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CHAO CHENG

TitleProfessor
InstitutionBaylor College of Medicine
DepartmentDepartment of Medicine
AddressOne Baylor Plaza
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    R01CA269764     (CHENG, CHAO)Dec 8, 2022 - Nov 30, 2027
    NIH
    An innovative integrated computational framework using gene signatures for patient stratification
    Role: Principal Investigator
    R21CA227996     (CHENG, CHAO)Apr 1, 2019 - Mar 31, 2021
    NIH
    Computational Identification of new candidate drugs for lung cancer treatment
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. 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, Wang Z. Author Correction: Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nat Commun. 2025 Feb 24; 16(1):1916. PMID: 39994256; PMCID: PMC11850708.
      Citations:    Fields:    
    2. Li C, Nguyen TT, Li JR, Song X, Fujimoto J, Little L, Gumb C, Chow CB, Wistuba II, Futreal AP, Zhang J, Hubert SM, Heymach JV, Wu J, Amos CI, Zhang J, Cheng C. Multiregional transcriptomic profiling provides improved prognostic insight in localized non-small cell lung cancer. NPJ Precis Oncol. 2024 Oct 05; 8(1):225. PMID: 39369068; PMCID: PMC11455871.
      Citations: 2     
    3. Li JR, Shaw V, Lin Y, Wang X, Aminu M, Li Y, Wu J, Zhang J, Amos CI, Cheng C. The prognostic effect of infiltrating immune cells is shaped by proximal M2 macrophages in lung adenocarcinoma. Mol Cancer. 2024 Sep 04; 23(1):185. PMID: 39232758; PMCID: PMC11373246.
      Citations: 4     Fields:    Translation:HumansCells
    4. Shaw V, Zhang B, Tang M, Peng W, Amos C, Cheng C. Racial and socioeconomic disparities in survival improvement of eight cancers. BJC Rep. 2024 Mar 11; 2(1):21. PMID: 39516676; PMCID: PMC11524065.
      Citations: 6     
    5. Li JR, Arsang-Jang S, Cheng Y, Sun F, D'Souza A, Dhakal B, Hari P, Huang Q, Auer P, Li Y, Urrutia R, Zhan F, Shaughnessy JD, Janz S, Dong J, Cheng C. Enhancing prognostic power in multiple myeloma using a plasma cell signature derived from single-cell RNA sequencing. Blood Cancer J. 2024 03 06; 14(1):38. PMID: 38443358; PMCID: PMC10915134.
      Citations:    Fields:    Translation:HumansCells
    6. Lin Y, Burt BM, Lee HS, Nguyen TT, Jang HJ, Lee C, Hong W, Ripley RT, Amos CI, Cheng C. Clonal gene signatures predict prognosis in mesothelioma and lung adenocarcinoma. NPJ Precis Oncol. 2024 Feb 23; 8(1):47. PMID: 38396241; PMCID: PMC10891127.
      Citations: 1     
    7. 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, Wang Z. Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nat Commun. 2024 Feb 08; 15(1):1199. PMID: 38331912; PMCID: PMC10853168.
      Citations:    
    8. Li C, Zhang J, Cheng C. TimiGP: An R package to depict the tumor microenvironment from bulk transcriptomics. STAR Protoc. 2023 12 15; 4(4):102742. PMID: 38019649; PMCID: PMC10698325.
      Citations:    
    9. Li C, Zhang B, Schaafsma E, Reuben A, Wang L, Turk MJ, Zhang J, Cheng C. TimiGP: Inferring cell-cell interactions and prognostic associations in the tumor immune microenvironment through gene pairs. Cell Rep Med. 2023 07 18; 4(7):101121. PMID: 37467716; PMCID: PMC10394258.
      Citations:    
    10. Wolf BK, Zhao Y, McCray A, Hawk WH, Deary LT, Sugiarto NW, LaCroix IS, Gerber SA, Cheng C, Wang X. Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nat Struct Mol Biol. 2023 01; 30(1):10-21. PMID: 36522426; PMCID: PMC10513740.
      Citations:    
    11. Nguyen TT, Lee HS, Burt BM, Amos CI, Cheng C. A combination of intrinsic and extrinsic features improves prognostic prediction in malignant pleural mesothelioma. Br J Cancer. 2022 11; 127(9):1691-1700. PMID: 35999269; PMCID: PMC9596423.
      Citations:    
    12. Cui M, Cheng C, Zhang L. High-throughput proteomics: a methodological mini-review. Lab Invest. 2022 11; 102(11):1170-1181. PMID: 35922478; PMCID: PMC9362039.
      Citations:    
    13. Li JR, Tang M, Li Y, Amos CI, Cheng C. Genetic variants associated mRNA stability in lung. BMC Genomics. 2022 Mar 11; 23(1):196. PMID: 35272635; PMCID: PMC8915503.
      Citations:    Fields:    Translation:Cells
    14. Yao K, Tong CY, Cheng C. A framework to predict the applicability of Oncotype DX, MammaPrint, and E2F4 gene signatures for improving breast cancer prognostic prediction. Sci Rep. 2022 02 09; 12(1):2211. PMID: 35140308; PMCID: PMC8828770.
      Citations:    
    15. Schaafsma E, Takacs EM, Kaur S, Cheng C, Kurokawa M. Predicting clinical outcomes of cancer patients with a p53 deficiency gene signature. Sci Rep. 2022 01 25; 12(1):1317. PMID: 35079034; PMCID: PMC8789768.
      Citations:    
    16. Nguyen TT, Lee HS, Burt BM, Wu J, Zhang J, Amos CI, Cheng C. A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma. Genome Med. 2022 01 12; 14(1):5. PMID: 35016696; PMCID: PMC8753834.
      Citations:    Fields:    Translation:Humans
    17. Zhao Y, Dong Y, Hong W, Jiang C, Yao K, Cheng C. Computational modeling of chromatin accessibility identified important epigenomic regulators. BMC Genomics. 2022 Jan 08; 23(1):19. PMID: 34996354; PMCID: PMC8742372.
      Citations:    Fields:    Translation:HumansCells
    18. Zhang B, Yao K, Cheng C. A network-based integration for understanding racial disparity in prostate cancer. Transl Oncol. 2022 Mar; 17:101327. PMID: 34998235; PMCID: PMC8738961.
      Citations:    
    19. Hong W, Li A, Liu Y, Xiao X, Christiani DC, Hung RJ, McKay J, Field J, Amos CI, Cheng C. Clonal Hematopoiesis Mutations in Patients with Lung Cancer Are Associated with Lung Cancer Risk Factors. Cancer Res. 2022 01 15; 82(2):199-209. PMID: 34815255; PMCID: PMC8815061.
      Citations:    Fields:    Translation:Humans
    20. 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, Usherwood EJ, Wong SL, Phillips JD, Shirai K, Angeles CV, Yan S, Curiel TJ, Huang YH, Cheng C, Turk MJ. Resident memory CD8+ T?cells in regional lymph nodes mediate immunity to metastatic melanoma. Immunity. 2021 09 14; 54(9):2117-2132.e7. PMID: 34525340; PMCID: PMC9015193.
      Citations:    
    21. Schaafsma E, Zhang B, Schaafsma M, Tong CY, Zhang L, Cheng C. Impact of Oncotype DX testing on ER+ breast cancer treatment and survival in the first decade of use. Breast Cancer Res. 2021 07 17; 23(1):74. PMID: 34274003; PMCID: PMC8285794.
      Citations:    Fields:    
    22. Schaafsma E, Fugle CM, Wang X, Cheng C. Pan-cancer association of HLA gene expression with cancer prognosis and immunotherapy efficacy. Br J Cancer. 2021 Aug; 125(3):422-432. PMID: 33981015; PMCID: PMC8329209.
      Citations: 1     Fields:    
    23. Zhang B, Yao K, Zhou E, Zhang L, Cheng C. Chr20q Amplification Defines a Distinct Molecular Subtype of Microsatellite Stable Colorectal Cancer. Cancer Res. 2021 04 15; 81(8):1977-1987. PMID: 33619118; PMCID: PMC8137593.
      Citations:    
    24. Schaafsma E, Zhao Y, Zhang L, Li Y, Cheng C. MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers. Mol Cancer Res. 2021 03; 19(3):414-428. PMID: 33234576; PMCID: PMC7925347.
      Citations: 2     Fields:    Translation:Humans
    25. Schaafsma E, Zhao Y, Wang Y, Varn FS, Zhu K, Yang H, Cheng C. Whole transcriptome signature for prognostic prediction (WTSPP): application of whole transcriptome signature for prognostic prediction in cancer. Lab Invest. 2020 10; 100(10):1356-1366. PMID: 32144347; PMCID: PMC7483260.
      Citations: 1     Fields:    Translation:HumansCells
    26. 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 RJ. VISTA is a checkpoint regulator for na?ve T cell quiescence and peripheral tolerance. Science. 2020 01 17; 367(6475). PMID: 31949051; PMCID: PMC7391053.
      Citations: 47     Fields:    Translation:AnimalsCells
    27. Xie F, Zhang J, Wang J, Reuben A, Xu W, Yi X, Varn FS, Ye Y, Cheng J, Yu M, Wang Y, Liu Y, Xie M, Du P, Ma K, Ma X, Zhou P, Yang S, Chen Y, Wang G, Xia X, Liao Z, Heymach JV, Wistuba II, Futreal PA, Ye K, Cheng C, Xia T. Multifactorial Deep Learning Reveals Pan-Cancer Genomic Tumor Clusters with Distinct Immunogenomic Landscape and Response to Immunotherapy. Clin Cancer Res. 2020 06 15; 26(12):2908-2920. PMID: 31911545; PMCID: PMC7299824.
      Citations: 7     Fields:    Translation:Humans
    28. Qin C, He X, Zhao Y, Tong CY, Zhu KY, Sun Y, Cheng C. Systematic computational identification of prognostic cytogenetic markers in neuroblastoma. BMC Med Genomics. 2019 12 12; 12(1):192. PMID: 31831008; PMCID: PMC6909636.
      Citations:    Fields:    Translation:Humans
    29. 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, Pusztai L, Febbraio M, Cheng C, Kinlaw WB, Kurokawa M, Sotiriou C. CD36-Mediated Metabolic Rewiring of Breast Cancer Cells Promotes Resistance to HER2-Targeted Therapies. Cell Rep. 2019 12 10; 29(11):3405-3420.e5. PMID: 31825825; PMCID: PMC6938262.
      Citations: 36     Fields:    Translation:HumansAnimalsCells
    30. Schaafsma E, Yuan Y, Zhao Y, Cheng C. Computational STAT3 activity inference reveals its roles in the pancreatic tumor microenvironment. Sci Rep. 2019 12 03; 9(1):18257. PMID: 31796877; PMCID: PMC6890662.
      Citations: 5     Fields:    Translation:Humans
    31. Wang Y, Franks JM, Whitfield ML, Cheng C. BioMethyl: an R package for biological interpretation of DNA methylation data. Bioinformatics. 2019 10 01; 35(19):3635-3641. PMID: 30799505; PMCID: PMC6761945.
      Citations: 9     Fields:    Translation:Cells
    32. 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. A Transcriptionally Definable Subgroup of Triple-Negative Breast and Ovarian Cancer Samples Shows Sensitivity to HSP90 Inhibition. Clin Cancer Res. 2020 01 01; 26(1):159-170. PMID: 31558472; PMCID: PMC6942625.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    33. Zhao Y, Carter R, Natarajan S, Varn FS, Compton DA, Gawad C, Cheng C, Godek KM. Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells. BMC Med Genomics. 2019 05 31; 12(1):79. PMID: 31151460; PMCID: PMC6545015.
      Citations: 11     Fields:    Translation:HumansCells
    34. 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. Characterizing the heterogeneity in 5-aminolevulinic acid-induced fluorescence in glioblastoma. J Neurosurg. 2020 06 01; 132(6):1706-1714. PMID: 31125970.
      Citations: 5     Fields:    
    35. 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. Hypoxia-Induced VISTA Promotes the Suppressive Function of Myeloid-Derived Suppressor Cells in the Tumor Microenvironment. Cancer Immunol Res. 2019 07; 7(7):1079-1090. PMID: 31088847; PMCID: PMC6606337.
      Citations: 51     Fields:    Translation:HumansAnimalsCells
    36. Qi X, Jiao Y, Cheng C, Qian F, Chen Z, Wu Q. H22954, a novel long non-coding RNA down-regulated in AML, inhibits cancer growth in a BCL-2-dependent mechanism. Cancer Lett. 2019 07 10; 454:26-36. PMID: 30959078.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    37. Chen Y, Wang Y, Salas LA, Miller TW, Mark K, Marotti JD, Kettenbach AN, Cheng C, Christensen BC. Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier. Breast Cancer Res. 2019 01 25; 21(1):14. PMID: 30683142; PMCID: PMC6347811.
      Citations: 2     Fields:    Translation:HumansCells
    38. Ung MH, MacKenzie TA, Onega TL, Amos CI, Cheng C. Statins associate with improved mortality among patients with certain histological subtypes of lung cancer. Lung Cancer. 2018 12; 126:89-96. PMID: 30527197; PMCID: PMC6296763.
      Citations: 9     Fields:    Translation:Humans
    39. Kamal Y, Cheng C, Frost HR, Amos CI. Predictors of disease aggressiveness influence outcome from immunotherapy treatment in renal clear cell carcinoma. Oncoimmunology. 2019; 8(1):e1500106. PMID: 30546942; PMCID: PMC6287778.
      Citations: 10     Fields:    
    40. Mortezaei Z, Cazier JB, Mehrabi AA, Cheng C, Masoudi-Nejad A. Novel putative drugs and key initiating genes for neurodegenerative disease determined using network-based genetic integrative analysis. J Cell Biochem. 2019 04; 120(4):5459-5471. PMID: 30302804.
      Citations: 2     Fields:    Translation:Humans
    41. Gorlov I, Orlow I, Ringelberg C, Hernando E, Ernstoff MS, Cheng C, Her S, Parker JS, Thompson CL, Gerstenblith MR, Berwick M, Amos C. Identification of gene expression levels in primary melanoma associated with clinically meaningful characteristics. Melanoma Res. 2018 10; 28(5):380-389. PMID: 29975213; PMCID: PMC6448582.
      Citations: 8     Fields:    Translation:Humans
    42. Varn FS, Schaafsma E, Wang Y, Cheng C. Genomic Characterization of Six Virus-Associated Cancers Identifies Changes in the Tumor Immune Microenvironment and Altered Genetic Programs. Cancer Res. 2018 11 15; 78(22):6413-6423. PMID: 30254145; PMCID: PMC6239894.
      Citations: 20     Fields:    Translation:HumansCells
    43. Zhao Y, Schaafsma E, Gorlov IP, Hernando E, Thomas NE, Shen R, Turk MJ, Berwick M, Amos CI, Cheng C. A Leukocyte Infiltration Score Defined by a Gene Signature Predicts Melanoma Patient Prognosis. Mol Cancer Res. 2019 01; 17(1):109-119. PMID: 30171176; PMCID: PMC6318018.
      Citations: 19     Fields:    Translation:HumansCells
    44. Shee K, Jiang A, Varn FS, Liu S, Traphagen NA, Owens P, Ma CX, Hoog J, Cheng C, Golub TR, Straussman R, Miller TW. Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER+ breast cancer. FASEB J. 2019 02; 33(2):1644-1657. PMID: 30161001; PMCID: PMC6338642.
      Citations: 7     Fields:    Translation:HumansCells
    45. Zhao Y, Schaafsma E, Cheng C. Applications of ENCODE data to Systematic Analyses via Data Integration. Curr Opin Syst Biol. 2018 Oct; 11:57-64. PMID: 31011690; PMCID: PMC6474416.
      Citations: 1     
    46. Zhao Y, Zurawel AA, Jenkins NP, Duennwald ML, Cheng C, Kettenbach AN, Supattapone S. Comparative Analysis of Mutant Huntingtin Binding Partners in Yeast Species. Sci Rep. 2018 06 22; 8(1):9554. PMID: 29934597; PMCID: PMC6015068.
      Citations: 4     Fields:    Translation:Animals
    47. Kuklinski LF, Yan S, Li Z, Fisher JL, Cheng C, Noelle RJ, Angeles CV, Turk MJ, Ernstoff MS. VISTA expression on tumor-infiltrating inflammatory cells in primary cutaneous melanoma correlates with poor disease-specific survival. Cancer Immunol Immunother. 2018 Jul; 67(7):1113-1121. PMID: 29737375; PMCID: PMC11028124.
      Citations: 35     Fields:    Translation:HumansCells
    48. Varn FS, Tafe LJ, Amos CI, Cheng C. Computational immune profiling in lung adenocarcinoma reveals reproducible prognostic associations with implications for immunotherapy. Oncoimmunology. 2018; 7(6):e1431084. PMID: 29872556; PMCID: PMC5980421.
      Citations: 19     Fields:    
    49. Rahme GJ, Luikart BW, Cheng C, Israel MA. A recombinant lentiviral PDGF-driven mouse model of proneural glioblastoma. Neuro Oncol. 2018 02 19; 20(3):332-342. PMID: 29016807; PMCID: PMC5817944.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    50. 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. Therapeutically targeting tumor microenvironment-mediated drug resistance in estrogen receptor-positive breast cancer. J Exp Med. 2018 03 05; 215(3):895-910. PMID: 29436393; PMCID: PMC5839765.
      Citations: 23     Fields:    Translation:HumansAnimalsCells
    51. Lin A, Yin J, Cheng C, Yang Z, Yang H. Decreased expression of FOXA2 promotes eutopic endometrial cell proliferation and migration in patients with endometriosis. Reprod Biomed Online. 2018 Feb; 36(2):181-187. PMID: 29233503.
      Citations: 6     Fields:    Translation:Humans
    52. Almiron Bonnin DA, Havrda MC, Lee MC, Liu H, Zhang Z, Nguyen LN, Harrington LX, Hassanpour S, Cheng C, Israel MA. Secretion-mediated STAT3 activation promotes self-renewal of glioma stem-like cells during hypoxia. Oncogene. 2018 02 22; 37(8):1107-1118. PMID: 29155422; PMCID: PMC5851110.
      Citations: 35     Fields:    Translation:AnimalsCells
    53. Wang Y, Ung MH, Cantor S, Cheng C. Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer. Sci Rep. 2017 Nov 16; 7(1):15742. PMID: 29146938; PMCID: PMC5691048.
      Citations: 5     Fields:    Translation:HumansCells
    54. Zhao Y, Varn FS, Cai G, Xiao F, Amos CI, Cheng C. A P53-Deficiency Gene Signature Predicts Recurrence Risk of Patients with Early-Stage Lung Adenocarcinoma. Cancer Epidemiol Biomarkers Prev. 2018 01; 27(1):86-95. PMID: 29141854; PMCID: PMC5839302.
      Citations: 23     Fields:    Translation:Humans
    55. Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY. Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines. Nat Genet. 2017 Oct; 49(10):1428-1436. PMID: 28869592.
      Citations: 92     Fields:    Translation:HumansCells
    56. Wang Y, Ung MH, Xia T, Cheng W, Cheng C. Cancer cell line specific co-factors modulate the FOXM1 cistrome. Oncotarget. 2017 Sep 29; 8(44):76498-76515. PMID: 29100329; PMCID: PMC5652723.
      Citations: 6     Fields:    
    57. Tian A, Benchabane H, Wang Z, Zimmerman C, Xin N, Perochon J, Kalna G, Sansom OJ, Cheng C, Cordero JB, Ahmed Y. Intestinal stem cell overproliferation resulting from inactivation of the APC tumor suppressor requires the transcription cofactors Earthbound and Erect wing. PLoS Genet. 2017 Jul; 13(7):e1006870. PMID: 28708826; PMCID: PMC5510812.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    58. Mark KMK, Varn FS, Ung MH, Qian F, Cheng C. The E2F4 prognostic signature predicts pathological response to neoadjuvant chemotherapy in breast cancer patients. BMC Cancer. 2017 05 02; 17(1):306. PMID: 28464832; PMCID: PMC5414335.
      Citations: 10     Fields:    Translation:Humans
    59. Cai G, Xiao F, Cheng C, Li Y, Amos CI, Whitfield ML. Population effect model identifies gene expression predictors of survival outcomes in lung adenocarcinoma for both Caucasian and Asian patients. PLoS One. 2017; 12(4):e0175850. PMID: 28426704; PMCID: PMC5398559.
      Citations: 4     Fields:    Translation:Humans
    60. Beattie SR, Mark KMK, Thammahong A, Dhingra S, Caffrey-Carr AK, Cheng C, Black CC, Bowyer P, Bromley MJ, Obar JJ, Cramer RA, Ries LNA, Goldman GH. Filamentous fungal carbon catabolite repression supports metabolic plasticity and stress responses essential for disease progression. PLoS Pathog. 2017 Apr; 13(4):e1006340. PMID: 28423062; PMCID: PMC5411099.
      Citations: 40     Fields:    Translation:Animals
    61. Nowak EC, Lines JL, Varn FS, Deng J, Sarde A, Mabaera R, Kuta A, Le Mercier I, Cheng C, Noelle RJ. Immunoregulatory functions of VISTA. Immunol Rev. 2017 03; 276(1):66-79. PMID: 28258694; PMCID: PMC5702497.
      Citations: 76     Fields:    Translation:HumansAnimals
    62. Almiron Bonnin DA, Ran C, Havrda MC, Liu H, Hitoshi Y, Zhang Z, Cheng C, Ung M, Israel MA. Insulin-Mediated Signaling Facilitates Resistance to PDGFR Inhibition in Proneural hPDGFB-Driven Gliomas. Mol Cancer Ther. 2017 04; 16(4):705-716. PMID: 28138037.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    63. Varn FS, Wang Y, Mullins DW, Fiering S, Cheng C. Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment. Cancer Res. 2017 03 15; 77(6):1271-1282. PMID: 28126714; PMCID: PMC5798883.
      Citations: 68     Fields:    Translation:HumansCells
    64. Andrews E, Wang Y, Xia T, Cheng W, Cheng C. Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. PLoS Comput Biol. 2017 01; 13(1):e1005340. PMID: 28103241; PMCID: PMC5289608.
      Citations: 5     Fields:    Translation:Humans
    65. Yang CC, Chen MH, Lin SY, Andrews EH, Cheng C, Liu CC, Chen JJ. Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data. BMC Genomics. 2017 01 10; 18(1):61. PMID: 28068916; PMCID: PMC5223348.
      Citations:    Fields:    Translation:HumansCells
    66. Ung MH, Wang GL, Varn FS, Cheng C. Application of pharmacologically induced transcriptomic profiles to interrogate PI3K-Akt-mTOR pathway activity associated with cancer patient prognosis. Oncotarget. 2016 Dec 20; 7(51):84142-84154. PMID: 27589846; PMCID: PMC5356650.
      Citations: 3     Fields:    Translation:HumansCells
    67. Posternak V, Ung MH, Cheng C, Cole MD. MYC Mediates mRNA Cap Methylation of Canonical Wnt/?-Catenin Signaling Transcripts By Recruiting CDK7 and RNA Methyltransferase. Mol Cancer Res. 2017 02; 15(2):213-224. PMID: 27899423; PMCID: PMC5290160.
      Citations: 16     Fields:    Translation:HumansCells
    68. Wang Y, Mark KM, Ung MH, Kettenbach A, Miller T, Xu W, Cheng W, Xia T, Cheng C. Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer. Genome Med. 2016 10 27; 8(1):114. PMID: 27788678; PMCID: PMC5084341.
      Citations: 2     Fields:    Translation:HumansCells
    69. Chesmore KN, Bartlett J, Cheng C, Williams SM. Complex Patterns of Association between Pleiotropy and Transcription Factor Evolution. Genome Biol Evol. 2016 10 23; 8(10):3159-3170. PMID: 27635052; PMCID: PMC5174740.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    70. Ung MH, Varn FS, Cheng C. In silico frameworks for systematic pre-clinical screening of potential anti-leukemia therapeutics. Expert Opin Drug Discov. 2016 Dec; 11(12):1213-1222. PMID: 27689915; PMCID: PMC5180445.
      Citations: 2     Fields:    Translation:HumansAnimals
    71. Varn FS, Mullins DW, Arias-Pulido H, Fiering S, Cheng C. Adaptive immunity programmes in breast cancer. Immunology. 2017 Jan; 150(1):25-34. PMID: 27564847; PMCID: PMC5341497.
      Citations: 24     Fields:    Translation:HumansAnimalsCells
    72. Liu X, Yu P, Cheng C, Potash JB, Han S. GLITTER: a web-based application for gene link inspection through tissue-specific coexpression. Sci Rep. 2016 09 14; 6:33460. PMID: 27623690; PMCID: PMC5022062.
      Citations: 2     Fields:    Translation:Humans
    73. Kato M, Kashem MA, Cheng C. An intestinal microRNA modulates the homeostatic adaptation to chronic oxidative stress in C. elegans. Aging (Albany NY). 2016 09 12; 8(9):1979-2005. PMID: 27623524; PMCID: PMC5076448.
      Citations: 10     Fields:    Translation:AnimalsCells
    74. Yang CC, Andrews EH, Chen MH, Wang WY, Chen JJ, Gerstein M, Liu CC, Cheng C. iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data. BMC Genomics. 2016 08 12; 17(1):632. PMID: 27519564; PMCID: PMC4983039.
      Citations: 1     Fields:    Translation:HumansCells
    75. Ung MH, Liu CC, Cheng C. Integrative analysis of cancer genes in a functional interactome. Sci Rep. 2016 06 30; 6:29228. PMID: 27356765; PMCID: PMC4928112.
      Citations: 4     Fields:    Translation:Humans
    76. Canfield K, Wells W, Geradts J, Kinlaw WB, Cheng C, Kurokawa M. Inverse association between MDM2 and HUWE1 protein expression levels in human breast cancer and liposarcoma. Int J Clin Exp Pathol. 2016; 9(6):6342-6349. PMID: 29375730; PMCID: PMC5782804.
      Citations: 8     Fields:    
    77. Petrone A, Adamo ME, Cheng C, Kettenbach AN. Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics. Mol Cell Proteomics. 2016 07; 15(7):2448-61. PMID: 27134283; PMCID: PMC4937516.
      Citations: 34     Fields:    Translation:HumansCells
    78. Yan KK, Wang D, Sethi A, Muir P, Kitchen R, Cheng C, Gerstein M. Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs. Cell Syst. 2016 Mar 23; 2(3):147-157. PMID: 27047991; PMCID: PMC4817108.
      Citations: 7     Fields:    
    79. Ung MH, Sun CH, Weng CW, Huang CC, Lin CC, Liu CC, Cheng C. Integrated Drug Expression Analysis for leukemia: an integrated in silico and in vivo approach to drug discovery. Pharmacogenomics J. 2017 07; 17(4):351-359. PMID: 26975228; PMCID: PMC5243857.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    80. Rahme GJ, Zhang Z, Young AL, Cheng C, Bivona EJ, Fiering SN, Hitoshi Y, Israel MA. PDGF Engages an E2F-USP1 Signaling Pathway to Support ID2-Mediated Survival of Proneural Glioma Cells. Cancer Res. 2016 05 15; 76(10):2964-76. PMID: 26951930.
      Citations: 16     Fields:    Translation:HumansAnimalsCells
    81. Yang H, Yin J, Ficarrotta K, Hsu SH, Zhang W, Cheng C. Aberrant expression and hormonal regulation of Galectin-3 in endometriosis women with infertility. J Endocrinol Invest. 2016 Jul; 39(7):785-91. PMID: 26886939; PMCID: PMC4906070.
      Citations: 2     Fields:    Translation:HumansCells
    82. Cheng C, Lou S, Andrews EH, Ung MH, Varn FS. Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value. Mol Cancer Res. 2016 Apr; 14(4):332-43. PMID: 26856934; PMCID: PMC5033644.
      Citations: 3     Fields:    Translation:HumansCells
    83. Varn FS, Andrews EH, Mullins DW, Cheng C. Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles. Nat Commun. 2016 Jan 04; 7:10248. PMID: 26725977; PMCID: PMC4725766.
      Citations: 24     Fields:    Translation:HumansAnimals
    84. Varn FS, Andrews EH, Cheng C. Systematic analysis of hematopoietic gene expression profiles for prognostic prediction in acute myeloid leukemia. Sci Rep. 2015 Nov 24; 5:16987. PMID: 26598031; PMCID: PMC4657053.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    85. Zhang S, Zhou J, Hu H, Gong H, Chen L, Cheng C, Zeng J. A deep learning framework for modeling structural features of RNA-binding protein targets. Nucleic Acids Res. 2016 Feb 29; 44(4):e32. PMID: 26467480; PMCID: PMC4770198.
      Citations: 67     Fields:    Translation:Cells
    86. Liu YC, Li JR, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu SD, Huang CC, Cheng C, Liu CC, Huang HD. CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res. 2016 Jan 04; 44(D1):D209-15. PMID: 26450965; PMCID: PMC4702939.
      Citations: 166     Fields:    Translation:Humans
    87. Yang H, Kang K, Cheng C, Mamillapalli R, Taylor HS. Integrative Analysis Reveals Regulatory Programs in Endometriosis. Reprod Sci. 2015 Sep; 22(9):1060-72. PMID: 26134036; PMCID: PMC5933170.
      Citations: 9     Fields:    Translation:HumansCells
    88. Ung MH, Varn FS, Cheng C. IDEA: Integrated Drug Expression Analysis-Integration of Gene Expression and Clinical Data for the Identification of Therapeutic Candidates. CPT Pharmacometrics Syst Pharmacol. 2015 Jul; 4(7):415-25. PMID: 26312165; PMCID: PMC4544055.
      Citations: 3     Fields:    
    89. Cheng C, Varn FS, Marsit CJ. E2F4 Program Is Predictive of Progression and Intravesical Immunotherapy Efficacy in Bladder Cancer. Mol Cancer Res. 2015 Sep; 13(9):1316-24. PMID: 26032289; PMCID: PMC4734892.
      Citations: 7     Fields:    Translation:HumansCells
    90. Ung MH, Varn FS, Lou S, Cheng C. Regulators associated with clinical outcomes revealed by DNA methylation data in breast cancer. PLoS Comput Biol. 2015 May; 11(5):e1004269. PMID: 25996148; PMCID: PMC4440643.
      Citations: 3     Fields:    Translation:HumansCells
    91. Wang D, Yan KK, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein MB. Loregic: a method to characterize the cooperative logic of regulatory factors. PLoS Comput Biol. 2015 Apr; 11(4):e1004132. PMID: 25884877; PMCID: PMC4401777.
      Citations: 9     Fields:    Translation:HumansAnimals
    92. Cheng C, Andrews E, Yan KK, Ung M, Wang D, Gerstein M. An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome. Genome Biol. 2015 Mar 31; 16:63. PMID: 25880651; PMCID: PMC4404648.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    93. Varn FS, Ung MH, Lou SK, Cheng C. Integrative analysis of survival-associated gene sets in breast cancer. BMC Med Genomics. 2015 Mar 12; 8:11. PMID: 25881247; PMCID: PMC4359519.
      Citations: 10     Fields:    Translation:Humans
    94. Balboni AL, Cherukuri P, Ung M, DeCastro AJ, Cheng C, DiRenzo J. p53 and ?Np63a Coregulate the Transcriptional and Cellular Response to TGF? and BMP Signals. Mol Cancer Res. 2015 Apr; 13(4):732-42. PMID: 25700283; PMCID: PMC4398640.
      Citations: 10     Fields:    Translation:HumansCells
    95. Fan Y, Wu J, Ung MH, De Lay N, Cheng C, Ling J. Protein mistranslation protects bacteria against oxidative stress. Nucleic Acids Res. 2015 Feb 18; 43(3):1740-8. PMID: 25578967; PMCID: PMC4330365.
      Citations: 41     Fields:    Translation:Cells
    96. Tan J, Ung M, Cheng C, Greene CS. Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders. Pac Symp Biocomput. 2015; 132-43. PMID: 25592575; PMCID: PMC4299935.
      Citations: 47     Fields:    Translation:HumansCells
    97. Khaleel SS, Andrews EH, Ung M, DiRenzo J, Cheng C. E2F4 regulatory program predicts patient survival prognosis in breast cancer. Breast Cancer Res. 2014 Dec 02; 16(6):486. PMID: 25440089; PMCID: PMC4303196.
      Citations: 35     Fields:    Translation:HumansCells
    98. Greene CS, Tan J, Ung M, Moore JH, Cheng C. Big data bioinformatics. J Cell Physiol. 2014 Dec; 229(12):1896-900. PMID: 24799088; PMCID: PMC5604462.
      Citations: 45     Fields:    Translation:Humans
    99. Chung D, Barker BM, Carey CC, Merriman B, Werner ER, Lechner BE, Dhingra S, Cheng C, Xu W, Blosser SJ, Morohashi K, Mitchell TK, Haas H, Mitchell AP, Cramer RA, Mazurie A. ChIP-seq and in vivo transcriptome analyses of the Aspergillus fumigatus SREBP SrbA reveals a new regulator of the fungal hypoxia response and virulence. PLoS Pathog. 2014 Nov; 10(11):e1004487. PMID: 25375670; PMCID: PMC4223079.
      Citations: 87     Fields:    Translation:AnimalsCells
    100. Hurley JM, Dasgupta A, Emerson JM, Zhou X, Ringelberg CS, Knabe N, Lipzen AM, Lindquist EA, Daum CG, Barry KW, Grigoriev IV, Smith KM, Galagan JE, Bell-Pedersen D, Freitag M, Cheng C, Loros JJ, Dunlap JC. Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Proc Natl Acad Sci U S A. 2014 Dec 02; 111(48):16995-7002. PMID: 25362047; PMCID: PMC4260557.
      Citations: 60     Fields:    Translation:AnimalsCells
    101. Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, 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, Hammonds A, Harrow J, Hoskins RA, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, 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, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, 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, Djebali S, Guig? R, Howald C, Lagarde J, Pervouchine D, Tanzer A. Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28; 512(7515):445-8. PMID: 25164755; PMCID: PMC4155737.
      Citations: 144     Fields:    Translation:HumansAnimalsCells
    102. Yan KK, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M. OrthoClust: an orthology-based network framework for clustering data across multiple species. Genome Biol. 2014 Aug 28; 15(8):R100. PMID: 25249401; PMCID: PMC4289247.
      Citations: 17     Fields:    Translation:AnimalsCells
    103. 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. Comparative analysis of regulatory information and circuits across distant species. Nature. 2014 Aug 28; 512(7515):453-6. PMID: 25164757; PMCID: PMC4336544.
      Citations: 87     Fields:    Translation:HumansAnimalsCells
    104. Yang H, Li D, Cheng C. Relating gene expression evolution with CpG content changes. BMC Genomics. 2014 Aug 20; 15:693. PMID: 25142157; PMCID: PMC4148958.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    105. Mishra BP, Zaffuto KM, Artinger EL, Org T, Mikkola HK, Cheng C, Ernst P, Djabali M. The histone methyltransferase activity of MLL1 is dispensable for hematopoiesis and leukemogenesis. Cell Rep. 2014 May 22; 7(4):1239-47. PMID: 24813891; PMCID: PMC4120120.
      Citations: 70     Fields:    Translation:AnimalsCells
    106. Ung M, Ma X, Johnson KC, Christensen BC, Cheng C. Effect of estrogen receptor a binding on functional DNA methylation in breast cancer. Epigenetics. 2014 Apr; 9(4):523-32. PMID: 24434785; PMCID: PMC4121363.
      Citations: 17     Fields:    Translation:HumansCells
    107. Cheng C, Moore J, Greene C. Applications of bioinformatics to non-coding RNAs in the era of next-generation sequencing. Pac Symp Biocomput. 2014; 412-6. PMID: 24297566; PMCID: PMC3900277.
      Citations: 3     Fields:    Translation:Humans
    108. Tzeng DT, Tseng YT, Ung M, Liao IE, Liu CC, Cheng C. DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data. Nucleic Acids Res. 2014 Jan; 42(Database issue):D178-83. PMID: 24302579; PMCID: PMC3965116.
      Citations: 1     Fields:    Translation:HumansCells
    109. Johnson KC, Koestler DC, Cheng C, Christensen BC. Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation. Epigenetics. 2014 Feb; 9(2):268-75. PMID: 24196486; PMCID: PMC3962537.
      Citations: 33     Fields:    Translation:HumansCells
    110. Li D, Sulovari A, Cheng C, Zhao H, Kranzler HR, Gelernter J. Association of gamma-aminobutyric acid A receptor a2 gene (GABRA2) with alcohol use disorder. Neuropsychopharmacology. 2014 Mar; 39(4):907-18. PMID: 24136292; PMCID: PMC3924525.
      Citations: 48     Fields:    Translation:Humans
    111. Grant GD, Brooks L, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML. Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors. Mol Biol Cell. 2013 Dec; 24(23):3634-50. PMID: 24109597; PMCID: PMC3842991.
      Citations: 100     Fields:    Translation:HumansCells
    112. Cheng C, Fu Y, Shen L, Gerstein M. Identification of yeast cell cycle regulated genes based on genomic features. BMC Syst Biol. 2013 Jul 29; 7:70. PMID: 23895232; PMCID: PMC3734186.
      Citations: 2     Fields:    Translation:AnimalsCells
    113. Zhu M, Liu CC, Cheng C. REACTIN: regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. BMC Genomics. 2013 Jul 26; 14:504. PMID: 23885756; PMCID: PMC3750236.
      Citations: 14     Fields:    Translation:HumansCells
    114. Cheng C, Ung M, Grant GD, Whitfield ML. Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. PLoS Comput Biol. 2013; 9(7):e1003132. PMID: 23874175; PMCID: PMC3708869.
      Citations: 4     Fields:    Translation:HumansCells
    115. Yin J, Wu N, Zeng F, Cheng C, Kang K, Yang H. Paeonol induces apoptosis in human ovarian cancer cells. Acta Histochem. 2013 Oct; 115(8):835-9. PMID: 23768958.
      Citations: 8     Fields:    Translation:HumansCells
    116. Artinger EL, Mishra BP, Zaffuto KM, Li BE, Chung EK, Moore AW, Chen Y, Cheng C, Ernst P. An MLL-dependent network sustains hematopoiesis. Proc Natl Acad Sci U S A. 2013 Jul 16; 110(29):12000-5. PMID: 23744037; PMCID: PMC3718146.
      Citations: 44     Fields:    Translation:HumansCells
    117. Yip KY, Cheng C, Gerstein M. Machine learning and genome annotation: a match meant to be? Genome Biol. 2013 May 29; 14(5):205. PMID: 23731483; PMCID: PMC4053789.
      Citations: 24     Fields:    Translation:Humans
    118. Yang CC, Buck MJ, Chen MH, Chen YF, Lan HC, Chen JJ, Cheng C, Liu CC. Discovering chromatin motifs using FAIRE sequencing and the human diploid genome. BMC Genomics. 2013 May 08; 14:310. PMID: 23656909; PMCID: PMC3655836.
      Citations: 2     Fields:    Translation:HumansCells
    119. Kittler R, Zhou J, Hua S, Ma L, Liu Y, Pendleton E, Cheng C, Gerstein M, White KP. A comprehensive nuclear receptor network for breast cancer cells. Cell Rep. 2013 Feb 21; 3(2):538-51. PMID: 23375374.
      Citations: 46     Fields:    Translation:HumansCells
    120. Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012 Sep 26; 13(9):R48. PMID: 22950945; PMCID: PMC3491392.
      Citations: 145     Fields:    Translation:HumansCells
    121. Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 06; 489(7414):91-100. PMID: 22955619; PMCID: PMC4154057.
      Citations: 750     Fields:    Translation:HumansCells
    122. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616; PMCID: PMC3439153.
      Citations: 7176     Fields:    Translation:HumansAnimalsCells
    123. Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Birney E, Weng Z, Snyder M, Gerstein M, Guig? R. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012 Sep; 22(9):1658-67. PMID: 22955978; PMCID: PMC3431483.
      Citations: 98     Fields:    Translation:HumansCells
    124. Yang H, Lei C, Cheng C, Feng Y, Zhang W, Petracco RG, Sak S. The antiapoptotic effect of galectin-3 in human endometrial cells under the regulation of estrogen and progesterone. Biol Reprod. 2012 Aug; 87(2):39. PMID: 22674388.
      Citations: 8     Fields:    Translation:HumansCells
    125. Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Birney E, Weng Z, Guig? R. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012 Jun 13; 13(9):R53. PMID: 22950368; PMCID: PMC3491397.
      Citations: 118     Fields:    Translation:HumansCells
    126. Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M. Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol. 2011 Nov; 7(11):e1002190. PMID: 22125477; PMCID: PMC3219617.
      Citations: 50     Fields:    Translation:Animals
    127. Yang H, Cheng C, Zhang W. Average rank-based score to measure deregulation of molecular pathway gene sets. PLoS One. 2011; 6(11):e27579. PMID: 22096597; PMCID: PMC3212578.
      Citations: 5     Fields:    Translation:HumansCells
    128. Cheng C, Shou C, Yip KY, Gerstein MB. Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors. Genome Biol. 2011 Nov 07; 12(11):R111. PMID: 22060676; PMCID: PMC3334597.
      Citations: 11     Fields:    Translation:AnimalsCells
    129. Cheng C, Min R, Gerstein M. TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. Bioinformatics. 2011 Dec 01; 27(23):3221-7. PMID: 22039215; PMCID: PMC3223362.
      Citations: 34     Fields:    Translation:AnimalsCells
    130. Cheng C, Gerstein M. Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Res. 2012 Jan; 40(2):553-68. PMID: 21926158; PMCID: PMC3258143.
      Citations: 66     Fields:    Translation:AnimalsCells
    131. Yang H, Taylor HS, Lei C, Cheng C, Zhang W. Hormonal regulation of galectin 3 in trophoblasts and its effects on endometrium. Reprod Sci. 2011 Nov; 18(11):1118-27. PMID: 21555510.
      Citations: 6     Fields:    Translation:HumansCells
    132. ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222; PMCID: PMC3079585.
      Citations: 732     Fields:    Translation:HumansCells
    133. 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, N?gre N. A cis-regulatory map of the Drosophila genome. Nature. 2011 Mar 24; 471(7339):527-31. PMID: 21430782; PMCID: PMC3179250.
      Citations: 295     Fields:    Translation:AnimalsCells
    134. Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M. A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol. 2011; 12(2):R15. PMID: 21324173; PMCID: PMC3188797.
      Citations: 54     Fields:    Translation:HumansAnimalsCells
    135. Pang K, Cheng C, Xuan Z, Sheng H, Ma X. Understanding protein evolutionary rate by integrating gene co-expression with protein interactions. BMC Syst Biol. 2010 Dec 30; 4:179. PMID: 21190591; PMCID: PMC3022652.
      Citations: 6     Fields:    Translation:HumansCells
    136. 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, 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, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, 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, Dos? AC, R?tsch G. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010 Dec 24; 330(6012):1775-87. PMID: 21177976; PMCID: PMC3142569.
      Citations: 561     Fields:    Translation:AnimalsCells
    137. 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. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res. 2011 Feb; 21(2):276-85. PMID: 21177971; PMCID: PMC3032931.
      Citations: 38     Fields:    Translation:AnimalsCells
    138. Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. 2011 Feb; 21(2):245-54. PMID: 21177963; PMCID: PMC3032928.
      Citations: 142     Fields:    Translation:AnimalsCells
    139. Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB. Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Res. 2010 Nov; 38(20):6997-7007. PMID: 20615899; PMCID: PMC2978362.
      Citations: 15     Fields:    Translation:HumansCells
    140. 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. Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol. 2010 Apr 01; 6(4):e1000730. PMID: 20369013; PMCID: PMC2848541.
      Citations: 85     Fields:    Translation:HumansCells
    141. Ge H, Wei M, Fabrizio P, Hu J, Cheng C, Longo VD, Li LM. Comparative analyses of time-course gene expression profiles of the long-lived sch9Delta mutant. Nucleic Acids Res. 2010 Jan; 38(1):143-58. PMID: 19880387; PMCID: PMC2800218.
      Citations: 6     Fields:    Translation:AnimalsCells
    142. Cheng C, Bhardwaj N, Gerstein M. The relationship between the evolution of microRNA targets and the length of their UTRs. BMC Genomics. 2009 Sep 14; 10:431. PMID: 19751524; PMCID: PMC2758905.
      Citations: 51     Fields:    Translation:HumansAnimalsCells
    143. Cheng C, Fu X, Alves P, Gerstein M. mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer. Genome Biol. 2009; 10(9):R90. PMID: 19723326; PMCID: PMC2768979.
      Citations: 52     Fields:    Translation:Humans
    144. Cheng C, Li LM, Alves P, Gerstein M. Systematic identification of transcription factors associated with patient survival in cancers. BMC Genomics. 2009 May 15; 10:225. PMID: 19442316; PMCID: PMC2686740.
      Citations: 8     Fields:    Translation:Humans
    145. Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev. 2009 Mar 01; 23(5):619-32. PMID: 19240126; PMCID: PMC2658521.
      Citations: 76     Fields:    Translation:AnimalsCells
    146. Cheng C, Li LM. Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One. 2008 Apr 23; 3(4):e1989. PMID: 18431476; PMCID: PMC2291556.
      Citations: 53     Fields:    Translation:HumansCells
    147. Ge H, Cheng C, Li LM. A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays. BMC Bioinformatics. 2008 Apr 14; 9:194. PMID: 18410691; PMCID: PMC2375129.
      Citations: 7     Fields:    Translation:Cells
    148. Cheng C, Li LM. Systematic identification of cell cycle regulated transcription factors from microarray time series data. BMC Genomics. 2008 Mar 03; 9:116. PMID: 18315882; PMCID: PMC2315658.
      Citations: 16     Fields:    Translation:Animals
    149. Wei M, Fabrizio P, Hu J, Ge H, Cheng C, Li L, Longo VD. Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9. PLoS Genet. 2008 Jan; 4(1):e13. PMID: 18225956; PMCID: PMC2213705.
      Citations: 223     Fields:    Translation:AnimalsCells
    150. Cheng C, Yan X, Sun F, Li LM. Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics. 2007 Nov 16; 8:452. PMID: 18021409; PMCID: PMC2194743.
      Citations: 50     Fields:    Translation:Cells
    151. Cheng C, Fabrizio P, Ge H, Wei M, Longo VD, Li LM. Significant and systematic expression differentiation in long-lived yeast strains. PLoS One. 2007 Oct 31; 2(10):e1095. PMID: 17971858; PMCID: PMC2039703.
      Citations: 13     Fields:    Translation:AnimalsCells
    152. Cheng C, Fabrizio P, Ge H, Longo VD, Li LM. Inference of transcription modification in long-live yeast strains from their expression profiles. BMC Genomics. 2007 Jul 06; 8:219. PMID: 17617911; PMCID: PMC1949827.
      Citations: 19     Fields:    Translation:AnimalsCells
    153. Cheng C, Ma X, Yan X, Sun F, Li LM. MARD: a new method to detect differential gene expression in treatment-control time courses. Bioinformatics. 2006 Nov 01; 22(21):2650-7. PMID: 16928738.
      Citations: 4     Fields:    Translation:Animals
    154. Fabrizio P, Gattazzo C, Battistella L, Wei M, Cheng C, McGrew K, Longo VD. Sir2 blocks extreme life-span extension. Cell. 2005 Nov 18; 123(4):655-67. PMID: 16286010.
      Citations: 180     Fields:    Translation:AnimalsCells
    155. Cheng C, Li LM. Sub-array normalization subject to differentiation. Nucleic Acids Res. 2005; 33(17):5565-73. PMID: 16204457; PMCID: PMC1243797.
      Citations: 9     Fields:    Translation:HumansAnimals
    156. Ye X, Ji C, Huang Q, Cheng C, Tang R, Xu J, Zeng L, Dai J, Wu Q, Gu S, Xie Y, Mao Y. Isolation and characterization of a human putative receptor protein kinase cDNA STYK1. Mol Biol Rep. 2003 Jun; 30(2):91-6. PMID: 12841579.
      Citations: 9     Fields:    Translation:HumansCells
    157. Ye X, Xu J, Cheng C, Yin G, Zeng L, Ji C, Gu S, Xie Y, Mao Y. Isolation and characterization of a novel human putative anemia-related gene homologous to mouse sideroflexin. Biochem Genet. 2003 Apr; 41(3-4):119-25. PMID: 12670026.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    158. Cheng C, Xu J, Ye X, Dai J, Wu Q, Zeng L, Wang L, Zhao W, Ji C, Gu S, Xie Y, Mao Y. Cloning, expression and characterization of a novel human VMP gene. Mol Biol Rep. 2002 Sep; 29(3):281-6. PMID: 12463420.
      Citations: 2     Fields:    Translation:HumansCells
    159. Cheng C, Zhou ZX, Xu M, Zhao W, Xu J, Zeng L, Huang Y, Wu QH, Dai JF, Ying K, Xie Y, Mao YM. [Tumor relevance analysis of a highly conserved gene by using gene microarray hybridization]. Yi Chuan. 2002 May; 24(3):227-31. PMID: 16126669.
      Citations:    Fields:    
    160. Cheng C, Ying K, Xu M, Zhao W, Zhou Z, Huang Y, Wang W, Xu J, Zeng L, Xie Y, Mao Y. Cloning and characterization of a novel human transcription factor AP-2 beta like gene (TFAP2BL1). Int J Biochem Cell Biol. 2002 Jan; 34(1):78-86. PMID: 11733187.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    161. Wang W, Huang Y, Zhou Z, Tang R, Zhao W, Zeng L, Xu M, Cheng C, Gu S, Ying K, Xie Y, Mao Y. Identification and characterization of AGTRAP, a human homolog of murine Angiotensin II Receptor-Associated Protein (Agtrap). Int J Biochem Cell Biol. 2002 Jan; 34(1):93-102. PMID: 11733189.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    162. Xu J, Zhou Z, Zeng L, Huang Y, Zhao W, Cheng C, Xu M, Xie Y, Mao Y. Cloning, expression and characterization of a novel human REPS1 gene. Biochim Biophys Acta. 2001 Dec 03; 1522(2):118-21. PMID: 11750063.
      Citations: 9     Fields:    Translation:HumansCells
    163. Xu M, Zhou Z, Cheng C, Zhao W, Tang R, Huang Y, Wang W, Xu J, Zeng L, Xie Y, Mao Y. Cloning and characterization of a novel human TEKTIN1 gene. Int J Biochem Cell Biol. 2001 Dec; 33(12):1172-82. PMID: 11606253.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    164. Wu Q, Xu M, Cheng C, Zhou Z, Huang Y, Zhao W, Zeng L, Xu J, Fu X, Ying K, Xie Y, Mao Y. Molecular cloning and characterization of a novel Dehydrogenase/reductase (SDR family) member 1 genea from human fetal brain. Mol Biol Rep. 2001; 28(4):193-8. PMID: 12153138.
      Citations: 1     Fields:    Translation:HumansCells
    165. Zeng L, Zhou Z, Xu J, Zhao W, Wang W, Huang Y, Cheng C, Xu M, Xie Y, Mao Y. Molecular cloning, structure and expression of a novel nuclear RNA-binding cyclophilin-like gene (PPIL4) from human fetal brain. Cytogenet Cell Genet. 2001; 95(1-2):43-7. PMID: 11978968.
      Citations: 7     Fields:    Translation:HumansCells
    166. Huang Y, Tang R, Dai J, Gu S, Zhao W, Cheng C, Xu M, Zhou Z, Ying K, Xi Y, Mao Y. A novel human hydroxysteroid dehydrogenase like 1 gene (HSDL1) is highly expressed in reproductive tissues. Mol Biol Rep. 2001; 28(4):185-91. PMID: 12153137.
      Citations: 8     Fields:    Translation:HumansCells
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