Search Results - "Davidson, Nadia"

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes by Davidson, Nadia M, Oshlack, Alicia

“…Next generation sequencing has made it possible to perform differential gene expression studies in non-model organisms. For these studies, the need for a…”
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SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes by Davidson, Nadia M, Hawkins, Anthony D K, Oshlack, Alicia

“…Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable…”
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JAFFA: High sensitivity transcriptome-focused fusion gene detection by Davidson, Nadia M, Majewski, Ian J, Oshlack, Alicia

“…Genomic instability is a hallmark of cancer and, as such, structural alterations and fusion genes are common events in the cancer landscape. RNA sequencing…”
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JAFFAL: detecting fusion genes with long-read transcriptome sequencing by Davidson, Nadia M, Chen, Ying, Sadras, Teresa, Ryland, Georgina L, Blombery, Piers, Ekert, Paul G, Göke, Jonathan, Oshlack, Alicia

“…In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with their…”
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RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome by Ayers, Katie L, Davidson, Nadia M, Demiyah, Diana, Roeszler, Kelly N, Grützner, Frank, Sinclair, Andrew H, Oshlack, Alicia, Smith, Craig A

“…Birds have a ZZ male: ZW female sex chromosome system and while the Z-linked DMRT1 gene is necessary for testis development, the exact mechanism of sex…”
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MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data by Cmero, Marek, Schmidt, Breon, Majewski, Ian J, Ekert, Paul G, Oshlack, Alicia, Davidson, Nadia M

“…Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify…”
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Flexiplex: a versatile demultiplexer and search tool for omics data by Cheng, Oliver, Ling, Min Hao, Wang, Changqing, Wu, Shuyi, Ritchie, Matthew E, Göke, Jonathan, Amin, Noorul, Davidson, Nadia M

“…Abstract Motivation The process of analyzing high throughput sequencing data often requires the identification and extraction of specific target sequences…”
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Unusual PDGFRB fusion reveals novel mechanism of kinase activation in Ph-like B-ALL by Sadras, Teresa, Jalud, Fatimah B., Kosasih, Hansen J., Horne, Christopher R., Brown, Lauren M., El-Kamand, Sam, de Bock, Charles E., McAloney, Lachlan, Ng, Ashley P., Davidson, Nadia M., Ludlow, Louise E. A., Oshlack, Alicia, Cowley, Mark J., Khaw, Seong L., Murphy, James M., Ekert, Paul G.

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Novel CDKL5 targets identified in human iPSC-derived neurons by Massey, Sean, Ang, Ching-Seng, Davidson, Nadia M., Quigley, Anita, Rollo, Ben, Harris, Alexander R., Kapsa, Robert M. I., Christodoulou, John, Van Bergen, Nicole J.

“…CDKL5 Deficiency Disorder (CDD) is a debilitating epileptic encephalopathy disorder affecting young children with no effective treatments. CDD is caused by…”
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Correction: Novel CDKL5 targets identified in human iPSC-derived neurons by Massey, Sean, Ang, Ching-Seng, Davidson, Nadia M., Quigley, Anita, Rollo, Ben, Harris, Alexander R., Kapsa, Robert M. I., Christodoulou, John, Van Bergen, Nicole J.

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ALLSorts: a RNA-Seq subtype classifier for B-Cell Acute Lymphoblastic Leukemia by Schmidt, Breon, Brown, Lauren M., Ryland, Georgina L., Lonsdale, Andrew, Kosasih, Hansen J., Ludlow, Louise E., Majewski, Ian J., Blombery, Piers, Ekert, Paul G., Davidson, Nadia M., Oshlack, Alicia

“…B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. Subtypes within B-ALL are distinguished by characteristic structural variants…”
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Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq by Ayers, Katie L, Lambeth, Luke S, Davidson, Nadia M, Sinclair, Andrew H, Oshlack, Alicia, Smith, Craig A

“…Despite some advances in recent years, the genetic control of gonadal sex differentiation during embryogenesis is still not completely understood. To identify…”
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Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis by Davidson, Nadia M, Oshlack, Alicia

“…RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the…”
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Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing by Farlie, Peter G., Davidson, Nadia M., Baker, Naomi L., Raabus, Mai, Roeszler, Kelly N., Hirst, Claire, Major, Andrew, Mariette, Mylene M., Lambert, David M., Oshlack, Alicia, Smith, Craig A.

“…The ratites are a distinctive clade of flightless birds, typified by the emu and ostrich that have acquired a range of unique anatomical characteristics since…”
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Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing by Majewski, Ian J, Mittempergher, Lorenza, Davidson, Nadia M, Bosma, Astrid, Willems, Stefan M, Horlings, Hugo M, de Rink, Iris, Greger, Liliana, Hooijer, Gerrit KJ, Peters, Dennis, Nederlof, Petra M, Hofland, Ingrid, de Jong, Jeroen, Wesseling, Jelle, Kluin, Roelof JC, Brugman, Wim, Kerkhoven, Ron, Nieboer, Frank, Roepman, Paul, Broeks, Annegien, Muley, Thomas R, Jassem, Jacek, Niklinski, Jacek, van Zandwijk, Nico, Brazma, Alvis, Oshlack, Alicia, van den Heuvel, Michel, Bernards, René

“…Oncogenic fusion genes that involve kinases have proven to be effective targets for therapy in a wide range of cancers. Unfortunately, the diagnostic…”
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Human yolk sac-like haematopoiesis generates RUNX1- and GFI1/1B-dependent blood and SOX17-positive endothelium by Bruveris, Freya F, Ng, Elizabeth S, Leitoguinho, Ana Rita, Motazedian, Ali, Vlahos, Katerina, Sourris, Koula, Mayberry, Robyn, McDonald, Penelope, Azzola, Lisa, Davidson, Nadia M, Oshlack, Alicia, Stanley, Edouard G, Elefanty, Andrew G

“…The genetic regulatory network controlling early fate choices during human blood cell development are not well understood. We used human pluripotent stem cell…”
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Fast and accurate differential transcript usage by testing equivalence class counts [version 1; peer review: 3 approved with reservations] by Cmero, Marek, Davidson, Nadia M, Oshlack, Alicia

“…Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differential gene expression is the…”
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Erratum to: SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes by Davidson, Nadia M, Hawkins, Anthony D K, Oshlack, Alicia

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The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia by Brown, Lauren M., Lonsdale, Andrew, Zhu, Andrea, Davidson, Nadia M., Schmidt, Breon, Hawkins, Anthony, Wallach, Elise, Martin, Michelle, Mechinaud, Francoise M., Khaw, Seong Lin, Bartolo, Ray C., Ludlow, Louise E.A., Challis, Jackie, Brooks, Ian, Petrovic, Vida, Venn, Nicola C., Sutton, Rosemary, Majewski, Ian J., Oshlack, Alicia, Ekert, Paul G.

“…Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy, and implementation of risk-adapted therapy has been instrumental in the dramatic…”
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Using equivalence class counts for fast and accurate testing of differential transcript usage [version 2; peer review: 2 approved, 1 approved with reservations] by Cmero, Marek, Davidson, Nadia M, Oshlack, Alicia

“…Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differential gene expression is the…”
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