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

10.1186/1471-2164-12-259
Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing
Cited by: 97
Author(s): Jordi Durbán, Paula Juárez, Yamileth Angulo, Bruno Lomonte, Marietta Flores-Dı́az, Alberto Alape-Girón, Mahmood Sasa, Libia Sanz, José Marı́a Gutiérrez, Joaquı́n Dopazo, Ana Conesa, Juan J. Calvete
Software Mentions: 1
Published: over 13 years ago
10.1186/1471-2164-14-78
Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development
Cited by: 43
Author(s): M.A.N. Passos, V.O. Cruz, F.L. Emediato, Cristiane C. Teixeira, Vânia Cristina Rennó Azevedo, Ana Cristina Miranda Brasileiro, Édson Perito Amorim, Cláudia Fortes Ferreira, N. F. Martins, Roberto Coiti Togawa, G. J. Pappas Júnior, Orzenil Bonfim da Silva, Robert G. Miller
Software Mentions: 1
Published: almost 12 years ago
10.1186/1471-2164-13-406
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective
Cited by: 36
Author(s): Aureliano Bombarely, Kieron D. Edwards, Juan Pablo Sanchez-Tamburrino, Lukas A. Mueller
Software Mentions: 1
Published: over 12 years ago
10.1080/23802359.2017.1318686
Mitochondrial genome divergence between beluga whales in Baffin Bay and the Sea of Okhotsk
Cited by: 1
Author(s): Mikkel Skovrind, José Alfredo Samaniego Castruita, Mads Peter Heide‐Jørgensen, Love Dalén, Eline D. Lorenzen
Software Mentions: 1
Published: almost 8 years ago
10.1080/23802359.2019.1629343
Complete chloroplast genome of the Meconopsis quintuplinervia (Papaveraceae), a traditional medicine of Tibetan
Cited by: 1
Author(s): Binduo Xu, Hengbo Kang, Shuai Luo, Qian Yang, Zhe Zhao, Fangfang Peng, Zhan‐Lin Liu
Software Mentions: 1
Published: over 5 years ago
10.1080/23802359.2019.1693297
The complete chloroplast genome sequence of <i>Pinus cembra</i> L. (Pinaceae)
Cited by: 1
Author(s): Thomas Schott, Hilke Schroeder, Katrin Schöning-Stierand, Birgit Kersten
Software Mentions: 1
Published: over 5 years ago
10.1080/23802359.2019.1689863
Characterization of the complete plastid genome of <i>Acer tsinglingense</i>, an endemic tree species in China
Cited by: 3
Author(s): Peng-Bin Dong, Yu Liu, Qi-Yuan Gao, Ting Yang, Xueyi Chen, Jiayu Yang, Qianhan Shang, Min-Feng Fang
Software Mentions: 1
Published: over 5 years ago
10.1080/23802359.2017.1280706
The complete mitochondrial genome of the White-Nose Syndrome pathogen, Pseudogymnoascus destructans
Cited by: 1
Author(s): Adrian Forsythe, Jianping Xu
Software Mentions: 1
Published: almost 8 years ago
10.1080/23802359.2019.1688697
Characterization of the complete plastid genome of fireweed, Epilobium angustifolium, Shaanxi, China
Cited by: 0
Author(s): Yuli Li, Shiyi Tang, Yu Cheng Dai, Yuting Jiang, Baoguo Li
Software Mentions: 1
Published: over 5 years ago
10.1080/23802359.2021.1872440
Characteristic and phylogenetic analyses of chloroplast genome for <i>Ephedra monosperma</i> (Ephedraceae), an important medicinal species
Cited by: 0
Author(s): Ye Zhao, Yida Fan, Yanci Yang
Software Mentions: 1
Published: almost 4 years ago
10.1186/1471-2164-14-211
Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools
Cited by: 42
Author(s): Veljo Kisand, Teresa Lettieri
Software Mentions: 1
Published: almost 12 years ago
10.1080/23802359.2017.1422396
The complete mitochondrial genome of<i>Psammomys obesus</i>(Rodentia: Muridae)
Cited by: 2
Author(s): Yanhong Lan, Mengjia Liu, Yi Cao
Software Mentions: 1
Published: almost 7 years ago
10.1080/23802359.2021.1960915
The complete mitogenome of the <i>Amolops jinjiangensis</i> (Anura: Ranidae)
Cited by: 1
Author(s): Ziwen Wang, Jun Ping, Yun Xia, Xiaomao Zeng, Jianghong Ran
Software Mentions: 1
Published: over 3 years ago
10.1080/23802359.2018.1437806
Mitochondrial genome of an Allegheny Woodrat (<i>Neotoma magister</i>)
Cited by: 3
Author(s): Mandy Schofield, Joseph E. Duchamp, Jeffery L. Larkin, Timothy J. Smyser, Jacqueline Doyle
Software Mentions: 1
Published: almost 7 years ago
10.1080/23802359.2018.1495122
The complete nucleotide sequence of chloroplast genome of <i>Euphorbia kansui</i> (Euphorbiaceae), an endemic herb in China
Cited by: 3
Author(s): Mi‐Li Liu, Fan Wu, Yue Wu, Yingjuan Wang, Zhong-Hu Li
Software Mentions: 1
Published: over 6 years ago
10.1080/23802359.2020.1772136
The whole genome assembly and evolution analyze of carmine radish (Raphanus sativus L.) Mitochondrion
Cited by: 0
Author(s): Hua Peng, Jian Gao
Software Mentions: 1
Published: over 4 years ago
10.1080/23802359.2020.1791018
The complete plastid genome sequence of Gleditsia sinensis, an ancient medicinal tree in China
Cited by: 1
Author(s): Ji-Qing Bai, Lei Yang, Su Gao, Weixing Zhu, Luqi Huang
Software Mentions: 1
Published: over 4 years ago
10.3390/microorganisms7100396
Fatal Elephant Endotheliotropic Herpesvirus Infection of Two Young Asian Elephants
Cited by: 11
Author(s): Selvaraj Pavulraj, Kathrin Eschke, Adriane Prahl, Michael Flügger, Jakob Trimpert, Petra B. van den Doel, Sandro Andreotti, Sabine Kaessmeyer, Nikolaus Osterrieder, Walid Azab
Software Mentions: 1
Published: about 5 years ago
10.3390/microorganisms8111685
Lysogenization of a Lactococcal Host with Three Distinct Temperate Phages Provides Homologous and Heterologous Phage Resistance
Cited by: 10
Author(s): Sofía Ruiz‐Cruz, Elvina Parlindungan, Andrea Erazo Garzon, Mona Alqarni, Gabriele Andrea Lugli, Marco Ventura, Douwe van Sinderen, Jennifer Mahony
Software Mentions: 1
Published: about 4 years ago
10.1186/1471-2164-13-S7-S8
Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs)
Cited by: 36
Author(s): Gagan Garg, Shoba Ranganathan
Software Mentions: 1
Published: almost 12 years ago
10.1186/1471-2164-10-547
De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley
Cited by: 74
Author(s): Burkhard Steuernagel, Stefan Taudien, Heidrun Gundlach, Michael Seidel, Ruvini Ariyadasa, Daniela Schulte, A. Petzold, Marius Felder, Andreas Graner, Uwe Scholz, Klaus Mayer, Matthias Platzer, Nils Stein
Software Mentions: 1
Published: about 15 years ago
10.1186/1471-2164-15-964
A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)
Cited by: 33
Author(s): Xiaolan Rao, Nick Krom, Yuhong Tang, Thomas Widiez, Daphna Havkin‐Frenkel, Faith C. Belanger, Richard A. Dixon, Fang Chen
Software Mentions: 1
Published: almost 11 years ago
10.1186/1471-2105-9-433
Reranking candidate gene models with cross-species comparison for improved gene prediction
Cited by: 8
Author(s): Qian Liu, Koby Crammer, Fernando Pereira, David S. Roos
Software Mentions: 1
Published: about 16 years ago
10.3390/microorganisms9091869
In Vitro and In Vivo Assessment of the Potential of Escherichia coli Phages to Treat Infections and Survive Gastric Conditions
Cited by: 2
Author(s): Joanna Kaczorowska, Eoghan Casey, Gabriele Andrea Lugli, Marco Ventura, David J. Clarke, Douwe van Sinderen, Jennifer Mahony
Software Mentions: 1
Published: about 3 years ago
10.1128/MRA.00027-20
Draft Genome Sequence of Staphylococcus pseudintermedius Strain 13-13613, Isolated from a Case of Canine Pyoderma
Cited by: 1
Author(s): Inga Eichhorn, Antina Lübke‐Becker, Antje-Maria Lapschies, Megan E. Jacob, Wolfgang Bäumer, Marcus Fulde
Software Mentions: 1
Published: almost 5 years ago
10.1128/MRA.01136-18
First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
Cited by: 5
Author(s): Mustafa Ababneh, Helena Lage Ferreira, Mohammad Khalifeh, David L. Suarez, Claudio L. Afonso
Software Mentions: 1
Published: almost 6 years ago
10.1128/MRA.00887-18
High-Quality Draft Genome Sequence of Xanthomonas arboricola pv. juglandis CPBF 1521, Isolated from Leaves of a Symptomatic Walnut Tree in Portugal without a Past of Phytosanitary Treatment
Cited by: 5
Author(s): Clovis Torres Fernandes, Jochen Blom, Joël F. Pothier, Fernando Tavares
Software Mentions: 1
Published: about 6 years ago
10.1128/MRA.00157-19
Draft Genome Sequence of Xylaria longipes DSM 107183, a Saprotrophic Ascomycete Colonizing Hardwood
Cited by: 2
Author(s): Enrico Büttner, Anna Maria Gebauer, Martin Hofrichter, Christiane Liers, Harald Kellner
Software Mentions: 1
Published: over 5 years ago
10.1128/MRA.00845-19
Draft Genome Sequence of Xylaria hypoxylon DSM 108379, a Ubiquitous Fungus on Hardwood
Cited by: 2
Author(s): Enrico Büttner, Christiane Liers, Martin Hofrichter, Anna Maria Gebauer, Harald Kellner
Software Mentions: 1
Published: about 5 years ago
10.1186/1471-2164-15-774
Identification of male-specific amh duplication, sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia (Oreochromis niloticus)
Cited by: 96
Author(s): Orly Eshel, Andrey Shirak, Lior Dor, Mark Band, Tatyana Zak, Michal Markovich-Gordon, Vered Chalifa‐Caspi, E. Feldmesser, J. I. Weller, Eyal Seroussi, Gideon Hulata, Ron Maymon
Software Mentions: 1
Published: about 10 years ago
10.1128/MRA.00262-20
Draft Genome Sequence of the Ascomycete Xylaria multiplex DSM 110363
Cited by: 0
Author(s): Enrico Büttner, Christiane Liers, Anne Richter, Martin Hofrichter, Harald Kellner
Software Mentions: 1
Published: over 4 years ago
10.1128/MRA.00921-18
High-Quality Draft Genome Sequence of Xanthomonas sp. Strain CPBF 424, a Walnut-Pathogenic Strain with Atypical Features
Cited by: 7
Author(s): Clovis Torres Fernandes, Jochen Blom, Joël F. Pothier, Fernando Tavares
Software Mentions: 1
Published: about 6 years ago
10.1128/MRA.01635-18
Complete Genome Sequence of Lactococcus lactis subsp. cremoris 3107, Host for the Model Lactococcal P335 Bacteriophage TP901-1
Cited by: 4
Author(s): Andrea Erazo Garzon, Jennifer Mahony, Francesca Bottacini, Philip Kelleher, Douwe van Sinderen
Software Mentions: 1
Published: almost 6 years ago
10.1128/MRA.01125-18
Draft Genome Sequence of Bacillus coagulans ZB29, a Commercial Probiotic Strain
Cited by: 1
Author(s): Darshana Chauhan, Y.C. Patel, Jayraj Doshi, Rashesh D. Doshi, Anjali Bose
Software Mentions: 1
Published: almost 6 years ago
10.1128/MRA.00846-19
Complete Genome Sequences of Four <i>Microbacterium</i> Strains Isolated from Metal- and Radionuclide-Rich Soils
Cited by: 2
Author(s): Philippe Ortet, Nicolas Gallois, Justine Long, Séverine Zirah, Catherine Berthomieu, Jean Armengaud, Béatrice Alpha-Bazin, Mohamed Barakat, Virginie Chapon
Software Mentions: 1
Published: about 5 years ago
10.1128/MRA.00285-20
Resequencing of the Red Alga Cyanidioschyzon merolae: Strain Differences and Mitochondrial Sequence Corrections
Cited by: 0
Author(s): Naoki Sato, Takashi Moriyama, Natsumi Mori-Moriyama
Software Mentions: 1
Published: over 4 years ago
10.1128/MRA.00601-20
Draft Genome Sequence of Collimonas pratensis Strain PMB3(1), an Effective Mineral-Weathering and Chitin-Hydrolyzing Bacterial Strain
Cited by: 4
Author(s): Laura Picard, Philippe Oger, Marie‐Pierre Turpault, Stéphane Uroz
Software Mentions: 1
Published: about 4 years ago
10.1128/MRA.00885-18
Sequences of Seven Complete Genomes of Human Parvovirus B19
Cited by: 0
Author(s): Yuhuan Qiu, Zhidan Zhao, Jianming Qiu
Software Mentions: 1
Published: about 6 years ago
10.1186/1471-2164-12-623
Polyphenism in social insects: insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris
Cited by: 61
Author(s): Thomas J. Colgan, James C. Carolan, Stephen Bridgett, Seirian Sumner, Mark Blaxter, Mark J. F. Brown
Software Mentions: 1
Published: almost 13 years ago
10.1186/1471-2164-14-407
Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon
Cited by: 69
Author(s): Michele Vidotto, Alessandro Grapputo, Elisa Boscari, Federica Barbisan, Alessandro Coppe, Gilberto Grandi, Abhishek Kumar, Leonardo Congiu
Software Mentions: 1
Published: almost 12 years ago
10.1186/1471-2164-12-206
Identification of ovule transcripts from the Apospory-Specific Genomic Region (ASGR)-carrier chromosome
Cited by: 19
Author(s): Yajuan Zeng, Joann A. Conner, Peggy Ozias‐Akins
Software Mentions: 1
Published: over 13 years ago
10.1128/MRA.00871-20
Genome Sequence of Bifidobacterium breve INIA P734 (CECT 8178), a Strain Isolated from Human Breast Milk
Cited by: 4
Author(s): Lidia Rodrigo-Torres, Eva Rodríguez, Ángela Peirotén, Susana Langa, Margarita Médina, David R. Arahal, Rosa Aznar, Juan Luís Arqués
Software Mentions: 1
Published: almost 4 years ago
10.1128/MRA.00416-19
Draft Genome Sequences of 16 Strains of Escherichia Cryptic Clade II Isolated from Intertidal Sediment in Hong Kong
Cited by: 5
Author(s): Zhiyong Shen, Xiu Pei Koh, Yanping Yu, Chun Fai Woo, Yigang Tong, S. S. Lau
Software Mentions: 1
Published: over 5 years ago
10.1128/MRA.01306-20
Genome Sequence of the Versatile Deadwood Decomposer Xylaria grammica IHIA82
Cited by: 1
Author(s): Enrico Büttner, Virginia Wambui Kimani, Harald Kellner, Martin Hofrichter, Christiane Liers
Software Mentions: 1
Published: almost 4 years ago
10.1128/MRA.00570-19
Draft Genome Sequences of 12 Monophasic Salmonella enterica subsp. enterica Serotype Typhimurium 1,4,[5],12:i:− Strains Isolated from Wild Griffon Vultures in Eastern Spain
Cited by: 1
Author(s): Clara Marín, Giuseppe D’Auria, Llúcia Martínez-Priego, Francisco Marco‐Jiménez
Software Mentions: 1
Published: about 5 years ago
10.1186/1471-2164-14-538
Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis
Cited by: 34
Author(s): Alberto Pallavicini, Adriana Canapa, Marco Barucca, Jessica Alföldi, Maria Assunta Biscotti, Francesco Buonocore, Gianluca De Moro, Federica Di Palma, Anna Maria Fausto, Marikò Forconi, Marco Gerdol, Daisy Monica Makapedua, Jason Turner-Meier, Ettore Olmo, Giuseppe Scapigliati
Software Mentions: 1
Published: over 11 years ago
10.1186/1471-2164-15-129
Comparative genomics of unintrogressed Campylobacter coli clades 2 and 3
Cited by: 36
Author(s): Caroline P. A. Skarp-de Haan, Alejandra Culebro, Thomas Schott, Joana Revez, Elke K. H. Schweda, Marja‐Liisa Hänninen, Mirko Rossi
Software Mentions: 1
Published: almost 11 years ago
10.1128/MRA.01637-18
Draft Genome Sequences of a Putative Prokaryotic Consortium (IPPAS B-1204) Consisting of a Cyanobacterium ( <i>Leptolyngbya</i> sp.) and an Alphaproteobacterium ( <i>Porphyrobacter</i> sp.)
Cited by: 3
Author(s): Kirill S. Mironov, Pavel A. Leusenko, Vera V. Ustinova, К. Болатхан, B. K. Zayadan, Elena V. Kupriyanova, Maria Shumskaya, Maria A. Sinetova, Dmitry A. Los
Software Mentions: 1
Published: over 5 years ago
10.1128/MRA.00210-21
Nearly Complete Genome Sequences of Two Bluetongue Viruses Isolated during the 2020 Outbreak in the Grand Duchy of Luxembourg
Cited by: 1
Author(s): Frank Vandenbussche, Manon Bourg, Élisabeth Mathijs, David Lefebvre, Ilse De Leeuw, Andy Haegeman, Laetitia Aerts, Steven Van Borm, Kris De Clercq
Software Mentions: 1
Published: over 3 years ago
10.1186/1471-2164-14-787
Genomes of “Spiribacter”, a streamlined, successful halophilic bacterium
Cited by: 40
Author(s): Mario López‐Pérez, Rohit Ghai, María José León, Ángel Rodríguez-Olmos, José Luis Copa-Patiño, Juán Soliveri, Cristina Sánchez‐Porro, António Ventosa, Francisco Rodrı́guez-Valera
Software Mentions: 1
Published: about 11 years ago
10.1128/MRA.00249-19
Draft Genome Sequence of the Wood-Staining Ascomycete Chlorociboria aeruginascens DSM 107184
Cited by: 2
Author(s): Enrico Büttner, Christiane Liers, Anna Maria Gebauer, Jérôme Collemare, Jorge C. Navarro-Muñoz, Martin Hofrichter, Harald Kellner
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0053632
Transcriptome Exploration in Leymus chinensis under Saline-Alkaline Treatment Using 454 Pyrosequencing
Cited by: 39
Author(s): Yueru Sun, Fawei Wang, Nan Wang, Yanjun Dong, Qi Liu, Lei Zhao, Huan Chen, Weican Liu, Hai-Long Yin, Xiaomei Zhang, Yanxi Yuan, Haiyan Li
Software Mentions: 1
Published: almost 12 years ago
10.1128/MRA.00682-19
Draft Genome Sequence of Mycolicibacterium sp. Strain CH28, a Potential Degrader of Diisopropyl Ether, Isolated from Pharmaceutical Wastewater
Cited by: 2
Author(s): Ingrid Zsilinszky, Péter Gyula, Zoltán Bihari, Balázs Fehér, Zsolt Szabó
Software Mentions: 1
Published: about 5 years ago
10.1186/s12864-017-3537-5
Genetic and functional characterisation of the lactococcal P335 phage-host interactions
Cited by: 27
Author(s): Jennifer Mahony, Joana Oliveira, Barry Collins, Laurens Hanemaaijer, Gabriele Andrea Lugli, Horst Neve, Marco Ventura, Thijs R. H. M. Kouwen, Christian Cambillau, Douwe van Sinderen
Software Mentions: 1
Published: almost 8 years ago
10.1186/1471-2164-15-67
Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat
Cited by: 16
Author(s): Andrzej K. Noyszewski, Farhad Ghavami, Loai M. Alnemer, Afshin Soltani, Yong Gu, Naxin Huo, Steven W. Meinhardt, Penny M.A. Kianian, Shahryar F. Kianian
Software Mentions: 1
Published: almost 11 years ago
10.1128/MRA.01404-18
Draft Genome Sequences for Five <i>Photorhabdus</i> Bacterial Symbionts of Entomopathogenic <i>Heterorhabditis</i> Nematodes Isolated from India
Cited by: 5
Author(s): Vishal Singh Somvanshi, Bhumika Dubay, Jyoti Kushwah, R Sivakumar, Udayakumar S. Vishnu, Jagadesan Sankarasubramanian, Jeyaprakash Rajendhran, Uma Rao
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pone.0151434
Transcriptome Analysis of an Insecticide Resistant Housefly Strain: Insights about SNPs and Regulatory Elements in Cytochrome P450 Genes
Cited by: 11
Author(s): Khalid Mahmood, Dorte H. Højland, Torben Asp, Michael Kristensen
Software Mentions: 1
Published: over 8 years ago
10.1128/MRA.00185-20
Coding-Complete Genome Sequence of an African Swine Fever Virus Strain Liv13/33 Isolate from Experimental Transmission between Pigs and Ornithodoros moubata Ticks
Cited by: 7
Author(s): Amélie Chastagner, Rémi Pereira De Oliveira, Evelyne Hutet, Mireille Le Dimna, Frédéric Paboeuf, Pierrick Lucas, Yannick Blanchard, Linda K. Dixon, Laurence Vial, Marie‐Frédérique Le Potier
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0087648
Diversity of Conotoxin Gene Superfamilies in the Venomous Snail, Conus victoriae
Cited by: 100
Author(s): Samuel D. Robinson, Helena Safavi-­Hemami, Lachlan McIntosh, Anthony W. Purcell, Raymond S. Norton, Anthony T. Papenfuss
Software Mentions: 1
Published: almost 11 years ago
10.1186/1471-2164-14-294
Sex-biased gene expression in the brown alga Fucus vesiculosus
Cited by: 37
Author(s): Maria João Fernandes Martins, Catarina Mota, Gareth A. Pearson
Software Mentions: 1
Published: over 11 years ago
10.1186/1471-2164-13-640
Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa
Cited by: 61
Author(s): Arwa Shahin, Martijn van Kaauwen, Danny Esselink, Joachim W. Bargsten, J.M. van Tuyl, R.G.F. Visser, Paul Arens
Software Mentions: 1
Published: about 12 years ago
10.1590/0074-02760180586
Aporé virus, a novel mammarenavirus (Bunyavirales: Arenaviridae) related to highly pathogenic virus from South America
Cited by: 7
Author(s): Jorlan Fernandes, Alexandro Guterres, Renata Carvalho de Oliveira, Rodrigo Jardim, Alberto M. R. Dávila, Roger Hewson, Elba Regina Sampaio de Lemos
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pone.0083542
Assessment of the Geographic Origins of Pinewood Nematode Isolates via Single Nucleotide Polymorphism in Effector Genes
Cited by: 27
Author(s): Joana Figueiredo, Maria José Simões, Paula Fernanda Gomes, Cristina Barroso, Diogo Pinho, Luci Conceição, Luís Fonseca, Isabel Abrantes, Miguel Pinheiro, Conceição Egas
Software Mentions: 1
Published: almost 11 years ago
10.1590/0074-02760190020
Diversity of metallo-β-lactamase-encoding genes found in distinct species of Acinetobacter isolated from the Brazilian Amazon Region
Cited by: 13
Author(s): Danielle Murici Brasiliense, Rodrigo Cayô, Ana Paula Streling, Carolina Silva Nodari, Rafael Ribeiro Barata, Poliana Silva Lemos, Janaína Mota de Vasconcelos Massafra, Yan Correa, Igor Rafael dos Santos Magalhães, Ana Cristina Gales, Roberta Nice Salgado Sodré
Software Mentions: 1
Published: almost 6 years ago
10.1590/0074-02760160010
Draft genome of the Leptospira interrogans strains, Acegua, RCA, Prea, and Capivara, obtained from wildlife maintenance hosts and infected domestic animals
Cited by: 14
Author(s): Frederico Schmitt Kremer, Marcus Redü Eslabão, Sérgio Jorge, Natasha Rodrigues de Oliveira, Julia Labonde, Monize N. P Santos, Leonardo Garcia Monte, André Alex Grassmann, C. E. Cunha, Karine M. Forster, Luisa Zanolli Moreno, Andréa Micke Moreno, Vinícius Farias Campos, Alan J. A. McBride, Luciano S. Pinto, Odir A. Dellagostin
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0174506
Phylogenetic analysis of family Neisseriaceae based on genome sequences and description of Populibacter corticis gen. nov., sp. nov., a member of the family Neisseriaceae, isolated from symptomatic bark of Populus × euramericana canker
Cited by: 19
Author(s): Yong Li, Xue Han, Sheng-qi Sang, Cai-li Lin, Xi-zhuo Wang
Software Mentions: 1
Published: over 7 years ago
10.1590/0074-02760180051
Genome sequence of a multidrug-resistant Corynebacterium striatum isolated from bloodstream infection from a nosocomial outbreak in Rio de Janeiro, Brazil
Cited by: 10
Author(s): Juliana Nunes Ramos, Izabel dos Santos Rodrigues, Paulo Victor Pereira Baio, João Flávio Carneiro Veras, Rommel Thiago Jucá Ramos, Luis Gustavo Carvalho Pacheco, Vasco Azevedo, Raphael Hirata Júnior, Michel Abanto, Ana Luíza Mattos‐Guaraldi, Verônica Viana Vieira
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2164-11-694
A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences
Cited by: 59
Author(s): Tonia S. Schwartz, Hongseok Tae, Youngik Yang, Keithanne Mockaitis, John L. Van Hemert, Stephen R. Proulx, Jeong Hyeon Choi, Anne M. Bronikowski
Software Mentions: 1
Published: almost 14 years ago
10.1186/1471-2164-12-629
A pilot study for channel catfish whole genome sequencing and de novo assembly
Cited by: 26
Author(s): Yanliang Jiang, Jianguo Lü, Eric Peatman, Huseyin Kucuktas, Shikai Liu, Shaolin Wang, Fenyong Sun, Zhanjiang Liu
Software Mentions: 1
Published: almost 13 years ago
10.1186/1471-2164-14-120
High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L
Cited by: 168
Author(s): Régine Delourme, Cyril Falentin, Berline Fopa Fomeju, Marie Boillot, Gilles Lassalle, Isabelle André, Jorge Duarte, Valérie Gauthier, Nicole Lucante, Amandine Marty, Maryline Pauchon, Jean-Philippe Pichon, Nicolas Ribière, Gwenn Trotoux, Philippe Blanchard, Nathalie Rivière, Jean‐Pierre Martinant, Jérôme Pauquet
Software Mentions: 1
Published: almost 12 years ago
10.1186/1471-2164-14-178
Deep sequencing for de novo construction of a marine fish (Sparus aurata)transcriptome database with a large coverage of protein-coding transcripts
Cited by: 76
Author(s): Josep Àlvar Calduch-Giner, Azucena Bermejo-Nogales, Laura Benedito-Palos, Itziar Estensoro, Gabriel F. Ballester‐Lozano, Ariadna Sitjà‐Bobadilla, Jaume Pérez‐Sánchez
Software Mentions: 1
Published: over 11 years ago
10.1155/2017/4097425
The Draft Genome of the Non-Host-Associated<i>Methanobrevibacter arboriphilus</i>Strain DH1 Encodes a Large Repertoire of Adhesin-Like Proteins
Cited by: 5
Author(s): Anja Poehlein, Rolf Daniel, Henning Seedorf
Software Mentions: 1
Published: almost 8 years ago
10.3390/ma13235575
Production of Greener High-Strength Concrete Using Russian Quartz Sandstone Mine Waste Aggregates
Cited by: 41
Author(s): Alexander Tolstoy, Valery Lesovik, Roman Fediuk, Mugahed Amran, G. Murali, Nikolai Vatin, Yuriy Vasilev
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0123298
Rapid High Resolution Genotyping of Francisella tularensis by Whole Genome Sequence Comparison of Annotated Genes (“MLST+”)
Cited by: 38
Author(s): Markus Antwerpen, Karola Prior, Alexander Mellmann, Sebastian Höppner, Wolf D. Splettstoesser, Dag Harmsen
Software Mentions: 1
Published: over 9 years ago
10.3390/ma10080956
Enhanced Corrosion Resistance of Carbon Steel in Hydrochloric Acid Solution by Eriobotrya Japonica Thunb. Leaf Extract: Electrochemical Study
Cited by: 18
Author(s): Wenjing Yang, Qihui Wang, Ke Xu, Yuebang Yin, Hebin Bao, Xueming Li, Lidan Niu, Shiqi Chen
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0106116
Mycoplasma ovipneumoniae - A Primary Cause of Severe Pneumonia Epizootics in the Norwegian Muskox (Ovibos moschatus) Population
Cited by: 35
Author(s): Kjell Handeland, Torstein Tengs, Branko Kokotovic, Turid Vikøren, Roger D. Ayling, Bjarne Bergsjø, Ólöf Sigurðardóttir, Tord Bretten
Software Mentions: 1
Published: about 10 years ago
10.3390/md13106472
Matrix Production, Pigment Synthesis, and Sporulation in a Marine Isolated Strain of Bacillus pumilus
Cited by: 5
Author(s): Blanda Di Luccia, Antonio Riccio, Adele Vanacore, Loredana Baccigalupi, Antonio Molinaro, Ezio Ricca
Software Mentions: 1
Published: about 9 years ago
10.1186/1471-2164-11-559
High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus
Cited by: 114
Author(s): Raúl Bettencourt, Miguel Pinheiro, Conceição Egas, Paula Fernanda Gomes, Mafalda Afonso, Timothy M. Shank, Ricardo Serrão Santos
Software Mentions: 1
Published: about 14 years ago
10.1186/s12864-017-3955-4
Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family
Cited by: 72
Author(s): Gabriele Andrea Lugli, Christian Milani, Francesca Turroni, Sabrina Duranti, Leonardo Mancabelli, Marta Mangifesta, Chiara Ferrario, Monica Marianna Modesto, Paola Mattarelli, Jiří Killer, Douwe van Sinderen, Marco Ventura
Software Mentions: 1
Published: over 7 years ago
10.3390/md10020258
Recruitment of Glycosyl Hydrolase Proteins in a Cone Snail Venomous Arsenal: Further Insights into Biomolecular Features of Conus Venoms
Cited by: 26
Author(s): Aude Violette, Adrijana Leonardi, David Piquemal, Yves Terrat, Daniel Biass, Sébastien Dutertre, Florian Noguier, Frédéric Ducancel, Reto Stöcklin, Igor Križaj, Philippe Favreau
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.pone.0085480
Deep Sequencing-Based Analysis of the Cymbidium ensifolium Floral Transcriptome
Cited by: 56
Author(s): Xiaobai Li, Jianxun Luo, Tang Yan, Xinghua Lin, Feng Jin, Dehui Qin, Chongbo Sun, Min Xie
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0040592
Characterization of Pro-Inflammatory Flagellin Proteins Produced by Lactobacillus ruminis and Related Motile Lactobacilli
Cited by: 57
Author(s): Bridget A. Neville, Brian M. Forde, Marcus J. Claesson, Trevor Darby, Avril Coghlan, Ken Nally, R. Paul Ross, Paul W. O’Toole
Software Mentions: 1
Published: over 12 years ago
10.1186/1471-2164-15-574
Whole genome sequence comparison of vtx2-converting phages from Enteroaggregative Haemorrhagic Escherichia coli strains
Cited by: 14
Author(s): Laura Grande, Valeria Michelacci, Rosangela Tozzoli, P. Ranieri, Antonella Maugliani, Alfredo Caprioli, Stefano Morabito
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0118741
Correction: GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers
Cited by: 0
Author(s):
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0200104
First chloroplast genomics study of Phoenix dactylifera (var. Naghal and Khanezi): A comparative analysis
Cited by: 12
Author(s): Abdul Latif Khan, Sajjad Asaf, In‐Jung Lee, Ahmed Al‐Harrasi, Ahmed Al‐Rawahi
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0030370
CAPRG: Sequence Assembling Pipeline for Next Generation Sequencing of Non-Model Organisms
Cited by: 5
Author(s): Arun K. Rawat, Mohamed O. Elasri, Kurt A. Gust, Glover Eugene George, Don Pham, Leona D. Scanlan, Chris D. Vulpe, Edward J. Perkins
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.pone.0083823
In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups
Cited by: 70
Author(s): Tarini Shankar Ghosh, Satarupa Sengupta, G. Balakrish Nair, Sharmila S. Mande
Software Mentions: 1
Published: almost 11 years ago
10.1186/1476-511X-9-55
A high-fat meal impairs muscle vasodilatation response to mental stress in humans with Glu27 beta2-adrenoceptor polymorphism
Cited by: 2
Author(s): Mmg Gowdak, Mateus Camaroti Laterza, Maria Urbana Pinto Brandão Rondon, Ivani C. Trombetta, Alexandre C. Pereira, José Eduardo Krieger, Carlos Eduardo Negrão
Software Mentions: 1
Published: almost 15 years ago
10.1371/journal.pone.0088615
Transcriptome Analysis of the Scleractinian Coral Stylophora pistillata
Cited by: 48
Author(s): Sarit Karako-Lampert, Didier Zoccola, Mali Salmon‐Divon, Mark Katzenellenbogen, Sylvie Tambutté, Anthony Bertucci, Ove Høegh-Guldberg, Emeline Deleury, Denis Allemand, Oren Levy
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0222457
Rapid evolution of Mexican H7N3 highly pathogenic avian influenza viruses in poultry
Cited by: 15
Author(s): Sungsu Youk, Donghun Lee, Helena Lage Ferreira, Claudio L. Afonso, Ángel E. Absalón, David E. Swayne, David L. Suarez, Mary J. Pantin‐Jackwood
Software Mentions: 1
Published: about 5 years ago
10.1186/1471-2164-12-56
Pyrosequencing the transcriptome of the greenhouse whitefly, Trialeurodes vaporariorum reveals multiple transcripts encoding insecticide targets and detoxifying enzymes
Cited by: 99
Author(s): Nikos Karatolos, Yannick Pauchet, Paul Wilkinson, Ritika Chauhan, I. Denholm, Kevin Gorman, David R. Nelson, Chris Bass, Richard H. ffrench-Constant, Martin S. Williamson
Software Mentions: 1
Published: almost 14 years ago
10.1186/s12864-014-1192-7
Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms
Cited by: 30
Author(s): Bin He, Shirong Zhao, Yuehong Chen, Qinghua Cao, Changhe Wei, Xiaoyu Cheng, Yizheng Zhang
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pone.0055090
Transcriptome Analysis of Cytokinin Response in Tomato Leaves
Cited by: 33
Author(s): Xiulin Shi, S. Dutta Gupta, Ingrid Lindquist, Connor Cameron, Joann Mudge, Aaron M. Rashotte
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pone.0067221
Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya
Cited by: 71
Author(s): Yury M. Shtarkman, Zeynep A. Koçer, Robyn Edgar, Ram Veerapaneni, Tom D’Elia, Paul F. Morris, Scott O. Rogers
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0177896
Genomic abundance is not predictive of tandem repeat localization in grass genomes
Cited by: 4
Author(s): Paul Bilinski, Yonghua Han, Matthew B. Hufford, Anne Lorant, Pingdong Zhang, Matt C. Estep, Jiming Jiang, Jeffrey Ross‐Ibarra
Software Mentions: 1
Published: over 7 years ago
10.3390/brainsci10090655
Non-Immersive Virtual Reality for Post-Stroke Upper Extremity Rehabilitation: A Small Cohort Randomized Trial
Cited by: 20
Author(s): Roxana Miclăuş, Nadinne Roman, Silviu Caloian, B.I. Mitoiu, Oana Suciu, Roxana Ramona Onofrei, Ecaterina Pavel, Andrea Elena Neculau
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pone.0109952
Species-Specific Viromes in the Ancestral Holobiont Hydra
Cited by: 53
Author(s): Juris A. Grasis, Tim Lachnit, Friederike Anton-Erxleben, Yan Wei Lim, Robert Schmieder, Sebastian Fraune, Sören Franzenburg, Santiago Insua, GloriaMay Machado, Matthew Haynes, Mark Little, Robert B. Kimble, Philip Rosenstiel, Forest Rohwer, Thomas C. G. Bosch
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0232667
Adaptation to unstable coordination patterns in individual and joint actions
Cited by: 1
Author(s): Thomas Wolf, Natalie Sebanz, Günther Knoblich
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0112617
Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome
Cited by: 21
Author(s): Nicolas Tchitchek, David Safronetz, Angela L. Rasmussen, Craig Martens, Kimmo Virtaneva, Stephen F. Porcella, Heinz Feldmann, Hideki Ebihara, Michael G. Katze
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0090914
How to Kill the Honey Bee Larva: Genomic Potential and Virulence Mechanisms of Paenibacillus larvae
Cited by: 88
Author(s): Marvin Djukic, Elżbieta Brzuszkiewicz, Anne Fünfhaus, Jörn Voss, Kathleen Gollnow, Lena Poppinga, Heiko Liesegang, Eva Garcia‐Gonzalez, Elke Genersch, Rolf Daniel
Software Mentions: 1
Published: over 10 years ago