bioconductor: MIRA | Projects | Ecosyste.ms: Papers

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 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: about 12 years ago

10.4049/jimmunol.1401980

Definition of the Cattle Killer Cell Ig–like Receptor Gene Family: Comparison with Aurochs and Human Counterparts
Cited by: 26
Author(s): Nicholas D. Sanderson, Paul J. Norman, Lisbeth A. Guethlein, Shirley A. Ellis, Christina L. Williams, Matthew Breen, Steven D. E. Park, David A. Magee, Farbod Babrzadeh, Andrew Warry, Michael Watson, Daniel G. Bradley, David E. MacHugh, Peter Parham, John A. Hammond
Software Mentions: 3
Published: over 9 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 6 years ago

10.1038/s41396-018-0215-9

Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome
Cited by: 28
Author(s): Zachary Armstrong, Keith Mewis, Feng Liu, Connor Morgan-Lang, Melanie Scofield, Evan W Durno, Hong Ming Chen, Kevin Mehr, Stephen G. Withers, Steven J. Hallam
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-4470-y

Features of the organization of bread wheat chromosome 5BS based on physical mapping
Cited by: 10
Author(s): Е. А. Салина, Mikhail A. Nesterov, Zeev Frenkel, A. A. Kiseleva, E. M. Timonova, Federica Magni, Jan Vrána, Jan Šafář, Hana Šimková, Jaroslav Doležel, Abraham B. Korol, E. M. Sergeeva
Software Mentions: 3
Published: over 6 years ago

10.3390/toxins5122456

Evolution Stings: The Origin and Diversification of Scorpion Toxin Peptide Scaffolds
Cited by: 76
Author(s): Kartik Sunagar, Eivind A. B. Undheim, Angelo H. C. Chan, Ivan Koludarov, Sergio A. Muñoz-Gómez, Agostinho Antunes, Bryan G. Fry
Software Mentions: 3
Published: over 10 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: almost 9 years ago

10.3390/toxins5122488

A Proteomics and Transcriptomics Investigation of the Venom from the Barychelid Spider Trittame loki (Brush-Foot Trapdoor)
Cited by: 64
Author(s): Eivind A.B. Undheim, Kartik Sunagar, Volker Herzig, Laurence Kely, Dolyce H. W. Low, Timothy N. W. Jackson, Alun Jones, Nyoman D. Kurniawan, Glenn F. King, Syed Abid Ali, Agostinho Antunes, Tim Ruder, Bryan G. Fry
Software Mentions: 3
Published: over 10 years ago

10.1038/s41396-019-0545-2

The Green Revolution shaped the population structure of the rice pathogen Xanthomonas oryzae pv. oryzae
Cited by: 29
Author(s): Ian Lorenzo Quibod, Genelou Atieza-Grande, Eula Gems Oreiro, Denice Palmos, Marian Hanna R. Nguyen, Sapphire Coronejo, Ei Ei Aung, Cipto Nugroho, Verónica Román-Reyna, M. R. G. Burgos, Pauline Capistrano, Sylvestre G. Dossa, Geoffrey Onaga, Caesar Saloma, Casiana Vera Cruz, Ricardo Oliva
Software Mentions: 3
Published: over 4 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: about 5 years ago

10.1038/s41598-021-83664-5

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution
Cited by: 22
Author(s): Maria Alejandra Serna-Sánchez, Oscar Alejandro Pérez‐Escobar, Diego Bogarín, María Fernanda Torres-Jimenez, Astrid Catalina Álvarez-Yela, Juliana E. Arcila-Galvis, Climbiê Ferreira Hall, Fábio de Barros, Fábio Pinheiro, Steven Dodsworth, Mark W. Chase, Alexandre Antonelli, Tatiana Arias
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-020-61305-7

Root transcriptome reveals efficient cell signaling and energy conservation key to aluminum toxicity tolerance in acidic soil adapted rice genotype
Cited by: 12
Author(s): Wricha Tyagi, Julia S. Yumnam, Debashish Sen, Mayank Rai
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-021-87457-8

Low biological fluctuation of mitochondrial CpG and non-CpG methylation at the single-molecule level
Cited by: 21
Author(s): Chloe D. Goldsmith, Jesús Rafael Rodríguez‐Aguilera, Ines El-Rifai, Adrien Jarretier-Yuste, Valérie Hervieu, Olivier Raineteau, Pierre Saintigny, Victoria Chagoya de Sánchez, Robert Dante, Gabriel Ichim, Héctor Hernández-Vargas
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-018-21560-1

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources
Cited by: 40
Author(s): Sarika Jaiswal, Tushar J. Antala, M. K. Mandavia, Meenu Chopra, Rahul Singh Jasrotia, R. S. Tomar, Jashminkumar Kheni, U. B. Angadi, Mir Asif Iquebal, B. A. Golakia, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0214227

A viral metagenomic survey identifies known and novel mammalian viruses in bats from Saudi Arabia
Cited by: 31
Author(s): Nischay Mishra, Shamsudeen F. Fagbo, Abdulaziz N. Alagaili, Adam Nitido, Simon H. Williams, James Ng, Bohyun Lee, Abdulkareem Durosinlorun, Joel A. Garcia, Komal Jain, Vishal Kapoor, Jonathan H. Epstein, Thomas Briese, Ziad A. Memish, Kevin J. Olival, W. Ian Lipkin
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-43796-1

Long-lived Temnothorax ant queens switch from investment in immunity to antioxidant production with age
Cited by: 36
Author(s): Matteo Negroni, Susanne Foitzik, Barbara Feldmeyer
Software Mentions: 3
Published: about 5 years ago

10.1186/1751-0473-8-23

Combining de novo and reference-guided assembly with scaffold_builder
Cited by: 54
Author(s): Genivaldo Gueiros Z. Silva, Bas E. Dutilh, T. David Matthews, Keri Elkins, Robert Schmieder, Elizabeth A. Dinsdale, Robert A. Edwards
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-017-14239-6

Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)
Cited by: 82
Author(s): José F. Sánchez-Sevilla, José G. Vallarino, Sonia Osorio, Aureliano Bombarely, David Posé, Catharina Merchante, Miguel A. Botella, Iraida Amaya, Victoriano Valpuesta
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.0030054

Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
Cited by: 87
Author(s): Axel Bernal, Koby Crammer, Artemis G. Hatzigeorgiou, Fernando Pereira
Software Mentions: 3
Published: about 17 years ago

10.1002/pld3.232

Draft genomes of two outcrossing wild rice, <i>Oryza rufipogon</i> and <i>O. longistaminata</i> , reveal genomic features associated with mating‐system evolution
Cited by: 8
Author(s): Wei Li, Qun‐Jie Zhang, Ting Zhu, Yan Tong, Kui Li, Cong Shi, Yun Zhang, Yun‐Long Liu, Jianjun Jiang, Yuan Liu, Enhua Xia, Hui Huang, Liping Zhang, Dan Zhang, Chao Shi, Wenkai Jiang, Yanjie Zhao, Shu‐Yan Mao, Jun-Ying Jiao, Peng Xu, Lili Yang, Li‐Zhi Gao
Software Mentions: 3
Published: almost 4 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: over 12 years ago

10.1038/s41598-017-18341-7

Discovering viral genomes in human metagenomic data by predicting unknown protein families
Cited by: 13
Author(s): Mauricio Barrientos‐Somarribas, David N. Messina, Christian Pou, Fredrik Lysholm, Annelie Bjerkner, Tobias Allander, Björn Andersson, Erik L. L. Sonnhammer
Software Mentions: 3
Published: over 6 years ago

10.1186/1944-3277-9-22

Genome sequence of Coxiella burnetii strain Namibia
Cited by: 12
Author(s): Mathias C. Walter, Caroline Öhrman, Kerstin Myrtennäs, Andreas Sjödin, Mona Byström, Pär Larsson, Anna Macellaro, Mats Forsman, Dimitrios Frangoulidis
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj.3558

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology
Cited by: 59
Author(s): Benjamin J. Tully, Rohan Sachdeva, Elaina D. Graham, John F. Heidelberg
Software Mentions: 3
Published: almost 7 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: over 10 years ago

10.12688/wellcomeopenres.14438.2

Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum
Cited by: 5
Author(s): Mary Dias, Chitra Pattabiraman, Shilpa Siddappa, Malali Gowda, Anita Shet, Derek J. Smith, Barbara Muehlemann, Krishnapriya Tamma, Tom Solomon, Terry C. Jones, Sudhir Krishna
Software Mentions: 3
Published: over 5 years ago

10.1093/gbe/evv144

Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition
Cited by: 27
Author(s): John A. Burns, Amber Paasch, Apurva Narechania, Eun-Soo Kim
Software Mentions: 3
Published: almost 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: almost 12 years ago

10.1186/s12864-016-2565-x

Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome
Cited by: 14
Author(s): Aimee Benjamin, Benjamin B. Green, B.A. Crooker, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: about 8 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: almost 13 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: about 12 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: over 5 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: about 8 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: over 5 years ago

10.3389/fmicb.2021.613529

Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria
Cited by: 37
Author(s): Melissa E K Haines, Francesca E Hodges, Janet Y. Nale, Jennifer Mahony, Douwe van Sinderen, Joanna Kaczorowska, Bandar Alrashid, Mahmuda Akter, Nathan Brown, Dominic Sauvageau, Thomas Sicheritz-Pontén, Anisha M. Thanki, Andrew Millard, Edouard E. Galyov, Martha R.J. Clokie
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2105-15-211

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
Cited by: 446
Author(s): Marten Boetzer, Walter Pirovano
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-11-731

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea
Cited by: 50
Author(s): Josep F. Abril, Francesc Cebrià, Gustavo Rodríguez-Esteban, Thomas Horn, Susanna Fraguas, B. Calvo, Kerstin Bartscherer, Emili Saló
Software Mentions: 2
Published: over 13 years ago

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: about 8 years ago

10.3389/fmicb.2015.00084

Novel Flp pilus biogenesis-dependent natural transformation
Cited by: 32
Author(s): Angel Angelov, Paul M. P. van Bergen, Florian Nadler, Philipp Hornburg, Antoni Lichev, Maria Übelacker, Fiona Pachl, Bernhard Küster, Wolfgang Liebl
Software Mentions: 2
Published: over 9 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: over 6 years ago

10.1186/1471-2164-13-599

Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening
Cited by: 49
Author(s): Carla S. Santos, Miguel Pinheiro, Ana Isabel Silva, Conceição Egas, Marta W. Vasconcelos
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-11-543

Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate
Cited by: 126
Author(s): Jon Jerlström-Hultqvist, Oscar Franzén, Johan Ankarklev, Feifei Xu, Eva Nohýnková, Jan O. Andersson, Staffan G. Svärd, Björn Andersson
Software Mentions: 2
Published: over 13 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: over 8 years ago

10.1186/s12864-015-1331-9

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release
Cited by: 42
Author(s): Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne Da Silva, Jean‐Charles Leplé, Florent Murat, S. Ueno, Jérôme Bartholome, Céline Lalanne, François Ehrenmann, Céline Noirot, Christian Burban, Valérie Leger, Joëlle Amselem, Caroline Belser, Hadi Quesneville, Michael Stierschneider, Silvia Fluch, Lasse Feldhahn, Mika Tarkka, Sylvie Herrmann, François Buscot, Christophe Klopp, Antoine Kremer, Jérôme Salse, Jean‐Marc Aury, Christophe Plomion
Software Mentions: 2
Published: about 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: over 3 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: almost 10 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: over 11 years ago

10.1186/1471-2164-11-703

Gene discovery in the horned beetle Onthophagus taurus
Cited by: 38
Author(s): Jeong Hyeon Choi, Teiya Kijimoto, Emilie C. Snell‐Rood, Hongseok Tae, Youngik Yang, Armin P. Moczek, Justen Andrews
Software Mentions: 2
Published: over 13 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: about 10 years ago

10.1186/1471-2164-11-635

Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered european eel
Cited by: 85
Author(s): Alessandro Coppe, J. M. Pujolar, Grégory E. Maes, Peter Larsen, Michael Møller Hansen, Louis Bernatchez, Lorenzo Zane, Stefania Bortoluzzi
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2105-14-S15-S16

Finishing bacterial genome assemblies with Mix
Cited by: 41
Author(s): Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand‐Pugnet, Florence Tardy, Christine Citti, Virginie Dupuy, Macha Nikolski
Software Mentions: 2
Published: over 10 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: almost 4 years ago

10.1186/1471-2164-11-384

Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
Cited by: 167
Author(s): Sheng Guo, Yi Zheng, Je‐Gun Joung, Shiqiang Liu, Zhonghua Zhang, Oswald Crasta, Bruno W. S. Sobral, Yong Xu, Sanwen Huang, Zhangjun Fei
Software Mentions: 2
Published: almost 14 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: over 8 years ago

10.1186/1471-2164-14-793

Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum)
Cited by: 38
Author(s): Yang Ping Lee, Federico M. Giorgi, Marc Lohse, Kotryna Kvederavičiūtė, Sven Klages, Björn Usadel, Irute Meskiene, Richard Reinhardt, Dirk K. Hincha
Software Mentions: 2
Published: over 10 years ago

10.1128/AEM.00139-16

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone
Cited by: 8
Author(s): Kevin C. Lee, Matthew B. Stott, Peter F. Dunfield, Curtis Huttenhower, Ian R. McDonald, Xochitl C. Morgan
Software Mentions: 2
Published: almost 8 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: almost 12 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: about 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: over 11 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: about 8 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: about 12 years ago

10.1186/s12859-017-1927-y

Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data
Cited by: 50
Author(s): Kosai Al-Nakeeb, Thomas Nordahl Petersen, Thomas Sicheritz-Pontén
Software Mentions: 2
Published: over 6 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: almost 11 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: over 5 years ago

10.3389/fmicb.2014.00750

Current strategies for mobilome research
Cited by: 26
Author(s): Tue Sparholt Jørgensen, Anne S. Kiil, Mette Sif Hansen, Søren J. Sørensen, Lars Hansen
Software Mentions: 2
Published: over 9 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: about 9 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: over 12 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: about 10 years ago

10.3390/md11030830

The CHROMEVALOA Database: A Resource for the Evaluation of Okadaic Acid Contamination in the Marine Environment Based on the Chromatin-Associated Transcriptome of the Mussel Mytilus galloprovincialis
Cited by: 22
Author(s): Victoria Suárez-Ulloa, Juan Fernández‐Tajes, Vanessa Aguiar‐Pulido, Ciro Rivera-Casas, Rodrigo González-Romero, Juan Ausió, Josefina Méndez, Julián Dorado, José M. Eirín‐López
Software Mentions: 2
Published: about 11 years ago

10.1186/s12862-015-0434-x

Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
Cited by: 12
Author(s): Barbara Feldmeyer, Bastian Greshake, Elisabeth Funke, Ingo Ebersberger, Markus Pfenninger
Software Mentions: 2
Published: almost 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: about 11 years ago

10.1186/s12864-016-2528-2

Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b
Cited by: 18
Author(s): Andrej Benjak, Swapna Uplekar, Ming Zhang, Jérémie Piton, Stewart T. Cole, Claudia Sala
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2164-15-357

Transcriptomic changes during regeneration of the central nervous system in an echinoderm
Cited by: 68
Author(s): Vladimir Mashanov, Olga Zueva, José E. García‐Arrarás
Software Mentions: 2
Published: over 10 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: almost 10 years ago

10.1186/s13068-016-0471-8

Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq
Cited by: 31
Author(s): Yuan Fu, Michele Poli, Gaurav Sablok, Bo Wang, Yanchun Liang, Nicola La Porta, Violeta Velikova, Francesco Loreto, Mingai Li, Claudio Varotto
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-017-3972-3

Transcriptome profiling of tobacco (Nicotiana tabacum) pollen and pollen tubes
Cited by: 23
Author(s): Lei Liu Conze, Sofia Berlin, Aude Le Bail, Benedikt Kost
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12864-016-2515-7

HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads
Cited by: 16
Author(s): Anas Al-okaily
Software Mentions: 2
Published: about 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: over 11 years ago

10.1186/bcr2233

Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer
Cited by: 133
Author(s): Stefania Tommasi, Deborah L Karm, Xiwei Wu, Yun Yen, Gerd P. Pfeifer
Software Mentions: 2
Published: about 15 years ago

10.3390/life10120356

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota
Cited by: 10
Author(s): Lucía Muggia, Claudio Gennaro Ametrano, Katja Sterflinger, Donatella Tesei
Software Mentions: 2
Published: over 3 years ago

10.3390/life10100228

The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers
Cited by: 21
Author(s): Soyeon Kim, Joo Won Lee, Young‐Seok Park
Software Mentions: 2
Published: over 3 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: over 11 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: over 2 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: over 11 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: over 9 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: over 7 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: over 5 years ago

10.1186/1471-2164-15-371

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing
Cited by: 37
Author(s): José B. Pereira-Leal, Isabel A. Abreu, Cláudia S. Alabaça, Maria Helena Almeida, Paulo Almeida, Tânia Almeida, Isabel Amorim, Susana de Sousa Araújo, Herlânder Azevedo, Aleix Badia, Dora Batista, Andreas Böhn, Tiago Capote, Isabel Carrasquinho, Inês Chaves, Ana Cristina Coelho, María José Costa, Rita Costa, A. Cravador, Conceição Egas, Carlos Faro, Ana Margarida Fortes, Ana S. Fortunato, Maria João Gaspar, Sónia Gonçalves, José Graça, M. Horta, Vera Inácio, José Leitão, Teresa Lino-Neto, Liliana Marum, José Matos, Diogo Mendonça, Andreia Miguel, Celia María Gonzalo Miguel, Leonor Morais-Cecílio, Isabel Neves, Filomena Nóbrega, Maria Margarida Oliveira, Rute Oliveira, M. S. Pais, Jorge A P Paiva, Octávio S. Paulo, Miguel Pinheiro, João Raimundo, José C. Ramalho, Ana Isabel Ribeiro, Teresa Ribeiro, Margarida Rocheta, Ana Isabel Rodrigues, José Carlos Rodrígues, Nelson J. M. Saibo, Tatiana Santo, Ana Clara Santos, Paula Sá–Pereira, Mónica Sebastiana, Fernanda Simões, Rómulo Sacramento Sobral, R. M. Tavares, Rita Teresa Teixeira, Carolina Varela, Manuela Veloso, Cândido Pinto Ricardo
Software Mentions: 2
Published: over 10 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: over 8 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: about 6 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: almost 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: over 5 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: about 13 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: almost 13 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: about 11 years ago

10.1186/s12864-015-1519-z

Genome assembly using Nanopore-guided long and error-free DNA reads
Cited by: 162
Author(s): Mohammed‐Amin Madoui, Stéfan Engelen, Corinne Cruaud, Caroline Belser, Laurie Bertrand, Adriana Alberti, Arnaud Lemainque, Patrick Wincker, Jean‐Marc Aury
Software Mentions: 2
Published: about 9 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: over 8 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: over 9 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: about 12 years ago

Projects: bioconductor: MIRA

Papers Mentioning MIRA 856