Representative peer-reviewed publications

Co-first author; Corresponding author

• Li J, Liu W, Mojumdar K, Kim H, Zhou Z, Ju Z, Kumar SV, Ng P, Chen, H, Davies MA, Lu Y, Akbani R, Mills GB, Liang H (2024)
  An Expanded Quantitative Protein Expression Atlas of Human Cancers
  Nature Cancer in press
• Lin W, Luo Y, Wu J, Zhang H, Jin G, Guo C, Zhou H, Liang H, Xu X (2023)
  Loss of ADAR1 in macrophages in combination with interferon gamma suppresses tumor growth by remodeling the tumor microenvironment
  Journal for ImmunoTherapy of Cancer 11(11): e007402 [PDF]
• Luo Y, Liang H (2023)
  Single-cell dissection of tumor microenvironmental response and resistance to cancer therapy
  Trends in Genetics 39(10):758-772 [PDF]
• Shen X, Gao X, Luo Y, Xu Q, Fan Y, Hong S, Huang Z, Liu X, Wang Q, Wang D, Lu L, Wu C, Liang H, Wang L (2023)
  Cxxc finger protein 1 maintains homesostasis and functin of intenstinal group 3 innate lymphoid cells with aging
  Nature Aging 3(8):965-981 [PDF]
• Li L, Gu Y, Zhang M, Shi X, Li Z, Xu X, Sun T, Dong Y, Xue C, Zhu X, Lv R, Jiao K, Ji X, Wang L, Zhang Y, Liang Z, Jin Y, Yin R, Wu M, Liang H (2023)
  HRD Effects on First-line Adjuvant Chemotherapy and PARPi Maintenance Therapy in Chinese Ovarian Cancer Patients
  NPJ Precision Oncology 7(1):51 [PDF]
• Chen J, Liu K, Luo Y, Kang M, Wang J, Chen G, Qi J, Wu W, Wang B, Han Y, Shi L, Wang K, Han X, Ma X, Liu W, Ding Y, Wang L, Liang H, Wang L, Chen J (2023)
  Single-cell Profiling of Tumor Immune Microenvironment Reveals Immune Irresponsiveness in Gastric Signet-ring Cell Carcinoma
  Gastroentology 165(1):88-103 [PDF]
• Peng X, Zhang S, Wang Y, Zhou Z, Yu Z, Zhong Z, Zhang L, Chen Z, Claret FX, Elkabets M, Wang F, Wang R, Liang H, Lin W, Kong D (2023)
  Stellettin B sensitizes glioblastoma to DNA-damaging treatments by suppressing PI3K-mediated homologous recombination repair
  Advanced Science 10(3):e2205529 [PDF]
• Zhou Z, Chen MM, Luo Y, Mojumdar K, Peng X, Chen H, Kumar S, Akbani R, Lu Y, Liang H (2022)
  Tumor-intrinsic SIRPA Promotes Sensitivity to Checkpoint Inhibition Immunotherapy in Melanoma
  Cancer Cell 40(11):1324-1340 [PDF]
• Peng X, Luo Y, Li H, Guo X, Chen H, Ji X, Liang H (2022)
  RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells
  PLoS Genetics18(3):e1010130 [PDF]
• Li J, Lu H, Ng PK, Pantazi A, Ip CK, Jeong K, Amador B, Tran R, Tsang Y, 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 (2022)
  A functional genomic approach to actionable gene fusions for precision oncology
  Science Advances 8(6):eabm2382 [PDF]
• Lin J, Peng X, Dong K, Long J Guo X, Li H, Bai Y, , Yang X, Wang D, Lu X, Mao Y, Sang X, Ji X, Zhao H, Liang H (2021)
  Genomic characterization of co-existing neoplasia and carcinoma lesions reveals distinct evolutionary paths of gallbladder cancer
  Nature Communications 12(1):4753 [PDF]
• Zong X, Zhang Y, Peng X, Cao D, Yu M, Wang J, Li H, Guo X, Liang H, Yang J (2021)
  Analysis of the genomic landscape of Yolk Sac tumors reveals mechanisms of evolution and chemoresistance
  Nature Communications 12(1):3579 [PDF]
• Li J, Chen H, Wang Y, Chen MM, Liang H (2021)
  Next-generation analystics for omics data
  Cancer Cell 39(1): 3-6 [PDF]
• Zhao W, Li J, Chen MM, Luo Y, Ju Z, Nesser NK, Johnson-Camacho K, Boniface CT, Lawrence Y, Pande NY, Spellman PT, Davies MA, Herlyn M, Gray JW, von Euw E, Slamon DJ, Schultz A, Kumar SV, Korkut A, Akbani R, Lu Y, Brugge JS, Mills GB, Liang H (2020)
  Large-scale characterization of drug responses of clinically relevant proteins in cancer cell lines
  Cancer Cell 38(6): 829-843 [PDF]
• Chen H, Liang H (2020)
  A high-resolution map of human enhancer RNA loci characterizes super-enhancer activities in cancer
  Cancer Cell 38(5): 701-715 [PDF]
• Li Z, Gao X, Peng X, Chen MM, Li Z, Wei B, Wen X, Wei B, Dong Y, Bu Z, Wu A, Wu Q, Zhang L, Li Z, Liu Y, Jia S, Zhang L, Tang L, Shan F, Lv G, Shen L, Ji X, Liang H, Ji J (2020)
  Multi-omics characterization of molecular features of gastric cancer correlated with response to neoadjuvant chemotherapy
  Science Advances 6 (9): e4211 [PDF]
• Chen H, Li J, Wang Y, Ng PK, Tsang TH, Shaw KR, Mills GB, Liang H (2020)
  Comprehensive Assessment of Computational Algorithms in Predicting Cancer Driver Mutations
  Genome Biology 21 (1): 43 [PDF]
• 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 H-L, Nakagawa H, Park K, Campbell PJ, Liang H; PCAWG Consortium (2020)
  Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers
  Nature Genetics 52 (3): 342-352 [PDF]
• Xu X, Wang Y, Mojumdar K, Zhou Z, Jeong K, Mangala LS, Yu S, Tsang YH, Lu Y, Lopez-Berestein G, Sood AK, Mills GB, Liang H (2019)
  A-to-I edited miRNA-379-5p inhibits cell proliferation through CD97-induced apoptosis
  The Journal of Clinical Investigation 129(12): 5343-5356 [PDF]
• Gao GF, Parker JS, Reynolds SM, Silva TC, Wang L, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MK, Mungall AJ, Robertson G, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z, The Genomic Data Analysis Network, Liang H, Noble MS(2019)
  Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons
  Cell Systems 9(1):24-34.e10 [PDF]
• Ye Y, Hu Q, Chen H, Liang K, Yuan Y, Xiang Y, Ruan H, Zhang Z, Song A, Zhang H, Liu L, Diao L, Lou Y, Zhou B, Wang L, Zhou S, Gao J, Jonasch E, Lin SH, Xia Y, Lin C, Yang L, Mills GB, Liang H, Han L (2019)
  Characterization of Hypoxia-associated Molecular Features to Aid Hypoxia-Targeted Therapy
  Nature Metabolism 1: 431-444 [PDF]
• Wang Y, Xu X, Maglic D, Dill MT, Mojumdar K, Ng P, 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, The Cancer Genome Atlas Research Network, Camargo F, Liang H (2018)
  Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer
  Cell Reports 25(5):1304-1317 [PDF]
• Zhang H, Wang Y, Li J, Chen H, He X, Liang H, Lu J (2018)
  Biosynthetic Energy Cost for Amino Acids Decreases in Cancer Evolution
  Nature Communications 9(1):4124 [PDF]
• Chen H, Li C, Zhou Z, Liang H (2018)
  Fast Evolving Human-specific Neural Enhancers are Associated with Aging-related Diseases
  Cell Systems 6(5):604-611 [PDF]
• Peng X, Xu Y, Wang Y, Hawke D, Yu S, Han L, Zhou Z, Jeong KJ, Tsang YH, Zhang M, Lu Y, Hwu P, Scott KL, Liang H, Mills GB (2018)
  A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer
  Cancer Cell 33: 450-462 [PDF]
• Chen H, Li C, Peng X, Zhou Z, Weinstein JN, The Cancer Genome Atlas Research Network, Liang H (2018)
  A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
  Cell 173(2):386-399 [PDF]
• Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN, The Cancer Genome Atlas Research Network, Bathe OF, Liang H (2018)
  Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers
  Cell Reports 23(1):255-269 [PDF]
• Ge Z, Leighton JS, Wang Y, Peng X, Chen Z, Chen H, Sun Y, Yao F, Li J, Zhang H, Liu J, Shriver CD, Hu H, The Cancer Genome Atlas Research Network, Piwnica-Worms H, Ma L, Liang H (2018)
  Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types
  Cell Reports 23(1):213-226 [PDF]
• Ng P, Li J, Jeong K, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip C, Ju Z, Wester M, Yu S, Li Y, Vellano C, Schultz N, Karchin R, Ding L, Lu Y, Cheung L, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB (2018)
  Systematic Functional Annotation of Somatic Mutations in Cancer
  Cancer Cell 33, 450-462 [PDF]
• Deng J, Chen H, Zhou D, Zhang J, Chen Y, Liu Q, Ai D, Zhu H, Chu L, Ren W, Zhang X, Xia Y, Sun M, Zhang H, Li J, Peng X, Li L, Han L, Lin H, Cai X, Xiang J, Chen S, Sun Y, Zhang Y, Zhang J, Chen H, Zhao Y, Liu Y, Liang H, Zhao K (2017)
  Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations
  Nature Communications 8(1):1533 [PDF]
• Li J, Akbani R, Zhao W, Lu Y, Weinstein JN, Mills GB, Liang H (2017)
  Explore, visualize and analyze functional cancer proteomic data using The Cancer Proteome Atlas
  Cancer Research 77(21):e51-54 [PDF]
• Wang Y, Xu X, Yu S, Jeong KJ, Zhou Z, Han L, Tsang YH, Li J, Chen H, Mangala LS, Yuan Y, Eterovic AK, Lu Y, Sood AK, Scott KL, Mills GB, Liang H (2017)
  Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers
  Genome Research 27(7):1112-1125 [PDF]
• Li J, Zhao W, Akbani R, Liu W, Ju Z, Ling S, Vellano CP, Roebuck P, Yu Q, Eterovic AK, Byers LA, Davies MA, Deng W, Vashisht Gopal YN, Chen G, von Euw EM, Slamon D, Conklin D, Heymach JV, Minna JD, Myers JN, Lu Y, Mills GB, Liang H (2017)
  Characterization of human cancer cell lines by reverse phase protein arrays
  Cancer Cell 31(2): 225-239 [PDF]
• Yuan Y, Liu L, Chen H, Wang Y, Xu Y, Mao H, Li J, Mills GB, Shu Y, Li L, Liang H (2016)
  Comprehensive characterization of molecular differences in cancer between male and female patients
  Cancer Cell 29(5): 711-722 [PDF]
• Chang HR, Nam S, Kook MC, Kim KT, Liu X, Yao H, Jung HR, Lemos R Jr, Seo HH, Park HS, Gim Y, Hong D, Huh I, Kim YW, Tan D, Liu CG, Powis G, Park T, Liang H, Kim YH (2016)
  HNF4α is a therapeutic target that links AMPK to WNT signaling in early-stage gastric cancer
  Gut 65(1):19-32 [PDF]
• Han L, Diao L, Yu S, Xu X, Li J, Zhang R, Yang Y , Werner HM, Eterovic KA, Yuan Y, Li J, Nair N, Minelli R, Tsang Y, Cheung LW, Jeong KJ, Roszik J, Ju Z, Woodman S, Lu Y, Scott KL, Li JB, Mills GB, Liang H (2015)
  The genomic landscape and clinical relevance of A-to-I RNA editing in human cancers
  Cancer Cell 28(5):515-528 [PDF]
• Yang JY, Werner HM, Li J, Westin SN, Lu Y, Halle MK, Trovik J, Salvesen HB, Mills GB, Liang H (2015)
  Integrative protein-based prognostic model for early-stage endormetrioid endometrial cancer
  Clinical Cancer Research 22(2): 513-523 [PDF]
• Li J, Han L, Roebuck P, Diao L, Liu L, Yuan Y, Weinstein JN, Liang H (2015)
  TANRIC: an interactive open platform to explore the function of lncRNAs in cancer
  Cancer Research 75(18):3728-37 [PDF]
• Han L, Yuan Y, Zheng S, Yang Y, Li J, Edgerton ME, Diao L, Xu Y, Verhaak RG, Liang H (2014)
  The Pan-Cancer analysis of pseudogene expression analysis reveals biologically and clinically relevant tumor subtypes
  Nature Communications 5:3963 [PDF]
• Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, Han L, Huang X, Lawrence MS, Weinstein JN, Stuart JM, Mills GB, Garraway LA, Margolin AA, Getz G, Liang H (2014)
  Assessing the clinical utility of cancer genomic and proteomic data across tumor types
  Nature Biotechnology 32 (7): 644-52 [PDF]
• Yang Y, Han L, Yuan Y, Li J, Hei N, Liang H (2014)
  Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types
  Nature Communications 5:3231 [PDF]

• Li J, Lu Y, Akbani R, Ju Z, Roebuck PL, Liu W, Yang JY, Broom BM, Verhaak RG, Kane DW, Wakefield C, Weinstein JN, Mills GB, Liang H (2013)

  TCPA: a resource for cancer functional proteomics data

  Nature Methods 10 (11): 1046-1047 [PDF]
• Liang H , Cheung LW, Li J, Ju Z, Yu S, Stemke-Hale K, Dogruluk T, Lu Y, Liu X, Gu C, Guo W, Scherer SE, Carter H, Westin SN, Dyer MD, Verhaak RG, Zhang F, Karchin R, Liu CG, Lu KH, Broaddus RR, Scott KL, Hennessy BT, Mills GB (2012)

  Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer

  Genome Research 22(11): 2020-2129 [PDF]