Li
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0052492

SNP Design from 454 Sequencing of Podosphaera plantaginis Transcriptome Reveals a Genetically Diverse Pathogen Metapopulation with High Levels of Mixed-Genotype Infection
Cited by: 68
Author(s): Charlotte Tollenaere, Hanna Susi, Jussi Nokso-Koivisto, Patrik Koskinen, Ayco J. M. Tack, Petri Auvinen, Lars Paulín, Mikko J. Frilander, Rainer Lehtonen, Anna‐Liisa Laine
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0205995

Two novel temperate bacteriophages infecting Streptococcus pyogenes: Their genomes, morphology and stability
Cited by: 11
Author(s): Marek Harhala, Jakub Barylski, Kinga Humińska-Lisowska, Dorota Lecion, Jacek Wojciechowicz, Karolina Lahutta, Mateja Kus, Andrew M. Kropinski, Sylwia Nowak, Grzegorz Nowicki, Katarzyna Hodyra-Stefaniak, Krystyna Dąbrowska
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0164468

Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by ‘Entotheonella’
Cited by: 33
Author(s): Yu Nakashima, Yoko Egami, Masanari Kimura, Toshiyuki Wakimoto, Ikuro Abe
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0151001

Pyrosequencing the Midgut Transcriptome of the Banana Weevil Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) Reveals Multiple Protease-Like Transcripts
Cited by: 11
Author(s): Arnubio Valencia, Haichuan Wang, Álvaro Soto, Manuel Aristizábal, Jorge W. Arboleda, Seong‐il Eyun, Daniel D. Noriega, Blair D. Siegfried
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0091591

Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
Cited by: 30
Author(s): Feng Wang, Danlei Li, Zhiying Wang, Airong Dong, Lihong Liu, Buyong Wang, Qiaoli Chen, Xiaohan Liu
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0119835

Nuclear-Cytoplasmic Conflict in Pea (Pisum sativum L.) Is Associated with Nuclear and Plastidic Candidate Genes Encoding Acetyl-CoA Carboxylase Subunits
Cited by: 38
Author(s): В. С. Богданова, Olga O. Zaytseva, A. V. Mglinets, Natalia V. Shatskaya, Oleg E. Kosterin, Gennady V. Vasiliev
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0034953

Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome
Cited by: 527
Author(s): Kirandeep Bhullar, Nicholas Waglechner, A Pawłowski, Kalinka Koteva, Eric D. Banks, Michael D. Johnston, Hazel A. Barton, Gerard D. Wright
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0116381

Isolation and Functional Characterization of the Novel Clostridium botulinum Neurotoxin A8 Subtype
Cited by: 59
Author(s): Skadi Kull, Katharina Schulz, Jasmin Weisemann, Sebastian Kirchner, Tanja Schreiber, Alexander Bollenbach, Piotr Wojtek Dabrowski, Andreas Nitsche, Suzanne R. Kalb, Martin B. Dorner, John R. Barr, Andreas Rummel, Brigitte G. Dorner
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0103787

Virulence and Draft Genome Sequence Overview of Multiple Strains of the Swine Pathogen Haemophilus parasuis
Cited by: 37
Author(s): Susan L. Brockmeier, Karen B. Register, Joanna S. Kuehn, Tracy L. Nicholson, Crystal L. Loving, Darrell O. Bayles, Sarah M. Shore, Gregory J. Phillips
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0146832

Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus “Ferrovum”
Cited by: 37
Author(s): Sophie R. Ullrich, Anja Poehlein, Judith S. Tischler, Carolina González, Francisco J. Ossandon, Rolf Daniel, David S. Holmes, Michael Schlömann, Martin Mühling
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0086039

Comprehensive Transcriptome Assembly of Chickpea (Cicer arietinum L.) Using Sanger and Next Generation Sequencing Platforms: Development and Applications
Cited by: 84
Author(s): Himabindu Kudapa, Sarwar Azam, Andrew Sharpe, Bunyamin Tar’an, Rong Li, Benjamin Deonovic, Connor Cameron, Andrew Farmer, Steven B. Cannon, Rajeev K. Varshney
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0037553

Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates
Cited by: 66
Author(s): Shatavia S. Morrison, Tiffany C. Williams, Aurora A. Cain, Brett Froelich, Casey A. Taylor, Craig Baker‐Austin, David W. Verner–Jeffreys, Rachel Hartnell, James D. Oliver, Cynthia Gibas
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0141561

Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing
Cited by: 104
Author(s): Mark Klinger, François Pépin, Jen Wilkins, Thomas Asbury, Tobias Wittkop, Jianbiao Zheng, Martin Moorhead, Malek Faham
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0049202

Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology
Cited by: 32
Author(s): Florian Leese, Philipp Brand, Andrey Rozenberg, Christoph Mayer, Shobhit Agrawal, Johannes Dambach, Lars Dietz, Jana S. Doemel, William P. Goodall-Copstake, Christoph Held, Jennifer A. Jackson, Kathrin P. Lampert, Katrin Linse, Jan Niklas Macher, Jennifer Nolzen, Michael J. Raupach, Nicole T. Rivera, Christoph D. Schubart, Sebastian Striewski, Ralph Tollrian, Chester J. Sands
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0151270

Antimicrobial Combinations against Pan-Resistant Acinetobacter baumannii Isolates with Different Resistance Mechanisms
Cited by: 62
Author(s): Gleice Cristina Leite, Maura Salaroli de Oliveira, Lauro Vieira Perdigão Neto, Cristiana Kamia Dias Rocha, Thaís Guimarães, Camila Rizek, Anna S. Levin, Sílvia Figueiredo Costa
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0192672

Co-circulation of all the four dengue virus serotypes and detection of a novel clade of DENV-4 (genotype I) virus in Pune, India during 2016 season
Cited by: 70
Author(s): Shubham Shrivastava, Divya Tiraki, Arundhati Diwan, Sanjay Lalwani, Meera Modak, Akhilesh C. Mishra, Vidya A. Arankalle
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0188768

Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers
Cited by: 30
Author(s): Fabrice Touzain, Laëtitia Le Devendec, Claire de Boisséson, Sandrine Baron, Éric Jouy, Agnès Perrin-Guyomard, Yannick Blanchard, Isabelle Kempf
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0043986

Identification of a Novel Bat Papillomavirus by Metagenomics
Cited by: 44
Author(s): Herman Tse, Alan K.L. Tsang, Hoi-Wah Tsoi, Andy S. P. Leung, Chi-Chun Ho, Susanna K. P. Lau, Patrick C. Y. Woo, Kwok‐Yung Yuen
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0197426

The long-term impact of community mobilisation through participatory women's groups on women's agency in the household: A follow-up study to the Makwanpur trial
Cited by: 12
Author(s): Lu Gram, Jolene Skordis‐Worrall, Dharma S Manandhar, Daniel Strachan, Joanna Morrison, Naomi Saville, David Osrin, Kirti Man Tumbahangphe, Anthony Costello, Michelle Heys
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0033840

De-Novo Assembly and Analysis of the Heterozygous Triploid Genome of the Wine Spoilage Yeast Dekkera bruxellensis AWRI1499
Cited by: 111
Author(s): Chris Curtin, Anthony R. Borneman, Paul J. Chambers, Isak S. Pretorius
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0042637

Transcriptome Analysis and SSR/SNP Markers Information of the Blunt Snout Bream (Megalobrama amblycephala)
Cited by: 171
Author(s): Zexia Gao, Wei Luo, Liu Hong, Cong Zeng, Xiaolian Liu, Shaokui Yi, Weimin Wang
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0088618

Transcriptome Data Reveal Syndermatan Relationships and Suggest the Evolution of Endoparasitism in Acanthocephala via an Epizoic Stage
Cited by: 40
Author(s): Alexandra R. Wey-Fabrizius, Holger Herlyn, Benjamin Rieger, David Rosenkranz, Alexander Witek, David Welch, Ingo Ebersberger, Thomas Hankeln
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0107777

Plasmidome Interchange between Clostridium botulinum, Clostridium novyi and Clostridium haemolyticum Converts Strains of Independent Lineages into Distinctly Different Pathogens
Cited by: 45
Author(s): Hanna Skarin, Bo Segerman
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0029626

Functional Divergence in the Genus Oenococcus as Predicted by Genome Sequencing of the Newly-Described Species, Oenococcus kitaharae
Cited by: 23
Author(s): Anthony R. Borneman, Jane McCarthy, Paul J. Chambers, Eveline Bartowsky
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0055185

Genomic and Secretomic Analyses Reveal Unique Features of the Lignocellulolytic Enzyme System of Penicillium decumbens
Cited by: 143
Author(s): Guodong Liu, Lei Zhang, Xiaomin Wei, Gen Zou, Yuqi Qin, Liang Ma, Jie Li, Huajun Zheng, Shengyue Wang, Chengshu Wang, Luying Xun, Guoping Zhao, Zhihua Zhou, Yinbo Qu
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0058628

The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii
Cited by: 76
Author(s): Daniel N. Farrugia, Liam D. H. Elbourne, Karl A. Hassan, Bart A. Eijkelkamp, Sasha G. Tetu, Melissa H. Brown, Bhumika S. Shah, Anton Y. Peleg, Bridget C. Mabbutt, Ian T. Paulsen
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0064856

Genome Implosion Elicits Host-Confinement in Alcaligenaceae: Evidence from the Comparative Genomics of Tetrathiobacter kashmirensis, a Pathogen in the Making
Cited by: 8
Author(s): Wriddhiman Ghosh, Md. Akhtarul Alam, Chayan Roy, Prosenjit Pyne, Ashish George, Ranadhir Chakraborty, Saikat Majumder, Atima Agarwal, Sheolee Chakraborty, Subrata Majumdar, Shamba Gupta
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0054576

Agent of Whirling Disease Meets Orphan Worm: Phylogenomic Analyses Firmly Place Myxozoa in Cnidaria
Cited by: 57
Author(s): Maximilian P. Nesnidal, Martin Helmkampf, Iris Bruchhaus, Mansour El-Matbouli, Bernhard Hausdorf
Software Mentions: 1
Published: over 11 years ago

10.1007/s00018-016-2173-6

Comparative genomics of drug resistance in Trypanosoma brucei rhodesiense
Cited by: 22
Author(s): Graf F, Philipp Ludin, Christian Arquint, Roman Schmidt, Nora Schaub, Christina Kunz Renggli, Jane C. Munday, Jessica Krezdorn, Nicola Baker, David Horn, Oliver Balmer, Adalgisa Caccone, Harry P. de Koning, Pascal Mäser
Software Mentions: 1
Published: about 8 years ago

10.1093/cdj/bsy017

Sustainability of community-based women’s groups: reflections from a participatory intervention for newborn and maternal health in Nepal
Cited by: 19
Author(s): Annemijn E C Sondaal, Kirti Man Tumbahangphe, Rishi Neupane, Dharma S Manandhar, Anthony Costello, Joanna Morrison
Software Mentions: 1
Published: about 6 years ago

10.1155/2021/9975078

Improving Loanword Identification in Low-Resource Language with Data Augmentation and Multiple Feature Fusion
Cited by: 1
Author(s): Chenggang Mi, Shaolin Zhu, Rui Nie
Software Mentions: 1
Published: about 3 years ago

10.1186/s40649-016-0032-0

Text normalization for named entity recognition in Vietnamese tweets
Cited by: 3
Author(s): Vu Nguyen, Hien Nguyen, Václav Snåšel
Software Mentions: 1
Published: over 7 years ago

10.1186/s13031-017-0134-9

The role of public health information in assistance to populations living in opposition and contested areas of Syria, 2012–2014
Cited by: 23
Author(s): Emma Diggle, Wilhelmina Welsch, Richard Sullivan, Gerbrand Alkema, Abdihamid Warsame, M Wafai, Mohammed Jasem, Abdulkarim Ekzayez, Rachael Cummings, Preeti Patel
Software Mentions: 1
Published: over 6 years ago

Projects: bioconductor: MIRA

Papers Mentioning MIRA 856