• Co-first author; Corresponding author

2016

• Yuan Y, Liu L, Chen H, Wang Y, Xu Y, Mao H, Li J, Mills GB, Shu Y, Li L, Liang H
  Comprehensive characterization of molecular differences in cancer between male and female patients
  Cancer Cell 29(5): 711-722 [PDF]
• Xu-Monette ZY, Deng Q, Manyam GC, Tzankov A, Zou1 D, Visco C, Dybkær K, Zhang L, Liang H, Montes-Moreno S, Chiu A, Orazi A, Zu Y, Bhagat G, Richards KL, His ED, Choi WWL, van Krieken JH, Huh J, Ponzoni M, Ferreri AJM, Parsons BM, Møller MB, Wang S, Miranda RN, Piris MA, Winter JN, Medeiros LJ, Li Y, Young KH
  Clinical and biological significance of MYC genomic mutations in de novo diffuse large B-cell lymphoma
  Clinical Cancer Research (in press)
• Liu X, Xiao Z, Han L, Lee S, Wang W, Lee H, Zhuang L, Chen J, Lin HK, Liang H, Gan B
  LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress
  Nature Cell Biology 18(4):431-442 [PDF]
• Powell E, Shao J, Cai S, Mistry N, Yuan Y, Tieu T, Decker K, Chen HC, Do KA, Heffernan TP, Edwards J, Liang H, Piwnica-Worms D, Piwnica-Worms H
  p53 deficiency linked to B-cell translocation gene-2 (BTG2) loss enhances metastatic potential by promoting tumor growth in primary and metastatic sites in patient-derived xenograft (PDX) models of triple negative breast cancer
  Breast Cancer Research 18:13 [PDF]
• Redis RS, Vela LE, Lu W, de Oliveira JF, Ivan C, Rodriguez-Aguayo C, Adamoski D, Pasculli B, Taguchi A,   Chen Y, Fernandez AF, Valledor L,  Roosbroeck KV, Chang S, Shah M, Kinnebrew G, Han L, Atlasi Y,  Cheung LH, Monroig P, Ramirez MS, Catela-Ivkovic T, Van L, Ling H, Gafa R, Kapitanovic S, Lanza G,  Bankson JA, Huang P, Lai SY, Rosenblum MG, Radovich M, Ivan M, Bartholomeusz G, Liang H, Fraga M, Widger WR, Hanash S, Berindan-Neagoe I, Lopez-Berestein G, Ambrosio AL, Gomes Dias AM, Calin GA

  Allele-specific reprograming of cancer metabolism by the long non-coding RNA, CCAT2

  Molecular Cell 61(4):520-534 [PDF]
• Lin A, Li C, Xing Z, Hu Q, Liang K, Han L, Wang C, Hawke DH, Wang S, Zhang Y, Wei Y, Ma G, Park PK, Zhou J, Zhou Y, Hu Z, Zhou Y, Mark JR, Liang H, Hung MC, Lin C, Yang L
  The LINK-A lncRNA activates normoxic HIF1α signaling in triple-negative breast cancer
  Nature Cell Biology 18(2):213-24 [PDF]
• Han L, Liang H
  RNA editing in cancer: mechanistic, prognostic and therapeutic implications
  Molecular and Celluar Oncology (in press)
• Cancer Genome Atlas Research Network (including Liang H).
  Comprehensive molecular characterization of papillary renal cell carcinoma
  The New England Journal of Medicine 374(2):135-145 [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

  HNF4α is a therapeutic target that links AMPK to WNT signaling in early-stage gastric cancer

  Gut 65(1):19-32 [PDF]

2015

• Fang X, Wei J, He X, An P, Wang H, Jiang L, Shao D, Liang H, Li Y, Wang F, Min J
  Landscape of dietary factors associated with risk of gastric cancer: a systematic review and dose-response meta-analysis of prospective cohort studies
  European Journal of Cancer 51(18):2820-32 [PDF]
• Han L, Diao L, Yu S, Xu X, Li J, Zhang R, Yang Y, Werner HM, Eterovic AK, 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 28(5):515-528 [PDF]
• Ferrajoli I, Ivan C, Ciccone M, Shimizu M, Kita Y, Ohtsuka M, D'Abundo L, Qiang J, Lerner S, Nouraee N,  Rabe KG, Rassenti LZ, Roosbroeck KV, Manning JT, Yuan Y, Zhang X, Shanafelt TD, Wierda WG,  Sabbioni S, Tarrand JJ, Estrov Z, Radovich M, Liang H, Negrini H, Kipps TJ, Kay NE, Keating M, Calin GA
  Epstein-Barr virus microRNAs are expressed in patients with chronic lymphocytic leukemia and correlate with overall survival
  E-Biomedicine 2(6):572-582 [PDF]
• Yang JY, Werner HM, Li J, Westin SN, Lu Y, Halle MK, Trovik J, Salvesen HB, Mills GB, Liang H
  Integrative protein-based prognostic model for early-stage endormetrioid endometrial cancer
  Clinical Cancer Research 22(2): 513-523 [PDF]
• Li J, Han L, Roebuck L, Diao L, Liu L, Yuan Y, Weinstein JN, Liang H
  TANRIC: an interactive open platform to explore the function of lncRNAs in cancer
  Cancer Research 75(18):3728-37 [PDF]

• Colla S, Ong DS, Ogoti Y, Marchesini M, Mistry NA, Clise-Dwyer K, Ang SA, Storti P, Viale A, Giuliani N, Ruisaard K, Ganan Gomez I, Bristow CA, Estecio M, Weksberg DC, Ho TW, Hu B, Genovese G, Pettazzoni P, Multani AS, Jiang S, Hua S, Ryan MC, Carugo A, Nezi L, Wei Y, Yang H, D'Anca M, Zhang L. Gaddis S, Gong T, Horner JW, Heffernan TP, Jones P, Cooper LJ, Liang H, Kantarjian H, Wang YA, Chin L, Bueso-Ramos C, Garcia-Manero G, DePinho RA
  Telomere dysfunction drives aberrant hematopoietic differentiation and myelodysplastic syndrome
  Cancer Cell 27(5): 644-657 [PDF]
• Wang J, Paris PL, Chen J, Nyo V, Yao H, Frazier ML, Killary AM, Liu CG, Liang H, Mathy C, Bondata S, Kirkwood K, Sen S
  Next generation sequencing of pancreatic cyst fluid microRNAs from low grade-benign and high grade-invasive lesions
  Cancer Letters 356(2):404-409 [PDF]
• Nam S, Chang HR, Jung HR, Gim Y, Kim NY, Grailhe R, Seo HR, Park HS, Balch C, Lee J, Park I, Jung SY, Jeong KC, Powis G, Liang H, Lee ES, Ro J, Kim YH
  A pathway-based approach for identifying biomarkers of tumor progression to trastuzumab-resistant breast cancer
  Cancer Letters 356 (2): 880-890 [PDF]

• Zhang P, Wang L, Rodriguez-Aguayo C, Yuan Y, Debeb BG, Chen D, Sun Y, You MJ, Liu Y, Dean DC, Woodward WA,  Liang H, Yang X, Lopez-Berestein G, Sood AK, Hu Y, Ang KK, Chen J, Ma L
  miR-205 acts as a tumor radiosensitizer by targeting ZEB1 and Ubc13
  Nature Communications 5:5671 [PDF]
• Cheung LW, Yu S, Zhang D, Li J, Ng PK, Panupinthu N, Mitra S, Ju Z, Yu Q, Liang H, Hawke DH, Lu Y, Broaddus RR, Mills GB
  Naturally occurring neomorphic PIK3R1 mutations activate the MAPK pathway, dictating therapeutic response to MAPK pathway inhibitors
  Cancer Cell 26(4): 479-494 [PDF]
• Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B,  Kim M, Wang T, Heiser L, Realubit R, Mattioli M, Alvarez MJ, Shen Y, NCI-DREAM Community (including Liang H), Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A
  A community computational challenge to predict the activity of pairs of compounds
  Nature Biotechnology 32(12): 1213-1222 [PDF]
• Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-fin M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community (including Liang H), Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G
  A community effort to assess and improve drug sensitivity prediction algorithms.
  Nature Biotechnology 32(12): 1202-1212 [PDF]
• 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, Roberston AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA; Cancer Genome Atlas Research Network (including Liang H), Benz CC, Perou CM, Stuart JM
  Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of orgin
  Cell 158(4):929-944[PDF]
• Wang Y, Waters J, Leung ML, Unruth A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin N
  Clonal evolution in breast cancer revealed by single nucleus genome sequencing
  Nature 512(7513):155-160[PDF]
• Zhang P, Wei Y, Wang L, Debeb BG, Yuan Y, Zhang J, Yuan J, Wang M, Chen D, Sun Y, Woodward WA, Liu Y, Dean DC, Liang H, Hu Y, Ang KK, Hung MC, Chen J, Ma L
  ATM-mediated stabilization of ZEB1 promotes DNA damage response and radioresistance through CHK1
  Nature Cell Biology 16(9):864-975 [PDF]
• Han L, Yuan Y, Zheng S, Yang Y, Li J, Edgerton ME, Diao L, Xu Y, Verhaak RG, Liang H
  The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumor subtypes
  Nature Communications 5: 3963 [PDF]
  Highlighted in new article " Analysis finds value in pseudogenes", Cancer Discovey 4: 978-979
• 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

  Assessing the clinical utility of cancer genomic and proteomic data across tumor types

  Nature Biotechnology 32(7):644-52[PDF]
• Akbani R, Ng PK, Werner HM, Shahmoradgoli M, Zhang F, Ju Z, Liu W, Yang JY, Yoshihara K, Li J, Ling S, Seviour EG, Ram PT, Minna JD, Diao L, Tong P, Heymach JV, Hill SM, Dondeligner F, Städler N, Byers LA, Meric-Bernstam F, Weinstein JN, Broom BM, Verhaak RG, Liang H, Mukherjee S, Lu Y, Mills GB

  A pan-cancer proteomic perspective on The Cancer Genome Atlas

  Nature Communications 5:3887 [PDF]
• Nam S, Chang HR, Kim KT, Kook MC, Hong D, Kwon CH, Jung HR, Park HS, Powis G, Liang H, Park T,  Kim YH
  PATHOME: an algorithm for accurately detecting differentially expressed subpathways
  Oncogene 33(41):4941-51 [PDF]
• Chen D, Sun Y, Yuan Y, Zhang J, You J, Teruya-Feldstein J, Wang M, Kah KJ, Gupta S, Liang H, Ma L
  miR-100 induces epithelial-mesenchymal transition but suppresses tumorigenesis, migration and invasion
  PLoS Genetics 10(2):1004177 [PDF]
• Piao H, Yuan Y, Wang M, Sun Y, Liang H, Ma L
  α-catenin acts as a tumor suppressor in E-cadherin-negative basal-like breast cancer by inhibiting NF-κB signaling
  Nature Cell Biology16(3):245-54 [PDF]
• Yang Y, Han L, Yuan Y, Li J, Hei N, Liang H
  Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types
  Nature Communications 5:3231 [PDF]

2013

• Bailey AM, Zhan L, Maru D,  Shureiqi I, Pickering CR, Izzo J, He N, Wei C, Baladandayuthapani V, Liang H,  Kopetz S, Powis P, Guo G
  FXR silencing in human colon cancer by DNA methylation and KRAS signaling
  American Journal of Physiology -Gastrointestinal and Liver Physiology 306(1):G48-58 [PDF]
• Mao Y, Chen H, Liang H, Meric-Bernstam F, Mills GB, Chen K
  CanDrA: cancer-specific driver missense mutation annotation with optimized features
  PLoS One 8(10): e77945 [PDF]
• Cancer Genome Atlas Research Network (including Liang H), Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM
  The Cancer Genome Atlas Pan-Cancer analysis project
  Nature Genetics 45(10): 1113-1120 [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
  TCPA: a resource for cancer functional proteomics data
  Nature Methods 10 (11): 1046-1047 [PDF]
• Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA
  Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
  Nature Genetics 45(10): 1121-26 [PDF]
• Cancer Genome Atlas Research Network (including Liang H as a key contributor)
  Integrated genomic characterization of endometrial carcinoma
  Nature 497 (7447): 67-73 [PDF]
• Liang H, Kim YH [invited review]
  Identifying molecular drivers of gastic cancer through next-generation sequencing
  Cancer Letters 340 (2): 241-246 [PDF] MDLinx news
• Liang H, Landweber LF [invited review]
  Dual coding regions in human alternatively spliced genes (version 2.0)
  Encyclopedia of Life Sciences John Wiley & Sons, Ltd

2012

• Li Y, Zhang L, Ball RL, Liang X, Li J, Lin Z, Liang H
  Comparative analysis of somatic copy-number alterations across different human cancer types reveals two distinct classes of breakpoint hotspots
  Human Molecular Genetics 21(22): 4957-4965 [PDF]
• Chen D, Sun Y, Wei Y, Zhang P, Rezaeian AH, Teruya-Feldstein J, Gupta S, Liang H, Lin HK, Hung MC, Ma L
  LIFR is a breast cancer metastasis suppressor upstream of the Hippo-YAP pathway and a prognostic marker
  Nature Medicine 18(10): 1511-1517 [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.
  Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer
  Genome Research 22(11): 2020-2129 [PDF]
• Yuan Y, Norris C, Xu Y, Tsui KW, Ji Y, Liang H
  BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data
  BMC Genomics13(Suppl 8): S9 [PDF] [Software]
• Li J, Roebuck P, Grünewald S, Liang H
  SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data
  Nucleic Acids Research 40(W):W123-126 [PDF] [Webserver]
• Kim YH , Liang H , Liu X, Lee JS, Cho JY, Cheong JH, Kim H, Li M, Downey TJ, Sun Y, Sun J, Dyer MD, Beasley EM, Noh SH, Weinstein JN, Liu CG, Powis G
  AMPKα modulation in cancer progression: multilayer integrative analysis of the whole transcriptome in Asian gastric cancer
  Cancer Research 72(10): 2512-21 [PDF] GEN news
• Yuan Y, Xu Y, Xu J, Ball RL, Liang H

  Predicting the lethal phenotype of knockout mouse by integrating comprehensive genomic data

  Bioinformatics 28(9): 1246-52 [PDF]

2011

• Yun J, Frankenberger CA, Kuo WL, Boelens MC, Eves EM, Cheng N, Liang H, Li WH, Ishwaran H, Minn AJ , Rosner MR

  Signaling pathway for RKIP and Let-7 regulates and predicts metastatic breast cancer

  EMBO Journal 30(21): 4500-14 [PDF]
• Cheung LW , Hennessy BT, Li J, Yu S, Myers AP, Djordjevic B, Lu Y, Stemke-Hale K, Dyer MD, Zhang F, Ju Z, Cantley LC, Scherer SE, Liang H, Lu K, Broaddus RR, Mills GB

  High frequency of PIK3R1 and PIK3R2 mutations in endometrial cancer elucidates a Novel mechanism for regulation of PTEN protein stability

  Cancer Discovery 1(2): 170-185 [PDF] [Comment] [Interview]
• Ji Y, Xu Y, Zhang Q, Tsui KW, Yuan Y, Norris C, Liang S, Liang H

  BM-map: Bayesian mapping of multireads for next-generation sequencing data

  Biometrics 67(4): 1215-24 [PDF]

• Lin Z, Wu WS, Liang H, Woo Y, Li WH

  The spatial distributions of cis-regulatory elements in yeast promoters and its implications fortranscriptional regulation

  BMC Genomics 11: 581 [PDF]
• Liang H [invited commentary]

  Decoding the dual-coding region: Key factors influencing the translational potential of a two-ORF-containing transcript

  Cell Research 20(5): 508-509 [PDF]

• Li YD, Liang H, Gu Z, Lin Z, Guan W, Li Y, Li WH

  Detecting positive selection in the dudding yeast genome

  Journal of Evolutionary Biology 22(12): 2430-2437 [PDF]
• Liang H, Li W-H

  Functional compensation by duplicated genes in mouse

  Trends in Genetics 25(10): 441-442 [PDF] [Supplementary Files]
• Liang H, Li W-H

  Lowly expressed human microRNA genes evolve rapidly

  Molecular Biology and Evolution 26(6) 1195-1198 [PDF]

• Liang H, Lin YS, Li WH

  Fast evolution of core promoters in primate genomes

  Molecular Biology and Evolution 25 (6): 1239-1244 [PDF]
• Liang H, Landweber LF [invited review]

  Dual coding regions in human alternatively spliced genes

  Encyclopedia of Life Sciences John Wiley & Sons, Ltd [PDF]
• Liang H, Fernández A. [invited review]

  Evolutionary constraints imposed by gene dosage balance

  Frontiers in Bioscience 13: 4373-4378 [PDF]

• Liang H, Li WH

  MicroRNA regulation of human protein protein interaction network

  RNA 13 (9): 1402-1408 [PDF] [Supplementary Files]
• Liang H, Li WH

  Gene essentiality, duplicability and protein connectivity in human and mouse

  Trends in Genetics 23(8): 375-378 [PDF] [Supplementary Files]
• Saunders MA, Liang H, Li WH

  Human polymorphism at microRNAs and microRNA target sites

  PNAS 104 (9): 3300-3305 [PDF] [Supplementary Files]
  Selected by Faculty of 1000 Biology
• Liang H, Landweber LF

  Hypothesis: RNA editing of microRNA target sites in humans?

  RNA 13(4): 463-467 [PDF] [Supplementary Files]

• Liang H, Zhou W, Landweber LF

  SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis

  Nucleic Acids Research 34: W382-384 [PDF] [Web Server]
  Selected as the most popular bioserver at www.eBioinfogen.com
• Liang H, Landweber LF

  A genome-wide study of dual coding regions in human alternatively spliced genes

  Genome Research 16(2): 190-196 [PDF] [Supplementary Files]
  Highlighted in Briefings in Bioinformatics 7(2): 198-199 [PDF]

• Chang WJ, Bryson PD, Liang H, Shin MK, Landweber LF

  The evolutionary origin of a complex scrambled gene

  PNAS 102(42): 15149-15154 [PDF] [Supplementary Files]
• Liang H, Landweber LF, Fresco JR

  Are stop codons recognized by base triplets in the large ribosomal RNA subunit?

  RNA 11(10): 1478-1484 [PDF]
• Liang H, Landweber LF

  Molecular mimicry: quantitative methods to study structural similarity between protein and RNA

  RNA 11(8): 1167-1172 [PDF] [Supplementary Files]
• Liang H, Cavalcanti AR, Landweber LF

  Conservation of tandem stop codons in yeasts

  Genome Biology 6(4): R31 [PDF] [Supplementary Files]
• Liang H, Wong J, Bao Q, Cavalcanti AR, Landweber LF

  Decoding the decoding region: analysis of the eukaryotic release factor (eRF1) stop Codon-binding residues

  Journal of Molecular Evolution 60(3): 337-344 [PDF]