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Publications

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 Rep. 2017 Dec 5;21(10):2965-2977. doi: 10.1016/j. celrep.2017.07.048.

Chen YC, Farzadfard F, Gharaei N, Chen WCW, Cao J, Lu TK. Randomized CRISPR-Cas Transcriptional Perturbation Screening Reveals Protective Genes against Alpha-Synuclein Toxicity. Mol Cell. 2017 Oct 5;68(1):247-257.e5. doi: 10.1016/j.molcel.2017.09.014.

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. Sci Rep. 2017 Aug 1;7(1):6993. doi:10.1038/s41598-017-07481-5.

Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 2017 Jun;14(6):577-580. doi: 10.1038/nmeth.4286.

Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A,Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun;14(6):573-576. doi: 10.1038/nmeth.4225.

Cairns J, Ung CY, da Rocha EL, Zhang C, Correia C, Weinshilboum R, Wang L, Li H. A network-based phenotype mapping approach to identify genes that modulate drug response phenotypes. Sci Rep. 2016 Nov 14;6:37003. doi: 10.1038/srep37003.

Wong AS, Choi GC, Lu TK. Deciphering Combinatorial Genetics. Annu Rev Genet. 2016 Nov 23;50:515-538. Epub 2016 Oct 6. Review.

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 Jun 2;44(10):e100. doi: 10.1093/nar/gkw166.

Wong AS, Choi GC, Cui CH, Pregernig G, Milani P, Adam M, Perli SD, Kazer SW, Gaillard A, Hermann M, Shalek AK, Fraenkel E, Lu TK. Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM. Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):2544-9. doi: 10.1073/pnas.1517883113.

Wong AS, Choi GC, Cheng AA, Purcell O, Lu TK. Massively parallel high-order combinatorial genetics in human cells. Nat Biotechnol. 2015 Sep;33(9):952-61. doi: 10.1038/nbt.3326.

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. doi: 10.1016/j.cell.2015.08.037.

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. doi: 10.1093/hmg/ddu202.

Cheng AA, Ding H, Lu TK. Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics. Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12462-7. doi: 10.1073/pnas.1400093111.

Cahan P, Morris SA, Collins JJ, Daley GQ. Defining cellular identity through network biology. Cell Cycle. 2014;13(21):3313-4. doi: 10.4161/15384101.2014.972918.

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):903-915. doi: 10.1016/j. cell.2014.07.020.

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. doi: 10.1016/j.cell.2014.07.021.

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.doi:10.1126/scitranslmed.3007048.

Lorenz DR, Cantor CR, Collins JJ. A network biology approach to aging in yeast. Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1145-50. doi: 10.1073/pnas.0812551106.

Ergün A, Lawrence CA, Kohanski MA, Brennan TA, Collins JJ. A network biology approach to prostate cancer. Mol Syst Biol. 2007;3:82.

di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliott SJ, Schaus SE, Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol. 2005 Mar;23(3):377-83.

Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science. 2003 Jul 4;301(5629):102-5.

Tegner J, Yeung MK, Hasty J, Collins JJ. Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5944-9.