Jun Li, Ph.D.

Peer-Reviewed Articles

1. 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.
2. Hahn AW, Menk AV, Rivadeneira DB, Augustin RC, Xu M, Li J, Wu X, Mishra AK, Gide TN, Quek C, Zang Y, Spencer CN, Menzies AM, Daniel CR, Hudgens CW, Nowicki T, Haydu LE, Khan MAW, Gopalakrishnan V, Burton EM, Malke J, Simon JM, Bernatchez C, Putluri N, Woodman SE, Vashisht Gopal YN, Guerrieri R, Fischer GM, Wang J, Wani KM, Thompson JF, Lee JE, Hwu P, Ajami N, Gershenwald JE, Long GV, Scolyer RA, Tetzlaff MT, Lazar AJ, Schadendorf D, Wargo JA, Kirkwood JM, DeBerardinis RJ, Liang H, Futreal A, Zhang J, Wilmott JS, Peng W, Davies MA, Delgoffe GM, Najjar YG, McQuade JL. Obesity Is Associated with Altered Tumor Metabolism in Metastatic Melanoma. Clinical Cancer Research 29(1):154-164, 2023. e-Pub 2023. PMID: 36166093.
3. Li J*, Lu H*, Ng PK*, Pantazi A*, Ip CKM, Jeong KJ, Amador B, Tran R, Tsang YH, Yang L, Song X, Dogruluk T, Ren X, Hadjipanayis A, Bristow CA, Lee S, Kucherlapati M, Parfenov M, Tang J, Seth S, Mahadeshwar HS, Mojumdar K, Zeng D, Zhang J, Protopopov A, Seidman JG, Creighton CJ, Lu Y, Sahni N, Shaw KR, Meric-Bernstam F, Futreal A, Chin L, Scott KL, Kucherlapati R, Mills GB, Liang H. A functional genomic approach to actionable gene fusions for precision oncology. Science Advances 8(6):eabm2382, 2022. e-Pub 2022. PMID: 35138907.
4. Li J, Chen H, Wang Y, Chen MM, Liang H. Next-Generation Analytics for Omics Data. Cancer Cell 39(1):3-6, 2021. e-Pub 2021. PMID: 32976776.
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. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. Zhao W*, Li J*, Chen MM, Luo Y, Ju Z, Nesser NK, Johnson-Camacho K, Boniface CT, Lawrence Y, Pande NT, Davies MA, Herlyn M, Muranen T, Zervantonakis IK, von Euw E, Schultz A, Kumar SV, Korkut A, Spellman PT, Akbani R, Slamon DJ, Gray JW, Brugge JS, Lu Y, Mills GB, Liang H. Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines. Cancer Cell 38(6):829-843.e4, 2020. e-Pub 2020. PMID: 33157050.
16. Chen MM, Li J, Mills GB, Liang H. Predicting Cancer Cell Line Dependencies from the Protein Expression Data of Reverse-Phase Protein Arrays. JCO Clinical Cancer Informatics 4:357-366, 2020. e-Pub 2020. PMID: 32330068.
17. Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, Consortium P. Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers. Nature Genetics 52(3):342-352, 2020. e-Pub 2020. PMID: 32024997.
18. 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.
19. Chen H, Li J, Wang Y, Ng PK, Tsang YH, Shaw KR, Mills GB, Liang H. Comprehensive assessment of computational algorithms in predicting cancer driver mutations. Genome Biology 21(1):43, 2020. e-Pub 2020. PMID: 32079540.
20. Chen MM, Li J, Wang Y, Akbani R, Lu Y, Mills GB, Liang H. TCPA v3.0: An Integrative Platform to Explore the Pan-cancer Analysis of Functional Proteomic Data. Molecular & Cellular Proteomics 18(8 suppl 1):S15-S25, 2019. e-Pub 2019. PMID: 31201206.
21. Zhang H, Wang Y, Li J, Chen H, He X, Zhang H, Liang H, Lu J. Biosynthetic energy cost for amino acids decreases in cancer evolution. Nature Communications 9(1), 2018. e-Pub 2018. PMID: 30297703.
22. Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, Ju Z, Hansel D, de Velasco G, Pennathur A, Andersen JB, O'Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P, Cherniack AD, Deng C, Resar L, CGARN (including Li J), Weinstein JN, Mishra L, Akbani R. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily. Cell Systems 7(4):422-437.e7, 2018. e-Pub 2018. PMID: 30268436.
23. Wang Y, Xu X, Maglic D, Dill MT, Mojumdar K, Ng PK, Jeong KJ, Tsang YH, Moreno D, Bhavana VH, Peng X, Ge Z, Chen H, Li J, Chen Z, Zhang H, Han L, Du D, Creighton CJ, Mills GB, Research Network CGA, Camargo F, Liang H. Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer. Cell Reports 25(5):1304-1317.e5, 2018. e-Pub 2018. PMID: 30380420.
24. Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, CGARN (including Li J), Rätsch G. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell 34(2):211-224.e6, 2018. e-Pub 2018. PMID: 30078747.
25. Zhao W, Li J, Akbani R, Liang H, Mills GB. Credentialing Individual Samples for Proteogenomic Analysis. Molecular & Cellular Proteomics 17(8):1515-1530, 2018. e-Pub 2018. PMID: 29716986.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
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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.