May 15, 2018

Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., Islam, S. M. A., Lopez-Bigas, N., Klimczak, L. J., McPherson, J. R., Morganella, S., Sabarinathan, R., Wheeler, D. A., Mustonen, V., … Getz, G. (2018). The Repertoire of Mutational Signatures in Human Cancer. https://doi.org/10.1101/322859

Clinical OMICs / Mar 01, 2020

Cancer Gets a Global Genomic Map: The Pan-Cancer Analysis of Whole Genomes incorporated 2,658 whole genomes, 38 tumor types, 1,188 transcriptomes, and 1,300 scientists from 37 countries. (2020). Clinical OMICs, 7(2), 12–15. https://doi.org/10.1089/clinomi.07.02.14

Feb 05, 2018

Rubanova, Y., Shi, R., Harrigan, C. F., Li, R., Wintersinger, J., Sahin, N., Deshwar, A., & Morris, Q. (2018). TrackSig: reconstructing evolutionary trajectories of mutations in cancer. https://doi.org/10.1101/260471

Aug 27, 2017

Li, Y., Roberts, N. D., Weischenfeldt, J., Wala, J. A., Shapira, O., Schumacher, S. E., Khurana, E., Korbel, J., Imielinski, M., Beroukhim, R., & Campbell, P. J. (2017). Patterns of structural variation in human cancer. https://doi.org/10.1101/181339

Cancer Research / Jul 01, 2018

Cortés-Ciriano, I., Lee, J.-K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C.-Z., Pellman, D. S., & Park, P. J. (2018). Abstract LB-378: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Cancer Research, 78(13_Supplement), LB-378-LB-378. https://doi.org/10.1158/1538-7445.am2018-lb-378

Sep 20, 2017

Sabarinathan, R., Pich, O., Martincorena, I., Rubio-Perez, C., Juul, M., Wala, J., Schumacher, S., Shapira, O., Sidiropoulos, N., Waszak, S. M., Tamborero, D., Mularoni, L., Rheinbay, E., Hornshøj, H., Deu-Pons, J., Muiños, F., Bertl, J., Guo, Q., … Creighton, C. J. (2017). The whole-genome panorama of cancer drivers. https://doi.org/10.1101/190330

Aug 24, 2017

Rodriguez-Martin, B., Alvarez, E. G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y. S., Temes, J., Garcia-Souto, D., Detering, H., Li, Y., Rodriguez-Castro, J., Dueso-Barroso, A., Bruzos, A. L., Dentro, S. C., Blanco, M. G., Contino, G., … Ardeljan, D. (2017). Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours. https://doi.org/10.1101/179705

Nov 08, 2018

Zapatka, M., Borozan, I., Brewer, D. S., Iskar, M., Grundhoff, A., Alawi, M., Desai, N., Sültmann, H., Moch, H., Cooper, C. S., Eils, R., Ferretti, V., & Lichter, P. (2018). The landscape of viral associations in human cancers. https://doi.org/10.1101/465757

Sep 03, 2017

Calabrese, C., Davidson, N. R., Fonseca, N. A., He, Y., Kahles, A., Lehmann, K.-V., Liu, F., Shiraishi, Y., Soulette, C. M., Urban, L., Demircioğlu, D., Greger, L., Li, S., Liu, D., Perry, M. D., Xiang, L., Zhang, F., … Zhang, J. (2017). Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types. https://doi.org/10.1101/183889

Nature Genetics / Feb 11, 2020

Yuan, Y., Ju, Y. S., Kim, Y., Li, J., Wang, Y., Yoon, C. J., Yang, Y., Martincorena, I., Creighton, C. J., Weinstein, J. N., Xu, Y., Han, L., Kim, H.-L., Nakagawa, H., Park, K., Campbell, P. J., & Liang, H. (2020). Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nature Genetics, 55(5), 893–893. https://doi.org/10.1038/s41588-020-0587-4

Aug 22, 2017

Akdemir, K. C., Li, Y., Verhaak, R. G., Beroukhim, R., Cambell, P., Chin, L., & Futreal, P. A. (2017). Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer. https://doi.org/10.1101/179176

Nov 05, 2017

Jiao, W., Atwal, G., Polak, P., Karlic, R., Cuppen, E., Danyi, A., de Ridder, J., van Herpen, C., Lolkema, M. P., Steeghs, N., Getz, G., Morris, Q. D., & Stein, L. D. (2017). A deep learning system can accurately classify primary and metastatic cancers based on patterns of passenger mutations. https://doi.org/10.1101/214494

Jun 20, 2017

Carlevaro-Fita, J., Lanzós, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J. S., & Johnson, R. (2017). Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC). https://doi.org/10.1101/152769

Aug 23, 2018

Paczkowska, M., Barenboim, J., Sintupisut, N., Fox, N. C., Zhu, H., Abd-Rabbo, D., Boutros, P. C., & Reimand, J. (2018). Integrative pathway enrichment analysis of multivariate omics data. https://doi.org/10.1101/399113

Hematology, Transfusion and Cell Therapy / Jan 01, 2022

Shibeeb, S., & Khan, A. (2022). ABO blood group association and COVID-19. COVID-19 susceptibility and severity: a review. Hematology, Transfusion and Cell Therapy, 44(1), 70–75. https://doi.org/10.1016/j.htct.2021.07.006

Jun 30, 2017

Sieverling, L., Hong, C., Koser, S. D., Ginsbach, P., Kleinheinz, K., Hutter, B., Braun, D. M., Cortés-Ciriano, I., Xi, R., Kabbe, R., Park, P. J., Eils, R., Schlesner, M., Rippe, K., Jones, D. T. W., Brors, B., & Feuerbach, L. (2017). Genomic footprints of activated telomere maintenance mechanisms in cancer. https://doi.org/10.1101/157560

Jan 28, 2019

Bhandari, V., Li, C. H., Bristow, R. G., & Boutros, P. C. (2019). Divergent mutational processes distinguish hypoxic and normoxic tumours. https://doi.org/10.1101/531996

Aug 07, 2018

Reyna, M. A., Haan, D., Paczkowska, M., Verbeke, L. P. C., Vazquez, M., Kahraman, A., Pulido-Tamayo, S., Barenboim, J., Wadi, L., Dhingra, P., Shrestha, R., Getz, G., Lawrence, M. S., Pedersen, J. S., Rubin, M. A., Wheeler, D. A., Brunak, S., Izarzugaza, J. M., … Khurana, E. (2018). Pathway and network analysis of more than 2,500 whole cancer genomes. https://doi.org/10.1101/385294

Jan 23, 2019

Li, C. H., Prokopec, S. D., Sun, R. X., Yousif, F., Schmitz, N., & Boutros, P. C. (2019). Sex Differences in Oncogenic Mutational Processes. https://doi.org/10.1101/528968

Jan 12, 2017

Zhang, Y., Chen, F., Fonseca, N. A., He, Y., Fujita, M., Nakagawa, H., Zhang, Z., Brazma, A., & Creighton, C. J. (2017). Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements. https://doi.org/10.1101/099861

Nov 06, 2017

Shuai, S., Gallinger, S., & Stein, L. (2017). DriverPower: Combined burden and functional impact tests for cancer driver discovery. https://doi.org/10.1101/215244

Jul 04, 2023

Ji, S., Zhu, T., Sethia, A., & Wang, W. (2023). Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples. https://doi.org/10.1101/2023.07.04.547569

Aug 04, 2017

Cmero, M., Ong, C. S., Yuan, K., Schröder, J., Mo, K., Corcoran, N. M., Papenfuss, A. T., Hovens, C. M., Markowetz, F., & Macintyre, G. (2017). SVclone: inferring structural variant cancer cell fraction. https://doi.org/10.1101/172486

Sep 07, 2017

Yakneen, S., Waszak, S. M., Gertz, M., & Korbel, J. O. (2017). Enabling rapid cloud-based analysis of thousands of human genomes via Butler. https://doi.org/10.1101/185736

European Heart Journal / Oct 01, 2022

Kotanidis, C. P., Xie, C., Siddique, M., Burnham, K., Lockstone, H., Kotronias, R., West, H., Rodrigues, J., Adlam, D., Neubauer, S., Channon, K., Deanfield, J., Ho, L. P., & Antoniades, C. (2022). Constructing custom-made radiotranscriptomic signatures from CT angiograms: an application in COVID-19 vascular inflammation. European Heart Journal, 43(Supplement_2). https://doi.org/10.1093/eurheartj/ehac544.198

BMC Genomics / Oct 07, 2023

Amarasinghe, H. E., Zhang, P., Whalley, J. P., Allcock, A., Migliorini, G., Brown, A. C., Scozzafava, G., & Knight, J. C. (2023). Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance. BMC Genomics, 24(1). https://doi.org/10.1186/s12864-023-09663-0

Human Molecular Genetics / Mar 29, 2018

Strachan, T., & Read, A. (2018). Genetic Manipulation of Animals for Modeling Disease and Investigating Gene Function. Human Molecular Genetics, 639–675. https://doi.org/10.4324/9780203833544-20

Genome Medicine / Sep 12, 2023

Zhang, J.-Y., Whalley, J. P., Knight, J. C., Wicker, L. S., Todd, J. A., & Ferreira, R. C. (2023). SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile. Genome Medicine, 15(1). https://doi.org/10.1186/s13073-023-01227-x

Annals of Surgery / Jul 27, 2023

Torrance, H. D., Zhang, P., Longbottom, E. R., Mi, Y., Whalley, J. P., Allcock, A., Kwok, A. J., Cano-Gamez, E., Geoghegan, C. G., Burnham, K. L., Antcliffe, D. B., Davenport, E. E., Pearse, R. M., O’Dwyer, M. J., Hinds, C. J., Knight, J. C., & Gordon, A. C. (2023). A Transcriptomic Approach to Understand Patient Susceptibility to Pneumonia After Abdominal Surgery. Annals of Surgery. https://doi.org/10.1097/sla.0000000000006050

Jan 28, 2023

Torrance, H. D., Zhang, P., Longbottom, E. R., Mi, Y., Whalley, J. P., Allcock, A., Kwok, A. J., Cano-Gamez, E., Geoghegan, C. G., Burnham, K. L., Antcliffe, D. B., Davenport, E. E., Pearse, R. M., O’Dwyer, M. J., Hinds, C. J., Knight, J. C., & Gordon, A. C. (2023). A transcriptomic approach to understand patient susceptibility to pneumonia after abdominal surgery. https://doi.org/10.1101/2023.01.25.23284914

Dec 23, 2022

Weeratunga, P., Denney, L., Bull, J. A., Repapi, E., Sergeant, M., Etherington, R., Vuppussetty, C., Turner, G. D. H., Clelland, C., Cross, A., Issa, F., de Andrea, C. E., Bermejo, I. M., Sims, D., McGowan, S., Zurke, Y.-X., Ahern, D. J., Gamez, E. C., … Ho, L.-P. (2022). Unbiased single cell spatial analysis localises inflammatory clusters of immature neutrophils-CD8 T cells to alveolar progenitor cells in fatal COVID-19 lungs. https://doi.org/10.1101/2022.12.21.22283654

Intensive Care Medicine / Sep 14, 2022

Fish, M., Rynne, J., Jennings, A., Lam, C., Lamikanra, A. A., Ratcliff, J., Cellone-Trevelin, S., Timms, E., Jiriha, J., Tosi, I., Pramanik, R., Simmonds, P., Seth, S., Williams, J., Gordon, A. C., Knight, J., Smith, D. J., Whalley, J., … Harrison, D. (2022). Coronavirus disease 2019 subphenotypes and differential treatment response to convalescent plasma in critically ill adults: secondary analyses of a randomized clinical trial. Intensive Care Medicine, 48(11), 1525–1538. https://doi.org/10.1007/s00134-022-06869-w

Aug 09, 2022

Mi, Y., Burnham, K. L., Charles, P. D., Heilig, R., Vendrell, I., Whalley, J., Torrance, H. D., Antcliffe, D. B., May, S. M., Neville, M. J., Berridge, G., Hutton, P., Goh, C., Radhakrishnan, J., Nesvizhskii, A., Yu, F., Davenport, E. E., McKechnie, S., … Davies, R. (2022). High-throughput mass spectrometry maps the sepsis plasma proteome and differences in response. https://doi.org/10.1101/2022.08.07.22278495

The Lancet Digital Health / Oct 01, 2022

Kotanidis, C. P., Xie, C., Alexander, D., Rodrigues, J. C. L., Burnham, K., Mentzer, A., O’Connor, D., Knight, J., Siddique, M., Lockstone, H., Thomas, S., Kotronias, R., Oikonomou, E. K., Badi, I., Lyasheva, M., Shirodaria, C., Lumley, S. F., Constantinides, B., Sanderson, N., … Lin, W.-H. (2022). Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19. The Lancet Digital Health, 4(10), e705–e716. https://doi.org/10.1016/s2589-7500(22)00132-7

Nature Communications / Jul 14, 2022

Gilchrist, J. J., Makino, S., Naranbhai, V., Sharma, P. K., Koturan, S., Tong, O., Taylor, C. A., Watson, R. A., de los Aires, A. V., Cooper, R., Lau, E., Danielli, S., Hameiri-Bowen, D., Lee, W., Ng, E., Whalley, J., Knight, J. C., & Fairfax, B. P. (2022). Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-31626-4

Genome Biology / Jun 24, 2022

Zhang, P., Amarasinghe, H. E., Whalley, J. P., Tay, C., Fang, H., Migliorini, G., Brown, A. C., Allcock, A., Scozzafava, G., Rath, P., Davies, B., & Knight, J. C. (2022). Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance. Genome Biology, 23(1). https://doi.org/10.1186/s13059-022-02702-1

Cell / Mar 01, 2022

Ahern, D. J., Ai, Z., Ainsworth, M., Allan, C., Allcock, A., Angus, B., Ansari, M. A., Arancibia-Cárcamo, C. V., Aschenbrenner, D., Attar, M., Baillie, J. K., Barnes, E., Bashford-Rogers, R., Bashyal, A., Beer, S., Berridge, G., Beveridge, A., Bibi, S., Bicanic, T., … Zurke, Y.-X. (2022). A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell, 185(5), 916-938.e58. https://doi.org/10.1016/j.cell.2022.01.012

PLOS Computational Biology / Aug 03, 2021

Zhang, J.-Y., Roberts, H., Flores, D. S. C., Cutler, A. J., Brown, A. C., Whalley, J. P., Mielczarek, O., Buck, D., Lockstone, H., Xella, B., Oliver, K., Corton, C., Betteridge, E., Bashford-Rogers, R., Knight, J. C., Todd, J. A., & Band, G. (2021). Using de novo assembly to identify structural variation of eight complex immune system gene regions. PLOS Computational Biology, 17(8), e1009254. https://doi.org/10.1371/journal.pcbi.1009254

May 11, 2021

May 11, 2021

Gilchrist, J. J., Makino, S., Naranbhai, V., Lau, E., Danielli, S., Hameiri-Bowen, D., Lee, W., Ng, E., Whalley, J., Knight, J. C., & Fairfax, B. P. (2021). Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity. https://doi.org/10.1101/2021.05.10.443088

Scientific Reports / Feb 19, 2021

Navarro-Guerrero, E., Tay, C., Whalley, J. P., Cowley, S. A., Davies, B., Knight, J. C., & Ebner, D. (2021). Genome-wide CRISPR/Cas9-knockout in human induced Pluripotent Stem Cell (iPSC)-derived macrophages. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-82137-z

Feb 04, 2021

Zhang, J.-Y., Roberts, H., Flores, D. S. C., Cutler, A. J., Brown, A. C., Whalley, J. P., Mielczarek, O., Buck, D., Lockstone, H., Xella, B., Oliver, K., Corton, C., Betteridge, E., Bashford-Rogers, R., Knight, J. C., Todd, J. A., & Band, G. (2021). Using de novo assembly to identify structural variation of complex immune system gene regions. https://doi.org/10.1101/2021.02.03.429586

Nature Communications / Oct 07, 2020

Whalley, J. P., Buchhalter, I., Rheinbay, E., Raine, K. M., Stobbe, M. D., Kleinheinz, K., Werner, J., Beltran, S., Gut, M., Hübschmann, D., Hutter, B., Livitz, D., Perry, M. D., Rosenberg, M., Saksena, G., Trotta, J.-R., Eils, R., Gerhard, D. S., Campbell, P. J., … Gut, I. G. (2020). Framework for quality assessment of whole genome cancer sequences. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-18688-y

Nature Communications / Sep 21, 2020

Bailey, M. H., Meyerson, W. U., Dursi, L. J., Wang, L.-B., Dong, G., Liang, W.-W., Weerasinghe, A., Li, S., Li, Y., Kelso, S., Akbani, R., Anur, P., Bailey, M. H., Buchanan, A., Chiotti, K., Covington, K., Creason, A., Ding, L., … Ellrott, K. (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-18151-y

Nature Communications / Aug 28, 2020

Li, C. H., Prokopec, S. D., Sun, R. X., Yousif, F., Schmitz, N., Al-Shahrour, F., Atwal, G., Bailey, P. J., Biankin, A. V., Boutros, P. C., Campbell, P. J., Chang, D. K., Cooke, S. L., Deshpande, V., Faltas, B. M., Faquin, W. C., Garraway, L., Getz, G., … Grimmond, S. M. (2020). Sex differences in oncogenic mutational processes. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17359-2

Nature Genetics / Feb 05, 2020

Cortés-Ciriano, I., Lee, J. J.-K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C.-Z., Pellman, D. S., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Beroukhim, R., Boutros, P. C., Bowtell, D. D. L., Brors, B., Burns, K. H., … Campbell, P. J. (2020). Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics, 52(3), 331–341. https://doi.org/10.1038/s41588-019-0576-7

Nature Genetics / Feb 05, 2020

Yuan, Y., Ju, Y. S., Kim, Y., Li, J., Wang, Y., Yoon, C. J., Yang, Y., Martincorena, I., Creighton, C. J., Weinstein, J. N., Xu, Y., Han, L., Kim, H.-L., Nakagawa, H., Park, K., Campbell, P. J., Liang, H., Aaltonen, L. A., … Abascal, F. (2020). Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nature Genetics, 52(3), 342–352. https://doi.org/10.1038/s41588-019-0557-x

Nature Genetics / Feb 05, 2020

Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Boutros, P. C., Bowtell, D. D. L., Brors, B., Burns, K. H., Campbell, P. J., … Chan, K. (2020). Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nature Genetics, 52(3), 294–305. https://doi.org/10.1038/s41588-019-0564-y

Nature Genetics / Feb 05, 2020

Rodriguez-Martin, B., Alvarez, E. G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y. S., Temes, J., Garcia-Souto, D., Detering, H., Li, Y., Rodriguez-Castro, J., Dueso-Barroso, A., Bruzos, A. L., Dentro, S. C., Blanco, M. G., Contino, G., … Ardeljan, D. (2020). Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics, 52(3), 306–319. https://doi.org/10.1038/s41588-019-0562-0

Nature Biotechnology / Feb 05, 2020

Yakneen, S., Waszak, S. M., Aminou, B., Bartolome, J., Boroevich, K. A., Boyce, R., Brooks, A. N., Buchanan, A., Buchhalter, I., Butler, A. P., Byrne, N. J., Cafferkey, A., Campbell, P. J., Chen, Z., Cho, S., Choi, W., Clapham, P., Davis-Dusenbery, B. N., … De La Vega, F. M. (2020). Butler enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, 38(3), 288–292. https://doi.org/10.1038/s41587-019-0360-3

Nature Genetics / Feb 05, 2020

Zapatka, M., Borozan, I., Brewer, D. S., Iskar, M., Grundhoff, A., Alawi, M., Desai, N., Sültmann, H., Moch, H., Alawi, M., Borozan, I., Brewer, D. S., Cooper, C. S., Desai, N., Eils, R., Ferretti, V., Grundhoff, A., Iskar, M., … Kleinheinz, K. (2020). The landscape of viral associations in human cancers. Nature Genetics, 52(3), 320–330. https://doi.org/10.1038/s41588-019-0558-9

Nature / Feb 05, 2020

Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S. C., Gonzalez, S., Rosebrock, D., Mitchell, T. J., Rubanova, Y., Anur, P., Yu, K., Tarabichi, M., Deshwar, A., Wintersinger, J., Kleinheinz, K., Vázquez-García, I., Haase, K., Jerman, L., Sengupta, S., … Macintyre, G. (2020). The evolutionary history of 2,658 cancers. Nature, 578(7793), 122–128. https://doi.org/10.1038/s41586-019-1907-7

Nature Communications / Feb 05, 2020

Jiao, W., Atwal, G., Polak, P., Karlic, R., Cuppen, E., Al-Shahrour, F., Atwal, G., Bailey, P. J., Biankin, A. V., Boutros, P. C., Campbell, P. J., Chang, D. K., Cooke, S. L., Deshpande, V., Faltas, B. M., Faquin, W. C., Garraway, L., Getz, G., … Grimmond, S. M. (2020). A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature Communications, 11(1). https://doi.org/10.1038/s41467-019-13825-8

Nature / Feb 05, 2020

Rheinbay, E., Nielsen, M. M., Abascal, F., Wala, J. A., Shapira, O., Tiao, G., Hornshøj, H., Hess, J. M., Juul, R. I., Lin, Z., Feuerbach, L., Sabarinathan, R., Madsen, T., Kim, J., Mularoni, L., Shuai, S., Lanzós, A., Herrmann, C., … Maruvka, Y. E. (2020). Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature, 578(7793), 102–111. https://doi.org/10.1038/s41586-020-1965-x

Communications Biology / Feb 05, 2020

Carlevaro-Fita, J., Lanzós, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J. S., Abascal, F., Amin, S. B., Bader, G. D., Barenboim, J., Beroukhim, R., Bertl, J., Boroevich, K. A., Brunak, S., Campbell, P. J., Carlevaro-Fita, J., Chakravarty, D., Chan, C. W. Y., … Chen, K. (2020). Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications Biology, 3(1). https://doi.org/10.1038/s42003-019-0741-7

Nature Communications / Feb 05, 2020

Shuai, S., Abascal, F., Amin, S. B., Bader, G. D., Bandopadhayay, P., Barenboim, J., Beroukhim, R., Bertl, J., Boroevich, K. A., Brunak, S., Campbell, P. J., Carlevaro-Fita, J., Chakravarty, D., Chan, C. W. Y., Chen, K., Choi, J. K., Deu-Pons, J., Dhingra, P., … Diamanti, K. (2020). Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications, 11(1). https://doi.org/10.1038/s41467-019-13929-1

Nature Communications / Feb 05, 2020

Bhandari, V., Li, C. H., Bristow, R. G., Boutros, P. C., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., … Alawi, M. (2020). Divergent mutational processes distinguish hypoxic and normoxic tumours. Nature Communications, 11(1). https://doi.org/10.1038/s41467-019-14052-x

Nature / Feb 05, 2020

Calabrese, C., Davidson, N. R., Demircioğlu, D., Fonseca, N. A., He, Y., Kahles, A., Lehmann, K.-V., Liu, F., Shiraishi, Y., Soulette, C. M., Urban, L., Calabrese, C., Davidson, N. R., Demircioğlu, D., Fonseca, N. A., He, Y., Kahles, A., … Lehmann, K.-V. (2020). Genomic basis for RNA alterations in cancer. Nature, 578(7793), 129–136. https://doi.org/10.1038/s41586-020-1970-0

Nature Communications / Feb 05, 2020

Sieverling, L., Hong, C., Koser, S. D., Ginsbach, P., Kleinheinz, K., Hutter, B., Braun, D. M., Cortés-Ciriano, I., Xi, R., Kabbe, R., Park, P. J., Eils, R., Schlesner, M., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Beroukhim, R., Boutros, P. C., … Bowtell, D. D. L. (2020). Genomic footprints of activated telomere maintenance mechanisms in cancer. Nature Communications, 11(1). https://doi.org/10.1038/s41467-019-13824-9

Nature Communications / Feb 05, 2020

Zhang, Y., Chen, F., Fonseca, N. A., He, Y., Fujita, M., Nakagawa, H., Zhang, Z., Brazma, A., Amin, S. B., Awadalla, P., Bailey, P. J., Brazma, A., Brooks, A. N., Calabrese, C., Chateigner, A., Cortés-Ciriano, I., Craft, B., Craft, D., … Creighton, C. 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). https://doi.org/10.1038/s41467-019-13885-w

Nature Communications / Feb 05, 2020

Cmero, M., Yuan, K., Ong, C. S., Schröder, J., Adams, D. J., Anur, P., Beroukhim, R., Boutros, P. C., Bowtell, D. D. L., Campbell, P. J., Cao, S., Christie, E. L., Cun, Y., Dawson, K. J., Demeulemeester, J., Dentro, S. C., Deshwar, A. G., Donmez, N., … Drews, R. M. (2020). Inferring structural variant cancer cell fraction. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14351-8

Nature Communications / Feb 05, 2020

Paczkowska, M., Barenboim, J., Sintupisut, N., Fox, N. S., Zhu, H., Abd-Rabbo, D., Mee, M. W., Boutros, P. C., Abascal, F., Amin, S. B., Bader, G. D., Beroukhim, R., Bertl, J., Boroevich, K. A., Brunak, S., Campbell, P. J., Carlevaro-Fita, J., Chakravarty, D., … Chan, C. W. Y. (2020). Integrative pathway enrichment analysis of multivariate omics data. Nature Communications, 11(1). https://doi.org/10.1038/s41467-019-13983-9

Nature Communications / Feb 05, 2020

Reyna, M. A., Haan, D., Paczkowska, M., Verbeke, L. P. C., Vazquez, M., Kahraman, A., Pulido-Tamayo, S., Barenboim, J., Wadi, L., Dhingra, P., Shrestha, R., Getz, G., Lawrence, M. S., Pedersen, J. S., Rubin, M. A., Wheeler, D. A., Brunak, S., Izarzugaza, J. M. G., … Khurana, E. (2020). Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14367-0

Nature / Feb 05, 2020

Li, Y., Roberts, N. D., Wala, J. A., Shapira, O., Schumacher, S. E., Kumar, K., Khurana, E., Waszak, S., Korbel, J. O., Haber, J. E., Imielinski, M., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Beroukhim, R., Boutros, P. C., Bowtell, D. D. L., Brors, B., … Burns, K. H. (2020). Patterns of somatic structural variation in human cancer genomes. Nature, 578(7793), 112–121. https://doi.org/10.1038/s41586-019-1913-9

Nature Communications / Feb 05, 2020

Rubanova, Y., Shi, R., Harrigan, C. F., Li, R., Wintersinger, J., Sahin, N., Deshwar, A. G., Dentro, S. C., Leshchiner, I., Gerstung, M., Jolly, C., Haase, K., Tarabichi, M., Wintersinger, J., Deshwar, A. G., Yu, K., Gonzalez, S., Rubanova, Y., … Macintyre, G. (2020). Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14352-7

Nature / Feb 05, 2020

Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Tian Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., Islam, S. M. A., Lopez-Bigas, N., Klimczak, L. J., McPherson, J. R., Morganella, S., Sabarinathan, R., Wheeler, D. A., Mustonen, V., … Alexandrov, L. B. (2020). The repertoire of mutational signatures in human cancer. Nature, 578(7793), 94–101. https://doi.org/10.1038/s41586-020-1943-3

Nature / Feb 05, 2020

Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., … von Mering, C. (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793), 82–93. https://doi.org/10.1038/s41586-020-1969-6

PLOS Computational Biology / Nov 25, 2019

Stobbe, M. D., Thun, G. A., Diéguez-Docampo, A., Oliva, M., Whalley, J. P., Raineri, E., & Gut, I. G. (2019). Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer. PLOS Computational Biology, 15(11), e1007496. https://doi.org/10.1371/journal.pcbi.1007496

May 22, 2017

Whalley, J. P., Buchhalter, I., Rheinbay, E., Raine, K. M., Kleinheinz, K., Stobbe, M. D., Werner, J., Beltran, S., Gut, M., Huebschmann, D., Hutter, B., Livitz, D., Perry, M., Rosenberg, M., Saksena, G., Trotta, J.-R., Eils, R., Korbel, J., Gerhard, D. S., … Gut, I. G. (2017). Framework for quality assessment of whole genome, cancer sequences. https://doi.org/10.1101/140921