tidybulk: an R tidy framework for modular transcriptomic data analysis
Mangiola, Stefano, Molania, Ramyar, Dong, Ruining, Doyle, Maria A, Papenfuss, Anthony T
Published in Genome Biology (22.01.2021)
Published in Genome Biology (22.01.2021)
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CONTRA: copy number analysis for targeted resequencing
JASON LI, LUPAT, Richard, AMARASINGHE, Kaushalya C, THOMPSON, Ella R, DOYLE, Maria A, RYLAND, Georgina L, TOTHILL, Richard W, HALGAMUGE, Saman K, CAMPBELL, Ian G, GORRINGE, Kylie L
Published in Bioinformatics (Oxford, England) (15.05.2012)
Published in Bioinformatics (Oxford, England) (15.05.2012)
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RNA-Seq Data Analysis in Galaxy
Batut, Bérénice, van den Beek, Marius, Doyle, Maria A., Soranzo, Nicola
Published in Methods in molecular biology (Clifton, N.J.) (01.01.2021)
Published in Methods in molecular biology (Clifton, N.J.) (01.01.2021)
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Book Chapter
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Exome sequencing identifies rare deleterious mutations in DNA repair genes FANCC and BLM as potential breast cancer susceptibility alleles
Thompson, Ella R, Doyle, Maria A, Ryland, Georgina L, Rowley, Simone M, Choong, David Y H, Tothill, Richard W, Thorne, Heather, Barnes, Daniel R, Li, Jason, Ellul, Jason, Philip, Gayle K, Antill, Yoland C, James, Paul A, Trainer, Alison H, Mitchell, Gillian, Campbell, Ian G
Published in PLoS genetics (01.09.2012)
Published in PLoS genetics (01.09.2012)
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The RNA workbench 2.0: next generation RNA data analysis
Fallmann, Jörg, Videm, Pavankumar, Bagnacani, Andrea, Batut, Bérénice, Doyle, Maria A, Klingstrom, Tomas, Eggenhofer, Florian, Stadler, Peter F, Backofen, Rolf, Grüning, Björn
Published in Nucleic acids research (02.07.2019)
Published in Nucleic acids research (02.07.2019)
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Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors
Ryland, Georgina L, Hunter, Sally M, Doyle, Maria A, Caramia, Franco, Li, Jason, Rowley, Simone M, Christie, Michael, Allan, Prue E, Stephens, Andrew N, Bowtell, David D L, Campbell, Ian G, Gorringe, Kylie L
Published in Genome medicine (07.08.2015)
Published in Genome medicine (07.08.2015)
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Id2 and E Proteins Orchestrate the Initiation and Maintenance of MLL-Rearranged Acute Myeloid Leukemia
Ghisi, Margherita, Kats, Lev, Masson, Frederick, Li, Jason, Kratina, Tobias, Vidacs, Eva, Gilan, Omer, Doyle, Maria A., Newbold, Andrea, Bolden, Jessica E., Fairfax, Kirsten A., de Graaf, Carolyn A., Firth, Matthew, Zuber, Johannes, Dickins, Ross A., Corcoran, Lynn M., Dawson, Mark A., Belz, Gabrielle T., Johnstone, Ricky W.
Published in Cancer cell (11.07.2016)
Published in Cancer cell (11.07.2016)
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Genomic characterisation of Eμ-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene
Lefebure, Marcus, Tothill, Richard W., Kruse, Elizabeth, Hawkins, Edwin D., Shortt, Jake, Matthews, Geoffrey M., Gregory, Gareth P., Martin, Benjamin P., Kelly, Madison J., Todorovski, Izabela, Doyle, Maria A., Lupat, Richard, Li, Jason, Schroeder, Jan, Wall, Meaghan, Craig, Stuart, Poortinga, Gretchen, Cameron, Don, Bywater, Megan, Kats, Lev, Gearhart, Micah D., Bardwell, Vivian J., Dickins, Ross A., Hannan, Ross D., Papenfuss, Anthony T., Johnstone, Ricky W.
Published in Nature communications (06.03.2017)
Published in Nature communications (06.03.2017)
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Identification of attractive drug targets in neglected-disease pathogens using an in silico approach
Crowther, Gregory J, Shanmugam, Dhanasekaran, Carmona, Santiago J, Doyle, Maria A, Hertz-Fowler, Christiane, Berriman, Matthew, Nwaka, Solomon, Ralph, Stuart A, Roos, David S, Van Voorhis, Wesley C, Agüero, Fernán
Published in PLoS neglected tropical diseases (24.08.2010)
Published in PLoS neglected tropical diseases (24.08.2010)
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Germline whole exome sequencing of a family with appendiceal mucinous tumours presenting with pseudomyxoma peritonei
Lung, Mei Sim, Mitchell, Catherine A, Doyle, Maria A, Lynch, Andrew C, Gorringe, Kylie L, Bowtell, David D L, Campbell, Ian G, Trainer, Alison H
Published in BMC cancer (01.05.2020)
Published in BMC cancer (01.05.2020)
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Prevalence of PALB2 mutations in Australian familial breast cancer cases and controls
Thompson, Ella R, Gorringe, Kylie L, Rowley, Simone M, Wong-Brown, Michelle W, McInerny, Simone, Li, Na, Trainer, Alison H, Devereux, Lisa, Doyle, Maria A, Li, Jason, Lupat, Richard, Delatycki, Martin B, Mitchell, Gillian, James, Paul A, Scott, Rodney J, Campbell, Ian G
Published in Breast cancer research : BCR (19.08.2015)
Published in Breast cancer research : BCR (19.08.2015)
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Interfacing Seurat with the R tidy universe
Mangiola, Stefano, Doyle, Maria A, Papenfuss, Anthony T
Published in Bioinformatics (Oxford, England) (18.11.2021)
Published in Bioinformatics (Oxford, England) (18.11.2021)
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Molecular comparison of pure ovarian fibroma with serous benign ovarian tumours
Hunter, Sally M, Dall, Genevieve V, Doyle, Maria A, Lupat, Richard, Li, Jason, Allan, Prue, Rowley, Simone M, Bowtell, David, Campbell, Ian G, Gorringe, Kylie L
Published in BMC research notes (22.07.2020)
Published in BMC research notes (22.07.2020)
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Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes
Doyle, Maria A, Gasser, Robin B, Woodcroft, Ben J, Hall, Ross S, Ralph, Stuart A
Published in BMC genomics (03.04.2010)
Published in BMC genomics (03.04.2010)
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PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories
Doig, Kenneth D, Fellowes, Andrew, Bell, Anthony H, Seleznev, Andrei, Ma, David, Ellul, Jason, Li, Jason, Doyle, Maria A, Thompson, Ella R, Kumar, Amit, Lara, Luis, Vedururu, Ravikiran, Reid, Gareth, Conway, Thomas, Papenfuss, Anthony T, Fox, Stephen B
Published in Genome medicine (24.04.2017)
Published in Genome medicine (24.04.2017)
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Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment
Li, Jason, Doyle, Maria A, Saeed, Isaam, Wong, Stephen Q, Mar, Victoria, Goode, David L, Caramia, Franco, Doig, Ken, Ryland, Georgina L, Thompson, Ella R, Hunter, Sally M, Halgamuge, Saman K, Ellul, Jason, Dobrovic, Alexander, Campbell, Ian G, Papenfuss, Anthony T, McArthur, Grant A, Tothill, Richard W
Published in PloS one (01.04.2014)
Published in PloS one (01.04.2014)
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The Drug Vehicle and Solvent N-Methylpyrrolidone Is an Immunomodulator and Antimyeloma Compound
Shortt, Jake, Hsu, Andy K., Martin, Benjamin P., Doggett, Karen, Matthews, Geoffrey M., Doyle, Maria A., Ellul, Jason, Jockel, Tina E., Andrews, Daniel M., Hogg, Simon J., Reitsma, Andrea, Faulkner, David, Bergsagel, P. Leif, Chesi, Marta, Heath, Joan K., Denny, William A., Thompson, Philip E., Neeson, Paul J., Ritchie, David S., McArthur, Grant A., Johnstone, Ricky W.
Published in Cell reports (Cambridge) (22.05.2014)
Published in Cell reports (Cambridge) (22.05.2014)
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Massively parallel sequencing and analysis of the Necator americanus transcriptome
Cantacessi, Cinzia, Mitreva, Makedonka, Jex, Aaron R, Young, Neil D, Campbell, Bronwyn E, Hall, Ross S, Doyle, Maria A, Ralph, Stuart A, Rabelo, Elida M, Ranganathan, Shoba, Sternberg, Paul W, Loukas, Alex, Gasser, Robin B
Published in PLoS neglected tropical diseases (01.05.2010)
Published in PLoS neglected tropical diseases (01.05.2010)
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MicroRNA genes and their target 3'-untranslated regions are infrequently somatically mutated in ovarian cancers
Ryland, Georgina L, Bearfoot, Jennifer L, Doyle, Maria A, Boyle, Samantha E, Choong, David Y H, Rowley, Simone M, Tothill, Richard W, Gorringe, Kylie L, Campbell, Ian G
Published in PloS one (20.04.2012)
Published in PloS one (20.04.2012)
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LeishCyc: a biochemical pathways database for Leishmania major
Doyle, Maria A, MacRae, James I, De Souza, David P, Saunders, Eleanor C, McConville, Malcolm J, Likić, Vladimir A
Published in BMC systems biology (05.06.2009)
Published in BMC systems biology (05.06.2009)
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