Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software von Cameron, Daniel L., Di Stefano, Leon, Papenfuss, Anthony T.

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GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly von Cameron, Daniel L, Schröder, Jan, Penington, Jocelyn Sietsma, Do, Hongdo, Molania, Ramyar, Dobrovic, Alexander, Speed, Terence P, Papenfuss, Anthony T

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A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast von Pal, Bhupinder, Chen, Yunshun, Vaillant, François, Capaldo, Bianca D, Joyce, Rachel, Song, Xiaoyu, Bryant, Vanessa L, Penington, Jocelyn S, Di Stefano, Leon, Tubau Ribera, Nina, Wilcox, Stephen, Mann, Gregory B, Papenfuss, Anthony T, Lindeman, Geoffrey J, Smyth, Gordon K, Visvader, Jane E

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MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect von Esposito, Daniel, Weile, Jochen, Shendure, Jay, Starita, Lea M, Papenfuss, Anthony T, Roth, Frederick P, Fowler, Douglas M, Rubin, Alan F

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GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing von Cameron, Daniel L, Baber, Jonathan, Shale, Charles, Valle-Inclan, Jose Espejo, Besselink, Nicolle, van Hoeck, Arne, Janssen, Roel, Cuppen, Edwin, Priestley, Peter, Papenfuss, Anthony T

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Targeting of the Tumor Suppressor GRHL3 by a miR-21-Dependent Proto-Oncogenic Network Results in PTEN Loss and Tumorigenesis von Darido, Charbel, Georgy, Smitha R., Wilanowski, Tomasz, Dworkin, Sebastian, Auden, Alana, Zhao, Quan, Rank, Gerhard, Srivastava, Seema, Finlay, Moira J., Papenfuss, Anthony T., Pandolfi, Pier Paolo, Pearson, Richard B., Jane, Stephen M.

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A statistical framework for analyzing deep mutational scanning data von Rubin, Alan F, Gelman, Hannah, Lucas, Nathan, Bajjalieh, Sandra M, Papenfuss, Anthony T, Speed, Terence P, Fowler, Douglas M

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Determination of RNA structural diversity and its role in HIV-1 RNA splicing von Tomezsko, Phillip J., Corbin, Vincent D. A., Gupta, Paromita, Swaminathan, Harish, Glasgow, Margalit, Persad, Sitara, Edwards, Matthew D., Mcintosh, Lachlan, Papenfuss, Anthony T., Emery, Ann, Swanstrom, Ronald, Zang, Trinity, Lan, Tammy C. T., Bieniasz, Paul, Kuritzkes, Daniel R., Tsibris, Athe, Rouskin, Silvi

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Complementarity and redundancy of IL-22-producing innate lymphoid cells von Rankin, Lucille C, Girard-Madoux, Mathilde J H, Seillet, Cyril, Mielke, Lisa A, Kerdiles, Yann, Fenis, Aurore, Wieduwild, Elisabeth, Putoczki, Tracy, Mondot, Stanislas, Lantz, Olivier, Demon, Dieter, Papenfuss, Anthony T, Smyth, Gordon K, Lamkanfi, Mohamed, Carotta, Sebastian, Renauld, Jean-Christophe, Shi, Wei, Carpentier, Sabrina, Soos, Tim, Arendt, Christopher, Ugolini, Sophie, Huntington, Nicholas D, Belz, Gabrielle T, Vivier, Eric

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tidybulk: an R tidy framework for modular transcriptomic data analysis von Mangiola, Stefano, Molania, Ramyar, Dong, Ruining, Doyle, Maria A, Papenfuss, Anthony T

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Malaria parasite DNA-harbouring vesicles activate cytosolic immune sensors von Sisquella, Xavier, Ofir-Birin, Yifat, Pimentel, Matthew A., Cheng, Lesley, Abou Karam, Paula, Sampaio, Natália G., Penington, Jocelyn Sietsma, Connolly, Dympna, Giladi, Tal, Scicluna, Benjamin J., Sharples, Robyn A., Waltmann, Andreea, Avni, Dror, Schwartz, Eli, Schofield, Louis, Porat, Ziv, Hansen, Diana S., Papenfuss, Anthony T., Eriksson, Emily M., Gerlic, Motti, Hill, Andrew F., Bowie, Andrew G., Regev-Rudzki, Neta

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The Hippo pathway oncoprotein YAP promotes melanoma cell invasion and spontaneous metastasis von Zhang, Xiaomeng, Yang, Lie, Szeto, Pacman, Abali, Gamze Kuser, Zhang, Youfang, Kulkarni, Aishwarya, Amarasinghe, Kaushalya, Li, Jason, Vergara, Ismael A., Molania, Ramyar, Papenfuss, Anthony T., McLean, Catriona, Shackleton, Mark, Harvey, Kieran F.

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Detection of cell-free microbial DNA using a contaminant-controlled analysis framework von Zozaya-Valdés, Enrique, Wong, Stephen Q, Raleigh, Jeanette, Hatzimihalis, Athena, Ftouni, Sarah, Papenfuss, Anthony T, Sandhu, Shahneen, Dawson, Mark A, Dawson, Sarah-Jane

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Diversity of conotoxin gene superfamilies in the venomous snail, Conus victoriae von Robinson, Samuel D, Safavi-Hemami, Helena, McIntosh, Lachlan D, Purcell, Anthony W, Norton, Raymond S, Papenfuss, Anthony T

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Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer von Trigos, Anna S, Pearson, Richard B, Papenfuss, Anthony T, Goode, David L

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MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer von Cipponi, Arcadi, Goode, David L., Bedo, Justin, McCabe, Mark J., Pajic, Marina, Croucher, David R., Rajal, Alvaro Gonzalez, Junankar, Simon R., Saunders, Darren N., Lobachevsky, Pavel, Papenfuss, Anthony T., Nessem, Danielle, Nobis, Max, Warren, Sean C., Timpson, Paul, Cowley, Mark, Vargas, Ana C., Qiu, Min R., Generali, Daniele G., Keerthikumar, Shivakumar, Nguyen, Uyen, Corcoran, Niall M., Long, Georgina V., Blay, Jean-Yves, Thomas, David M.

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T-Cell Receptor Therapy in the Treatment of Ovarian Cancer: A Mini Review von Wu, Jessica W Y, Dand, Sudiksha, Doig, Lachlan, Papenfuss, Anthony T, Scott, Clare L, Ho, Gwo, Ooi, Joshua D

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Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins von Trigos, Anna S, Bongiovanni, Felicia, Zhang, Yangyi, Zethoven, Maia, Tothill, Richard, Pearson, Richard, Papenfuss, Anthony T, Goode, David L

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Circulating tumour DNA reflects treatment response and clonal evolution in chronic lymphocytic leukaemia von Yeh, Paul, Hunter, Tane, Sinha, Devbarna, Ftouni, Sarah, Wallach, Elise, Jiang, Damian, Chan, Yih-Chih, Wong, Stephen Q., Silva, Maria Joao, Vedururu, Ravikiran, Doig, Kenneth, Lam, Enid, Arnau, Gisela Mir, Semple, Timothy, Wall, Meaghan, Zivanovic, Andjelija, Agarwal, Rishu, Petrone, Pasquale, Jones, Kate, Westerman, David, Blombery, Piers, Seymour, John F., Papenfuss, Anthony T., Dawson, Mark A., Tam, Constantine S., Dawson, Sarah-Jane

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The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen-encoding var genes von Tonkin-Hill, Gerry Q, Trianty, Leily, Noviyanti, Rintis, Nguyen, Hanh H T, Sebayang, Boni F, Lampah, Daniel A, Marfurt, Jutta, Cobbold, Simon A, Rambhatla, Janavi S, McConville, Malcolm J, Rogerson, Stephen J, Brown, Graham V, Day, Karen P, Price, Ric N, Anstey, Nicholas M, Papenfuss, Anthony T, Duffy, Michael F

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