How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
Schurch, Nicholas J, Schofield, Pietá, Gierliński, Marek, Cole, Christian, Sherstnev, Alexander, Singh, Vijender, Wrobel, Nicola, Gharbi, Karim, Simpson, Gordon G, Owen-Hughes, Tom, Blaxter, Mark, Barton, Geoffrey J
Published in RNA (Cambridge) (01.06.2016)
Published in RNA (Cambridge) (01.06.2016)
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Journal Article
Genome wide association and genomic prediction for growth traits in juvenile farmed Atlantic salmon using a high density SNP array
Tsai, Hsin-Yuan, Hamilton, Alastair, Tinch, Alan E, Guy, Derrick R, Gharbi, Karim, Stear, Michael J, Matika, Oswald, Bishop, Steve C, Houston, Ross D
Published in BMC genomics (18.11.2015)
Published in BMC genomics (18.11.2015)
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Journal Article
Benefits and pitfalls of captive conservation genetic management: Evaluating diversity in scimitar-horned oryx to support reintroduction planning
Ogden, Rob, Chuven, Justin, Gilbert, Tania, Hosking, Caroline, Gharbi, Karim, Craig, Mark, Al Dhaheri, Shaikha Salem, Senn, Helen
Published in Biological conservation (01.01.2020)
Published in Biological conservation (01.01.2020)
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Journal Article
Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping
Gautier, Mathieu, Foucaud, Julien, Gharbi, Karim, Cézard, Timothée, Galan, Maxime, Loiseau, Anne, Thomson, Marian, Pudlo, Pierre, Kerdelhué, Carole, Estoup, Arnaud
Published in Molecular ecology (01.07.2013)
Published in Molecular ecology (01.07.2013)
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Journal Article
The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
Gautier, Mathieu, Yamaguchi, Junichi, Foucaud, Julien, Loiseau, Anne, Ausset, Aurélien, Facon, Benoit, Gschloessl, Bernhard, Lagnel, Jacques, Loire, Etienne, Parrinello, Hugues, Severac, Dany, Lopez-Roques, Celine, Donnadieu, Cecile, Manno, Maxime, Berges, Helene, Gharbi, Karim, Lawson-Handley, Lori, Zang, Lian-Sheng, Vogel, Heiko, Estoup, Arnaud, Prud’homme, Benjamin
Published in Current biology (22.10.2018)
Published in Current biology (22.10.2018)
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Journal Article
Mapping and validation of the major sex-determining region in Nile tilapia (Oreochromis niloticus L.) Using RAD sequencing
Palaiokostas, Christos, Bekaert, Michaël, Khan, Mohd G Q, Taggart, John B, Gharbi, Karim, McAndrew, Brendan J, Penman, David J
Published in PloS one (11.07.2013)
Published in PloS one (11.07.2013)
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Journal Article
Genomic prediction of host resistance to sea lice in farmed Atlantic salmon populations
Tsai, Hsin-Yuan, Hamilton, Alastair, Tinch, Alan E, Guy, Derrick R, Bron, James E, Taggart, John B, Gharbi, Karim, Stear, Michael, Matika, Oswald, Pong-Wong, Ricardo, Bishop, Steve C, Houston, Ross D
Published in Genetics selection evolution (Paris) (29.06.2016)
Published in Genetics selection evolution (Paris) (29.06.2016)
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Journal Article
Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing
Gonen, Serap, Lowe, Natalie R, Cezard, Timothé, Gharbi, Karim, Bishop, Stephen C, Houston, Ross D
Published in BMC genomics (27.02.2014)
Published in BMC genomics (27.02.2014)
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Journal Article
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
Gilroy, Rachel, Ravi, Anuradha, Getino, Maria, Pursley, Isabella, Horton, Daniel L, Alikhan, Nabil-Fareed, Baker, Dave, Gharbi, Karim, Hall, Neil, Watson, Mick, Adriaenssens, Evelien M, Foster-Nyarko, Ebenezer, Jarju, Sheikh, Secka, Arss, Antonio, Martin, Oren, Aharon, Chaudhuri, Roy R, La Ragione, Roberto, Hildebrand, Falk, Pallen, Mark J
Published in PeerJ (San Francisco, CA) (06.04.2021)
Published in PeerJ (San Francisco, CA) (06.04.2021)
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Journal Article
Author Correction: A simple and robust real-time qPCR method for the detection of PIK3CA mutations
Alvarez-Garcia, Virginia, Bartos, Clare, Keraite, Ieva, Trivedi, Urmi, Brennan, Paul M., Kersaudy-Kerhoas, Maïwenn, Gharbi, Karim, Oikonomidou, Olga, Leslie, Nicholas R.
Published in Scientific reports (06.08.2021)
Published in Scientific reports (06.08.2021)
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Journal Article
Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing
Palaiokostas, Christos, Bekaert, Michaël, Davie, Andrew, Cowan, Mairi E, Oral, Münevver, Taggart, John B, Gharbi, Karim, McAndrew, Brendan J, Penman, David J, Migaud, Hervé
Published in BMC genomics (20.08.2013)
Published in BMC genomics (20.08.2013)
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Journal Article
Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
Gierliński, Marek, Cole, Christian, Schofield, Pietà, Schurch, Nicholas J, Sherstnev, Alexander, Singh, Vijender, Wrobel, Nicola, Gharbi, Karim, Simpson, Gordon, Owen-Hughes, Tom, Blaxter, Mark, Barton, Geoffrey J
Published in Bioinformatics (Oxford, England) (15.11.2015)
Published in Bioinformatics (Oxford, England) (15.11.2015)
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Journal Article
Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids
McGowan, Jamie, Kilias, Estelle S, Alacid, Elisabet, Lipscombe, James, Jenkins, Benjamin H, Gharbi, Karim, Kaithakottil, Gemy G, Macaulay, Iain C, McTaggart, Seanna, Warring, Sally D, Richards, Thomas A, Hall, Neil, Swarbreck, David
Published in PLoS genetics (05.10.2023)
Published in PLoS genetics (05.10.2023)
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Journal Article
Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes
Wright, David J, Hall, Nicola A L, Irish, Naomi, Man, Angela L, Glynn, Will, Mould, Arne, Angeles, Alejandro De Los, Angiolini, Emily, Swarbreck, David, Gharbi, Karim, Tunbridge, Elizabeth M, Haerty, Wilfried
Published in BMC genomics (10.01.2022)
Published in BMC genomics (10.01.2022)
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Journal Article
Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon
Tsai, Hsin-Yuan, Matika, Oswald, Edwards, Stefan McKinnon, Antolín-Sánchez, Roberto, Hamilton, Alastair, Guy, Derrick R, Tinch, Alan E, Gharbi, Karim, Stear, Michael J, Taggart, John B, Bron, James E, Hickey, John M, Houston, Ross D
Published in G3 : genes - genomes - genetics (01.04.2017)
Published in G3 : genes - genomes - genetics (01.04.2017)
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Journal Article
A simple and robust real-time qPCR method for the detection of PIK3CA mutations
Alvarez-Garcia, Virginia, Bartos, Clare, Keraite, Ieva, Trivedi, Urmi, Brennan, Paul M., Kersaudy-Kerhoas, Maïwenn, Gharbi, Karim, Oikonomidou, Olga, Leslie, Nicholas R.
Published in Scientific reports (09.03.2018)
Published in Scientific reports (09.03.2018)
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Journal Article
Maternal inheritance of deltamethrin resistance in the salmon louse Lepeophtheirus salmonis (Krøyer) is associated with unique mtDNA haplotypes
Carmona-Antoñanzas, Greta, Bekaert, Michaël, Humble, Joseph L, Boyd, Sally, Roy, William, Bassett, David I, Houston, Ross D, Gharbi, Karim, Bron, James E, Sturm, Armin
Published in PloS one (12.07.2017)
Published in PloS one (12.07.2017)
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Journal Article
Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters ( Crassostrea gigas and Ostrea edulis )
Gutierrez, Alejandro P, Turner, Frances, Gharbi, Karim, Talbot, Richard, Lowe, Natalie R, Peñaloza, Carolina, McCullough, Mark, Prodöhl, Paulo A, Bean, Tim P, Houston, Ross D
Published in G3 : genes - genomes - genetics (01.07.2017)
Published in G3 : genes - genomes - genetics (01.07.2017)
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Journal Article