Publications

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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.
  14. 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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  15. 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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  16. 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.
  17. 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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  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. 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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  20. 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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  21. 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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  22. 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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  23. 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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  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. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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 02
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  47. 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. J Med Genet 2015 Jan; 52 (1):10-6 Epub 2014 Nov 04
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  48. 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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  49. 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. Sci Rep. 2014; 4:7519. Epub 2014 Dec 17.
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  50. Shih YH , Zhang Y , Ding Y , Ross CA , Li H , Olson TM , Xu X . Cardiac transcriptome and dilated cardiomyopathy genes in zebrafish. Circ Cardiovasc Genet 2015 Apr; 8 (2):261-9 Epub 2015 Jan 11
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  51. 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. 2015 Jan; 55(1):76-90. Epub 2014 Jun 08.
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  52. 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 Epub 2015 May 11
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  53. 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 . Dickson DW, Boylan KB, Li H, Petrucelli L. Distinct brain transcriptome profiles in C9orf72-associated and sporadic ALS. Nat Neurosci 2015 Aug; 18 (8):1175-82 Epub 2015 July 20
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  54. Diefenbach CS , Li H , Hong F , Gordon LI , Fisher RI , Bartlett NL , Crump M , Gascoyne RD , Wagner H Jr, Stiff PJ , Cheson BD , Stewart DA , Kahl BS , Friedberg JW , Blum KA , Habermann TM , Tuscano JM , Hoppe RT , Horning SJ , Advani RH . Evaluation of the International Prognostic Score (IPS-7) and a Simpler Prognostic Score (IPS-3) for advanced Hodgkin lymphoma in the modern era. Br J Haematol 2015 Nov; 171 (4):530-8 Epub 2015 Sept 07
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  55. 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 Epub 2015 Sept 10
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  56. Li H , Zhu H , Wallack M , Mwamburi M , Abdul-Hay SO , Leissring MA , Qiu WQ . Age and its association with low insulin and high amyloid-beta peptides in blood. J Alzheimers Dis 2015; 49 (1):129-37
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  57. Maurer MJ , Jais JP , Ghesquieres H , Witzig TE , Hong F , Haioun C , Thompson CA , Thieblemont C , Micallef IN , Porrata LF , Ribrag V , Nowakowski GS , Casasnovas O , Bologna S , Morschhauser F , Morrison VA , Peterson BA , Macon WR , Copie-Bergman C , Feldman AL , Syrbu SI , Kurtin PJ , Gascoyne RD , Li H , Allmer C , Kahl BS , Ansell SM , Slager SL , Link BK , Salles G , Habermann TM , Tilly H , Cerhan JR . SI, Kurtin PJ, Gascoyne RD, Li H, Allmer C, Kahl BS, Ansell SM, Slager SL, Link BK, Salles G, Habermann TM, Tilly H, Cerhan JR. Personalized risk prediction for event-free survival at 24 months in patients with diffuse large B-cell lymphoma. Am J Hematol 2016 Feb; 91 (2):179-84 Epub 2015 Nov 26
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  58. Burnside ES , Drukker K , Li H , Bonaccio E , Zuley M , Ganott M , Net JM , Sutton EJ , Brandt KR , Whitman GJ , Conzen SD , Lan L , Ji Y , Zhu Y , Jaffe CC , Huang EP , Freymann JB , Kirby JS , Morris EA , Giger ML . Using computer-extracted image phenotypes from tumors on breast magnetic resonance imaging to predict breast cancer pathologic stage. Cancer 2016 Mar 1; 122 (5):748-57 Epub 2015 Nov 30
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  59. 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. Proc Natl Acad Sci U S A. 2016 Jan 5; 113(1):E7-E15. Epub 2015 Dec 14.
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  60. da Rocha EL , Ung CY , McGehee CD , Correia C , Li H . NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities. Nucleic Acids Res 2016 Mar 14 [Epub ahead of print]
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  61. 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 Dev 2016 May 1; 25 (9):740-7 Epub 2016 Apr 11
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  62. Li H , Sun SR , Yap JQ , Chen JH , Qian Q . 0.9% saline is neither normal nor physiological. J Zhejiang Univ Sci B 2016 Mar; 17 (3):181-7
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  63. Wu D , Wang M , Wang X , Yin N , Song T , Li H , Zhang F , Zhang Y , Ye Z , Yu J , Wang DM , Zhao Z . Maternal transmission effect of a PDGF-C SNP on nonsyndromic cleft lip with or without palate from a Chinese population. PLoS One 2012; 7 (9):e46477 Epub 2012 Sept 28
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  64. 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. Nat Genet 2016 May; 48 (5):581-6 Epub 2016 Mar 21
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  65. Kottyan LC , Zoller EE , Bene J , Lu X , Kelly JA , Rupert AM , Lessard CJ , Vaughn SE , Marion M , Weirauch MT , Namjou B , Adler A , Rasmussen A , Glenn S , Montgomery CG , Hirschfield GM , Xie G , Coltescu C , Amos C , Li H , Ice JA , Nath SK , Mariette X , Bowman S , Rischmueller M , Lester S , Brun JG , Goransson LG , Harboe E , Omdal R , Cunninghame-Graham DS , Vyse T , Miceli-Richard C , Brennan MT , Lessard JA , Wahren-Herlenius M , Kvarnstrom M , Illei GG , Witte T , Jonsson R , Eriksson P , Nordmark G , Ng WF , Anaya JM , Rhodus NL , Segal BM , Merrill JT , James JA , Guthridge JM , Scofield RH , Alarcon-Riquelme M , Bae SC , Boackle SA , Criswell LA , Gilkeson G , Kamen DL , Jacob CO , Kimberly R , Brown E , Edberg J , Alarcon GS , Reveille JD , Vila LM , Petri M , Ramsey-Goldman R , Freedman BI , Niewold T , Stevens AM , Tsao BP , Ying J , Mayes MD , Gorlova OY , Wakeland W , Radstake T , Martin E , Martin J , Siminovitch K , Moser Sivils KL , Gaffney PM , Langefeld CD , Harley JB , Kaufman KM . The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. Hum Mol Genet 2015 Jan 15; 24 (2):582-96 Epub 2014 Sept 08
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  66. Chuong MD , Hallemeier CL , Jabbour SK , Yu J , Badiyan S , Merrell KW , Mishra MV , Li H , Verma V , Lin SH . Improving Outcomes for Esophageal Cancer using Proton Beam Therapy. Int J Radiat Oncol Biol Phys 2016 May 1; 95 (1):488-97 Epub 2015 Dec 14
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  67. Matney JE , Park PC , Li H , Court LE , Zhu XR , Dong L , Liu W , Mohan R . Perturbation of water-equivalent thickness as a surrogate for respiratory motion in proton therapy Journal Of Applied Clinical Medical Physics 2016; 17 (2):368-78