Selected Publications

  1. Zhang Z, Jing J, Ye Y, Chen Z, Jing Y, Li S, Hong W, Ruan H, Liu Y, Hu Q, Wang J, Li W, Lin C, Diao L#, Zhou Y#, Han L#. Characterization of the dual functional effects of heat shock proteins (HSPs) in cancer hallmarks to aid development of HSP inhibitors. Genome Medicine, 2020, 12: 101. PMID: 33225964
  2. Zhang Z#, Hong W, Ruan H, Jing Y, Li S, Liu Y, Wang J, Li W, Diao L#, Han L#: HeRA: an atlas of enhancer RNAs across human tissues. Nucleic Acids Reseach, 2020, gkaa940, PMID: 33119754
  3. Jing Y, Liu J, Ye Y, Pan L, Deng H, Wang Y, Yang Y, Diao L, Lin SH, Mills GB, Zhuang G#, Xue X#, Han L#. Multi-omics prediction of immune-related adverse events during checkpoint immunotherapy. Nature Communications, 2020, 11: 4946, PMID: 33009409
  4. Ye Y, Kuang X, Xie Z, Liang L, Zhang Z, Zhang Y, Ma F, Gao Q, Chang R, Lee H, Zhao S, Su J, Li H, Peng J, Chen H, Yin M, Peng C, Yang N, Wang J, Liu J, Liu H#, Han L#, Chen X#. Small-molecule MMP2/MMP9 inhibitor SB-3CT modulates tumor immune surveillance by regulating PD-L1. Genome Medicine, 2020, 12: 83, PMID: 32988398
  5. Kuang X, Li H, Liang L, Ye Y, Zhang Y, Li J, Ma F, Fu Z, Chen X, Tang Z, Peng J, Tao J, Fang F, Wang Y, Lei G, Zhao S, Su J, Yang N, Peng C, Xu X, Hung M, Han L#, Liu H#, Liu J#, Chen X#. The beneficial role of Sunitinib in tumor immune surveillance by regulating tumor PD-L1. Advanced Science (in press)
  6. Jing Y#, Diao L#, Han L#. Adverse events associated with potential drugs for COVID-19: a case study from real-world data. Briefings in Bioinformatics, 2020, bbaa234, PMID: 33003194
  7. Liu Y, Ruan H, Li S, Ye Y, Hong W, Gong J, Zhang Z, Jing Y, Zhang X#, Diao L#, Han L#. The genetic and pharmacogenomic landscape of snoRNAs in human cancer. Molecular Cancer, 2020, 19: 108, PMID: 32576192
  8. Ye Y, Jing Y, Li L, Mills GB, Diao L#, Liu H#, Han L#. Sex-associated molecular differences for cancer immunotherapy. Nature Communications, 2020, 11: 1779, PMID: 32286310
  9. Ye Y, Zhang Z, Liu Y, Diao L#, Han L#: A Multi-Omics Perspective of Quantitative Trait Loci in Precision Medicine. Trends in Genetics, 2020, 36: 318-336, PMID: 32294413 (Feature review)
  10. Li S, Zhang Z, Han L#: 3D Spheroids Propel Tumor Characterization. Trends in Cancer, 2020, PMID: 32423684
  11. Chang G*, Shi L*, Ye Y*, Shi H, Zeng L, Tiwary S, Huse JT, Huo L, Ma L, Ma Y, Zhang S, Zhu J, Xie V, Li P, Han L, He C#, Huang S#. YTHDF3 Induces the Translation of m6A-Enriched Gene Transcripts to Promote Breast Cancer Brain Metastasis. Cancer Cell, 2020, PMID: 33125861
  12. Chen Z, Li S, Shen M, Lu X, Bao C, Chen D, Ding J, Wang Q, Huang S, Cong W, Han L#, He X#. The Mutational and Transcriptional Landscapes of Hepatocarcinogenesis in a Rat Model. iScience, 2020, 23, 101690, PMID: 33163943
  13. Zhang Y, Li Y, Hu Q, Xi Y, Xing Z, Zhang Z, Huang LA, Wu J, Liang K, Nguyen TK, Egranov SD, Sun C, Zhao Z, Hawke DH, Li J, Sun D, Kin JJ, Zhang P, Cheng J, Farida A, Hung Mien-Chie, Han L, Darabi R, Lin C, Yang L. LncRNA H19 Alleviates Muscular Dystrophy Through Stabilizing Dystrophin. Nature Cell Biology, 2020, 22: 1332-1345, PMID: 33106653
  14. Liang T, Han L, Guo L: Rewired Functional Regulatory Networks Among miRNA Isoforms (isomiRs) From let-7 and miR-10 Gene Families in Cancer. Computational and Structural Biotechnology Journal, 2020, 18: 1238-1248, PMID: 32542110
  15. Wang Y, Yao F, Wang L, Li Z, Ren Z, Li D, Zhang M, Han L, Wang SQ, Zhou B, Wang L: Single-cell Analysis of Murine Fibroblasts Identifies Neonatal to Adult Switching That Regulates Cardiomyocyte Maturation. Nature Communications. 2020, 11:2585, PMID: 32444791
  16. Huang T, Cheng X, Chahoud J, Sarhan A, Tamboli P, Rao P, Guo M, Manyam G, Zhang L, Xiang Y, Han L, Shang X, Deng P, Luo Y, Lu X, Feng S, Ferrer MM, Alan Wang Y, DePinho RA, Pettaway CA, Lu X. Effective combinatorial immunotherapy for penile squamous cell carcinoma. Nature Communications, 2020, 11:2124, PMID: 32358507
  17. Liu H, Kuang X, Zhang Y, Ye Y, Li J, Liang L, Xie Z, Weng L, Guo J, Li H, Ma F, Chen X, Zhao S, Su J, Yang N, Fang F, Xie Y, Tao J, Zhang J, Chen M, Peng C, Sun L, Zhang X, Liu J, Han L, Xu X, Hung MC, Chen X. ADORA1 Inhibition Promotes Tumor Immune Evasion by Regulating the ATF3-PD-L1 Axis. Cancer Cell, 2020, 37: 324-339, PMID: 32183950
  18. 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: Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers. Nature Genetics, 2020, 52: 342-352. PMID: 32024997
  19. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (including Han L): Pan-cancer analysis of whole genomes. Nature, 2020, 578: 82-93. PMID: 32025007
  20. Wang L, Yu P, Zhou B, Song J, Li Z, Zhang M, Guo G, Wang Y, Chen X, Han L, Hu S. Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function. Nature Cell Biology, 2020, 22:108-119. PMID: 31915373
  21. Zhang Z#, Li S, Han L#. Resolving Spliceosomal Malfunctions Advances RNA-Based Therapeutics. Trends in Molecular Medicine, 2019. PMID: 31836419
  22. Zhang Z, Lee JH, Ruan H, Ye Y, Krakowiak J, Hu Q, Xiang Y, Gong J, Zhou B, Wang L, Lin C, Diao L, Mills GB, Li W#, Han L#. Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer. Nature Communications, 2019, 10: 4562. PMID: 31594934
  23. Ruan H, Xiang Y, Ko J, Li S, Jing Y, Zhu X, Ye Y, Zhang Z, Mills T, Feng J, Liu CJ, Jing J, Cao J, Zhou B, Wang L, Zhou Y, Lin C, Guo AY, Chen X, Diao L, Li W, Chen Z, He X, Mills GB, Blackburn MR, Han L#. Comprehensive characterization of circular RNAs in ~1000 human cancer cell lines. Genome Medicine, 2019, 11: 55. PMID: 31446897
  24. Ruan H, Liao Y, Ren Z, Mao L, Yao F, Yu P, Ye Y, Zhang Z, Li S, Xu H, Liu J, Diao L, Zhou B, Han L#, Wang L#. Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitment. BMC Biology. 2019, 17: 89. PMID: 31722692
  25. Hong W, Ruan H, Zhang Z, Ye Y, Liu Y, Li S, Jing Y, Zhang H, Diao L, Liang H, Han L#. Nucleic Acids Research. 2019. PMID: 31586392
  26. Li S, Zhang Z, Han L#: Molecular Treasures of Cancer Cell Lines. Trends in Molecular Medicine, 2019 PMID: 31255475
  27. Ye Y, Hu Q, Chen H, Liang K, Yuan 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 S, Xia Y, Lin C, Yang L#, Mills GB#, Liang H#, Han L#: Characterization of Hypoxia-associated Molecular Features to Aid Hypoxia-Targeted Therapy. Nature Metabolism, 2019
  28. Hu Q, Ye Y, Chan LC, Liang K, Li Y, Evans K, Pan Y, Zhang Y, Xia W, Liu J, Gong J, Chatterjee S, Han L#, Lin C#, Yang L#: Oncogenic LncRNA Down-regulates Cancer Cell Antigen Presentation and Intrinsic Tumor Suppression. Nature Immunology, 2019
  29. Li S, Han L: Circular RNAs as promising biomarkers in cancer: detection, function, and beyond. Genome Medicine, 2019, 11:15. PMID: 30894216
  30. Liu Z, Li H, He L, Xiang Y, Tian C, Li C, Tan P, Jing J, Tian Y, Du L, Huang Y, Han L#, Li M#, Zhou Y#: Discovery of Small-Molecule Inhibitors of the HSP90-Calcineurin-NFAT Pathway against Glioblastoma. Cell Chemical Biology, 2019, 26: 352-365.E7. PMID: 3063926
  31. Weng T, Ko J, Masamha CP, Xia Z, Xiang Y, Chen NY, Molina JG, Collum S, Mertens TC, Luo F, Philip K, Davies J, Huang J, Wilson C, Thandavarayan RA, Bruckner BA, Jyothula SS, Volcik KA, Li L, Han L, Li W, Assassi S, Karmouty-Quintana H, Wagner EJ, Blackburn MR: Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation. Journal of Clinical Investigation. 2019. PMID: 30830875
  32. Li Y, Hu Q, Li C, Liang K, Xiang Y, Hsiao H, Nguyen TK, Park PK, Egranov SD, Ambati CR, Putluri N, Hawke DH, Han L, Hung MC, Danesh FR, Yang L, Lin C: PTEN-induced partial epithelial-mesenchymal transition drives diabetic kidney disease. Journal of Clinical Investigation. 2019. PMID: 30741721
  33. Hu Q, Li C, Wang S, Li Y, Wen B, Zhang Y, Liang K, Yao J, Ye Y, Hsiao H, Nguyen TK, Park PK, Egranov SD, Hawke DH, Marks JR, Han L, Hung MC, Zhang B, Lin C, Yang L: LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition. Cell Research. 2019. PMID: 30631154
  34. Zhang Z, Ye Y, Gong J, Ruan H, Liu CJ, Xiang Y, Cai C, Guo AY, Ling J, Diao L#, Weinstein JN#, Han L#: Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers. Communications Biology. 2018, 1:234. PMID: 30588513
  35. Xiang Y, Ye Y, Zhang Z, Han L#: Maximizing the utility of cancer transcriptomic data. Trends in Cancer, 2018, 4:823-837. PMID: 30470304
  36. Tan P, Ye Y, He L, Xie J, Jing J, Ma G, Pan H, Han L#, Han W#, Zhou Y#: TRIM59 promotes breast cancer motility by suppressing p62-selective autophagic degradation of PDCD10. PLoS Biology, 2018, e3000051. PMID: 30408026
  37. Tian J, Wang Z, Mei S, Yang N, Yang Y, Ke J, Zhu Y, Gong Y, Zou D, Peng X, Wang X, Wan H, Zhong R, Chang J, Gong J, Han L#, Miao X#: CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer. Nucleic Acids Research, 2018, gky954
  38. Gong J, Wan H, Mei S, Ruan H, Zhang Z, Liu C, Guo AY, Diao L#, Miao X#, Han L#: Pancan-meQTL: a database to systematically evaluate the effects of genetic variants on methylation in human cancer. Nucleic Acids Research, 2018, gky814
  39. 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; Cancer Genome Atlas Research Network, Camargo F, Liang H: Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer. Cell Reports, 2018: 1304-1317
  40. Zhang J, Tan P, Guo L, Gong J, Ma J, Li J, Lee M, Fang S, Jing J, Johnson G, Sun D, Cao WM, Dashwood R, Han L, Zhou Y, Dong WG, Huang Y: p53-dependent autophagic degradation of TET2 modulates cancer therapeutic resistance. Oncogene, 2018
  41. Zhang M, Fritsche J, Roszik J, Williams LJ, Peng X, Chiu Y, Tsou CC, Hoffgaard F, Goldfinger V, Schoor O, Talukder A, Forget MA, Haymaker C, Bernatchez C, Han L, Tsang YH, Kong K, Xu X, Scott KL, Singh-Jasuja H, Lizee G, Liang H, Weinschenk T, Mills GB, Hwu P: RNA editing derived epitopes function as cancer antigens to elicit immune responses. Nature Communications, 2018:3919
  42. 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, ResarL; Cancer Genome Atlas Research Network (including Han L), 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, 2018 (In press)
  43. Yuan X, Yao F, Zhang T, Ren Z, Zhou B, Liu F, Liao Y, Han L, Diao L, Li Y, He F, Wang L: THO Complex–Dependent Posttranscriptional Control Contributes to Vascular Smooth Muscle Cell Fate Decision. Circulation Research, 2018,123:538–549
  44. 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: Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers. Nature Genetics, 2018 (In press)
  45. Xing Z, Zhang Y, Liang K, Yan L, Xiang Y, Li C, Hu Q, Putluri V, Putluri N, Coarfa C, Sreekumar A, Park PK, Nguyen TK, Wang S, Zhou J, Zhou Y, Marks JR, Hawke DH, Hung MC, Yang L, Han L, Ying H, Lin C: Long Non-coding RNA-directed Glycolysis Augmentation in Breast Cancer. Cancer Research, 2018:4524-4532
  46. Liu CJ, Hu FF, Xia M, Han L, Zhang Q, Guo AY: GSCALite: A Web Server for Gene Set Cancer Analysis. Bioinformatics, 2018, bty411
  47. Huang J, Weng T, Ko J, Chen NY, Xiang Y, Volcik K, Han L, Blackburn MR, Lu X: Suppression of cleavage factor in 25 promotes the proliferation of lung cancer cells through alternative polyadenylation. Biochem Biophys Res Commun, 2018
  48. Peng X, Xu X, Wang Y, Hawke DH, Yu S, Han L, Zhou Z, MojumdarK, Jeong KJ, Labrie M, Tsang TH, Zhang M, Lu Y, Hwu P, Scott KL, Liang H, Mills GB: A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer. Cancer Cell, 2018, 14: 817-828
  49. Zhao N, Cao J, Xu L, Tang Q, Dobrolecki LE, Lv X, Talukdar M, Lu Y, Wang X, Hu DZ, Shi Q, Xiang Y, Wang Y, Liu X, Bu W, Jiang Y, Li M, Gong Y, Sun Z, Ying H, Yuan B, Lin X, Feng XH, Hartig SM, Li F, Shen H, Chen Y, Han L, Zeng Q, Patterson JB, Kaipparettu BA, Putluri N, Sicheri F, Rosen JM, Lewis MT, Chen X: Pharmacological targeting of MYC-regulated IRE1/XBP1 pathway suppresses MYC-driven breast cancer. Journal of Clinical Investigation, 2018, 128: 1283-1299
  50. Ye Y, Xiang Y, Ozguc FM, Kim Y, Liu CJ, Park PK, Hu Q, Diao L, Lou Y, Lin C, Guo AY, Zhou B, Wang L, Chen Z, Takahashi JS, Mills GB, Yoo SH, Han L#: The genomic landscape and pharmacogenomic interactions of clock genes in cancer chronotherapy. Cell Systems, 2018, 6: 314-328
  51. Ruan H, Han L#. Regulatory RNA Editing Sites in Cancer: Prediction and Beyond. EBioMedicine. 2018, 27:7-8
  52. Gong J, Li Y, Liu CJ, Xiang Y, Li C, Ye Y, Zhang Z, Hawke DH, Park PK, Diao L, Putkey JA, Yang L, Guo AY#, Lin C#, Han L#: A pan-cancer analysis of the expression and clinical relevance of small nucleolar RNA in human cancer. Cell Reports, 2017, 21: 1968-1981
  53. Xiang Y, Ye Y, Lou Y, Yang Y, Cai C, Zhang Z, Mills T, Chen NY, Kim Y, Ozguc FM, Diao L, Karmouty-Quintana H, Xia Y, Blackburn M, Kellems R, Chen Z, Yoo SH, Shyu AB, Mills GB, Han L#: Comprehensive characterization of alternative polyadenylation in human cancer. Journal of the National Cancer Institute, 2017, djx223
  54. Gong J, Mei S, Liu C, Xiang Y, Ye Y, Zhang Z, Feng J, Liu R, Diao L, Guo AY, Miao X, Han L#: PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types. Nucleic Acids Research, 2017, gkx861
  55. Xia S, Feng J, Chen K, Ma Y, Gong J, Cai F, Jin Y, Gao Y, Xia L, Chang H, Wei L, Han L#, He C#: CSCD: A database for cancer-specific circular RNAs. Nucleic Acids Research, 2017, gkx863
  56. Feng J*, Xiang Y*, Xia S*, Liu H, Wang J, Ozguc FM, Lei L, Kong R, Diao L, He C, Han L#: CircView: A Visualization and Exploration Tool for Circular RNAs. Briefings in Bioinformatics, 2017, bbx070
  57. Vannini I, Wise PM, Challagundla KB, Plousiou M, Raffini M, Bandini E, Fanini F, Paliaga G, Crawford M, Ferracin M, Ivan C, Fabris L, Davuluri RV, Guo Z, Cortez MA, Zhang X, Chen L, Zhang S, Fernandez-
  58. Cymering C, Han L, Carloni S, Salvi S, Ling H, Murtadha M, Neviani P, Gitlitz BJ, Laird-Offringa IA, Nana-Sinkam P, Negrini M, Liang H, Amadori D, Cimmino A, Calin GA, Fabbri M: Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs. Nature Communications, 2017, 8: 1801
  59. Xiao Z, Han L, Lee H, Zhuang L, Zhang Y, Baddour J, Nagrath D, Wood C, Gu J, Wu X, Liang H, Gan B: Energy stress-induced lncRNA FILNC1 represses c-Myc-mediated energy metabolism and inhibits renal tumor development. Nature Communications, 2017, 8:783
  60. 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 J, Liang H, Zhao K: Comparative Genomic Analysis of Esophageal Squamous Cell Carcinoma between Asian and Caucasian Patient Populations. Nature Communications, 2017, 8:1553
  61. Chen C-Y, Zhang Y, Xiang Y, Han L, Shyu A-B: Antagonistic actions of two human Pan3 isoforms on global mRNA turnover. RNA, 2017, 23: 1404-1418
  62. Sun K, D’Alessandro A, Ahmed MH, Zhang Y, Song A, Ko TP, Nemkov T, Reisz JA, Wu H, Adebiyi M, Peng Z, Gong J, Liu H, Huang A, Wen
  63. YE, Wen AQ, Berka V, Bogdanov MV, Abdulmalik O, Han L, Tsai AL, Idowu M, Juneja HS, Kellems RE, Dowhan W, Hansen KC, Safo MK, Xia Y: Structural and Functional Insight of Sphingosine 1-Phosphate-Mediated Pathogenic Metabolic Reprogramming in Sickle Cell Disease. Scientific Reports, 2017,
  64. 7 :15281
  65. Guo Y, Han L, Shen Q: Recent Advances in High Throughput Sequencing Analysis. International Journal of Genomics, 2017: 2454780
  66. Wang Y, Xu X, Yu S, Kang 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: Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers. Genome Research, 2017, 27: 1112-1125
  67. The Cancer Genome Atlas Research Network (Including Han L): Integrated genomic and molecular characterization of cervical cancer. Nature, 2017, 10.1038/nature21386
  68. Lei L, Xia S, Liu D, Li X, Feng J, Zhu Y, Hu J, Xia L, Guo L, Chen F, Cheng H, Chen K, Hu H, Chen X, Li F, Zhong S, Mittal N, Yang G, Qian Z, Han L#, He C#: Genome-wide characterization of lncRNAs in acute myeloid leukemia. Briefings in Bioinformatics, 2017, bbx007
  69. Lin A, Hu Q, Li C, Xing Z, Ma G, Wang C, Li J, Yao J, Liang K, Wang S, Park P, Marks J, Zhou Y, Zhou J, Hung MC, Liang H, Hu Z, Shen H, Hawke DH, Han L, Zhou Y, Lin C, Yang L: PtdIns (3,4,5)P3-lncRNA interaction exaggerates AKT activation and confers resistance to AKT inhibitors. Nature Cell Biology, 2017, 19: 238-251
  70. Li C, Wang S, Xing Z, Lin A, Liang K, Song J, Hu Q, Yao J, Chen Z, Park P, Hawke DH, Zhou J, Zhou Y, Zhang S, Liang H, Hung MC, Gallick G, Han L, Lin C, and Yang L: A ROR1-HER3-LncRNA signaling axis modulates the Hippo-YAP pathway to regulate bone metastasis. Nature Cell Biology, 2017, 19: 106-119
  71. Song A, Zhang Y, Han L, Yegutkin G, Liu H, Sun K, D’Alessandro A, Li J, Karmouty-Quintana H, Iriyama T, Weng T, Zhao S, Wang W, Wu H, Nemkov T, Subudhi A, Jameson-Van Houten S, Julian CG, Lovering AT, Hansen KC, Zhang H, Bogdanov M, Dowhan W, Jin J, Kellems RE, Eltzschig HK, Blackburn M, Roach RC, Xia Y: Erythrocytes retain hypoxic adenosine response for faster acclimatization upon re-ascent. Nature Communications, 2017, 8: 14108
  72. Gong J, Liu C, Liu W, Xiang Y, Diao L, Guo AY, Han L#: LNCediting: a database for functional effects of RNA editing in lncRNAs. Nucleic Acid Research. 2016, gkw835
  73. Xia S, Feng J, Lei L, Hu J, Xia L, Wang J, Xiang Y, Liu L, Zhong S, Han L#, He C#: Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes. Briefings in Bioinformatics. 2016, bbw081.
  74. Jiang HJ, Lee HS, Burt BM, Lee GK, Yoon KA, Park YY, Sohn BH, Kim SB, Kim MS, Lee JM, Joo J, Kim SC, Yoo JS, Na KJ, Choi YL, Oark JL, Kim SY, Lee YS, Han L, Liang H, Mak D, Burks JK, Zo J, Sugarbaker DJ, Shim YM, Lee JS: Integrated Genomic Analysis of Recurrence-Associated Small Non-coding RNAs in Oesophageal Cancer. 2016, pii: gutjnl-2015-311238
  75. Marini A, Lena AM, Panatta E, Ivan C, Han L, Liang H, Annicchiarico-Petruzzelli M, Di Daniele N, Calin GA, Candi E, Melino G: Ultraconserved long non-coding RNA uc.63 in breast cancer. Oncotarget. 2016, 8: 35669
  76. Zhou B, Wang L, Zhang S, Bennett BD, He F, Zhang Y, Xiong C, Han L, Diao L, Li P, Fargo DC, Cox AD, Hu G: INO80 governs super enhancer-mediated oncogenic transcription and tumor growth in melanoma. Genes & Development. 2016, 30:1440-53
  77. Liu X, Xiao ZD, Han L, Zhang J, Lee SW, Wang W, Lee H, Zhuang L, Chen J, Lin HK, Wang J, Liang H, Gan B:
  78. LncRNANBR2 engages a metabolic checkpoint by regulating AMPK under energy stress. Nature Cell Biology, 2016, 18: 431-442
  79. Redis RS, Vela LE, Lu W, Ferreira de Oliveira J, Ivan C, Rodriguez-Aguayo C, Adamoski D, Pasculli B, Taguchi A, Chen Y, Fernandez AF, Valledor L, Van Roosbroeck K, Chang S, Shah M, Kinnebrew G, Han L, Atlasi Y, Cheung LH, Huang GY, Monroig P, Ramirez MS, Catela Ivkovic T, Van L, Ling H, Gafà R, Kapitanovic S, Lanza G, Bankson JA, Huang P, Lai SY, Bast RC, Rosenblum MG, Radovich M, Ivan M, Bartholomeusz G, Liang H, Fraga MF, Widger WR, Hanash S, Berindan-Neagoe I, Lopez-Berestein G, Ambrosio AL, Gomes Dias SM, Calin GA: Allele-Specific Reprogramming of Cancer Metabolism by the Long Non-coding RNA CCAT2. Molecular Cell, 2016, 18: 520-534.
  80. Lin A, Li C, Xing Z, Ma G, Hu Q, Liang K, Han L, Wang C, Hawke DH, Wang S, Zhang Y, Wei Y, Park P, Zhou J, Zhou Y, Marks J, Hu Z, Hung MC, Liang H, Zou Y, Lin C, Yang L: The LINK-A lncRNA Activates Normoxic HIF1α Signaling in Triple-negative Breast Cancer. Nature Cell Biology, 2016, 18: 213-224.
  81. Han L, Liang H: RNA Editing in Cancer: Mechanistic, Prognostic and Therapeutic Implications. Molecular & Cellular Oncology (Invited author’s view)
  82. 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: The genomic landscape and clinical relevance of A-to-I RNA editing in human cancers. Cancer Cell, 2015, 28: 515-528.
  83. Li J*, Han L*, Roebuck P, Diao L, Liu L, Yuan Y, Weinstein J, Liang H: TANRIC: An Interactive Open Platform to Explore the Function of LncRNAs in Cancer. Cancer Research, 2015, 75: 3728-3733.
  84. Vickers KC, Roteta LA, Hucheson-Dilks H, Han L, and Guo Y: Mining diverse small RNA species in the deep transcriptome. Trends Biochemical Sciences, 2015. 40: 4-7.
  85. Lee WH, Nguyen P, Hu S, Liang G, Ong SG, Han L, Sanchez-Freire V, Lee AS, Vasanawala M, Segall G, and Wu JC: Variable activation of the DNA damage response pathways in patients undergoing single-photon emission computed tomography myocardial perfusion imaging. Circulation Cardiovascular Imaging, 2015. 8: e002851.
  86. Han L#, Guo Y, Su Z, Zheng S, and Lu Z: Advances in Computational Genomics. BioMed Research International,2015: 187803.
  87. Han L, Vickers KC, Samuels DC, and Guo Y: Alternative applications for distinct RNA sequencing strategies. Briefings in Bioinformatics, 2015. 16: 629-639.
  88. Yuan Y, VanAllen 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, and Liang, H: Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nature Biotechnology, 2014. 32: 644-52.
  89. Yang Y, Han L, Yuan Y, Li J, Hei N, and Liang H: Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types. Nature Communications, 2014. 5: 3231.
  90. Wang L, Du Y, Ward JM, Shimbo T, Lackford B, Zheng X, Miao YL, Zhou B, Han L, Fargo DC, Jothi R, Williams CJ, Wade PA, and Hu G: INO80 facilitates pluripotency gene activation in embryonic stem cell self-renewal, reprogramming, and blastocyst development. Cell Stem Cell, 2014. 14: 575-91.
  91. Luo X*, Huang L*, Han L*, Luo Z, Hu F, Tieu R, and Gan L: Systematic prioritization and integrative analysis of copy number variations in schizophrenia reveal key schizophrenia susceptibility genes. Schizophrenia Bulletin, 2014. 40: 1285-99.
  92. Hoadley KA, Yau C, Wolf DM, 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 LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Cancer Genome Atlas Research Network (Including Han L), Benz CC, Perou CM, and Stuart JM: Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell, 2014. 158: 929-44.
  93. Han L, Yuan Y, Zheng S, Yang Y, Li J, Edgerton ME, Diao L, Xu Y, Verhaak RG, and Liang H: The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant
  94. tumor sub-types. Nature Communications, 2014. 5: 3963.
  95. Costello JC, Heiser LM, Georgii E, Gonen M, Menden MP, Wang NJ, Bansal M, Ammad-ud
  96. dinM, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, NCI DREAM Community (Including Han L), Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, and Stolovitzky G: A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology, 2014. 32: 1202-12.
  97. Wang L, Miao YL, Zheng X, Lackford B, Zhou B, Han L, Yao C, Ward JM, Burkholder A, Lipchina I, Fargo DC, Hochedlinger K, Shi Y, Williams CJ, and Hu G: The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming. Cell Stem Cell, 2013. 13: 676-90.
  98. Samuels DC*, Han L*, Li J, Quanghu S, Clark TA, Shyr Y, and Guo Y: Finding the lost treasures in exome sequencing data. Trends in Genetics, 2013. 29: 593-9.
  99. Lan F, Lee AS, Liang P, Sanchez-Freire V, Nguyen PK, Wang L, Han L, Yen M, Wang Y, Sun N, Abilez OJ, Hu S, Ebert AD, Navarrete EG, Simmons CS, Wheeler M, Pruitt B, Lewis R, Yamaguchi Y, Ashley EA, Bers DM, Robbins RC, Longaker MT, and Wu JC: Abnormal calcium handling properties underlie familial hypertrophic cardiomyopathy pathology in patient-specific induced pluripotent stem cells. Cell Stem Cell, 2013. 12: 101-13.
  100. Hu S, Wilson KD, Ghosh Z, Han L, Wang Y, Lan F, Ransohoff KJ, Burridge P, and Wu JC:
  101. MicroRNA-302 increases reprogramming efficiency via repression of NR2F2. Stem Cells, 2013. 31: 259-68.
  102. Erdogan B, Bosompem A, Peng D, Han L, Smith E, Kennedy ME, Alford CE, Wu H, Zhao Z, Mosse CA, El-Rifai W, and Kim AS: Methylation of promoters of microRNAs and their host genes in myelodysplastic syndromes. Leukemia & Lymphoma, 2013. 54: 2720-7.
  103. Dey D*, Han L*, Bauer M, Sanada F, Oikonomopoulos A, Hosoda T, Unno K, De Almeida P, Leri A, and Wu JC: Dissecting the molecular relationship among various cardiogenic progenitor cells. Circulation Research, 2013. 112: 1253-62.
  104. Cancer Genome Atlas Research Network (Including Han L), Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, and Stuart JM: The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics, 2013. 45: 1113-20.
  105. Xia J*, Han L*, and Zhao Z: Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. BMC Genomics, 2012. 13 Suppl 8: S7.
  106. Sun N, Yazawa M, Liu J, Han L, Sanchez-Freire V, Abilez OJ, Navarrete EG, Hu S, Wang L, Lee A, Pavlovic A, Lin S, Chen R, Hajjar RJ, Snyder MP, Dolmetsch RE, Butte MJ, Ashley EA, Longaker MT, Robbins RC, and Wu JC: Patient-specific induced pluripotent stem cells as a model for familial dilated cardiomyopathy. Science Translational Medicine, 2012. 4: 130ra47.
  107. Liu J, Narsinh KH, Lan F, Wang L, Nguyen PK, Hu S, Lee A, Han L, Gong Y, Huang M, Nag D, Rosenberg J, Chouldechova A, Robbins RC, and Wu JC: Early stem cell engraftment predicts late cardiac functional recovery: preclinical insights from molecular imaging. Circulation Cardiovascular Imaging, 2012. 5: 481-90.
  108. Lan F, Liu J, Narsinh KH, Hu S, Han L, Lee AS, Karow M, Nguyen PK, Nag D, Calos MP, Robbins RC, and Wu JC: Safe genetic modification of cardiac stem cells using a site-specific integration technique. Circulation, 2012. 126: S20-8.
  109. Gu M, Nguyen PK, Lee AS, Xu D, Hu S, Plews JR, Han L, Huber BC, Lee WH, Gong Y, de Almeida PE, Lyons J, Ikeno F, Pacharinsak C, Connolly AJ, Gambhir SS, Robbins RC, Longaker MT, and Wu JC: Microfluidic single-cell analysis shows that porcine induced pluripotent stem cell-derived endothelial cells improve myocardial function by paracrine activation. Circulation Research, 2012. 111: 882-93.
  110. Du X*, Han L*, Guo AY, and Zhao Z: Features of methylation and gene expression in the promoter-associated CpG islands using human methylome data. Comparative and Functional Genomics, 2012. 2012: 598987.
  111. Lee AS, Xu D, Plews JR, Nguyen PK, Nag D, Lyons JK, Han L, Hu S, Lan F, Liu J, Huang M, Narsinh KH, Long CT, de Almeida PE, Levi B, Kooreman N, Bangs C, Pacharinsak C, Ikeno F, Yeung AC, Gambhir SS, Robbins RC, Longaker MT, and Wu JC: Preclinical derivation and imaging of autologously transplanted canine induced pluripotent stem cells. Journal of Biological Chemistry, 2011. 286: 32697-704.
  112. Dey D, Inayathullah M, Lee AS, LeMieux MC, Zhang X, Wu Y, Nag D, De Almeida PE, Han L, Rajadas J, and Wu JC: Efficient gene delivery of primary human cells using peptide linked polyethylenimine polymer hybrid. Biomaterials, 2011. 32: 4647-58.
  113. Su Z, Han L, and Zhao Z: Conservation and divergence of DNA methylation in eukaryotes. Epigenetics, 2011. 6: 134-140.
  114. Sun J, Han L, and Zhao Z: Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis. Artificial Intelligence in Medicine, 2010. 48: 99-106.
  115. Han L, Zheng S, Sun S, Huang T, and Zhao Z: Genome-Wide DNA Methylation Profiling in 40 Breast cancer cell lines. Lecture Notes in Computer Science, 2010. 6215.
  116. Zhao Z, and Han L: CpG islands: algorithms and applications in methylation studies. Biochemical and Biophysical Research Communications, 2009. 382: 643-5.
  117. Han L, and Zhao Z: Contrast features of CpG islands in the promoter and other regions in the dog genome. Genomics, 2009. 94: 117-24.
  118. Han L, and Zhao Z: CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? BMC Bioinformatics, 2009. 10: 65.
  119. Han L, and Zhao Z: Comparative analysis of CpG islands in four fish genomes. Comparative and Functional Genomics, 2008: 565631.
  120. Han L, Yang R, Su B, and Zhao Z: An SVM-based algorithm for classifying promoter-associated CpG islands in the human and mouse genomes. Lecture Notes in Artificial Intelligence, 2008. 5227: 6.
  121. Han L, Su B, Li WH, and Zhao Z: CpG island density and its correlations with genomic features in mammalian genomes. Genome Biology, 2008. 9: R79.
  122. Jiang C*, Han L*, Su B, Li WH, and Zhao Z: Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Molecular Biology and Evolution, 2007. 24: 1991-2000.