Lucinda Antonacci-Fulton

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Lucinda Antonacci-Fulton

Assistant Professor of Genetics

 https://orcid.org/0000-0001-6429-4288
    • 219512
      Citations
    1993 …2024

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    • 2024

      A genetic association study of circulating coagulation factor VIII and von Willebrand factor levels

      Trans-Omics for Precision Medicine (TOPMed) program, The INVENT Consortium, de Vries, P. S., Reventun, P., Brown, M. R., Heath, A. S., Huffman, J. E., Le, N. Q., Bebo, A., Brody, J. A., Temprano-Sagrera, G., Raffield, L. M., Ozel, A. B., Thibord, F., Jain, D., Lewis, J. P., Rodriguez, B. A. T., Pankratz, N., Taylor, K. D. & Polasek, O. & 182 others, Chen, M. H., Yanek, L. R., Carrasquilla, G. D., Marioni, R. E., Kleber, M. E., Trégouët, D. A., Yao, J., Li-Gao, R., Joshi, P. K., Trompet, S., Martinez-Perez, A., Ghanbari, M., Howard, T. E., Reiner, A. P., Arvanitis, M., Ryan, K. A., Bartz, T. M., Rudan, I., Faraday, N., Linneberg, A., Ekunwe, L., Davies, G., Delgado, G. E., Suchon, P., Guo, X., Rosendaal, F. R., Klaric, L., Noordam, R., van Rooij, F., Curran, J. E., Wheeler, M. M., Osburn, W. O., O'Connell, J. R., Boerwinkle, E., Beswick, A., Psaty, B. M., Kolcic, I., Souto, J. C., Becker, L. C., Hansen, T., Doyle, M. F., Harris, S. E., Moissl, A. P., Deleuze, J. F., Rich, S. S., van Hylckama Vlieg, A., Campbell, H., Stott, D. J., Soria, J. M., de Maat, M. P. M., Almasy, L., Brody, L. C., Auer, P. L., Abe, N., Abecasis, G., Aguet, F., Albert, C., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Ardlie, K., Arking, D., Arnett, D. K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Ayas, N., Balasubramanian, A., Barnard, J., Barnes, K., Barr, R. G., Barron-Casella, E., Barwick, L., Beaty, T., Beck, G., Becker, D., Becker, L., Beer, R., Beitelshees, A., Benjamin, E., Benos, T., Bezerra, M., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Blue, N., Bowden, D. W., Bowler, R., Brody, J., Broeckel, U., Broome, J., Brown, D., Bunting, K., Burchard, E., Bustamante, C., Buth, E., Cade, B., Cardwell, J., Carey, V., Carrier, J., Carson, A. P., Carty, C., Casaburi, R., Casas Romero, J. P., Casella, J., Castaldi, P., Chaffin, M., Chang, C., Chang, Y. C., Chasman, D., Chavan, S., Chen, B. J., Chen, W. M., Ida Chen, Y. D., Cho, M., Choi, S. H., Chuang, L. M., Chung, M., Chung, R. H., Clish, C., Comhair, S., Conomos, M., Cornell, E., Correa, A., Crandall, C., Crapo, J., Cupples, L. A., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., David, S., Davis, C., Daya, M., de Andrade, M., de las Fuentes, L., de Vries, P., DeBaun, M., Deka, R., DeMeo, D., Devine, S., Dinh, H., Doddapaneni, H., Duan, Q., Dugan-Perez, S., Duggirala, R., Durda, J. P., Dutcher, S. K., Eaton, C., El Boueiz, A., Ellinor, P., Emery, L., Erzurum, S., Farber, C., Farek, J., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Frazar, C., Fu, M., Fullerton, S. M., Fulton, L., Gabriel, S., Gan, W., Gao, S., Gao, Y., Gass, M., Geiger, H., Gelb, B., Geraci, M., Germer, S., Gerszten, R., Gu, C. C., Rao, D. C. & Sung, Y. J., May 2 2024, In: Blood. 143, 18, p. 1845-1855 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      2 Scopus citations

    • Human whole-exome genotype data for Alzheimer’s disease

      Leung, Y. Y., Naj, A. C., Chou, Y. F., Valladares, O., Schmidt, M., Hamilton-Nelson, K., Wheeler, N., Lin, H., Gangadharan, P., Qu, L., Clark, K., Kuzma, A. B., Lee, W. P., Cantwell, L., Nicaretta, H., van der Lee, S., English, A., Kalra, D., Muzny, D. & Skinner, E. & 121 others, Doddapeneni, H., Dinh, H., Hu, J., Santibanez, J., Jayaseelan, J., Worley, K., Gibbs, R. A., Lee, S., Dugan-Perez, S., Korchina, V., Nasser, W., Liu, X., Han, Y., Zhu, Y., Liu, Y., Khan, Z., Zhu, C., Sun, F. J., Jun, G. R., Chung, J., Farrell, J., Zhang, X., Banks, E., Gupta, N., Gabriel, S., Butkiewicz, M., Benchek, P., Smieszek, S., Song, Y., Vardarajan, B., Reitz, C., Reyes-Dumeyer, D., Tosto, G., De Jager, P. L., Barral, S., Ma, Y., Beiser, A., Liu, C. T., Dupuis, J., Lunetta, K., Cupples, L. A., Choi, S. H., Chen, Y., Mez, J., Vanderspek, A., Ikram, M. A., Ahmad, S., Faber, K., Foroud, T., Mlynarski, E., Schmidt, H., Schmidt, R., Kunkle, B., Rajabli, F., Beecham, G., Vance, J. M., Adams, L. D., Cuccaro, M., Mena, P., Booth, B. M., Renton, A., Goate, A., Marcora, E., Stine, A., Feolo, M., Launer, L. J., Koboldt, D. C., Wilson, R. K., van Duijn, C., Amin, N., Kapoor, M., Salerno, W., Bennett, D. A., Xia, L. C., Malamon, J., Mosley, T. H., Satizabal, C., Jan Bressler, B., Jian, X., Nato, A. Q., Horimoto, A. R., Wang, B., Psaty, B., Witten, D., Tsuang, D., Blue, E., Wijsman, E., Sohi, H., Nguyen, H., Bis, J. C., Rice, K., Brown, L., Dorschner, M., Saad, M., Navas, P., Nafikov, R., Thornton, T., Day, T., Haut, J., Sha, J., Zhang, N., Iqbal, T., Zhao, Y., Below, J. E., Larson, D. E., Appelbaum, E., Waligorski, J., Antonacci-Fulton, L., Fulton, R. S., Haines, J., Farrer, L., Seshadri, S., Brkanac, Z., Cruchaga, C., Pericak-Vance, M., Mayeux, R. P., Bush, W. S., Destefano, A., Martin, E., Schellenberg, G. D. & Wang, L. S., Dec 2024, In: Nature communications. 15, 1, 684.

      Research output: Contribution to journal › Article › peer-review

      Open Access

    • Pangenome graph construction from genome alignments with Minigraph-Cactus

      Human Pangenome Reference Consortium, Apr 2024, In: Nature Biotechnology. 42, 4, p. 663-673 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      51 Scopus citations
    • 2023

      Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis

      NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Apr 27 2023, In: Nature. 616, 7958, p. 755-763 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      32 Scopus citations

    • A draft human pangenome reference

      Liao, W. W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., Buonaiuto, S., Chang, X. H., Cheng, H., Chu, J., Colonna, V., Eizenga, J. M., Feng, X., Fischer, C., Fulton, R. S. & Garg, S. & 99 others, Groza, C., Guarracino, A., Harvey, W. T., Heumos, S., Howe, K., Jain, M., Lu, T. Y., Markello, C., Martin, F. J., Mitchell, M. W., Munson, K. M., Mwaniki, M. N., Novak, A. M., Olsen, H. E., Pesout, T., Porubsky, D., Prins, P., Sibbesen, J. A., Sirén, J., Tomlinson, C., Villani, F., Vollger, M. R., Antonacci-Fulton, L. L., Baid, G., Baker, C. A., Belyaeva, A., Billis, K., Carroll, A., Chang, P. C., Cody, S., Cook, D. E., Cook-Deegan, R. M., Cornejo, O. E., Diekhans, M., Ebert, P., Fairley, S., Fedrigo, O., Felsenfeld, A. L., Formenti, G., Frankish, A., Gao, Y., Garrison, N. A., Giron, C. G., Green, R. E., Haggerty, L., Hoekzema, K., Hourlier, T., Ji, H. P., Kenny, E. E., Koenig, B. A., Kolesnikov, A., Korbel, J. O., Kordosky, J., Koren, S., Lee, H. J., Lewis, A. P., Magalhães, H., Marco-Sola, S., Marijon, P., McCartney, A., McDaniel, J., Mountcastle, J., Nattestad, M., Nurk, S., Olson, N. D., Popejoy, A. B., Puiu, D., Rautiainen, M., Regier, A. A., Rhie, A., Sacco, S., Sanders, A. D., Schneider, V. A., Schultz, B. I., Shafin, K., Smith, M. W., Sofia, H. J., Abou Tayoun, A. N., Thibaud-Nissen, F., Tricomi, F. F., Wagner, J., Walenz, B., Wood, J. M. D., Zimin, A. V., Bourque, G., Chaisson, M. J. P., Flicek, P., Phillippy, A. M., Zook, J. M., Eichler, E. E., Haussler, D., Wang, T., Jarvis, E. D., Miga, K. H., Garrison, E., Marschall, T., Hall, I. M., Li, H. & Paten, B., May 11 2023, In: Nature. 617, 7960, p. 312-324 13 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      271 Scopus citations

    • Clonal haematopoiesis and risk of chronic liver disease

      NHLBI TOPMed Hematology Working Group, Apr 27 2023, In: Nature. 616, 7958, p. 747-754 8 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      71 Scopus citations

    • Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma

      NHLBI Trans-Omics in Precision Medicine (TOPMed) Consortium, Recto, K., Kachroo, P., Huan, T., Van Den Berg, D., Lee, G. Y., Bui, H., Lee, D. H., Gereige, J., Yao, C., Hwang, S. J., Joehanes, R., Weiss, S. T., Abe, N., Abecasis, G., Aguet, F., Albert, C., Almasy, L., Alonso, A. & Ament, S. & 181 others, Anderson, P., Anugu, P., Applebaum-Bowden, D., Ardlie, K., Arking, D., Arnett, D. K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Ayas, N., Balasubramanian, A., Barnard, J., Barnes, K., Barr, R. G., Barron-Casella, E., Barwick, L., Beaty, T., Beck, G., Becker, D., Becker, L., Beer, R., Beitelshees, A., Benjamin, E., Benos, T., Bezerra, M., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Blue, N., Boerwinkle, E., Bowden, D. W., Bowler, R., Brody, J., Broeckel, U., Broome, J., Brown, D., Bunting, K., Burchard, E., Bustamante, C., Buth, E., Cade, B., Cardwell, J., Carey, V., Carrier, J., Carson, A. P., Carty, C., Casaburi, R., Casas Romero, J. P., Casella, J., Castaldi, P., Chaffin, M., Chang, C., Chang, Y. C., Chasman, D., Chavan, S., Chen, B. J., Chen, W. M., Ida Chen, Y. D., Cho, M., Choi, S. H., Chuang, L. M., Chung, M., Chung, R. H., Clish, C., Comhair, S., Conomos, M., Cornell, E., Correa, A., Crandall, C., Crapo, J., Cupples, L. A., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., David, S., Davis, C., Daya, M., de Andrade, M., de las Fuentes, L., de Vries, P., DeBaun, M., Deka, R., DeMeo, D., Devine, S., Dinh, H., Doddapaneni, H., Duan, Q., Dugan-Perez, S., Duggirala, R., Durda, J. P., Dutcher, S. K., Eaton, C., Ekunwe, L., El Boueiz, A., Ellinor, P., Emery, L., Erzurum, S., Farber, C., Farek, J., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Frazar, C., Fu, M., Fullerton, S. M., Fulton, L., Gabriel, S., Gan, W., Gao, S., Gao, Y., Gass, M., Geiger, H., Gelb, B., Geraci, M., Germer, S., Gerszten, R., Ghosh, A., Gibbs, R., Gignoux, C., Gladwin, M., Glahn, D., Gogarten, S., Gong, D. W., Goring, H., Graw, S., Gray, K. J., Grine, D., Gross, C., Gu, C. C., Guan, Y., Guo, X., Gupta, N., Haessler, J., Hall, M., Han, Y., Hanly, P., Harris, D., Hawley, N. L., He, J., Heavner, B., Heckbert, S., Hernandez, R., Herrington, D., Hersh, C., Hidalgo, B., Hixson, J., Hobbs, B., Hokanson, J., Hong, E., Hoth, K., Hsiung, C., Hu, J., Hung, Y. J., Huston, H., Hwu, C. M., Irvin, M. R., Jackson, R., Jain, D., Jaquish, C., Johnsen, J., Johnson, A., Johnson, C., Johnston, R., Jones, K., Kang, H. M., Kaplan, R., Kardia, S., Kelly, S., Kenny, E., Kessler, M., Khan, A., Khan, Z., Kim, W., Rao, D. C. & Sung, Y. J., Sep 2023, In: EBioMedicine. 95, 104758.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      3 Scopus citations

    • Increased mutation and gene conversion within human segmental duplications

      Human Pangenome Reference Consortium, Abel, H. J., Antonacci-Fulton, L. L., Fulton, R. S., Hall, I., Liao, W. W., Regier, A., Tomlinson, C. & Wang, T., May 11 2023, In: Nature. 617, 7960, p. 325-334 10 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      29 Scopus citations

    • Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

      Human Pangenome Reference Consortium, Aug 28 2023, In: Cell Reports Methods. 3, 8, 100543.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      3 Scopus citations

    • Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies

      NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Jan 2023, In: Nature Genetics. 55, 1, p. 154-164 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      18 Scopus citations

    • Recombination between heterologous human acrocentric chromosomes

      Human Pangenome Reference Consortium, Abel, H. J., Antonacci-Fulton, L. L., Fulton, R. S., Hall, I., Liao, W. W., Regier, A. & Wang, T., May 11 2023, In: Nature. 617, 7960, p. 335-343 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      38 Scopus citations
    • 2022

      A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies

      NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & TOPMed Lipids Working Group, Dec 2022, In: Nature Methods. 19, 12, p. 1599-1611 13 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      37 Scopus citations

    • Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data

      TOPMed Anthropometry Working Group & NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mar 2022, In: Nature Genetics. 54, 3, p. 263-273 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      151 Scopus citations

    • Nine out of ten samples were mistakenly switched by The Orang-utan Genome Consortium

      Banes, G. L., Fountain, E. D., Karklus, A., Fulton, R. S., Antonacci-Fulton, L. & Nelson, J. O., Dec 2022, In: Scientific data. 9, 1, 485.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      2 Scopus citations

    • Rare coding variants in 35 genes associate with circulating lipid levels—A multi-ancestry analysis of 170,000 exomes

      AMP-T2D-GENES, Myocardial Infarction Genetics Consortium, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & NHLBI TOPMed Lipids Working Group, Jan 6 2022, In: American journal of human genetics. 109, 1, p. 81-96 16 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      21 Scopus citations

    • Semi-automated assembly of high-quality diploid human reference genomes

      Human Pangenome Reference Consortium, Cody, S., Fulton, R. S., Fulton, L. L., Li, D., Lindsay, T., Regier, A., Stitziel, N. O., Wang, T. & Hall, I., Nov 17 2022, In: Nature. 611, 7936, p. 519-531 13 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      80 Scopus citations

    • Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer

      Cui Zhou, D., Jayasinghe, R. G., Chen, S., Herndon, J. M., Iglesia, M. D., Navale, P., Wendl, M. C., Caravan, W., Sato, K., Storrs, E., Mo, C. K., Liu, J., Southard-Smith, A. N., Wu, Y., Naser Al Deen, N., Baer, J. M., Fulton, R. S., Wyczalkowski, M. A., Liu, R. & Fronick, C. C. & 46 others, Fulton, L. A., Shinkle, A., Thammavong, L., Zhu, H., Sun, H., Wang, L. B., Li, Y., Zuo, C., McMichael, J. F., Davies, S. R., Appelbaum, E. L., Robbins, K. J., Chasnoff, S. E., Yang, X., Reeb, A. N., Oh, C., Serasanambati, M., Lal, P., Varghese, R., Mashl, J. R., Ponce, J., Terekhanova, N. V., Yao, L., Wang, F., Chen, L., Schnaubelt, M., Lu, R. J. H., Schwarz, J. K., Puram, S. V., Kim, A. H., Song, S. K., Shoghi, K. I., Lau, K. S., Ju, T., Chen, K., Chatterjee, D., Hawkins, W. G., Zhang, H., Achilefu, S., Chheda, M. G., Oh, S. T., Gillanders, W. E., Chen, F., DeNardo, D. G., Fields, R. C. & Ding, L., Sep 2022, In: Nature Genetics. 54, 9, p. 1390-1405 16 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      93 Scopus citations

    • Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals

      Tahir, U. A., Katz, D. H., Avila-Pachecho, J., Bick, A. G., Pampana, A., Robbins, J. M., Yu, Z., Chen, Z. Z., Benson, M. D., Cruz, D. E., Ngo, D., Deng, S., Shi, X., Zheng, S., Eisman, A. S., Farrell, L., Hall, M. E., Correa, A., Tracy, R. P. & Durda, P. & 410 others, Taylor, K. D., Liu, Y., Johnson, W. C., Guo, X., Yao, J., Chen, Y. D. I., Manichaikul, A. W., Ruberg, F. L., Blaner, W. S., Jain, D., Bouchard, C., Sarzynski, M. A., Rich, S. S., Rotter, J. I., Wang, T. J., Wilson, J. G., Clish, C. B., Natarajan, P., Gerszten, R. E., Abe, N., Abecasis, G., Aguet, F., Albert, C., Almasy, L., Alonso, A., Ament, S., Anderson, P., Anugu, P., Applebaum-Bowden, D., Ardlie, K., Arking, D., Arnett, D. K., Ashley-Koch, A., Aslibekyan, S., Assimes, T., Auer, P., Avramopoulos, D., Ayas, N., Balasubramanian, A., Barnard, J., Barnes, K., Barr, R. G., Barron-Casella, E., Barwick, L., Beaty, T., Beck, G., Becker, D., Becker, L., Beer, R., Beitelshees, A., Benjamin, E., Benos, T., Bezerra, M., Bielak, L., Bis, J., Blackwell, T., Blangero, J., Blue, N., Boerwinkle, E., Bowden, D. W., Bowler, R., Brody, J., Broeckel, U., Broome, J., Brown, D., Bunting, K., Burchard, E., Bustamante, C., Buth, E., Cade, B., Cardwell, J., Carey, V., Carrier, J., Carson, A., Carty, C., Casaburi, R., Romero, J. P. C., Casella, J., Castaldi, P., Chaffin, M., Chang, C., Chang, Y. C., Chasman, D., Chavan, S., Chen, B. J., Chen, W. M., Cho, M., Choi, S. H., Chuang, L. M., Chung, M., Chung, R. H., Comhair, S., Conomos, M., Cornell, E., Crandall, C., Crapo, J., Cupples, L. A., Curran, J., Curtis, J., Custer, B., Damcott, C., Darbar, D., David, S., Davis, C., Daya, M., de Andrade, M., Fuentes, L. D. L., de Vries, P., DeBaun, M., Deka, R., DeMeo, D., Devine, S., Dinh, H., Doddapaneni, H., Duan, Q., Dugan-Perez, S., Duggirala, R., Dutcher, S. K., Eaton, C., Ekunwe, L., El Boueiz, A., Ellinor, P., Emery, L., Erzurum, S., Farber, C., Farek, J., Fingerlin, T., Flickinger, M., Fornage, M., Franceschini, N., Frazar, C., Fu, M., Fullerton, S. M., Fulton, L., Gabriel, S., Gan, W., Gao, S., Gao, Y., Gass, M., Geiger, H., Gelb, B., Geraci, M., Germer, S., Ghosh, A., Gibbs, R., Gignoux, C., Gladwin, M., Glahn, D., Gogarten, S., Gong, D. W., Goring, H., Graw, S., Gray, K. J., Grine, D., Gross, C., Gu, C. C., Guan, Y., Gupta, N., Haessler, J., Han, Y., Hanly, P., Harris, D., Hawley, N. L., He, J., Heavner, B., Heckbert, S., Hernandez, R., Herrington, D., Hersh, C., Hidalgo, B., Hixson, J., Hobbs, B., Hokanson, J., Hong, E., Hoth, K., Hsiung, C., Hu, J., Hung, Y. J., Huston, H., Hwu, C. M., Irvin, M. R., Jackson, R., Jaquish, C., Johnsen, J., Johnson, A., Johnston, R., Jones, K., Kang, H. M., Kaplan, R., Kardia, S., Kelly, S., Kenny, E., Kessler, M., Khan, A., Khan, Z., Kim, W., Kimoff, J., Kinney, G., Konkle, B., Kooperberg, C., Kramer, H., Lange, C., Lange, E., Lange, L., Laurie, C., Laurie, C., LeBoff, M., Lee, J., Lee, S., Lee, W. J., LeFaive, J., Levine, D., Levy, D., Lewis, J., Li, X., Li, Y., Lin, H., Lin, H., Lin, X., Liu, S., Liu, Y., Loos, R. J. F., Lubitz, S., Lunetta, K., Luo, J., Magalang, U., Mahaney, M., Make, B., Manning, A., Manson, J. A., Martin, L., Marton, M., Mathai, S., Mathias, R., May, S., McArdle, P., McDonald, M. L., McFarland, S., McGarvey, S., McGoldrick, D., McHugh, C., McNeil, B., Mei, H., Meigs, J., Menon, V., Mestroni, L., Metcalf, G., Meyers, D. A., Mignot, E., Mikulla, J., Min, N., Minear, M., Minster, R. L., Mitchell, B. D., Moll, M., Momin, Z., Montasser, M. E., Montgomery, C., Muzny, D., Mychaleckyj, J. C., Nadkarni, G., Naik, R., Naseri, T., Nekhai, S., Nelson, S. C., Neltner, B., Nessner, C., Nickerson, D., Nkechinyere, O., North, K., O’Connell, J., O’Connor, T., Ochs-Balcom, H., Okwuonu, G., Pack, A., Paik, D. T., Palmer, N., Pankow, J., Papanicolaou, G., Parker, C., Peloso, G., Peralta, J. M., Perez, M., Perry, J., Peters, U., Peyser, P., Phillips, L. S., Pleiness, J., Pollin, T., Post, W., Becker, J. P., Boorgula, M. P., Preuss, M., Psaty, B., Qasba, P., Qiao, D., Qin, Z., Rafaels, N., Raffield, L., Rajendran, M., Ramachandran, V. S., Rao, D. C., Rasmussen-Torvik, L., Ratan, A., Redline, S., Reed, R., Reeves, C., Regan, E., Reiner, A., Reupena, M. S., Rice, K., Robillard, R., Robine, N., Dan Roden, R., Roselli, C., Ruczinski, I., Runnels, A., Russell, P., Ruuska, S., Sabino, E. C., Saleheen, D., Salimi, S., Salvi, S., Salzberg, S., Sandow, K., Sankaran, V. G., Santibanez, J., Schwander, K., Schwartz, D., Sciurba, F., Seidman, C., Seidman, J., Sériès, F., Sheehan, V., Sherman, S. L., Shetty, A., Shetty, A., Sheu, W. H. H., Shoemaker, M. B., Silver, B., Silverman, E., Skomro, R., Smith, A. V., Smith, J., Smith, J., Smith, N., Smith, T., Smoller, S., Snively, B., Snyder, M., Sofer, T., Sotoodehnia, N., Stilp, A. M., Storm, G., Streeten, E., Su, J. L., Sung, Y. J., Sylvia, J., Szpiro, A., Taliun, D., Tang, H., Taub, M., Taylor, M., Taylor, S., Telen, M., Thornton, T. A., Threlkeld, M., Tinker, L., Tirschwell, D., Tishkoff, S., Tiwari, H., Tong, C., Tsai, M., Vaidya, D., Van Den Berg, D., VandeHaar, P., Vrieze, S., Walker, T., Wallace, R., Walts, A., Wang, F. F., Wang, H., Wang, J., Watson, K., Watt, J., Weeks, D. E., Weinstock, J., Weir, B., Weiss, S. T., Weng, L. C., Wessel, J., Willer, C., Williams, K., Williams, L. K., Wilson, C., Winterkorn, L., Wong, Q., Wu, J., Xu, H., Yanek, L., Yang, I., Yu, K., Zekavat, S. M., Zhang, Y., Zhao, S. X., Zhao, W., Zhu, X., Ziv, E., Zody, M. & Zoellner, S., Dec 2022, In: Nature communications. 13, 1, 4923.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      15 Scopus citations

    • Whole genome sequence analysis of blood lipid levels in >66,000 individuals

      NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 2022, In: Nature communications. 13, 1, 5995.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      25 Scopus citations
    • 2021

      A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

      NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Oct 2021, In: Nature Genetics. 53, 10, p. 1504-1516 13 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      68 Scopus citations

    • Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices

      NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & FinnGen, Dec 1 2021, In: Nature communications. 12, 1, 2182.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      13 Scopus citations

    • Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium

      NHLBI SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS), Dec 2021, In: Genome medicine. 13, 1, 66.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      22 Scopus citations

    • Genome sequencing unveils a regulatory landscape of platelet reactivity

      NHLBI Trans-Omics for Precision (TOPMed) Consortium, Dec 1 2021, In: Nature communications. 12, 1, 3626.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      31 Scopus citations

    • Genomic Profiling of Lung Adenocarcinoma in Never-Smokers

      Devarakonda, S., Li, Y., Martins Rodrigues, F., Sankararaman, S., Kadara, H., Goparaju, C., Lanc, I., Pepin, K., Waqar, S. N., Morgensztern, D., Ward, J., Masood, A., Fulton, R., Fulton, L., Gillette, M. A., Satpathy, S., Carr, S. A., Wistuba, I., Pass, H. & Wilson, R. K. & 2 others, Ding, L. & Govindan, R., Nov 20 2021, In: Journal of Clinical Oncology. 39, 33, p. 3747-3758 12 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      56 Scopus citations

    • Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

      NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Feb 11 2021, In: Nature. 590, 7845, p. 290-299 10 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      905 Scopus citations

    • Variant-specific inflation factors for assessing population stratification at the phenotypic variance level

      NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 1 2021, In: Nature communications. 12, 1, 3506.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      7 Scopus citations

    • Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program

      TOPMed Sleep Working Group & NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Dec 2021, In: Genome medicine. 13, 1, 136.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      19 Scopus citations
    • 2020

      A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

      PCAWG Tumor Subtypes and Clinical Translation Working Group, PCAWG Consortium, 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. & 182 others, Grimmond, S. M., Haider, S., Hoadley, K. A., Jiao, W., Kaiser, V. B., Karlic, R., Kato, M., Kübler, K., Lazar, A. J., Li, C. H., Louis, D. N., Margolin, A., Martin, S., Nahal-Bose, H. K., Nielsen, G. P., Nik-Zainal, S., Omberg, L., P’ng, C., Perry, M. D., Polak, P., Rheinbay, E., Rubin, M. A., Semple, C. A., Sgroi, D. C., Shibata, T., Siebert, R., Smith, J., Stein, L. D., Stobbe, M. D., Sun, R. X., Thai, K., Wright, D. W., Wu, C. L., Yuan, K., Zhang, J., Danyi, A., de Ridder, J., van Herpen, C., Lolkema, M. P., Steeghs, N., Getz, G., Morris, Q. D., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Beroukhim, R., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Bowtell, D. D. L., Boyault, S., Boyce, R., Boyd, J., Brazma, A., Brennan, P., Brewer, D. S., Brinkman, A. B., Bristow, R. G., Broaddus, R. R., Brock, J. E., Brock, M., Broeks, A., Brooks, A. N., Brooks, D., Brors, B., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 728.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      133 Scopus citations

    • Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

      PCAWG Consortium, PCAWG Drivers and Functional Interpretation Working Group, PCAWG-Structural Variation Working Group, 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. & 183 others, Herrmann, C., Maruvka, Y. E., Shen, C., Amin, S. B., Bandopadhayay, P., Bertl, J., Boroevich, K. A., Busanovich, J., Carlevaro-Fita, J., Chakravarty, D., Chan, C. W. Y., Craft, D., Dhingra, P., Diamanti, K., Fonseca, N. A., Gonzalez-Perez, A., Guo, Q., Hamilton, M. P., Haradhvala, N. J., Hong, C., Isaev, K., Johnson, T. A., Juul, M., Kahles, A., Kahraman, A., Kim, Y., Komorowski, J., Kumar, K., Kumar, S., Lee, D., Lehmann, K. V., Li, Y., Liu, E. M., Lochovsky, L., Park, K., Pich, O., Roberts, N. D., Saksena, G., Schumacher, S. E., Sidiropoulos, N., Sieverling, L., Sinnott-Armstrong, N., Stewart, C., Tamborero, D., Tubio, J. M. C., Umer, H. M., Uusküla-Reimand, L., Wadelius, C., Wadi, L., Yao, X., Zhang, C. Z., Zhang, J., Haber, J. E., Hobolth, A., Imielinski, M., Kellis, M., Lawrence, M. S., von Mering, C., Nakagawa, H., Raphael, B. J., Rubin, M. A., Sander, C., Stein, L. D., Stuart, J. M., Tsunoda, T., Wheeler, D. A., Johnson, R., Reimand, J., Gerstein, M., Khurana, E., Campbell, P. J., López-Bigas, N., Weischenfeldt, J., Beroukhim, R., Martincorena, I., Pedersen, J. S., Getz, G., Bader, G. D., Barenboim, J., Brunak, S., Chen, K., Choi, J. K., Deu-Pons, J., Fink, J. L., Frigola, J., Gambacorti-Passerini, C., Garsed, D. W., Gut, I. G., Haan, D., Harmanci, A. O., Helmy, M., Hodzic, E., Izarzugaza, J. M. G., Kim, J. K., Korbel, J. O., Larsson, E., Li, S., Li, X., Lou, S., Marchal, K., Martinez-Fundichely, A., McGillivray, P. D., Meyerson, W., Muiños, F., Paczkowska, M., Park, K., Pons, T., Pulido-Tamayo, S., Reyes-Salazar, I., Reyna, M. A., Rubio-Perez, C., Sahinalp, S. C., Salichos, L., Shackleton, M., Shrestha, R., Valencia, A., Vazquez, M., Verbeke, L. P. C., Wang, J., Warrell, J., Waszak, S. M., Wu, G., Yu, J., Zhang, X., Zhang, Y., Zhao, Z., Zou, L., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Boutros, P. C., Bowtell, D. D. L., Brors, B., Burns, K. H., Chan, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Frenkel-Morgenstern, M., Gordenin, D. A., Hutter, B., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Lee, E. A., Lee, J. J. K., Lynch, A. G., Macintyre, G., Markowetz, F., Meyerson, M., Miyano, S., Navarro, F. C. P., Ossowski, S., Park, P. J., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, S. A., Rodriguez-Martin, B., Scully, R., Torrents, D., Villasante, I., Waddell, N., Yang, L., Yoon, S. S., Zamora, J., Aaltonen, L. A., Abeshouse, A., Aburatani, H., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Feb 6 2020, In: Nature. 578, 7793, p. 102-111 10 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      373 Scopus citations

    • Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

      PCAWG Drivers and Functional Interpretation Group, PCAWG Consortium, Carlevaro-Fita, J., Lanzós, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J. S., Johnson, R., Abascal, F., Amin, S. B., Bader, G. D., Barenboim, J., Beroukhim, R., Bertl, J., Boroevich, K. A., Brunak, S., Campbell, P. J., Chakravarty, D. & Chan, C. W. Y. & 182 others, Chen, K., Choi, J. K., Deu-Pons, J., Dhingra, P., Diamanti, K., Fink, J. L., Fonseca, N. A., Frigola, J., Gambacorti-Passerini, C., Garsed, D. W., Gerstein, M., Getz, G., Gonzalez-Perez, A., Guo, Q., Gut, I. G., Haan, D., Hamilton, M. P., Haradhvala, N. J., Harmanci, A. O., Helmy, M., Herrmann, C., Hess, J. M., Hobolth, A., Hodzic, E., Hornshøj, H., Isaev, K., Izarzugaza, J. M. G., Johnson, T. A., Juul, M., Juul, R. I., Kahles, A., Kahraman, A., Kellis, M., Khurana, E., Kim, J., Kim, J. K., Kim, Y., Komorowski, J., Korbel, J. O., Kumar, S., Larsson, E., Lawrence, M. S., Lee, D., Lehmann, K. V., Li, S., Li, X., Lin, Z., Liu, E. M., Lochovsky, L., Lou, S., Madsen, T., Marchal, K., Martincorena, I., Martinez-Fundichely, A., Maruvka, Y. E., McGillivray, P. D., Meyerson, W., Muiños, F., Mularoni, L., Nakagawa, H., Nielsen, M. M., Paczkowska, M., Park, K., Park, K., Pich, O., Pons, T., Pulido-Tamayo, S., Raphael, B. J., Reimand, J., Reyes-Salazar, I., Reyna, M. A., Rheinbay, E., Rubin, M. A., Rubio-Perez, C., Sabarinathan, R., Sahinalp, S. C., Saksena, G., Salichos, L., Sander, C., Schumacher, S. E., Shackleton, M., Shapira, O., Shen, C., Shrestha, R., Shuai, S., Sidiropoulos, N., Sieverling, L., Sinnott-Armstrong, N., Stein, L. D., Stuart, J. M., Tamborero, D., Tiao, G., Tsunoda, T., Umer, H. M., Uusküla-Reimand, L., Valencia, A., Vazquez, M., Verbeke, L. P. C., Wadelius, C., Wadi, L., Wang, J., Warrell, J., Waszak, S. M., Weischenfeldt, J., Wheeler, D. A., Wu, G., Yu, J., Zhang, J., Zhang, X., Zhang, Y., Zhao, Z., Zou, L., von Mering, C., Aaltonen, L. A., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Communications Biology. 3, 1, 56.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      147 Scopus citations

    • Combined burden and functional impact tests for cancer driver discovery using DriverPower

      PCAWG Drivers and Functional Interpretation Working Group, PCAWG Consortium, 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. & 182 others, Diamanti, K., Feuerbach, L., Fink, J. L., Fonseca, N. A., Frigola, J., Gambacorti-Passerini, C., Garsed, D. W., Gerstein, M., Getz, G., Guo, Q., Gut, I. G., Haan, D., Hamilton, M. P., Haradhvala, N. J., Harmanci, A. O., Helmy, M., Herrmann, C., Hess, J. M., Hobolth, A., Hodzic, E., Hong, C., Hornshøj, H., Isaev, K., Izarzugaza, J. M. G., Johnson, R., Johnson, T. A., Juul, M., Juul, R. I., Kahles, A., Kahraman, A., Kellis, M., Khurana, E., Kim, J., Kim, J. K., Kim, Y., Komorowski, J., Korbel, J. O., Kumar, S., Lanzós, A., Larsson, E., Lawrence, M. S., Lee, D., Lehmann, K. V., Li, S., Li, X., Lin, Z., Liu, E. M., Lochovsky, L., Lou, S., Madsen, T., Marchal, K., Martincorena, I., Martinez-Fundichely, A., Maruvka, Y. E., McGillivray, P. D., Meyerson, W., Muiños, F., Mularoni, L., Nakagawa, H., Nielsen, M. M., Paczkowska, M., Park, K., Park, K., Pedersen, J. S., Pons, T., Pulido-Tamayo, S., Raphael, B. J., Reimand, J., Reyes-Salazar, I., Reyna, M. A., Rheinbay, E., Rubin, M. A., Rubio-Perez, C., Sahinalp, S. C., Saksena, G., Salichos, L., Sander, C., Schumacher, S. E., Shackleton, M., Shapira, O., Shen, C., Shrestha, R., Shuai, S., Sidiropoulos, N., Sieverling, L., Sinnott-Armstrong, N., Stein, L. D., Stuart, J. M., Tamborero, D., Tiao, G., Tsunoda, T., Umer, H. M., Uusküla-Reimand, L., Valencia, A., Vazquez, M., Verbeke, L. P. C., Wadelius, C., Wadi, L., Wang, J., Warrell, J., Waszak, S. M., Weischenfeldt, J., Wheeler, D. A., Wu, G., Yu, J., Zhang, J., Zhang, X., Zhang, Y., Zhao, Z., Zou, L., von Mering, C., Gallinger, S., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 734.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      25 Scopus citations

    • Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

      PCAWG-Structural Variation Working Group, PCAWG Consortium, 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. & 182 others, Campbell, P. J., Chan, K., Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gerstein, M., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Koh, Y., Korbel, J. O., Kumar, K., Lee, E. A., Li, Y., Lynch, A. G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Miyano, S., Nakagawa, H., Navarro, F. C. P., Ossowski, S., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, N. D., Roberts, S. A., Rodriguez-Martin, B., Schumacher, S. E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Torrents, D., Tubio, J. M. C., Villasante, I., Waddell, N., Wala, J. A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S. S., Zamora, J., Park, P. J., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Muyas, F. & Werner, J., Mar 1 2020, In: Nature Genetics. 52, 3, p. 331-341 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      408 Scopus citations

    • Comprehensive molecular characterization of mitochondrial genomes in human cancers

      PCAWG Consortium, 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. & 181 others, 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Beroukhim, R., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Bowtell, D. D. L., Boyault, S., Boyce, R., Boyd, J., Brazma, A., Brennan, P., Brewer, D. S., Brinkman, A. B., Bristow, R. G., Broaddus, R. R., Brock, J. E., Brock, M., Broeks, A., Brooks, A. N., Brooks, D., Brors, B., Brunak, S., Bruxner, T. J. C., Bruzos, A. L., Buchanan, A., Buchhalter, I., Buchholz, C., Bullman, S., Burke, H., Burkhardt, B., Burns, K. H., Busanovich, J., Bustamante, C. D., Butler, A. P., Butte, A. J., Byrne, N. J., Børresen-Dale, A. L., Caesar-Johnson, S. J., Cafferkey, A., Cahill, D., Calabrese, C., Caldas, C., Calvo, F., Camacho, N., Campbell, P. J., Campo, E., Cantù, C., Cao, S., Carey, T. E., Carlevaro-Fita, J., Carlsen, R., Cataldo, I., Cazzola, M., Cebon, J., Cerfolio, R., Chadwick, D. E., Chakravarty, D., Chalmers, D., Chan, C. W. Y., Chan, K., Chan-Seng-Yue, M., Chandan, V. S., Chang, D. K., Chanock, S. J., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Mar 1 2020, In: Nature Genetics. 52, 3, p. 342-352 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      248 Scopus citations

    • Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

      PCAWG-Structural Variation Working Group, PCAWG Consortium, 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. & 182 others, Chan, K., Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gerstein, M., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Korbel, J. O., Kumar, K., Lee, E. A., Lee, J. J. K., Li, Y., Lynch, A. G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Meyerson, M., Miyano, S., Nakagawa, H., Navarro, F. C. P., Ossowski, S., Park, P. J., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, N. D., Roberts, S. A., Rodriguez-Martin, B., Schumacher, S. E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Torrents, D., Tubio, J. M. C., Villasante, I., Waddell, N., Wala, J. A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S. S., Zamora, J., Zhang, C. Z., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Muyas, F. & Werner, J., Mar 1 2020, In: Nature Genetics. 52, 3, p. 294-305 12 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      158 Scopus citations

    • Divergent mutational processes distinguish hypoxic and normoxic tumours

      PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 737.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      88 Scopus citations

    • Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale

      NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium & TOPMed Lipids Working Group, Sep 1 2020, In: Nature Genetics. 52, 9, p. 969-983 15 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      126 Scopus citations

    • Genomic basis for RNA alterations in cancer

      PCAWG Transcriptome Core Group, PCAWG Transcriptome Working Group, PCAWG Consortium, 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., Greger, L., Li, S., Liu, D., Perry, M. D., Xiang, Q. & Zhang, F. & 183 others, Zhang, J., Bailey, P., Erkek, S., Hoadley, K. A., Hou, Y., Huska, M. R., Kilpinen, H., Korbel, J. O., Marin, M. G., Markowski, J., Nandi, T., Pan-Hammarström, Q., Pedamallu, C. S., Siebert, R., Stark, S. G., Su, H., Tan, P., Waszak, S. M., Yung, C., Zhu, S., Awadalla, P., Creighton, C. J., Meyerson, M., Ouellette, B. F. F., Wu, K., Yang, H., Brazma, A., Brooks, A. N., Göke, J., Rätsch, G., Schwarz, R. F., Stegle, O., Zhang, Z., Amin, S. B., Chateigner, A., Cortés-Ciriano, I., Craft, B., Frenkel-Morgenstern, M., Goldman, M., Khurana, E., Lamaze, F. C., Li, C., Li, X., Li, X., Liu, X., Nielsen, M. M., Ojesina, A. I., Park, P. J., Pedersen, J. S., Teh, B. T., Wang, J., Xiong, H., Yakneen, S., Ye, C., Zhang, X., Zheng, L., Zhu, J., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Beroukhim, R., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Bowtell, D. D. L., Boyault, S., Boyce, R., Boyd, J., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Feb 6 2020, In: Nature. 578, 7793, p. 129-136 8 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      273 Scopus citations

    • Genomic footprints of activated telomere maintenance mechanisms in cancer

      PCAWG-Structural Variation Working Group, PCAWG Consortium, 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. & 182 others, Bowtell, D. D. L., Brors, B., Burns, K. H., Campbell, P. J., Chan, K., Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gerstein, M., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Korbel, J. O., Kumar, K., Lee, E. A., Lee, J. J. K., Li, Y., Lynch, A. G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Meyerson, M., Miyano, S., Nakagawa, H., Navarro, F. C. P., Ossowski, S., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, N. D., Roberts, S. A., Rodriguez-Martin, B., Schumacher, S. E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Torrents, D., Tubio, J. M. C., Villasante, I., Waddell, N., Wala, J. A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S. S., Zamora, J., Zhang, C. Z., Brors, B., Rippe, K., Jones, D. T. W., Feuerbach, L., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Muyas, F. & Werner, J., Dec 1 2020, In: Nature communications. 11, 1, 733.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      77 Scopus citations

    • High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

      PCAWG Transcriptome Working Group, PCAWG-Structural Variation Working Group, PCAWG Consortium, 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. & 183 others, Craft, D., Creighton, C. J., Davidson, N. R., Demircioğlu, D., Erkek, S., Fonseca, N. A., Frenkel-Morgenstern, M., Goldman, M. J., Greger, L., Göke, J., He, Y., Hoadley, K. A., Hou, Y., Huska, M. R., Kahles, A., Khurana, E., Kilpinen, H., Korbel, J. O., Lamaze, F. C., Lehmann, K. V., Li, C., Li, S., Li, X., Li, X., Liu, D., Liu, F., Liu, X., Marin, M. G., Markowski, J., Meyerson, M., Nandi, T., Nielsen, M. M., Ojesina, A. I., Ouellette, B. F. F., Pan-Hammarström, Q., Park, P. J., Pedamallu, C. S., Pedersen, J. S., Perry, M. D., Rätsch, G., Schwarz, R. F., Shiraishi, Y., Siebert, R., Soulette, C. M., Stark, S. G., Stegle, O., Su, H., Tan, P., Teh, B. T., Urban, L., Wang, J., Waszak, S. M., Wu, K., Xiang, Q., Xiong, H., Yakneen, S., Yang, H., Ye, C., Yung, C. K., Zhang, F., Zhang, J., Zhang, X., Zhang, Z., Zheng, L., Zhu, J., Zhu, 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., Chan, K., Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Garsed, D. W., Gerstein, M., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Korbel, J. O., Kumar, K., Lee, E. A., Lee, J. J. K., Li, Y., Lynch, A. G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Miyano, S., Nakagawa, H., Navarro, F. C. P., Ossowski, S., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, N. D., Roberts, S. A., Rodriguez-Martin, B., Schumacher, S. E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Torrents, D., Tubio, J. M. C., Villasante, I., Waddell, N., Wala, J. A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S. S., Zamora, J., Zhang, C. Z., Creighton, C. J., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Muyas, F. & Werner, J., Dec 1 2020, In: Nature communications. 11, 1, 736.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      51 Scopus citations

    • Inferring structural variant cancer cell fraction

      PCAWG Evolution and Heterogeneity Working Group, PCAWG Consortium, 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. & 182 others, Drews, R. M., Eils, R., Fan, Y., Fittall, M. W., Garsed, D. W., Gerstung, M., Getz, G., Gonzalez, S., Ha, G., Haase, K., Imielinski, M., Jerman, L., Ji, Y., Jolly, C., Kleinheinz, K., Lee, J., Lee-Six, H., Leshchiner, I., Livitz, D., Malikic, S., Martincorena, I., Mitchell, T. J., Morris, Q. D., Mustonen, V., Oesper, L., Peifer, M., Peto, M., Raphael, B. J., Rosebrock, D., Rubanova, Y., Sahinalp, S. C., Salcedo, A., Schlesner, M., Schumacher, S. E., Sengupta, S., Shi, R., Shin, S. J., Spellman, P. T., Spiro, O., Stein, L. D., Tarabichi, M., Van Loo, P., Vembu, S., Vázquez-García, I., Wang, W., Wedge, D. C., Wheeler, D. A., Wintersinger, J. A., Yang, T. P., Yao, X., Yu, K., Zhu, H., Corcoran, N. M., Papenfuss, T., Hovens, C. M., Markowetz, F., Macintyre, G., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Boyault, S., Boyce, R., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 730.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      29 Scopus citations

    • Inherited causes of clonal haematopoiesis in 97,691 whole genomes

      NHLBI Trans-Omics for Precision Medicine Consortium, Oct 29 2020, In: Nature. 586, 7831, p. 763-768 6 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      391 Scopus citations

    • Integrative pathway enrichment analysis of multivariate omics data

      PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 735.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      119 Scopus citations

    • Mapping and characterization of structural variation in 17,795 human genomes

      NHGRI Centers for Common Disease Genomics, Jul 2 2020, In: Nature. 583, 7814, p. 83-89 7 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      162 Scopus citations

    • Pan-cancer analysis of whole genomes

      The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Feb 6 2020, In: Nature. 578, 7793, p. 82-93 12 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      1766 Scopus citations

    • Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

      PCAWG-Structural Variation Working Group, PCAWG Consortium, 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. & 182 others, Ardeljan, D., Tojo, M., Roberts, N. D., Zumalave, S., Edwards, P. A., Weischenfeldt, J., Puiggròs, M., Chong, Z., Chen, K., Lee, E. A., Wala, J. A., Raine, K. M., Butler, A., Waszak, S. M., Navarro, F. C. P., Schumacher, S. E., Monlong, J., Maura, F., Bolli, N., Bourque, G., Gerstein, M., Park, P. J., Wedge, D. C., Beroukhim, R., Torrents, D., Korbel, J. O., Martincorena, I., Fitzgerald, R. C., Van Loo, P., Kazazian, H. H., Burns, K. H., Campbell, P. J., Tubio, J. M. C., Akdemir, K. C., Boutros, P. C., Bowtell, D. D. L., Brors, B., Chan, K., Cortés-Ciriano, I., Dunford, A. J., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Kazanov, M. D., Klimczak, L. J., Koh, Y., Kumar, K., Lee, J. J. K., Lynch, A. G., Macintyre, G., Markowetz, F., Martinez-Fundichely, A., Meyerson, M., Miyano, S., Nakagawa, H., Ossowski, S., Pearson, J. V., Rippe, K., Roberts, S. A., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Villasante, I., Waddell, N., Yang, L., Yao, X., Yoon, S. S., Zhang, C. Z., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Mar 1 2020, In: Nature Genetics. 52, 3, p. 306-319 14 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      250 Scopus citations

    • Pathway and network analysis of more than 2500 whole cancer genomes

      PCAWG Drivers and Functional Interpretation Working Group, PCAWG Consortium, 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. & 182 others, Khurana, E., Marchal, K., von Mering, C., Sahinalp, S. C., Valencia, A., Abascal, F., Amin, S. B., Bader, G. D., Bandopadhayay, P., Beroukhim, R., Bertl, J., Boroevich, K. A., Busanovich, J., Campbell, P. J., Carlevaro-Fita, J., Chakravarty, D., Chan, C. W. Y., Chen, K., Choi, J. K., Deu-Pons, J., Diamanti, K., Feuerbach, L., Fink, J. L., Fonseca, N. A., Frigola, J., Gambacorti-Passerini, C., Garsed, D. W., Gerstein, M., Guo, Q., Gut, I. G., Hamilton, M. P., Haradhvala, N. J., Harmanci, A. O., Helmy, M., Herrmann, C., Hess, J. M., Hobolth, A., Hodzic, E., Hong, C., Hornshøj, H., Isaev, K., Johnson, R., Johnson, T. A., Juul, M., Juul, R. I., Kahles, A., Kellis, M., Kim, J., Kim, J. K., Kim, Y., Komorowski, J., Korbel, J. O., Kumar, S., Lanzós, A., Larsson, E., Lee, D., Lehmann, K. V., Li, S., Li, X., Lin, Z., Liu, E. M., Lochovsky, L., Lou, S., Madsen, T., Martincorena, I., Martinez-Fundichely, A., Maruvka, Y. E., McGillivray, P. D., Meyerson, W., Muiños, F., Mularoni, L., Nakagawa, H., Nielsen, M. M., Park, K., Park, K., Pons, T., Reyes-Salazar, I., Rheinbay, E., Rubio-Perez, C., Saksena, G., Salichos, L., Sander, C., Schumacher, S. E., Shackleton, M., Shapira, O., Shen, C., Shuai, S., Sidiropoulos, N., Sieverling, L., Sinnott-Armstrong, N., Stein, L. D., Tamborero, D., Tiao, G., Tsunoda, T., Umer, H. M., Uusküla-Reimand, L., Wadelius, C., Wang, J., Warrell, J., Waszak, S. M., Weischenfeldt, J., Wu, G., Yu, J., Zhang, J., Zhang, X., Zhang, Y., Zhao, Z., Zou, L., Reimand, J., Stuart, J. M., Raphael, B. J., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 729.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      69 Scopus citations

    • Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig

      PCAWG Evolution and Heterogeneity Working Group, PCAWG Consortium, 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. & 182 others, Macintyre, G., Adams, D. J., Anur, P., Beroukhim, R., Boutros, P. C., Bowtell, D. D., Campbell, P. J., Cao, S., Christie, E. L., Cmero, M., Cun, Y., Dawson, K. J., Demeulemeester, J., Donmez, N., Drews, R. M., Eils, R., Fan, Y., Fittall, M., Garsed, D. W., Getz, G., Ha, G., Imielinski, M., Jerman, L., Ji, Y., Kleinheinz, K., Lee, J., Lee-Six, H., Livitz, D. G., Malikic, S., Markowetz, F., Martincorena, I., Mitchell, T. J., Mustonen, V., Oesper, L., Peifer, M., Peto, M., Raphael, B. J., Rosebrock, D., Sahinalp, S. C., Salcedo, A., Schlesner, M., Schumacher, S., Sengupta, S., Shi, R., Shin, S. J., Spiro, O., Stein, L. D., Vázquez-García, I., Vembu, S., Wheeler, D. A., Yang, T. P., Yao, X., Yuan, K., Zhu, H., Wang, W., Morris, Q. D., Spellman, P. T., Wedge, D. C., Van Loo, P., Morris, Q. D., 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., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Ding, L., Fulton, L. A., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 731.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      30 Scopus citations

    • Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

      MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4748.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      32 Scopus citations

    • Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

      Hughes, J. F., Skaletsky, H., Pyntikova, T., Koutseva, N., Raudsepp, T., Brown, L. G., Bellott, D. W., Cho, T. J., Dugan-Rocha, S., Khan, Z., Kremitzki, C., Fronick, C., Graves-Lindsay, T. A., Fulton, L., Warren, W. C., Wilson, R. K., Owens, E., Womack, J. E., Murphy, W. J. & Muzny, D. M. & 4 others, Worley, K. C., Chowdhary, B. P., Gibbs, R. A. & Page, D. C., Nov 18 2020, In: Genome research. 31, 12, p. 1716-1726 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      27 Scopus citations

    • Sex differences in oncogenic mutational processes

      PCAWG Tumour Subtypes and Clinical Translation & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4330.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      62 Scopus citations