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: bioconductor: MIRA

https://packages.ecosyste.ms/registries/bioconductor.org/packages/MIRA

Methylation-Based Inference of Regulatory Activity
1 version
Latest release: about 1 year ago
1 dependent package
8,474 downloads total

Papers Mentioning MIRA 856

10.3389/fmicb.2016.00248
Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island
Cited by: 23
Author(s): Eduard Fadeev, Fabio De Pascale, Alessandro Vezzi, Sariel Hübner, Dikla Aharonovich, Daniel Sher
Software Mentions: 2
Published: over 8 years ago
10.3389/fgene.2014.00190
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome
Cited by: 34
Author(s): Joanna Moreton, Stephen Dunham, Richard D. Emes
Software Mentions: 2
Published: over 10 years ago
10.3389/fgene.2015.00361
Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes
Cited by: 52
Author(s): Joanna Moreton, Abril Izquierdo, Richard D. Emes
Software Mentions: 2
Published: almost 9 years ago
10.3389/fcimb.2018.00375
Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples
Cited by: 34
Author(s): Corinne P. Oechslin, Nicole Lenz, Nicole Liechti, Sarah Ryter, Philipp Agyeman, Rémy Bruggmann, Stephen L. Leib, Christian Beuret
Software Mentions: 2
Published: about 6 years ago
10.1093/bioinformatics/bty083
MIRA: an R package for DNA methylation-based inference of regulatory activity
Cited by: 18
Author(s): John T. Lawson, Eleni M. Tomazou, Christoph Bock, Nathan C. Sheffield
Software Mentions: 2
Published: over 6 years ago
10.1093/jac/dkv119
Within-host diversity of MRSA antimicrobial resistances
Cited by: 51
Author(s): Kinga I. Stańczak-Mrozek, Anusha Manne, Gwenan M. Knight, Katherine A. Gould, Adam A. Witney, Jodi A. Lindsay
Software Mentions: 2
Published: over 9 years ago
10.3389/fcimb.2020.527102
The Most Frequently Used Sequencing Technologies and Assembly Methods in Different Time Segments of the Bacterial Surveillance and RefSeq Genome Databases
Cited by: 25
Author(s): Bo Segerman
Software Mentions: 2
Published: about 4 years ago
10.3389/fbioe.2020.01024
Characterization of Highly Mucus-Adherent Non-GMO Derivatives of Lacticaseibacillus rhamnosus GG
Cited by: 6
Author(s): Pia Rasinkangas, Hanne L. P. Tytgat, Jarmo Ritari, Justus Reunanen, Seppo Salminen, Airi Palva, François P. Douillard, Willem M. de Vos
Software Mentions: 2
Published: over 4 years ago
10.3389/fbioe.2015.00141
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
Cited by: 28
Author(s): Rodrigo García-López, Jorge F. Vázquez-Castellanos, Andrés Moya
Software Mentions: 2
Published: about 9 years ago
10.1038/srep30158
The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features
Cited by: 28
Author(s): Songtao Gui, Zhihua Wu, Hongyuan Zhang, Yinzhen Zheng, Zhixuan Zhu, Dequan Liang, Yi Ding
Software Mentions: 2
Published: over 8 years ago
10.1186/s12864-015-1893-6
Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates
Cited by: 41
Author(s): Johan Ankarklev, Oscar Franzén, Dimitra Peirasmaki, Jon Jerlström-Hultqvist, Marianne Lebbad, Jan O. Andersson, Björn Andersson, Staffan G. Svärd
Software Mentions: 2
Published: about 9 years ago
10.1186/1471-2164-15-901
Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation
Cited by: 10
Author(s): Andrew Toseland, Simon Moxon, Thomas Möck, Vincent Moulton
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0042039
Next-Generation Sequencing of the Porcine Skeletal Muscle Transcriptome for Computational Prediction of MicroRNA Gene Targets
Cited by: 8
Author(s): T. G. McDaneld, Ted Smith, Gregory P Harhay, Ralph T. Wiedmann
Software Mentions: 2
Published: over 12 years ago
10.1186/1471-2164-15-68
From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes
Cited by: 25
Author(s): Andrew Clarke, Stefan Prost, Jo‐Ann L. Stanton, W. Timothy J. White, Matt Kaplan, Elizabeth Matisoo-Smith
Software Mentions: 2
Published: almost 11 years ago
10.1186/1756-0500-4-254
The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones
Cited by: 7
Author(s): Paula Moolhuijzen, A.E. Lew-Tabor, Jess A. T. Morgan, M. Rodriguez-Valle, Daniel G. Peterson, Scot E. Dowd, Felix D. Guerrero, M. Bellgard, R. Appels
Software Mentions: 2
Published: over 13 years ago
10.3389/fmicb.2018.02933
Genome Analysis of Haplotype D of Candidatus Liberibacter Solanacearum
Cited by: 9
Author(s): Leron Katsir, Zhepu Ruan, Diego Santos-García, Alon Piasezky, Jiandong Jiang, Noa Sela, Shiri Freilich, Ofir Bahar
Software Mentions: 2
Published: almost 6 years ago
10.1186/1471-2164-15-245
Characterization of the transcriptome and temperature-induced differential gene expression in QPX, the thraustochytrid parasite of hard clams
Cited by: 20
Author(s): Ewelina Rubin, Arnaud Tanguy, Mickael Perrigault, Emmanuelle Pales Espinosa, Bassem Allam
Software Mentions: 2
Published: over 10 years ago
10.1038/s41598-019-46914-1
Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago
Cited by: 56
Author(s): Stephen Sameroff, Rafal Tokarz, Roxanne A. Charles, Komal Jain, Alexandra Oleynik, Xiaoyu Che, Karla Georges, Christine V. F. Carrington, W. Ian Lipkin, C.A.L. Oura
Software Mentions: 2
Published: over 5 years ago
10.1128/genomeA.01169-14
Exploring the Genome of a Butyric Acid Producer, Clostridium butyricum INCQS635
Cited by: 1
Author(s): Thiago Bruce, Fernanda Gomes Leite, Diogo A. Tschoeke, Mauro Sayão de Miranda, Nei Pereira, Rogério Valle, Cristiane C. Thompson, Fabiano L. Thompson
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12864-020-06906-2
Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element
Cited by: 16
Author(s): Ze Chen, Yibo Xuan, Guangcai Liang, Xiaolong Yang, Zhou Yu, Stephen C. Barker, Samuel Kelava, Wenjun Bu, Jingze Liu, Shan Gao
Software Mentions: 2
Published: over 4 years ago
10.1186/s12870-015-0596-0
Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants
Cited by: 59
Author(s): Jillian M. Hagel, Jeremy S. Morris, Eun-Jeong Lee, Isabel Desgagné‐Penix, Crystal D. Bross, Lihong Chang, Xue Chen, Scott C. Farrow, Ye Zhang, Jung Soh, Christoph Wilhelm Sensen, Peter J. Facchini
Software Mentions: 2
Published: about 9 years ago
10.1186/1471-2164-14-465
Assessing De Novo transcriptome assembly metrics for consistency and utility
Cited by: 107
Author(s): Shawn T. O’Neil, Scott J. Emrich
Software Mentions: 2
Published: almost 12 years ago
10.1186/1471-2229-10-96
Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes
Cited by: 83
Author(s): Ruth Timme, Charles F. Delwiche
Software Mentions: 2
Published: almost 15 years ago
10.1371/journal.pone.0068200
Transcriptome Characterisation of the Ant Formica exsecta with New Insights into the Evolution of Desaturase Genes in Social Hymenoptera
Cited by: 15
Author(s): Hélène Badouin, Khalid Belkhir, Emma Gregson, Juan Galindo, Liselotte Sundström, Stephen J. Martin, Roger K. Butlin, Carole Smadja
Software Mentions: 2
Published: over 11 years ago
10.1186/s12870-016-0777-5
Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars
Cited by: 39
Author(s): Luciana Souto Mofatto, F. de A. Carneiro, Natália Gomes Vieira, Karoline Estefani Duarte, Ramón Vidal, Jean Carlos Alekcevetch, Michelle G. Cotta, Jean‐Luc Verdeil, Fabienne Lapeyre-Montès, Marc Lartaud, Thierry Leroy, Fabien De Bellis, David Pot, Gustavo Costa Rodrigues, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Alan Carvalho Andrade, Pierre Marraccini
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0017418
A De Novo Expression Profiling of Anopheles funestus, Malaria Vector in Africa, Using 454 Pyrosequencing
Cited by: 51
Author(s): Richard I. Gregory, Alistair C. Darby, Helen Irving, Mamadou B. Coulibaly, Margaret Hughes, Lizette L. Koekemoer, Maureen Coetzee, Hilary Ranson, Janet Hemingway, Neil Hall, Charles S. Wondji
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0155441
Comparative Mitogenomics of Leeches (Annelida: Clitellata): Genome Conservation and Placobdella-Specific trnD Gene Duplication
Cited by: 18
Author(s): Alejandro Oceguera‐Figueroa, Alejandro Manzano-Marı́n, Sebastian Kvist, Andrés Moya, Mark E. Siddall, Amparo Latorre
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0035152
Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics
Cited by: 119
Author(s): Peifeng Ji, Guiming Liu, Jian Xu, Xumin Wang, Jiong-Tang Li, Zixia Zhao, Xiaofeng Zhang, Yan Zhang, Peng Xu, Xin Sun
Software Mentions: 2
Published: over 12 years ago
10.1186/1471-2164-12-234
Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring
Cited by: 120
Author(s): Massimo Milan, Alessandro Coppe, Richard Reinhardt, M. Leonor Cancela, Ricardo B. Leite, Carlos Saavedra, Claudio Ciofi, Guido Chelazzi, Tomaso Patarnello, Stefania Bortoluzzi, Luca Bargelloni
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0051188
Evaluating de Bruijn Graph Assemblers on 454 Transcriptomic Data
Cited by: 24
Author(s): Xianwen Ren, Tao Liu, Jie Dong, Lu Sun, Jian Yang, Yafang Zhu, Qi Jin
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0040683
Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes
Cited by: 44
Author(s): M. M. Swanson, B. Reavy, Kira S. Makarova, Peter J. A. Cock, D. W. Hopkins, L. Torrance, Eugene V. Koonin, Michael Taliansky
Software Mentions: 2
Published: over 12 years ago
10.1186/1471-2229-14-46
A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement
Cited by: 35
Author(s): Rong He, Fernanda Salvato, Park Jeong-Jin, Minjeong Kim, William M. Nelson, Tiago Santana Balbuena, Mark R. Willer, John A. Crow, Greg May, Carol Soderlund, Jay J. Thelen, David R. Gang
Software Mentions: 2
Published: almost 11 years ago
10.1186/1471-2164-15-126
Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea
Cited by: 93
Author(s): Jorge Duarte, Nathalie Rivière, Alain Baranger, Grégoire Aubert, Judith Burstin, Laurent Cornet, Clément Lavaud, Isabelle Lejeune‐Hénaut, Jean‐Pierre Martinant, Jean-Philippe Pichon, Marie‐Laure Pilet‐Nayel, Gilles Boutet
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0126416
Combining GWAS and RNA-Seq Approaches for Detection of the Causal Mutation for Hereditary Junctional Epidermolysis Bullosa in Sheep
Cited by: 15
Author(s): Aroa Suárez-Vega, Julio Benavides, Valentín Pérez Pérez, Gwenola Tosser‐Klopp, Christophe Klopp, Stephen J. Keennel, Juan José Arranz
Software Mentions: 2
Published: over 9 years ago
10.1080/23802359.2019.1692719
The mitochondrial genome of a wild toxic mushroom, Russula subnigricans
Cited by: 1
Author(s): Fei Yu, Yongjie Zhang, Jiankun Liang
Software Mentions: 2
Published: over 5 years ago
10.1186/s12864-017-4379-x
De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
Cited by: 58
Author(s): Madeleine Carruthers, Andrey A. Yurchenko, Julian J. Augley, Colin E. Adams, Paweł Herzyk, Kathryn R. Elmer
Software Mentions: 2
Published: almost 7 years ago
10.7717/peerj.207
An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke,<i>Fasciolopsis buski</i>(Lankester, 1857) Looss, 1899
Cited by: 18
Author(s): Devendra Kumar Biswal, Sudeep Ghatani, Jollin Andrea Shylla, R. K. Sahu, Nandita Mullapudi, Alok Bhattacharya, Veena Tandon
Software Mentions: 2
Published: about 11 years ago
10.1371/journal.pone.0029814
SNP Discovery and Development of a High-Density Genotyping Array for Sunflower
Cited by: 99
Author(s): Eleni Bachlava, Christopher A. Taylor, Shunxue Tang, John E. Bowers, Jennifer R. Mandel, John M. Burke, Steven J. Knapp
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0092202
A Microarray-Based Analysis of Gametogenesis in Two Portuguese Populations of the European Clam Ruditapes decussatus
Cited by: 14
Author(s): Joana Sousa, Massimo Milan, Luca Bargelloni, Marianna Pauletto, Domitília Matias, Sandra Joaquim, Ana Margarete Matias, Virgile Quillien, Alexandra Leitão, Arnaud Huvet
Software Mentions: 2
Published: over 10 years ago
10.1186/s12870-015-0534-1
Characterization of the cork oak transcriptome dynamics during acorn development
Cited by: 21
Author(s): Andreia Miguel, Jose J De Vega, Liliana Marum, Inês Chaves, Tatiana Santo, José Leitão, Maria Carolina Varela, Celia María Gonzalo Miguel
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0057459
Metagenomic Detection of Viral Pathogens in Spanish Honeybees: Co-Infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses
Cited by: 89
Author(s): Fredrik Granberg, Marina Vicente-Rubiano, Consuelo Rubio-Guerri, Oskar E. Karlsson, Deborah Kukielka, Sándor Bélak, José Manuel Sánchez-Vizcaíno
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0142814
Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes
Cited by: 4
Author(s): Joshua J. Faber-Hammond, Manoj P. Samanta, Elizabeth A. Whitchurch, Dustin P. Manning, Joseph A. Sisneros, Allison B. Coffin
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0031410
Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach
Cited by: 76
Author(s): Marvin Mundry, Erich Bornberg‐Bauer, Michael Sammeth, Philine G. D. Feulner
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0051263
Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes
Cited by: 14
Author(s): Agnès Dettaı̈, Cyril Gallut, Sophie Brouillet, Joël Pothier, Guillaume Lecointre, Régis Debruyne
Software Mentions: 2
Published: almost 12 years ago
10.1186/1471-2164-15-96
Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood
Cited by: 144
Author(s): K. G. Frey, J. Enrique Herrera-Galeano, C. L. Redden, Truong Luu, Stephanie L. Servetas, Alfred Mateczun, Vishwesh Mokashi, Kimberly A. Bishop‐Lilly
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0022751
Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology
Cited by: 692
Author(s): Alexander Mellmann, Dag Harmsen, Craig Cummings, Emily B. Zentz, Shana R. Leopold, Alain Rico, Karola Prior, Rafael Szczepanowski, Yongmei Ji, Wenlan Zhang, Stephen McLaughlin, John Henkhaus, Benjamin Leopold, Martina Bielaszewska, Rita Prager, Pius Brzoska, Richard Moore, Simone M Guenther, Jonathan M. Rothberg, Helge Karch
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0212769
Genome and secretome of Chondrostereum purpureum correspond to saprotrophic and phytopathogenic life styles
Cited by: 11
Author(s): Rocío Reina, Harald Kellner, Jaqueline Hess, Nico Jehmlich, Inmaculada García-Romera, Elisabet Aranda, Martin Hofrichter, Christiane Liers
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0256126
Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data
Cited by: 1
Author(s): Anna Victória Silvério Righetto Mauad, Leila do Nascimento Vieira, Valter A. Baura, Eduardo Balsanelli, Emanuel Maltempi de Souza, Mark W. Chase, Eric de Camargo Smidt
Software Mentions: 2
Published: about 3 years ago
10.3390/pathogens3020258
High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology
Cited by: 25
Author(s): Ségolène Caboche, Christophe Audebert, David Hot
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0044858
Gamma Irradiation Does Not Induce Detectable Changes in DNA Methylation Directly following Exposure of Human Cells
Cited by: 32
Author(s): Christoph Lahtz, Steven Bates, Yong Jiang, Arthur X. Li, Xiwei Wu, Maria A. Hahn, Gerd P. Pfeifer
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pone.0105221
Elevated Levels of Circulating DNA in Cardiovascular Disease Patients: Metagenomic Profiling of Microbiome in the Circulation
Cited by: 140
Author(s): Vasudevan Dinakaran, Andiappan Rathinavel, Pushpanathan Muthuirulan, R Sivakumar, Paramasamy Gunasekaran, Jeyaprakash Rajendhran
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0112998
Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and Other Angiosperms for Marker Choice
Cited by: 34
Author(s): Nadja Korotkova, Lars Nauheimer, Hasmik Ter-Voskanyan, Martin Allgaier, Thomas Borsch
Software Mentions: 2
Published: about 10 years ago
10.1186/1471-2105-12-453
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
Cited by: 119
Author(s): Yi Zheng, Liangjun Zhao, Junping Gao, Zhangjun Fei
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0202338
Validation of a Kinect V2 based rehabilitation game
Cited by: 47
Author(s): Mengxuan Ma, Rachel Proffitt, Marjorie Skubic
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0065953
Unbiased Approach for Virus Detection in Skin Lesions
Cited by: 55
Author(s): Davit Bzhalava, Hanna Katarina Lilith Johansson, Johanna Ekström, Helena Faust, Birgitta Moller, Carina Eklund, Peter Nordin, Bo Stenquist, John Paoli, Bengt Persson, Ola Forslund, Joakim Dillner
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0058068
SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species
Cited by: 74
Author(s): Rebekah E. Oliver, Nicholas A. Tinker, Gerard R. Lazo, Shiaoman Chao, Eric N. Jellen, M. L. Carson, H. W. Rines, D. E. Obert, Joseph D. Lutz, Irene Shackelford, Abraham B. Korol, Charlene P. Wight, Kyle M. Gardner, Jiro Hattori, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael Bonman, Jean‐Luc Jannink, Mark E. Sorrells, Gina Brown-Guedira, J. W. Mitchell Fetch, Stephen A. Harrison, Catherine Howarth, Amir M. H. Ibrahim, F. L. Kolb, Marcia McMullen, J. Paul Murphy, H. W. Ohm, B. G. Rossnagel, Weikai Yan, Kelci Miclaus, Jordan Hiller, Peter J. Maughan, Rachel R. Redman Hulse, Joseph M. Anderson, Emir Islamovic, Eric W. Jackson
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0205582
De novo assembly of wheat root transcriptomes and transcriptional signature of longitudinal differentiation
Cited by: 5
Author(s): Ghana S. Challa, Wanlong Li
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0170676
Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics
Cited by: 18
Author(s): Rafael Azevedo Baraúna, Rommel Thiago Jucá Ramos, Adonney Allan de Oliveira Veras, Kenny C. Pinheiro, Leandro de Jesus Benevides, Marcus Vinícius Canário Viana, Luís Carlos Guimarães, Judy M. Edman, Sharon J. Spier, Vasco Azevedo, Artur M. S. Silva
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0052302
SNP Detection from De Novo Transcriptome Sequencing in the Bivalve Macoma balthica: Marker Development for Evolutionary Studies
Cited by: 24
Author(s): Eric Pante, Audrey Rohfritsch, Vanessa Becquet, Khalid Belkhir, Nicolas Bierne, Pascale Garcia
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0104651
Genome Analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: A Rhizobacterium That Improves Plant Growth and Stress Management
Cited by: 79
Author(s): Adnan Niazi, Shahid Manzoor, Shashidar Asari, Sarosh Bejai, Johan Meijer, Erik Bongcam‐Rudloff
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0035269
Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals
Cited by: 203
Author(s): Till Bayer, Manuel Aranda, Shinichi Sunagawa, Lauren K. Yum, Michael K. DeSalvo, Erika Lindquist, Mary Alice Coffroth, Christian R. Voolstra, Mónica Medina
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0122074
Comparative Genomic Analysis of Two Novel Sporadic Shiga Toxin-Producing Escherichia coli O104:H4 Strains Isolated 2011 in Germany
Cited by: 12
Author(s): Erhard Tietze, Piotr Wojtek Dabrowski, Rita Prager, Aleksandar Radonić, Angelika Fruth, Philipp Auraß, Andreas Nitsche, Martin Mielke, Antje Flieger
Software Mentions: 2
Published: over 9 years ago
10.3390/v10080429
Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes
Cited by: 9
Author(s): Cecilia Oluseyi Osunmakinde, Ramganesh Selvarajan, Timothy Sibanda, Bhekie B. Mamba, Titus A.M. Msagati
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0018844
Relationship between Gene Body DNA Methylation and Intragenic H3K9me3 and H3K36me3 Chromatin Marks
Cited by: 127
Author(s): Maria A. Hahn, Xiwei Wu, Arthur X. Li, Torsten Hahn, Gerd P. Pfeifer
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0107014
GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers
Cited by: 28
Author(s): Sebastian Jünemann, Karola Prior, Andreas Albersmeier, Stefan P. Albaum, Jörn Kalinowski, Alexander Goesmann, Jens Stoye, Dag Harmsen
Software Mentions: 2
Published: about 10 years ago
10.1371/journal.pntd.0008492
Insecticide resistance and genetic structure of Aedes aegypti populations from Rio de Janeiro State, Brazil
Cited by: 10
Author(s): Rafi Ur Rahman, Luciano V. Cosme, Monique Melo Costa, Luana Carrara, José Bento Pereira Lima, Ademir Jesús Martins
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pgen.1005722
Escape from Lethal Bacterial Competition through Coupled Activation of Antibiotic Resistance and a Mobilized Subpopulation
Cited by: 44
Author(s): Reed M. Stubbendieck, Paul D. Straight
Software Mentions: 2
Published: almost 9 years ago
10.1186/1471-2105-15-126
Automated ensemble assembly and validation of microbial genomes
Cited by: 59
Author(s): Sergey Koren, Todd J. Treangen, Curtis Hill, Mihai Pop, Adam M. Phillippy
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pgen.1003393
A Gene Transfer Agent and a Dynamic Repertoire of Secretion Systems Hold the Keys to the Explosive Radiation of the Emerging Pathogen Bartonella
Cited by: 82
Author(s): Lionel Guy, Björn Nystedt, Christina Toft, Katarzyna Zaremba-Niedźwiedzka, Eva Berglund, Fredrik Granberg, Kristina Näslund, Ann‐Sofie Eriksson, Siv G. E. Andersson
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pntd.0004384
Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections
Cited by: 27
Author(s): Ehtesham Mofiz, Torsten Seemann, Melanie Bahlo, Deborah C. Holt, Bart J. Currie, Katja Fischer, Anthony T. Papenfuss
Software Mentions: 2
Published: almost 9 years ago
10.3390/v13010103
Surveillance and Genetic Characterization of Virulent Newcastle Disease Virus Subgenotype V.3 in Indigenous Chickens from Backyard Poultry Farms and Live Bird Markets in Kenya
Cited by: 10
Author(s): Henry M. Kariithi, Helena Lage Ferreira, Catharine N. Welch, Leonard O. Ateya, Auleria Ajiambo Apopo, Richard Zoller, Jeremy D. Volkening, Dawn Williams-Coplin, Darren J. Parris, Tim L. Olivier, Dana Goldenberg, Yatinder S. Binepal, Sonia M. Hernández, Claudio L. Afonso, David L. Suarez
Software Mentions: 2
Published: almost 4 years ago
10.1186/1471-2164-11-650
Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak
Cited by: 70
Author(s): S. Ueno, Grégoire Le Provost, Valérie Leger, Christophe Klopp, Céline Noirot, Jean‐Marc Frigério, Franck Salin, Jérôme Salse, Michaël Abrouk, Florent Murat, Oliver Brendel, Jérémy Derory, Pierre Abadie, Patrick Léger, Cyril Cabané, Aurélien Barré, Antoine de Daruvar, Arnaud Couloux, Patrick Wincker, Marie-Pierre Reviron, Antoine Kremer, Christophe Plomion
Software Mentions: 2
Published: almost 14 years ago
10.1111/1755-0998.12626
Strategies for complete plastid genome sequencing
Cited by: 104
Author(s): Alex D. Twyford, Rob W. Ness
Software Mentions: 2
Published: almost 8 years ago
10.1186/1476-4598-9-44
A Genome-wide screen identifies frequently methylated genes in haematological and epithelial cancers
Cited by: 89
Author(s): Thomas L. Dunwell, Luke B. Hesson, Tibor A. Rauch, Lihui Wang, Richard E. Clark, Ashraf Dallol, Dean Gentle, Daniel Catchpoole, Eamonn R. Maher, Gerd P. Pfeifer, Farida Latif
Software Mentions: 2
Published: over 14 years ago
10.1186/1471-2105-12-481
U-Compare bio-event meta-service: compatible BioNLP event extraction services
Cited by: 15
Author(s): Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Miwa Misawa, Sophia Ananiadou, Mariana Neves, Alberto Pascual-Montano, Arzucan Özgür, Dragomir Radev, Sebastian Riedel, Rune Sætre, Hong‐Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun’ichi Tsujii
Software Mentions: 2
Published: almost 13 years ago
10.1128/genomeA.01309-14
Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica
Cited by: 6
Author(s): Sandra Ronca, Aline Frossard, Leandro D. Guerrero, Thulani P. Makhalanyane, Jackie Aislabie, Don A. Cowan
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0066279
SVM-Based Prediction of Propeptide Cleavage Sites in Spider Toxins Identifies Toxin Innovation in an Australian Tarantula
Cited by: 31
Author(s): Emily S. Wong, Margaret H. Hardy, David Wood, Timothy L. Bailey, Glenn F. King
Software Mentions: 2
Published: over 11 years ago
10.1080/23802359.2021.1918029
Characteristic and phylogenetic analyses of chloroplast genome for <i>Syringa komarowii</i> C.K.Schneid. (Oleaceae) from Huoditang, China, an important horticultural plant
Cited by: 1
Author(s): Yongqin Cheng, Zaimin Jiang, Jing Cai
Software Mentions: 1
Published: over 3 years ago
10.1080/23802359.2019.1687031
The complete chloroplast genome sequence of <i>Mentha canadensis</i> (Labiatae), a traditional Chinese herbal medicine
Cited by: 1
Author(s): Huaizhu Li, Lin Yang, Ji-Qing Bai, An Qiuyan, Dou Liu, Rui-Xue She
Software Mentions: 1
Published: almost 5 years ago
10.1186/1471-2164-11-242
Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
Cited by: 54
Author(s): Niranjan Nagarajan, Constance E. Cook, MariaPia Di Bonaventura, Hong Ge, Allen L. Richards, Kimberly A. Bishop‐Lilly, Robert DeSalle, Timothy D. Read, Mihai Pop
Software Mentions: 1
Published: over 14 years ago
10.1080/23802359.2020.1866452
Characteration and comparative analysis of the whole chloroplast genomes of five common millet (<i>Panicum miliaceum</i>)
Cited by: 1
Author(s): Xiaoan Cao, Sichen Liu, Zhixin Mu, Qiao Zhang
Software Mentions: 1
Published: over 3 years ago
10.1080/23802359.2019.1636728
The complete chloroplast genome sequence of <i>Liparis japonica</i> (Orchidaceae)
Cited by: 6
Author(s): Jianfang Li, Qian Yang, Zhan‐Lin Liu
Software Mentions: 1
Published: over 5 years ago
10.1186/s12864-017-3739-x
No evidence for a bovine mastitis Escherichia coli pathotype
Cited by: 48
Author(s): Andreas Leimbach, Anja Poehlein, John Vollmers, Dennis Görlich, Rolf Daniel, Ulrich Dobrindt
Software Mentions: 1
Published: over 7 years ago
10.1080/23802359.2016.1275844
The complete mitochondrial genome of a cryptic amphipod species from the <i>Gammarus fossarum</i> complex
Cited by: 11
Author(s): Jan Niklas Macher, Florian Leese, Alexander Weigand, Andrey Rozenberg
Software Mentions: 1
Published: almost 8 years ago
10.1080/23802359.2017.1285207
The complete mitochondrial genome of the subsocial cockroach<i>Nauphoeta cinerea</i>and phylogenomic analyses of Blattodea mitogenomes suggest reclassification of superfamilies
Cited by: 5
Author(s): Ana Teresa Nogueira Dumans, Danielle Bertino Grimaldi, Carolina Furtado, Ednildo A. Machado, Francisco Prosdocimi
Software Mentions: 1
Published: almost 8 years ago
10.1186/1471-2164-15-1139
A genome-guided analysis of energy conservation in the thermophilic, cytochrome-free acetogenic bacterium Thermoanaerobacter kivui
Cited by: 55
Author(s): Verena Hess, Anja Poehlein, Marie Charlotte Weghoff, Rolf Daniel, Volker Müller
Software Mentions: 1
Published: almost 10 years ago
10.1080/23802359.2017.1339212
The mitochondrial genomes of Atlas Geckos (<i>Quedenfeldtia</i>): mitogenome assembly from transcriptomes and anchored hybrid enrichment datasets
Cited by: 6
Author(s): Mariana L. Lyra, Ulrich Joger, Ulrich Schulte, Tahar Slimani, El Hassan El Mouden, Abdellah Bouazza, Sven Künzel, Alan R. Lemmon, Emily Moriarty Lemmon, Miguel Vences
Software Mentions: 1
Published: almost 8 years ago
10.1080/23802359.2019.1627930
Complete chloroplast genome of a Chinese endemic species <i>Corydalis trisecta</i> Franch. (Papaveraceae)
Cited by: 6
Author(s): Nazish Kanwal, Xiao Zhang, Nawal Afzal, Jia Yang, Zhong-Hu Li, Guifang Zhao
Software Mentions: 1
Published: over 5 years ago
10.1186/s12864-019-5482-y
Genome analysis identifies a spontaneous nonsense mutation in ppsD leading to attenuation of virulence in laboratory-manipulated Mycobacterium tuberculosis
Cited by: 6
Author(s): Shyamasree De Majumdar, Kriti Sikri, Payel Ghosh, Neetika Jaisinghani, Malobi Nandi, Sheetal Gandotra, Shekhar C. Mande, Jaya Sivaswami Tyagi
Software Mentions: 1
Published: almost 6 years ago
10.1186/1471-2164-11-695
Deep sequencing of New World screw-worm transcripts to discover genes involved in insecticide resistance
Cited by: 33
Author(s): Rumão Batista Nunes de Carvalho, Ana Maria Lima de Azeredo-Espin, Tatiana Teixeira Torres
Software Mentions: 1
Published: almost 14 years ago
10.1080/23802359.2017.1347830
The mitochondrial genomes of three species of poison frogs (Anura: Dendrobates)
Cited by: 2
Author(s): Mariana L. Lyra, Eugenia Sanchez, Sven Kuenzel, Stefan Loetters, Célio F. B. Haddad, Miguel Vences
Software Mentions: 1
Published: over 7 years ago
10.1080/23802359.2019.1693924
The complete chloroplast genome of <i>Forsythia mira</i>, an endemic medicinal shrub in China
Cited by: 2
Author(s): Su Gao, Ji-Qing Bai, Mi‐Li Liu, Pengfei Wang, Na Li, Lei Yang, Xiaoping Wang, Zhong-Hu Li
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12864-019-5587-3
Genome and proteome of the chlorophyll f-producing cyanobacterium Halomicronema hongdechloris: adaptative proteomic shifts under different light conditions
Cited by: 21
Author(s): Min Chen, Miguel A. Hernández‐Prieto, Patrick C. Loughlin, Yaqiong Li, Robert D. Willows
Software Mentions: 1
Published: over 5 years ago
10.1080/23802359.2021.1878958
The complete molecular sequence of chloroplast genome of <i>Lablab purpureus</i> (L.) Sweet
Cited by: 2
Author(s): Na Li, Ji-Qing Bai, Su Gao, Lei Yang, Jing Li, Shao-Bing Du, Xiaoping Wang
Software Mentions: 1
Published: over 3 years ago
10.1080/23802359.2018.1457993
Complete mitochondrial genome of Sargassum yezoense (Sargassaceae, Phaeophyceae)
Cited by: 0
Author(s): Kyeong Mi Kim, Jin-Tak Choi, Hwan Su Yoon, Hyeong Seok Jang, Ji Won Hong
Software Mentions: 1
Published: almost 7 years ago
10.1186/1471-2164-13-387
Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection
Cited by: 83
Author(s): P. M. Guimarães, Ana Cristina Miranda Brasileiro, Carolina Vianna Morgante, Andressa Cunha Quintana Martins, George J. Pappas, Orzenil B. Silva, Roberto Coiti Togawa, Soraya C. M. Leal‐Bertioli, Ana Cláudia Guerra Araújo, Márcio de Carvalho Moretzsohn, David J. Bertioli
Software Mentions: 1
Published: over 12 years ago
10.1080/23802359.2016.1197077
Complete mitochondrial genome sequencing of central Indian domestic pig
Cited by: 4
Author(s): Ajit Singh, Kajal Kumar Jadav, Dharmendra Kumar, Nidhi Rajput, Awadh Bihari Srivastav, B. C. Sarkhel
Software Mentions: 1
Published: almost 9 years ago
10.1080/23802359.2021.1917311
Characterization of the DNA molecular sequence of complete plastid genome of Paeonia rockii subsp. taibaishanica, an endemic species in China
Cited by: 1
Author(s): Peng-Bin Dong, Li Zhang, Zhao-Ping Lu, Yuan Wang, Xiaoyu Song, Jiu-Xia Wang, Dan He, Xiaofeng Lei, Ma-Li Wang, Min-Feng Fang, Zhong-Hu Li
Software Mentions: 1
Published: over 3 years ago
10.1080/23802359.2019.1704643
The complete plastome sequence of <i>Platanthera japonica</i> (Orchidaceae): an endangered medicinal and ornamental plant
Cited by: 2
Author(s): Xiao Zhang, Huaizhu Li, H. Z. Huang, Qiaoli Wang
Software Mentions: 1
Published: almost 5 years ago
10.1080/23802359.2018.1521312
Characterization of the whole plastid genome sequence of Abies chensiensis (Pinaceae), an endangered endemic conifer in China
Cited by: 1
Author(s): Mi‐Li Liu, Ji-Qing Bai, Wan-Lin Dong, Ruonan Wang, Peng-Bin Dong, Ning Wang, Hongyan Liu, Min-Feng Fang
Software Mentions: 1
Published: over 6 years ago