Hu Li Lab Mayo Clinic

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Publications

  1. Weiskittel TM, Ung CY, Correia C, Zhang C, Li H. De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens. Genome Research. 2021 Dec.
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  2. Sturmlechner I, Zhang C, Sine CC, van Deursen EJ, Jeganathan KB, Hamada N, Grasic J, Friedman D, Stutchman JT, Can I, Hamada M, Lim DY, Lee JH, Ordog T, Laberge RM, Shapiro V, Baker DJ, Li H, van Deursen JM. p21 produces a bioactive secretome that places stressed cells under immunosurveillance. Science. 2021 Oct 29;374(6567):eabb3420.
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  3. Cheon IS, Li C, Son YM, Goplen NP, Wu Y, Cassmann T, Wang Z, Wei X, Tang J, Li Y, Marlow H, Hughes S, Hammel L, Cox TM, Goddery E, Ayasoufi K, Weiskopf D, Boonyaratanakornkit J, Dong H, Li H, Chakraborty R, Johnson AJ, Edell E, Taylor JJ, Kaplan MH, Sette A, Bartholmai BJ, Kern R, Vassallo R, Sun J. Immune Signatures Underlying Post-acute COVID-19 Lung Sequelae. Science Immunology. 2021 Nov 12;6(65):eabk1741.
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  4. Ung CY, Weiskittel TM, Correia C, Kaufmann SH, Li H. Manifold Medicine: A Schema that Expands Treatment Dimensionality. Drug Discovery Today. 2021 Sep 29;S1359-6446(21)00423-2.
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  5. Zhao J, Yao K, Yu H, Zhang L, Xu Y, Chen L, Sun Z, Zhu Y, Zhang C, Qian Y, Ji S, Zhang M, Cheng J, Correia C, Weiskittel T, Lin D, Zhao Y, Chandrasekaran S, Fu X, Zhang D, Fan H, Xie W, Li H, Hu Z, Zhang J. Metabolic remodeling during early murine embryo development. Nature Metabolism. 2021 Oct;3(10):1372-1384.
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  6. Gautam P, Hamashima K, Chen Y, Zeng YY, Makovoz B, Parikh BH, Lee HY, Lau KA, Su X, Wong RCB, Chan WK, Li H, Blenkinsop TA, Loh YH. Multi-species single-cell transcriptomic analysis of ocular compartment regulons. Nature Communications. 2021 Sep 28;12(1):5675.
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  7. Childs BG, Zhang C, Shuja F, Sturmlechner I, Trewartha S, Velasco1 RF, Baker D, Li H, van Deursen JM. Senescent cells suppress innate smooth muscle cell repair functions in atherosclerosis. Nature Aging. 2021 Aug;1(8):698-714.
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  8. Jiang L, Lin W, Zhang C, Ash PEA, Verma M, Kwan J, van Vliet E, Yang Z, Lourdes Cruz A, Boudeau S, Maziuk BF, Lei S, Song J, Alvarez VE, Hovde S, Abisambra JF, Kuo MH, Kanaan N, Murray ME, Crary JF, Zhao J, Cheng JX, Petrucelli L, Li H, Emili A, Wolozin B. Interaction of tau with HNRNPA2B1 and N6-methyladenosine RNA mediates the progression of tauopathy. Molecular Cell. 2021 Oct 21;81(20):4209-4227.e12.
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  9. Ahn KS, O'Brien DR, Kim YH, Kim TS, Yamada H, Park JW, Park SJ, Kim SH, Zhang C, Li H, Kang KJ, Roberts LR. Associations of Serum Tumor Biomarkers with Integrated Genomic and Clinical Characteristics of Hepatocellular Carcinoma. Liver Cancer 2021;10:593-605.
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  10. Hurley RM, McGehee CD, Nesic K, Correia C, Weiskittel TM, Kelly RL, Venkatachalam A, Hou X, Pathoulas NM, Meng XW, Kondrashova O, Radke MR, Schneider PA, Flatten KS, Peterson KL, Becker MA, Wong EM, Southey MS, Alexander Dobrovic AD, Lin KK, Thomas C Harding TC, McNeish I, Ross CA, Wagner JM, Wakefield MJ, Scott CL, Haluska P, Wahner Hendrickson AE, Karnitz LM, Swisher EM, Li H, Weroha SJ, Kaufmann SH. Characterization of a RAD51C-Silenced High Grade Serous Ovarian Cancer Model During Development of PARP Inhibitor Resistance. NAR Cancer. 2021 Sep; 3 (3):zcab028.
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  11. Sun Z, Yu H, Zhao J, Tan T, Pan H, Zhu Y, Chen L, Zhang C, Zhang L, Lei A, Xu Y, Bi X, Huang X, Gao B, Wang L, Correia C, Chen M, Sun Q, Feng Y, Shen L, Wu H, Wang J, Shen X, Daley GQ, Li H, Zhang J. LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells. Protein Cell. 2021 Jul 31.
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  12. Weiskittel TM, Correia C, Yu G, Ung CY, Kaufmann SH, Billadeau DD, Li H. The Trifecta of Single Cell, Systems Biology, and Machine Learning Approaches. Genes (Basel). 2021 Jul 20;12(7):1098.
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  13. Dong Z, Yeo KS, Lopez G, Zhang C, Dankert Eggum E, Rokita JL, Ung CY, Levee T, Her ZP, Howe C, Hou X, van Ree J, Li S, He S, Tao T, Fritchie K, Torres-Mora J, Lehman J, Meves A, Razidlo G, Rathi K, Weroha SJ, Look AT, van Deursen J, Li H, Westendorf J, Maris J, Zhu S. GAS7 Deficiency Promotes Metastasis of MYCN-driven Neuroblastoma. Cancer Research. 2021 Jun 1; 81 (11):2995-3007.
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  14. Monie D, Correia C, Ung CY, Zhang C, Vile R, Li H. Modular network mechanism of CCN1-associated resistance to HSV-1-derived oncolytic immunovirotherapies for glioblastomas. Sci Rep. 2021 May 27;11(1):11198.
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  15. Cairns J, Ingle JN, Kalari KR, Goetz MP, Weinshilboum RM, Gao H, Li H, Ghanat Bari M, Wang L. Anastrozole regulates fatty acid synthase in breast cancer. Mol Cancer Ther. 2021; molcanther.0509.2021.
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  16. Ding H, Vincelette N, McGehee C, Kohorst M, Koh B, Venkatachalam A, Meng XW, Schneider P, Flatten K, Peterson K, Correia C, Lee SH, Patnaik M, Webster J, Ghiaur G, Smith B, Karp J, Keith Pratz, Li H, Karnitz L, Kaufmann S. CDK2-mediated TNFa Upregulation as a Mechanism of Selective Cytotoxicity in Acute Leukemia. Cancer Research. 2021 May 15; 81 (10):2666-2678.
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  17. Meng-Lin K, Ung CY, Weiskittel TM, Chen A, Zhang C, Correia C, Li H. Machine Learning and Systems Biology Approaches to Characterize Dosage-Based Gene Dependencies in Cancer Cells. J Bioinform Syst Biol. 2021; 4 (1): 13-32.
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  18. Hamashima K, Gautam P, Lau KA, Khiong CW, Blenkinsop TA, Li H, Loh YH. Potential Modes of COVID-19 Transmission From Human Eye Revealed by Single-cell Atlas. bioRxiv. 2020.05.09.085613.
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  19. Crist AM, Hinkle KM, Wang X, Moloney CM, Matchett BJ, Labuzan SA, Frankenhauser I, Azu NO, Liesinger AM, Lesser ER, Serie DJ, Quicksall ZS, Patel TA, Carnwath TP, DeTure M, Tang X, Petersen RC, Duara R, Graff-Radford NR, Allen M, Carrasquillo MM, Li H, Ross OA, Ertekin-Taner N, Dickson DW, Asmann YW, Carter RE, Murray ME. Transcriptomic analysis to identify genes associated with selective hippocampal vulnerability in Alzheimer's disease. Nature Communications. 2021 Apr 19; 12 (1):2311.
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  20. Horn IP, Marks DL, Koenig AN, Hogenson TL, Almada LL, Goldstein LE, Romecin Duran PA, Vera R, Vrabel AM, Cui G, Rabe KG, Bamlet WR, Mer G, Sicotte H, Zhang C, Li H, Petersen GM, Fernandez-Zapico ME. A rare germline CDKN2A variant (47T>G; p16-L16R) predisposes carriers to pancreatic cancer by reducing cell cycle inhibition. J Biol Chem. 2021 Apr 3;100634.
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  21. Monie DD, Bhandarkar AR, Parney IF, Correia C, Sarkaria JN, Vile RG, Li H. Synthetic and systems biology principles in the design of programmable oncolytic virus immunotherapies for glioblastoma multiforme. Neurosurgical Focus. 2021 Feb;50(2):E10.
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  22. Li X, Guo X, Zhu Y, Wei G, Zhang Y, Li Z, Xu H, Cui J, Wu W, He J, Ritchie ME, Weiskittel TM, Li H, Yu H, Ding L, Shao M, Luo Q, Xu X, Teng X, Chang AH, Zhang J, Huang H, Hu Y. Single cell transcriptomic analysis reveals BCMA CAR-T cell dynamics in a patient with refractory primary plasma cell leukemia. Molecular Therapy. 2021 Feb 3; 29 (2):645-657.
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  23. Aggen D, Ager C, Obradovic A, Chowdhury N, Ghasemzadeh A, Mao W, Chaimowitz M, Lopez-Bujanda Z, Spina C, Hawley J, Dallos M, Zhang C, Wang V, Li H, Guo X, Drake C. Blocking Interleukin-1 Beta Promotes Tumor Regression and Remodeling of the Myeloid Compartment in a Renal Cell Carcinoma Model: Multi-Dimensional Analyses. Clinical Cancer Research. 2021 Jan 15; 27 (2):608-621.
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  24. Pietrobono S, Anichini G, Sala C, Manetti F, Almada LL, Pepe S, Carr RM, Paradise BD, Sarkaria JN, Davila JI, Tofani L, Battisti I, Arrigoni G, Ying L, Zhang C, Li H, Meves A, Fernandez-Zapico ME, Stecca B. ST3GAL1 is a target of the SOX2-GLI1 transcriptional complex and promotes melanoma metastasis through AXL. Nature Communications. 2020 Nov 17;11(1):5865.
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  25. Wang HF , Warrier T, Farran CA , Zheng ZH , Xing QR, Fullwood MJ, Zhang LF, Li H, Xu J, Lim TM, Loh YH. Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen. Cell Reports. 2020 Oct 27;33(4):108309.
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  26. Limzerwala JF, Jeganathan KB, Kloeber JA, Davies BA, Zhang C, Sturmlechner I, Zhong J, Velasco RF, Fields AP, Yuan Y, Baker DJ, Zhou D, Li H, Katzmann DJ, van Deursen JM. FoxM1 insufficiency hyperactivates Ect2-RhoA-mDia1 signaling to drive cancer. Nature Cancer. 2020; 1:1010-1024.
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  27. Xing QR, El Farran CA, Gautam P, Chuah YS, Warrier T, Toh CXD, Kang NY, Sugii S, Chang YT, Xu J, Collins JJ, Daley GQ, Li H, Zhang LF, Loh YH. Diversification of Reprogramming Trajectories Revealed by Parallel Single-cell Transcriptome and Chromatin Accessibility Sequencing. Science Advances. 2020 Sep 11;6(37):eaba1190.
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  28. Zhou Y, Han C, Wang E, Lorch AH, Serafin V, Cho BK, Guttierrez Diaz BT, Calvo J, Fang C, Khodadadi-Jamayran A, Tabaglio T, Marier C, Kuchmiy A, Sun L, Yacu G, Filip SK, Jin Q, Takahashi YH, Amici DR, Rendleman EJ, Rawat R, Bresolin S, Paganin M, Zhang C, Li H, Kandela I, Politanska Y, Abdala-Valencia H, Mendillo ML, Zhu P, Palhais B, Van Vlierberghe P, Taghon T, Aifantis I, Goo YA, Guccione E, Heguy A, Tsirigos A, Wee KB, Mishra RK, Pflumio F, Accordi B, Basso G, Ntziachristos P. Posttranslational regulation of the exon skipping machinery controls aberrant splicing in leukemia. Cancer Discovery. 2020 Sep; 10 (9):1388-1409.
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  29. Ho MF, Zhang C, Zhang L, Wei L, Zhou Y, Moon I, Geske JR, Choi DS, Biernacka J, Frye M, Wen Z, Karpyak VM, Li H, Weinshilboum R. TSPAN5 influences serotonin and kynurenine: pharmacogenomic mechanisms related to alcohol use disorder and acamprosate treatment response. Mol Psychiatry. 2020 Aug 4
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  30. Xing QR, El Farran CA, Zeng YY, Yi Y, Warrier T, Gautam P, Collins JJ, Xu J, Droge P, Koh CG, Li H, Zhang LF, Loh YH Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility. Genome Research. 2020 Jul;30(7):1027-1039.
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  31. Cairns J, Ingle JN, Dudenkov TTM, Kalari KR, Carlson EE, Na J, Buzdar AU, Robson ME, Ellis MJ, Goss PE, Shepherd LE, Goodnature B, Goetz MP, Weinshilboum RM, Li H, Ghanat Bari M, Wang L. Pharmacogenomics of aromatase inhibitors in postmenopausal breast cancer and additional mechanisms of anastrozole action. JCI Insight. 2020 Jul 23.
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  32. Zhao W, Lei A, Tian L, Wang X, Correia C, Weiskittel T, Li H, Trounson A, Fu Q, Yao K, Zhang J. Strategies for Genetically Engineering Hypoimmunogenic Universal Pluripotent Stem Cells. iScience. 2020 May 17; 23 (6):101162.
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  33. Lu J, Zhu X, Shui JE, Xiong L, Gierahn T, Zhang C, Wood M, Hally S, Love JC, Li H, Crawford BC, Mou H, Lerou PH. Rho/SMAD/mTOR triple inhibition enables long-term expansion of human neonatal tracheal aspirate-derived airway basal cell-like cells. Pediatr Res. 2020 May 4 Epub 2020 May 04.
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  34. Monie DD, Zhang C, Correia C, Ung C, Vile RG, Li H. Network-guided bioengineering of oncolytic immunovirotherapies for glioblastoma. J Immunol 2020 May 1, 204(1 Supplement)169.17.
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  35. Skamagki M, Zhang C, Liu Z, Li H, Zhao R, Kim K. Reprogramming of Pluripotency-Specific microRNA Signatures Is Not Essential to Generate Inducible Pluripotent Stem Cells. Cell Reprogram 2020 Feb; 22 (1):1-2.
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  36. Sieben CJ, Jeganathan KB, Nelson GG, Sturmlechner I, Zhang C, van Deursen W, Bakker B, Foijer F, Li H, Baker DJ, van Deursen JM. BubR1 allelic effects drive phenotypic heterogeneity in mosaic-variegated aneuploidy progeria syndrome. Journal of Clinical Investigation. 2020 Jan 2;130(1):171-188.
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  37. Apicco DJ, Zhang C, Maziuk B, Jiang L, Ballance HI, Boudeau S, Ung CY, Li H, Wolozin B. Dysregulation of RNA splicing in tauopathies. Cell Reports. 2019 Dec 24;29(13):4377-4388.e4.
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  38. Kanakkanthara A, Kurmi K, Ekstrom TL, Hou X, Purfeerst ER, Heinzen EP, Correia C, Huntoon CJ, O'Brien D, Wahner Hendrickson AE, Dowdy SC, Li H, Oberg AL, Hitosugi T, Kaufmann SH, Weroha SJ, Karnitz LM.. BRCA1 Deficiency Upregulates NNMT, Which Reprograms Metabolism and Sensitizes Ovarian Cancer Cells to Mitochondrial Metabolic Targeting Agents. Cancer Res. 2019 Dec 1; 79 (23):5920-5929.
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  39. Cabral DJ, Penumutchu S, Reinhart EM, Zhang C, Korry BJ, Wurster JI, Nilson R, Guang A, Sano WH, Rowan-Nash AD, Li H, Belenky P. Microbial metabolism modulates antibiotic susceptibility within the murine gut microbiome. Cell Metabolism. 2019 Oct 1;30(4):800-823.e7.
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  40. Neavin DR, Lee JH, Liu D, Ye Z, Li H, Wang L, Ordog T, Weinshilboum RM. Nucleotide Polymorphisms at a Distance from Aryl Hydrocarbon Receptor (AHR) Binding Sites Influence AHR Ligand-Dependent Gene Expression. Drug Metab Dispos. 2019 Sep; 47 (9):983-994.
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  41. Ung CY, Ghanat Bari M, Zhang C, Liang J, Correia C, Li H. Regulostat Inferelator: A novel network biology platform to uncover molecular devices that predetermine cellular response phenotypes. Nucleic Acids Research. 2019 Aug 22;47(14):e82.
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  42. Aziz K, Limzerwala JF, Sturmlechner I, Hurley E, Zhang C, Jeganathan KB, Nelson G, Bronk S, Velasco RF, van Deursen EJ, O'Brien DR, Kocher JA, Youssef SA, van Ree JH, de Bruin A, van den Bos H, Spierings DCJ, Foijer F, van de Sluis B, Roberts LR, Gores G, Li H, van Deursen JM. Ccne1 Overexpression Causes Chromosome Instability in Liver Cells and Liver Tumor Development in Mice. Gastroenterology. 2019 Jul;157(1):210-226.e12.
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  43. Tu X, Qin B, Zhang Y, Zhang C, Kahila M, Nowsheen S, Yin P, Yuan J, Pei H, Li H, Yu J, Song Z, Zhou Q, Zhao F, Liu J, Zhang C, Dong H, Mutter RW, Lou Z. PD-L1 (B7-H1) Competes with the RNA Exosome to Regulate the DNA Damage Response and Can Be Targeted to Sensitize to Radiation or Chemotherapy. Mol Cell. 2019 Jun 20;74(6):1215-1226.e4.
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  44. Ho MF, Zhang C, Zhang L, Li H, Weinshilboum RM. Ketamine and Active Ketamine Metabolites Regulate STAT3 and the Type I Interferon Pathway in Human Microglia: Molecular Mechanisms Linked to the Antidepressant Effects of Ketamine. Front Pharmacol. 2019; 10:1302.
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  45. Sun Z, Zhao J, Yu H, Zhang C, Li H, Zeng Z, Zhang J Metabolomics in Stem Cell Biology Research. Methods Mol Biol. 2019 1975:321-330.
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  46. Liu Z, Che P, Mercado JJ, Hackney JR, Friedman GK, Zhang C, You Z, Zhao X, Ding Q, Kim K, Li H, Liu Z, Markert JM, Nabors B, Gillespie GY, Zhao R, Han X. Characterization of iPSCs derived from low grade gliomas revealed early regional chromosomal amplifications during gliomagenesis. J Neurooncol. 2019 Jan;141(2):289-301.
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  47. Wang L, Gao J, Siedlak SL, Torres S, Jiang Y, Xie F, Liu J, Liang J, Fujioka H, Perry G, Zhang C, Li H, Wang X. Mitofusin 2 Regulates Axonal Transport of Calpastatin to Prevent Neuromuscular Synaptic Elimination in Skeletal Muscles. Cell Metabolism. 2018 Sep 4;28(3):400-414.e8.
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  48. Shrestha S, Zhang C, Jerde CR, Nie Q, Li H, Offer SM, Diasio RB. Gene-specific variant classifier (DPYD-Varifier) to identify deleterious alleles of dihydropyrimidine dehydrogenase. Clinical Pharmacology & Therapeutics. 2018 Oct;104(4):709-718.
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  49. Maziuk BF, Apicco DJ, Lourdes Cruz A, Jiang L, Ash PEA, Lummertz Rocha E, Zhang C, Yu WH, Leszyk J, Abisambra JF, Li H, Wolozin B. RNA binding proteins co-localize with small tau inclusions in tauopathy. Acta Neuropathologica Communications. 2018 Aug 1;6(1):71.
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  50. Spadafora R, Lu J, Khetani RS, Zhang C, Iberg A, Li H, Shi Y, Lerou P. Lung Resident Mesenchymal Stromal Cells Reveal Transcriptional Dynamics of Lung Development in Preterm Infants. American Journal of Respiratory and Critical Care Medicine. 2018 Oct 1;198(7):961-964.
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  51. Fang HT, El Farran CA, Xing QR, Zhang LF, Li Hu, Lim B, Loh YH. Global H3.3 dynamic deposition defines its bimodal role in cell fate transition. Nature Communications. 2018 Apr 18;9(1):1537.
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  52. Childs BG, Li H, van Deursen JM. Senescent cells: a therapeutic target for cardiovascular disease. Journal of Clinical Investigation. 2018 Apr 2;128(4):1217-1228.
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  53. Ho MF, Lummertz da Rocha E, Zhang C, Ingle J, Goss P, Shepherd L, Kubo M, Wang L, Li H, Weinshilboum R. TCL1A, a novel transcription factor and a co-regulator of NF-small ka, CyrillicB p65: SNP and estrogen-dependence. Journal of Pharmacology and Experimental Therapeutics. 2018 Jun;365(3):700-710.
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  54. Lummertz da Rocha E, Rowe RG, Lundin V, Malleshaiah M, Jha DK, Rambo CR, Li H, North TE, Collins JJ, Daley GQ. Reconstruction of complex single-cell trajectories using CellRouter. Nature Communications. 2018 Mar 1; 9 (1):892.
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  55. Kasendra M, Tovaglieri A, Sontheimer-Phelps A, Jalili-Firoozinezhad S, Bein A, Chalkiadaki A, Scholl W, Zhang C, Rickner H, Richmond CA, Li H, Breault DT, Ingber DE. Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids. Scientific Reports. 2018 Feb 13;8(1):2871.
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  56. Zhang J, Zhao J, Dahan P, Lu V, Zhang C, Li H, Teitell MA. Metabolism in Pluripotent Stem Cells and Early Mammalian Development. Cell Metabolism. 2018 Feb 6;27(2):332-338.
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  57. Lu J, Baccei A, Lummertz da Rocha E, Guillermier C, McManus S, Finney LA, Zhang C, Steinhauser ML, Li H, Lerou PH. Single-cell RNA sequencing reveals metallothionein heterogeneity during hESC differentiation to definitive endoderm. Stem Cell Research. 2018 Apr;28:48-55.
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  58. Apicco DJ, Ash PEA, Maziuk B, LeBlang C, Medalla M, Abdullatif AA, Ferragud A, Botelho E, Ballance HI, Dhawan U, Boudeau S, Cruz AL, Kashy D, Wong A, Goldberg LR, Yazdani N, Zhang C, Ung CY, Tripodis Y, Kanaan NM, Ikezu T, Cottone P, Leszyk J, Li H, Luebke J, Bryant CD, Wolozin B. Reducing the RNA binding protein TIA1 protects against tau-mediated neurodegeneration in vivo. Nature Neuroscience. 2018 Jan;21(1):72-80.
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  59. Chandrasekaran S, Zhang J, Sun Z, Zhang L, Ross CA, Huang YC, Asara JM, Li H, Daley GQ, Collins JJ. Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling. Cell Reports. 2017 Dec 5;21(10):2965-2977.
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  60. Zhang C, Skamagki M, Liu Z, Ananthanarayanan A, Zhao R, Li H, Kim K. Biological significance of suppression of oxidative phosphorylation in induced pluripotent stem cells. Cell Reports. 2017 Nov 21;21(8):2058-2065.
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  61. Ebbert MTW, Ross CA, Pregent LJ, Lank RJ, Zhang C, Katzman RB, Jansen-West K, Song Y, Lummertz da Rocha E, Palmucci C, Desaro P, Robertson AE, Caputo AM, Dickson DW, Boylan KB, Rademakers R, Ordog T, Li H, Belzil VV. Conserved DNA methylation combined with differential frontal cortex and cerebellar expression distinguishes C9orf72-associated and sporadic ALS, and implicates SERPINA1 in disease. Acta Neuropathologica. 2017 Nov;134(5):715-728.
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  62. Liu Z, Zhang C, Skamagki M, Khodadadi-Jamayran A, Zhang W, Kong D, Chang CW, Feng J, Han X, Townes TM, Li H, Kim K, Zhao R. Elevated p53 Activities Restrict Differentiation Potential of MicroRNA-Deficient Pluripotent Stem Cells. Stem Cell Reports. 2017 Nov 14;9(5):1604-1617.
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  63. Skamagki M, Zhang C, Ross CA, Ananthanarayanan A, Liu Z, Mu Q, Basu U, Wang J, Zhao R, Li H, Kim K. RNA Exosome Complex-Mediated Control of Redox Status in Pluripotent Stem Cells. Stem Cell Reports. 2017 Oct 10;9(4):1053-1061.
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  64. Zhu S, Zhang X, Weichert-Leahey N, Dong Z, Zhang C, Lopez G, Tao T, He S, Wood AC, Oldridge D, Ung CY, van Ree JH, Khan A, Salazar BM, Lummertz da Rocha E, Zimmerman MW, Guo F, Cao H, Hou X, Weroha SJ, Perez-Atayde AR, Neuberg DS, Meves A, McNiven MA, van Deursen JM, Li H, Maris JM, Look AT. LMO1 Synergizes with MYCN to Promote Neuroblastoma Initiation and Metastasis. Cancer Cell. 2017 Sep 11;32(3):310-323.e5.
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  65. Skamagki M, Correia C, Yeung P, Baslan T, Beck S, Zhang C, Ross CA, Dang L, Liu Z, Giunta S, Chang TP, Wang J, Ananthanarayanan A, Bohndorf M, Bosbach B, Adjaye J, Funabiki H, Kim J, Lowe S, Collins JJ, Lu CW, Li H, Zhao R, Kim K. ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors. Nature Cell Biology. 2017 Sep;19(9):1037-1048.
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  66. Zhang J, Li H, Trounson A, Wu JC, Nioi P. Combining hiPSCs and Human Genetics: Major Applications in Drug Development. Cell Stem Cell. 2017 Aug 3;21(2):161-165.
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  67. Ghanat Bari M, Ung CY, Zhang C, Zhu S, Li H. Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks. Scientific Reports. 2017 Aug 1;7(1):6993.
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  68. Zhang X, Dong Z, Zhang C, Ung CY, He S, Tao T, Oliveira AM, Meves A, Ji B, Look AT, Li H, Neel BG, Zhu S. Critical Role for GAB2 in Neuroblastoma Pathogenesis through the Promotion of SHP2/MYCN Cooperation. Cell Reports. 2017 Mar 21;18(12):2932-2942.
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  69. Liu Z, Zhang C, Khodadadi-Jamayran A, Dang L, Han X, Kim K, Li H, Zhao R. Canonical microRNAs enable differentiation, protect against DNA damage, and promote cholesterol biosynthesis in neural stem cells. Stem Cells and Development. 2017 Feb 1;26(3):177-188.
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  70. Gao X, Lee HY, Lummertz da Rocha E, Zhang C, Lu YF, Li D, Feng Y, Ezike J, Elmes RR, Barrasa MI, Cahan P, Li H, Daley GQ, Lodish HF. TGF-beta inhibitors stimulate red blood cell production by enhancing self-renewal of BFU-E erythroid progenitors. Blood. 2016 Dec 8;128(23):2637-2641.
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  71. Cheng H, Ang HY, A El Farran C, Li P, Fang HT, Liu TM, Kong SL, Chin ML, Ling WY, Lim EK, Li H, Huber T, Loh KM, Loh YH, Lim B. Reprogramming mouse fibroblasts into engraftable myeloerythroid and lymphoid progenitors. Nature Communications. 2016 Nov 21;7:13396.
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  72. Cairns J, Ung CY, Lummertz da Rocha E, Zhang C, Correia C, Weinshilboum R, Wang L, Li H. A network-based phenotype mapping approach to identify genes that modulate drug response phenotypes. Scientific Reports. 2016 Nov 14;6:37003.
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  73. Wang W, Wang L, Lu J, Siedlak SL, Fujioka H, Liang J, Jiang S, Ma X, Jiang Z, Lummertz da Rocha E, Sheng M, Choi H, Lerou PH, Li H, Wang X. The inhibition of TDP-43 mitochondrial localization blocks its neuronal toxicity. Nature Medicine. 2016 Aug;22(8):869-878.
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  74. Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, Ross CA, Cacchiarelli D, Xia Q, Seligson M, Shinoda G, Xie W, Cahan P, Wang L, Ng SC, Tintara S, Trapnell C, Onder T, Loh YH, Mikkelsen T, Sliz P, Teitell MA, Asara JM, Marto JA, Li H, Collins JJ, Daley GQ. LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. Cell Stem Cell. 2016 Jul 7;19(1):66-80.
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  75. Toh CD, Chan JW, Chong ZS, Wang HF, Guo HC, Satapathy S, Ma D, Goh GY, Khattar E, Yang L, Tergaonkar V, Chang YT, Collins JJ, Daley GQ, Wee KB, Farran CA, Li H, Lim YP, Bard FA, Loh YH. RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming. Cell Reports. 2016 Jun 21;15(12):2597-607.
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  76. Lummertz da Rocha E, Ung CY, Mcgehee CD, Correia C, Li H. NetDecoder: A Network-based Platform to Decode Context-Specific Biological Networks and Gene Activities. Nucleic Acids Research. 2016 Jun 2;44(10):e100.
    View PubMed  NetDecoder Portal
  77. Cohen NR, Ross CA, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, Collins JJ. A role for the bacterial GATC methylome in antibiotic stress survival. Nature Genetics. 2016 May 48(5):581-586.
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  78. Vanderweyde T, Apicco DJ, Youmans-Kidder K, Ash PE, Cook C, Lummertz da Rocha E, Jansen-West K, Frame AA, Citro A, Leszyk J, Ivanov P, Abisambra JF, Steffen M, Li H, Petrucelli L, Wolozin B. Interaction of tau with the RNA-binding Protein TIA1 Regulates tau Pathophysiology and Toxicity. Cell Reports. 2016 May 17;15(7):1455-66.
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  79. Lu J, Li H, Baccei A, Sasaki T, Gilbert DM, Lerou PH. Influence of ATM-mediated DNA damage response on genomic variation in human induced pluripotent stem cells. Stem Cells and Development. 2016 May 1;25(9):740-7.
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  80. Kim HJ, Li H, Collins JJ, Ingber DE. Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip. Proceedings of the National Academy of Sciences of the United States of America. 2016 Jan 5; 113(1):E7-E15.
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  81. Yang BX, El Farran CA, Guo HC, Yu T, Fang HT, Wang HF, Schlesinger S, Seah YF, Goh GY, Neo SP, Li Y, Lorincz MC, Tergaonkar V, Lim TM, Chen L, Gunaratne J, Collins JJ, Goff SP, Daley GQ, Li H, Bard FA, Loh YH. Systematic identification of factors for provirus silencing in embryonic stem cells. Cell. 2015 Sep 24; 163(1):230-45.
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  82. Prudencio M, Belzil VV, Batra R, Ross CA, Gendron TF, Pregent LJ, Murray ME, Overstreet KK, Piazza-Johnston AE, Desaro P, Bieniek KF, DeTure M, Lee WC, Biendarra SM, Davis MD, Baker MC, Perkerson RB, van Blitterswijk M, Stetler CT, Rademakers R, Link CD, Dickson DW, Boylan KB, Li H, Petrucelli L. Distinct brain transcriptome profiles in C9orf72-associated and sporadic ALS. Nature Neuroscience. 2015 Aug; 18(8):1175-82.
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  83. Lee HY, Gao X, Barrasa MI, Li H, Elmes RR, Peters LL, Lodish HF. PPAR-alpha and glucocorticoid receptor synergize to promote erythroid progenitor self-renewal. Nature. 2015 Jun 25; 522(7557):474-7.
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  84. Shih YH, Zhang Y, Ding Y, Ross CA, Li H, Olson TM, Xu X. Cardiac transcriptome and dilated cardiomyopathy genes in zebrafish. Circulation: Cardiovascular Genetics. 2015 Apr; 8(2):261-9.
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  85. Chen CD, Li H, Liang J, Hixson K, Zeldich E, Abraham CR. The anti-aging and tumor suppressor protein Klotho enhances differentiation of a human oligodendrocytic hybrid cell line. Journal of Molecular Neuroscience. 2015 Jan; 55(1):76-90.
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  86. Wu L, Schaid DJ, Sicotte H, Wieben ED, Li H, Petersen GM. Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations. Journal of Medical Genetics. 2015 Jan; 52(1):10-6.
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  87. Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature. 2014 Dec 4; 516(7529):56-61.
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  88. Dusonchet J, Li H, Guillily M, Liu M, Stafa K, Derada Troletti C, Boon JY, Saha S, Glauser L, Mamais A, Citro A, Youmans KL, Liu L, Schneider BL, Aebischer P, Yue Z, Bandopadhyay R, Glicksman MA, Moore DJ, Collins JJ, Wolozin B. A Parkinson's disease gene regulatory network identifies the signaling protein RGS2 as a modulator of LRRK2 activity and neuronal toxicity. Human Molecular Genetics. 2014 Sep 15; 23(18):4887-905.
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  89. Colvin TA, Gabai VL, Gong J, Calderwood SK, Li H, Gummuluru S, Matchuk ON, Smirnova SG, Orlova NV, Zamulaeva IA, Garcia-Marcos M, Li X, Young ZT, Rauch JN, Gestwicki JE, Takayama S, Sherman MY. Hsp70-Bag3 interactions regulate cancer-related signaling networks. Cancer Research. 2014 Sep 1; 74(17):4731-40.
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  90. Cahan P, Li H, Morris SA, Lummertz da Rocha E, Daley GQ, Collins JJ. CellNet: network biology applied to stem cell engineering. Cell. 2014 Aug 14; 158(4):903-15.
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  91. Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ. Dissecting engineered cell types and enhancing cell fate conversion via CellNet. Cell. 2014 Aug 14; 158(4):889-902.
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  92. Lang AH, Li H, Collins JJ, Mehta P. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes. PLOS Computational Biology. 2014 Aug; 10(8):e1003734.
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  93. Lu Y, Loh YH, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CX, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell. 2014 Jul 3; 15(1):92-101.
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  94. Tan HK, Toh CX, Ma D, Yang B, Liu TM, Lu J, Wong CW, Tan TK, Li H, Syn C, Tan EL, Lim B, Lim YP, Cook SA, Loh YH. Human finger-prick induced pluripotent stem cells facilitate the development of stem cell banking. Stem Cells Translational Medicine. 2014 May; 3(5):586-98.
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  95. Lu J, Li H, Hu M, Sasaki T, Baccei A, Gilbert DM, Liu JS, Collins JJ, Lerou PH. The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming. Cell Reports. 2014 Apr 10; 7(1):70-8.
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  96. Jasuja R, Costello JC, Singh R, Gupta V, Spina CS, Toraldo G, Jang H, Li H, Serra C, Guo W, Chauhan P, Narula NS, Guarneri T, Ergun A, Travison TG, Collins JJ, Bhasin S. Combined administration of testosterone plus an ornithine decarboxylase inhibitor as a selective prostate-sparing anabolic therapy. Aging Cell. 2014 Apr; 13(2):303-10.
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  97. Ma H, Ng HM, Teh X, Li H, Lee YH, Chong YM, Loh YH, Collins JJ, Feng B, Yang H, Wu Q. Zfp322a Regulates Mouse ES Cell Pluripotency and Enhances Reprogramming Efficiency. PLOS Genetics. 2014 Feb; 10(2):e1004038.
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  98. Brock A, Krause S, Li H, Kowalski M, Goldberg MS, Collins JJ, Ingber DE. Silencing HoxA1 by intraductal injection of siRNA lipidoid nanoparticles prevents mammary tumor progression in mice. Science Translational Medicine. 2014 Jan 1; 6(217):217ra2.
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  99. Pandey SP, Winkler JA, Li H, Camacho DM, Collins JJ, Walker GC. Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics. 2014; 15:121.
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  100. Faucon PC, Pardee K, Kumar RM, Li H, Loh YH, Wang X. Gene networks of fully connected triads with complete auto-activation enable multistability and stepwise stochastic transitions. PLoS One. 2014; 9(7):e102873.
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  101. Ma H, Ow JR, Tan BC, Goh Z, Feng B, Loh YH, Fedele M, Li H, Wu Q. The dosage of Patz1 modulates reprogramming process. Scientific Reports. 2014; 4:7519.
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  102. Doulatov S, Vo LT, Chou SS, Kim PG, Arora N, Li H, Hadland BK, Bernstein ID, Collins JJ, Zon LI, Daley GQ. Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. Cell Stem Cell. 2013 Oct 3; 13(4):459-70.
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  103. Griffith RM, Li H, Zhang N, Favazza TL, Fulton AB, Hansen RM, Akula JD. Next-generation sequencing analysis of gene regulation in the rat model of retinopathy of prematurity. Documenta Ophthalmologica. 2013 Aug; 127(1):13-31.
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  104. Chen CD, Sloane JA, Li H, Aytan N, Giannaris EL, Zeldich E, Hinman JD, Dedeoglu A, Rosene DL, Bansal R, Luebke JI, Kuro-o M, Abraham CR. The antiaging protein Klotho enhances oligodendrocyte maturation and myelination of the CNS. Journal of Neuroscience. 2013 Jan 30; 33(5):1927-39.
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  105. Ung CY, Lam SH, Zhang X, Li H, Zhang L, Li B, Gong Z. Inverted expression profiles of sex-biased genes in response to toxicant perturbations and diseases. PLoS One. 2013; 8(2):e56668.
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  106. McKinney-Freeman S, Cahan P, Li H, Lacadie SA, Huang HT, Curran M, Loewer S, Naveiras O, Kathrein KL, Konantz M, Langdon EM, Lengerke C, Zon LI, Collins JJ, Daley GQ. The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell. 2012 Nov 2; 11(5):701-14.
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  107. Brock A, Goh HT, Yang B, Lu Y, Li H, Loh YH. Cellular reprogramming: a new technology frontier in pharmaceutical research. Pharmaceutical Research. 2012 Jan; 29(1):35-52.
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  108. Ferree A, Guillily M, Li H, Smith K, Takashima A, Squillace R, Weigele M, Collins JJ, Wolozin B. Regulation of physiologic actions of LRRK2: focus on autophagy. Neurodegenerative Diseases. 2012; 10(1-4):238-41.
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  109. Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, Huo H, Loh YH, Aryee MJ, Lensch MW, Li H, Collins JJ, Feinberg AP, Daley GQ. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nature Biotechnology. 2011 Dec; 29(12):1117-9.
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  110. Ung CY, Lam SH, Zhang X, Li H, Ma J, Zhang L, Li B, Gong Z. Existence of inverted profile in chemically responsive molecular pathways in the zebrafish liver. PLoS One. 2011; 6(11):e27819.
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  111. Loh YH, Yang L, Yang JC, Li H, Collins JJ, Daley GQ. Genomic approaches to deconstruct pluripotency. Annual Review of Genomics and Human Genetics. 2011; 12:165-85.
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  112. Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell. 2010 Nov 5; 7(5):618-30.
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  113. Loh YH, Hartung O, Li H, Guo C, Sahalie JM, Manos PD, Urbach A, Heffner GC, Grskovic M, Vigneault F, Lensch MW, Park IH, Agarwal S, Church GM, Collins JJ, Irion S, Daley GQ. Reprogramming of T cells from human peripheral blood. Cell Stem Cell. 2010 Jul 2; 7(1):15-9.
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  114. Rao H, Li Z, Li X, Ma X, Ung C, Li H, Liu X, Chen Y. Identification of small molecule aggregators from large compound libraries by support vector machines. Journal of Computational Chemistry. 2010 Mar; 31(4):752-63.
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  115. Li H, Ung CY, Ma XH, Liu XH, Li BW, Low BC, Chen YZ. Pathway sensitivity analysis for detecting pro-proliferation activities of oncogenes and tumor suppressors of epidermal growth factor receptor-extracellular signal-regulated protein kinase pathway at altered protein levels. CANCER. 2009 Sep 15; 115(18):4246-63.
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  116. Li H, Ung CY, Ma XH, Li BW, Low BC, Cao ZW, Chen YZ. Simulation of crosstalk between small GTPase RhoA and EGFR-ERK signaling pathway via MEKK1. Bioinformatics. 2009 Feb 1; 25(3):358-64.
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  117. Ung CY, Li H, Ma XH, Jia J, Li BW, Low BC, Chen YZ. Simulation of the regulation of EGFR endocytosis and EGFR-ERK signaling by endophilin-mediated RhoA-EGFR crosstalk. FEBS Letters. 2008 Jun 25; 582(15):2283-90.
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  118. Li H, Yap CW, Ung CY, Xue Y, Li ZR, Han LY, Lin HH, Chen YZ. Machine learning approaches for predicting compounds that interact with therapeutic and ADMET related proteins. Journal of Pharmaceutical Sciences. 2007 Nov; 96(11):2838-60.
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  119. Yap CW, Li H, Ji ZL, Chen YZ. Regression methods for developing QSAR and QSPR models to predict compounds of specific pharmacodynamic, pharmacokinetic and toxicological properties. Mini-Reviews in Medicinal Chemistry. 2007 Nov; 7(11):1097-107.
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  120. Li ZR, Han LY, Xue Y, Yap CW, Li H, Jiang L, Chen YZ. MODEL-molecular descriptor lab: a web-based server for computing structural and physicochemical features of compounds. Biotechnology and Bioengineering. 2007 Jun 1; 97(2):389-96.
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  121. Ung CY, Li H, Cao ZW, Li YX, Chen YZ. Are herb-pairs of traditional Chinese medicine distinguishable from others? Pattern analysis and artificial intelligence classification study of traditionally defined herbal properties. Journal of Ethnopharmacology. 2007 May 4; 111(2):371-7.
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  122. Ung CY, Li H, Kong CY, Wang JF, Chen YZ. Usefulness of traditionally defined herbal properties for distinguishing prescriptions of traditional Chinese medicine from non-prescription recipes. Journal of Ethnopharmacology. 2007 Jan 3; 109(1):21-8.
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  123. Ung CY, Li H, Yap CW, Chen YZ. In silico prediction of pregnane X receptor activators by machine learning approaches. Molecular Pharmacology. 2007 Jan; 71(1):158-68.
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  124. Chen X, Li H, Yap CW, Ung CY, Jiang L, Cao ZW, Li YX, Chen YZ. Computer prediction of cardiovascular and hematological agents by statistical learning methods. Cardiovascular and Hematological Agents in Medicinal Chemistry. 2007 Jan; 5(1):11-9.
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  125. Cui J, Han LY, Li H, Ung CY, Tang ZQ, Zheng CJ, Cao ZW, Chen YZ. Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties. Molecular Immunology. 2007 Jan; 44(4):514-20.
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  126. Chen X, Zhou H, Liu YB, Wang JF, Li H, Ung CY, Han LY, Cao ZW, Chen YZ. Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation. British Journal of Pharmacology. 2006 Dec; 149(8):1092-103.
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  127. Li H, Ung CY, Yap CW, Xue Y, Li ZR, Chen YZ. Prediction of estrogen receptor agonists and characterization of associated molecular descriptors by statistical learning methods. Journal of Molecular Graphics and Modelling. 2006 Nov; 25(3):313-23.
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  128. Xue Y, Li H, Ung CY, Yap CW, Chen YZ. Classification of a diverse set of Tetrahymena pyriformis toxicity chemical compounds from molecular descriptors by statistical learning methods. Chemical Research in Toxicology. 2006 Aug; 19(8):1030-9.
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  129. Yap CW, Xue Y, Li H, Li ZR, Ung CY, Han LY, Zheng CJ, Cao ZW, Chen YZ. Prediction of compounds with specific pharmacodynamic, pharmacokinetic or toxicological property by statistical learning methods. Mini-Reviews in Medicinal Chemistry. 2006 Apr; 6(4):449-59.
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  130. Zheng CJ, Han LY, Chen X, Cao ZW, Cui J, Lin HH, Zhang HL, Li H, Chen YZ. Information of ADME-associated proteins and potential application for pharmacogenetic prediction of drug responses. Current Pharmacogenomics and Personalized Medicine. 2006; 4(2):79-85.
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  131. Li H, Yap CW, Xue Y, Li ZR, Ung CY, Han LY, Chen YZ. Statistical Learning Approach for Predicting Specific Pharmacodynamic, Pharmacokinetic or Toxicological Properties of Pharmaceutical Agents. Drug Development Research. 2006; 66(4):245-59.
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  132. Han LY, Zheng CJ, Lin HH, Cui J, Li H, Zhang HL, Tang ZQ, Chen YZ. Prediction of functional class of novel plant proteins by a statistical learning method. New Phytologist. 2005 Oct; 168(1):109-21.
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  133. Li H, Yap CW, Ung CY, Xue Y, Cao ZW, Chen YZ. Effect of selection of molecular descriptors on the prediction of blood-brain barrier penetrating and nonpenetrating agents by statistical learning methods. Journal of Chemical Information and Modeling. 2005 Sep-Oct; 45(5):1376-84.
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  134. Li H, Ung CY, Yap CW, Xue Y, Li ZR, Cao ZW, Chen YZ. Prediction of genotoxicity of chemical compounds by statistical learning methods. Chemical Research in Toxicology. 2005 Jun; 18(6):1071-80.
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Book Chapters

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

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