Explore our research highlights and publications

Research Highlight

Publications:

  1. Zhou Z#, Chen MJM#, Luo Y#, Mojumda K, Peng X, Chen H, Kumar SV, Akbani R, Lu Y and Liang H* (2022). Tumor-intrinsic SIRPA Promotes Checkpoint Inhibition Immunotherapy in Melanoma. Cancer Cell, 40 (11), 1324-1340. e8. doi: 10.1016/j.ccell.2022.10.012
  2. Li J#, Chen H#, Wang Y#, Chen MJM#, Liang H* (2021). Next-Generation Analytics for Omics Data. Cancer Cell, 39 (1), 3-6. doi: 10.1016/j.ccell.2020.09.002
  3. Chen MJM, Li J, Mills GB, and Liang H* (2020). Predicting Cancer Cell Line Dependencies From the Protein Expression Data of Reverse-Phase Protein Arrays. JCO Clinical Cancer Informatics, 4: 357-366. doi: 10.1200/CCI.19.00144
  4. Li Z#, Gao X#, Peng X#, Chen MJM#, Wei B, Wen X, Wei B, Dong Y, Bu Z, Wu A, Wu Q, Tang L, Li Z, Liu Y, Zhang L, Jia S, Zhang L, Shan F, Zhang J, Wu X, Ji X, Ji K, Wu X, Shi J, Xing X, Wu J, 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 Chemothery. Science Advances, 6 (9), eaay4211. doi: 10.1126/sciadv.aay4211
  5. Chen MJM#, Li J#, Wang Y, Akbani R, Lu Y, Mills GB, and Liang H* (2019). TCPA v3.0: An Integrative Platform to Explore the Pan-cancer Analysis of Functional Proteomic Data. Molecular & Cellular Proteomics, 18 (8), S15-S25. doi: 10.1074/mcp.RA118.001260
  6. Chen MJM#, Chen LK#, Lai YS, Lin YY, Wu DC, Tung YA, Liu KY, Shih HT, Chen YJ, Lin YL, Ma LT, Huang JL, Wu PC, Hong MY, Chu FH, Wu JT*, Li WH*, Chen CY* (2016). Integrating RNA-seq and ChIP-seq Data to Characterize Long Non-coding RNAs in Drosophila melanogaster. BMC Genomics, 17(1):220. doi: 10.1186/s12864-016-2457-0
  7. Chen MJM, Chou LC, Hsieh TT, Lee DD, Liu KW, Yu CY, Oyang YJ, Tsai HK* and Chen CY* (2012). De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae. Bioinformatics, 28 (5): 701-708. doi: 10.1093/bioinformatics/bts002
  8. Recep Bayraktar, Yitao Tang, Mihnea P Dragomir, Cristina Ivan, Xinxin Peng, Linda Fabris, Jianhua Zhang, Alessandro Carugo, Serena Aneli, Jintan Liu, Mei-Ju May Chen, Sanjana Srinivasan, Iman Sahnoune, Emine Bayraktar, Kadir C Akdemir, Meng Chen, Pranav Narayanan, Wilson Huang, Leonie Florence Ott, Agda Karina Eterovic, Oscar Eduardo Villarreal, Mohammad Moustaf Mohammad, Michael D Peoples, Danielle M Walsh, Jon Andrew Hernandez, Margaret B Morgan, Kenna R Shaw, Jennifer S Davis, David Menter, Constantine S Tam, Paul Yeh, Sarah-Jane Dawson, Laura Z Rassenti, Thomas J Kipps, Tanja Kunej, Zeev Estrov, Simon A Joosse, Luca Pagani, Catherine Alix-Panabières, Klaus Pantel, Alessandra Ferajoli, Andrew Futreal, Ignacio I Wistuba, Milan Radovich, Scott Kopetz, Michael J Keating, Giulio F Draetta, John S Mattick, Han Liang, George A Calin (2025). The mutational landscape and functional effects of noncoding ultraconserved elements in human cancers. Science Advances, 11(8), eado2830. doi: 10.1126/sciadv.eado2830
  9. Bakr A*, Corte GD#, Veselinov O#, Kelekçi S#, Chen MJM#, Lin YY, Cross A, Syed R, Iacovone M, Sigismondo G, Goyal A, Lutsik P, Weichenhan D, Plass C, Popanda O and Schmezer P (2024). ARID1A promotes chromatin loop formation at double-strand breaks and simultaneously regulates epigenetic marks for DSB repair and transcription silencing. Nucleic Acids Research, gkae233. doi: 10.1093/nar/gkae233
  10. Fujita M, Chen MJM, Siwak DR, Sasagawa S, Oosawa-Tatsuguchi A, Arihiro K, Ono A, Miura R, Maejima K, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Lee JS, Lu Y, Mills GB, Liang H, Nishizuka SS and Nakagawa H* (2022). Proteo-genomic characterization of virus-associated liver cancers reveals potential subtypes and therapeutic targets. Nature Communications, 13 (1), 6481. doi: 10.1038/s41467-022-34249-x
  11. Yao F*, Deng Y, Zhao Y, Mei Y, Zhang Y, Liu X, Martinez C, Su X, Rosato RR, Teng H, Hang Q, Yap S, Chen D, Wang Y, Chen MJM, Zhang M, Liang H, Xie D, Chen X, Zhu H, Chang JC, You MJ, Sun, Y, Gan B, Ma L* (2021). A targetable LIFR−NF-κB−LCN2 axis controls liver tumorigenesis and vulnerability to ferroptosis. Nature Communications, 12 (1), 7333. doi: 10.1038/s41467-021-27452-9
  12. Chen ME, Tsai MH, Huang HT, Tsai CC, Chen MJM, Yang DS, Yang TZ, Wang J, Huang RN* (2021). Transcriptome profiling reveals the developmental regulation of NaCl-treated Forcipomiya taiwana eggs. BMC Genomics, 22, 1-14. doi: 10.1186/s12864-021-08096-x
  13. Mei Y, Chen MJM, Liang H, and Ma L* (2021). A four-gene signature for predicting survival and immunotherapeutic responses based on immune classification of melanoma. Communications Biology, 4 (1), 383. doi: 10.1038/s42003-021-01911-x
  14. Zhao W#, Li J#, Chen MJM, Ju Z, Nesser NK, Johnson-Camacho K, Boniface CT, Lawrence Y, Pande NT, Davies MA, Herlyn M, Muranen T, Zervantonakis I, Von Euw E, Schultz A, Kumar SV, Korkut A, Spellman PT, Akbani R, Slamon DJ, Gray JW, Brugge JS, Lu Y, Mills GB*, and Liang H* (2020). Large-scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines. Cancer Cell, 38 (6), 829-843. e4. doi: 10.1016/j.ccell.2020.10.008
  15. Ko CJ, Hsu TW, Wu SR, Lan SW, Hsiao TF, Lin HY, Lin HH, Tu HF, Lee CF, Huang CC, Chen MJM, Hsiao PW, Huang HP, and Lee MS* (2020). Inhibition of TMPRSS2 by HAI-2 reduces prostate cancer cell invasion and metastasis. Oncogene, 39 (37), 5950-5963. doi: 10.1038/s41388-020-01413-w
  16. Oeyen JP*, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MJM, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni HV, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SC, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, von Reumont BM, Rosendale AJ, Simao FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B*, Niehuis O* (2020). Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera. Genome Biology and Evolution, 12 (7), 1099-1188. doi: 10.1093/gbe/evaa106
  17. Panfilio KA*, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang C, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan-Perez S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao Y, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter M, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S (2019). Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biology, 20, 1-26. doi: 10.1186/s13059-019-1660-0
  18. Poynton HC*, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DST, Murali SC, Chen S, Glastad KM, Goodisman MAD, Werren JH, Vineis JH, Bowen JL, Friedrich M, Jones J, Robertson HM, Feyereisen R, Mechler-Hickson A, Mathers N, Lee CE, Colbourne JK, Biales A, Johnston JS, Wellborn GA, Rosendale AJ, Cridge AG, Munoz-Torres MC, Bain PA, Manny AR, Major KM, Lambert FN, Vulpe CD, Tuck P, Blalock BJ, Lin YY, Smith ME, Ochoa-Acuna H, Chen MJM, Childers CP, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Gibbs RA, Richards S (2018). The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. Environmental Science and Technology, 52(10):6009-6022. doi: 10.1021/acs.est.8b00837
  19. Schoville SD*, Chen YH, Andersson MN, Benoit JB, Bhandari A, Bowsher JH, Brevik K, Cappelle K, Chen MJM, Childers AK, Childers C, Christiaens O, Clements J, Didion EM, Elpidina EN, Engsontia P, Friedrich M, Garcia-Robles I, Gibbs RA, Goswami C, Grapputo A, Gruden K, Grynberg M, Henrissat B, Jennings EC, Jones JW, Kalsi M, Khan SA, Kumar A, Li F, Lombard V, Ma X, Martynov A, Miller NJ, Mitchell RF, Munoz-Torres M, Muszewska A, Oppert B, Palli SR, Panfilio KA, Pauchet Y, Perkin LC, Petek M, Poelchau MF, Record E, Rinehart JP, Robertson HM, Rosendale AJ, Ruiz-Arroyo VM, Smagghe G, Szendrei Z, Thomas GWC, Torson AS, Jentzsch IMV, Weirauch MT, Yates AD, Yocum GD, Yoon JS, and Richards S (2018). A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Scientific Reports, 8 (1), 1931. doi: 10.1038/s41598-018-20154-1
  20. Saha S*, Hosmani PS*, Villalobos-Ayala K, Miller S, Shippy T, Flores M, Rosendale A, Cordola C, Bell T, Mann H, DeAvila G, DeAvila D, Moore Z, Buller K, Ciolkevich K, Nandyal S, Mahoney R, Voorhis JV, Dunlevy M, Farrow D, Hunter D, Morgan T, Shore K, Guzman V, Izsak A, Dixon DE, Cridge A, Cano L, Cao X, Jiang H, Leng N, Johnson S, Cantarel BL, Richards S, English A, Shatters RG, Childers C, Chen MJ, Hunter W, Cilia M, Mueller LA, Munoz-Torres M, Nelson D, Poelchau MF, Benoit JB, Wiersma-Koch H, D’Elia T, Brown SJ (2017). Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. Database, 2017, 1–20. doi: 10.1093/database/bax032
  21. Hung KH, Su ST, Chen CY, Hsu PH, Huang SY, Wu WJ, Chen MJM, Chen HY, Wu PC, Lin FR, Tsai MD, Lin KI* (2016). Aiolos collaborates with Blimp-1 to regulate the survival of multiple myeloma cells. Cell Death and Differentiation, 23 (7), 1175-1184. doi: 10.1038/cdd.2015.167
  22. Hsu JC*, Lin YY, Chang CC, Hua KH, Chen MJM, Huang LH, Chen CY* (2016). Discovery of Organophosphate Resistance-Related Genes in Well-known Resistance Mechanisms of the Diamondback Moth (Plutella xylostella) by RNA-Seq. Journal of Economic Entomology, 109 (3), 1378-1386. doi: 10.1093/jee/tow070
  23. Kuo TCY, Hu CC, Chien TY, Chen MJM, Feng HT, Chen LFO, Chen CY, Hsu JC (2015). Discovery of genes related to formothion resistance in oriental fruit fly (Bactrocera dorsalis) by a constrained functional genomics analysis. Insect Molecular Biology, 24(3): 338-347. doi: 10.1111/imb.12161
  24. Chen WY, Shih HT, Liu KY, Shih ZS, Chen LK, Tsai TH, Chen MJ, Liu H, Tan BCM, Chen CY, Lee HH, Loppin B, Aït‐Ahmed O, Wu JT* (2015). Intellectual disability‐associated dBRWD3 regulates gene expression through inhibition of HIRA/YEM‐mediated chromatin deposition of histone H3. 3. EMBO Reports, 16 (4), 528-538. doi: 10.15252/embr.201439092
  25. Rajendran SK, Lin IW, Chen MJM, Chen CY, and Yeh KW* (2014). Differential activation of sporamin expression in response to abiotic mechanical wounding and biotic herbivore attack in the sweet potato. BMC Plant Biology, 14 (1), 1-21. doi: 10.1186/1471-2229-14-112
  26. Meyer P*, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, DREAM 6&7 Parameter Estimation consortium, Sauro HM, Stolovitzky G and Saez-Rodriguez J* (2014). Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Systems Biology, 8 (1), 13. doi: 10.1186/1752-0509-8-13
  27. Meyer P*, Siwo G, Zeevi D, Sharon E, Norel R, DREAM6 Promoter Prediction Consortium, Segal E and Stolovitzky G (2013). Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome Research, 23 (11), 1928-1937. doi: 10.1101/gr.157420.113
  28. Hsu JC, Chien TY#, Hu CC#, Chen MJM#, Wu WJ, Feng HT, Haymer DS and Chen CY* (2012). Discovery of Genes Related to Insecticide Resistance in Bactrocera dorsalis by Functional Genomic Analysis of a De Novo Assembled Transcriptome. PLoS ONE, 7(8): e40950. doi: 10.1371/journal.pone.0040950
  29. Liu HC, Shih LY, Chen MJM, Wnag CC, Yeh TC, Lin TH, Chen CY, Lin CJ and Liang DC* (2011). Expression of HOXB genes is significantly different in acute myeloid leukemia with a partial tandem duplication of MLL vs. a MLL translocation: a cross-laboratory study. Cancer Genetics, 204 (5): 252-259. doi: 10.1016/j.cancergen.2011.02.003
  30. Liu LY, Chen CY, Chen MJM#, Tsai MS#, Lee CHS#, Phang TL, Chang LY, Kuo WH, Hwa HL, Lien HC, Jung SM, Lin YS, Chang KJ and Hsieh FJ* (2009). Statistical identification of gene association by CID in application of constructing ER regulatory network. BMC Bioinformatics, 10 (1), 85. doi: 10.1186/1471-2105-10-85
  31. Chen CY, Tsai HK, Hsu CM, Chen MJM, Hung HG, Huang GTW, Li WH* (2008). Discovering gapped binding sites of yeast transcription factors. Proceedings of the National Academy of Sciences of the United States of America, 105 (7), 2527-2532. doi: 10.1073/pnas.0712188105
  32. Chen MJM, Lin H, Chiang LM, Childers CP*, and Poelchau MF* (2019). The GFF3toolkit: QC and Merge Pipeline for Genome Annotation. In Insect Genomics: Methods and Protocols, pp. 75-87. doi: 10.1007/978-1-4939-8775-7_7
  33. Poelchau MF*, Chen MJM, Lin YY, and Childers CP* (2018). Navigating the i5k Workspace@NAL: A Resource for Arthropod Genomes. In Eukaryotic Genomic Databases: Methods and Protocols, pp. 557-577. doi: 10.1007/978-1-4939-7737-6_18
  34. Chen MJM (2016). Characterizing Long Non-coding RNAs in Drosophila melanogaster. PhD thesis, NTU. doi: 10.6342/NTU201601384
  35. Chen MJM (2009). Incorporating Motif Discovery in Investigation of Transcription Factor Cooperativity in Saccharomyces Cerevisiae. Master thesis, NTU. doi: 10.6342/NTU.2009.03156