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113 results for Oshlack,+Alicia

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Select record 21
ArticlesPeer ReviewedFull Text
Transcript length bias in RNA-seq data confounds systems biology
Author / Creator:Oshlack, Alicia ; Wakefield, Matthew J
Publisher:England: BioMed Central Ltd
Journal title:Biology direct, 2009-04, Vol.4 (14), p.14-14
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ArticlesPeer ReviewedFull Text
Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data
Author / Creator:Sadedin, Simon P ; Oshlack, Alicia
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2019-04, Vol.20 (1), p.78-78, Article 78
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Evaluation of variability in human kidney organoids
Author / Creator:Phipson, Belinda ; Er, Pei X. ; Combes, Alexander N. ; Forbes, Thomas A. ; Howden, Sara E. ; Zappia, Luke ; Yen, Hsan-Jan ; Lawlor, Kynan T. ; Hale, Lorna J. ; Sun, Jane ; Wolvetang, Ernst ; Takasato, Minoru ; Oshlack, Alicia ; Little, Melissa H.
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2019-01, Vol.16 (1), p.79-87
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ArticlesPeer ReviewedFull Text
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes
Author / Creator:Davidson, Nadia M ; Hawkins, Anthony D K ; Oshlack, Alicia
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2017-08, Vol.18 (1), p.148-148, Article 148
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ArticlesPeer ReviewedFull Text
STRetch: detecting and discovering pathogenic short tandem repeat expansions
Author / Creator:Dashnow, Harriet ; Lek, Monkol ; Phipson, Belinda ; Halman, Andreas ; Sadedin, Simon ; Lonsdale, Andrew ; Davis, Mark ; Lamont, Phillipa ; Clayton, Joshua S ; Laing, Nigel G ; MacArthur, Daniel G ; Oshlack, Alicia
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2018-08, Vol.19 (1), p.121-121, Article 121
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Select record 26
ArticlesPeer ReviewedFull Text
SuperFreq: Integrated mutation detection and clonal tracking in cancer
Author / Creator:Flensburg, Christoffer ; Sargeant, Tobias ; Oshlack, Alicia ; Majewski, Ian J
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2020-02, Vol.16 (2), p.e1007603-e1007603
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Select record 27
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Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability
Author / Creator:de Mendoza, Alex ; Nguyen, Trung Viet ; Ford, Ethan ; Poppe, Daniel ; Buckberry, Sam ; Pflueger, Jahnvi ; Grimmer, Matthew R. ; Stolzenburg, Sabine ; Bogdanovic, Ozren ; Oshlack, Alicia ; Farnham, Peggy J. ; Blancafort, Pilar ; Lister, Ryan
Publisher:London: BioMed Central Ltd
Journal title:Genome Biology, 2022-07, Vol.23 (1), p.163-163, Article 163
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Select record 28
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Gene length and detection bias in single cell RNA sequencing protocols
Author / Creator:Phipson, Belinda ; Zappia, Luke ; Oshlack, Alicia
Publisher:England: Faculty of 1000 Ltd
Journal title:F1000 research, 2017, Vol.6, p.595-595
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Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Author / Creator:Patrick, Ralph ; Humphreys, David T. ; Janbandhu, Vaibhao ; Oshlack, Alicia ; Ho, Joshua W.K. ; Harvey, Richard P. ; Lo, Kitty K.
Publisher:London: BioMed Central Ltd
Journal title:Genome Biology, 2020-07, Vol.21 (1), p.167-167, Article 167
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Select record 30
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JAFFA: High sensitivity transcriptome-focused fusion gene detection
Author / Creator:Davidson, Nadia M ; Majewski, Ian J ; Oshlack, Alicia
Publisher:England: BioMed Central Ltd
Journal title:Genome medicine, 2015-05, Vol.7 (1), p.43-43, Article 43
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ArticlesPeer ReviewedFull Text
JAFFAL: detecting fusion genes with long-read transcriptome sequencing
Author / Creator:Davidson, Nadia M ; Chen, Ying ; Sadras, Teresa ; Ryland, Georgina L ; Blombery, Piers ; Ekert, Paul G ; Göke, Jonathan ; Oshlack, Alicia
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2022-01, Vol.23 (1), p.10-10, Article 10
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Select record 32
ArticlesPeer ReviewedFull Text
splatPop: simulating population scale single-cell RNA sequencing data
Author / Creator:Azodi, Christina B ; Zappia, Luke ; Oshlack, Alicia ; McCarthy, Davis J
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2021-12, Vol.22 (1), p.341-341, Article 341
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Select record 33
ArticlesPeer ReviewedFull Text
Nephron progenitor commitment is a stochastic process influenced by cell migration
Author / Creator:Lawlor, Kynan T ; Zappia, Luke ; Lefevre, James ; Park, Joo-Seop ; Hamilton, Nicholas A ; Oshlack, Alicia ; Little, Melissa H ; Combes, Alexander N
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2019-01, Vol.8
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Select record 34
ArticlesPeer ReviewedFull Text
MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data
Author / Creator:Cmero, Marek ; Schmidt, Breon ; Majewski, Ian J ; Ekert, Paul G ; Oshlack, Alicia ; Davidson, Nadia M
Publisher:England: BioMed Central
Journal title:Genome Biology, 2021-10, Vol.22 (1), p.296-296, Article 296
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Select record 35
ArticlesPeer ReviewedFull Text
Toblerone: detecting exon deletion events in cancer using RNA-seq [version 1; peer review: 2 approved]
Author / Creator:Lonsdale, Andrew ; Halman, Andreas ; Brown, Lauren ; Kosasih, Hansen ; Ekert, Paul ; Oshlack, Alicia
Publisher:London: Faculty of 1000 Ltd
Journal title:F1000 research, 2023, Vol.12, p.130-130
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Select record 36
ArticlesPeer ReviewedFull Text
NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network
Author / Creator:Anderson, David J. ; Kaplan, David I. ; Bell, Katrina M. ; Koutsis, Katerina ; Haynes, John M. ; Mills, Richard J. ; Phelan, Dean G. ; Qian, Elizabeth L. ; Leitoguinho, Ana Rita ; Arasaratnam, Deevina ; Labonne, Tanya ; Ng, Elizabeth S. ; Davis, Richard P. ; Casini, Simona ; Passier, Robert ; Hudson, James E. ; Porrello, Enzo R. ; Costa, Mauro W. ; Rafii, Arash ; Curl, Clare L. ; Delbridge, Lea M. ; Harvey, Richard P. ; Oshlack, Alicia ; Cheung, Michael M. ; Mummery, Christine L. ; Petrou, Stephen ; Elefanty, Andrew G. ; Stanley, Edouard G. ; Elliott, David A.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2018-04, Vol.9 (1), p.1373-13, Article 1373
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Select record 37
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RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome
Author / Creator:Ayers, Katie L ; Davidson, Nadia M ; Demiyah, Diana ; Roeszler, Kelly N ; Grützner, Frank ; Sinclair, Andrew H ; Oshlack, Alicia ; Smith, Craig A
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology (Online Edition), 2013-03, Vol.14 (3), p.R26-R26, Article R26
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Select record 38
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Slinker: Visualising novel splicing events in RNA-Seq data [version 1; peer review: 3 approved]
Author / Creator:Schmidt, Breon ; Cmero, Marek ; Ekert, Paul ; Davidson, Nadia ; Oshlack, Alicia
Publisher:England: Faculty of 1000 Ltd
Journal title:F1000 research, 2021, Vol.10, p.1255-1255
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Select record 39
ArticlesPeer ReviewedFull Text
Gene regulation in primates evolves under tissue-specific selection pressures
Author / Creator:Blekhman, Ran ; Oshlack, Alicia ; Chabot, Adrien E ; Smyth, Gordon K ; Gilad, Yoav
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2008-11, Vol.4 (11), p.e1000271-e1000271
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Select record 40
ArticlesPeer ReviewedFull Text
Using equivalence class counts for fast and accurate testing of differential transcript usage [version 2; peer review: 2 approved, 1 approved with reservations]
Author / Creator:Cmero, Marek ; Davidson, Nadia M ; Oshlack, Alicia
Publisher:England: Faculty of 1000 Ltd
Journal title:F1000 research, 2019, Vol.8, p.265-265
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Transcript length bias in RNA-seq data confounds systems biology

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Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data

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Evaluation of variability in human kidney organoids

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SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

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STRetch: detecting and discovering pathogenic short tandem repeat expansions

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SuperFreq: Integrated mutation detection and clonal tracking in cancer

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Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability

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Gene length and detection bias in single cell RNA sequencing protocols

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Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

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JAFFA: High sensitivity transcriptome-focused fusion gene detection

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JAFFAL: detecting fusion genes with long-read transcriptome sequencing

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splatPop: simulating population scale single-cell RNA sequencing data

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Nephron progenitor commitment is a stochastic process influenced by cell migration

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MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

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Toblerone: detecting exon deletion events in cancer using RNA-seq [version 1; peer review: 2 approved]

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NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network

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RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

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Slinker: Visualising novel splicing events in RNA-Seq data [version 1; peer review: 3 approved]

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Gene regulation in primates evolves under tissue-specific selection pressures

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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]

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