Dr John Pearson
Adjunct Senior Fellow
Institute for Molecular Bioscience
Journal Articles
Kaladharan, Sid, Vidgen, Miranda E., Pearson, John V., Donoghue, Victoria K., Whiteman, David C., Waddell, Nicola and Pratt, Gregory (2021). Ask the people: developing guidelines for genomic research with Aboriginal and Torres Strait Islander peoples. BMJ Global Health, 6 (11) e007259, 1-8. doi: 10.1136/bmjgh-2021-007259
Yap, Melvyn, Johnston, Rebecca L., Foley, Helena, MacDonald, Samual, Kondrashova, Olga, Tran, Khoa A., Nones, Katia, Koufariotis, Lambros T., Bean, Cameron, Pearson, John V., Trzaskowski, Maciej and Waddell, Nicola (2021). Verifying explainability of a deep learning tissue classifier trained on RNA-seq data. Scientific Reports, 11 (1) 2641. doi: 10.1038/s41598-021-81773-9
Zhang, Yiqun, Chen, Fengju, Fonseca, Nuno A., He, Yao, Fujita, Masashi, Nakagawa, Hidewaki, Zhang, Zemin, Brazma, Alvis, Amin, Samirkumar B., Awadalla, Philip, Bailey, Peter J., Brazma, Alvis, Brooks, Angela N., Calabrese, Claudia, Chateigner, Aurélien, Cortés-Ciriano, Isidro, Craft, Brian, Craft, David, Creighton, Chad J., Davidson, Natalie R., Demircioğlu, Deniz, Erkek, Serap, Fonseca, Nuno A., Frenkel-Morgenstern, Milana, Goldman, Mary J., Greger, Liliana, Göke, Jonathan, He, Yao, Hoadley, Katherine A. ... Creighton, Chad J. (2020). High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nature Communications, 11 (1) 736. doi: 10.1038/s41467-019-13885-w
Sieverling, Lina, Hong, Chen, Koser, Sandra D., Ginsbach, Philip, Kleinheinz, Kortine, Hutter, Barbara, Braun, Delia M., Cortés-Ciriano, Isidro, Xi, Ruibin, Kabbe, Rolf, Park, Peter J., Eils, Roland, Schlesner, Matthias, Akdemir, Kadir C., Alvarez, Eva G., Baez-Ortega, Adrian, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D. L., Brors, Benedikt, Burns, Kathleen H., Campbell, Peter J., Chan, Kin, Chen, Ken, Cortés-Ciriano, Isidro, Dueso-Barroso, Ana, Dunford, Andrew J., Edwards, Paul A., Estivill, Xavier ... PCAWG-Structural Variation Working Group (2020). Genomic footprints of activated telomere maintenance mechanisms in cancer. Nature Communications, 11 (1) 733. doi: 10.1038/s41467-019-13824-9
Campbell, Peter J., Getz, Gad, Korbel, Jan O., Stuart, Joshua M., Jennings, Jennifer L., Stein, Lincoln D., Perry, Marc D., Nahal-Bose, Hardeep K., Ouellette, B. F. Francis, Li, Constance H., Rheinbay, Esther, Nielsen, G. Petur, Sgroi, Dennis C., Wu, Chin-Lee, Faquin, William C., Deshpande, Vikram, Boutros, Paul C., Lazar, Alexander J., Hoadley, Katherine A., Louis, David N., Dursi, L. Jonathan, Yung, Christina K., Bailey, Matthew H., Saksena, Gordon, Raine, Keiran M., Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun ... Hamdy, Freddie C. (2020). Pan-cancer analysis of whole genomes. Nature, 578 (7793), 82-93. doi: 10.1038/s41586-020-1969-6
Akdemir, Kadir C., Le, Victoria T., Chandran, Sahaana, Li, Yilong, Verhaak, Roel G., Beroukhim, Rameen, Campbell, Peter J., Chin, Lynda, Dixon, Jesse R., Futreal, P. Andrew, Alvarez, Eva G., Baez-Ortega, Adrian, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D. L., Brors, Benedikt, Burns, Kathleen H., Chan, Kin, Chen, Ken, Cortes-Ciriano, Isidro, Dueso-Barroso, Ana, Dunford, Andrew J., Edwards, Paul A., Estivill, Xavier, Etemadmoghadam, Dariush, Feuerbach, Lars, Fink, J. Lynn, Frenkel-Morgenstern, Milana, Garsed, Dale W. ... Zhang, Cheng-Zhong (2020). Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nature Genetics, 52 (3), 294-305. doi: 10.1038/s41588-019-0564-y
Rodriguez-Martin, Bernardo, Alvarez, Eva G., Baez-Ortega, Adrian, Zamora, Jorge, Supek, Fran, Demeulemeester, Jonas, Santamarina, Martin, Ju, Young Seok, Temes, Javier, Garcia-Souto, Daniel, Detering, Harald, Li, Yilong, Rodriguez-Castro, Jorge, Dueso-Barroso, Ana, Bruzos, Alicia L., Dentro, Stefan C., Blanco, Miguel G., Contino, Gianmarco, Ardeljan, Daniel, Tojo, Marta, Roberts, Nicola D., Zumalave, Sonia, Edwards, Paul A. W., Weischenfeldt, Joachim, Puiggros, Montserrat, Chong, Zechen, Chen, Ken, Lee, Eunjung Alice, Wala, Jeremiah A. ... Zhang, Cheng-Zhong (2020). Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics, 52 (3), 306-319. doi: 10.1038/s41588-019-0562-0
Wilmott, James S., Johansson, Peter A., Newell, Felicity, Waddell, Nicola, Ferguson, Peter, Quek, Camelia, Patch, Ann-Marie, Nones, Katia, Shang, Ping, Pritchard, Antonia L., Kazakoff, Stephen, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Xu, Qinying, Saw, Robyn P. M., Spillane, Andrew J., Stretch, Jonathan R., Shannon, Kerwin F., Kefford, Richard F., Menzies, Alexander M., Long, Georgina V., Thompson, John F., Pearson, John V., Mann, Graham J., Hayward, Nicholas K. and Scolyer, Richard A. (2019). Whole genome sequencing of melanomas in adolescent and young adults reveals distinct mutation landscapes and the potential role of germline variants in disease susceptibility. International Journal of Cancer, 144 (5), 1049-1060. doi: 10.1002/ijc.31791
Hayward, Nicholas K., Wilmott, James S., Waddell, Nicola, Johansson, Peter A., Field, Matthew A., Nones, Katia, Patch, Ann-Marie, Kakavand, Hojabr, Alexandrov, Ludmil B., Burke, Hazel, Jakrot, Valerie, Kazakoff, Stephen, Holmes, Oliver, Leonard, Conrad, Sabarinathan, Radhakrishnan, Mularoni, Loris, Wood, Scott, Xu, Qinying, Waddell, Nick, Tembe, Varsha, Pupo, Gulietta M., De Paoli-Iseppi, Ricardo, Vilain, Ricardo E., Shang, Ping, Lau, Loretta M. S., Dagg, Rebecca A., Schramm, Sarah-Jane, Pritchard, Antonia, Dutton-Regester, Ken ... Mann, Graham J. (2017). Whole-genome landscapes of major melanoma subtypes. Nature, 545 (7653), 175-180. doi: 10.1038/nature22071
Scarpa, Aldo, Chang, David K., Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T., Johns, Amber L., Miller, David K., Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O., Cingarlini, Sara, Vicentini, Caterina, McKay, Skye, Quinn, Michael C.J., Bruxner, Timothy J.C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J., Anderson, Matthew J., Fink, J. Lynn ... Grimmond, Sean M. (2017). Whole-genome landscape of pancreatic neuroendocrine tumours. Nature, 543 (7643), 65-71. doi: 10.1038/nature21063
Humphris, Jeremy L., Patch, Ann-Marie, Nones, Katia, Bailey, Peter J., Johns, Amber L., McKay, Skye, Chang, David K., Miller, David K., Pajic, Marina, Kassahn, Karin S., Quinn, Michael C. J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Stone, Andrew, Wilson, Peter J., Anderson, Matthew, Fink, J. Lynn, Holmes, Oliver, Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Waddell, Nick, Wood, Scott, Mead, Ronald S. ... Biankin, Andrew V. (2017). Hypermutation in pancreatic cancer. Gastroenterology, 152 (1), 68-74.e2. doi: 10.1053/j.gastro.2016.09.060
Secrier, Maria, Li, Xiaodun, De Silva, Nadeera, Eldridge, Matthew D., Contino, Gianmarco, Bornschein, Jan, Macrae, Shona, Grehan, Nicola, O'Donovan, Maria, Miremadi, Ahmad, Yang, Tsun-Po, Bower, Lawrence, Chettouh, Hamza, Crawte, Jason, Galeano-Dalmau, Núria, Grabowska, Anna, Saunders, John, Underwood, Tim, Waddell, Nicola, Barbour, Andrew P., Nutzinger, Barbara, Achilleos, Achilleas, Edwards, Paul A. W., Lynch, Andy G., Tavare, Simon, Fitzgerald, Rebecca C., Noorani, Ayesha, Elliott, Rachael Fels, Weaver, Jamie ... Grimmond, Sean M. (2016). Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance. Nature Genetics, 48 (10), 1131-1141. doi: 10.1038/ng.3659
Johansson, Peter A., Pritchard, Antonia L., Patch, Ann-Marie, Wilmott, James S., Pearson, John V., Waddell, Nicola, Scolyer, Richard A., Mann, Graham J. and Hayward, Nicholas K. (2016). Mutation load in melanoma is affected by MC1R genotype. Pigment Cell & Melanoma Research, 30 (2), 255-258. doi: 10.1111/pcmr.12571
Li, Jun, Woods, Susan L., Healey, Sue, Beesley, Jonathan, Chen, Xiaoqing, Lee, Jason S., Sivakumaran, Haran, Wayte, Nicci, Nones, Katia, Waterfall, Joshua J., Pearson, John, Patch, Anne-Marie, Senz, Janine, Ferreira, Manuel A., Kaurah, Pardeep, Mackenzie, Robertson, Heravi-Moussavi, Alireza, Hansford, Samantha, Lannagan, Tamsin R. M., Spurdle, Amanda B., Simpson, Peter T., da Silva, Leonard, Lakhani, Sunil R., Clouston, Andrew D., Bettington, Mark, Grimpen, Florian, Busuttil, Rita A., Di Costanzo, Natasha, Boussioutas, Alex ... Chenevix-Trench, Georgia (2016). Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. American Journal of Human Genetics, 98 (5), 830-842. doi: 10.1016/j.ajhg.2016.03.001
Gingras, Marie-Claude, Covington, Kyle R., Chang, David K., Donehower, Lawrence A., Gill, Anthony J., Ittmann, Michael M., Creighton, Chad J., Johns, Amber L., Shinbrot, Eve, Dewal, Ninad, Fisher, William E., Pilarsky, Christian, Grutzmann, Robert, Overman, Michael J., Jamieson, Nigel B., Van Buren II, George, Drummond, Jennifer, Walker, Kimberly, Hampton, Oliver A., Xi, Liu, Muzny, Donna M., Doddapaneni, Harsha, Lee, Sandra L., Bellair, Michelle, Hu, Jianhong, Han, Yi, Dinh, Huyrn H., Dahdouli, Mike, Samra, Jaswinder S. ... Gibbs, Richard A. (2016). Ampullary cancers harbor the tumor suppressor gene ELF3 and exhibit frequent WNT Dysregulation. Cell Reports, 14 (4), 907-919. doi: 10.1016/j.celrep.2015.12.005
Alioto, Tyler S., Buchhalter, Ivo, Derdak, Sophia, Hutter, Barbara, Eldridge, Matthew D., Hovig, Eivind, Heisler, Lawrence E., Beck, Timothy A., Simpson, Jared T., Tonon, Laurie, Sertier, Anne-Sophie, Patch, Ann-Marie, Jager, Natalie, Ginsbach, Philip, Drews, Ruben, Paramasivam, Nagarajan, Kabbe, Rolf, Chotewutmontri, Sasithorn, Diessl, Nicolle, Previti, Christopher, Schmidt, Sabine, Brors, Benedikt, Feuerbach, Lars, Heinold, Michael, Grobner, Susanne, Korshunov, Andrey, Tarpey, Patrick S., Butler, Adam P., Hinton, Jonathan ... Gut, Ivo G. (2015). A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Communications, 6 (10001) 10001, 10001. doi: 10.1038/ncomms10001
Patch, Ann-Marie, Christie, Elizabeth L., Etemadmoghadam, Dariush, Garsed, Dale W., George, Joshy, Fereday, Sian, Nones, Katia, Cowin, Prue, Alsop, Kathryn, Bailey, Peter J., Kassahn, Karin S., Newell, Felicity, Quinn, Michael C. J., Kazakoff, Stephen, Quek, Kelly, Wilhelm-Benartzi, Charlotte, Curry, Ed, Leong, Huei San, Australian Ovarian Cancer Study Group, Hamilton, Anne, Mileshkin, Linda, Au-Yeung, George, Kennedy, Catherine, Hung, Jillian, Chiew, Yoke-Eng, Harnett, Paul, Friedlander, Michael, Quinn, Michael, Pyman, Jan ... Bowtell, David D. L. (2015). Corrigendum: Whole-genome characterization of chemoresistant ovarian cancer. Nature, 527 (7578), 398-398. doi: 10.1038/nature15716
Saunus, Jodi M., Quinn, MIchael C. J., Patch, Ann-Marie, Pearson, John V., Bailey, Peter J., Nones, Katia, McCart Reed, Amy E., Miller, David, Peter J. Wilson, Al-Ejeh, Fares, Mariasegaram, Mythily, Lau, Queenie, Withers, Teresa, Jeffree, Rosalind L., Reid, Lynne E., Da Silva, Leonard, Matsika, Admire, Niland, Colleen M., Cummings, Margaret C., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Anderson, Matthew J., Fink, J. Lynn ... Lakhani, Sunil R. (2015). Integrated genomic and transcriptomic analysis of human brain metastases identifies recurrently altered pathways of potential clinical significance. Journal of Pathology, 237 (3), 363-378. doi: 10.1002/path.4583
Creixell, Pau, Reimand, Juri, Haider, Syed, Wu, Guanming, Shibata, Tatsuhiro, Vazquez, Miguel, Mustonen, Ville, Gonzalez-Perez, Abel, Pearson, John, Sander, Chris, Raphael, Benjamin J., Marks, Debora S., Ouellette, B. F. Francis, Valencia, Alfonso, Bader, Gary D., Boutros, Paul C., Stuart, Joshua M., Linding, Rune, Lopez-Bigas, Nuria, Stein, Lincoln D. and International Cancer Genome Consortium (2015). Pathway and network analysis of cancer genomes. Nature Methods, 12 (7), 615-621. doi: 10.1038/nmeth.3440
Patch, Ann-Marie, Christie, Elizabeth L., Etemadmoghadam, Dariush, Garsed, Dale W., George, Joshy, Fereday, Sian, Nones, Katia, Cowin, Prue, Alsop, Kathryn, Bailey, Peter J., Kassahn, Karin S., Newell, Felicity, Quinn, Michael C. J., Kazakoff, Stephen, Quek, Kelly, Wilhelm-Benartzi, Charlotte, Curry, Ed, Leong, Huei San, The Australian Ovarian Cancer Study Group, Hamilton, Anne, Mileshkin, Linda, Au-Yeung, George, Kennedy, Catherine, Hung, Jillian, Chiew, Yoke-Eng, Harnett, Paul, Friedlander, Michael, Quinn, Michael, Pyman, Jan ... Bowtell, David D. L. (2015). Whole-genome characterization of chemoresistant ovarian cancer. Nature, 521 (7553), 489-494. doi: 10.1038/nature14410
Nagaraj, Shiv Hiriyur, Waddell, Nicola, Madugundu, Anil K., Wood, Scott, Jones, Alun, Mandyam, Ramya, Nones, Katia, Pearson, John and Grimmond, Sean M. (2015). PGTools: a software suite for proteogenomic data analysis and visualization. Journal of Proteome Research, 14 (5), 2255-2266. doi: 10.1021/acs.jproteome.5b00029
Waddell, Nicola, Pajic, Marina, Patch, Anne-Marie, Chang, David K, Kassahn, Karin S, Bailey, Peter, Johns, Amber L, Miller, David, Nones, Katia, Quek, Kelly, Quinn, Michael C. J, Robertson, Alan J, Fadlullah, Muhammad Z.H, Bruxner, Tim J.C, Christ, Angelika N, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Wilson, Peter J, Markham, Emma, Cloonan, Nicole, Anderson, Matthew J, Fink, J. Lynn, Holmes, Oliver, Kazakoff, Stephen H, Leonard, Conrad ... Grimmond, Sean M (2015). Whole genomes redefine the mutational landscape of pancreatic cancer. Nature, 518 (7540), 495-501. doi: 10.1038/nature14169
Nones, Katia, Waddell, Nicola, Wayte, Nicci, Patch, Ann-Marie, Bailey, Peter, Newell, Felicity, Holmes, Oliver, Fink, J. Lynn, Quinn, Michael C. J., Tang, Yue Hang, Lampe, Guy, Quek, Kelly, Loffler, Kelly A., Manning, Suzanne, Idrisoglu, Senel, Miller, David, Xu, Qinying, Waddell, Nick, Wilson, Peter J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Nourse, Craig, Nourbakhsh, Ehsan, Anderson, Matthew, Kazakoff, Stephen, Leonard, Conrad, Wood, Scott, Simpson, Peter T. ... Barbour, Andrew P. (2014). Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nature Communications, 5 (1) 6224, 5224.1-5224.9. doi: 10.1038/ncomms6224
Nones, Katia, Waddell, Nic, Song, Sarah, Patch, Ann-Marie, Miller, David, Johns, Amber, Wu, Jianmin, Kassahn, Karin S., Wood, David, Bailey, Peter, Fink, Lynn, Manning, Suzanne, Christ, Angelika N., Nourse, Craig, Kazakoff, Stephen, Taylor, Darrin, Leonard, Conrad, Chang, David K., Jones, Marc D., Thomas, Michelle, Watson, Clare, Pinese, Mark, Cowley, Mark, Rooman, Ilse, Pajic, Marina, Butturini, Giovanni, Malpaga, Anna, Corbo, Vincenzo, Crippa, Stefano ... Grimmond, Sean M. (2014). Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling. International Journal of Cancer, 2014 (5), 1110-1118. doi: 10.1002/ijc.28765
Quek, Kelly, Nones, Katia, Patch, Ann-Marie, Fink, J. Lynn, Newell, Felicity, Cloonan, Nicole, Miller, David, Fadlullah, Muhammad Z. H., Kassahn, Karin, Christ, Angelika N., Bruxner, Timothy J. C., Manning, Suzanne, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Steptoe, Anita, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Qinying, Australian Pancreatic Cancer Genome Initiative, Wilson, Peter, Biankin, Andrew V., Pearson, John V., Waddell, Nic and Grimmond, Sean M. (2014). A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing. BioTechniques, 57 (1), 31-38. doi: 10.2144/000114189
Johns, Amber L., Miller, David K., Simpson, Skye H., Gill, Anthony J., Kassahn, Karin S., Humphris, Jeremy L., Samra, Jaswinder S., Tucker, Katherine, Andrews, Lesley, Chang, David K., Waddell, Nicola, Pajic, Marina, Australian Pancreatic Cancer Genome Initiative, Pearson, John V., Grimmond, Sean M., Biankin, Andrew V. and Zeps, Nikolajs (2014). Returning individual research results for genome sequences of pancreatic cancer. Genome Medicine, 6 (5) 42, 1-8. doi: 10.1186/gm558
Kassahn, Karin S., Holmes, Oliver, Nones, Katia, Patch, Ann-Marie, Miller, David K., Christ, Angelika K., Harliwong, Ivon, Bruxner, Timothy J., Xu, Qinying, Anderson, Matthew, Wood, Scott, Leonard, Conrad, Taylor, Darrin, Newell, Felicity, Song, Sarah, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Steptoe, Anita, Pajic, Marina, Cowley, Mark J., Pinese, Mark, Chang, David K., Gill, Anthony J., Johns, Amber L., Wu, Jianmin, Wilson, Peter J. ... Pearson, John V. (2013). Somatic point mutation calling in low cellularity tumors. PloS One, 8 (11) e74380, e74380.1-e74380.10. doi: 10.1371/journal.pone.0074380
Gonzalez-Perez, Abel, Mustonen, Ville, Reva, Boris, Ritchie, Graham R. S., Creixell, Pau, Karchin, Rachel, Vazquez, Miguel, Fink, J. Lynn, Kassahn, Karin S., Pearson, John V., Bader, Gary D., Boutros, Paul C., Muthuswamy, Lakshmi, Ouellette, B. F. Francis, Reimand, Jüri, Linding, Rune, Shibata, Tatsuhiro, Valencia, Alfonso, Butler, Adam, Dronov, Serge, Flicek, Paul, Shannon, Nick B., Carter, Hannah, Ding, Li, Sander, Chris, Stuart, Josh M., Stein, Lincoln D. and Lopez-Bigas, Nuria (2013). Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods, 10 (8), 723-729. doi: 10.1038/nmeth.2562
Chou, Angela, Waddell, Nicola, Cowley, Mark J., Gill, Anthony J., Chang, David K., Patch, Ann-Marie, Nones, Katia, Wu, Jianmin, Pinese, Mark, Johns, Amber L., Miller, David K., Kassahn, Karin S., Nagrial, Adnan M., Wasan, Harpreet, Goldstein, David, Toon, Christopher W., Chin, Venessa, Chantrill, Lorraine, Humphris, Jeremy, Mead, R. Scott, Rooman, Ilse, Samra, Jaswinder S., Pajic, Marina, Musgrove, Elizabeth A., Pearson, John V., Morey, Adrienne L., Grimmond, Sean M. and Biankin, Andrew V. (2013). Clinical and molecular characterization of HER2 amplified-pancreatic cancer. Genome Medicine, 5 (8) 78, 78.1-78.10. doi: 10.1186/gm482
Alexandrov, Ludmil B., Nik-Zainal, Serena, Wedge, David C., Aparicio, Samuel A. J. R., Behjati, Sam, Biankin, Andrew V., Bignell, Graham R., Bolli, Niccolo, Borg, Ake, Borresen-Dale, Anne-Lise, Boyault, Sandrine, Burkhardt, Birgit, Butler, Adam P., Caldas, Carlos, Davies, Helen R., Desmedt, Christine, Eils, Roland, Eyfjord, Jorunn Erla, Foekens, John A., Greaves, Mel, Hosoda, Fumie, Hutter, Barbara, Ilicic, Tomislav, Imbeaud, Sandrine, Imielinsk, Marcin, Jaeger, Natalie, Jones, David T. W., Jones, David, Knappskog, Stian ... Stratton, Michael R. (2013). Signatures of mutational processes in human cancer. Nature, 500 (7463), 415-421. doi: 10.1038/nature12477
Biankin, Andrew V., Waddell, Nicola, Kassahn, Karin S., Gingras, Marie-Claude, Muthuswamy, Lakshmi B., Johns, Amber L., Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Wu, Jianmin, Chang, David K., Cowley, Mark J., Gardiner, Brooke B., Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Pajic, Marina, Scarlett, Christopher J., Gill, Anthony J., Pinho, Andreia V., Rooman, Ilse, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad ... Grimmond, Sean M. (2012). Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature, 491 (7424), 399-405. doi: 10.1038/nature11547
Song, Sarah, Nones, Katia, Miller, David, Harliwong, Ivon, Kassahn, Karin S., Pinese, Mark, Pajic, Marina, Gill, Anthony J., Johns, Amber L., Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Qinying, Newell, Felicity, Cowley, Mark J., Wu, Jianmin, Wilson, Peter, Fink, Lynn, Biankin, Andrew V., Waddell, Nic, Grimmond, Sean M. and Pearson, John V. (2012). qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS One, 7 (9) e45835, e45835.1-e45835.7. doi: 10.1371/journal.pone.0045835
Clarke, Laura, Zheng-Bradley, Xiangqun, Smith, Richard, Kulesha, Eugene, Xiao, Chunlin, Toneva, Iliana, Vaughan, Brendan, Preuss, Don, Leinonen, Rasko, Shumway, Martin, Sherry, Stephen, Flicek, Paul, The 1000 Genomes Project Consortium and Pearson, John (2012). The 1000 Genomes Project: data management and community access. Nature Methods, 9 (5), 459-462. doi: 10.1038/NMETH.1974
Mann, Karen M., Ward, Jerrold M., Yew, Christopher Chin Kuan, Kovochich, Anne, Dawson, David W., Black, Michael A., Brett, Benjamin T., Sheetz, Benjamin T., Dupuy, Adam J., Chang, David K., Biankin, Andrew V., Waddell, Nicola, Kassahn, Karin S., Grimmond, Sean M., Rust, Alistair G., Adams, David J., Jenkins, Nancy A., Copeland, Neal G., Australian Pancreatic Cancer Genome Initiative, Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi ... Pearson, John V. (2012). Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. Proceedings of the National Academy of Sciences of the United States of America, 109 (16), 5934-5941. doi: 10.1073/pnas.1202490109
Cowley, Mark J., Pinese, Mark, Kassahn, Karin S., Waddell, Nic, Pearson, John V., Grimmond, Sean M., Biankin, Andrew V., Hautaniemi, Sampsa and Wu, Jianmin (2012). PINA v2.0: Mining interactome modules. Nucleic Acids Research, 40 (D1), D862-D865. doi: 10.1093/nar/gkr967
Wood, David L. A., Xu, Qinying, Pearson, John V., Cloonan, Nicole and Grimmond, Sean M. (2011). X-MATE: a flexible system for mapping short read data. Bioinformatics, 27 (4) btq698, 580-581. doi: 10.1093/bioinformatics/btq698
Hudson, T. J., Anderson, W., Aretz, A., Barker, A. D., Grimmond, S. M., Pearson, J. V., Cloonan, N., Gardiner, B. A., Waddell, N. J., Wilson, P. J., Wainwright, B. J. and The International Cancer Genome Consortium (2010). International network of cancer genome projects. Nature, 464 (7291), 993-998. doi: 10.1038/nature08987
McGregor, B., Pfitzner, J., Zhu, G., Grace, M., Eldridge, A., Pearson, J., Mayne, C., Aitken, J. F., Green, A. C. and Martin, N. G. (1999). Genetic and environmental contributions to size, color, shape, and other characteristics of melanocytic naevi in a sample of adolescent twins.. Genetic Epidemiology, 16 (1), 40-53. doi: 10.1002/(SICI)1098-2272(1999)16:1<40::AID-GEPI4>3.0.CO;2-1
Conference Papers
Leonard, Conrad, Wood, Scott, Holmes, Oliver, Waddell, Nic, Gorse, Dominique, Hansen, David P. and Pearson, John V. (2019). Running genomic analyses in the cloud. Annual Australian national conference for Health Informatics HIC 2019, Melbourne, VIC Australia, 12 – 14 August 2019. IOS Press. doi: 10.3233/SHTI190787
Saunus, J. M., Quinn, M. C. J., Patch, A. M., Pearson, J. V., Bailey, P. J., Cloonan, N., Nones, K., Miller, D., Mariasegaram, M., Lau, Q., Jeffree, L., Khanna, K. K., Chenevix-Trench, G., Grimmond, S. M., Simpson, P. T., Waddell, N. and Lakhani, S. R. (2015). Genomic and transcriptomic landscapes of human brain metastases. 15th International Biennial Congress of the Metastasis Research Society, Heidelberg, Germany, June 28th–July 1st, 2014. Dordrecht, Netherlands: Springer Netherlands. doi: 10.1007/s10585-015-9708-3
Data Collection
Pearson, John (2014). Next-Generation Sequencing of COLO-829 Tumour/Normal Melanoma Cell Line Pair. The University of Queensland. (Collection)