Sachet Ashok Shukla

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Sachet Ashok Shukla

Assistant Professor

 https://orcid.org/0000-0003-2445-3584
    Calculated based on number of publications stored in Pure and citations from Scopus
    20112024

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    • Article

      A cloning and expression system to probe T-cell receptor specificity and assess functional avidity to neoantigens

      Hu, Z., Anandappa, A. J., Sun, J., Kim, J., Leet, D. E., Bozym, D. J., Chen, C., Williams, L., Shukla, S. A., Zhang, W., Tabbaa, D., Steelman, S., Olive, O., Livak, K. J., Kishi, H., Muraguchi, A., Guleria, I., Stevens, J., Lane, W. J., Burkhardt, U. E., & 6 othersFritsch, E. F., Neuberg, D., Ott, P. A., Keskin, D. B., Hacohen, N. & Wu, C. J., Nov 1 2018, In: Blood. 132, 18, p. 1911-1921 11 p.

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

      Open Access
      44 Scopus citations

    • A functional screen identifies miRs that induce radioresistance in glioblastomas

      Moskwa, P., Zinn, P. O., Choi, Y. E., Shukla, S. A., Fendler, W., Chen, C. C., Lu, J., Golub, T. R., Hjelmeland, A. & Chowdhury, D., Dec 1 2014, In: Molecular Cancer Research. 12, 12, p. 1767-1778 12 p.

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

      Open Access
      27 Scopus citations

    • An immunogenic personal neoantigen vaccine for patients with melanoma

      Ott, P. A., Hu, Z., Keskin, D. B., Shukla, S. A., Sun, J., Bozym, D. J., Zhang, W., Luoma, A., Giobbie-Hurder, A., Peter, L., Chen, C., Olive, O., Carter, T. A., Li, S., Lieb, D. J., Eisenhaure, T., Gjini, E., Stevens, J., Lane, W. J., Javeri, I., & 20 othersNellaiappan, K., Salazar, A. M., Daley, H., Seaman, M., Buchbinder, E. I., Yoon, C. H., Harden, M., Lennon, N., Gabriel, S., Rodig, S. J., Barouch, D. H., Aster, J. C., Getz, G., Wucherpfennig, K., Neuberg, D., Ritz, J., Lander, E. S., Fritsch, E. F., Hacohen, N. & Wu, C. J., Jul 13 2017, In: Nature. 547, 7662, p. 217-221 5 p.

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

      1905 Scopus citations

    • A secreted PD-L1 splice variant that covalently dimerizes and mediates immunosuppression

      Mahoney, K. M., Shukla, S. A., Patsoukis, N., Chaudhri, A., Browne, E. P., Arazi, A., Eisenhaure, T. M., Pendergraft, W. F., Hua, P., Pham, H. C., Bu, X., Zhu, B., Hacohen, N., Fritsch, E. F., Boussiotis, V. A., Wu, C. J. & Freeman, G. J., Mar 13 2019, In: Cancer Immunology, Immunotherapy. 68, 3, p. 421-432 12 p.

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

      Open Access
      88 Scopus citations

    • Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer

      Strickland, K. C., Howitt, B. E., Shukla, S. A., Rodig, S., Ritterhouse, L. L., Liu, J. F., Garber, J. E., Chowdhury, D., Wu, C. J., D'Andrea, A. D., Matulonis, U. A. & Konstantinopoulos, P. A., Mar 22 2016, In: Oncotarget. 7, 12, p. 13587-13598 12 p.

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

      Open Access
      464 Scopus citations

    • Association of polymerase e-mutated and microsatellite-instable endometrial cancers with neoantigen load, number of tumor-infiltrating lymphocytes, and expression of PD-1 and PD-L1

      Howitt, B. E., Shukla, S. A., Sholl, L. M., Ritterhouse, L. L., Watkins, J. C., Rodig, S., Stover, E., Strickland, K. C., D'Andrea, A. D., Wu, C. J., Matulonis, U. A. & Konstantinopoulos, P. A., Dec 2015, In: JAMA Oncology. 1, 9, p. 1319-1323 5 p.

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

      Open Access
      498 Scopus citations

    • Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade

      Shukla, S. A., Bachireddy, P., Schilling, B., Galonska, C., Zhan, Q., Bango, C., Langer, R., Lee, P. C., Gusenleitner, D., Keskin, D. B., Babadi, M., Mohammad, A., Gnirke, A., Clement, K., Cartun, Z. J., Van Allen, E. M., Miao, D., Huang, Y., Snyder, A., Merghoub, T., & 12 othersWolchok, J. D., Garraway, L. A., Meissner, A., Weber, J. S., Hacohen, N., Neuberg, D., Potts, P. R., Murphy, G. F., Lian, C. G., Schadendorf, D., Hodi, F. S. & Wu, C. J., Apr 19 2018, In: Cell. 173, 3, p. 624-633.e8

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

      Open Access
      108 Scopus citations

    • CDKN2A alterations and response to immunotherapy in solid tumors

      Adib, E., Nassar, A. H., Akl, E. W., Alaiwi, S. A., Nuzzo, P. V., Mouhieddine, T. H., Sonpavde, G., Haddad, R. I., Mouw, K. W., Giannakis, M., Hodi, F. S., Shukla, S. A., Gusev, A., Braun, D. A., Choueiri, T. K. & Kwiatkowski, D. J., Jul 15 2021, In: Clinical Cancer Research. 27, 14, p. 4025-4035 11 p.

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

      Open Access
      45 Scopus citations

    • Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

      McGranahan, N., Furness, A. J. S., Rosenthal, R., Ramskov, S., Lyngaa, R., Saini, S. K., Jamal-Hanjani, M., Wilson, G. A., Birkbak, N. J., Hiley, C. T., Watkins, T. B. K., Shafi, S., Murugaesu, N., Mitter, R., Akarca, A. U., Linares, J., Marafioti, T., Henry, J. Y., Van Allen, E. M., Miao, D., & 16 othersSchilling, B., Schadendorf, D., Garraway, L. A., Makarov, V., Rizvi, N. A., Snyder, A., Hellmann, M. D., Merghoub, T., Wolchok, J. D., Shukla, S. A., Wu, C. J., Peggs, K. S., Chan, T. A., Hadrup, S. R., Quezada, S. A. & Swanton, C., Mar 25 2016, In: Science. 351, 6280, p. 1463-1469 7 p.

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

      Open Access
      2245 Scopus citations

    • Comprehensive analysis of cancer-associated somatic mutations in class i HLA genes

      Shukla, S. A., Rooney, M. S., Rajasagi, M., Tiao, G., Dixon, P. M., Lawrence, M. S., Stevens, J., Lane, W. J., Dellagatta, J. L., Steelman, S., Sougnez, C., Cibulskis, K., Kiezun, A., Hacohen, N., Brusic, V., Wu, C. J. & Getz, G., Oct 1 2015, In: Nature biotechnology. 33, 11, p. 1152-1158 7 p.

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

      Open Access
      464 Scopus citations

    • Comprehensive genomic characterization of squamous cell lung cancers

      Hammerman, P. S., Voet, D., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E. S., Gabriel, S., Getz, G., Imielinski, M., Helman, E., Hernandez, B., Pho, N. H., Meyerson, M., Chu, A., Hye-Chun, J. E., Mungall, A. J., & 316 othersPleasance, E., Robertson, A. G., Sipahimalani, P., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chuah, E., Coope, R. J. N., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, K., Nip, K. M., Olshen, A., Schein, J. E., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R., Zeng, T., Zhao, Y., Jones, S. J. M., Marra, M. A., Saksena, G., Cherniack, A. D., Schumacher, S. E., Tabak, B., Carter, S. L., Nguyen, H., Onofrio, R. C., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Protopopov, A., Zhang, J., Hadjipanayis, A., Lee, S., Xi, R., Yang, L., Ren, X., Zhang, H., Shukla, S., Chen, P. C., Haseley, P., Lee, E., Chin, L., Park, P. J., Kucherlapati, R., Socci, N. D., Liang, Y., Schultz, N., Borsu, L., Lash, A. E., Viale, A., Sander, C., Ladanyi, M., Auman, J. T., Hoadley, K. A., Wilkerson, M. D., Shi, Y., Liquori, C., Meng, S., Li, L., Turman, Y. J., Topal, M. D., Tan, D., Waring, S., Buda, E., Walsh, J., Jones, C. D., Mieczkowski, P. A., Singh, D., Wu, J., Gulabani, A., Dolina, P., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M. G., Stuart, J., Mose, L. E., Jefferys, S. R., Balu, S., O'Connor, B. D., Chiang, D., Liu, J., Chiang, D. Y., Hayes, D. N., Perou, C. M., Cope, L., Weisenberger, D., Danilova, L., Weisenberger, D. J., Maglinte, D. T., Pan, F., Van Den Berg, D. J., Triche, T., Herman, J. G., Baylin, S. B., Laird, P. W., Noble, M., Gehlenborg, N., DiCara, D., Zhang, J., Wu, C. J., Liu, S. Y., Zou, L., Lin, P., Cho, J., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Sinha, R., Ciriello, G., Cerami, E., Gross, B., Jacobsen, A., Gao, J., Aksoy, B. A., Weinhold, N., Ramirez, R., Taylor, B. S., Antipin, Y., Reva, B., Mo, Q., Seshan, V., Paik, P. K., Akbani, R., Zhang, N., Broom, B. M., Casasent, T., Unruh, A., Wakefield, C., Cason, R. C., Baggerly, K. A., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Ng, S., Goldstein, T., Waltman, P., Sokolov, A., Collisson, E., Ellrott, K., Collisson, E. A., Zerbino, D., Ma, S., Craft, B., Du, Y., Cabanski, C., Walter, V., Marron, J. S., Liu, Y., Wang, K., Prins, J. F., Creighton, C. J., Zhang, Y., Travis, W. D., Rekhtman, N., Yi, J., Aubry, M. C., Cheney, R., Dacic, S., Flieder, D., Funkhouser, W., Illei, P., Myers, J., Tsao, M. S., Penny, R., Mallery, D., Shelton, T., Hatfield, M., Morris, S., Yena, P., Shelton, C., Sherman, M., Paulauskis, J., Govindan, R., Azodo, I., Beer, D., Bose, R., Byers, L. A., Carbone, D., Chang, L. W., Chun, E., Ding, L., Heymach, J., Ida, C., Johnson, B., Jurisica, I., Kaufman, J., Kosari, F., Kwiatkowski, D., Maher, C. A., Pao, W., Peifer, M., Robertson, G., Rusch, V., Siegfried, J., Sougnez, C., Thomas, R. K., Tomaszek, S., Vaske, C., Wheeler, D., Wigle, D. A., Wilks, C., Zhang, J. J., Jensen, M. A., Sfeir, R., Kahn, A. B., Chu, A. L., Kothiyal, P., Wang, Z., Snyder, E. E., Pontius, J., Pihl, T. D., Backus, M., Walton, J., Baboud, J., Berton, D. L., Nicholls, M. C., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P. A., Alonso, S., Sanbhadti, R. N., Barletta, S. P., Greene, J. M., Pot, D. A., Bandarchi-Chamkhaleh, B., Boyd, J., Weaver, J., Azodo, I. A., Tomaszek, S. C., Yang, P., Brock, M. V., Rogers, K., Rutledge, M., Brown, T., Lee, B., Shin, J., Trusty, D., Dhir, R., Siegfried, J. M., Potapova, O., Fedosenko, K. V., Zakowski, M., Nemirovich-Danchenko, E., Iacocca, M. V., Brown, J., Rabeno, B., Czerwinski, C., Petrelli, N., Fan, Z., Todaro, N., Eckman, J., Rathmell, W. K., Thorne, L. B., Huang, M., Boice, L., Hill, A., Curley, E., Morrison, C., Gaudioso, C., Bartlett, J. M. S., Kodeeswaran, S., Zanke, B., Sekhon, H., David, K., Juhl, H., Le, X. V., Kohl, B., Thorp, R., Tien, N. V., Bang, N. V., Sussman, H., Phu, B. D., Hajek, R., Hung, N. P., Khan, K. Z., Muley, T., Mills Shaw, K. R., Sheth, M., Yang, L., Demchok, J. A., Davidsen, T., Buetow, K., Eley, G., Ferguson, M., Dillon, L. A. L., Schaefer, C., Guyer, M. S., Ozenberger, B. A., Palchik, J. D., Peterson, J., Sofia, H. J., Thomson, E., Johnson, B. E. & Shen, R., Sep 27 2012, In: Nature. 489, 7417, p. 519-525 7 p.

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

      3134 Scopus citations

    • Comprehensive molecular characterization of human colon and rectal cancer

      Muzny, D. M., Bainbridge, M. N., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., Kovar, C. L., Lewis, L. R., Morgan, M. B., Newsham, I. F., Reid, J. G., Santibanez, J., Shinbrot, E., Trevino, L. R., Wu, Y. Q., Wang, M., Gunaratne, P., Donehower, L. A., Creighton, C. J., Wheeler, D. A., & 293 othersGibbs, R. A., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E. S., Gabriel, S., Ding, L., Fulton, R. S., Koboldt, D. C., Wylie, T., Walker, J., Dooling, D. J., Fulton, L., Delehaunty, K. D., Fronick, C. C., Demeter, R., Mardis, E. R., Wilson, R. K., Chu, A., Chun, H. J. E., Mungall, A. J., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chuah, E., Coope, R. J. N., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Schein, J. E., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R., Zeng, T., Zhao, Y., Jones, S. J. M., Marra, M. A., Bass, A. J., Ramos, A. H., Saksena, G., Cherniack, A. D., Schumacher, S. E., Tabak, B., Carter, S. L., Pho, N. H., Nguyen, H., Onofrio, R. C., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Meyerson, M., Protopopov, A., Hadjipanayis, A., Lee, E., Xi, R., Yang, L., Ren, X., Sathiamoorthy, N., Chen, P. C., Haseley, P., Xiao, Y., Lee, S., Seidman, J., Chin, L., Park, P. J., Kucherlapati, R., Todd Auman, J., Hoadley, K. A., Du, Y., Wilkerson, M. D., Shi, Y., Liquori, C., Meng, S., Li, L., Turman, Y. J., Topal, M. D., Tan, D., Waring, S., Buda, E., Walsh, J., Jones, C. D., Mieczkowski, P. A., Singh, D., Wu, J., Gulabani, A., Dolina, P., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M., Mose, L. E., Jefferys, S. R., Balu, S., O'Connor, B. D., Prins, J. F., Chiang, D. Y., Neil Hayes, D., Perou, C. M., Hinoue, T., Weisenberger, D. J., Maglinte, D. T., Pan, F., Berman, B. P., Van Den Berg, D. J., Shen, H., Triche, T., Baylin, S. B., Laird, P. W., Getz, G., Noble, M., Voat, D., Gehlenborg, N., Dicara, D., Zhang, J., Zhang, H., Wu, C. J., Liu, S. Y., Shukla, S., Zhou, L., Lin, P., Park, R. W., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Thorsson, V., Reynolds, S. M., Bernard, B., Kreisberg, R., Lin, J., Iype, L., Bressler, R., Erkkilä, T., Gundapuneni, M., Liu, Y., Norberg, A., Robinson, T., Yang, D., Zhang, W., Shmulevich, I., De Ronde, J. J., Schultz, N., Cerami, E., Ciriello, G., Goldberg, A. P., Gross, B., Jacobsen, A., Gao, J., Kaczkowski, B., Sinha, R., Arman Aksoy, B., Antipin, Y., Reva, B., Shen, R., Taylor, B. S., Ladanyi, M., Sander, C., Akbani, R., Zhang, N., Broom, B. M., Casasent, T., Unruh, A., Wakefield, C., Hamilton, S. R., Craig Cason, R., Baggerly, K. A., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Zachary Sanborn, J., Vaske, C. J., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Ng, S., Goldstein, T., Ellrott, K., Collisson, E., Cozen, A. E., Zerbino, D., Wilks, C., Craft, B., Spellman, P., Penny, R., Shelton, T., Hatfield, M., Morris, S., Yena, P., Shelton, C., Sherman, M., Paulauskis, J., Gastier-Foster, J. M., Bowen, J., Ramirez, N. C., Black, A., Pyatt, R., Wise, L., White, P., Bertagnolli, M., Brown, J., Chan, T. A., Chu, G. C., Czerwinski, C., Denstman, F., Dhir, R., Dörner, A., Fuchs, C. S., Guillem, J. G., Iacocca, M., Juhl, H., Kaufman, A., Iii, B. K., Van Le, X., Mariano, M. C., Medina, E. N., Meyers, M., Nash, G. M., Paty, P. B., Petrelli, N., Rabeno, B., Richards, W. G., Solit, D., Swanson, P., Temple, L., Tepper, J. E., Thorp, R., Vakiani, E., Weiser, M. R., Willis, J. E., Witkin, G., Zeng, Z., Zinner, M. J., Zornig, C., Jensen, M. A., Sfeir, R., Kahn, A. B., Chu, A. L., Kothiyal, P., Wang, Z., Snyder, E. E., Pontius, J., Pihl, T. D., Ayala, B., Backus, M., Walton, J., Whitmore, J., Baboud, J., Berton, D. L., Nicholls, M. C., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P. A., Alonso, S., Sanbhadti, R. N., Barletta, S. P., Greene, J. M., Pot, D. A., Shaw, K. R. M., Dillon, L. A. L., Buetow, K., Davidsen, T., Demchok, J. A., Eley, G., Ferguson, M., Fielding, P., Schaefer, C., Sheth, M., Yang, L., Guyer, M. S., Ozenberger, B. A., Palchik, J. D., Peterson, J., Sofia, H. J. & Thomson., E., Jul 19 2012, In: Nature. 487, 7407, p. 330-337 8 p.

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

      6415 Scopus citations

    • Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

      Robertson, A. G., Kim, J., Al-Ahmadie, H., Bellmunt, J., Guo, G., Cherniack, A. D., Hinoue, T., Laird, P. W., Hoadley, K. A., Akbani, R., Castro, M. A. A., Gibb, E. A., Kanchi, R. S., Gordenin, D. A., Shukla, S. A., Sanchez-Vega, F., Hansel, D. E., Czerniak, B. A., Reuter, V. E., Su, X., & 153 othersde Sa Carvalho, B., Chagas, V. S., Mungall, K. L., Sadeghi, S., Pedamallu, C. S., Lu, Y., Klimczak, L. J., Zhang, J., Choo, C., Ojesina, A. I., Bullman, S., Leraas, K. M., Lichtenberg, T. M., Wu, C. J., Schultz, N., Getz, G., Meyerson, M., Mills, G. B., McConkey, D. J., Albert, M., Alexopoulou, I., Ally, A., Antic, T., Aron, M., Balasundaram, M., Bartlett, J., Baylin, S. B., Beaver, A., Birol, I., Boice, L., Bootwalla, M. S., Bowen, J., Bowlby, R., Brooks, D., Broom, B. M., Bshara, W., Burks, E., Cárcano, F. M., Carlsen, R., Carvalho, A. L., Castle, E. P., Castro, P., Catto, J. W., Chesla, D. W., Chuah, E., Chudamani, S., Cortessis, V. K., Cottingham, S. L., Crain, D., Curley, E., Daneshmand, S., Demchok, J. A., Dhalla, N., Djaladat, H., Eckman, J., Egea, S. C., Engel, J., Felau, I., Ferguson, M. L., Gardner, J., Gastier-Foster, J. M., Gerken, M., Gomez-Fernandez, C. R., Harr, J., Hartmann, A., Herbert, L. M., Ho, T. H., Holt, R. A., Hutter, C. M., Jones, S. J. M., Jorda, M., Kahnoski, R. J., Kasaian, K., Kwiatkowski, D. J., Lai, P. H., Lane, B. R., Lerner, S. P., Liu, J., Lolla, L., Lotan, Y., Lucchesi, F. R., Ma, Y., Machado, R. D., Maglinte, D. T., Mallery, D., Marra, M. A., Martin, S. E., Mayo, M., Meraney, A., Moinzadeh, A., Moore, R. A., Mora Pinero, E. M., Morris, S., Morrison, C., Mungall, A. J., Myers, J. B., Naresh, R., O'Donnell, P. H., Parekh, D. J., Parfitt, J., Paulauskis, J. D., Sekhar Pedamallu, C., Penny, R. J., Pihl, T., Porten, S., Quintero-Aguilo, M. E., Ramirez, N. C., Rathmell, W. K., Rieger-Christ, K., Saller, C., Salner, A., Sandusky, G., Scapulatempo-Neto, C., Schein, J. E., Schuckman, A. K., Shelton, C., Shelton, T., Simko, J., Singh, P., Sipahimalani, P., Smith, N. D., Sofia, H. J., Sorcini, A., Stanton, M. L., Steinberg, G. D., Stoehr, R., Su, X., Sullivan, T., Sun, Q., Tam, A., Tarnuzzer, R., Tarvin, K., Taubert, H., Thiessen, N., Thorne, L., Tse, K., Tucker, K., Van Den Berg, D. J., van Kessel, K. E., Wach, S., Wan, Y., Wang, Z., Weinstein, J. N., Weisenberger, D. J., Wise, L., Wong, T., Wu, Y., Yang, L., Zach, L. A., Zenklusen, J. C., Zhang, J., Zmuda, E. & Zwarthoff, E. C., Oct 19 2017, In: Cell. 171, 3, p. 540-556.e25

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

      Open Access
      1478 Scopus citations

    • Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC network

      Zeng, Z., Fu, J., Cibulskis, C., Jhaveri, A., Gumbs, C., Das, B., Sanchez-Espiridion, B., Janssens, S., Taing, L., Wang, J., Lindsay, J., Vilimas, T., Zhang, J., Tokheim, C., Sahu, A., Jiang, P., Yan, C., Duose, D. Y., Cerami, E., Chen, L., & 28 othersCohen, D., Chen, Q., Enos, R., Huang, X., Lee, J. J., Liu, Y., Neuberg, D. S., Nguyen, C., Patterson, C., Sarkar, S., Shukla, S., Tang, M., Tsuji, J., Uduman, M., Wang, X., Weirather, J. L., Yu, J., Yu, J., Zhang, J., Zhang, J., Meerzaman, D., Thurin, M., Futreal, A., Karlovich, C., Gabriel, S. B., Wistuba, I. I., Shirley Liu, X. & Wu, C. J., Sep 15 2021, In: Clinical Cancer Research. 27, 18, p. 5049-5061 13 p.

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

      Open Access
      5 Scopus citations

    • Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect

      Bachireddy, P., Ennis, C., Nguyen, V. N., Gohil, S. H., Clement, K., Shukla, S. A., Forman, J., Barkas, N., Freeman, S., Bavli, N., Elagina, L., Leshchiner, I., Mohammad, A. W., Mathewson, N. D., Keskin, D. B., Rassenti, L. Z., Kipps, T. J., Brown, J. R., Getz, G., Ho, V. T., & 7 othersGnirke, A., Neuberg, D., Soiffer, R. J., Ritz, J., Alyea, E. P., Kharchenko, P. V. & Wu, C. J., Sep 16 2020, In: Science translational medicine. 12, 561, eabb7661.

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

      Open Access
      16 Scopus citations

    • Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

      Campbell, J. D., Alexandrov, A., Kim, J., Wala, J., Berger, A. H., Pedamallu, C. S., Shukla, S. A., Guo, G., Brooks, A. N., Murray, B. A., Imielinski, M., Hu, X., Ling, S., Akbani, R., Rosenberg, M., Cibulskis, C., Ramachandran, A., Collisson, E. A., Kwiatkowski, D. J., Lawrence, M. S., & 10 othersWeinstein, J. N., Verhaak, R. G. W., Wu, C. J., Hammerman, P. S., Cherniack, A. D., Getz, G., Artyomov, M. N., Schreiber, R., Govindan, R. & Meyerson, M., Jun 1 2016, In: Nature Genetics. 48, 6, p. 607-616 10 p.

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

      Open Access
      828 Scopus citations

    • Epigenomic charting and functional annotation of risk loci in renal cell carcinoma

      Nassar, A. H., Abou Alaiwi, S., Baca, S. C., Adib, E., Corona, R. I., Seo, J. H., Fonseca, M. A. S., Spisak, S., El Zarif, T., Tisza, V., Braun, D. A., Du, H., He, M., Flaifel, A., Alchoueiry, M., Denize, T., Matar, S. G., Acosta, A., Shukla, S., Hou, Y., & 16 othersSteinharter, J., Bouchard, G., Berchuck, J. E., O’Connor, E., Bell, C., Nuzzo, P. V., Mary Lee, G. S., Signoretti, S., Hirsch, M. S., Pomerantz, M., Henske, E., Gusev, A., Lawrenson, K., Choueiri, T. K., Kwiatkowski, D. J. & Freedman, M. L., Dec 2023, In: Nature communications. 14, 1, 346.

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

      Open Access
      9 Scopus citations

    • Evolution and impact of subclonal mutations in chronic lymphocytic leukemia

      Landau, D. A., Carter, S. L., Stojanov, P., McKenna, A., Stevenson, K., Lawrence, M. S., Sougnez, C., Stewart, C., Sivachenko, A., Wang, L., Wan, Y., Zhang, W., Shukla, S. A., Vartanov, A., Fernandes, S. M., Saksena, G., Cibulskis, K., Tesar, B., Gabriel, S., Hacohen, N., & 6 othersMeyerson, M., Lander, E. S., Neuberg, D., Brown, J. R., Getz, G. & Wu, C. J., Feb 14 2013, In: Cell. 152, 4, p. 714-726 13 p.

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

      Open Access
      1120 Scopus citations

    • Expression of T-Cell exhaustion molecules and human endogenous retroviruses as predictive biomarkers for response to nivolumab in metastatic clear cell renal cell carcinoma

      Ficial, M., Jegede, O. A., Angelo, M. S., Hou, Y., Flaifel, A., Pignon, J. C., Braun, D. A., Wind-Rotolo, M., Sticco-Ivins, M. A., Catalano, P. J., Freeman, G. J., Sharpe, A. H., Hodi, F. S., Motzer, R. J., Wu, C. J., Atkins, M. B., McDermott, D. F., Shukla, S. A., Choueiri, T. K. & Signoretti, S., Mar 1 2021, In: Clinical Cancer Research. 27, 5, p. 1371-1380 10 p.

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

      Open Access
      43 Scopus citations

    • Genetic mechanisms of immune evasion in colorectal cancer

      Grasso, C. S., Giannakis, M., Wells, D. K., Hamada, T., Mu, X. J., Quist, M., Nowak, J. A., Nishihara, R., Qian, Z. R., Inamura, K., Morikawa, T., Nosho, K., Abril-Rodriguez, G., Connolly, C., Escuin-Ordinas, H., Geybels, M. S., Grady, W. M., Hsu, L., Hu-Lieskovan, S., Huyghe, J. R., & 32 othersKim, Y. J., Krystofinski, P., Leiserson, M. D. M., Montoya, D. J., Nadel, B. B., Pellegrini, M., Pritchard, C. C., Puig-Saus, C., Quist, E. H., Raphael, B. J., Salipante, S. J., Shin, D. S., Shinbrot, E., Shirts, B., Shukla, S., Stanford, J. L., Sun, W., Tsoi, J., Upfill-Brown, A., Wheeler, D. A., Wu, C. J., Yu, M., Zaidi, S. H., Zaretsky, J. M., Gabriel, S. B., Lander, E. S., Garraway, L. A., Hudson, T. J., Fuchs, C. S., Ribas, A., Ogino, S. & Peters, U., Jun 2018, In: Cancer discovery. 8, 6, p. 730-749 20 p.

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      Open Access
      338 Scopus citations

    • Genomic alterations during the in situ to invasive ductal breast carcinoma transition shaped by the immune system

      Trinh, A., Gil Del Alcazar, C. R., Shukla, S. A., Chin, K., Chang, Y. H., Thibault, G., Eng, J., Jovanovic, B., Aldaz, C. M., Park, S. Y., Jeong, J., Wu, C., Gray, J. & Polyak, K., Apr 2021, In: Molecular Cancer Research. 19, 4, p. 623-635 13 p.

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

      Open Access
      21 Scopus citations

    • Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

      Giannakis, M., Mu, X. J., Shukla, S. A., Qian, Z. R., Cohen, O., Nishihara, R., Bahl, S., Cao, Y., Amin-Mansour, A., Yamauchi, M., Sukawa, Y., Stewart, C., Rosenberg, M., Mima, K., Inamura, K., Nosho, K., Nowak, J. A., Lawrence, M. S., Giovannucci, E. L., Chan, A. T., & 10 othersNg, K., Meyerhardt, J. A., Van Allen, E. M., Getz, G., Gabriel, S. B., Lander, E. S., Wu, C. J., Fuchs, C. S., Ogino, S. & Garraway, L. A., Apr 26 2016, In: Cell Reports. 15, 4, p. 857-865 9 p.

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

      Open Access
      561 Scopus citations

    • Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

      Van Allen, E. M., Miao, D., Schilling, B., Shukla, S. A., Blank, C., Zimmer, L., Sucker, A., Hillen, U., Foppen, M. H. G., Goldinger, S. M., Utikal, J., Hassel, J. C., Weide, B., Kaehler, K. C., Loquai, C., Mohr, P., Gutzmer, R., Dummer, R., Gabriel, S., Wu, C. J., & 2 othersSchadendorf, D. & Garraway, L. A., Oct 9 2015, In: Science. 350, 6257, p. 207-211 5 p.

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      Open Access
      2002 Scopus citations

    • Germline variants associated with toxicity to immune checkpoint blockade

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      Open Access
      36 Scopus citations

    • HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia

      Lai, T. H., Ozer, H. G., Gasparini, P., Nigita, G., Distefano, R., Yu, L., Ravikrishnan, J., Yilmaz, S., Gallegos, J., Shukla, S., Puduvalli, V., Woyach, J., Lapalombella, R., Blachly, J., Byrd, J. C. & Sampath, D., Jun 1 2023, In: Blood Advances. 7, 12, p. 2897-2911 15 p.

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      Open Access
      3 Scopus citations

    • HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study

      Naranbhai, V., Viard, M., Dean, M., Groha, S., Braun, D. A., Labaki, C., Shukla, S. A., Yuki, Y., Shah, P., Chin, K., Wind-Rotolo, M., Mu, X. J., Robbins, P. B., Gusev, A., Choueiri, T. K., Gulley, J. L. & Carrington, M., Jan 2022, In: The lancet oncology. 23, 1, p. 172-184 13 p.

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      Open Access
      47 Scopus citations

    • Integrated genomic analyses of ovarian carcinoma

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    • Integrated genomic characterization of the human immunome in cancer

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      Open Access
      11 Scopus citations

    • Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia

      Wang, L., Fan, J., Francis, J. M., Georghiou, G., Hergert, S., Li, S., Gambe, R., Zhou, C. W., Yang, C., Xiao, S., Cin, P. D., Bowden, M., Kotliar, D., Shukla, S. A., Brown, J. R., Neuberg, D., Alessi, D. R., Zhang, C. Z., Kharchenko, P. V., Livak, K. J., & 1 othersWu, C. J., Aug 2017, In: Genome research. 27, 8, p. 1300-1311 12 p.

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      Open Access
      59 Scopus citations

    • Integrative functional genomics identifies RINT1 as a novel GBM oncogene

      Quayle, S. N., Chheda, M. G., Shukla, S. A., Wiedemeyer, R., Tamayo, P., Dewan, R. W., Zhuang, L., Huang-Hobbs, E., Haidar, S., Xiao, Y., Ligon, K. L., Hahn, W. C. & Chin, L., Nov 2012, In: Neuro-oncology. 14, 11, p. 1325-1331 7 p.

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      13 Scopus citations

    • Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma

      Bakouny, Z., Braun, D. A., Shukla, S. A., Pan, W., Gao, X., Hou, Y., Flaifel, A., Tang, S., Bosma-Moody, A., He, M. X., Vokes, N., Nyman, J., Xie, W., Nassar, A. H., Abou Alaiwi, S., Flippot, R., Bouchard, G., Steinharter, J. A., Nuzzo, P. V., Ficial, M., & 33 othersSant’Angelo, M., Forman, J., Berchuck, J. E., Dudani, S., Bi, K., Park, J., Camp, S., Sticco-Ivins, M., Hirsch, L., Baca, S. C., Wind-Rotolo, M., Ross-Macdonald, P., Sun, M., Lee, G. S. M., Chang, S. L., Wei, X. X., McGregor, B. A., Harshman, L. C., Genovese, G., Ellis, L., Pomerantz, M., Hirsch, M. S., Freedman, M. L., Atkins, M. B., Wu, C. J., Ho, T. H., Linehan, W. M., McDermott, D. F., Heng, D. Y. C., Viswanathan, S. R., Signoretti, S., Van Allen, E. M. & Choueiri, T. K., Dec 1 2021, In: Nature communications. 12, 1, 808.

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      Open Access
      78 Scopus citations

    • Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma

      Braun, D. A., Hou, Y., Bakouny, Z., Ficial, M., Sant’ Angelo, M., Forman, J., Ross-Macdonald, P., Berger, A. C., Jegede, O. A., Elagina, L., Steinharter, J., Sun, M., Wind-Rotolo, M., Pignon, J. C., Cherniack, A. D., Lichtenstein, L., Neuberg, D., Catalano, P., Freeman, G. J., Sharpe, A. H., & 6 othersMcDermott, D. F., Van Allen, E. M., Signoretti, S., Wu, C. J., Shukla, S. A. & Choueiri, T. K., Jun 1 2020, In: Nature medicine. 26, 6, p. 909-918 10 p.

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      Open Access
      476 Scopus citations

    • Investigation of antigen-specific T-cell receptor clusters in human cancers

      Zhang, H., Liu, L., Zhang, J., Chen, J., Ye, J., Shukla, S., Qiao, J., Zhan, X., Chen, H., Wu, C. J., Fu, Y. X. & Li, B., Mar 15 2020, In: Clinical Cancer Research. 26, 6, p. 1359-1371 13 p.

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      Open Access
      74 Scopus citations

    • Irrecist for the evaluation of candidate biomarkers of response to nivolumab in metastatic clear cell renal cell carcinoma: Analysis of a phase II prospective clinical trial

      Pignon, J. C., Jegede, O., Shukla, S. A., Braun, D. A., Horak, C. E., Wind-Rotolo, M., Ishii, Y., Catalano, P. J., Grosha, J., Flaifel, A., Novak, J. S., Mahoney, K. M., Freeman, G. J., Sharpe, A. H., Stephen Hodi, F., Motzer, R. J., Choueiri, T. K., Wu, C. J., Atkins, M. B., McDermott, D. F., & 1 othersSignoretti, S., Apr 1 2019, In: Clinical Cancer Research. 25, 7, p. 2174-2184 11 p.

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

      Open Access
      74 Scopus citations

    • Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

      The Tumor Neoantigen Selection Alliance, Oct 29 2020, In: Cell. 183, 3, p. 818-834.e13

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      Open Access
      252 Scopus citations

    • Landscape of tumor-infiltrating T cell repertoire of human cancers

      Li, B., Li, T., Pignon, J. C., Wang, B., Wang, J., Shukla, S. A., Dou, R., Chen, Q., Hodi, F. S., Choueiri, T. K., Wu, C., Hacohen, N., Signoretti, S., Liu, J. S. & Liu, X. S., Jul 1 2016, In: Nature Genetics. 48, 7, p. 725-732 8 p.

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      Open Access
      222 Scopus citations

    • Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma

      George, S., Miao, D., Demetri, G. D., Adeegbe, D., Rodig, S. J., Shukla, S., Lipschitz, M., Amin-Mansour, A., Raut, C. P., Carter, S. L., Hammerman, P., Freeman, G. J., Wu, C. J., Ott, P. A., Wong, K. K. & Van Allen, E. M., Feb 21 2017, In: Immunity. 46, 2, p. 197-204 8 p.

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

      Open Access
      376 Scopus citations

    • Mammalian SWI/SNF complex genomic alterations and immune checkpoint blockade in solid tumors

      Alaiwi, S. A., Nassar, A. H., Xie, W., Bakouny, Z., Berchuck, J. E., Braun, D. A., Baca, S. C., Nuzzo, P. V., Flippot, R., Mouhieddine, T. H., Spurr, L. F., Li, Y. Y., Li, T., Flaifel, A., Steinharter, J. A., Margolis, C. A., Vokes, N. I., Du, H., Shukla, S. A., Cherniack, A. D., & 12 othersSonpavde, G., Haddad, R. I., Awad, M. M., Giannakis, M., Hodi, F. S., Liu, X. S., Signoretti, S., Kadoch, C., Freedman, M. L., Kwiatkowski, D. J., Van Allen, E. M. & Choueiri, T. K., Aug 1 2020, In: Cancer Immunology Research. 8, 8, p. 1075-1084 10 p.

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

      Open Access
      47 Scopus citations

    • Metabolomic adaptations and correlates of survival to immune checkpoint blockade

      Li, H., Bullock, K., Gurjao, C., Braun, D., Shukla, S. A., Bossé, D., Lalani, A. K. A., Gopal, S., Jin, C., Horak, C., Wind-Rotolo, M., Signoretti, S., McDermott, D. F., Freeman, G. J., Van Allen, E. M., Schreiber, S. L., Stephen Hodi, F., Sellers, W. R., Garraway, L. A., Clish, C. B., & 2 othersChoueiri, T. K. & Giannakis, M., Dec 1 2019, In: Nature communications. 10, 1, 4346.

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      Open Access
      147 Scopus citations

    • microRNA regulatory network inference identifies miR-34a as a novel regulator of TGF-β signaling in glioblastoma

      Genovese, G., Ergun, A., Shukla, S. A., Campos, B., Hanna, J., Ghosh, P., Quayle, S. N., Rai, K., Colla, S., Ying, H., Wu, C. J., Sarkar, S., Xiao, Y., Zhang, J., Zhang, H., Kwong, L., Dunn, K., Wiedemeyer, W. R., Brennan, C., Zheng, H., & 3 othersRimm, D. L., Collins, J. J. & Chin, L., Aug 2012, In: Cancer discovery. 2, 8, p. 736-749 14 p.

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      Open Access
      96 Scopus citations

    • Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer

      Weber, Z. T., Collier, K. A., Tallman, D., Forman, J., Shukla, S., Asad, S., Rhoades, J., Freeman, S., Parsons, H. A., Williams, N. O., Barroso-Sousa, R., Stover, E. H., Mahdi, H., Cibulskis, C., Lennon, N. J., Ha, G., Adalsteinsson, V. A., Tolaney, S. M. & Stover, D. G., Dec 2021, In: Genome medicine. 13, 1, 89.

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

      Open Access
      7 Scopus citations

    • Molecular and genetic properties of tumors associated with local immune cytolytic activity

      Rooney, M. S., Shukla, S. A., Wu, C. J., Getz, G. & Hacohen, N., Jan 15 2015, In: Cell. 160, 1-2, p. 48-61 14 p.

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      Open Access
      2535 Scopus citations

    • Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

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

      Open Access
      905 Scopus citations

    • Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma

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

      Open Access
      237 Scopus citations

    • Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma

      Oliveira, G., Stromhaug, K., Klaeger, S., Kula, T., Frederick, D. T., Le, P. M., Forman, J., Huang, T., Li, S., Zhang, W., Xu, Q., Cieri, N., Clauser, K. R., Shukla, S. A., Neuberg, D., Justesen, S., MacBeath, G., Carr, S. A., Fritsch, E. F., Hacohen, N., & 6 othersSade-Feldman, M., Livak, K. J., Boland, G. M., Ott, P. A., Keskin, D. B. & Wu, C. J., Aug 5 2021, In: Nature. 596, 7870, p. 119-125 7 p.

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

      Open Access
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      Shukla, S. A., Howitt, B. E., Wu, C. J. & Konstantinopoulos, P. A., Feb 1 2017, In: Gynecologic Oncology Reports. 19, p. 42-45 4 p.

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

      Open Access
      23 Scopus citations

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      Braun, D. A., Street, K., Burke, K. P., Cookmeyer, D. L., Denize, T., Pedersen, C. B., Gohil, S. H., Schindler, N., Pomerance, L., Hirsch, L., Bakouny, Z., Hou, Y., Forman, J., Huang, T., Li, S., Cui, A., Keskin, D. B., Steinharter, J., Bouchard, G., Sun, M., & 15 othersPimenta, E. M., Xu, W., Mahoney, K. M., McGregor, B. A., Hirsch, M. S., Chang, S. L., Livak, K. J., McDermott, D. F., Shukla, S. A., Olsen, L. R., Signoretti, S., Sharpe, A. H., Irizarry, R. A., Choueiri, T. K. & Wu, C. J., May 10 2021, In: Cancer cell. 39, 5, p. 632-648.e8

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      Open Access
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    • Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche

      Baldominos, P., Barbera-Mourelle, A., Barreiro, O., Huang, Y., Wight, A., Cho, J. W., Zhao, X., Estivill, G., Adam, I., Sanchez, X., McCarthy, S., Schaller, J., Khan, Z., Ruzo, A., Pastorello, R., Richardson, E. T., Dillon, D., Montero-Llopis, P., Barroso-Sousa, R., Forman, J., & 7 othersShukla, S. A., Tolaney, S. M., Mittendorf, E. A., von Andrian, U. H., Wucherpfennig, K. W., Hemberg, M. & Agudo, J., May 12 2022, In: Cell. 185, 10, p. 1694-1708.e19

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      Open Access
      97 Scopus citations

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      Open Access
      628 Scopus citations

    • RNase H–dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis

      Li, S., Sun, J., Allesøe, R., Datta, K., Bao, Y., Oliveira, G., Forman, J., Jin, R., Olsen, L. R., Keskin, D. B., Shukla, S. A., Wu, C. J. & Livak, K. J., Aug 1 2019, In: Nature protocols. 14, 8, p. 2571-2594 24 p.

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

      Open Access
      22 Scopus citations