Publications

  1. 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. Hum Mol Genet. 2014 Sep 15; 23(18):4887-905. Epub 2014 May 2
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  2. 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 Res. 2014 Sep 1; 74(17):4731-40. Epub 2014 Jul 03.
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  3. 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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  4. 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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  5. Lang AH, Li H, Collins JJ, Mehta P. Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes. PLoS Comput Biol. 2014 Aug; 10(8):e1003734. Epub 2014 Aug 14.
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  6. 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. Epub 2014 May 08.
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  7. 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. J Mol Neurosci. 2014 Jun 08.
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  8. 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 Transl Med. 2014 May; 3(5):586-98. Epub 2014 Mar 19.
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  9. 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 Rep. 2014 Apr 10; 7(1):70-8. Epub 2014 Mar 27.
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  10. 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. Epub 2013 Dec 04.
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  11. 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 Genet. 2014 Feb; 10(2):e1004038. Epub 2014 Feb 13.
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  12. 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. Sci Transl Med. 2014 Jan 1; 6(217):217ra2.
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  13. 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. Epub 2014 Feb 11.
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  14. 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. Epub 2014 Jul 24.
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  15. 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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  16. 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. Doc Ophthalmol. 2013 Aug; 127(1):13-31. Epub 2013 Jun 18.
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  17. 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. J Neurosci. 2013 Jan 30; 33(5):1927-39.
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  18. 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. Epub 2013 Feb 14.
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  19. 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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  20. Brock A, Goh HT, Yang B, Lu Y, Li H, Loh YH. Cellular reprogramming: a new technology frontier in pharmaceutical research. Pharm Res. 2012 Jan; 29(1):35-52. Epub 2011 Nov 9
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  21. 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. Neurodegener Dis. 2012; 10(1-4):238-41. Epub 2011 Dec 23.
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  22. 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. Nat Biotechnol. 2011 Dec; 29(12):1117-9. Epub 2011 Nov 27
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  23. Loh YH, Yang L, Yang JC, Li H, Collins JJ, Daley GQ. Genomic approaches to deconstruct pluripotency. Annu Rev Genomics Hum Genet. 2011; 12:165-85.
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  24. 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. Epub 2011 Nov 29
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  25. 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. Epub 2010 Sep 30
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  26. 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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  27. 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. J Comput Chem. 2010 Mar; 31(4):752-63.
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  28. 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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  29. 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. Epub 2008 Dec 11.
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  30. 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 Lett. 2008 Jun 25; 582(15):2283-90. Epub 2008 May 27.
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  31. 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 Rev Med Chem. 2007 Nov; 7(11):1097-107.
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  32. 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. J Pharm Sci. 2007 Nov; 96(11):2838-60.
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  33. 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. Biotechnol Bioeng. 2007 Jun 1; 97(2):389-96.
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  34. 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. J Ethnopharmacol. 2007 May 4; 111(2):371-7. Epub 2006 Dec 16.
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  35. 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. J Ethnopharmacol. 2007 Jan 3; 109(1):21-8. Epub 2006 Jun 29.
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  36. 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. Mol Immunol. 2007 Jan; 44(4):514-20. Epub 2006 Mar 23
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  37. Ung CY, Li H, Yap CW, Chen YZ. In silico prediction of pregnane X receptor activators by machine learning approaches. Mol Pharmacol. 2007 Jan; 71(1):158-68. Epub 2006 Sep 26.
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  38. 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. Cardiovasc Hematol Agents Med Chem. 2007 Jan; 5(1):11-9.
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  39. 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. Br J Pharmacol. 2006 Dec; 149(8):1092-103. Epub 2006 Nov 06.
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  40. 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. J Mol Graph Model. 2006 Nov; 25(3):313-23. Epub 2006 Feb 23.
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  41. 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. Chem Res Toxicol. 2006 Aug; 19(8):1030-9.
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  42. 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 Rev Med Chem. 2006 Apr; 6(4):449-59.
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  43. 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 Dev. Res. 2006; 66(4):245-59.
  44. 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. 2006; 4(2):79-85.
  45. 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 Phytol. 2005 Oct; 168(1):109-21.
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  46. 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. J Chem Inf Model. 2005 Sep-Oct; 45(5):1376-84.
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  47. Li H, Ung CY, Yap CW, Xue Y, Li ZR, Cao ZW, Chen YZ. Prediction of genotoxicity of chemical compounds by statistical learning methods. Chem Res Toxicol. 2005 Jun; 18(6):1071-80.
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