Jun Li, Ph.D.

Peer-Reviewed Articles

1. Liu W*, Li J*, Tang Y, Liu C, Song M, Ju Z, Kumar SV, Lu Y, Akbani R, Mills G, Liang H. DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis. Nature Communications, 2025. e-Pub 2025. PMID: 40050282.
2. Li J, Liu W, Kim H, Mojumdar K, Zhou Z, Ju Z, Kumar SV, Ng PK, Davies MA, Lu Y, Akbani R, Mills GB, Liang H. A protein expression atlas on tissue samples and cell lines from cancer patients provides insights into tumor heterogeneity and dependencies. Nature Cancer, 2024. e-Pub 2024. PMID: 39227745.
3. Jiao, W, Atwal, G, Polak, P, Karlic, R, Cuppen, E, Al-Shahrour, F, Atwal, G, Bailey, PJ, Biankin, AV, Boutros, PC, Campbell, PJ, Chang, DK, Cooke, SL, Lazar, A, Akbani, R, Aldape, KD, Broaddus, R, Borresen-Dale, A, Cao, S, Chakravarty, D, Chen, K, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Futreal, A, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Myklebost, O, Park, K, Plass, C, Sood, AK, Su, X, Thompson, A, Van Loo, P, Wang, L, Wang, W, Weinstein, JN, Yuan, Y, Zhu, H. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32024849.
4. Cmero, M, Yuan, K, Ong, CS, Schröder, J, Adams, DJ, Anur, P, Beroukhim, R, Boutros, PC, Bowtell, DD, Campbell, PJ, Cao, S, Christie, EL, Cun, Y, Dawson, KJ, Demeulemeester, J, Eils, R, Fan, Y, Van Loo, P, Wang, W, Zhu, H, Akbani, R, Aldape, KD, Broaddus, R, Borresen-Dale, A, Chakravarty, D, Chen, K, Chen, Y, Czerniak, BA, El-Naggar, AK, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Myklebost, O, Park, K, Plass, C, Sood, AK, Su, X, Thompson, A, Wang, L, Weinstein, JN, Yuan, Y. Inferring structural variant cancer cell fraction. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32024845.
5. Sieverling, L, Hong, C, Koser, S, Ginsbach, P, Kleinheinz, K, Hutter, B, Braun, DM, Cortés-Ciriano, I, Xi, R, Kabbe, R, Park, PJ, Eils, R, Schlesner, M, Akdemir, KC, Alvarez, EG, Chen, K, Akbani, R, Aldape, KD, Broaddus, R, Borresen-Dale, A, Cao, S, Chakravarty, D, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Myklebost, O, Park, K, Plass, C, Sood, AK, Su, X, Thompson, A, Van Loo, P, Wang, L, Wang, W, Weinstein, JN, Yuan, Y, Zhu, H. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32024817.
6. Shuai, S, Abascal, F, Amin, S, Bader, GD, Bandopadhayay, P, Barenboim, J, Beroukhim, R, Bertl, J, Boroevich, KA, Brunak, S, Campbell, PJ, Carlevaro-Fita, J, Chakravarty, D, Chan, CY, Chen, K, Choi, JK, Deu-Pons, J, Dhingra, P, Park, K, Akbani, R, Aldape, KD, Broaddus, R, Borresen-Dale, A, Cao, S, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Sood, AK, Su, X, Thompson, A, Van Loo, P, Wang, L, Wang, W, Weinstein, JN, Yuan, Y, Zhu, H. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32024818.
7. Li, CH, Prokopec, SD, Sun, RX, Yousif, F, Schmitz, N, Al-Shahrour, F, Atwal, G, Bailey, PJ, Biankin, AV, Boutros, PC, Campbell, PJ, Eils, R, Myklebost, O, Borresen-Dale, A, Plass, C, Akbani, R, Akdemir, KC, Aldape, KD, Broaddus, R, Cao, S, Chakravarty, D, Chen, K, Chen, Y, Chong, Z, Czerniak, BA, El-Naggar, AK, Fan, Y, Futreal, A, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Park, K, Sood, AK, Su, X, Thompson, A, Ueno, NT, Van Loo, P, Wang, L, Wang, W, Weinstein, JN, Yuan, Y, Zhu, H. Sex differences in oncogenic mutational processes. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32859912.
8. Bailey, M, Meyerson, WU, Dursi, LJ, Wang, LB, Dong, G, Liang, WW, Weerasinghe, A, Li, S, Kelso, S, Akbani, R, Anur, P, Bailey, MH, Buchanan, A, Chiotti, K, Covington, KR, Creason, A, Ding, L, Ellrott, K, Huse, J, Wang, W, Weinstein, JN, Chen, K, Chong, Z, Akdemir, KC, Aldape, KD, Cao, S, Chakravarty, D, Chen, Y, Chong, Z, Czerniak, BA, El-Naggar, AK, Fan, Y, Futreal, A, Gershenwald, JE, Han, L, von Kalle, C, Krishnamurthy, S, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Park, K, Sood, AK, Su, X, Thompson, A, Van Loo, P, Wang, L, Yuan, Y, Zhu, H. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32958763.
9. Zhang, Y, Chen, F, Fonseca, NA, He, Y, Fujita, M, Nakagawa, H, Zhang, Z, Brazma, A, Amin, SB, Awadalla, P, Bailey, PJ, Brazma, A, Brooks, AN, Calabrese, C, Chateigner, A, Cortés-Ciriano, I, Akdemir, KC, Chen, K, Akbani, R, Aldape, KD, Broaddus, R, Borresen-Dale, A, Cao, S, Chakravarty, D, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Plass, C, Sood, AK, Su, X, Thompson, A, Van Loo, P, Wang, L, Wang, W, Weinstein, JN, Yuan, Y, Zhu, H. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32024823.
10. Rubanova, Y, Shi, R, Harrigan, CF, Li, R, Wintersinger, J, Sahin, N, Deshwar, AG, Dentro, SC, Leshchiner, I, Gerstung, M, Jolly, C, Haase, K, Tarabichi, M, Wintersinger, J, Cao, S, Eils, R, Fan, Y, Zhu, H, Wang, W, Van Loo, P, Akbani, R, Aldape, KD, Borresen-Dale, A, Chakravarty, D, Chen, K, Chen, Y, Czerniak, BA, El-Naggar, AK, Futreal, A, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Myklebost, O, Park, K, Plass, C, Sood, AK, Su, X, Thompson, A, Wang, L, Weinstein, JN, Yuan, Y. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32024834.
11. Reyna, MA, Haan, D, Paczkowska, M, Verbeke, LP, Vazquez, M, Kahraman, A, Pulido-Tamayo, S, Barenboim, J, Wadi, L, Dhingra, P, Shrestha, R, Getz, G, Lawrence, MS, Pedersen, JS, Rubin, MA, Chakravarty, D, Chen, K, Park, K, Akbani, R, Aldape, KD, Borresen-Dale, A, Cao, S, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Futreal, A, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Plass, C, Sood, AK, Su, X, Thompson, A, Van Loo, P, Wang, L, Wang, W, Weinstein, JN, Yuan, Y, Zhu, H. Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32024854.
12. Campbell, PJ, Getz, G, Korbel, JO, Stuart, JM, Jennings, JL, Stein, L, Perry, MD, Nahal-Bose, HK, Ouellette, BF, Li, CH, Rheinbay, E, Nielsen, GP, Lazar, A, Wang, W, Van Loo, P, Weinstein, JN, Fan, Y, Chen, K, Chong, Z, Eils, R, Chakravarty, D, Park, K, Plass, C, Akdemir, KC, Cao, S, Zhu, H, Chen, Y, Han, L, Li, J, Yuan, Y, Liang, H, Su, X, Lichter, P, Borresen-Dale, A, Krishnamurthy, S, Thompson, A, Ueno, NT, von Kalle, C, Futreal, A, Akbani, R, Aldape, KD, Broaddus, R, Czerniak, BA, El-Naggar, AK, Gershenwald, JE, Huse, J, Lu, Y, Mills, GB, Sood, AK, Wang, L. Pan-cancer analysis of whole genomes. Nature 578(7793):82-93, 2020. e-Pub 2020. PMID: 32025007.
13. Paczkowska, M, Barenboim, J, Sintupisut, N, Fox, NS, Zhu, H, Abd-Rabbo, D, Mee, MW, Boutros, PC, Abascal, F, Amin, S, Bader, GD, Beroukhim, R, Bertl, J, Boroevich, KA, Chakravarty, D, Chen, K, Park, K, Akbani, R, Aldape, KD, Broaddus, R, Borresen-Dale, A, Cao, S, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Futreal, A, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Lazar, A, Li, J, Liang, H, Lichter, P, Lu, Y, Mills, GB, Plass, C, Sood, AK, Su, X, Thompson, A, Van Loo, P, Wang, L, Wang, W, Weinstein, JN, Yuan, Y, Zhu, H. Integrative pathway enrichment analysis of multivariate omics data. Nature communications 11(1), 2020. e-Pub 2020. PMID: 32024846.
14. Liu, Y, Sethi, NS, Hinoue, T, Schneider, BG, Cherniack, AD, Sanchez-Vega, F, Seoane, JA, Farshidfar, F, Akbani, R, Kanchi, RS, Mishra, L, Lazar, A, Wistuba, II, Liu, Y, Zhang, W, Broom, BM, Ju, Z, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer cell 33(4):721-735.e8, 2018. e-Pub 2018. PMID: 29622466.
15. Taylor, A, Shih, J, Ha, G, Gao, GF, Zhang, X, Berger, AC, Schumacher, SE, Wang, C, Lazar, A, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer cell 33(4):676-689.e3, 2018. e-Pub 2018. PMID: 29622463.
16. Wang, Z, Yang, B, Zhang, M, Guo, W, Wu, Z, Wang, Y, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer cell 33(4):706-720.e9, 2018. e-Pub 2018. PMID: 29622465.
17. Hoadley, KA, Yau, C, Hinoue, T, Wolf, D, Lazar, A, Drill, E, Shen, R, Taylor, A, Cherniack, AD, Thorsson, V, Akbani, R, Bowlby, R, Wong, C, Wistuba, II, Liu, Y, Zhang, W, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell 173(2):291-304.e6, 2018. e-Pub 2018. PMID: 29625048.
18. Sanchez-Vega, F, Mina, M, Armenia, J, Chatila, WK, Luna, A, La, KC, Liang, H, Lazar, A, Kwong, L, Frederick, MJ, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 173(2):321-337.e10, 2018. e-Pub 2018. PMID: 29625050.
19. Bailey, M, Tokheim, C, Porta-Pardo, E, Sengupta, S, Wang, Z, Liang, H, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A, Chen, K. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell 173(2):371-385.e18, 2018. e-Pub 2018. PMID: 29625053.
20. Chen, H, Li, C, Peng, X, Zhou, Z, Weinstein, JN, Caesar-Johnson, SJ, Demchok, JA, Felau, I, Kasapi, M, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A, Liang, H. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell 173(2):386-399.e12, 2018. e-Pub 2018. PMID: 29625054.
21. Ding, L, Bailey, M, Porta-Pardo, E, Thorsson, V, Colaprico, A, Bertrand, D, Akbani, R, Mills, GB, Lazar, A, Liu, Y, Zhang, W, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell 173(2):305-320.e10, 2018. e-Pub 2018. PMID: 29625049.
22. Huang, KL, Mashl, RJ, Wu, Y, Ritter, DI, Wang, J, Oh, C, Paczkowska, M, Kim, T, Logothetis, CJ, Wistuba, II, Chen, K, Liu, Y, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, von Deimling, A, Meric-Bernstam, F. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell 173(2):355-370.e14, 2018. e-Pub 2018. PMID: 29625052.
23. Liu, J, Lichtenberg, TM, Hoadley, KA, Poisson, LM, Lazar, A, Cherniack, AD, Kovatich, AJ, Scapulatempo, CN, Wistuba, II, Carvalho, AL, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, von Deimling, A. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell 173(2):400-416.e11, 2018. e-Pub 2018. PMID: 29625055.
24. Malta, TM, Sokolov, A, Gentles, AJ, Burzykowski, T, Poisson, LM, Weinstein, JN, Kaminska, B, Huelsken, J, Mishra, L, Lazar, A, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell 173(2):338-354.e15, 2018. e-Pub 2018. PMID: 29625051.
25. Campbell, JD, Yau, C, Liu, Y, Akbani, R, Byers, LA, Kanchi, RS, Gay, CM, Diao, L, Ma, W, Lazar, A, Flores, ER, Tsai, KY, Wistuba, II, Zhang, W, Broom, BM, Ju, Z, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Pickering, CR. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Reports 23(1):194-212.e6, 2018. e-Pub 2018. PMID: 29617660.
26. Chiu, HS, Somvanshi, S, Patel, E, Chen, TW, Singh, VP, Zorman, B, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A, Sood, AK. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Reports 23(1):297-312.e12, 2018. e-Pub 2018. PMID: 29617668.
27. Gao, Q, Liang, WW, Foltz, SM, Mutharasu, G, Jayasinghe, R, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A, Chen, K. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Reports 23(1):227-238.e3, 2018. e-Pub 2018. PMID: 29617662.
28. Jayasinghe, R, Cao, S, Gao, Q, Wendl, MC, Vo, NS, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A, Chen, K. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Reports 23(1):270-281.e3, 2018. e-Pub 2018. PMID: 29617666.
29. Knijnenburg, T, Wang, L, Zimmermann, MT, Chambwe, N, Gao, GF, Cherniack, AD, Liu, Y, Akbani, R, Weinstein, JN, Li, L, Mills, GB, Zhang, W, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Uppore Kukkillaya, AR, Zhang, J, Liu, X, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Reports 23(1):239-254.e6, 2018. e-Pub 2018. PMID: 29617664.
30. Ricketts, CJ, de Cubas, AA, Fan, H, Smith, CC, Lang, M, Reznik, E, Akbani, R, Kanchi, RS, Mills, GB, Tamboli, P, Liu, Y, Zhang, W, Broom, BM, Ju, Z, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Reports 23(1):313-326.e5, 2018. e-Pub 2018. PMID: 29617669.
31. Saltz, JH, Gupta, R, Hou, L, Kurc, T, Singh, PK, Nguyen, V, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A, Uppore Kukkillaya, AR. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Reports 23(1):181-193.e7, 2018. e-Pub 2018. PMID: 29617659.
32. Seiler, M, Peng, S, Agrawal, AA, Palacino, J, Teng, T, Zhu, P, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell Reports 23(1):282-296.e4, 2018. e-Pub 2018. PMID: 29617667.
33. Way, GP, Sanchez-Vega, F, La, KC, Armenia, J, Chatila, WK, Luna, A, Wistuba, II, von Deimling, A, Carvalho, AL, Scapulatempo, CN, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Reports 23(1):172-180.e3, 2018. e-Pub 2018. PMID: 29617658.
34. Ellrott, K, Bailey, M, Saksena, G, Covington, KR, Kandoth, C, Stewart, C, Liu, Y, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Carvalho, AL, Fregnani, JG, Reis, RV, Scapulatempo, CN, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, Wistuba, II, von Deimling, A. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Systems 6(3):271-281.e7, 2018. e-Pub 2018. PMID: 29596782.
35. Schaub, FX, Dhankani, V, Berger, AC, Trivedi, M, Richardson, AB, Shaw, R, Zhao, W, Zhang, X, Liu, Y, Wistuba, II, Zhang, W, Akbani, R, Broom, BM, Ju, Z, Kanchi, RS, Korkut, A, Li, J, Liang, H, Ling, S, Liu, W, Lu, Y, Mills, GB, Uppore Kukkillaya, AR, Weinstein, JN, Zhang, J, Liu, X, Wang, L, Fregnani, JG, Reis, RV, Ajani, JA, Behrens, MC, Bondaruk, J, Broaddus, R, Czerniak, BA, Esmaeli, B, Fujimoto, J, Gershenwald, JE, Guo, CC, Lazar, A, Logothetis, CJ, Meric-Bernstam, F, Moran, C, Ramondetta, LM, Rice, DC, Sood, AK, Tamboli, P, Thompson, T, Troncoso, P, Tsao, A, von Deimling, A. Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Systems 6(3):282-300.e2, 2018. e-Pub 2018. PMID: 29596783.
36. Xu-Monette, Z, Deng, Q, Manyam, GC, Tzankov, A, Li, L, Xia, Y, Wang, XX, Zou, D, Visco, C, Dybkær, K, Li, J, Zhang, L, Liang, H, Montes-Moreno, S, Chiu, A, Orazi, A, Zu, Y, Bhagat, G, Richards, KL, Hsi, ED, Choi, WW, Van Krieken, JH, Huh, J, Ponzoni, M, Ferreri, AJ, Parsons, BM, Møller, MB, Wang, S, Miranda, R, Piris, MA, Winter, JN, Medeiros, LJ, Li, Y, Young, KH. Clinical and biologic significance of MYC genetic mutations in de novo diffuse large B-cell lymphoma. Clinical Cancer Research 22(14):3593-3605, 2016. e-Pub 2016. PMID: 26927665.
37. Hoadley, KA, Yau, C, Wolf, D, Cherniack, AD, Tamborero, D, Ng, S, Leiserson, MD, Niu, B, McLellan, MD, Uzunangelov, V, Zhang, J, Kandoth, C, Akbani, R, Shen, H, Omberg, L, Chu, A, Margolin, AA, Van't Veer, L, Lopez-Bigas, N, Laird, PW, Byers, LA, Mills, GB, Weinstein, JN, Aldape, KD, Baggerly, KA, Bristow, C, Broom, BM, Chin, L, Edgerton, ME, Hamilton, SR, Han, L, Ju, Z, Kim, H, Li, J, Liang, H, Liu, W, Liu, Y, Lorenzi, PL, Lu, Y, McGuire, SE, Song, X, Su, X, Verhaak, R, Wu, C, Wu, C, Yao, J, Yuan, Y, Zhang, W, Zhao, W, Zheng, S. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 158(4):929-944, 2014. e-Pub 2014. PMID: 25109877.

Book Chapters

1. Siwak DR, Li J, Akbani R, Liang H, Lu Y. Analytical Platforms 3: Processing Samples via the RPPA Pipeline to Generate Large-Scale Data for Clinical Studies. In: Adv Exp Med Biol. Springer, 113-147, 2019.
2. Labrie M, Fang Y, Kendsersky ND, Li J, Liang H, Westin SN, Mitri Z, Mills GB. Using Reverse Phase Protein Array (RPPA) to Identify and Target Adaptive Resistance. In: Adv Exp Med Biol. Springer, 251-266, 2019.