bioconductor: MIRA | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-12-S3-S14

In silico secretome analysis approach for next generation sequencing transcriptomic data
Cited by: 30
Author(s): Gagan Garg, Shoba Ranganathan
Software Mentions: 1
Published: almost 14 years ago

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

10.1186/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

10.1186/1471-2164-12-629

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

10.1186/1471-2164-13-640

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

10.1186/1471-2164-15-67

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

10.1186/1471-2164-15-129

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

10.1186/1471-2164-14-407

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

10.1186/1471-2164-15-964

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

10.1186/1471-2164-10-547

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

10.1186/1471-2164-14-78

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

10.1186/1471-2164-13-387

Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection
Cited by: 83
Author(s): P. M. Guimarães, Ana Cristina Miranda Brasileiro, Carolina Vianna Morgante, Andressa Cunha Quintana Martins, George J. Pappas, Orzenil B. Silva, Roberto Coiti Togawa, Soraya C. M. Leal‐Bertioli, Ana Cláudia Guerra Araújo, Márcio de Carvalho Moretzsohn, David J. Bertioli
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-11-695

Deep sequencing of New World screw-worm transcripts to discover genes involved in insecticide resistance
Cited by: 33
Author(s): Rumão Batista Nunes de Carvalho, Ana Maria Lima de Azeredo-Espin, Tatiana Teixeira Torres
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-15-768

Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak
Cited by: 31
Author(s): Joana Revez, Ann-Katrin Llarena, Thomas Schott, Markku Kuusi, Marjaana Hakkinen, Rauni Kivistö, Marja‐Liisa Hänninen, Mirko Rossi
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2164-14-753

Life based on phosphite: a genome-guided analysis of Desulfotignum phosphitoxidans
Cited by: 34
Author(s): Anja Poehlein, Rolf Daniel, Bernhard Schink, Diliana D. Simeonova
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-15-238

High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species
Cited by: 17
Author(s): Louise Brousseau, Alexandra Tinaut, Caroline Duret, Tiange Lang, Pauline Garnier‐géré, Ivan Scotti
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-1981-7

Integration of Ixodes ricinus genome sequencing with transcriptome and proteome annotation of the naïve midgut
Cited by: 37
Author(s): Wibke J. Cramaro, Dominique Revets, Oliver Hunewald, Regina Sinner, Anna L. Reye, Claude P. Muller
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-015-1294-x

Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis
Cited by: 66
Author(s): Kian Lam Tan, Yung-Chie Tan, Li-Yen Chang, Kok Wei Lee, Siti Sarah Nor'e, Wai-Yan Yee, Mohd Noor Mat Isa, Faizatul Lela Jafar, Chee-Choong Hoh, Sazaly AbuBakar
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-019-5713-2

Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features
Cited by: 5
Author(s): Yu-Feng Huang, Tzu-Han Chen, Zih-Ting Chang, Tai-Chuan Wang, Se Jin Lee, Jong Cheol Kim, Jae Soo Kim, King-Wah Chiu, Yu‐Shin Nai
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-13-266

De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus
Cited by: 87
Author(s): Yijun Zhou, Fei Gao, Ran Liu, Jinchao Feng, Hongjie Li
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-12-77

Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology
Cited by: 85
Author(s): Rebekah E. Oliver, Gerard R. Lazo, Joseph D. Lutz, Marc Rubenfield, Nicholas A. Tinker, Joseph M. Anderson, Nicole H Wisniewski Morehead, Dinesh Adhikary, Eric N. Jellen, Peter J. Maughan, Gina L Brown Guedira, Shiaoman Chao, Aaron D. Beattie, M. L. Carson, H. W. Rines, D. E. Obert, J. Michael Bonman, Eric W. Jackson
Software Mentions: 1
Published: almost 14 years ago

10.1186/1471-2164-14-227

Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis
Cited by: 104
Author(s): Yunyuan Xu, Zheng Zhang, Mengxi Wang, Jianhe Wei, Hongjiang Chen, Zhi‐Hui Gao, Chun Sui, Hongmei Luo, Xingli Zhang, Yun Yang, Hua Meng, Wenlan Li
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-15-112

Genome-wide transcriptome analysis of Chinese pollination-constant nonastringent persimmon fruit treated with ethanol
Cited by: 37
Author(s): Chun Luo, Qinglin Zhang, Zhitian Luo
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-15-97

Insights into naturally minimised Streptomyces albus J1074 genome
Cited by: 134
Author(s): Nestor Zaburannyi, Mariia Rabyk, Bohdan Ostash, Victor Fedorenko, Andriy Luzhetskyy
Software Mentions: 1
Published: almost 11 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

10.1186/1471-2164-15-574

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

10.1186/1471-2164-11-559

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

10.1186/1471-2164-11-694

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

10.1186/1471-2164-14-294

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/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

10.1186/1471-2164-14-787

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

10.1186/1471-2164-14-538

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

10.1186/1471-2164-12-623

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

10.1186/1471-2164-15-774

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

10.1186/1471-2164-13-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

10.1186/1471-2164-14-211

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

10.1186/1471-2164-12-259

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/s12864-019-5587-3

Genome and proteome of the chlorophyll f-producing cyanobacterium Halomicronema hongdechloris: adaptative proteomic shifts under different light conditions
Cited by: 21
Author(s): Min Chen, Miguel A. Hernández‐Prieto, Patrick C. Loughlin, Yaqiong Li, Robert D. Willows
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5482-y

Genome analysis identifies a spontaneous nonsense mutation in ppsD leading to attenuation of virulence in laboratory-manipulated Mycobacterium tuberculosis
Cited by: 6
Author(s): Shyamasree De Majumdar, Kriti Sikri, Payel Ghosh, Neetika Jaisinghani, Malobi Nandi, Sheetal Gandotra, Shekhar C. Mande, Jaya Sivaswami Tyagi
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-15-1139

A genome-guided analysis of energy conservation in the thermophilic, cytochrome-free acetogenic bacterium Thermoanaerobacter kivui
Cited by: 55
Author(s): Verena Hess, Anja Poehlein, Marie Charlotte Weghoff, Rolf Daniel, Volker Müller
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-017-3739-x

No evidence for a bovine mastitis Escherichia coli pathotype
Cited by: 48
Author(s): Andreas Leimbach, Anja Poehlein, John Vollmers, Dennis Görlich, Rolf Daniel, Ulrich Dobrindt
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-11-242

Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
Cited by: 54
Author(s): Niranjan Nagarajan, Constance E. Cook, MariaPia Di Bonaventura, Hong Ge, Allen L. Richards, Kimberly A. Bishop‐Lilly, Robert DeSalle, Timothy D. Read, Mihai Pop
Software Mentions: 1
Published: over 14 years ago

10.1186/s12864-016-2626-1

The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus
Cited by: 18
Author(s): Cláudia S. L. Vicente, Francisco X. Nascimento, Yoriko Ikuyo, Peter J. A. Cock, Manuel Mota, Koichi Hasegawa
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-1775-y

Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids
Cited by: 47
Author(s): Enrique Ibarra-Laclette, Alfonso Méndez-Bravo, Claudia Anahí Pérez-Torres, Victor A. Albert, Keithanne Mockaitis, Aruna Kilaru, Rodolfo López-Gómez, Jacob Israel Cervantes-Luevano, Luis Herrera-Estrella
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-016-2604-7

Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni
Cited by: 26
Author(s): Peter R. Sternes, Anthony R. Borneman
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-1821-9

De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis
Cited by: 15
Author(s): Enrique Ibarra-Laclette, Flor Zamudio-Hernández, Claudia Anahí Pérez-Torres, Victor A. Albert, Enrique Ramı́rez-Chávez, Jorge Molina‐Torres, Araceli Fernández-Cortés, Carlos L. Calderón‐Vázquez, José Luis Olivares‐Romero, Alfredo Herrera‐Estrella, Luis Herrera‐Estrella
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-13-219

Genome-wide SNP identification in multiple morphotypes of allohexaploid tall fescue (Festuca arundinacea Schreb)
Cited by: 16
Author(s): Melanie L. Hand, Noel O. I. Cogan, John W. Forster
Software Mentions: 1
Published: over 12 years ago

10.1186/s12913-020-05280-9

Establishing injury surveillance in emergency departments in Nepal: protocol for mixed methods prospective study
Cited by: 5
Author(s): Dan Magnus, Santosh Bhatta, Julie Mytton, Elisha Joshi, Emma Bird, Sumiksha Bhatta, Sunil Raja Manandhar, Sunil Kumar Joshi
Software Mentions: 1
Published: over 4 years ago

10.1186/1755-8794-4-82

Identification of DNA methylation changes associated with human gastric cancer
Cited by: 53
Author(s): Jung Hoon Park, Jinah Park, Jung Kyoon Choi, Jaemyun Lyu, Min Soo Bae, Young Gun Lee, Jae Bum Bae, Dong Yoon Park, Han Kwang Yang, Tae You Kim, Young-Joon Kim
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12866-015-0460-2

Molecular epidemiology and characterization of an outbreak causing Klebsiella pneumoniae clone carrying chromosomally located bla CTX-M-15 at a German University-Hospital
Cited by: 24
Author(s): Stephen E. Mshana, Moritz Fritzenwanker, Linda Falgenhauer, Eugen Domann, Torsten Hain, Trinad Chakraborty, Can Imirzalioglu
Software Mentions: 1
Published: over 9 years ago

10.1186/s12866-021-02090-9

Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection
Cited by: 7
Author(s): Maria Kulecka, Edyta Waker, Filip Ambrożkiewicz, Agnieszka Paziewska, Karolina Skubisz, Patrycja Cybula, Łukasz Targoński, Michał Mikula, Jan Walewski, Jerzy Ostrowski
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2180-14-192

Distinguishing highly-related outbreak-associated Clostridium botulinum type A(B) strains
Cited by: 23
Author(s): Brian Raphael, T. Brian Shirey, Carolina Lúquez, Susan E. Maslanka
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2180-13-74

Mealybugs nested endosymbiosis: going into the ‘matryoshka’ system in Planococcus citri in depth
Cited by: 35
Author(s): Sergio López-Madrigal, Amparo Latorre, Manuel Porcar, Andrés Moya, Rosario Gil
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2229-14-179

BeMADS1 is a key to delivery MADSs into nucleus in reproductive tissues-De novo characterization of Bambusa edulis transcriptome and study of MADS genes in bamboo floral development
Cited by: 34
Author(s): Ming-Che Shih, Ming-Lun Chou, Jin-Jun Yue, Cheng-Tran Hsu, Wen-Shin Chang, Swee-Suak Ko, De-Chih Liao, Yao‐Ting Huang, Jeremy J.W. Chen, Jiangang Yuan, Xiaoping Gu, Chun-Shin Lin
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2229-14-2

The temporal foliar transcriptome of the perennial C3 desert plant Rhazya stricta in its natural environment
Cited by: 26
Author(s): Steven Yates, Igor Chernukhin, Rubén Álvarez-Fernández, Ulrike Bechtold, Mohammed N. Baeshen, Nabih A. Baeshen, Mohammad Z Mutwakil, Jamal S. M. Sabir, Tracy Lawson, Philip M. Mullineaux
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2229-14-43

Genetic analysis of safflower domestication
Cited by: 33
Author(s): Stephanie A. Pearl, John E. Bowers, Sebastian Reyes-Chin-Wo, Richard W. Michelmore, John M. Burke
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12870-014-0407-z

“The usual suspects”- analysis of transcriptome sequences reveals deviating B gene activity in C. vulgaris bud bloomers
Cited by: 4
Author(s): Anne Behrend, Thomas Borchert, Annette Hohe
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2229-13-13

Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies
Cited by: 22
Author(s): Barbara J. Bliss, Stefan Wanke, Abdelali Barakat, Saravanaraj Ayyampalayam, Norman J. Wickett, P. Kerr Wall, Yuannian Jiao, Lena Landherr, Paula E. Ralph, Yi Hu, Christoph Neinhuis, Jim Leebens‐Mack, K. Arumuganathan, Sandra W. Clifton, Siela N. Maximova, Hong Mā, Claude W. dePamphilis
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2393-5-6

Women's health groups to improve perinatal care in rural Nepal
Cited by: 95
Author(s): Joanna Morrison, Suresh Tamang, Natasha Mesko, David Osrin, Bhim P. Shrestha, Madan Manandhar, Dharma S Manandhar, Hilary Standing, Anthony Costello
Software Mentions: 1
Published: over 19 years ago

10.1186/1756-0500-7-69

RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis
Cited by: 29
Author(s): Keng See Chow, Ahmad-Kamal Ghazali, Chee-Choong Hoh, Zainorlina Mohd-Zainuddin
Software Mentions: 1
Published: almost 11 years ago

10.1186/1756-0500-5-243

Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes
Cited by: 7
Author(s): Mohammed Sahli, Tetsuo Shibuya
Software Mentions: 1
Published: over 12 years ago

10.1186/1756-0500-4-411

Sequencing of BAC pools by different next generation sequencing platforms and strategies
Cited by: 14
Author(s): Stefan Taudien, Burkhard Steuernagel, Ruvini Ariyadasa, Daniela Schulte, Thomas Schmutzer, Marco Groth, Marius Felder, A. Petzold, Uwe Scholz, Klaus Mayer, Nils Stein, Matthias Platzer
Software Mentions: 1
Published: about 13 years ago

10.1186/1756-0500-5-79

SNP markers retrieval for a non-model species: a practical approach
Cited by: 22
Author(s): Arwa Shahin, Thomas van Gurp, Sander Peters, R.G.F. Visser, J.M. van Tuyl, Paul Arens
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12917-017-1239-5

No evidence of enteric viral involvement in the new neonatal porcine diarrhoea syndrome in Danish pigs
Cited by: 21
Author(s): Nicole Bakkegård Goecke, Charlotte Kristiane Hjulsager, Hanne Kongsted, Mette Boye, Simon Rasmussen, Fredrik Granberg, Thea Kølsen Fischer, S E Midgley, Lasse Dam Rasmussen, Øystein Angen, Jan Kresten Nielsen, Sven Erik Lind Jorsal, Lars Erik Larsen
Software Mentions: 1
Published: about 7 years ago

10.1186/s12917-017-1211-4

Phylogenetic assessment reveals continuous evolution and circulation of pigeon-derived virulent avian avulaviruses 1 in Eastern Europe, Asia, and Africa
Cited by: 39
Author(s): Mahmoud Sabra, Kiril M. Dimitrov, Iryna V. Goraichuk, Abdul Wajid, Poonam Sharma, Dawn Williams-Coplin, Asma Basharat, Shafqat Fatima Rehmani, Denys Muzyka, Patti J. Miller, Claudio L. Afonso
Software Mentions: 1
Published: about 7 years ago

10.1136/bmjgh-2018-001024

Long-term impact of community-based participatory women’s groups on child and maternal mortality and child disability: follow-up of a cluster randomised trial in rural Nepal
Cited by: 4
Author(s): Michelle Heys, Lu Gram, Angie Wade, Edward James Norman Haworth, David Osrin, Khadkha Sagar, Deepti Shrestha, Rishi Neupane, Dhruba Adhikari, Ramesh Adhikari, Bharat Budhathoki, Dharma S Manandhar, Anthony Costello
Software Mentions: 1
Published: almost 6 years ago

10.3762/bjnano.10.63

Enhancement in thermoelectric properties due to Ag nanoparticles incorporated in Bi2Te3 matrix
Cited by: 7
Author(s): Seema Gupta, D. C. Agarwal, Sivaiah Bathula, Sankarakumar Amrithpandian, K. Asokan, Ajay Dhar, B. K. Panigrahi, D.K. Avasthi, Vinay Gupta
Software Mentions: 1
Published: over 5 years ago

10.1186/s13040-016-0090-8

Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads
Cited by: 20
Author(s): Liang Ma, Castle Raley, Xin Zheng, Geetha Kutty, Emile Gogineni, Brad T. Sherman, Qiang Sun, Xiongfong Chen, Thomas Skelly, Kristine Jones, Robert M. Stephens, Bin Zhou, William Lau, Calvin A. Johnson, Tomozumi Imamichi, Minkang Jiang, Robin Dewar, Richard A. Lempicki, Bao Tran, Joseph A. Kovacs, Da Wei Huang
Software Mentions: 1
Published: over 8 years ago

10.1093/bioinformatics/btt273

GAGE-B: an evaluation of genome assemblers for bacterial organisms
Cited by: 138
Author(s): Tanja Magoč, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg
Software Mentions: 1
Published: over 11 years ago

10.1093/bioinformatics/bts613

Reference-independent comparative metagenomics using cross-assembly: crAss
Cited by: 57
Author(s): Bas E. Dutilh, Robert Schmieder, James Nulton, Ben Felts, Peter Salamon, Robert A. Edwards, John L. Mokili
Software Mentions: 1
Published: about 12 years ago

10.6026/97320630014031

Current Bioinformatics resources in combating infectious diseases
Cited by: 13
Author(s): Amr T. M. Saeb
Software Mentions: 1
Published: almost 7 years ago

10.3390/biology2020629

Ecology of Subglacial Lake Vostok (Antarctica), Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice
Cited by: 54
Author(s): Scott O. Rogers, Yury M. Shtarkman, Zeynep A. Koçer, Robyn Edgar, Ram Veerapaneni, Tom D’Elia
Software Mentions: 1
Published: over 11 years ago

10.3390/biology2010206

Microbial Analyses of Ancient Ice Core Sections from Greenland and Antarctica
Cited by: 35
Author(s): Caitlin Knowlton, Ram Veerapaneni, Tom D’Elia, Scott O. Rogers
Software Mentions: 1
Published: almost 12 years ago

10.1155/2021/6662027

Genome Features and In Vitro Activity against Influenza A and SARS-CoV-2 Viruses of Six Probiotic Strains
Cited by: 9
Author(s): И. В. Соловьева, T. N. Ilyicheva, Vasiliy Y. Marchenko, Oleg V. Pyankov, А. Г. Точилина, Irina V. Belova, В. А. Жирнов, Н. И. Бормотов, М. О. Скарнович, А. Г. Дурыманов, С. Б. Молодцова, Ekaterina Filippova, A. S. Ovchinnikova, Anastasia V Magerramova, Alexander B. Ryzhikov, Rinat А. Maksyutov
Software Mentions: 1
Published: over 3 years ago

10.3390/biomedicines8120605

A Novel Nonsense Mutation in FGB (c.1421G>A; p.Trp474Ter) in the Beta Chain of Fibrinogen Causing Hypofibrinogenemia with Bleeding Phenotype
Cited by: 25
Author(s): Tomáš Šimurda, R. Vilar, Jana Žolková, Eliška Ceznerová, Zuzana Kolková, Dušan Loderer, Marguerite Neerman-Arbez, Alessandro Casini, Monika Brunclíková, Ingrid Škorňová, Miroslava Dobrotová, Marián Grendár, Ján Staško, Peter Kubisz
Software Mentions: 1
Published: almost 4 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

10.1186/1476-511X-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

10.3390/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

10.3390/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

10.3390/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

10.3390/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

10.1590/0074-02760180051

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

10.1590/0074-02760160010

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

10.1590/0074-02760190020

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

10.1590/0074-02760180586

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

10.1128/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

10.1128/MRA.01404-18

Draft Genome Sequences for Five Photorhabdus Bacterial Symbionts of Entomopathogenic Heterorhabditis 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

10.1128/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

10.1128/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

10.1128/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

10.1128/MRA.01637-18

Draft Genome Sequences of a Putative Prokaryotic Consortium (IPPAS B-1204) Consisting of a Cyanobacterium ( Leptolyngbya sp.) and an Alphaproteobacterium ( Porphyrobacter 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.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

10.1128/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.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.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.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

10.1128/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.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.00846-19

Complete Genome Sequences of Four Microbacterium 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.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

Projects: bioconductor: MIRA

Papers Mentioning MIRA 856