bioconductor: MIRA | Projects | Ecosyste.ms: Papers

10.1093/gbe/evz003

Repeated Evolution Versus Common Ancestry: Sex Chromosome Evolution in the Haplochromine CichlidPseudocrenilabrus philander
Cited by: 25
Author(s): Astrid Böhne, Alexandra Anh‐Thu Weber, Jelena Rajkov, Michael Rechsteiner, Andrin Riss, Bernhard Egger, Walter Salzburger
Software Mentions: 10
Published: almost 6 years ago

10.1093/database/bay027

Maser: one-stop platform for NGS big data from analysis to visualization
Cited by: 38
Author(s): Sonoko Kinjo, Norikazu Monma, Sadahiko Misu, Norikazu Kitamura, Junichi Imoto, Kazutoshi Yoshitake, Takashi Gojobori, Kazuho Ikeo
Software Mentions: 10
Published: almost 7 years ago

10.1038/s41598-017-14576-6

Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
Cited by: 37
Author(s): Meiser Anjuli, Jürgen Otte, Imke Schmitt, Francesco Dal Grande
Software Mentions: 9
Published: about 7 years ago

10.1186/s12864-019-5692-3

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains
Cited by: 14
Author(s): Marc Lorentzen, Hugo Campbell-Sills, Tue Sparholt Jørgensen, Tue Kjærgaard Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen, Patrick Lucas
Software Mentions: 9
Published: over 5 years ago

10.1590/1678-4685-GMB-2016-0230

Approaches for in silico finishing of microbial genome sequences
Cited by: 17
Author(s): Frederico Schmitt Kremer, Alan J. A. McBride, Luciano da Silva Pinto
Software Mentions: 8
Published: over 7 years ago

10.1186/s40168-019-0626-5

Choice of assembly software has a critical impact on virome characterisation
Cited by: 94
Author(s): Thomas D.S. Sutton, Adam G. Clooney, Feargal J. Ryan, R. Paul Ross, Colin Hill
Software Mentions: 8
Published: almost 6 years ago

10.1186/s12864-017-4429-4

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains
Cited by: 27
Author(s): Luis A. Amador, Aline Primot, Édouard Cadieu, Alain Roulet, Frédérique Barloy-Hubler
Software Mentions: 7
Published: almost 7 years ago

10.1186/1471-2164-12-227

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
Cited by: 144
Author(s): Susanne U. Franssen, Ranjit Shrestha, Andrea Bräutigam, Erich Bornberg‐Bauer, Andreas Weber
Software Mentions: 7
Published: over 13 years ago

10.7554/eLife.56689

Genome streamlining in a minute herbivore that manipulates its host plant
Cited by: 30
Author(s): Robert Greenhalgh, Wannes Dermauw, Joris J. Glas, Stéphane Rombauts, Nicky Wybouw, Jainy Thomas, Juan M. Alba, Ellen J. Pritham, Saioa Legarrea, René Feyereisen, Yves Van de Peer, Thomas Van Leeuwen, Richard M. Clark, Merijn R. Kant
Software Mentions: 7
Published: about 4 years ago

10.1186/s13059-019-1768-2

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes
Cited by: 60
Author(s): Geoffrey M. Attardo, Adly M. M. Abd-Alla, Álvaro Acosta-Serrano, James Allen, Rosemary Bateta, Joshua B. Benoit, Kostas Bourtzis, Jo Caers, Guy Caljon, Mikkel Christensen, David W. Farrow, Markus Friedrich, Aurélie Hua-Van, Emily C. Jennings, Denis M. Larkin, Daniel Lawson, Michael J. Lehane, Vasileios Panagiotis Lenis, Ernesto Lowy-Gallego, Rosaline W. Macharia, Anna R. Malacrida, Heather G. Marco, Daniel Masiga, G. Maslen, Irina Matetovici, Richard P Meisel, Irene K. Meki, Veronika Michalková, Wolfgang J. Miller, Patrick Minx, Paul O. Mireji, Lino Ometto, Andrew G. Parker, Rita V. M. Rio, Clair Rose, Andrew J. Rosendale, Omar Rota‐Stabelli, Grazia Savini, Liliane Schoofs, Francesca Scolari, Martin Swain, Peter Takáč, Chad Tomlinson, George Tsiamis, Jan Van Den Abbeele, Aurélien Vigneron, Jingwen Wang, Wesley C. Warren, Robert M. Waterhouse, Matthew T. Weirauch, Brian L. Weiss, Richard K. Wilson, Xin Zhao, Serap Aksoy
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.960

Swabs to genomes: a comprehensive workflow
Cited by: 30
Author(s): Madison I. Dunitz, Jenna M. Lang, Guillaume Jospin, Aaron E. Darling, Jonathan A. Eisen, David A. Coil
Software Mentions: 7
Published: over 9 years ago

10.1186/s13059-017-1367-z

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
Cited by: 9
Author(s): Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert, David Hot
Software Mentions: 6
Published: about 7 years ago

10.1093/gbe/evu149

Small but Powerful, the Primary Endosymbiont of Moss Bugs, Candidatus Evansia muelleri, Holds a Reduced Genome with Large Biosynthetic Capabilities
Cited by: 33
Author(s): Diego Santos-García, Amparo Latorre, Andrés Moya, George Gibbs, Viktor Hartung, Konrad Dettner, Stefan Martin Kuechler, Francisco J. Silva
Software Mentions: 6
Published: over 10 years ago

10.1089/cmb.2020.0081

GeneDMRs: An R Package for Gene-Based Differentially Methylated Regions Analysis
Cited by: 5
Author(s): Xiao Wang, Dan Hao, Haja N. Kadarmideen
Software Mentions: 6
Published: almost 4 years ago

10.7554/eLife.66797

Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers
Cited by: 6
Author(s): Kai He, Triston Eastman, Hannah Czolacz, Shuhao Li, Akio Shinohara, Shin-ichiro Kawada, Mark S. Springer, Michael Berenbrink, Kevin L. Campbell
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2164-12-619

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation
Cited by: 102
Author(s): Monica F. Poelchau, Julie A. Reynolds, David L. Denlinger, Christine G. Elsik, Peter Armbruster
Software Mentions: 6
Published: about 13 years ago

10.1038/sdata.2017.44

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Cited by: 119
Author(s): Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao Qi Zhang, Roberto A. Barrero, Qisen Zhang, Lin Li, Micha Bayer, Dan Bolser, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz‐Amatriaín, Rachid Ounit, Steve Wanamaker, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Dharanya Sampath, Darren Heavens, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K. McCooke, Cong Tan, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse Poland, M. Bellgard, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Peter Langridge, Gary J. Muehlbauer, Paul J. Kersey, Matthew D. Clark, Mario Cáccamo, Alan H. Schulman, Matthias Platzer, Timothy J. Close, Mats Hansson, Guoping Zhang, Ilka Braumann, Chengdao Li, Robbie Waugh, Uwe Scholz, Nils Stein, Martin Mascher
Software Mentions: 6
Published: over 7 years ago

10.1093/gbe/evu133

Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracellular Life
Cited by: 77
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 6
Published: over 10 years ago

10.1186/gb-2013-14-2-r16

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration
Cited by: 104
Author(s): Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Höffner, Marcus Krüger, Panagiotis A. Tsonis, Thilo Borchardt, Thomas Braun
Software Mentions: 6
Published: almost 12 years ago

10.3390/ijms22189824

Species-Specific Humoral Immune Responses in Sheep and Goats upon Small Ruminant Lentivirus Infections Inversely Correlate with Protection against Virus Replication and Pathological Lesions
Cited by: 2
Author(s): Rodolphe Michiels, Stefan Roels, Nick Vereecke, Élisabeth Mathijs, Laurent Mostin, Nick De Regge
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2164-14-100

A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover
Cited by: 19
Author(s): Istvàn Nagy, Susanne Barth, Jeanne Mehenni-Ciz, Michael T. Abberton, Dan Milbourne
Software Mentions: 5
Published: almost 12 years ago

10.3389/fpls.2012.00220

RNA-Seq Assembly – Are We There Yet?
Cited by: 79
Author(s): Simon Schliesky, Udo Gowik, Andreas P.M. Weber, Andrea Bräutigam
Software Mentions: 5
Published: almost 13 years ago

10.1186/1471-2164-15-704

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda
Cited by: 26
Author(s): Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin-Grenet, Florence Blanc, Clément François, Imène Séninet, Anthony Bretaudeau, Doriane Mutuel, Pierre-Alain Girard, Christelle Monsempès, Ghislaine Magdelenat, Frédérique Hilliou, René Feyereisen, Mylène Ogliastro, Anne-Nathalie Volkoff, Emmanuelle Jacquin‐Joly, Emmanuelle d’Alençon, Nicolas Nègre, Philippe Fournier
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-018-20262-y

Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes
Cited by: 15
Author(s): Austin Alleman, Barbara Feldmeyer, Susanne Foitzik
Software Mentions: 5
Published: almost 7 years ago

10.1016/j.chom.2020.01.004

Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner
Cited by: 79
Author(s): Mohammadali Khan Mirzaei, Anik Ashfaq Khan, Prakash Ghosh, Zofia E. Taranu, Mariia Taguer, Jinlong Ru, Rajashree Chowdhury, Md. Mamun Kabir, Li Deng, Dinesh Mondal, Corinne F. Maurice
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0092663

Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing
Cited by: 48
Author(s): Chong Wang, Markus A. Grohme, Brahim Mali, Ralph O. Schill, Marcus Frohme
Software Mentions: 5
Published: almost 11 years ago

10.1186/gb-2013-14-6-r66

Separating homeologs by phasing in the tetraploid wheat transcriptome
Cited by: 129
Author(s): Ksenia V. Krasileva, Vince Buffalo, Paul Bailey, Stephen Pearce, Sarah Ayling, Facundo Tabbita, Marcelo Soria, Shichen Wang, Eduard Akhunov, Cristóbal Uauy, Jorge Dubcovsky
Software Mentions: 5
Published: over 11 years ago

10.3389/fmicb.2019.02273

Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre
Cited by: 15
Author(s): Daniel Mende, Dominique Le Bœuf, Edward F. DeLong
Software Mentions: 5
Published: about 5 years ago

10.1186/1471-2164-11-571

Comparing de novo assemblers for 454 transcriptome data
Cited by: 240
Author(s): Sujai Kumar, Mark Blaxter
Software Mentions: 5
Published: about 14 years ago

10.1111/j.1365-294X.2012.05756.x

Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome‐wide digital gene expression analysis
Cited by: 83
Author(s): Tobias L. Lenz, Christophe Eizaguirre, Björn Rotter, Martin Kalbe, Manfred Milinski
Software Mentions: 5
Published: over 12 years ago

10.3389/fmicb.2016.01078

Region 4 of Rhizobium etli Primary Sigma Factor (SigA) Confers Transcriptional Laxity in Escherichia coli
Cited by: 1
Author(s): Orlando Santillán, Miguel A. Ramı́rez-Romero, Luis Lozano, Alberto Checa, Sergio Encarnación, Guillermo Dávila
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-13-136

A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica
Cited by: 60
Author(s): S. Ueno, Yoshinari Moriguchi, Kentaro Uchiyama, Tokuko Ujino‐Ihara, Norihiro Futamura, Tetsuya Sakurai, Kenji Shinohara, Yoshihiko Tsumura
Software Mentions: 4
Published: almost 13 years ago

10.3389/fmicb.2017.01786

Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter
Cited by: 31
Author(s): Oscar A. Sosa, Daniel J. Repeta, Sara Ferrón, Jessica A. Bryant, Daniel R. Mende, David M. Karl, Edward F. DeLong
Software Mentions: 4
Published: about 7 years ago

10.3390/mi8080233

Operation of a MOEMS Deformable Mirror in Cryo: Challenges and Results
Cited by: 5
Author(s): Frédéric Zamkotsian, Patrick Lanzoni, Rudy Barette, Michael A. Helmbrecht, Franck Marchis, Alex Teichman
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2016.00847

De novo Transcriptome Sequencing to Dissect Candidate Genes Associated with Pearl Millet-Downy Mildew (Sclerospora graminicola Sacc.) Interaction
Cited by: 36
Author(s): Kalyani S. Kulkarni, Harshvardhan N. Zala, Tejas C. Bosamia, Yogesh Shukla, Sushil Kumar, R. S. Fougat, Mruduka S. Patel, Narayanan Subhash, Chaitanya G. Joshi
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2020.00891

Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats
Cited by: 13
Author(s): Romain De Oliveira, Hélène Rimbert, François Balfourier, Jonathan Kitt, Emeric Dynomant, Jan Vrána, Jaroslav Doležel, Federica Cattonaro, Etienne Paux, Frédéric Choulet
Software Mentions: 4
Published: over 4 years ago

10.1186/2042-5783-3-2

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
Cited by: 109
Author(s): D.J. Edwards, Kathryn E. Holt
Software Mentions: 4
Published: over 11 years ago

10.1186/2042-5783-2-3

Metagenomics - a guide from sampling to data analysis
Cited by: 673
Author(s): Torsten Thomas, Jack Gilbert, Patrick Meyer
Software Mentions: 4
Published: almost 13 years ago

10.26508/lsa.201900331

Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis
Cited by: 18
Author(s): Florian Noack, Abhijeet Pataskar, Martin Schneider, Frank Buchholz, Vijay Tiwari, Federico Calegari
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0118231

Sugarcane Giant Borer Transcriptome Analysis and Identification of Genes Related to Digestion
Cited by: 12
Author(s): Fernando Campos de Assis Fonseca, Alexandre Augusto Pereira Firmino, Leonardo Lima Pepino Macedo, Roberta Ramos Coelho, José Dijair Antonino de Sousa Júnior, Orzenil B. Silva‐Junior, Roberto Coiti Togawa, George J. Pappas, Luiz Avelar Brandão de Góis, Maria Cristina Mattar da Silva, Maria Fátima Grossi-de-Sá
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12870-015-0663-6

Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome
Cited by: 40
Author(s): Amir Sherman, Mor Rubinstein, Ravit Eshed, Miri Benita, Mazal Ish-Shalom, Michal Sharabi-Schwager, Ada Rozen, David Saada, Yuval Cohen, Ron Ophir
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0044185

Sequencing and Characterization of Striped Venus Transcriptome Expand Resources for Clam Fishery Genetics
Cited by: 23
Author(s): Alessandro Coppe, Stefania Bortoluzzi, Giulia Murari, Ilaria A. M. Marino, Lorenzo Zane, Chiara Papetti
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0157600

De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies
Cited by: 43
Author(s): Timokratis Karamitros, Ian Harrison, Renata Piorkowska, Aris Katzourakis, Gkikas Magiorkinis, Jean L. Mbisa
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2229-11-131

From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)
Cited by: 101
Author(s): Grit Haseneyer, Thomas Schmutzer, Michael Seidel, Ruonan Zhou, Martin Mascher, C. C. Schön, Stefan Taudien, Uwe Scholz, Nils Stein, Klaus Mayer, Eva Bauer
Software Mentions: 4
Published: about 13 years ago

10.1186/s12864-015-1684-0

Hox cluster characterization of Banna caecilian (Ichthyophis bannanicus) provides hints for slow evolution of its genome
Cited by: 7
Author(s): Riga Wu, Qingfeng Li, Sen Meng, Peng Zhang, Dan Liang
Software Mentions: 4
Published: over 9 years ago

10.3390/v12111304

Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018
Cited by: 7
Author(s): Amélie Chastagner, Séverine Hervé, Stéphane Quéguiner, Edouard Hirchaud, Pierrick Lucas, Stéphane Gorin, Véronique Béven, Nicolas Barbier, Céline Deblanc, Yannick Blanchard, Gaëlle Simon
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-020-6672-3

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly
Cited by: 19
Author(s): Anthony Bayega, Haïg Djambazian, Konstantina T. Tsoumani, Maria‐Eleni Gregoriou, Efthimia Sagri, Elena Drosopoulou, Penelope Mavragani-Tsipidou, Kristina Giorda, George Tsiamis, Kostas Bourtzis, Spyridon Oikonomopoulos, Ken Dewar, Deanna M. Church, Alexie Papanicolaou, Kostas D. Mathiopoulos, Jiannis Ragoussis
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0088998

Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity
Cited by: 58
Author(s): Ron Ophir, Amir Sherman, Mor Rubinstein, Ravit Eshed, Michal Sharabi Schwager, Rotem Harel-Beja, Irit Bar-Ya’akov, Doron Holland
Software Mentions: 4
Published: almost 11 years ago

10.1186/1471-2164-12-285

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence
Cited by: 56
Author(s): José Blanca, Laura Pascual, Peio Ziarsolo, F. Nuez
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0147221

Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics
Cited by: 36
Author(s): Robert A. Syme, Kar‐Chun Tan, James K. Hane, Kejal N Dodhia, Thomas Stoll, Marcus L. Hastie, Eiko Furuki, Simon R. Ellwood, Angela H. Williams, Yew‐Foon Tan, Alison C. Testa, Jeffrey J. Gorman, Richard P. Oliver
Software Mentions: 4
Published: almost 9 years ago

10.1038/srep43149

The hidden perils of read mapping as a quality assessment tool in genome sequencing
Cited by: 4
Author(s): Burhan Lehri, Alan M. Seddon, Andrey V. Karlyshev
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pgen.1006777

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes
Cited by: 138
Author(s): Romain Blanc-Mathieu, Laetitia Perfus‐Barbeoch, Jean‐Marc Aury, Martine Da Rocha, Jérôme Gouzy, Erika Sallet, Cristina Martín-Jimenez, Marc Bailly‐Bechet, Philippe Castagnone‐Sereno, Jean‐François Flot, Djampa Kozlowski, Julie Cazareth, Arnaud Couloux, Corinne Da Silva, Julie Guy, Yujin Kim, Corinne Rancurel, Thomas Schiex, Pierre Abad, Patrick Wincker, Etienne G. J. Danchin
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-14-675

Efficient and accurate whole genome assembly and methylome profiling of E. coli
Cited by: 40
Author(s): Jason Powers, Victor Weigman, Jenny Shu, John Pufky, Donald Cox, Patrick Hurban
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2105-13-S17-S24

TranSeqAnnotator: large-scale analysis of transcriptomic data
Cited by: 6
Author(s): Ranjeeta Menon, Gagan Garg, Robin B. Gasser, Shoba Ranganathan
Software Mentions: 4
Published: about 12 years ago

10.1093/gbe/evaa216

Portiera Gets Wild: Genome Instability Provides Insights into the Evolution of Both Whiteflies and Their Endosymbionts
Cited by: 12
Author(s): Diego Santos-García, Natividad Mestre-Rincon, David Ouvrard, Einat Zchori-Fein, Shai Morin
Software Mentions: 4
Published: about 4 years ago

10.3390/toxins5112172

Three-Fingered RAVERs: Rapid Accumulation of Variations in Exposed Residues of Snake Venom Toxins
Cited by: 106
Author(s): Kartik Sunagar, Timothy N. W. Jackson, Eivind A. B. Undheim, Syed Abid Ali, Agostinho Antunes, Bryan G. Fry
Software Mentions: 4
Published: about 11 years ago

10.1186/1471-2164-13-549

Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes
Cited by: 17
Author(s): Heidrun Sigrid Windisch, Magnus Lucassen, Stephan Frickenhaus
Software Mentions: 4
Published: almost 13 years ago

10.7717/peerj.3569

Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?
Cited by: 42
Author(s): Malvina Kadlec, Baoheng Du, Nicholas C Le Maitre, Michael D. Pirie
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.1066

Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree
Cited by: 33
Author(s): Nagesh A. Kuravadi, Vijay A. Yenagi, Kannan Rangiah, H. B. Mahesh, Anantharamanan Rajamani, Meghana Deepak Shirke, Heikham Russiachand, Ramya Malarini Loganathan, Chandana Shankara Lingu, S Shilpa, Aishwarya Ramamurthy, B. N. Sathyanarayana, Malali Gowda
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0212755

Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing
Cited by: 9
Author(s): Fátima Gomes, Luciana Watanabe, João L.S.G. Vianez, Márcio Roberto Teixeira Nunes, Jedson Ferreira Cardoso, Clayton Pereira Silva de Lima, Horácio Schneider, Iracilda Sampaio
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-14-87

The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus
Cited by: 8
Author(s): Emanuel Heitlinger, Stephen Bridgett, Anna Montazam, Horst Taraschewski, Mark Blaxter
Software Mentions: 4
Published: almost 12 years ago

10.1155/2019/9565794

A Pathway Analysis Based on Genome-Wide DNA Methylation of Chinese Patients with Graves’ Orbitopathy
Cited by: 10
Author(s): Xin Zhong, Lin Hua, Yilin Yang, Tingting Shi, Wei Liu, Xiu Tuo, Li Yu, Xi Cao, Fengying Yang
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.3162

The genomic sequence ofExiguobacterium chiriqhuchastr. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Cited by: 14
Author(s): Ana Gutiérrez-Preciado, Carlos Vargas-Chávez, Mariana Reyes-Prieto, Omar Federico Ordoñez, Diego Santos-García, Tania Rosas-Pérez, Jorge Valdivia-Anistro, Eria A. Rebollar, Andrés Saralegui, Andrés Moya, Enrique Merino, Marı́a Eugenia Farı́as, Amparo Latorre, Valeria Souza
Software Mentions: 4
Published: over 7 years ago

10.3390/toxins5122621

Venom Down Under: Dynamic Evolution of Australian Elapid Snake Toxins
Cited by: 54
Author(s): Timothy N. W. Jackson, Kartik Sunagar, Eivind A. B. Undheim, Ivan Koludarov, Angelo H. C. Chan, Kate L. Sanders, Syed Abid Ali, Iwan Hendrikx, Nathan Dunstan, Bryan G. Fry
Software Mentions: 4
Published: about 11 years ago

10.1186/1471-2164-13-373

Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways
Cited by: 80
Author(s): Anthony R. Borneman, Jane McCarthy, Paul J. Chambers, Eveline Bartowsky
Software Mentions: 3
Published: almost 13 years ago

10.3389/fmicb.2018.02254

To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies
Cited by: 44
Author(s): Diego Santos-García, Ksenia Juravel, Shiri Freilich, Einat Zchori-Fein, Amparo Latorre, Andrés Moya, Shai Morin, Francisco J. Silva
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-12-99

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum
Cited by: 106
Author(s): Joshua P. Der, Michael S. Barker, Norman J. Wickett, Claude W. dePamphilis, Paul G. Wolf
Software Mentions: 3
Published: almost 14 years ago

10.1186/1743-422X-8-406

Sequencing of bovine herpesvirus 4 v.test strain reveals important genome features
Cited by: 18
Author(s): Léonor Palmeira, Bénédicte Machiels, Céline Lété, Alain Vanderplasschen, Laurent Gillet
Software Mentions: 3
Published: over 13 years ago

10.3389/fmicb.2017.01448

PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome
Cited by: 33
Author(s): Jade L. L. Teng, Man Lung Yeung, Elaine Chan, Lilong Jia, Chi Ho Lin, Yi Huang, Herman Tse, Samson S. Y. Wong, Pak C. Sham, Susanna K. P. Lau, Patrick C. Y. Woo
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-13-507

Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel
Cited by: 67
Author(s): J. M. Pujolar, Ilaria A. M. Marino, Massimo Milan, Alessandro Coppe, Grégory E. Maes, Fabrizio Capoccioni, Eleonora Ciccotti, Lieven Bervoets, Adrian Covaci, Claude Belpaire, Gordon Cramb, Tomaso Patarnello, Luca Bargelloni, Stefania Bortoluzzi, Lorenzo Zane
Software Mentions: 3
Published: almost 13 years ago

10.3389/fmicb.2018.03192

Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1
Cited by: 29
Author(s): Stephen Wandro, Andrew Oliver, Tara Gallagher, Claudia Weihe, Whitney England, Jennifer B. H. Martiny, Katrine Whiteson
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2105-10-447

Next generation transcriptomes for next generation genomes using est2assembly
Cited by: 56
Author(s): Alexie Papanicolaou, Remo Stierli, Richard H. ffrench-Constant, David G. Heckel
Software Mentions: 3
Published: about 15 years ago

10.1186/s12864-020-06801-w

The effect of variant interference on de novo assembly for viral deep sequencing
Cited by: 4
Author(s): Christina J. Castro, Rachel L. Marine, Edward Ramos, Terry Fei Fan Ng
Software Mentions: 3
Published: over 4 years ago

10.12688/f1000research.10443.1

ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services
Cited by: 7
Author(s): Espen Mikal Robertsen, Hubert Denise, Alex L. Mitchell, Alex Bateman, Lars Ailo Bongo, Nils Peder Willassen
Software Mentions: 3
Published: almost 8 years ago

10.3389/fgene.2018.00371

De novo Assembly and Transcriptome Characterization of Opisthopappus (Asteraceae) for Population Differentiation and Adaption
Cited by: 8
Author(s): Maofeng Chai, Shengnan Wang, Jie He, Wei Chen, Zelu Fan, Jia Li, Yiling Wang
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-021-02610-3

NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data
Cited by: 80
Author(s): Alessandro Montemurro, Viktoria Schuster, Helle Rus Povlsen, Amalie Kai Bentzen, Vanessa Isabell Jurtz, William D. Chronister, Austin Crinklaw, Sine Reker Hadrup, Ole Winther, Bjoern Peters, Leon Eyrich Jessen, Morten Nielsen
Software Mentions: 3
Published: over 3 years ago

10.1002/ece3.3918

A new strategy to infer circularity applied to four new complete frog mitogenomes
Cited by: 14
Author(s): Denis Jacob Machado, Daniel Janies, Cory Brouwer, Taran Grant
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0108550

A Comparison of Next Generation Sequencing Technologies for Transcriptome Assembly and Utility for RNA-Seq in a Non-Model Bird
Cited by: 35
Author(s): Findley R. Finseth, Richard G. Harrison
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-13-492

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat
Cited by: 35
Author(s): Andreas W. Schreiber, Matthew Hayden, Kerrie Forrest, Stephan Kong, Peter Langridge, Ute Baumann
Software Mentions: 3
Published: almost 13 years ago

10.3390/md10081765

The Transcriptome of Bathymodiolus azoricus Gill Reveals Expression of Genes from Endosymbionts and Free-Living Deep-Sea Bacteria
Cited by: 22
Author(s): Conceição Egas, Miguel Pinheiro, Paula Fernanda Gomes, Cristina Barroso, Raúl Bettencourt
Software Mentions: 3
Published: over 12 years ago

10.1002/evl3.22

Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins
Cited by: 29
Author(s): Rodrigo Pracana, Levantis Ilya, Carlos Martínez-Ruiz, Eckart Stolle, Anurag Priyam, Yannick Wurm
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2016.00143

Improved Environmental Genomes via Integration of Metagenomic and Single-Cell Assemblies
Cited by: 22
Author(s): Daniel R. Mende, Frank O. Aylward, John M. Eppley, Torben Nielsen, Edward F. DeLong
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0034225

Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology
Cited by: 60
Author(s): Yixing Wang, Xin Zeng, Niranjani J. Iyer, Douglas W. Bryant, Todd C. Mockler, Ramamurthy Mahalingam
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0088229

Comparative Variation within the Genome of Campylobacter jejuni NCTC 11168 in Human and Murine Hosts
Cited by: 29
Author(s): Dallas Thomas, Abdul G. Lone, L. Brent Selinger, Eduardo N. Taboada, Richard R. E. Uwiera, D. Wade Abbott, G. Douglas Inglis
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0230404

A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze
Cited by: 7
Author(s): Pedro Italo T. Silva, Orzenil B. Silva‐Junior, Lucileide Vilela Resende, V. A. de Sousa, A. V. de Aguiar, Dário Grattapaglia
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0098376

Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling
Cited by: 45
Author(s): Mónica Sebastiana, Bruno Miguel Vieira, Teresa Lino-Neto, Filipa Monteiro, Andreia Figueiredo, Lisete Sousa, M. S. Pais, R. M. Tavares, Octávio S. Paulo
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-017-4170-z

Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda
Cited by: 35
Author(s): Karina Lucas Silva‐Brandão, Renato J. Horikoshi, Daniel Bernardi, Celso Omoto, Antônio Figueira, Marcelo Mendes Brandão
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0215396

Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting
Cited by: 17
Author(s): Natalia Maria Silva, Aline Márcia Silva Araújo de Oliveira, Stefania Pegorin, Camila Escandura Giusti, Vitor Baptista Ferrari, Deibs Barbosa, Luciane Martins, Carlos L. Morais, João Carlos Setúbal, Suzan Pantaroto de Vasconcellos, da Silva, Júlio Cézar Franco de Oliveira, Renata C. Pascon, Cristina Viana-Niero
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-014-0357-3

NeatFreq: reference-free data reduction and coverage normalization for De Novosequence assembly
Cited by: 16
Author(s): Jamison McCorrison, Pratap Venepally, Indresh Singh, Derrick E. Fouts, Roger S. Lasken, Barbara A. Methé
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0248054

Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes
Cited by: 5
Author(s): Jaqueline Raquel de Almeida, Diego Mauricio Riaño-Pachón, Lívia Maria Franceschini, Isaneli Batista dos Santos, Jessica Aparecida Ferrarezi, Pedro Avelino Maia de Andrade, Cláudia Barros Monteiro-Vitorello, Carlos Alberto Labate, Maria Carolina Quecine
Software Mentions: 3
Published: almost 4 years ago

10.1186/1756-0500-7-132

STINGRAY: system for integrated genomic resources and analysis
Cited by: 5
Author(s): Glauber Wagner, Rodrigo Jardim, Diogo A. Tschoeke, Daniel R Loureiro, Kary Ocaña, Antonio Ribeiro, Vanessa Erichsen Emmel, Christian M. Probst, André Nóbrega Pitaluga, Edmundo C. Grisard, Maria Cláudia Cavalcanti, María Luiza Machado Campos, Marta Mattoso, Alberto M. R. Dávila
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0210356

Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome
Cited by: 27
Author(s): Víctor M. Guerrero-Sánchez, Ana M. Maldonado‐Alconada, Francisco Amil-Ruíz, Andrea Antonio Verardi, Jesús V. Jorrín‐Novo, María‐Dolores Rey
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0048855

Deep Sequencing Reveals Differences in the Transcriptional Landscapes of Fibers from Two Cultivated Species of Cotton
Cited by: 40
Author(s): Jean-Marc Lacape, Michel Claverie, Ramón Vidal, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Manuel Ruiz, M. Fleur du Pré, Danny Llewellyn, Yves Al-Ghazi, John Jacobs, Alexis Dereeper, Stéphanie Huguet, Marc Giband, Claire Lanaud
Software Mentions: 3
Published: about 12 years ago

10.1186/1471-2229-13-228

Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing
Cited by: 40
Author(s): Jin Zhang, Tracey A. Ruhlman, Jeffrey P. Mower, Robert K. Jansen
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0033802

Reconstructing Viral Genomes from the Environment Using Fosmid Clones: The Case of Haloviruses
Cited by: 85
Author(s): Inmaculada García-Heredia, Ana-Belén Martín-Cuadrado, Francisco J. M. Mojica, Fernando Santos, Álex Mira, Josefa Antón, Francisco Rodrı́guez-Valera
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0049455

Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species
Cited by: 104
Author(s): Susan Joseph, Prerak Desai, Yongmei Ji, Craig Cummings, Pei-Ju Rita Shih, Lovorka Degoricija, Alain Rico, Pius Brzoska, Stephen E. Hamby, Naqash Masood, Sumyya Hariri, Hana Sonbol, Nadia Chuzhanova, Michael McClelland, Manohar R. Furtado, Stephen Forsythe
Software Mentions: 3
Published: about 12 years ago

10.1186/1754-6834-7-66

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest
Cited by: 55
Author(s): Gotthard Kunze, Claude Gaillardin, Małgorzata Czernicka, Pascal Durrens, Tiphaine Martin, Erik Böer, Toni Gabaldón, José Almeida Cruz, Emmanuel Talla, Christian Marck, André Goffeau, Valérie Barbe, Philippe Baret, Keith Baronian, Sebastian Beier, Claudine Bleykasten, R. Bode, Serge Casarégola, Laurence Despons, Cécile Fairhead, Martin Giersberg, Przemysław Piotr Gierski, Urs Hähnel, Anja Hartmann, Dagmara Jankowska, Claire Jubin, Paul P. Jung, Ingrid Lafontaine, Véronique Leh-Louis, Marc Lemaire, Marina Marcet‐Houben, Martin Mascher, Guillaume Morel, Guy‐Franck Richard, Jan Riechen, Christine Sacerdot, Anasua Sarkar, Guilhem Savel, Joseph Schacherer, David James Sherman, Nils Stein, Marie Laure Straub, Agnès Thierry, Anke Trautwein-Schult, Benoît Vacherie, Éric Westhof, Sebastian Worch, Bernard Dujon, Jean Luc Souciet, Patrick Wincker, Uwe Scholz, Cécile Neuvéglise
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0129396

Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome
Cited by: 26
Author(s): Ching-Ping Lin, Chih‐Yuan Ko, Ching-I Kuo, Mao-Sen Liu, Roland Schafleitner, Long-Fang Oliver Chen
Software Mentions: 3
Published: over 9 years ago

10.1186/1755-8794-5-26

Screening significantly hypermethylated genes in fetal tissues compared with maternal blood using a methylated-CpG island recovery assay-based microarray
Cited by: 7
Author(s): Aihua Yin, Xiangzhong Zhang, Jing Wu, Lili Du, Tao He, Xiaozhuang Zhang
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0029696

Broad Phylogenomic Sampling and the Sister Lineage of Land Plants
Cited by: 234
Author(s): Ruth Timme, Tsvetan R. Bachvaroff, Charles F. Delwiche
Software Mentions: 3
Published: almost 13 years ago

Projects: bioconductor: MIRA

Papers Mentioning MIRA 856