Li Ding

View Scopus Profile

Li Ding

David English Smith Professorship in Medicine #3, Professor of Medicine, Professor of Genetics

 https://orcid.org/0000-0003-1517-2975

    Willing to Mentor

    Available to Mentor:

    PhD/MSTP Students

    • 188883
      Citations
    1996 …2025

    Research activity per year

    Search results

    • 2020

      Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (Nature Communications, (2020), 11, 1, (4748), 10.1038/s41467-020-18151-y)

      MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 6232.

      Research output: Contribution to journal › Comment/debate

      Open Access

    • 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
      150 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
      414 Scopus citations

    • Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer

      Cancer Genome Atlas Analysis Network, May 11 2020, In: Cancer Cell. 37, 5, p. 639-654.e6

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

      Open Access
      171 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
      252 Scopus citations

    • Discovery of driver non-coding splice-site-creating mutations in cancer

      Cao, S., Zhou, D. C., Oh, C., Jayasinghe, R. G., Zhao, Y., Yoon, C. J., Wyczalkowski, M. A., Bailey, M. H., Tsou, T., Gao, Q., Malone, A., Reynolds, S., Shmulevich, I., Wendl, M. C., Chen, F. & Ding, L., Dec 1 2020, In: Nature communications. 11, 1, 5573.

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

      Open Access
      22 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
      162 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
      90 Scopus citations

    • Erratum: Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (Cell (2019) 179(4) (964–983.e31), (S0092867419311237), (10.1016/j.cell.2019.10.007))

      Clinical Proteomic Tumor Analysis Consortium, Jan 9 2020, In: Cell. 180, 1, p. 207 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access
      39 Scopus citations

    • Evolution and structure of clinically relevant gene fusions in multiple myeloma

      Foltz, S. M., Gao, Q., Yoon, C. J., Sun, H., Yao, L., Li, Y., Jayasinghe, R. G., Cao, S., King, J., Kohnen, D. R., Fiala, M. A., Ding, L. & Vij, R., Dec 1 2020, In: Nature communications. 11, 1, 2666.

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

      Open Access
      33 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
      280 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
      78 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
      52 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
      30 Scopus citations

    • Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

      Children's Brain Tumor Network & Clinical Proteomic Tumor Analysis Consortium, Dec 23 2020, In: Cell. 183, 7, p. 1962-1985.e31

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

      Open Access
      189 Scopus citations

    • Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma

      Clinical Proteomic Tumor Analysis Consortium, Oct 20 2020, In: Cell Reports. 33, 3, 108276.

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

      Open Access
      89 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
      121 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
      1791 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
      259 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
      70 Scopus citations

    • Proteogenomic Characterization of Endometrial Carcinoma

      the Clinical Proteomic Tumor Analysis Consortium, Feb 20 2020, In: Cell. 180, 4, p. 729-748.e26

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

      Open Access
      288 Scopus citations

    • Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability

      Clinical Proteomic Tumor Analysis Consortium, Apr 21 2020, In: Cell Reports Medicine. 1, 1, 100004.

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

      Open Access
      57 Scopus citations

    • Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

      Clinical Proteomic Tumor Analysis Consortium, Jul 9 2020, In: Cell. 182, 1, p. 200-225.e35

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

      Open Access
      439 Scopus citations

    • Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy

      Clinical Proteomic Tumor Analysis Consortium, Nov 25 2020, In: Cell. 183, 5, p. 1436-1456.e31

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

      Open Access
      282 Scopus citations

    • Proteomic resistance biomarkers for pi3k inhibitor in triple negative breast cancer patient-derived xenograft models

      Guo, Z., Primeau, T., Luo, J., Zhang, C., Sun, H., Hoog, J., Gao, F., Huang, S., Edwards, D. P., Davies, S. R., Aft, R., Ding, L., Ellis, M. J., Li, S. & Ma, C. X., Dec 2020, In: Cancers. 12, 12, p. 1-14 14 p., 3857.

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

      Open Access
      11 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

    • 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
      66 Scopus citations

    • Systematic establishment of robustness and standards in patient-derived xenograft experiments and analysis

      NCI PDXNet Consortium, Jun 2020, In: Cancer research. 80, 11, p. 2286-2297 12 p.

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

      Open Access
      38 Scopus citations

    • The effects of common structural variants on 3D chromatin structure

      Shanta, O., Noor, A., Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., Fan, X., Wen, J., Handsaker, R. E., Fairley, S., Kronenberg, Z. N., Kong, X., Hormozdiari, F. & Lee, D. & 77 others, Wenger, A. M., Hastie, A. R., Antaki, D., Anantharaman, T., Audano, P. A., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C. S., Chong, Z., Chuang, N. T., Lambert, C. C., Church, D. M., Clarke, L., Farrell, A., Flores, J., Galeey, T., Gujral, M., Guryev, V., Heaton, W. H., Korlach, J., Kumar, S., Kwon, J. Y., Lam, E. T., Lee, J. E., Lee, J., Lee, W. P., Lee, S. P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K. M., Navarro, F. C. P., Nelson, B. J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A. W. C., Rosanio, G., Ryan, M., Stütz, A., Spierings, D. C. J., Ward, A., Welch, A. M. E., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C. L., Flicek, P., Chen, K., Gerstein, M. B., Kwok, P. Y., Lansdorp, P. M., Marth, G. T., Sebat, J., Shi, X., Bashir, A., Ye, K., Devine, S. E., Talkowski, M. E., Mills, R. E., Marschall, T., Korbel, J. O., Eichler, E. E., Lee, C. & Sebat, J., Jan 30 2020, In: BMC genomics. 21, 1, 95.

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

      Open Access
      20 Scopus citations

    • The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

      Human Tumor Atlas Network, Apr 16 2020, In: Cell. 181, 2, p. 236-249 14 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      308 Scopus citations

    • The landscape of viral associations in human cancers

      PCAWG Pathogens & PCAWG Consortium, Mar 1 2020, In: Nature Genetics. 52, 3, p. 320-330 11 p.

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

      Open Access
      254 Scopus citations

    • Tumor-on-a-chip platform to interrogate the role of macrophages in tumor progression

      Bi, Y., Shirure, V. S., Liu, R., Cunningham, C., Ding, L., Meacham, J. M., Goedegebuure, S. P., George, S. C. & Fields, R. C., Sep 1 2020, In: Integrative Biology. 12, 9, p. 221-232 12 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      45 Scopus citations

    • Whole exome sequencing reveals the maintained polyclonal nature from primary to metastatic malignant peripheral nerve sheath tumor in two patients with NF1

      Godec, A., Jayasinghe, R., Chrisinger, J. S. A., Prudner, B., Ball, T., Wang, Y., Srihari, D., Kaushal, M., Dietz, H., Zhang, X., Pekmezci, M., Dahiya, S., Tao, Y., Luo, J., Van Tine, B. A., Ding, L., Gutmann, D. H. & Hirbe, A. C., Jul 1 2020, In: Neuro-Oncology Advances. 2, p. I75-I84

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

      Open Access
      4 Scopus citations
    • 2019

      Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data

      The Genomic Data Analysis Network, Jul 24 2019, In: Cell Systems. 9, 1, p. 24-34.e10

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

      Open Access
      103 Scopus citations

    • CharGer: Clinical Characterization of Germline variants

      Scott, A. D., Huang, K. L., Weerasinghe, A., Mashl, R. J., Gao, Q., Martins Rodrigues, F., Wyczalkowski, M. A. & Ding, L., Mar 1 2019, In: Bioinformatics. 35, 5, p. 865-867 3 p.

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

      Open Access
      37 Scopus citations

    • Dynamic host immune response in virus-associated cancers

      Cao, S., Wylie, K. M., Wyczalkowski, M. A., Karpova, A., Ley, J., Sun, S., Mashl, R. J., Liang, W. W., Wang, X., Johnson, K., DiPersio, J. F., Gay, H., Ratner, L., Chen, F., Adkins, D. R. & Ding, L., Dec 1 2019, In: Communications Biology. 2, 1, 109.

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

      Open Access
      38 Scopus citations

    • Erratum: Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma (Cell (2019) 179(2) (561–577.e22), (S0092867419310037), (10.1016/j.cell.2019.08.052))

      Gao, Q., Zhu, H., Dong, L., Shi, W., Chen, R., Song, Z., Huang, C., Li, J., Dong, X., Zhou, Y., Liu, Q., Ma, L., Wang, X., Zhou, J., Liu, Y., Boja, E., Robles, A. I., Ma, W., Wang, P. & Li, Y. & 7 others, Ding, L., Wen, B., Zhang, B., Rodriguez, H., Gao, D., Zhou, H. & Fan, J., Nov 14 2019, In: Cell. 179, 5, p. 1240 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access
      108 Scopus citations

    • Framework for microRNA variant annotation and prioritization using human population and disease datasets

      Oak, N., Ghosh, R., Huang, K. L., Wheeler, D. A., Ding, L. & Plon, S. E., Jan 2019, In: Human mutation. 40, 1, p. 73-89 17 p.

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

      Open Access
      14 Scopus citations

    • Functional analysis of BARD1 missense variants in homology-directed repair and damage sensitivity

      Adamovich, A. I., Banerjee, T., Wingo, M., Duncan, K., Ning, J., Rodrigues, F. M., Huang, K. L., Lee, C., Chen, F., Ding, L. & Parvin, J. D., Mar 2019, In: PLoS genetics. 15, 3, e1008049.

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

      Open Access
      22 Scopus citations

    • Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

      Clinical Proteomic Tumor Analysis Consortium, Oct 31 2019, In: Cell. 179, 4, p. 964-983.e31

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

      Open Access
      420 Scopus citations

    • Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma

      Gao, Q., Zhu, H., Dong, L., Shi, W., Chen, R., Song, Z., Huang, C., Li, J., Dong, X., Zhou, Y., Liu, Q., Ma, L., Wang, X., Zhou, J., Liu, Y., Boja, E., Robles, A. I., Ma, W., Wang, P. & Li, Y. & 7 others, Ding, L., Wen, B., Zhang, B., Rodriguez, H., Gao, D., Zhou, H. & Fan, J., Oct 3 2019, In: Cell. 179, 2, p. 561-577.e22

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

      Open Access
      642 Scopus citations

    • Integrated transcriptomic–genomic tool Texomer profiles cancer tissues

      Wang, F., Zhang, S., Kim, T. B., Lin, Y. Y., Iqbal, R., Wang, Z., Mohanty, V., Sircar, K., Karam, J. A., Wendl, M. C., Meric-Bernstam, F., Weinstein, J. N., Ding, L., Mills, G. B. & Chen, K., May 1 2019, In: Nature Methods. 16, 5, p. 401-404 4 p.

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

      6 Scopus citations

    • Multi-platform discovery of haplotype-resolved structural variation in human genomes

      Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., Fan, X., Wen, J., Handsaker, R. E., Fairley, S., Kronenberg, Z. N., Kong, X., Hormozdiari, F., Lee, D., Wenger, A. M. & Hastie, A. R. & 77 others, Antaki, D., Anantharaman, T., Audano, P. A., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C. S., Chong, Z., Chuang, N. T., Lambert, C. C., Church, D. M., Clarke, L., Farrell, A., Flores, J., Galeev, T., Gorkin, D. U., Gujral, M., Guryev, V., Heaton, W. H., Korlach, J., Kumar, S., Kwon, J. Y., Lam, E. T., Lee, J. E., Lee, J., Lee, W. P., Lee, S. P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K. M., Navarro, F. C. P., Nelson, B. J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A. W. C., Qiu, Y., Rosanio, G., Ryan, M., Stütz, A., Spierings, D. C. J., Ward, A., Welch, A. M. E., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C. L., Ren, B., Flicek, P., Chen, K., Gerstein, M. B., Kwok, P. Y., Lansdorp, P. M., Marth, G. T., Sebat, J., Shi, X., Bashir, A., Ye, K., Devine, S. E., Talkowski, M. E., Mills, R. E., Marschall, T., Korbel, J. O., Eichler, E. E. & Lee, C., Dec 1 2019, In: Nature communications. 10, 1, 1784.

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

      Open Access
      522 Scopus citations

    • Predicting tumor response to PD-1 blockade

      Ding, L. & Chen, F., Aug 1 2019, In: New England Journal of Medicine. 381, 5, p. 477-479 3 p.

      Research output: Contribution to journal › Comment/debate

      22 Scopus citations

    • Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

      Clinical Proteomic Tumor Analysis Consortium, May 2 2019, In: Cell. 177, 4, p. 1035-1049.e19

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

      Open Access
      481 Scopus citations

    • Regulated phosphosignaling associated with breast cancer subtypes and druggability

      Huang, K. L., Wu, Y., Primeau, T., Wang, Y. T., Gao, Y., McMichael, J. F., Scott, A. D., Cao, S., Wendl, M. C., Johnson, K. J., Ruggles, K., Held, J., Payne, S. H., Davies, S., Dar, A., Kinsinger, C. R., Mesri, M., Rodriguez, H., Ellis, M. J. & Reid Townsend, R. & 6 others, Chen, F., Fenyö, D., Li, S., Liu, T., Carr, S. A. & Ding, L., 2019, In: Molecular and Cellular Proteomics. 18, 8, p. 1630-1650 21 p.

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

      Open Access
      13 Scopus citations
    • 2018

      A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

      The Cancer Genome Atlas Research Network, Apr 9 2018, In: Cancer Cell. 33, 4, p. 690-705.e9

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

      Open Access
      426 Scopus citations

    • An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

      The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 400-416.e11

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

      Open Access
      2226 Scopus citations