Publications

Research output from CMJM Lab

Leading Author Publications

2022

Tumor-intrinsic SIRPA Promotes Checkpoint Inhibition Immunotherapy in Melanoma

Zhou Z#, Chen MJM#, Luo Y#, Mojumda K, Peng X, Chen H, Kumar SV, Akbani R, Lu Y and Liang H*

Cancer Cell, 40 (11), 1324-1340. e8

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2021

Next-Generation Analytics for Omics Data

Li J#, Chen H#, Wang Y#, Chen MJM#, Liang H*

Cancer Cell, 39 (1), 3-6

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2020

Predicting Cancer Cell Line Dependencies From the Protein Expression Data of Reverse-Phase Protein Arrays

Chen MJM, Li J, Mills GB, and Liang H*

JCO Clinical Cancer Informatics, 4: 357-366

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2020

Multi-omics Characterization of Molecular Features of Gastric Cancer Correlated with Response to Neoadjuvant Chemotherapy

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*

Science Advances, 6 (9), eaay4211

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2019

TCPA v3.0: An Integrative Platform to Explore the Pan-cancer Analysis of Functional Proteomic Data

Chen MJM#, Li J#, Wang Y, Akbani R, Lu Y, Mills GB, and Liang H*

Molecular & Cellular Proteomics, 18 (8), S15-S25

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2016

Integrating RNA-seq and ChIP-seq Data to Characterize Long Non-coding RNAs in Drosophila melanogaster

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*

BMC Genomics, 17(1):220

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2012

De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae

Chen MJM, Chou LC, Hsieh TT, Lee DD, Liu KW, Yu CY, Oyang YJ, Tsai HK* and Chen CY*

Bioinformatics, 28 (5): 701-708

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Collaborative Publications

2025

The mutational landscape and functional effects of noncoding ultraconserved elements in human cancers

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

Science Advances, 11(8), eado2830

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2024

ARID1A promotes chromatin loop formation at double-strand breaks and simultaneously regulates epigenetic marks for DSB repair and transcription silencing

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

Nucleic Acids Research, gkae233

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2022

Proteo-genomic characterization of virus-associated liver cancers reveals potential subtypes and therapeutic targets

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*

Nature Communications, 13 (1), 6481

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2021

A targetable LIFR−NF-κB−LCN2 axis controls liver tumorigenesis and vulnerability to ferroptosis

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*

Nature Communications, 12 (1), 7333

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2021

Transcriptome profiling reveals the developmental regulation of NaCl-treated Forcipomiya taiwana eggs

Chen ME, Tsai MH, Huang HT, Tsai CC, Chen MJM, Yang DS, Yang TZ, Wang J, Huang RN*

BMC Genomics, 22, 1-14

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2021

A four-gene signature for predicting survival and immunotherapeutic responses based on immune classification of melanoma

Mei Y, Chen MJM, Liang H, and Ma L*

Communications Biology, 4 (1), 383

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2020

Large-scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines

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*

Cancer Cell, 38 (6), 829-843. e4

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2020

Inhibition of TMPRSS2 by HAI-2 reduces prostate cancer cell invasion and metastasis

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*

Oncogene, 39 (37), 5950-5963

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2020

Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera

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*

Genome Biology and Evolution, 12 (7), 1099-1188

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2019

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

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

Genome Biology, 20, 1-26

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2018

The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

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

Environmental Science and Technology, 52(10):6009-6022

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2018

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

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, 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

Scientific Reports, 8 (1), 1931

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2017

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

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 MJM, Hunter W, Cilia M, Mueller LA, Munoz-Torres M, Nelson D, Poelchau MF, Benoit JB, Wiersma-Koch H, D'Elia T, Brown SJ

Database, 2017, 1-20

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2016

Aiolos collaborates with Blimp-1 to regulate the survival of multiple myeloma cells

Hung KH, Su ST, Chen CY, Hsu PH, Huang SY, Wu WJ, Chen MJM, Chen HY, Wu PC, Lin FR, Tsai MD, Lin KI*

Cell Death and Differentiation, 23 (7), 1175-1184

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2016

Discovery of Organophosphate Resistance-Related Genes in Well-known Resistance Mechanisms of the Diamondback Moth (Plutella xylostella) by RNA-Seq

Hsu JC*, Lin YY, Chang CC, Hua KH, Chen MJM, Huang LH, Chen CY*

Journal of Economic Entomology, 109 (3), 1378-1386

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2015

Discovery of genes related to formothion resistance in oriental fruit fly (Bactrocera dorsalis) by a constrained functional genomics analysis

Kuo TCY, Hu CC, Chien TY, Chen MJM, Feng HT, Chen LFO, Chen CY, Hsu JC

Insect Molecular Biology, 24(3): 338-347

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2015

Intellectual disability-associated dBRWD3 regulates gene expression through inhibition of HIRA/YEM-mediated chromatin deposition of histone H3.3

Chen WY, Shih HT, Liu KY, Shih ZS, Chen LK, Tsai TH, Chen MJM, Liu H, Tan BCM, Chen CY, Lee HH, Loppin B, Ait-Ahmed O, Wu JT*

EMBO Reports, 16 (4), 528-538

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2014

Differential activation of sporamin expression in response to abiotic mechanical wounding and biotic herbivore attack in the sweet potato

Rajendran SK, Lin IW, Chen MJM, Chen CY, and Yeh KW*

BMC Plant Biology, 14 (1), 1-21

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2014

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

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*

BMC Systems Biology, 8 (1), 13

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2013

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Meyer P*, Siwo G, Zeevi D, Sharon E, Norel R, DREAM6 Promoter Prediction Consortium, Segal E and Stolovitzky G

Genome Research, 23 (11), 1928-1937

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2012

Discovery of Genes Related to Insecticide Resistance in Bactrocera dorsalis by Functional Genomic Analysis of a De Novo Assembled Transcriptome

Hsu JC, Chien TY#, Hu CC#, Chen MJM#, Wu WJ, Feng HT, Haymer DS and Chen CY*

PLoS ONE, 7(8): e40950

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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

Liu HC, Shih LY, Chen MJM, Wnag CC, Yeh TC, Lin TH, Chen CY, Lin CJ and Liang DC*

Cancer Genetics, 204 (5): 252-259

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2009

Statistical identification of gene association by CID in application of constructing ER regulatory network

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*

BMC Bioinformatics, 10 (1), 85

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2008

Discovering gapped binding sites of yeast transcription factors

Chen CY, Tsai HK, Hsu CM, Chen MJM, Hung HG, Huang GTW, Li WH*

Proceedings of the National Academy of Sciences of the United States of America, 105 (7), 2527-2532

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Book Chapters

2019

The GFF3toolkit: QC and Merge Pipeline for Genome Annotation

Chen MJM, Lin H, Chiang LM, Childers CP*, and Poelchau MF*

In: Insect Genomics: Methods and Protocols, pp. 75-87

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2018

Navigating the i5k Workspace@NAL: A Resource for Arthropod Genomes

Poelchau MF*, Chen MJM, Lin YY, and Childers CP*

In: Eukaryotic Genomic Databases: Methods and Protocols, pp. 557-577

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Theses & Dissertations

2016

Characterizing Long Non-coding RNAs in Drosophila melanogaster

Chen MJM

PhD thesis, NTU

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2009

Incorporating Motif Discovery in Investigation of Transcription Factor Cooperativity in Saccharomyces Cerevisiae

Chen MJM

Master thesis, NTU

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