Publications

All Publications

$ corresponding author; * co-first author

  • [221] DeepCG: A cell graph model for predicting prognosis in lung adenocarcinoma. Zhang B, Li C, Wu J, Zhang J and Cheng C$. Int J Cancer. 2024 Mar 1. doi: 10.1002/ijc.34901. [Pubmed]
  • [220] Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies. Li Y, Xiao X, Li J, Han Y, Cheng C, Fernandes GF, Slewitzke SE, Rosenberg SM, Zhu M, Byun J, Bosse Y, McKay JD, Albanes D, Lam S, Tardon A, Chen C, Bojesen SE, Landi MT, Johansson M, Risch A, Bickeboller H, Wichmann HE, Christiani DC, Rennert G, Arnold SM, Goodman GE, Field JK, Davies MPA, Shete S, Marchand LL, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Sun R, Zienolddiny S, Grankvist K, Johansson M, Caporaso NE, Cox A, Hong YC, Lazarus P, Schabath MB, Aldrich MC, Schwartz AG, Gorlov I, Purrington KS, Yang P, Liu Y, Bailey-Wilson JE, Pinney SM, Mandal D, Willey JC, Gaba C, Brennan P, Xia J, Shen H and Amos CI. Cancer Epidemiol Biomarkers Prev. 2024 Mar 1;33(3):389-399. doi:. [Pubmed]
  • [219] Clonal gene signatures predict prognosis in mesothelioma and lung adenocarcinoma. Lin Y, Burt BM, Lee HS, Nguyen TT, Jang HJ, Lee C, Hong W, Ripley RT, Amos CI$ and Cheng C$. NPJ Precis Oncol. 2024 Feb 23;8(1):47. doi: 10.1038/s41698-024-00531-y. [Pubmed]
  • [218] Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Han J, Dong Y, Zhu X, Reuben A, Zhang J, Xu J, Bai H, Duan J, Wan R, Zhao J, Bai J, Xia X, Yi X, Cheng C$, Wang J$ and Wang Z$. Nat Commun. 2024 Feb 8;15(1):1199. doi: 10.1038/s41467-024-45361-5. [Pubmed]
  • [217] UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors. Yang D, Geng T, Harrison AG, Cahoon JG, Xing J, Jiao B, Wang M, Cheng C, Hill RE, Wang H, Vella AT, Cheng G, Wang Y and Wang P. Nat Commun. 2024 Jan 26;15(1):780. doi: 10.1038/s41467-024-45141-1. [Pubmed]
  • [216] TimiGP: An R package to depict the tumor microenvironment from bulk transcriptomics. Li C, Zhang J and Cheng C$. STAR Protoc. 2023 Nov 27;4(4):102742. doi: 10.1016/j.xpro.2023.102742. [Pubmed]
  • [215] Focalizing regions of biomarker relevance facilitates biomarker prediction on histopathological images. Gan J, Wang H, Yu H, He Z, Zhang W, Ma K, Zhu L, Bai Y, Zhou Z, Yullie A, Bai X, Wang M, Yang D, Chen Y, Chen G, Lasenby J, Cheng C, Wu J, Zhang J, Wang X, Chen Y, Wang G and Xia T. iScience. 2023 Jun 29;26(10):107243. doi: 10.1016/j.isci.2023.107243. eCollection. [Pubmed]
  • [214] TimiGP: Inferring cell-cell interactions and prognostic associations in the tumor immune microenvironment through gene pairs. Li C, Zhang B, Schaafsma E, Reuben A, Wang L, Turk MJ, Zhang J$ and Cheng C$. Cell Rep Med. 2023 Jul 18;4(7):101121. doi: 10.1016/j.xcrm.2023.101121. [Pubmed]
  • [213] Predicting benefit from immune checkpoint inhibitors in patients with non-small-cell lung cancer by CT-based ensemble deep learning: a retrospective study. Saad MB, Hong L, Aminu M, Vokes NI, Chen P, Salehjahromi M, Qin K, Sujit SJ, Lu X, Young E, Al-Tashi Q, Qureshi R, Wu CC, Carter BW, Lin SH, Lee PP, Gandhi S, Chang JY, Li R, Gensheimer MF, Wakelee HA, Neal JW, Lee HS, Cheng C, Velcheti V, Lou Y, Petranovic M, Rinsurongkawong W, Le X, Rinsurongkawong V, Spelman A, Elamin YY, Negrao MV, Skoulidis F, Gay CM, Cascone T, Antonoff MB, Sepesi B, Lewis J, Wistuba II, Hazle JD, Chung C, Jaffray D, Gibbons DL, Vaporciyan A, Lee JJ, Heymach JV, Zhang J and Wu J. Lancet Digit Health. 2023 Jul;5(7):e404-e420. doi: 10.1016/S2589-7500(23)00082-1.. [Pubmed]
  • [212] Predicting Chemotherapy Benefit across Different Races in Early-Stage Breast Cancer Patients Using the Oncotype DX Score. Shaw VR, Amos CI and Cheng C$. Cancers (Basel). 2023 Jun 16;15(12):3217. doi: 10.3390/cancers15123217. [Pubmed]
  • [211] The ratio of intratumour to stromal infiltrating lymphocytes better predicts prognosis in breast cancer. Zhang B, Wang X and Cheng C$. Clin Transl Med. 2023 May;13(5):e1265. doi: 10.1002/ctm2.1265. [Pubmed]
  • [210] Mosaic chromosomal alterations is associated with increased lung cancer risk: insight from the INTEGRAL-ILCCO cohort analysis. Cheng C$, Hong W, Li Y, Xiao X, McKay J, Han Y, Byun J, Peng B, Albanes D, Lam S, Tardon A, Chen C, Bojesen SE, Landi MT, Johansson M, Risch A, Bickeboller H, Wichmann HE, Christiani DC, Rennert G, Arnold S, Goodman G, Field JK, Davies MP, Shete SS, Le Marchand L, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Zhu M, Shen H, Zienolddiny S, Grankvist K, Johansson M, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Brennan P, Li Y, Gorlova O, Gorlov I and Amos CI. J Thorac Oncol. 2023 May 5:S1556-0864(23)00527-0. doi:. [Pubmed]
  • [209] Immune infiltration in tumor and adjacent non-neoplastic regions co-determines patient clinical outcomes in early-stage lung cancer. Cheng C$, Nguyen TT, Tang M, Wang X, Jiang C, Liu Y, Gorlov I, Gorlova O, Iafrate J, Lanuti M, Christiani DC and Amos CI. J Thorac Oncol. 2023 May 3:S1556-0864(23)00526-9. doi:. [Pubmed]
  • [208] Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20. Preiss NK, Kamal Y, Wilkins OM, Li C, Kolling FW 4th, Trask HW, Usherwood YK, Cheng C$, Frost HR and Usherwood EJ. Life Sci Alliance. 2023 Jul 6;6(9):e202201683. doi: 10.26508/lsa.202201683. Print. [Pubmed]
  • [207] Methylation of nonessential genes in cutaneous melanoma - Rule Out hypothesis. Gorlov IP, Conway K, Edmiston SN, Parrish EA, Hao H, Amos CI, Tsavachidis S, Gorlova OY, Begg C, Hernando E, Cheng C$, Shen R, Orlow I, Luo L, Ernstoff MS, Kuan PF, Ollila DW, Tsai YS, Berwick M and Thomas NE. Melanoma Res. 2023 Jun 1;33(3):163-172. doi: 10.1097/CMR.0000000000000881. Epub. [Pubmed]
  • [206] T-Cell Receptor Optimization with Reinforcement Learning and Mutation Polices for Precision Immunotherapy. Chen Z, Min R, Guo H, Cheng C, Clancy T, Ning X. Research in Computational Molecular Biology: 27th Annual International Conference, RECOMB 2023, Istanbul, Turkey, April 16–19, 2023, Proceedings Apr 2023 Pages 174–191. [Link]
  • [205] Pathway-driven rare germline variants associated with transplant-associated thrombotic microangiopathy (TA-TMA). Zhang Z, Hong W, Wu Q, Tsavachidis S, Li JR, Amos CI, Cheng C$, Sartain SE, Afshar-Kharghan V, Dong JF, Bhatraju P, Martin PJ, Makar RS, Bendapudi PK and Li A. Thromb Res. 2023 May;225:39-46. doi: 10.1016/j.thromres.2023.03.001. Epub 2023. [Pubmed]
  • [204] Prognostic landscape of mitochondrial genome in myelodysplastic syndrome after stem-cell transplantation. Dong J, Buradagunta CS, Zhang T, Spellman S, Bolon YT, DeZern AE, Gadalla SM, Deeg HJ, Nazha A, Cutler C, Cheng C, Urrutia R, Auer P and Saber W. J Hematol Oncol. 2023 Mar 10;16(1):21. doi: 10.1186/s13045-023-01418-4. [Pubmed]
  • [203] Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins. Hong W, Zhao Y, Weng YL and Cheng C$. iScience. 2023 Feb 20;26(3):106250. doi: 10.1016/j.isci.2023.106250. eCollection. [Pubmed]
  • [202] Binding peptide generation for MHC Class I proteins with deep reinforcement learning. Chen Z, Zhang B, Guo H, Emani P, Clancy T, Jiang C, Gerstein M, Ning X, Cheng C$ and Min MR$. Bioinformatics. 2023 Feb 3;39(2):btad055. doi: 10.1093/bioinformatics/btad055. [Pubmed]
  • [201] A refined use of mutations to guide immunotherapy decisions. Cheng C and Amos CI. Nature. 2022 Dec;612(7941):639-641. doi: 10.1038/d41586-022-04448-z. [Pubmed]
  • [200] VISTA Targeting of T-cell Quiescence and Myeloid Suppression Overcomes Adaptive Resistance. Schaafsma E, Croteau W, ElTanbouly M, Nowak EC, Smits NC, Deng J, Sarde A, Webber CA, Rabadi D, Cheng C, Noelle R and Lines JL$. Cancer Immunol Res. 2023 Jan 3;11(1):38-55. doi: 10.1158/2326-6066.CIR-22-0116. [Pubmed]
  • [199] Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Wolf BK, Zhao Y, McCray A, Hawk WH, Deary LT, Sugiarto NW, LaCroix IS, Gerber SA, Cheng C$ and Wang X$. Nat Struct Mol Biol. 2023 Jan;30(1):10-21. doi: 10.1038/s41594-022-00880-x. Epub. [Pubmed]
  • [198] PD-L1 translocation to the plasma membrane enables tumor immune evasion through MIB2 ubiquitination. Yu X, Li W, Liu H, Wang X, Coarfa C, Cheng C, Yu X, Zeng Z, Cao Y, Young KH and Li Y. J Clin Invest. 2023 Feb 1;133(3):e160456. doi: 10.1172/JCI160456. [Pubmed]
  • [197] Microglia-Based Gene Expression Signature Highly Associated with Prognosis in Low-Grade Glioma. Schaafsma E, Jiang C, Nguyen T, Zhu K and Cheng C$. Cancers (Basel). 2022 Sep 30;14(19):4802. doi: 10.3390/cancers14194802. [Pubmed]
  • [196] Immune checkpoint gene VSIR predicts patient prognosis in acute myeloid leukemia and myelodysplastic syndromes. Yao K, Zhou E, Schaafsma E, Zhang B and Cheng C$. Cancer Med. 2022 Nov 16. doi: 10.1002/cam4.5409. [Pubmed]
  • [195] A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis. Feng X, Zhang X, Jiang S, Tang Y, Cheng C, Krishna PA, Wang X, Dai J, Zeng J, Xia T and Zhao D. Comput Struct Biotechnol J. 2022;20:5193-5202. doi: 10.1016/j.csbj.2022.08.044. [Pubmed]
  • [194] A combination of intrinsic and extrinsic features improves prognostic prediction in malignant pleural mesothelioma. Nguyen TT, Lee HS, Burt BM, Amos CI and Cheng C$. Br J Cancer. 2022 Aug 23. pii: 10.1038/s41416-022-01950-z. doi:. [Pubmed]
  • [193] High-throughput proteomics: a methodological mini-review. Cui M, Cheng C$ and Zhang L$. Lab Invest. 2022 Aug 3. pii: 10.1038/s41374-022-00830-7. doi:. [Pubmed]
  • [192] Structure Detection in Three-Dimensional Cellular Cryoelectron Tomograms by Reconstructing Two-Dimensional Annotated Tilt Series. Zeng X, Lin Z, Uddin MR, Zhou B, Cheng C, Zhang J, Freyberg Z and Xu M. J Comput Biol. 2022 Aug;29(8):932-941. doi: 10.1089/cmb.2021.0606. Epub 2022 Jul. [Pubmed]
  • [191] Patient-derived micro-organospheres enable clinical precision oncology. Ding S, Hsu C, Wang Z, Natesh NR, Millen R, Negrete M, Giroux N, Rivera GO, Dohlman A, Bose S, Rotstein T, Spiller K, Yeung A, Sun Z, Jiang C, Xi R, Wilkin B, Randon PM, Williamson I, Nelson DA, Delubac D, Oh S, Rupprecht G, Isaacs J, Jia J, Cheng C, Shen JP, Kopetz S, McCall S, Smith A, Gjorevski N, Walz AC, Antonia S, Marrer-Berger E, Clevers H, Hsu D, Shen X. Cell Stem Cell. 2022 Jun 2;29(6):905-917.e6. doi: 10.1016/j.stem.2022.04.006. Epub 2022 May 3. [Pubmed]
  • [190] The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract. Zhou Y, Gu B, Brichant G, Singh JP, Yang H, Chang H, Zhao Y, Cheng C, Liu ZW, Alderman MH 3rd, Lu L, Yang X, Gao XB, Taylor HS. BMC Biol. 2022 May 2;20(1):93. doi: 10.1186/s12915-022-01293-4. [Pubmed]
  • [189] Abnormal global alternative RNA splicing in COVID-19 patients. Wang C, Chen L, Chen Y, Jia W, Cai X, Liu Y, Ji F, Xiong P, Liang A, Liu R, Guan Y, Cheng Z, Weng Y, Wang W, Duan Y, Kuang D, Xu S, Cai H, Xia Q, Yang D, Wang MW, Yang X, Zhang J, Cheng C, Liu L, Liu Z, Liang R, Wang G, Li Z, Xia H, Xia T. PLoS Genet. 2022 Apr;18(4):e1010137. doi: 10.1371/journal.pgen.1010137. [Pubmed]
  • [188] Genetic variants associated mRNA stability in lung. Li JR, Tang M, Li Y, Amos CI and Cheng C$. BMC Genomics. 2022 Mar 11;23(1):196. doi: 10.1186/s12864-022-08405-y. [Pubmed]
  • [187] Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer. Yao K, Schaafsma E, Zhang B and Cheng C$. PLoS Comput Biol. 2022 Mar 9;18(3):e1009495. doi: 10.1371/journal.pcbi.1009495. [Pubmed]
  • [186] Deep-Precognitive Diagnosis: Preventing Future Pandemics by Novel Disease Detection with Biologicallyinspired Conv-Fuzzy Network. Chharia A, Upadhyay R, Kumar V, Cheng C, Zhang J, Wang T and Xu M IEEE Access. 2022 February 21. DOI: 10.1109/ACCESS.2022.3153059. [Link]
  • [185] Influence of T Cell-Mediated Immune Surveillance on Somatic Mutation Occurrences in Melanoma. Jiang C, Schaafsma E, Hong W, Zhao Y, Zhu K, Chao C and Cheng C$. Front Immunol. 2022 Jan 17;12:703821. doi: 10.3389/fimmu.2021.703821. eCollection. [Pubmed]
  • [184] Genome-wide interaction analysis identified low-frequency variants with sex disparity in lung cancer risk. Li Y, Xiao X, Li J, Byun J, Cheng C, Bosse Y, McKay J, Albanes D, Lam S, Tardon A, Chen C, Bojesen SE, Landi MT, Johansson M, Risch A, Bickeboller H, Wichmann HE, Christiani DC, Rennert G, Arnold S, Goodman G, Field JK, Davies MPA, Shete SS, Le Marchand L, Melander O, Brunnstrom H, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Shen H, Sun R, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Teare DM, Hong YC, Lazarus P, Schabath MB, Aldrich MC, Schwartz AG, Gorlov I, Purrington K, Yang P, Liu Y, Han Y, Bailey-Wilson JE, Pinney SM, Mandal D, Willey JC, Gaba C, Brennan P and Amos CI. Hum Mol Genet. 2022 Feb 9. pii: 6524820. doi: 10.1093/hmg/ddac030. [Pubmed]
  • [183] A framework to predict the applicability of Oncotype DX, MammaPrint, and E2F4 gene signatures for improving breast cancer prognostic prediction. Yao K, Tong CY and Cheng C$. Sci Rep. 2022 Feb 9;12(1):2211. doi: 10.1038/s41598-022-06230-7. [Pubmed]
  • [182] Clonal Hematopoiesis Mutations in Patients with Lung Cancer Are Associated with Lung Cancer Risk Factors. Hong W, Li A, Liu Y, Xiao X, Christiani DC, Hung RJ, McKay J, Field J, Amos CI and Cheng C$. Cancer Res. 2022 Jan 15;82(2):199-209. doi: 10.1158/0008-5472.CAN-21-1903. Epub. [Pubmed]
  • [181] A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma. Nguyen TT, Lee HS, Burt BM, Wu J, Zhang J, Amos CI and Cheng C$. Genome Med. 2022 Jan 12;14(1):5. doi: 10.1186/s13073-021-01010-w. [Pubmed]
  • [180] Immune infiltration difference between tumor and adjacent normal regions is prognostic for gastric cancer patients. Zhang B, Yao K and Cheng C$. Clinical and Translational Discovery. 2022 In press [Pubmed]
  • [179] Predicting clinical outcomes of cancer patients with a p53 deficiency gene signature. Schaafsma E, Takacs EM, Kaur S, Cheng C$ and Kurokawa M$. Sci Rep. 2022 Jan 25;12(1):1317. doi: 10.1038/s41598-022-05243-6. [Pubmed]
  • [178] Han J, Zhao Y, Shirai K, Molodtsov A, Kolling FW, Fisher JL, Zhang P, Yan S, Searles TG, Bader JM, Gui J, Cheng C, Ernstoff MS, Turk MJ and Angeles CV. Nat Cancer. 2021 Mar;2(3):300-311. doi: 10.1038/s43018-021-00180-1. [Pubmed]
  • [177] A B-Raf V600E gene signature for melanoma predicts prognosis and reveals sensitivity to targeted therapies. Yao K, Zhou E and Cheng C$. Cancer Med. 2022 Jan 19. doi: 10.1002/cam4.4491. [Pubmed]
  • [176] Computational modeling of chromatin accessibility identified important epigenomic regulators. Zhao Y, Dong Y, Hong W, Jiang C, Yao K and Cheng C$. BMC Genomics. 2022 Jan 8;23(1):19. doi: 10.1186/s12864-021-08234-5. [Pubmed]
  • [175] A network-based integration for understanding racial disparity in prostate cancer. Zhang B, Yao K and Cheng C$. Transl Oncol. 2022 Jan 5;17:101327. doi: 10.1016/j.tranon.2021.101327. [Pubmed]
  • [174] Artificial intelligence, machine learning, and deep learning for clinical outcome prediction. Pettit RW, Fullem R, Cheng C and Amos CI$. Emerg Top Life Sci. 2021 Dec 20. pii: 230519. doi: 10.1042/ETLS20210246. [Pubmed]
  • [173] The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics. Tang M, Abbas HA, Negrao MV, Ramineni M, Hu X, Hubert SM, Fujimoto J, Reuben A, Varghese S, Zhang J, Li J, Chow CW, Mao X, Song X, Lee WC, Wu J, Little L, Gumbs C, Behrens C, Moran C, Weissferdt A, Lee JJ, Sepesi B, Swisher S, Cheng C, Kurie J, Gibbons D, Heymach JV, Wistuba II, Futreal PA, Kalhor N and Zhang J. Nat Commun. 2021 Dec 6;12(1):7081. doi: 10.1038/s41467-021-27341-1. [Pubmed]
  • [172] Deep Learning Predicts EBV Status in Gastric Cancer Based on Spatial Patterns of Lymphocyte Infiltration. Zhang B, Yao K, Xu M, Wu J and Cheng C$. Cancers (Basel). 2021 Nov 29;13(23). pii: cancers13236002. doi:. [Pubmed]
  • [171] Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer. Chen M, Chen R, Jin Y, Li J, Hu X, Zhang J, Fujimoto J, Hubert SM, Gay CM, Zhu B, Tian Y, McGranahan N, Lee WC, George J, Hu X, Chen Y, Wu M, Behrens C, Chow CW, Pham HHN, Fukuoka J, Wu J, Parra ER, Little LD, Gumbs C, Song X, Wu CJ, Diao L, Wang Q, Cardnell R, Zhang J, Wang J, Le X, Gibbons DL, Heymach JV, Jack Lee J, William WN Jr, Cheng C, Glisson B, Wistuba I, Andrew Futreal P, Thomas RK, Reuben A, Byers LA and Zhang J. Nat Commun. 2021 Nov 17;12(1):6655. doi: 10.1038/s41467-021-26821-8. [Pubmed]
  • [170] B cell infiltration is highly associated with prognosis and an immune-infiltrated tumor microenvironment in neuroblastoma. Schaafsma E, Jiang C and Cheng C$. J Cancer Metastasis Treat. 2021;7(34). doi: 10.20517/2394-4722.2021.72. Epub 2021. [Pubmed]
  • [169] 9p21 loss confers a cold tumor immune microenvironment and primary resistance to immune checkpoint therapy. Han G, Yang G, Hao D, Lu Y, Thein K, Simpson BS, Chen J, Sun R, Alhalabi O, Wang R, Dang M, Dai E, Zhang S, Nie F, Zhao S, Guo C, Hamza A, Czerniak B, Cheng C, Siefker-Radtke A, Bhat K, Futreal A, Peng G, Wargo J, Peng W, Kadara H, Ajani J, Swanton C, Litchfield K, Ahnert JR, Gao J and Wang L. Nat Commun. 2021 Sep 23;12(1):5606. doi: 10.1038/s41467-021-25894-9. [Pubmed]
  • [168] Multimetric feature selection for analyzing multicategory outcomes of colorectal cancer: random forest and multinomial logistic regression models. Feng CH, Disis ML, Cheng C and Zhang L. Lab Invest. 2021 Sep 18. pii: 10.1038/s41374-021-00662-x. doi:. [Pubmed]
  • [167] SARS-CoV-2 Impairs Dendritic Cells and Regulates DC-SIGN Gene Expression in Tissues. Cai G, Du M, Bosse Y, Albrecht H, Qin F, Luo X, Androulakis XM, Cheng C, Nagarkatti M, Nagarkatti P, Christiani DC, Whitfield ML, Amos CI and Xiao F. Int J Mol Sci. 2021 Aug 26;22(17). pii: ijms22179228. doi: 10.3390/ijms22179228. [Pubmed]
  • [166] Resident memory CD8(+) T cells in regional lymph nodes mediate immunity to metastatic melanoma. Molodtsov AK, Khatwani N, Vella JL, Lewis KA, Zhao Y, Han J, Sullivan DE, Searles TG, Preiss NK, Shabaneh TB, Zhang P, Hawkes AR, Malik BT, Kolling FW 4th, Usherwood EJ, Wong SL, Phillips JD, Shirai K, Angeles CV, Yan S, Curiel TJ, Huang YH, Cheng C$ and Turk MJ$. Immunity. 2021 Sep 14;54(9):2117-2132.e7. doi: 10.1016/j.immuni.2021.08.019. [Pubmed]
  • [165] Pan-cancer association of HLA gene expression with cancer prognosis and immunotherapy efficacy. Schaafsma E, Fugle CM, Wang X and Cheng C$. Br J Cancer. 2021 Aug;125(3):422-432. doi: 10.1038/s41416-021-01400-2. Epub 2021. [Pubmed]
  • [164] Impact of Oncotype DX testing on ER+ breast cancer treatment and survival in the first decade of use. Schaafsma E, Zhang B, Schaafsma M, Tong CY, Zhang L and Cheng C$. Breast Cancer Res. 2021 Jul 17;23(1):74. doi: 10.1186/s13058-021-01453-4. [Pubmed]
  • [163] AutoEncoder-Based Computational Framework for Tumor Microenvironment Decomposition and Biomarker Identification in Metastatic Melanoma. Zhao Y, Dong Y, Sun Y and Cheng C$. Front Genet. 2021 May 27;12:665065. doi: 10.3389/fgene.2021.665065. eCollection. [Pubmed]
  • [162] Chr20q amplification defines a distinct molecular subtype of microsatellite stable colorectal cancer. Zhang B, Yao K, Zhou E, Zhang L and Cheng C$. Cancer Res. 2021 Feb 22;canres.4009.2020. [Pubmed]
  • [161] VISTA: A Target to Manage the Innate Cytokine Storm. ElTanbouly MA, Zhao Y, Schaafsma E, Burns CM, Mabaera R, Cheng C$ and Noelle RJ$. Front Immunol. 2021 Feb 11;11:595950. [Pubmed]
  • [160] Rare deleterious germline variants and risk of lung cancer. Liu Y, Xia J, McKay J, Tsavachidis S, Xiao X, Spitz MR, Cheng C, Byun J, Hong W, Li Y, Zhu D, Song Z, Rosenberg SM, Scheurer ME, Kheradmand F, Pikielny CW, Lusk CM, Schwartz AG, Wistuba, II, Cho MH, Silverman EK, Bailey-Wilson J, Pinney SM, Anderson M, Kupert E, Gaba C, Mandal D, You M, de Andrade M, Yang P, Liloglou T, Davies MPA, Lissowska J, Swiatkowska B, Zaridze D, Mukeria A, Janout V, Holcatova I, Mates D, Stojsic J, Scelo G, Brennan P, Liu G, Field JK, Hung RJ, Christiani DC, Amos CI. NPJ Precis Oncol. 2021 Feb 16;5(1):12. [Pubmed]
  • [159] Performance and efficiency of machine learning algorithms for analyzing rectangular biomedical data. Deng F, Huang J, Yuan X, Cheng C, Zhang L. Lab Invest. 2021 Apr;101(4):430-441. [Pubmed]
  • [158] A TMPRSS2-ERG gene signature predicts prognosis of patients with prostate adenocarcinoma. Zhou E, Zhang B, Zhu K, Schaafsma E, Kumar RD, and Cheng C$. Clin Transl Med. 2020 Dec;10(8):e216. [Pubmed]
  • [157] MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers. Schaafsma E, Zhao Y, Zhang L, Li Y, and Cheng C$. Mol Cancer Res. Mar;19(3):414-428 [Pubmed]
  • [156] Human genes differ by their UV sensitivity estimated through analysis of UV-induced silent mutations in melanoma. Gorlov IP, Amos CI, Tsavachidis S, Begg C, Hernando, E, Cheng C, Shen R, Orlow I, Luo L, Ernstoff MS, Parker J, Thomas NE, Gorlova OY and Berwick M. Hum Mutat.. 2020 Jul 9. [Pubmed]
  • [155] Transcriptional and proteomic insights into the host response in fatal COVID-19 cases. Wu M, Chen Y, Xia H, Wang C, Tan CY, Cai X, Liu Y, Ji F, Xiong P, Liu R, Guan Y, Duan Y, Kuang D, Xu S, Cai H, Xia Q, Yang, D, Wang MW, Chiu IM, Cheng C, Ahern PP, Liu L, Wang G, Surana NK, Xia T and Kasper DL. Proc Natl Acad Sci U S A. 2020 Oct 20. [Pubmed]
  • [154] A unified framework for integrative study of heterogeneous gene regulatory mechanisms. Cao Q, Zhang Z, Fu AX, Wu Q, Lee TL, Lo E, Cheng A, Cheng C, Leung D, Yip KY. Nature Machine Intelligence. 2020 July 27. 2:447–456. [Link]
  • [153] An integrative ENCODE resource for cancer genomics. Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci, A, Yan KK, Sethi A, Gursoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP and Gerstein M. Nat Commun. 2020 Jul 29; 11(1): 3696. [Pubmed]
  • [152] Gene signature-based prediction of triple-negative breast cancer patient response to Neoadjuvant chemotherapy. Zhao Y, Schaafsma E and Cheng C$. Cancer Med. 2020 Jul 21. [Pubmed]
  • [151] Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders. Pang K, Wang L, Wang W, Zhou J, Cheng C, Han K, Zoghbi HY and Liu Z. Genome Res. 2020 Jun; 30(6): 835-848. [Pubmed]
  • [150] An EGFR signature predicts cell line and patient sensitivity to multiple tyrosine kinase inhibitors. Cheng C$, Zhao Y, Schaafsma E, Weng YL and Amos C. Int J Cancer. 2020 May 14. [Pubmed]
  • [149] A gene expression-based immune signature for lung adenocarcinoma prognosis. Wang L, Luo X, Cheng C, Amos CI, Cai G and Xiao F. Cancer Immunol Immunother. 2020 Sep; 69(9): 1881-1890. [Pubmed]
  • [148] Whole transcriptome signature for prognostic prediction (WTSPP): application of whole transcriptome signature for prognostic prediction in cancer. Schaafsma E, Zhao Y, Wang Y, Varn FS, Zhu K, Yang H and Cheng C$. Lab Invest. 2020 Oct; 100(10): 1356-1366. [Pubmed]
  • [147] Gene signatures associated with genomic aberrations predict prognosis in neuroblastoma. He X, Qin C, Zhao Y, Zou L, Zhao H and Cheng C$. Cancer Commun (Lond). 2020 Mar; 40(2-3): 105-118. [Pubmed]
  • [146] VISTA is a checkpoint regulator for naïve T cell quiescence and peripheral tolerance. Eltanbouly MA, Zhao Y, Nowak E, Li J, Schaafsma E, Le Mercier I, Ceeraz S, Lines JL, Peng C, Carriere C, Huang X, Day M, Koehn B, Lee SW, Silva Morales M, Hogquist KA, Jameson SC, Mueller D, Rothstein J, Blazar BR, Cheng C$, Noelle R$. Science. 2020 Jan 17;367(6475). doi: 10.1126/science.aay0524. [Pubmed]
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  • [142] CD36-Mediated Metabolic Rewiring of Breast Cancer Cells Promotes Resistance to HER2-Targeted Therapies. Feng WW, Wilkins O, Bang S, Ung M, Li J, An J, Del Genio C, Canfield K, DiRenzo J, Wells W, Gaur A, Robey RB, Guo JY, Powles RL, Sotiriou C, Pusztai L, Febbraio M, Cheng C, Kinlaw WB, Kurokawa M. Cell Rep. 2019 Dec 10;29(11):3405-3420.e5. doi: 10.1016/j.celrep.2019.11.008. [Pubmed]
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  • [140] H22954, a novel long non-coding RNA down-regulated in AML, inhibits cancer growth in a BCL-2-dependent mechanism. Qi X, Jiao Y, Cheng C, Qian F, Chen Z, Wu Q. Cancer Lett. 2019 Jul 10;454:26-36. doi: 10.1016/j.canlet.2019.03.055. [Pubmed]
  • [139] A Novel putative drugs and key initiating genes for neurodegenerative disease determined using network-based genetic integrative analysis. Mortezaei Z, Cazier JB, Mehrabi AA, Cheng C, Masoudi-Nejad A$. J Cell Biochem.. 2019 Apr;120(4):5459-5471. doi: 10.1002/jcb.27825. [Pubmed]
  • [138] Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells. Zhao Y, Carter R, Natarajan S, Varn FS, Compton DA, Gawad C, Cheng C$, Godek KM$. J BMC Med Genomics. 2019 May 31;12(1):79. doi: 10.1186/s12920-019-0532-5. [Pubmed]
  • [137] A transcriptionally-definable subgroup of triple-negative breast and ovarian cancer samples shows sensitivity to HSP90 inhibition. Shee K, Wells JD, Ung M, Hampsch RA, Traphagen NA, Yang W, Liu SC, Zeldenrust MA, Wang L, Kalari KR, Yu J, Boughey JC, Demidenko E, Kettenbach AN, Cheng C, Goetz MP, Miller TW. J Clin Cancer Res. 2019 Sep 26. pii: clincanres.2213.2018. doi: 10.1158/1078-0432.CCR-18-2213. [Pubmed]
  • [136] BioMethyl: An R package for Biological Interpretation of DNA Methylation Data. Wang Y, Franks JM, Whitfield ML, Cheng C$. J Bioinformatics. 2019 Feb 25. pii: btz137. doi: 10.1093/bioinformatics/btz137. [Pubmed]
  • [135] Characterizing the heterogeneity in 5-aminolevulinic acid-induced fluorescence in glioblastoma. Almiron Bonnin DA, Havrda MC, Lee MC, Evans L, Ran C, Qian DC, Harrington LX, Valdes PA, Cheng C, Amos CI, Harris BT, Paulsen KD, Roberts DW, Israel MA. J Neurosurg. 2019 May 24:1-9. doi: 10.3171/2019.2.JNS183128. [Pubmed]
  • [134] Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier. Chen Y, Wang Y, Salas LA, Miller TW, Mark K, Marotti JD, Kettenbach AN, Cheng C$, Christensen BC$. Breast Cancer Res. 2019 Jan 25;21(1):14. doi: 10.1186/s13058-018-1090-z. [Pubmed]
  • [133] Hypoxia-Induced VISTA Promotes the Suppressive Function of Myeloid-Derived Suppressor Cells in the Tumor Microenvironment. Deng J, Li J, Sarde A, Lines JL, Lee YC, Qian DC, Pechenick DA, Manivanh R, Le Mercier I, Lowrey CH, Varn FS, Cheng C, Leib DA, Noelle RJ, Mabaera R. Cancer Immunol Res. 2019 May 14. doi: 10.1158/2326-6066.CIR-18-0507. [Pubmed]
  • [132] Statins associate with improved mortality among patients with certain histological subtypes of lung cancer. Ung MH, MacKenzie TA, Onega TL, Amos CI, Cheng C$. Lung Cancer. 2018 Dec;126:89-96. [Pubmed]
  • [131] Genomic characterization of six virus-associated cancers identifies changes in the tumor immune microenvironment and altered genetic programs. Varn F, Schaafsma E, Wang Y, Cheng C$. Cancer Res. 2018 Nov 15;78(22):6413-6423. [Pubmed]

2012-2018 (Dartmouth College)

  • [130] Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER+ breast cancer. Shee K, Jiang A, Varn F, Liu S, Traphagen N, Owens, P, Ma C, Hoog J, Cheng C, Golub T, Straussman R, Miller T. FASEB J. 2018 Aug 30:fj201801241R. [Pubmed]
  • [129] Applications of ENCODE data to Systematic Analyses via Data Integration. Zhao Y, Schaafsma E, Cheng C$. Current Opinion in Systems Biology. 2018 Oct;11:57-64. [Pubmed]
  • [128] A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis. Zhao Y, Schaafsma E, Gorlov IP, Hernando E, Thomas NE, Shen R, Turk MJ, Berwick M, Amos CI, Cheng C$. Mol Cancer Res. 2018 Aug 31. pii: molcanres.0173.2018. [Pubmed]
  • [127] A B cell-derived gene expression signature associates with an immunologically active tumor microenvironment and response to immune checkpoint blockade therapy. Varn F, Wang Y, Cheng C$. OncoImmunology. 2018 Sep 19;8(1):e1513440. [Pubmed]
  • [126] Predictors of disease aggressiveness influence outcome from immunotherapy treatment in renal clear cell carcinoma. Kamal Y, Cheng C, Frost HR, Amos CI. Oncoimmunology. 2018 Oct 16;8(1):e1500106. doi: 10.1080/2162402X.2018.1500106. [Pubmed]
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  • [124] VISTA expression on tumor-infiltrating inflammatory cells in primary cutaneous melanoma correlates with poor disease-specific survival. Kuklinski LF, Yan S, Li Z, Fisher JL, Cheng C, Noelle RJ, Angeles CV, Turk MJ, Ernstoff MS. Cancer Immunol Immunother. 2018 Jul;67(7):1113-1121. [Pubmed]
  • [123] Comparative Analysis of Mutant Huntingtin Binding Partners in Yeast Species. Zhao Y, Zurawel AA, Jenkins NP, Duennwald ML, Cheng C, Kettenbach AN, Supattapone S. Sci Rep. 2018 Jun 22;8(1):9554. [Pubmed]
  • [122] Computational immune profiling in lung adenocarcinoma reveals reproducible prognostic associations with implications for immunotherapy. Varn FS, Tafe LJ, Amos CI, Cheng C$. OncoImmunology. 2018; 215(3):895-910. [Pubmed]
  • [121] Therapeutically targeting tumor microenvironment-mediated drug resistance in estrogen receptor-positive breast cancer. Shee K, Yang W, Hinds JW, Hampsch RA, Varn FS, Traphagen NA, Patel K, Cheng C, Jenkins NP, Kettenbach AN, Demidenko E, Owens P, Faber AC, Golub TR, Straussman R, Miller TW. J Exp Med. 2018 Mar 15;7(6):e1431084. [Pubmed]
  • [120] Secretion-mediated STAT3 activation promotes self-renewal of glioma stem-like cells during hypoxia. Almiron AD, Havrda CM, Lee MC, Liu H, Zhang Z, Nguyen LN, Harrington LX, Hassanpour S, Cheng C, Israel AM. Oncogene. 2017 Nov 20. [Pubmed]
  • [119] Decreased expression of FOXA2 promotes eutopic endometrial cell proliferation and migration in patients with endometriosis. Lin A, Yin J, Cheng C, Yang Z, Yang H. Reproductive BioMedicine Online. 2017 Nov 22. [Pubmed]
  • [118] A P53-deficiency gene signature predicts recurrence risk of patients with early stage lung adenocarcinoma. Zhao Y, Varn FS, Cai G, Xiao F, Amos CI, Cheng C$. Cancer Epidemiol Biomarkers Prev. 2017 Nov 15. pii: cebp.0478. [Pubmed]
  • [117] Intestinal stem cell overproliferation resulting from inactivation of the APC tumor suppressor requires the transcription cofactors Earthbound and Erect wing. Tian A, Benchabane H, Wang Z, Zimmerman C, Xin N, Perochon J, Kalna G, Sansom OJ, Cheng C, Cordero JB, Ahmed Y. PLoS Genet. 2017 Jul 14;13(7):e1006870. [Pubmed]
  • [116] Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer. Wang Y, Ung HM, Cantor S, Cheng C$. Sci Rep. 2017 Nov 16;7(1):15742. [Pubmed]
  • [115] A recombinant lentiviral PDGF-driven mouse model of proneural glioblastoma. Rahme G, Luikart B, Cheng C, Israel M. Neuro-Ocology. 2017 Jul 7. doi: 10.1093/neuonc/nox129. [Pubmed]
  • [114] Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines. Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY. Nat Genet. 2017 Oct;49(10):1428-1436. [Pubmed]
  • [113] Comparative analyses of FOXM1 cistromes in diverse human cell lines reveals substantial impact of co-factors on genomic occupation. Wang Y, Ung HM, Xia T, Cheng W$, Cheng C$. Oncotarget. 2017 Aug 24;8(44):76498-76515. [Pubmed]
  • [112] The E2F4 prognostic signature predicts pathological response to neoadjuvant chemotherapy in breast cancer patients. Mark KMK, Varn FS, Ung MH, Qian F, Cheng C$. BMC cancer. 2017. 13(1):e1005340. [Pubmed]
  • [111] Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. Andrews E, Wang Y, Xia T, Cheng W, Cheng C$. PLoS computational biology. 2017. 17(1):306. [Pubmed]
  • [110] Immunoregulatory functions of VISTA. Nowak EC, Lines JL, Varn FS, Deng J, Sarde A, Mabaera R, Kuta A, Le Mercier I, Cheng C, Noelle RJ. Immunological reviews. 2017. 276(1):66-79. [Pubmed]
  • [109] Filamentous fungal carbon catabolite repression supports metabolic plasticity and stress responses essential for disease progression. Beattie SR, Mark KMK, Thammahong A, Ries LNA, Dhingra S, Caffrey-Carr AK, Cheng C, Black CC, Bowyer P, Bromley MJ, Obar JJ, Goldman GH, Cramer RA. PLoS pathogens. 2017. 13(4):e1006340. [Pubmed]
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  • [107] Insulin-mediated signaling facilitates resistance to PDGFR inhibition in proneural hPDGFB-driven gliomas. Almiron Bonnin DA, Ran C, Havrda MC, Liu H, Hitoshi Y, Zhang Z, Cheng C, Ung M, Israel MA. Mol Cancer Ther. 2017 Jan 30. pii: molcanther.0616.2016. doi: 10.1158/1535-7163.MCT-16-0616. [Pubmed]
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  • [105] Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data. Yang C, Chen M, Lin S, Andrews EH, Cheng C$, Liu C$, Chen JW$. BMC Genomics. 2016 [Pubmed]
  • [104] MYC Mediates mRNA Cap Methylation of Canonical Wnt/beta-catenin Signaling Transcripts by Recruiting CDK7 and RNA Methyltransferase. Posternak V, Ung MH, Cheng C, Cole MD. Mol Cancer Res. 2016 Nov 29. pii: molcanres.0247.2016. [Pubmed]
  • [103] In silico frameworks for systematic pre-clinical screening of potential anti-leukemia therapeutics. Ung M, Varn F, Cheng C$. Expert Opinion On Drug Discovery. 2016 Oct 11:1-10. [Pubmed]
  • [102] Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer. Wang Y, Mark K, Ung M, Kettenbach A, Miller T, Xu W, Cheng W, Xia T$, Cheng C$. Genome Medicine. 2016 Oct 27;8(1):114. [Pubmed]
  • [101] Complex patterns of association between pleiotropy with transcription factor evolution. Chesmore K, Bartlett J, Cheng C, Williams S. Genome Biology and Evolution. 2016 Sep 15. pii: evw228. [Pubmed]
  • [100]GLITTER: a web-based application for gene link inspection through tissue-specific coexpression. Liu X, Yu P, Cheng C, Potash J, Han S. Scientific Reports. 2016 Sep 14;6:33460. doi: 10.1038/srep33460. [Pubmed]
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  • [98] An intestinal microRNA modulates the homeostatic adaptation to chronic oxidative stress in C. elegans. Masaomi K, kashem A, Cheng C. Aging. 2016 Sep 12. doi: 10.18632/aging.101029. [Pubmed]
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  • [96] Application of pharmacologically induced transcriptomic profiles to interrogate PI3K-Akt-mTOR pathway activity associated with cancer patient prognosis. Ung MH, Wang G, Varn FS, Cheng C$. Oncotarget. 2016 Aug 31. doi: 10.18632/oncotarget.11776. [Pubmed]
  • [95] Inverse association between MDM2 and HUWE1protein expression levels in human breast cancer and liposarcoma. Canfield K, Wells W, Geradts J, Kinlaw WB, Kornbluth S, Cheng C, Kurokawa M. Int J Clin Exp Pathol. 2016;9(6):6342-6349. [Pubmed]
  • [94] Identification of candidate CDK1 substrates in mitosis by quantitative phosphoproteomics. Petrone A, Adamo ME, Cheng C, Kettenbach AN. Mol Cell Proteomics.. 2016 Jul;15(7):2448-61. doi: 10.1074/mcp.M116.059394. [Pubmed]
  • [93] Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs. Yan KK, Wang D, Sethi A, Muir P, Kitchen R, Cheng C, Gerstein M. Cell Syst. 2016 Mar 23;2(3):147-157. [Pubmed]
  • [92] Integrative analysis of cancer genes in a functional interactome. Ung MH, Liu C, Cheng C$. Scientific Reports. 2016 Jun 30;6:29228. doi: 10.1038/srep29228. [Pubmed]
  • [91] Aberrant expression and hormonal regulation of Galectin-3 in endometriosis women with infertility. Yang H, Yin J, Ficarrotta K, Hsu SH, Zhang W$, Cheng C$. J Endocrinol Invest. 2016 Jul;39(7):785-91. doi: 10.1007/s40618-016-0435-7. [Pubmed]
  • [90] Integrated Drug Expression Analysis for Leukemia -- An integrated in silico and in vivo approach to drug discovery. Ung MH, Sun C, Weng C, Huang C, Lin C$, Liu C$, Cheng C$. Pharmacogenomics. 2016 Mar 15. doi: 10.1038/tpj.2016.18. [Pubmed]
  • [89] PDGF Signaling Maintains Survival of Proneural Glioma. Rahmea G, Zhang Z, Young A, Hitoshi Y, Cheng C, Bivona E, Fiering S, Israel M. Cancer Research. 2016 Mar 7. pii: canres.2157. [Pubmed]
  • [88] Integrative Genomic Analyses Yields Cell Cycle Regulatory Programs with Prognostic Value. Molecular Cancer Res. Cheng C$, Lou S, Andrews EH, Ung MH, Varn FS. Molecular Cancer Res. 2016. Feb 8. pii: molcanres.0368. [Pubmed]
  • [87] Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles. Varn FS, Andrews EH, Mullins DW, Cheng C$. Nature Communications. 2016 Jan 4;7:10248. doi: 10.1038/ncomms10248. [Pubmed]
  • [86] Systematic identification of hematopoietic cell type-specific profiles for prognostic prediction in acute myeloid leukemia. Varn FS, Andrews EH, Cheng C$. Scientific Reports. 2015 Nov 24;5:16987. doi: 10.1038/srep16987. [Pubmed]
  • [85] A deep learning framework for modeling structural features of RNA-binding protein targets. Zhang S, Zhou J, Hu H, Gong H, Chen L, Cheng C$, Zeng J$. Nucleic Acids Research. 2016 Feb 29;44(4):e32. doi: 10.1093/nar/gkv1025. [Pubmed]
  • [84] Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. Tan J, Ung M, Cheng C, Greene C.S. Pac Symp Biocomput. 2015;20:132-43. [Pubmed]
  • [83] CircNet: a database of circular RNAs derived from transcriptome sequencing data. Liu YC, Li JR, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu SD, Huang CC, Cheng C, Liu CC, Huang HD. Nucleic Acids Res. 2015 Oct 7. pii: gkv940. [Pubmed]
  • [82] Integrative analysis reveals regulatory programs in endometriosis. Yang H, Kang K, Cheng C, Mamillapalli R, Hugh T. Reproductive Sciences. 2015 Sep;22(9):1060-72. doi: 10.1177/1933719115592709. [Pubmed]
  • [81] E2F4 Program is Predictive of Progression and Intravesical Immunotherapy Efficacy in Bladder Cancer. Cheng C$, Varn FS, Marsit, C. Mol Cancer Res. 2015 Sep;13(9):1316-24. doi: 10.1158/1541-7786.MCR-15-0120. [Pubmed]
  • [80] IDEA: Integrated Drug Expression Analysis - Integration of gene expression and clinical data for the identification of therapeutic candidates. Ung MH, Varn FS, Cheng C$. CPT: Pharmacometrics & Systems Pharmacology. 2015 Jul;4(7):415-25.[Pubmed]
  • [79] An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome. Cheng C$, Andrews E, Yan K, Ung M, Wang D, Gerstein M$. Genome Biol. 2015 Mar 31;16:63. doi: 10.1186/s13059-015-0624-2. [Pubmed]
  • [78] Regulators associated with clinical outcomes revealed by DNA methylation data in breast cancer. Ung MH, Varn FS, Lou S, Cheng C$. PLoS Comput Biol. 2015 May 21;11(5):e1004269. doi: 10.1371/journal.pcbi.1004269. [Pubmed]
  • [77] Loregic: A method to characterize the cooperative logic of regulatory factors. Wang D, Yan K, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein M. PLoS Comput Biol. 2015 Apr 17;11(4):e1004132. doi: 10.1371/journal.pcbi.1004132.. [Pubmed]
  • [76] Integrative analysis of survival-associated gene sets in breast cancer. Varn FS, Ung MH, Lou S, Cheng C$. BMC Medical Genomics. 2015, 8:11 doi:10.1186/s12920-015-0086-0. [Pubmed]
  • [75] Ensemble Learning Based Sparse High-Order Boltzmann Machines for Unsupervised Feature Interaction Identification. Min R, Ning X, Cheng C, Bonner A, Gerstein M. Machine Learning in Computational Biology (MLCB), Annual Conference on Neural Information Processing Systems (NIPS) 2014. [Link]
  • [74] Applications of bioinformatics to non-coding rnas in the era of next-generation sequencing. Cheng C, Moore J, Greene C. The Pacific Symposium on Biocomputing (PSB) 2014. [Pubmed]
  • [73] p53 and DeltaNp63alpa Co-regulate the Transcriptional and Cellular Response to TGFbeta and BMP Signals. Balboni AL, Cherukuri P, Ung M, DeCastro AJ, Cheng C, DiRenzo J. Mol Cancer Res. 2015 Feb 19. pii: molcanres.0152.2014. [Pubmed]
  • [72] Protein mistranslation protects bacteria against oxidative stress. Fan Y, Wu J, Ung MH, De Lay N, Cheng C, Ling J. Nucleic Acids Res. 2015 Jan 10. pii: gku1404. [Pubmed]
  • [71] ChIP-seq and In Vivo Transcriptome Analyses of the Aspergillus fumigatus SREBP SrbA Reveals a New Regulator of the Fungal Hypoxia Response and Virulence. Chung D, Barker BM, Carey CC, Merriman B, Werner ER, Lechner BE, Dhingra S, Cheng C, Xu W, Blosser SJ, Morohashi K, Mazurie A, Mitchell TK, Haas H, Mitchell AP, Cramer RA. PLoS Pathog. 2014 Nov 6;10(11):e1004487. [Pubmed]
  • [70] Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Hurleya J, Dasgupta A, Emersona J, Zhou X, Ringelberg C, Knabe N, Lipzen A, Lindquist W, Daum C, Barry K, Grigoriev I, Smith K, Galagand J, Bell-Pedersen D, Freitag M, Cheng C, J. Loros J, Dunlap J. Proc Natl Acad Sci U S A. 2014 Oct 31. [Pubmed]
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  • [67] Comparative analysis of regulatory information and circuits across diverse species. Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. Nature. 2014 August 28; 512: 453–456. [Pubmed]
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  • [65] Comparative analysis of the transcriptome across distant species. Gerstein MB*, Rozowsky J*, Yan KK*, Wang D*, Cheng C*, Brown B*, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Nature. 2014 August 28;512:445-448. [Pubmed]
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  • [63] The histone methyltransferase activity of MLL1 is dispensable for hematopoiesis and leukemogenesis. Mishra B, Zaffuto K, Artinger E, Org T, Mikkola H, Cheng C, Djabali M, Ernst P. Cell Rep. 2014 May 22;7(4):1239-47. [Pubmed]
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  • [60] DPRP: A database of phenotype-specific regulatory programs derived from transcription factor binding data. David TW*, Tseng Y*, Ung M, Liao I, Liu C, Cheng C$. Nucleic Acids Res. 2014 Jan;42(Database issue):D178-83. [Pubmed]
  • [59] Interpretable sparse high-order boltzmann machines for transcription factor interaction identification. Min R, Ning X, Cheng C, Gerstein M. Machine Learning in Computational Biology (MLCB), Annual Conference on Neural Information Processing Systems (NIPS) 2013. [Link]
  • [58] Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation. Johnson KC, Koestler DC, Cheng C, Christensen BC. Epigenetics. 2013 Nov 6;9(2). [Pubmed]
  • [57] Association of Gamma-Aminobutyric Acid A Receptor α 2 Gene (GABRA2) with Alcohol Use Disorder. Li D, Sulovari A, Cheng C, Zhao H, Kranzler HR, Gelernter J. Neuropsychopharmacology. 2013 Oct 18. [Pubmed]
  • [56] Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors. Grant GD, Brooks L 3rd, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML. Mol Biol Cell. 2013 Oct 9. [Pubmed]
  • [55] Identification of yeast cell cycle regulated genes based on genomic features. Cheng C$, Fu Y*, Shen L, Gerstein M. BMC Syst Biol. 2013 Jul 29;7(1):70. [Pubmed]
  • [54] REACTIN: Regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. Zhu M, Liu CC, Cheng C$. BMC Genomics. 2013 Jul 26;14(1):504. [Pubmed]
  • [53] Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. Cheng C$, Ung M, Grant G, Whitfield M. PLoS Computational Biology. 2013. [Pubmed]
  • [52] MLL1 coordinates proliferation with self-renewal in hematopoietic stem cells. Artinger E, Mishra B, Artinger K, Li B, Chung E, Moore A, Chen Y, Cheng C, Ernst P. Proc Natl Acad Sci U S A. 2013. [Pubmed]
  • [51] Discovering chromatin motifs using FAIRE sequencing and the human diploid genome. Yang C, Buck J.M, Chen M, Chen Y, Lan H, Cheng C, Chen J, Liu C. BMC Genomics. 2013 May 8;14:310. [Pubmed]
  • [50] Paeonol induces apoptosis in human ovarian cancer cells. Yin J, Wu N, Zeng F, Cheng C, Kang K, Yang H. Acta Histochemica. 2013 Jun 12. doi:pii: S0065-1281(13)00076-7. [Pubmed]
  • [49] Machine learning and genome annotation: A match meant to be? Kevin Y, Cheng C, Gerstein, M. Genome Biology. 2013 May 29;14(5):205. [Pubmed]

2008-2011 (Yale University)

  • [48] A Comprehensive Nuclear Receptor Network for Breast Cancer Cells. Kittler R, Zhou J, Hua S, Ma L, Liu Y, Pendleton E, Cheng C, Gerstein M, White KP. Cell Rep. 2013 Jan 30. [Pubmed]
  • [47] Modeling gene expression using chromatin features in various cellular contexts. Dong X, Greven M, Kundaje A, Djebali S, Brown BJ, Cheng C, Gerstein M, Guigó Serra R, Birney E, Weng Z. Genome Biology. 2012 Sep 5;13(9):R53. [Pubmed]
  • [46] The Anti-Apoptotic Effect of Galectin-3 in Human Endometrial Cells under the Regulation of Estrogen and Progesterone. Yang H, Lei C, Cheng C, Feng Y, Zhang W, Petracco RG, Sak S. Biol Reprod. 2012 Jun 6. [Pubmed]
  • [45] Analysis of the human regulatory network using ENCODE Data. Gerstein MB*, Kundaje A*, Hariharan M*, Landt SG*, Yan KK*, Cheng C*, Mu XJ*, Khurana E*, Rozowsky J*, Alexander R*, et al. Nature. 2012 Sep 6;489(7414):91-100. [Pubmed]
  • [44] An integrated encyclopedia of DNA elements in the human genome. The ENCODE Project Consortium. Nature. 2012 Sep 6;489(7414):57-74. [Pubmed]
  • [43] Genome-wide analysis of the binding sites of more than 100 transcription factors defines different types of genomic regions with distinct biological properties. Yip YK, Cheng C, Bhardwaj N, Brown BJ, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel JP, Snyder M and Gerstein M. Genome Biology. 2012 Sep 5;13(9):R48. [Pubmed]
  • [42] Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, et al. Genome Res. 2012 Sep;22(9):1658-67. [Pubmed]
  • [41] Average rank-based score to measure deregulation of molecular pathway gene sets. Yang H*, Cheng C*$, Zhang W. PLoS One. 2011;6(11):e27579. [Pubmed]
  • [40] Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Cheng C, Gerstein M. Nucleic Acids Research. 2011 Sep 16. [Pubmed]
  • [39] Genome-wide analysis of chromatin features identifies histone modification-sensitive and insensitive classes of yeast transcription factors. Cheng C*, Shou C*, Yip Y, Gerstein M. Genome Biology. 2011 Nov 7;12(11):R111. [Pubmed]
  • [38] A Probabilistic Method for identifying Transcription Factor Target Genes from ChIP-Seq Binding Profiles. Cheng C, Min R, Gerstein M. Bioinformatics. 2011 Dec 1;27(23):3221-7. [Pubmed]
  • [37] Construction and Analysis of an Integrated Regulatory Network Derived from High-throughput Sequencing Data. Cheng C, Yan, K, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu Z, Niu W, Alves P, Kato M, Snyder M, Gerstein M. PLoS Computational Biology. 2011 Nov;7(11):e1002190. [Pubmed]
  • [36] A User's Guide to the Encyclopedia of DNA Elements (ENCODE). The ENCODE Project Consortium. PLoS Biol. 2011 Apr;9(4):e1001046. [Pubmed]
  • [35] Hormonal Regulation of Galectin 3 in Trophoblasts and Its Effects on Endometrium. Yang H, Taylor HS, Lei C, Cheng C, Zhang W. Reprod Sci. 2011 May 9. [Pubmed]
  • [34] A cis-regulatory map of the Drosophila genome. Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP. Nature. 2011 Mar 24;471(7339):527-31. [Pubmed]
  • [33] A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M. Genome Biol. 2011 Feb 16;12(2):R15. [Pubmed]
  • [32] Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB. Genome Res. 2011 Feb;21(2):276-85. [Pubmed]
  • [31] Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Cheng C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V. Genome Res. 2011 Feb;21(2):245-54. [Pubmed]
  • [30] Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Gerstein MB*, Lu ZJ*, Van Nostrand EL*, Cheng C*, Arshinoff BI*, Liu T*, Yip KY*, Robilotto R*, Rechtsteiner A*, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. Science. 2010 Dec 24;330(6012):1775-87. (* co-first author) [Pubmed]
  • [29] Understanding protein evolutionary rate by integrating gene co-expression with protein interactions. Pang K, Cheng C, Xuan Z, Sheng H, Ma X. BMC Syst Biol. 2010 Dec 30;4:179. [Pubmed]
  • [28] Segmental duplications in the human genome reveal details of pseudogene formation. Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB. Nucleic Acids Res. 2010 Jul 8. [Pubmed]
  • [27] Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Wu Y, Li J, Hasina R, Cheng C, Lingen MW, Gerstein MB, Weichselbaum RR, Xing HR, Lussier YA. PLoS Comput Biol. 2010 Apr 1;6(4):e1000730. [Pubmed]
  • [26] Comparative analyses of time-course gene expression profiles of the long-lived sch9{Delta} mutant. Ge H, Wei M, Fabrizio P, Hu J, Cheng C, Longo VD, Li LM. Nucleic Acids Res. 2009 Oct 30. [Pubmed]
  • [25] The relationship between the evolution of microRNA targets and the length of their UTRs. Cheng C, Bhardwaj N, Gerstein M. BMC Genomics. 2009 Sep 14;10(1):431. [Pubmed]
  • [24] mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer. Cheng C*, Fu X*, Alves P, Gerstein M. Genome Biol. 2009 Sep 1;10(9):R90. [Pubmed]
  • [23] Systematic identification of transcription factors associated with patient survival in cancers. Cheng C, Li LM, Alves P, Gerstein M. BMC Genomics. 2009 May 15;10:225. [Pubmed]
  • [22] Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. Genes Dev. 2009 Mar 1;23(5):619-32. [Pubmed]

2002-2007 (University of Southern California)

  • [21] Inferring microRNA activities by combining gene expression with microRNA target prediction. Cheng C, Li LM. PLoS One. 2008 Apr 23;3(4):e1989. [Pubmed]
  • [20] A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays. Ge H, Cheng C, Li LM. BMC Bioinformatics. 2008 Apr 14;9:194. [Pubmed]
  • [19] Systematic identification of cell cycle regulated transcription factors from microarray time series data. Cheng C, Li LM. BMC Genomics. 2008 Mar 3;9:116. [Pubmed]
  • [18] Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9. Wei M, Fabrizio P, Hu J, Ge H, Cheng C, Li L, Longo VD. PLoS Genet. 2008 Jan;4(1):e13. [Pubmed]
  • [17] Inferring activity changes of transcription factors by binding association with sorted expression profiles. Cheng C, Yan X, Sun F, Li LM. BMC Bioinformatics. 2007 Nov 16;8:452. [Pubmed]
  • [16] Significant and systematic expression differentiation in long-lived yeast strains. Cheng C, Fabrizio P, Ge H, Wei M, Longo VD, Li LM. PLoS One. 2007 Oct 31;2(10):e1095. [Pubmed]
  • [15] Inference of transcription modification in long-live yeast strains from their expression profiles. Cheng C, Fabrizio P, Ge H, Longo VD, Li LM. BMC Genomics. 2007 Jul 6;8:219. [Pubmed]
  • [14] MARD: a new method to detect differential gene expression in treatment-control time courses. Cheng C, Ma X, Yan X, Sun F, Li LM. Bioinformatics. 2006, 22(21):2650-7. [Pubmed]
  • [13] Sub-array normalization subject to differentiation. Cheng C, Li LM. Nucleic Acids Res. 2005, 33(17):5565-73. [Pubmed]
  • [12] Sir2 blocks extreme life-span extension. Fabrizio P, Gattazzo C, Battistella L, Wei M, Cheng C, McGrew K, Longo VD. Cell. 2005, 123(4):548-50. [Pubmed]
  • [11] Isolation and characterization of a novel human putative anemia-related gene homologous to mouse sideroflexin. Ye X, Xu J, Cheng C, Yin G, Zeng L, et al. Biochem Genet. 2003, 41(3-4):119-25. [Pubmed]
  • [10] Isolation and characterization of a human putative receptor protein kinase cDNA STYK1. Ye X, Ji C, Huang Q, Cheng C, Tang R, et al. Mol Biol Rep. 2003, 30(2):91-6. [Pubmed]
  • [9] Cloning, expression and characterization of a novel human VMP gene. Cheng C, Xu J, Ye X, Dai J, Wu Q, Mao Y, et al. Mol Biol Rep. 2002, 29(3):281-6. [Pubmed]
  • [8] Cloning and characterization of a novel human transcription factor AP-2 beta like gene (TFAP2BL1). Cheng C, Ying K, Xu M, Zhao W, Zhou Z, et al. Int J Biochem Cell Biol. 2002, 34(1):78-86. [Pubmed]
  • [7] Identification and characterization of AGTRAP, a human homolog of murine Angiotensin II Receptor-Associated Protein (Agtrap). Wang W, Huang Y, Zhou Z, Tang R, Zhao W, Zeng L, Xu M, Cheng C, Gu S, Ying K, Xie Y, Mao Y. Int J Biochem Cell Biol. 2002 Jan;34(1):93-102. [Pubmed]
  • [6] Tumor Relevance Analysis of A Highly Conserved Gene by Using Gene Microarray Hybridization. Cheng C, Zhou Z, Xu M, Zhao W, Xu J, et al. Hereditas (BeiJing). 2002, 24(3): 227-231. [Pubmed]
  • [5] Cloning and characterization of a novel human TEKTIN1 gene. Xu M, Zhou Z, Cheng C, Zhao W, Tang R, et al. Int J Biochem Cell Biol. 2001, 33(12):1172-82. [Pubmed]
  • [4] Cloning, expression and characterization of a novel human REPS1 gene. Xu J, Zhou Z, Zeng L, Huang Y, Zhao W, Cheng C, Xu M, Xie Y, Mao Y. Biochim Biophys Acta. 2001 Dec 3;1522(2):118-21. [Pubmed]
  • [3] Molecular cloning and characterization of a novel Dehydrogenase/reductase (SDR family) member 1 genea from human fetal brain. Wu Q, Xu M, Cheng C, Zhou Z, Huang Y, et al. Mol Biol Rep. 2001, 28(4):193-8. [Pubmed]
  • [2] Molecular cloning, structure and expression of a novel nuclear RNA-binding cyclophilin-like gene (PPIL4) from human fetal brain. Zeng L, Zhou Z, Xu J, Zhao W, Wang W, Huang Y, Cheng C, Xu M, Xie Y, Mao Y. Cytogenet Cell Genet. 2001;95(1-2):43-7. [Pubmed
  • [1] A novel human hydroxysteroid dehydrogenase like 1 gene (HSDL1) is highly expressed in reproductive tissues. Huang Y, Tang R, Dai J, Gu S, Zhao W, Cheng C, Xu M, Zhou Z, Ying K, Xi Y, Mao Y. Mol Biol Rep. 2001;28(4):185-91. [Pubmed]

Other Publications

Book Chapters

  • [4] Cheng C and Worzel W. Chapter: Application of machine-learning methods to understand gene expression regulation. Book: Genetic Programming Theory and Practice XII. Springer, 2014. Edited by Rick Riolo, William Worzel and Mark Kotenchek.
  • [3] Ung M, Lou S, Varn F and Cheng C. Chapter: Integrative analysis identifies transcription factor-DNA methylation relationships and introduces new avenues for translating cancer epigenetics into the clinic. Book: Next Generation Sequencing in Cancer Research (Volume 2). Springer, 2014. Edited by Wei Wu and Hani Choudhry.
  • [2] Cheng C. Chapter: From transcription factor binding and histone modification to gene expression: integrative quantitative models. Book: Integrating omics data: statistical and computational methods. Cambridge Unversity Press, 2014. Edited by George C. Tseng, Xianghong Jasmine Zhou and Debashis Ghosh.
  • [1] Li, L. and Cheng, C., 2007. Chapter: Differentiation detection in microarray normalization. Book: Methods in Microarray Normalization (Drug Discovery Series), Edited by Phillip Stafford. [Link]

Patents

  • [1] Lei M. Li, Chao Cheng, Huanying Ge, SYSTEMS AND METHODS FOR ANALYZING MICROARRAYS. [Link]

Ph.D Thesis

  • Chao Cheng, Detecting and Understanding Differentiation of Microarray Expression Data. Computational and Molecular Biology, University of Southern California, 2006.

Masters Thesis

  • Chao Cheng, Symmetric and Trimmed Solutions of Simple Linear Regression. Department of Mathematics, University of Southern California, 2006.
  • Chao Cheng, Functional Analysis and Characterization of Human Dual Specific Phosphatases. Institute of Genetics, Life Science, Fudan University, 2002.

Questions or comments?

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