Li Ding

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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

    • 186634
      Citations
    1996 …2024

    Research activity per year

    Search results

    • 2024

      Combined KRAS-MAPK pathway inhibitors and HER2-directed drug conjugate is efficacious in pancreatic cancer

      Bulle, A., Liu, P., Seehra, K., Bansod, S., Chen, Y., Zahra, K., Somani, V., Khawar, I. A., Chen, H. P., Dodhiawala, P. B., Li, L., Geng, Y., Mo, C. K., Mahsl, J., Ding, L., Govindan, R., Davies, S., Mudd, J., Hawkins, W. G. & Fields, R. C. & 7 others, DeNardo, D. G., Knoerzer, D., Held, J. M., Grierson, P. M., Wang-Gillam, A., Ruzinova, M. B. & Lim, K. H., Dec 2024, In: Nature communications. 15, 1, 2503.

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

      Open Access
      3 Scopus citations

    • Comprehensive proteogenomic characterization of rare kidney tumors

      Clinical Proteomic Tumor Analysis Consortium, Li, G. X., Chen, L., Hsiao, Y., Mannan, R., Zhang, Y., Luo, J., Petralia, F., Cho, H., Hosseini, N., Leprevost, F. D. V., Calinawan, A., Li, Y., Anand, S., Dagar, A., Geffen, Y., Kumar-Sinha, C., Chugh, S., Le, A. & Ponce, S. & 83 others, Guo, S., Zhang, C., Schnaubelt, M., Al Deen, N. N., Chen, F., Caravan, W., Houston, A., Hopkins, A., Newton, C. J., Wang, X., Polasky, D. A., Haynes, S., Yu, F., Jing, X., Chen, S., Robles, A. I., Mesri, M., Thiagarajan, M., An, E., Getz, G. A., Linehan, W. M., Hostetter, G., Jewell, S. D., Chan, D. W., Wang, P., Omenn, G. S., Mehra, R., Ricketts, C. J., Ding, L., Chinnaiyan, A. M., Cieslik, M. P., Dhanasekaran, S. M., Zhang, H., Nesvizhskii, A. I., Lazar, A. J., Paulovich, A. G., Antczak, A., Green, A., Ma'ayan, A., Pruetz, B., Zhang, B., Reva, B., Druker, B. J., Goldthwaite, C. A., Birger, C., Mani, D. R., Chesla, D., Fenyö, D., Schadt, E. E., Wilson, G., Kołodziejczak, I., John, I., Hafron, J., Vo, J., Zaalishvili, K., Ketchum, K. A., Rodland, K. D., Nyce, K., Wiznerowicz, M., Domagalski, M. J., Anurag, M., Borucki, M., Gillette, M. A., Birrer, M. J., Edwards, N. J., Vatanian, N., VanderKolk, P., McGarvey, P. B., Dhir, R., Thangudu, R. R., Crispen, R., Smith, R. D., Payne, S. H., Cottingham, S., Cai, S., Carr, S. A., Liu, T., Le, T., Ma, W., Zhang, X., Lu, Y., Shutack, Y. & Zhang, Z., May 21 2024, In: Cell Reports Medicine. 5, 5, 101547.

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

      Open Access
      2 Scopus citations

    • DeST-OT: Alignment of Spatiotemporal Transcriptomics Data

      Halmos, P., Liu, X., Gold, J., Chen, F., Ding, L. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 434-437 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

      1 Scopus citations

    • Evaluation of Copanlisib in Combination with Eribulin in Triple-negative Breast Cancer Patient-derived Xenograft Models

      Guo, Z., Luo, J., Jay Mashl, R., Hoog, J., Maiti, P., Fettig, N., Davies, S. R., Aft, R., Held, J. M., Govindan, R., Ding, L., Li, S., von Morze, C., Wulf, G. M., Shoghi, K. I. & Ma, C. X., Jun 2024, In: Cancer research communications. 4, 6, p. 1430-1440 11 p.

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

      Open Access
      1 Scopus citations

    • Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics

      Ma, C., Balaban, M., Liu, J., Chen, S., Ding, L. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 466-469 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    • Pan-cancer proteogenomics characterization of tumor immunity

      Clinical Proteomic Tumor Analysis Consortium, Petralia, F., Ma, W., Yaron, T. M., Caruso, F. P., Tignor, N., Wang, J. M., Charytonowicz, D., Johnson, J. L., Huntsman, E. M., Marino, G. B., Calinawan, A., Evangelista, J. E., Selvan, M. E., Chowdhury, S., Rykunov, D., Krek, A., Song, X., Turhan, B. & Christianson, K. E. & 125 others, Lewis, D. A., Deng, E. Z., Clarke, D. J. B., Whiteaker, J. R., Kennedy, J. J., Zhao, L., Segura, R. L., Batra, H., Raso, M. G., Parra, E. R., Soundararajan, R., Tang, X., Li, Y., Yi, X., Satpathy, S., Wang, Y., Wiznerowicz, M., González-Robles, T. J., Iavarone, A., Gosline, S. J. C., Reva, B., Robles, A. I., Nesvizhskii, A. I., Mani, D. R., Gillette, M. A., Klein, R. J., Cieslik, M., Zhang, B., Paulovich, A. G., Sebra, R., Gümüş, Z. H., Hostetter, G., Fenyö, D., Omenn, G. S., Cantley, L. C., Ma'ayan, A., Lazar, A. J., Ceccarelli, M., Wang, P., Abelin, J., Aguet, F., Akiyama, Y., An, E., Anand, S., Anurag, M., Babur, Ö., Bavarva, J., Birger, C., Birrer, M. J., Cao, S., Carr, S. A., Chan, D. W., Chinnaiyan, A. M., Cho, H., Clauser, K., Colaprico, A., Zhou, D. C., da Veiga Leprevost, F., Day, C., Dhanasekaran, S. M., Ding, L., Domagalski, M. J., Dou, Y., Druker, B. J., Edwards, N., Ellis, M. J., Foltz, S. M., Francis, A., Geffen, Y., Getz, G., Heiman, D. I., Hong, R., Hu, Y., Huang, C., Jaehnig, E. J., Jewell, S. D., Ji, J., Jiang, W., Katsnelson, L., Ketchum, K. A., Kolodziejczak, I., Krug, K., Kumar-Sinha, C., Lei, J. T., Liang, W. W., Liao, Y., Lindgren, C. M., Liu, T., Liu, W., McDermott, J., McKerrow, W., Mesri, M., Mumphrey, M. B., Newton, C. J., Oldroyd, R., Payne, S. H., Pugliese, P., Rodland, K. D., Rodrigues, F. M., Ruggles, K. V., Savage, S. R., Schadt, E. E., Schnaubelt, M., Schraink, T., Schürer, S., Shi, Z., Smith, R. D., Song, F., Song, Y., Stathias, V., Storrs, E. P., Tan, J., Terekhanova, N. V., Thangudu, R. R., Thiagarajan, M., Wang, L. B., Wen, B., Wu, Y., Wyczalkowski, M. A., Yao, L., Li, Q. K., Zhang, H., Zhang, Q., Zhang, X. & Zhang, Z., Feb 29 2024, In: Cell. 187, 5, p. 1255-1277.e27

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

      Open Access
      13 Scopus citations

    • Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies

      Liu, Q., Zhang, J., Guo, C., Wang, M., Wang, C., Yan, Y., Sun, L., Wang, D., Zhang, L., Yu, H., Hou, L., Wu, C., Zhu, Y., Jiang, G., Zhu, H., Zhou, Y., Fang, S., Zhang, T., Hu, L. & Li, J. & 10 others, Liu, Y., Zhang, H., Zhang, B., Ding, L., Robles, A. I., Rodriguez, H., Gao, D., Ji, H., Zhou, H. & Zhang, P., Jan 4 2024, In: Cell. 187, 1, p. 184-203.e28

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

      27 Scopus citations

    • sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data

      Feng, J., Goedegebuure, S. P., Zeng, A., Bi, Y., Wang, T., Payne, P., Ding, L., DeNardo, D., Hawkins, W., Fields, R. C. & Li, F., Jan 2024, In: PLoS computational biology. 20, 1, e1011785.

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

      Open Access
      1 Scopus citations

    • Single-nucleotide variant calling in single-cell sequencing data with Monopogen

      Dou, J., Tan, Y., Kock, K. H., Wang, J., Cheng, X., Tan, L. M., Han, K. Y., Hon, C. C., Park, W. Y., Shin, J. W., Jin, H., Wang, Y., Chen, H., Ding, L., Prabhakar, S., Navin, N., Chen, R. & Chen, K., May 2024, In: Nature Biotechnology. 42, 5, p. 803-812 10 p.

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

      Open Access
      9 Scopus citations
    • 2023

      Animal Models and Their Role in Imaging-Assisted Co-Clinical Trials

      Peehl, D. M., Badea, C. T., Chenevert, T. L., Daldrup-Link, H. E., Ding, L., Dobrolecki, L. E., Houghton, A. M. G., Kinahan, P. E., Kurhanewicz, J., Lewis, M. T., Li, S., Luker, G. D., Ma, C. X., Manning, H. C., Mowery, Y. M., O’Dwyer, P. J., Pautler, R. G., Rosen, M. A., Roudi, R. & Ross, B. D. & 5 others, Shoghi, K. I., Sriram, R., Talpaz, M., Wahl, R. L. & Zhou, R., Apr 2023, In: Tomography (Ann Arbor, Mich.). 9, 2, p. 657-680 24 p.

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

      Open Access
      3 Scopus citations

    • Author Correction: The repertoire of mutational signatures in human cancer (Nature, (2020), 578, 7793, (94-101), 10.1038/s41586-020-1943-3)

      PCAWG Mutational Signatures Working Group, PCAWG Consortium, Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Tian Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., Islam, S. M. A., Lopez-Bigas, N., Klimczak, L. J., McPherson, J. R., Morganella, S., Sabarinathan, R., Wheeler, D. A. & Mustonen, V. & 182 others, Alexandrov, L. B., Bergstrom, E. N., Boot, A., Boutros, P., Chan, K., Covington, K. R., Fujimoto, A., Getz, G., Gordenin, D. A., Haradhvala, N. J., Huang, M. N., Islam, S. M. A., Kazanov, M., Kim, J., Klimczak, L. J., Lawrence, M., Martincorena, I., McPherson, J. R., Morganella, S., Mustonen, V., Nakagawa, H., Tian Ng, A. W., Polak, P., Prokopec, S., Roberts, S. A., Rozen, S. G., Sabarinathan, R., Saini, N., Shibata, T., Shiraishi, Y., Stratton, M. R., Teh, B. T., Vázquez-García, I., Wheeler, D. A., Wu, Y., Yousif, F., Yu, W., Getz, G., Rozen, S. 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., 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., Ding, L., Fulton, L. A., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Feb 16 2023, In: Nature. 614, 7948, p. E41

      Research output: Contribution to journal › Comment/debate

      Open Access
      4 Scopus citations

    • Author Correction: The evolutionary history of 2,658 cancers (Nature, (2020), 578, 7793, (122-128), 10.1038/s41586-019-1907-7)

      PCAWG Evolution & Heterogeneity Working Group, PCAWG Consortium, Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S. C., Gonzalez, S., Rosebrock, D., Mitchell, T. J., Rubanova, Y., Anur, P., Yu, K., Tarabichi, M., Deshwar, A., Wintersinger, J., Kleinheinz, K., Vázquez-García, I., Haase, K., Jerman, L. & Sengupta, S. & 182 others, Macintyre, G., Malikic, S., Donmez, N., Livitz, D. G., Cmero, M., Demeulemeester, J., Schumacher, S., Fan, Y., Yao, X., Lee, J., Schlesner, M., Boutros, P. C., Bowtell, D. D. L., Zhu, H., Getz, G., Imielinski, M., Beroukhim, R., Sahinalp, S. C., Ji, Y., Peifer, M., Markowetz, F., Mustonen, V., Yuan, K., Wang, W., Morris, Q. D., Dentro, S. C., Leshchiner, I., Gerstung, M., Jolly, C., Haase, K., Tarabichi, M., Wintersinger, J., Deshwar, A. G., Yu, K., Gonzalez, S., Rubanova, Y., Macintyre, G., Adams, D. J., Anur, P., Boutros, P. C., Campbell, P. J., Cao, S., Christie, E. L., Cmero, M., Cun, Y., Dawson, K. J., Demeulemeester, J., Donmez, N., Drews, R. M., 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., Wedge, D. C., Van Loo, P., 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., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Feb 16 2023, In: Nature. 614, 7948, p. E42

      Research output: Contribution to journal › Comment/debate

      Open Access
      2 Scopus citations

    • Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition (Nature Genetics, (2020), 52, 3, (306-319), 10.1038/s41588-019-0562-0)

      PCAWG-Structural Variation Working Group & PCAWG Consortium, Jun 2023, In: Nature Genetics. 55, 6, p. 1080 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access
      1 Scopus citations

    • Author Correction: Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma (Nature Communications, (2023), 14, 1, (1681), 10.1038/s41467-023-37211-7)

      Wu, Y., Terekhanova, N. V., Caravan, W., Naser Al Deen, N., Lal, P., Chen, S., Mo, C. K., Cao, S., Li, Y., Karpova, A., Liu, R., Zhao, Y., Shinkle, A., Strunilin, I., Weimholt, C., Sato, K., Yao, L., Serasanambati, M., Yang, X. & Wyczalkowski, M. & 22 others, Zhu, H., Zhou, D. C., Jayasinghe, R. G., Mendez, D., Wendl, M. C., Clark, D., Newton, C., Ruan, Y., Reimers, M. A., Pachynski, R. K., Kinsinger, C., Jewell, S., Chan, D. W., Zhang, H., Chaudhuri, A. A., Chheda, M. G., Humphreys, B. D., Mesri, M., Rodriguez, H., Hsieh, J. J., Ding, L. & Chen, F., Dec 2023, In: Nature communications. 14, 1, 2817.

      Research output: Contribution to journal › Comment/debate

      Open Access

    • Author Correction: Pan-cancer analysis of whole genomes (Nature, (2020), 578, 7793, (82-93), 10.1038/s41586-020-1969-6)

      The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E39

      Research output: Contribution to journal › Comment/debate

      Open Access
      1 Scopus citations

    • Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (Nature Genetics, (2020), 52, 3, (331-341), 10.1038/s41588-019-0576-7)

      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., Jun 2023, In: Nature Genetics. 55, 6, p. 1076 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access
      1 Scopus citations

    • Author Correction: Patterns of somatic structural variation in human cancer genomes (Nature, (2020), 578, 7793, (112-121), 10.1038/s41586-019-1913-9)

      PCAWG-Structural Variation Working Group & PCAWG Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E38

      Research output: Contribution to journal › Comment/debate

      Open Access
      2 Scopus citations

    • Author Correction: The landscape of viral associations in human cancers (Nature Genetics, (2020), 52, 3, (320-330), 10.1038/s41588-019-0558-9)

      PCAWG Pathogens, PCAWG Consortium, Zapatka, M., Borozan, I., Brewer, D. S., Iskar, M., Grundhoff, A., Alawi, M., Desai, N., Sültmann, H., Moch, H., Alawi, M., Borozan, I., Cooper, C. S., Desai, N., Eils, R., Ferretti, V., Grundhoff, A., Iskar, M. & Kleinheinz, K. & 182 others, Lichter, P., Nakagawa, H., Ojesina, A. I., Pedamallu, C. S., Schlesner, M., Su, X., Zapatka, M., Cooper, C. S., Ferretti, V., Lichter, P., 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., 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., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Jun 2023, In: Nature Genetics. 55, 6, p. 1077 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access

    • Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)

      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., May 2023, In: Nature Genetics. 55, 5, p. 892 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access
      2 Scopus citations

    • Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes (Nature Biotechnology, (2020), 38, 3, (288-292), 10.1038/s41587-019-0360-3)

      PCAWG Technical Working Group & PCAWG Consortium, Apr 2023, In: Nature Biotechnology. 41, 4, p. 577 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access

    • Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (Nature Genetics, (2020), 52, 3, (294-305), 10.1038/s41588-019-0564-y)

      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., Jun 2023, In: Nature Genetics. 55, 6, p. 1079 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access

    • Author Correction: Genomic basis for RNA alterations in cancer (Nature, (2020), 578, 7793, (129-136), 10.1038/s41586-020-1970-0)

      PCAWG Transcriptome Core Group, PCAWG Transcriptome Working Group & PCAWG Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E37

      Research output: Contribution to journal › Comment/debate

      Open Access

    • Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (Nature, (2020), 578, 7793, (102-111), 10.1038/s41586-020-1965-x)

      PCAWG Drivers and Functional Interpretation Working Group, PCAWG-Structural Variation Working Group & PCAWG Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E40

      Research output: Contribution to journal › Comment/debate

      Open Access
      2 Scopus citations

    • Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)

      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., Jun 2023, In: Nature Genetics. 55, 6, p. 1078 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access

    • Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma

      Puram, S. V., Mints, M., Pal, A., Qi, Z., Reeb, A., Gelev, K., Barrett, T. F., Gerndt, S., Liu, P., Parikh, A. S., Ramadan, S., Law, T., Mroz, E. A., Rocco, J. W., Adkins, D., Thorstad, W. L., Gay, H. A., Ding, L., Paniello, R. C. & Pipkorn, P. & 7 others, Jackson, R. S., Wang, X., Mazul, A., Chernock, R., Zevallos, J. P., Silva-Fisher, J. & Tirosh, I., Apr 2023, In: Nature Genetics. 55, 4, p. 640-650 11 p.

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

      21 Scopus citations

    • Clonal Hematopoiesis and Risk of Incident Lung Cancer

      Tian, R., Wiley, B., Liu, J., Zong, X., Truong, B., Zhao, S., Uddin, M. M., Niroula, A., Miller, C. A., Mukherjee, S., Heiden, B. T., Luo, J., Puri, V., Kozower, B. D., Walter, M. J., Ding, L., Link, D. C., Amos, C. I., Ebert, B. L. & Govindan, R. & 3 others, Natarajan, P., Bolton, K. L. & Cao, Y., Mar 1 2023, In: Journal of Clinical Oncology. 41, 7, p. 1423-1433 11 p.

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

      22 Scopus citations

    • Cross center single-cell RNA sequencing study of the immune microenvironment in rapid progressing multiple myeloma

      Pilcher, W., Thomas, B. E., Bhasin, S. S., Jayasinghe, R. G., Yao, L., Gonzalez-Kozlova, E., Dasari, S., Kim-Schulze, S., Rahman, A., Patton, J., Fiala, M., Cheloni, G., Kourelis, T., Dhodapkar, M. V., Vij, R., Mehr, S., Hamilton, M., Cho, H. J., Auclair, D. & Avigan, D. E. & 4 others, Kumar, S. K., Gnjatic, S., Ding, L. & Bhasin, M., Dec 2023, In: npj Genomic Medicine. 8, 1, 3.

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

      Open Access
      11 Scopus citations

    • Deep learning integrates histopathology and proteogenomics at a pan-cancer level

      Clinical Proteomic Tumor Analysis Consortium, Wang, J. M., Hong, R., Demicco, E. G., Tan, J., Lazcano, R., Moreira, A. L., Li, Y., Calinawan, A., Razavian, N., Schraink, T., Gillette, M. A., Omenn, G. S., An, E., Rodriguez, H., Tsirigos, A., Ruggles, K. V., Ding, L., Robles, A. I. & Mani, D. R. & 105 others, Rodland, K. D., Lazar, A. J., Liu, W., Fenyö, D., Aguet, F., Akiyama, Y., Anand, S., Anurag, M., Babur, Ö., Bavarva, J., Birger, C., Birrer, M. J., Cantley, L. C., Cao, S., Carr, S. A., Ceccarelli, M., Chan, D. W., Chinnaiyan, A. M., Cho, H., Chowdhury, S., Cieslik, M. P., Clauser, K. R., Colaprico, A., Zhou, D. C., da Veiga Leprevost, F., Day, C., Dhanasekaran, S. M., Domagalski, M. J., Dou, Y., Druker, B. J., Edwards, N., Ellis, M. J., Selvan, M. E., Foltz, S. M., Francis, A., Geffen, Y., Getz, G., Gonzalez Robles, T. J., Gosline, S. J. C., Gümüş, Z. H., Heiman, D. I., Hiltke, T., Hostetter, G., Hu, Y., Huang, C., Huntsman, E., Iavarone, A., Jaehnig, E. J., Jewell, S. D., Ji, J., Jiang, W., Johnson, J. L., Katsnelson, L., Ketchum, K. A., Kolodziejczak, I., Krug, K., Kumar-Sinha, C., Lei, J. T., Liang, W. W., Liao, Y., Lindgren, C. M., Liu, T., Ma, W., Rodrigues, F. M., McKerrow, W., Mesri, M., Nesvizhskii, A. I., Newton, C. J., Oldroyd, R., Paulovich, A. G., Payne, S. H., Petralia, F., Pugliese, P., Reva, B., Rykunov, D., Satpathy, S., Savage, S. R., Schadt, E. E., Schnaubelt, M., Schürer, S., Shi, Z., Smith, R. D., Song, X., Song, Y., Stathias, V., Storrs, E. P., Terekhanova, N. V., Thangudu, R. R., Thiagarajan, M., Tignor, N., Wang, L. B., Wang, P., Wang, Y., Wen, B., Wiznerowicz, M., Wu, Y., Wyczalkowski, M. A., Yao, L., Yaron, T. M., Yi, X., Zhang, B., Zhang, H., Zhang, Q., Zhang, X. & Zhang, Z., Sep 19 2023, In: Cell Reports Medicine. 4, 9, 101173.

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

      Open Access
      6 Scopus citations

    • Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma

      Wu, Y., Terekhanova, N. V., Caravan, W., Naser Al Deen, N., Lal, P., Chen, S., Mo, C. K., Cao, S., Li, Y., Karpova, A., Liu, R., Zhao, Y., Shinkle, A., Strunilin, I., Weimholt, C., Sato, K., Yao, L., Serasanambati, M., Yang, X. & Wyczalkowski, M. & 22 others, Zhu, H., Zhou, D. C., Jayasinghe, R. G., Mendez, D., Wendl, M. C., Clark, D., Newton, C., Ruan, Y., Reimers, M. A., Pachynski, R. K., Kinsinger, C., Jewell, S., Chan, D. W., Zhang, H., Chaudhuri, A. A., Chheda, M. G., Humphreys, B. D., Mesri, M., Rodriguez, H., Hsieh, J. J., Ding, L. & Chen, F., Dec 2023, In: Nature communications. 14, 1, 1681.

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

      Open Access
      14 Scopus citations

    • Epigenetic regulation during cancer transitions across 11 tumour types

      Terekhanova, N. V., Karpova, A., Liang, W. W., Strzalkowski, A., Chen, S., Li, Y., Southard-Smith, A. N., Iglesia, M. D., Wendl, M. C., Jayasinghe, R. G., Liu, J., Song, Y., Cao, S., Houston, A., Liu, X., Wyczalkowski, M. A., Lu, R. J. H., Caravan, W., Shinkle, A. & Naser Al Deen, N. & 24 others, Herndon, J. M., Mudd, J., Ma, C., Sarkar, H., Sato, K., Ibrahim, O. M., Mo, C. K., Chasnoff, S. E., Porta-Pardo, E., Held, J. M., Pachynski, R., Schwarz, J. K., Gillanders, W. E., Kim, A. H., Vij, R., DiPersio, J. F., Puram, S. V., Chheda, M. G., Fuh, K. C., DeNardo, D. G., Fields, R. C., Chen, F., Raphael, B. J. & Ding, L., Nov 9 2023, In: Nature. 623, 7986, p. 432-441 10 p.

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

      Open Access
      26 Scopus citations

    • Fibrosis induced by resident macrophages has divergent roles in pancreas inflammatory injury and PDAC

      Baer, J. M., Zuo, C., Kang, L. I., de la Lastra, A. A., Borcherding, N. C., Knolhoff, B. L., Bogner, S. J., Zhu, Y., Yang, L., Laurent, J., Lewis, M. A., Zhang, N., Kim, K. W., Fields, R. C., Yokoyama, W. M., Mills, J. C., Ding, L., Randolph, G. J. & DeNardo, D. G., Sep 2023, In: Nature immunology. 24, 9, p. 1443-1457 15 p.

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

      Open Access
      17 Scopus citations

    • High-dimensional deconstruction of pancreatic cancer identifies tumor microenvironmental and developmental stemness features that predict survival

      Storrs, E. P., Chati, P., Usmani, A., Sloan, I., Krasnick, B. A., Babbra, R., Harris, P. K., Sachs, C. M., Qaium, F., Chatterjee, D., Wetzel, C., Goedegebuure, S. P., Hollander, T., Anthony, H., Ponce, J., Khaliq, A. M., Badiyan, S., Kim, H., Denardo, D. G. & Lang, G. D. & 10 others, Cosgrove, N. D., Kushnir, V. M., Early, D. S., Masood, A., Lim, K. H., Hawkins, W. G., Ding, L., Fields, R. C., Das, K. K. & Chaudhuri, A. A., Dec 2023, In: npj Precision Oncology. 7, 1, 105.

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

      Open Access
      9 Scopus citations

    • Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

      Clinical Proteomic Tumor Analysis Consortium, Li, Y., Wu, Y., Lu, R. J. H., Chen, S., Zhao, Y., Caravan, W., Calinawan, A., Wyczalkowski, M. A., Wendl, M. C., Reimers, M. A., Pachynski, R., Van Tine, B. A., Chen, F., Ding, L. & Hsieh, J., Jan 9 2023, In: Cancer Cell. 41, 1, p. 139-163.e17

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

      Open Access
      78 Scopus citations

    • Immune Cell Deconvolution Reveals Possible Association of γδ T Cells with Poor Survival in Head and Neck Squamous Cell Carcinoma

      Parikh, A. S., Li, Y., Mazul, A., Yu, V. X., Thorstad, W., Rich, J., Paniello, R. C., Caruana, S. M., Troob, S. H., Jackson, R. S., Pipkorn, P., Zolkind, P., Qi, Z., Adkins, D., Ding, L. & Puram, S. V., Oct 2023, In: Cancers. 15, 19, 4855.

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

      Open Access

    • Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

      Clinical Proteomic Tumor Analysis Consortium, Sep 11 2023, In: Cancer Cell. 41, 9, p. 1567-1585.e7

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

      Open Access
      19 Scopus citations

    • Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

      Clinical Proteomic Tumor Analysis Consortium, Geffen, Y., Anand, S., Akiyama, Y., Yaron, T. M., Song, Y., Johnson, J. L., Govindan, A., Babur, Ö., Li, Y., Huntsman, E., Wang, L. B., Birger, C., Heiman, D. I., Zhang, Q., Miller, M., Maruvka, Y. E., Haradhvala, N. J., Calinawan, A. & Belkin, S. & 106 others, Kerelsky, A., Clauser, K. R., Krug, K., Satpathy, S., Payne, S. H., Mani, D. R., Gillette, M. A., Dhanasekaran, S. M., Thiagarajan, M., Mesri, M., Rodriguez, H., Robles, A. I., Carr, S. A., Lazar, A. J., Aguet, F., Cantley, L. C., Ding, L., Getz, G., An, E., Anurag, M., Bavarva, J., Birrer, M. J., Cao, S., Ceccarelli, M., Chan, D. W., Chinnaiyan, A. M., Cho, H., Chowdhury, S., Cieslik, M. P., Colaprico, A., da Veiga Leprevost, F., Day, C., Domagalski, M. J., Dou, Y., Druker, B. J., Edwards, N., Ellis, M. J., Fenyo, D., Foltz, S. M., Francis, A., Gonzalez Robles, T. J., Gosline, S. J. C., Gümüş, Z. H., Hiltke, T., Hong, R., Hostetter, G., Hu, Y., Huang, C., Iavarone, A., Jaehnig, E. J., Jewel, S. D., Ji, J., Jiang, W., Katsnelson, L., Ketchum, K. A., Kolodziejczak, I., Kumar-Sinha, C., Lei, J. T., Liang, W. W., Liao, Y., Lindgren, C. M., Liu, T., Liu, W., Ma, W., McKerrow, W., Nesvizhskii, A. I., Newton, C., Oldroyd, R., Omenn, G. S., Paulovich, A. G., Petralia, F., Pugliese, P., Reva, B., Rodland, K. D., Ruggles, K. V., Rykunov, D., Rodrigues, F. M., Savage, S. R., Schadt, E. E., Schnaubelt, M., Schraink, T., Shi, Z., Smith, R. D., Song, X., Stathias, V., Storrs, E. P., Schürer, S., Selvan, M. E., Tan, J., Terekhanova, N. V., Thangudu, R. R., Tignor, N., Wang, J. M., Wang, P., Wang, Y., Wen, B., Wiznerowicz, M., Wu, Y., Wyczalkowski, M. A., Yao, L., Yi, X., Zhang, B., Zhang, H., Zhang, X., Zhang, Z. & Zhou, D. C., Aug 31 2023, In: Cell. 186, 18, p. 3945-3967.e26

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

      Open Access
      37 Scopus citations

    • Pan-cancer proteogenomics connects oncogenic drivers to functional states

      Clinical Proteomic Tumor Analysis Consortium, Li, Y., Porta-Pardo, E., Tokheim, C., Bailey, M. H., Yaron, T. M., Stathias, V., Geffen, Y., Imbach, K. J., Cao, S., Anand, S., Akiyama, Y., Liu, W., Wyczalkowski, M. A., Song, Y., Storrs, E. P., Wendl, M. C., Zhang, W., Sibai, M. & Ruiz-Serra, V. & 104 others, Liang, W. W., Terekhanova, N. V., Rodrigues, F. M., Clauser, K. R., Heiman, D. I., Zhang, Q., Aguet, F., Calinawan, A. P., Dhanasekaran, S. M., Birger, C., Satpathy, S., Zhou, D. C., Wang, L. B., Baral, J., Johnson, J. L., Huntsman, E. M., Pugliese, P., Colaprico, A., Iavarone, A., Chheda, M. G., Ricketts, C. J., Fenyö, D., Payne, S. H., Rodriguez, H., Robles, A. I., Gillette, M. A., Kumar-Sinha, C., Lazar, A. J., Cantley, L. C., Getz, G., Ding, L., An, E., Anurag, M., Bavarva, J., Birrer, M. J., Calinawan, A., Ceccarelli, M., Chan, D. W., Chinnaiyan, A. M., Cho, H., Chowdhury, S., Cieslik, M. P., da Veiga Leprevost, F., Day, C., Domagalski, M. J., Dou, Y., Druker, B. J., Edwards, N., Ellis, M. J., Selvan, M. E., Foltz, S. M., Francis, A., Gonzalez Robles, T. J., Gosline, S. J. C., Gümüş, Z. H., Hiltke, T., Hong, R., Hostetter, G., Hu, Y., Huang, C., Huntsman, E., Jaehnig, E. J., Jewel, S. D., Ji, J., Jiang, W., Katsnelson, L., Ketchum, K. A., Kolodziejczak, I., Lei, J. T., Liao, Y., Lindgren, C. M., Liu, T., Ma, W., McKerrow, W., Nesvizhskii, A. I., Newton, C., Oldroyd, R., Omenn, G. S., Paulovich, A. G., Petralia, F., Reva, B., Rodland, K. D., Ruggles, K. V., Rykunov, D., Savage, S. R., Schadt, E. E., Schnaubelt, M., Schraink, T., Shi, Z., Smith, R. D., Song, X., Tan, J., Thangudu, R. R., Tignor, N., Wang, J. M., Wang, P., Wang, Y., Wen, B., Wiznerowicz, M., Yi, X., Zhang, B., Zhang, H., Zhang, X. & Zhang, Z., Aug 31 2023, In: Cell. 186, 18, p. 3921-3944.e25

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

      Open Access
      28 Scopus citations

    • Pharmaco-proteogenomic characterization of liver cancer organoids for precision oncology

      Ji, S., Feng, L., Fu, Z., Wu, G., Wu, Y., Lin, Y., Lu, D., Song, Y., Cui, P., Yang, Z., Sang, C., Song, G., Cai, S., Li, Y., Lin, H., Zhang, S., Wang, X., Qiu, S., Zhang, X. & Hua, G. & 14 others, Li, J., Zhou, J., Dai, Z., Wang, X., Ding, L., Wang, P., Gao, D., Zhang, B., Rodriguez, H., Fan, J., Clevers, H., Zhou, H., Sun, Y. & Gao, Q., Jul 26 2023, In: Science translational medicine. 15, 706, eadg3358.

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

      Open Access
      27 Scopus citations

    • Priorities to Promote Participant Engagement in the Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network

      the Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network, Apr 1 2023, In: Cancer Epidemiology Biomarkers and Prevention. 32, 4, p. 487-495 9 p.

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

      Open Access
      2 Scopus citations

    • Proteogenomic data and resources for pan-cancer analysis

      Clinical Proteomic Tumor Analysis Consortium, Li, Y., Dou, Y., Da Veiga Leprevost, F., Geffen, Y., Calinawan, A. P., Aguet, F., Akiyama, Y., Anand, S., Birger, C., Cao, S., Chaudhary, R., Chilappagari, P., Cieslik, M., Colaprico, A., Zhou, D. C., Day, C., Domagalski, M. J., Esai Selvan, M. & Fenyö, D. & 112 others, Foltz, S. M., Francis, A., Gonzalez-Robles, T., Gümüş, Z. H., Heiman, D., Holck, M., Hong, R., Hu, Y., Jaehnig, E. J., Ji, J., Jiang, W., Katsnelson, L., Ketchum, K. A., Klein, R. J., Lei, J. T., Liang, W. W., Liao, Y., Lindgren, C. M., Ma, W., Ma, L., MacCoss, M. J., Martins Rodrigues, F., McKerrow, W., Nguyen, N., Oldroyd, R., Pilozzi, A., Pugliese, P., Reva, B., Rudnick, P., Ruggles, K. V., Rykunov, D., Savage, S. R., Schnaubelt, M., Schraink, T., Shi, Z., Singhal, D., Song, X., Storrs, E., Terekhanova, N. V., Thangudu, R. R., Thiagarajan, M., Wang, L. B., Wang, J. M., Wang, Y., Wen, B., Wu, Y., Wyczalkowski, M. A., Xin, Y., Yao, L., Yi, X., Zhang, H., Zhang, Q., Zuhl, M., Getz, G., Ding, L., Nesvizhskii, A. I., Wang, P., Robles, A. I., Zhang, B., Payne, S. H., Lazar, A. J., Paulovich, A. G., Iavarone, A., Chinnaiyan, A. M., Druker, B. J., Kumar-Sinha, C., Newton, C. J., Huang, C., Mani, D. R., Smith, R. D., Huntsman, E., Schadt, E. E., An, E., Petralia, F., Hostetter, G., Omenn, G. S., Cho, H., Rodriguez, H., Kolodziejczak, I., Johnson, J. L., Bavarva, J., Tan, J., Rodland, K. D., Clauser, K. R., Krug, K., Cantley, L. C., Wiznerowicz, M., Ellis, M. J., Anurag, M., Mesri, M., Gillette, M. A., Birrer, M. J., Ceccarelli, M., Dhanasekaran, S. M., Edwards, N., Tignor, N., Babur, Ö., Gosline, S. J. C., Jewell, S. D., Satpathy, S., Chowdhury, S., Schürer, S., Carr, S. A., Liu, T., Hiltke, T., Yaron, T. M., Stathias, V., Liu, W., Zhang, X., Song, Y., Zhang, Z. & Chan, D. W., Aug 14 2023, In: Cancer Cell. 41, 8, p. 1397-1406 10 p.

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

      Open Access
      32 Scopus citations

    • Proteogenomic insights suggest druggable pathways in endometrial carcinoma

      Clinical Proteomic Tumor Analysis Consortium, Dou, Y., Katsnelson, L., Gritsenko, M. A., Hu, Y., Reva, B., Hong, R., Wang, Y. T., Kolodziejczak, I., Lu, R. J. H., Tsai, C. F., Bu, W., Liu, W., Guo, X., An, E., Arend, R. C., Bavarva, J., Chen, L., Chu, R. K. & Czekański, A. & 144 others, Davoli, T., Demicco, E. G., DeLair, D., Devereaux, K., Dhanasekaran, S. M., Dottino, P., Dover, B., Fillmore, T. L., Foxall, M., Hermann, C. E., Hiltke, T., Hostetter, G., Jędryka, M., Jewell, S. D., Johnson, I., Kahn, A. G., Ku, A. T., Kumar-Sinha, C., Kurzawa, P., Lazar, A. J., Lazcano, R., Lei, J. T., Li, Y., Liao, Y., Lih, T. S. M., Lin, T. T., Martignetti, J. A., Masand, R. P., Matkowski, R., McKerrow, W., Mesri, M., Monroe, M. E., Moon, J., Moore, R. J., Nestor, M. D., Newton, C., Omelchenko, T., Omenn, G. S., Payne, S. H., Petyuk, V. A., Robles, A. I., Rodriguez, H., Ruggles, K. V., Rykunov, D., Savage, S. R., Schepmoes, A. A., Shi, T., Shi, Z., Tan, J., Taylor, M., Thiagarajan, M., Wang, J. M., Weitz, K. K., Wen, B., Williams, C. M., Wu, Y., Wyczalkowski, M. A., Yi, X., Zhang, X., Zhao, R., Mutch, D., Chinnaiyan, A. M., Smith, R. D., Nesvizhskii, A. I., Wang, P., Wiznerowicz, M., Ding, L., Mani, D. R., Zhang, H., Anderson, M. L., Rodland, K. D., Zhang, B., Liu, T., Fenyö, D., Antczak, A., Anurag, M., Bauer, T., Birger, C., Birrer, M. J., Borucki, M., Cai, S., Calinawan, A., Carr, S. A., Castro, P., Cerda, S., Chan, D. W., Chesla, D., Cieslik, M. P., Cottingham, S., Dhir, R., Domagalski, M. J., Druker, B. J., Duffy, E., Edwards, N. J., Edwards, R., Ellis, M. J., Eschbacher, J., Fam, M., Fevrier-Sullivan, B., Francis, J., Freymann, J., Gabriel, S., Getz, G., Gillette, M. A., Godwin, A. K., Goldthwaite, C. A., Grady, P., Hafron, J., Hariharan, P., Hindenach, B., Hoadley, K. A., Huang, J., Ittmann, M. M., Johnson, A., Jones, C. D., Ketchum, K. A., Kirby, J., Le, T., Ma'ayan, A., Madan, R., Mareedu, S., McGarvey, P. B., Modugno, F., Montgomery, R., Nyce, K., Paulovich, A. G., Pruetz, B. L., Qi, L., Richey, S., Schadt, E. E., Shutack, Y., Singh, S., Smith, M., Tansil, D., Thangudu, R. R., Tobin, M., Um, K. S., Vatanian, N., Webster, A., Wilson, G. D., Wright, J., Zaalishvili, K., Zhang, Z. & Zhao, G., Sep 11 2023, In: Cancer Cell. 41, 9, p. 1586-1605.e15

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

      Open Access
      10 Scopus citations

    • Proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma

      Zhu, H., Lin, Y., Lu, D., Wang, S., Liu, Y., Dong, L., Meng, Q., Gao, J., Wang, Y., Song, N., Suo, Y., Ding, L., Wang, P., Zhang, B., Gao, D., Fan, J., Gao, Q. & Zhou, H., Aug 1 2023, In: National Science Review. 10, 8, nwad167.

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

      Open Access
      9 Scopus citations

    • Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)

      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., May 2023, In: Nature Genetics. 55, 5, p. 893 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access

    • Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

      Yao, L., Wang, J. T., Jayasinghe, R. G., O’Neal, J., Tsai, C. F., Rettig, M. P., Song, Y., Liu, R., Zhao, Y., Ibrahim, O. M., Fiala, M. A., Fortier, J. M., Chen, S., Gehrs, L., Rodrigues, F. M., Wendl, M. C., Kohnen, D., Shinkle, A., Cao, S. & Foltz, S. M. & 12 others, Zhou, D. C., Storrs, E., Wyczalkowski, M. A., Mani, S., Goldsmith, S. R., Zhu, Y., Hamilton, M., Liu, T., Chen, F., Vij, R., Ding, L. & DiPersio, J. F., Apr 15 2023, In: Cancer research. 83, 8, p. 1214-1233 20 p.

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

      Open Access
      12 Scopus citations

    • Single-cell transcriptomics reveals long noncoding RNAs associated with tumor biology and the microenvironment in pancreatic cancer

      Dang, H. X., Saha, D., Jayasinghe, R., Zhao, S., Coonrod, E., Mudd, J., Goedegebuure, S. P., Fields, R., Ding, L. & Maher, C. A., Dec 1 2023, In: NAR Cancer. 5, 4, zcad055.

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

      Open Access

    • Stromal and therapy-induced macrophage proliferation promotes PDAC progression and susceptibility to innate immunotherapy

      Zuo, C., Baer, J. M., Knolhoff, B. L., Belle, J. I., Liu, X., de la Lastra, A. A., Fu, C., Hogg, G. D., Kingston, N. L., Breden, M. A., Dodhiawala, P. B., Zhou, D. C., Lander, V. E., James, C. A., Ding, L., Lim, K. H., Fields, R. C., Hawkins, W. G., Weber, J. D. & Zhao, G. & 1 others, Denardo, D. G., Jun 5 2023, In: Journal of Experimental Medicine. 220, 6, e20212062.

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

      Open Access
      14 Scopus citations
    • 2022

      Author Correction: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment (Nature Communications, (2021), 12, 1, (5086), 10.1038/s41467-021-25177-3)

      The NCI PDXNet Consortium, Dec 2022, In: Nature communications. 13, 1, 294.

      Research output: Contribution to journal › Comment/debate

      Open Access
      2 Scopus citations

    • Cancer proteogenomics: current impact and future prospects

      Mani, D. R., Krug, K., Zhang, B., Satpathy, S., Clauser, K. R., Ding, L., Ellis, M., Gillette, M. A. & Carr, S. A., May 2022, In: Nature Reviews Cancer. 22, 5, p. 298-313 16 p.

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

      99 Scopus citations

    • Comprehensive Characterization of the Check for updates Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

      Yao, L., Jayasinghe, R. G., Lee, B. H., Bhasin, S. S., Pilcher, W., Doxie, D. B., Gonzalez-Kozlova, E., Dasari, S., Fiala, M. A., Pita-Juarez, Y., Strausbauch, M., Kelly, G., Thomas, B. E., Kumar, S. K., Cho, H. J., Anderson, E., Wendl, M., Dawson, T., D’souza, D. & Oh, S. T. & 17 others, Cheloni, G., Li, Y., DiPersio, J. F., Rahman, A. H., Dhodapkar, K. M., Kim-Schulze, S., Vij, R., Vlachos, I. S., Mehr, S., Hamilton, M., Auclair, D., Kourelis, T., Avigan, D., Dhodapkar, M. V., Gnjatic, S., Bhasin, M. K. & Ding, L., 2022, In: Cancer research communications. 2, 10, p. 1255-1265 11 p.

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

      Open Access
      14 Scopus citations

    • CS1 CAR-T targeting the distal domain of CS1 (SLAMF7) shows efficacy in high tumor burden myeloma model despite fratricide of CD8+CS1 expressing CAR-T cells

      O’Neal, J., Ritchey, J. K., Cooper, M. L., Niswonger, J., Sofía González, L., Street, E., Rettig, M. P., Gladney, S. W., Gehrs, L., Abboud, R., Prior, J. L., Haas, G. J., Jayasinghe, R. G., Ding, L., Ghobadi, A., Vij, R. & DiPersio, J. F., Jun 2022, In: Leukemia. 36, 6, p. 1625-1634 10 p.

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

      Open Access
      29 Scopus citations