Publications

1. Venkatachalam A, Correia C, Peterson K, Hou X, Schneider P, Strathman A, Flatten K, Sine C, Balczewski E, McGehee C, Larson M, Duffield L, Meng XW, Vincelette N, Ding H, Oberg A, Couch F, Swisher E, Li H, Weroha SJ, Kaufmann S. Proapoptotic activity of JNK-sensitive BH3-only proteins underpins ovarian cancer response to replication checkpoint inhibitors. Molecular Cancer, 2024 Sept. (Accepted)
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2. Zhang L, Weiskittel TM, Zhu Y, Xue D, Zhang H, Shen Y, Yu H, Li J, Hou L, Guo H, Dai Z, Li H, Zhang J. Comparative dissection of transcriptional landscapes of human iPSC-NK differentiation and NK cell development. Life Medicine, lnae032, 2024 Sept.
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3. Schultz DF, Davies BA, Payne JA, Martin CP, Minard AY, Childs BG, Zhang C, Jeganathan KB, Sturmlechner I, White TA, de Bruin A, Harkema L, Chen H, Davies MA, Jachim S, LeBrasseur NK, Piper RC, Li H, Baker DJ, van Deursen J, Billadeau DD, Katzmann DJ. Loss of HD-PTP function results in lipodystrophy, defective cellular signaling, and altered lipid homeostasis. J Cell Sci. 2024 Sep 15;137(18):jcs262032.
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4. Kamaraj US, Gautam P, Cheng T, Chin TS, Tay SK, Ho TH, Nadarajah R, Goh RCH, Wong SL, Mantoo S, Busmanis I, Li H, Le MT, Li QJ, Lim EH, Loh YH. Deciphering tumour microenvironment and elucidating the origin of cancer cells in ovarian clear cell carcinoma. bioRxiv [Preprint]. 2024 Aug 8:2024.08.06.606821.
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5. Ho MF, Zhang C, Cohan JS, Tuncturk M, Heider RM, Coombes BJ, Biernacka J, Moon I, Skime M, Ho AM, Ngo Q, Skillon C, Croakin PE, Oesterle TS, Karpyak VM, Li H, Weinshilboum R. IL17RB genetic variants are associated with acamprosate treatment response in patients with alcohol use disorder: A proteomics-informed genomics study. Brain Behav Immun. 2024 Aug:120:304-314.
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6. Khoury M, Guo Q, Furuta K, Correia C, Chady Meroueh C, Kim Lee HS, Warasnhe K, Perez LV, Mazar AP, Kim I, Noh YK, Holmes H, Romero MF, Sussman CR, Pavelko KD, Islam S, Bamidele AO, Hirsova P, Li H, Ibrahim SH. Glycogen Synthase Kinase 3 Activity Enhances Liver Inflammationin Metabolic Dysfunction Associated Steatohepatitis. JHEP Rep. 2024 Mar 26;6(6):101073.
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7. Gao H, Wei L, Indulkar S, Nguyen TTL, Liu D, Ho MF, Zhang C, Li H, Weinshilboum RM, Ingle JN, Wang L. Androgen receptor-mediated pharmacogenomic expression quantitative trait loci: implications for breast cancer response to AR-targeting therapy. Breast Cancer Res. 2024 Jul 4; 26 (1):111.
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8. Yu H, Zhao J, Shen Y, Lu Q, Liu Y, Li N, Chen M, Li H, Zhang J, Wang X. The dynamic landscape of enhancer-derived RNA during mammalian early embryo development. Cell Rep. 2024 Apr 8; 43 (4):114077.
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9. Ho MF, Zhang C, Moon I, Coombes BJ, Biernacka J, Skime M, Oesterle TS, Karpyak VM, Li H, Weinshilboum R. Molecular mechanisms involved in alcohol craving, IRF3, and endoplasmic reticulum stress: a multi-omics study. Transl Psychiatry. 2024 Mar 26;14(1):165.
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10. Xianyu Z, Correia C, Ung CY, Zhu S, Billadeau DD, Li H. The Rise of Hypothesis-Driven Artificial Intelligence in Oncology. Cancers (Basel). 2024 Feb 18;16(4):822.
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11. Wang M, Zhu B, Zhang C, Li C, Zhang R, Rathmell JC, Li H, Cui W, Hitosugi T, Sun J. Glutamine metabolism is required for optimal alveolar macrophage self-renewal. J Respir Biol Transl Med., 2024, 1 (1), 10004.
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12. Carneiro B, Cavalcante L, Mahalingam D, Saeed A, Safran H, Ma WW, Coveler A, Powell S, Bastos B, Davis E, Sahai V, Mikrut W, Longstreth J, Smith S, Weiskittel T, Li H, Borden B, Harvey RD, Sahebjam S, Cervantes A, Koukol A, Mazar A, Steeghs N, Kurzrock R, Giles F, Munster P. Phase 1 study of Elraglusib (9-ING-41), a glycogen synthase kinase-3b inhibitor, as monotherapy or combined with chemotherapy in patients with advanced malignancies. Clin Cancer Res. 2024 Feb 1;30(3):522-531.
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13. Monroe JM, Quach HQ, Punia S, Enninga EAL, Fedyshyn Y, Girsch JH, Fedyshyn B, Lemens M, Littlefield D, Behl S, Sintim-Aboagye E, Mejia Plazas MC, Yamaoka S, Ebihara H, Pandey A, Correia C, Ung CY, Li H, Vassallo R, Sun J, Johnson EL, Olson JE, Theel ES, Badley AD, Kennedy RB, Theiler RN, Chakraborty R. Vertical Transmission of SARS-CoV-2-Specific Antibodies and Cytokine Profiles in Pregnancy. J Infect Dis. 2024 Feb 14; 229 (2):473-484.
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14. Enninga EAL, Quach HQ, Jang JS, de Araujo Correia MCM, Fedyshyn Y, Fedyshyn B, Lemens M, Littlefield D, Behl S, Sintim-Aboagye E, Mejia Plazas MC, Cardenas MC, Chakraborty S, Yamaoka S, Ebihara H, Pandey A, Li H, Badley AD, Johnson EL, Sun J, Norgan AP, Theiler RN, Chakraborty R. Maternal SARS-CoV-2 Infection in Pregnancy Disrupts Gene Expression in Hofbauer Cells with Limited Impact on Cytotrophoblasts. PLoS Pathog. 2024 Feb 7; 20 (2):e1011990.
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15. Ng PI, Zhang C, Li H, Baker DJ. Senescence targeting methods impact Alzheimer's disease features in 3xTg mice. J Alzheimers Dis. 2024;97(4):1751-1763.
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16. Ung CY, Correia C, Li H, Adams CM, Westendorf JJ, Zhu S. The Multi-Organ Locked-State Model of Chronic Diseases and Systems Pharmacology Opportunities. Drug Discov Today. 2024 Jan;29(1):103825.
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17. Hu LS, D'Angelo F, Weiskittel TM, Caruso FP, Fortin Ensign SP, Blomquist MR, Flick MJ, Wang L, Sereduk CP, Meng-Lin K, De Leon G, Nespodzany A, Urcuyo JC, Gonzales AC, Curtin L, Lewis EM, Singleton KW, Dondlinger T, Anil A, Semmineh NB, Noviello T, Patel RA, Wang P, Wang J, Eschbacher JM, Hawkins-Daarud A, Jackson PR, Grunfeld IS, Elrod C, Mazza GL, McGee SC, Paulson L, Clark-Swanson K, Lassiter-Morris Y, Smith KA, Nakaji P, Bendok BR, Zimmerman RS, Krishna C, Patra DP, Patel NP, Lyons M, Neal M, Donev K, Mrugala MM, Porter AB, Beeman SC, Jensen TR, Schmainda KM, Zhou Y, Baxter LC, Plaisier CL, Li J, Li H, Lasorella A, Quarles CC, Swanson KR, Ceccarelli M, Iavarone A, Tran NL. Integrated molecular and multiparametric MRI mapping of high-grade glioma identifies regional biologic signatures. Nat Commun. 2023 Sep 28; 14 (1):6066.
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18. Hamashima K, Wong KW, Sam TW, Teo JHJ, Taneja R, Le MTN, Li QJ, Hanna JH, Li H, Loh YH. Single-nucleus multiomic mapping of m6A methylomes and transcriptomes in native populations of cells with sn-m6A-CT. Mol Cell. 2023 Aug 25;S1097-2765(23)00649-4.
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19. Prieto LI, Sturmlechner I, Graves SI, Zhang C, Goplen NP, Yi ES, Sun J, Goronzy JJ, Li H, Baker DJ. Senescent alveolar macrophages promote early onset lung cancer. Cancer Cell. 2023 Jul 10; 41 (7):1261-1275.e6.
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20. Meng-Lin K, Ung CY, Zhang C, Weiskittel TM, Wisniewski P, Zhang Z, Tan SH, Yeo KS, Zhu S, Correia C, Li H. SPIN-AI: A Deep Learning Model That Identifies Spatially Predictive Genes. Biomolecules. 2023 May 27;13(6):895.
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21. Ho MF, Zhang C, Moon I, Biernacka J, Coombes B, Skime M, Croarkin PE, Oesterle T, Karpyak VM, Li H, Weinshilboum R. Epigenetic regulation of GABA catabolism in iPSC-derived neurons: the molecular links between FGF21 and histone methylation. Mol Metab. 2023 Nov:77:101798.
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22. Li H, Zhang J, Loh YH, Billadeau DD. Editorial: Decoding Immunologic Complex Systems in Cancer: The Cutting-Edge Technologies Revolutionizing Cancer Immunology and Immunotherapy. Front Immunol. 2023 May 4;14:1208589.
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23. van Ree JH, Jeganathan KB, Fierro Velasco RO, Zhang C, Can I, Hamada M, Li H, Baker DJ, van Deursen JM. Hyperphosphorylated PTEN exerts oncogenic properties. Nat Commun. 2023 May 24;14(1):2983
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24. Weiskittel TM, Cao A, Meng-lin K, Lehmann ZJ, Feng B, Correia C, Zhang C, Wisniewski P, Zhu S, Ung CY, Li H. Network biology inspired machine learning features predict cancer gene targets and reveals target coordinating mechanisms. Pharmaceuticals (Basel). 2023 May 16;16(5):752.
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25. Correia C, Maurer M, McDonough S, Schneider P, Ross P, Novak A, Feldman A, Cerhan J, Slager S, Witzig T, Eckloff B, Li H, Nowakowski G, Kaufmann S. Relationship between BCL2 Mutations and Follicular Lymphoma Outcome in the Chemoimmunotherapy Era. Blood Cancer J. 2023 May 17;13(1):81.
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26. Ng PI, Zhang C, Li H, Baker DJ. Senescent microglia represent a subset of disease-associated microglia in P301S mice. J Alzheimers Dis. 2023;95(2):493-507.
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27. Zhang C, Guo Q, Chen L, Wu Z, Yan XJ, Zou C, Zhang Q, Tan J, Fang T, Rao Q, Li Y, Shen S, Deng M, Wang L, Gao H, Yu J, Li H, Zhang C, Nowsheen S, Kloeber J, Zhao F, Yin P, Teng C, Lin Z, Song K, Yao S, Yao L, Wu L, Zhang Y, Cheng X, Gao Q, Yuan J, Lou Z, Zhang JS. . A ribosomal gene panel predicting a novel synthetic lethality in non-BRCAness tumors. Signal Transduct Target Ther. 2023; 8 (1):183.
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28. Ung CY, Correia C, Billadeau DD, Zhu S, Li H. Manifold Epigenetics: A conceptual model that guides engineering strategies to improve whole-body regenerative health. Front Cell Dev Biol. 2023 Feb 14;11:1122422.
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29. Yi Y, Zeng Y, Sam TW, Hamashima K, Tan RJR, Warrier T, Phua JX, Taneja R, Liou YC, Li H, Xu J, Loh YH. Ribosomal proteins regulate 2-cell-stage transcriptome in mouse embryonic stem cells. Stem Cell Reports. 2023 Feb 14; 18 (2):463-474.
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30. Zhang Y, Black KE, Phung TN, Thundivalappil SR, Lin T, Wang W, Xu J, Zhang C, Hariri LP, Lapey A, Li H, Lerou PH, Ai X, Que J, Park JA, Hurley BP, Mou H. Human Airway Basal Cells Undergo Reversible Squamous Differentiation and Reshape Innate Immunity. Am J Respir Cell Mol Biol. 2023 Jun; 68 (6):664-678.
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31. Zhang Y, Lin T, Leung HM, Zhang C, Wilson-Mifsud B, Feldman MB, Puel A, Lanternier F, Couderc LJ, Danion F, Catherinot E, Salvator H, Tcherkian C, Givel C, Xu J, Tearney GJ, Vyas JM, Li H, Hurley BP, Mou H. STAT3 Mutation-Associated Airway Epithelial Defects in Job Syndrome. J Allergy Clin Immunol. 2023 Aug;152(2):538-550..
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32. Sturmlechner I, Sine CC, Jeganathan KB, Zhang C, Fierro Velasco RO, Baker DJ, Li H, van Deursen JM. Senescent cells limit p53 activity via multiple mechanisms to remain viable. Nature Communications. 2022 Jun 28;13(1):3722.
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33. Weiskittel TM, Ung CY, Correia C, Zhang C, Li H. De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens. Genome Research. 2022 Jan; 32 (1):124-134 Epub 2021 Dec 07.
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34. Warrier T, Farran C, Zeng Y, Ho B, Bao Q, Zheng Z, Bi X, Ng HH, Ong D, Chu J, Sanyal A, Fullwood M, Collins JJ, Li H, Xu J, Loh YH. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Nucleic Acids Research. 2022 Jul 1;gkac531.
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35. Zhang C, Correia C, Weiskittel T, Tan SH, Meng-Lin K, Yu GT, Yao J, Yeo KS, Zhu S, Ung CY, Li H. A knowledge-based discovery approach couples' artificial neural networks with weight engineering to uncover immune-related processes underpinning clinical traits of breast cancer. Front Immunol. 2022 Jul 14;13:920669.
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36. Ung CY, Levee TM, Zhang C, Correia C, Yeo KS, Li H, Zhu S. Gene utility recapitulates chromosomal aberrancies in advanced stage neuroblastoma. Comput Struct Biotechnol J. 2022 Jun 20;20:3291-3303.
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37. Nguyen TTL, Gao H, Liu D, Philips TJ, Ye Z, Lee JH, Shi GX, Copenhaver K, Zhang L, Wei L, Yu J, Zhang H, Barath A, Luong M, Zhang C, Gaspar-Maia A, Li H, Wang L, Ordog T, Weinshilboum RM. Glucocorticoids unmask silent non-coding genetic risk variants for common diseases. Nucleic Acids Res. 2022 Nov 18;gkac1045.
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38. Sun Z, Yu H, Zhao J, Tan T, Pan H, Zhu Y, Chen L, Zhang C, Zhang L, Lei A, Xu Y, Bi X, Huang X, Gao B, Wang L, Correia C, Chen M, Sun Q, Feng Y, Shen L, Wu H, Wang J, Shen X, Daley GQ, Li H, Zhang J. LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells. Protein Cell. 2022 Jul; 13 (7):490-512.
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39. Ho MF, Zhang C, Moon I, Zhu X, Coombes BJ, Biernacka J, Skime M, Oesterle TS, Karpyak VM, MD, Schmidt K, Gliske K, Ngo Q, Skillon C, Seppala MD, Li H, Weinshilboum RM. Single cell transcriptomics reveals distinct transcriptional responses to oxycodone and buprenorphine by iPSC-derived brain organoids from patients with opioid use disorder. Molecular Psychiatry. 2022 Oct.
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40. Hogenson TL, Xie H, Phillips WJ, Toruner MD, Li JJ, Horn IP, Kennedy DJ, Almada LL, Marks DL, Carr RM, Toruner M, Sigafoos AN, Koenig-Kappes AN, Olson RL, Tolosa EJ, Zhang C, Li H, Doles JD, Bleeker J, Barrett MT, Boyum JH, Kipp BR, Mahipal A, Hubbard JM, Scheffler Hanson TJ, Petersen GM, Dasari S, Oberg AL, Truty MJ, Graham RP, Levy MJ, Zhu M, Billadeau DD, Adjei AA, Dusetti N, Iovanna JL, Bekaii-Saab TS, Ma WW, Fernandez-Zapico ME. Culture media composition influences patient-derived organoids ability to predict therapeutic response in gastrointestinal cancers. JCI Insight. 2022 Oct 18;e158060.
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41. Li C, Liu Z, Zhang Z, Wang H, Friedman GK, Ding Q, Zhao X, Li H, Kim K, Yu X, Nabors BL, Han X, Zhao R. Generation of chromosome 1p/19q co-deletion by CRISPR/Cas9-guided genomic editing. Neuro-Oncology Advances. 2022 Aug 18;4(1):vdac131.
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42. Ung CY, Weiskittel TM, Correia C, Kaufmann SH, Li H. Manifold Medicine: A Schema that Expands Treatment Dimensionality. Drug Discovery Today. 2022 Jan; 27 (1):8-16 Epub 2021 Sept 29.
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43. Correia C, Weiskittel TM, Ung CY, Villasboas Bisneto JC, Billadeau DD, Kaufmann SH, Li H. Uncovering Pharmacological Opportunities for Cancer Stem Cells - A Systems Biology View. Front Cell Dev Biol. 2022 Mar 11;10:752326.
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44. Sturmlechner I, Zhang C, Sine CC, van Deursen EJ, Jeganathan KB, Hamada N, Grasic J, Friedman D, Stutchman JT, Can I, Hamada M, Lim DY, Lee JH, Ordog T, Laberge RM, Shapiro V, Baker DJ, Li H, van Deursen JM. p21 produces a bioactive secretome that places stressed cells under immunosurveillance. Science. 2021 Oct 29;374(6567):eabb3420.
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45. Gautam P, Hamashima K, Chen Y, Zeng YY, Makovoz B, Parikh BH, Lee HY, Lau KA, Su X, Wong RCB, Chan WK, Li H, Blenkinsop TA, Loh YH. Multi-species single-cell transcriptomic analysis of ocular compartment regulons. Nature Communications. 2021 Sep 28;12(1):5675.
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46. Cheon IS, Li C, Son YM, Goplen NP, Wu Y, Cassmann T, Wang Z, Wei X, Tang J, Li Y, Marlow H, Hughes S, Hammel L, Cox TM, Goddery E, Ayasoufi K, Weiskopf D, Boonyaratanakornkit J, Dong H, Li H, Chakraborty R, Johnson AJ, Edell E, Taylor JJ, Kaplan MH, Sette A, Bartholmai BJ, Kern R, Vassallo R, Sun J. Immune Signatures Underlying Post-acute COVID-19 Lung Sequelae. Science Immunology. 2021 Nov 12;6(65):eabk1741.
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47. Xing QR, El Farran CA, Gautam P, Chuah YS, Warrier T, Toh CXD, Kang NY, Sugii S, Chang YT, Xu J, Collins JJ, Daley GQ, Li H, Zhang LF, Loh YH. Diversification of Reprogramming Trajectories Revealed by Parallel Single-cell Transcriptome and Chromatin Accessibility Sequencing. Science Advances. 2020 Sep 11;6(37):eaba1190.
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48. Xing QR, El Farran CA, Zeng YY, Yi Y, Warrier T, Gautam P, Collins JJ, Xu J, Droge P, Koh CG, Li H, Zhang LF, Loh YH Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility. Genome Research. 2020 Jul;30(7):1027-1039.
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49. Dong Z, Yeo KS, Lopez G, Zhang C, Dankert Eggum E, Rokita JL, Ung CY, Levee T, Her ZP, Howe C, Hou X, van Ree J, Li S, He S, Tao T, Fritchie K, Torres-Mora J, Lehman J, Meves A, Razidlo G, Rathi K, Weroha SJ, Look AT, van Deursen J, Li H, Westendorf J, Maris J, Zhu S. GAS7 Deficiency Promotes Metastasis of MYCN-driven Neuroblastoma. Cancer Research. 2021 Jun 1; 81 (11):2995-3007.
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50. Zhao J, Yao K, Yu H, Zhang L, Xu Y, Chen L, Sun Z, Zhu Y, Zhang C, Qian Y, Ji S, Zhang M, Cheng J, Correia C, Weiskittel T, Lin D, Zhao Y, Chandrasekaran S, Fu X, Zhang D, Fan H, Xie W, Li H, Hu Z, Zhang J. Metabolic remodeling during early murine embryo development. Nature Metabolism. 2021 Oct;3(10):1372-1384.
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51. Childs BG, Zhang C, Shuja F, Sturmlechner I, Trewartha S, Fierro Velasco R, Baker D, Li H, van Deursen JM. Senescent cells suppress innate smooth muscle cell repair functions in atherosclerosis. Nature Aging. 2021 Aug;1(8):698-714.
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52. Jiang L, Lin W, Zhang C, Ash PEA, Verma M, Kwan J, van Vliet E, Yang Z, Lourdes Cruz A, Boudeau S, Maziuk BF, Lei S, Song J, Alvarez VE, Hovde S, Abisambra JF, Kuo MH, Kanaan N, Murray ME, Crary JF, Zhao J, Cheng JX, Petrucelli L, Li H, Emili A, Wolozin B. Interaction of tau with HNRNPA2B1 and N6-methyladenosine RNA mediates the progression of tauopathy. Molecular Cell. 2021 Oct 21;81(20):4209-4227.e12.
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53. Ahn KS, O'Brien DR, Kim YH, Kim TS, Yamada H, Park JW, Park SJ, Kim SH, Zhang C, Li H, Kang KJ, Roberts LR. Associations of Serum Tumor Biomarkers with Integrated Genomic and Clinical Characteristics of Hepatocellular Carcinoma. Liver Cancer 2021 Nov; 10 (6):593-605.
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54. Limzerwala JF, Jeganathan KB, Kloeber JA, Davies BA, Zhang C, Sturmlechner I, Zhong J, Velasco RF, Fields AP, Yuan Y, Baker DJ, Zhou D, Li H, Katzmann DJ, van Deursen JM. FoxM1 insufficiency hyperactivates Ect2-RhoA-mDia1 signaling to drive cancer. Nature Cancer. 2020; 1:1010-1024.
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55. Ding L, Roeck K, Zhang C, Zidek B, Rodman E, Hernandez-Barco Y, Zhang J, Bamlet WR, Oberg A, Zhang L, Bardeesy N, Li H, Billadeau DD. Nuclear GSK-3beta and oncogenic KRas lead to the retention of pancreatic ductal progenitor cells phenotypically similar to those seen in IPMN. Front Cell Dev Biol. 2022 May 13;10:853003.
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56. Wen T, Barham W, Li Y, Zhang H, Gicobi JK, Hirdler JB, Liu X, Ham H, Peterson Martinez KE, Lucien F, Lavoie RR, Li H, Correia C, Monie DD, An Z, Harrington SM, Wu X, Guo R, Dronca RS, Mansfield AS, Yan Y, Markovic SN, Park SS, Sun J, Qin H, Liu MC, Vasmatzis G, Billadeau DD, Dong H. NKG7 is a T-cell intrinsic therapeutic target for improving antitumor cytotoxicity and cancer immunotherapy. Cancer Immunol Res. 2022 Feb;10(2):162-181.
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57. Hurley RM, McGehee CD, Nesic K, Correia C, Weiskittel TM, Kelly RL, Venkatachalam A, Hou X, Pathoulas NM, Meng XW, Kondrashova O, Radke MR, Schneider PA, Flatten KS, Peterson KL, Becker MA, Wong EM, Southey MS, Alexander Dobrovic AD, Lin KK, Thomas C Harding TC, McNeish I, Ross CA, Wagner JM, Wakefield MJ, Scott CL, Haluska P, Wahner Hendrickson AE, Karnitz LM, Swisher EM, Li H, Weroha SJ, Kaufmann SH. Characterization of a RAD51C-Silenced High Grade Serous Ovarian Cancer Model During Development of PARP Inhibitor Resistance. NAR Cancer. 2021 Sep; 3 (3):zcab028.
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58. Ho MF, Zhang C, Moon I, Coombes BJ, Biernacka J, Skime M, Choi DS, Croarkin PE, Frye MA, Ngo Q, Skillon C, Oesterle TS, Karpyak VM, Li H, Weinshilboum RM Plasma TNFSF10 levels associated with acamprosate treatment response in patients with alcohol use disorder. Front Pharmacol. 2022; 13:986238.
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59. Ho MF, Zhang C, Wei L, Zhang L, Moon I, Geske J, Skime M, Choi DS, Biernaka J, Oesterle T, Frye M, Marvin S, Karpyak V, Li H, Weinshilboum R. Genetic Variants Associated with Acamprosate Treatment Response in Alcohol Use Disorder Patients: A Multiple Omics Study. British Journal of Pharmacology. 2022 Jan 11. doi: 10.1111/bph.15795.
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60. Weiskittel TM, Correia C, Yu G, Ung CY, Kaufmann SH, Billadeau DD, Li H. The Trifecta of Single Cell, Systems Biology, and Machine Learning Approaches. Genes (Basel). 2021 Jul 20;12(7):1098.
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61. Ho MF, Zhang C, Moon I, Wei L, Coombes B, Biernacka J, Skime M, Choi DS, Frye M, Schmidt K, Gliske K, Braughton J, Ngo Q, Skillon C, Seppala M, Oesterle T, Karpyak V, Li H, Weinshilboum R. Genome-wide association study for circulating FGF21 in patients with alcohol use disorder: molecular links between the SNHG16 locus and catecholamine metabolism. Molecular Metabolism. 2022 Jun 22;101534.
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62. Monie D, Correia C, Ung CY, Zhang C, Vile R, Li H. Modular network mechanism of CCN1-associated resistance to HSV-1-derived oncolytic immunovirotherapies for glioblastomas. Sci Rep. 2021 May 27;11(1):11198.
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63. Cairns J, Ingle JN, Kalari KR, Goetz MP, Weinshilboum RM, Gao H, Li H, Ghanat Bari M, Wang L. Anastrozole regulates fatty acid synthase in breast cancer. Mol Cancer Ther. 2022 Jan; 21 (1):206-216.
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64. Ding H, Vincelette N, McGehee C, Kohorst M, Koh B, Venkatachalam A, Meng XW, Schneider P, Flatten K, Peterson K, Correia C, Lee SH, Patnaik M, Webster J, Ghiaur G, Smith B, Karp J, Keith Pratz, Li H, Karnitz L, Kaufmann S. CDK2-mediated TNFa Upregulation as a Mechanism of Selective Cytotoxicity in Acute Leukemia. Cancer Research. 2021 May 15; 81 (10):2666-2678.
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65. Meng-Lin K, Ung CY, Weiskittel TM, Chen A, Zhang C, Correia C, Li H. Machine Learning and Systems Biology Approaches to Characterize Dosage-Based Gene Dependencies in Cancer Cells. J Bioinform Syst Biol. 2021; 4 (1): 13-32.
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66. Hamashima K, Gautam P, Lau KA, Khiong CW, Blenkinsop TA, Li H, Loh YH. Potential Modes of COVID-19 Transmission From Human Eye Revealed by Single-cell Atlas. bioRxiv. 2020.05.09.085613.
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67. Crist AM, Hinkle KM, Wang X, Moloney CM, Matchett BJ, Labuzan SA, Frankenhauser I, Azu NO, Liesinger AM, Lesser ER, Serie DJ, Quicksall ZS, Patel TA, Carnwath TP, DeTure M, Tang X, Petersen RC, Duara R, Graff-Radford NR, Allen M, Carrasquillo MM, Li H, Ross OA, Ertekin-Taner N, Dickson DW, Asmann YW, Carter RE, Murray ME. Transcriptomic analysis to identify genes associated with selective hippocampal vulnerability in Alzheimer's disease. Nature Communications. 2021 Apr 19; 12 (1):2311.
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68. Horn IP, Marks DL, Koenig AN, Hogenson TL, Almada LL, Goldstein LE, Romecin Duran PA, Vera R, Vrabel AM, Cui G, Rabe KG, Bamlet WR, Mer G, Sicotte H, Zhang C, Li H, Petersen GM, Fernandez-Zapico ME. A rare germline CDKN2A variant (47T>G; p16-L16R) predisposes carriers to pancreatic cancer by reducing cell cycle inhibition. J Biol Chem. 2021 Apr 3;100634.
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69. Monie DD, Bhandarkar AR, Parney IF, Correia C, Sarkaria JN, Vile RG, Li H. Synthetic and systems biology principles in the design of programmable oncolytic virus immunotherapies for glioblastoma multiforme. Neurosurgical Focus. 2021 Feb;50(2):E10.
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70. Li X, Guo X, Zhu Y, Wei G, Zhang Y, Li Z, Xu H, Cui J, Wu W, He J, Ritchie ME, Weiskittel TM, Li H, Yu H, Ding L, Shao M, Luo Q, Xu X, Teng X, Chang AH, Zhang J, Huang H, Hu Y. Single cell transcriptomic analysis reveals BCMA CAR-T cell dynamics in a patient with refractory primary plasma cell leukemia. Molecular Therapy. 2021 Feb 3; 29 (2):645-657.
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71. Aggen D, Ager C, Obradovic A, Chowdhury N, Ghasemzadeh A, Mao W, Chaimowitz M, Lopez-Bujanda Z, Spina C, Hawley J, Dallos M, Zhang C, Wang V, Li H, Guo X, Drake C. Blocking Interleukin-1 Beta Promotes Tumor Regression and Remodeling of the Myeloid Compartment in a Renal Cell Carcinoma Model: Multi-Dimensional Analyses. Clinical Cancer Research. 2021 Jan 15; 27 (2):608-621.
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155. Ung CY, Lam SH, Zhang X, Li H, Ma J, Zhang L, Li B, Gong Z. Existence of inverted profile in chemically responsive molecular pathways in the zebrafish liver. PLoS One. 2011; 6(11):e27819.
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156. Loh YH, Yang L, Yang JC, Li H, Collins JJ, Daley GQ. Genomic approaches to deconstruct pluripotency. Annual Review of Genomics and Human Genetics. 2011; 12:165-85.
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157. Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell. 2010 Nov 5; 7(5):618-30.
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158. Loh YH, Hartung O, Li H, Guo C, Sahalie JM, Manos PD, Urbach A, Heffner GC, Grskovic M, Vigneault F, Lensch MW, Park IH, Agarwal S, Church GM, Collins JJ, Irion S, Daley GQ. Reprogramming of T cells from human peripheral blood. Cell Stem Cell. 2010 Jul 2; 7(1):15-9.
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159. Rao H, Li Z, Li X, Ma X, Ung C, Li H, Liu X, Chen Y. Identification of small molecule aggregators from large compound libraries by support vector machines. Journal of Computational Chemistry. 2010 Mar; 31(4):752-63.
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160. Li H, Ung CY, Ma XH, Liu XH, Li BW, Low BC, Chen YZ. Pathway sensitivity analysis for detecting pro-proliferation activities of oncogenes and tumor suppressors of epidermal growth factor receptor-extracellular signal-regulated protein kinase pathway at altered protein levels. CANCER. 2009 Sep 15; 115(18):4246-63.
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161. Li H, Ung CY, Ma XH, Li BW, Low BC, Cao ZW, Chen YZ. Simulation of crosstalk between small GTPase RhoA and EGFR-ERK signaling pathway via MEKK1. Bioinformatics. 2009 Feb 1; 25(3):358-64.
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162. Ung CY, Li H, Ma XH, Jia J, Li BW, Low BC, Chen YZ. Simulation of the regulation of EGFR endocytosis and EGFR-ERK signaling by endophilin-mediated RhoA-EGFR crosstalk. FEBS Letters. 2008 Jun 25; 582(15):2283-90.
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163. Li H, Yap CW, Ung CY, Xue Y, Li ZR, Han LY, Lin HH, Chen YZ. Machine learning approaches for predicting compounds that interact with therapeutic and ADMET related proteins. Journal of Pharmaceutical Sciences. 2007 Nov; 96(11):2838-60.
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164. Yap CW, Li H, Ji ZL, Chen YZ. Regression methods for developing QSAR and QSPR models to predict compounds of specific pharmacodynamic, pharmacokinetic and toxicological properties. Mini-Reviews in Medicinal Chemistry. 2007 Nov; 7(11):1097-107.
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165. Li ZR, Han LY, Xue Y, Yap CW, Li H, Jiang L, Chen YZ. MODEL-molecular descriptor lab: a web-based server for computing structural and physicochemical features of compounds. Biotechnology and Bioengineering. 2007 Jun 1; 97(2):389-96.
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166. Ung CY, Li H, Cao ZW, Li YX, Chen YZ. Are herb-pairs of traditional Chinese medicine distinguishable from others? Pattern analysis and artificial intelligence classification study of traditionally defined herbal properties. Journal of Ethnopharmacology. 2007 May 4; 111(2):371-7.
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167. Ung CY, Li H, Kong CY, Wang JF, Chen YZ. Usefulness of traditionally defined herbal properties for distinguishing prescriptions of traditional Chinese medicine from non-prescription recipes. Journal of Ethnopharmacology. 2007 Jan 3; 109(1):21-8.
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168. Ung CY, Li H, Yap CW, Chen YZ. In silico prediction of pregnane X receptor activators by machine learning approaches. Molecular Pharmacology. 2007 Jan; 71(1):158-68.
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169. Chen X, Li H, Yap CW, Ung CY, Jiang L, Cao ZW, Li YX, Chen YZ. Computer prediction of cardiovascular and hematological agents by statistical learning methods. Cardiovascular and Hematological Agents in Medicinal Chemistry. 2007 Jan; 5(1):11-9.
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170. Cui J, Han LY, Li H, Ung CY, Tang ZQ, Zheng CJ, Cao ZW, Chen YZ. Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties. Molecular Immunology. 2007 Jan; 44(4):514-20.
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171. Chen X, Zhou H, Liu YB, Wang JF, Li H, Ung CY, Han LY, Cao ZW, Chen YZ. Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation. British Journal of Pharmacology. 2006 Dec; 149(8):1092-103.
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172. Li H, Ung CY, Yap CW, Xue Y, Li ZR, Chen YZ. Prediction of estrogen receptor agonists and characterization of associated molecular descriptors by statistical learning methods. Journal of Molecular Graphics and Modelling. 2006 Nov; 25(3):313-23.
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173. Xue Y, Li H, Ung CY, Yap CW, Chen YZ. Classification of a diverse set of Tetrahymena pyriformis toxicity chemical compounds from molecular descriptors by statistical learning methods. Chemical Research in Toxicology. 2006 Aug; 19(8):1030-9.
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174. Yap CW, Xue Y, Li H, Li ZR, Ung CY, Han LY, Zheng CJ, Cao ZW, Chen YZ. Prediction of compounds with specific pharmacodynamic, pharmacokinetic or toxicological property by statistical learning methods. Mini-Reviews in Medicinal Chemistry. 2006 Apr; 6(4):449-59.
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175. Zheng CJ, Han LY, Chen X, Cao ZW, Cui J, Lin HH, Zhang HL, Li H, Chen YZ. Information of ADME-associated proteins and potential application for pharmacogenetic prediction of drug responses. Current Pharmacogenomics and Personalized Medicine. 2006; 4(2):79-85.
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176. Li H, Yap CW, Xue Y, Li ZR, Ung CY, Han LY, Chen YZ. Statistical Learning Approach for Predicting Specific Pharmacodynamic, Pharmacokinetic or Toxicological Properties of Pharmaceutical Agents. Drug Development Research. 2006; 66(4):245-59.
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177. Han LY, Zheng CJ, Lin HH, Cui J, Li H, Zhang HL, Tang ZQ, Chen YZ. Prediction of functional class of novel plant proteins by a statistical learning method. New Phytologist. 2005 Oct; 168(1):109-21.
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178. Li H, Yap CW, Ung CY, Xue Y, Cao ZW, Chen YZ. Effect of selection of molecular descriptors on the prediction of blood-brain barrier penetrating and nonpenetrating agents by statistical learning methods. Journal of Chemical Information and Modeling. 2005 Sep-Oct; 45(5):1376-84.
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179. Li H, Ung CY, Yap CW, Xue Y, Li ZR, Cao ZW, Chen YZ. Prediction of genotoxicity of chemical compounds by statistical learning methods. Chemical Research in Toxicology. 2005 Jun; 18(6):1071-80.
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Book Chapters

1. Chen YZ, Yap CW, Li H. Chapter 8 Current QSAR Techniques for Toxicology. Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals. Ekins S. (Editor), John Wiley and Sons, 2007.
   
2. Chen YZ, Yap CW, Li H. Chapter 2 Protein Crystallography, Drug Design and Virtual Screening. Technology Platforms for New Drug Discovery and Development. Li QX (Editor), Higher Education Press, 2007.