My Bibliography

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Grasset EM, Dunworth M, Sharma G, Loth M, Tandurella J, Cimino-Mathews A, Gentz M, Bracht S, Haynes M, Fertig EJ, Ewald AJ. Triple-negative breast cancer metastasis involves complex epithelial-mesenchymal transition dynamics and requires vimentin. Sci Transl Med. 2022 Aug 3;14(656):eabn7571. doi: 10.1126/scitranslmed.abn7571. Epub 2022 Aug 3. PubMed PMID: 35921474; PubMed Central PMCID: PMC9801390.

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Matern W, Parker H, Danchik C, Hoover L, Bader J, Karakousis P. Genetic Determinants of Intrinsic Antibiotic Tolerance in Mycobacterium avium. Microbiology Spectrum. 2021 October; 9(2):-. doi: 10.1128/Spectrum.00246-21.

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Li L, Halpert G, Lerner MG, Hu H, Dimitrion P, Weiss MJ, He J, Philosophe B, Burkhart R, Burns WR, Wesson RN, MacGregor Cameron A, Wolfgang CL, Georgiades C, Kawamoto S, Azad NS, Yarchoan M, Meltzer SJ, Oshima K, Ensign LM, Bader JS, Selaru FM. Protein synthesis inhibitor omacetaxine is effective against hepatocellular carcinoma. JCI Insight. 2021 Jun 22;6(12). doi: 10.1172/jci.insight.138197. PubMed PMID: 34003798; PubMed Central PMCID: PMC8262474.

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Peng X, Bader JS, Avramopoulos D. Schizophrenia risk alleles often affect the expression of many genes and each gene may have a different effect on the risk: A mediation analysis. Am J Med Genet B Neuropsychiatr Genet. 2021 Jun;186(4):251-258. doi: 10.1002/ajmg.b.32841. Epub 2021 Mar 8. PubMed PMID: 33683021.

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Bader JS. The Panorama of Cancer Genetics. Cancer Res. 2021 May 15;81(10):2586-2587. doi: 10.1158/0008-5472.CAN-21-0885. PubMed PMID: 33999839; PubMed Central PMCID: PMC8293694.

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Bader J. The Panorama of Cancer Genetics. Cancer Research. 2021 May; 81(10):2586-2587. doi: 10.1158/0008-5472.CAN-21-0885.

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Lam AN, Peng X, Das D, Bader JS, Avramopoulos D. Transcriptomic data of Clozapine-treated Ngn2-induced Human Excitatory Neurons. Data Brief. 2021 Apr;35:106897. doi: 10.1016/j.dib.2021.106897. eCollection 2021 Apr. PubMed PMID: 33681435; PubMed Central PMCID: PMC7910509.

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Hahn WC, Bader JS, Braun TP, Califano A, Clemons PA, Druker BJ, Ewald AJ, Fu H, Jagu S, Kemp CJ, Kim W, Kuo CJ, McManus M, B Mills G, Mo X, Sahni N, Schreiber SL, Talamas JA, Tamayo P, Tyner JW, Wagner BK, Weiss WA, Gerhard DS. An expanded universe of cancer targets. Cell. 2021 Mar 4;184(5):1142-1155. doi: 10.1016/j.cell.2021.02.020. Review. PubMed PMID: 33667368; PubMed Central PMCID: PMC8066437.

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Hahn W, Bader J, Braun T, Califano A, Clemons P, Druker B, Ewald A, Fu H, Jagu S, Kemp C, Kim W, Kuo C, McManus M, B. Mills G, Mo X, Sahni N, Schreiber S, Talamas J, Tamayo P, Tyner J, Wagner B, Weiss W, Gerhard D, Dancik V, Gill S, Hua B, Sharifnia T, Viswanathan V, Zou Y, Dela Cruz F, Kung A, Stockwell B, Boehm J, Dempster J, Manguso R, Vazquez F, Cooper L, Du Y, Ivanov A, Lonial S, Moreno C, Niu Q, Owonikoko T, Ramalingam S, Reyna M, Zhou W, Grandori C, Shmulevich I, Swisher E, Cai J, Chan I, Dunworth M, Ge Y, Georgess D, Grasset E, Henriet E, Knútsdóttir H, Lerner M, Padmanaban V, Perrone M, Suhail Y, Tsehay Y, Warrier M, Morrow Q, Nechiporuk T, Long N, Saultz J, Kaempf A, Minnier J, Tognon C, Kurtz S, Agarwal A, Brown J, Watanabe-Smith K, Vu T, Jacob T, Yan Y, Robinson B, Lind E, Kosaka Y, Demir E, Estabrook J, Grzadkowski M, Nikolova O, Chen K, Deneen B, Liang H, Bassik M, Bhattacharya A, Brennan K, Curtis C, Gevaert O, Ji H, Karlsson K, Karagyozova K, Lo Y, Liu K, Nakano M, Sathe A, Smith A, Spees K, Wong W, Yuki K, Hangauer M, Kaufman D, Balmain A, Bollam S, Chen W, Fan Q, Kersten K, Krummel M, Li Y, Menard M, Nasholm N, Schmidt C, Serwas N, Yoda H, Ashworth A, Bandyopadhyay S, Bivona T, Eades G, Oberlin S, Tay N, Wang Y, Weissman J. An expanded universe of cancer targets. Cell. 2021 March; 184(5):1142-1155. doi: 10.1016/j.cell.2021.02.020.

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Das D, Peng X, Lam AN, Bader JS, Avramopoulos D. Transcriptome analysis of human induced excitatory neurons supports a strong effect of clozapine on cholesterol biosynthesis. Schizophr Res. 2021 Feb;228:324-326. doi: 10.1016/j.schres.2020.12.041. Epub 2021 Jan 24. PubMed PMID: 33497908; PubMed Central PMCID: PMC7987755.

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Hahn VS, Knutsdottir H, Luo X, Bedi K, Margulies KB, Haldar SM, Stolina M, Yin J, Khakoo AY, Vaishnav J, Bader JS, Kass DA, Sharma K. Myocardial Gene Expression Signatures in Human Heart Failure With Preserved Ejection Fraction. Circulation. 2021 Jan 12;143(2):120-134. doi: 10.1161/CIRCULATIONAHA.120.050498. Epub 2020 Oct 29. PubMed PMID: 33118835; PubMed Central PMCID: PMC7856095.

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Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ. Genetic interaction mapping informs integrative structure determination of protein complexes. Science. 2020 Dec 11;370(6522). doi: 10.1126/science.aaz4910. PubMed PMID: 33303586; PubMed Central PMCID: PMC7946025.

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Chan IS, Knútsdóttir H, Ramakrishnan G, Padmanaban V, Warrier M, Ramirez JC, Dunworth M, Zhang H, Jaffee EM, Bader JS, Ewald AJ. Cancer cells educate natural killer cells to a metastasis-promoting cell state. J Cell Biol. 2020 Sep 7;219(9). doi: 10.1083/jcb.202001134. PubMed PMID: 32645139; PubMed Central PMCID: PMC7480097.

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Padmanaban V, Grasset EM, Neumann NM, Fraser AK, Henriet E, Matsui W, Tran PT, Cheung KJ, Georgess D, Ewald AJ. Organotypic culture assays for murine and human primary and metastatic-site tumors. Nat Protoc. 2020 Aug;15(8):2413-2442. doi: 10.1038/s41596-020-0335-3. Epub 2020 Jul 20. PubMed PMID: 32690957; PubMed Central PMCID: PMC8202162.

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Zhang W, Mitchell LA, Bader JS, Boeke JD. Synthetic Genomes. Annu Rev Biochem. 2020 Jun 20;89:77-101. doi: 10.1146/annurev-biochem-013118-110704. Review. PubMed PMID: 32569517.

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Hasnain Z, Fraser AK, Georgess D, Choi A, Macklin P, Bader JS, Peyton SR, Ewald AJ, Newton PK. OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics. Bioinformatics. 2020 May 1;36(10):3292-3294. doi: 10.1093/bioinformatics/btaa096. PubMed PMID: 32091578; PubMed Central PMCID: PMC7214016.

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Mita P, Sun X, Fenyö D, Kahler DJ, Li D, Agmon N, Wudzinska A, Keegan S, Bader JS, Yun C, Boeke JD. BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells. Nat Struct Mol Biol. 2020 Feb;27(2):179-191. doi: 10.1038/s41594-020-0374-z. Epub 2020 Feb 10. PubMed PMID: 32042152; PubMed Central PMCID: PMC7082080.

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Mita P, Sun X, Fenyö D, Kahler D, Li D, Agmon N, Wudzinska A, Keegan S, Bader J, Yun C, Boeke J. BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells. Nature Structural & Molecular Biology. 2020 February; 27(2):179-191. doi: 10.1038/s41594-020-0374-z.

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Matern WM, Jenquin RL, Bader JS, Karakousis PC. Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure. Sci Rep. 2020 Jan 23;10(1):1095. doi: 10.1038/s41598-020-57845-7. PubMed PMID: 31974396; PubMed Central PMCID: PMC6978383.

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Matern W, Jenquin R, Bader J, Karakousis P. Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure. Scientific Reports. 2020 January; 10(1):-. doi: 10.1038/s41598-020-57845-7.

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Padmanaban V, Tsehay Y, Cheung KJ, Ewald AJ, Bader JS. Between-tumor and within-tumor heterogeneity in invasive potential. PLoS Comput Biol. 2020 Jan;16(1):e1007464. doi: 10.1371/journal.pcbi.1007464. eCollection 2020 Jan. PubMed PMID: 31961880; PubMed Central PMCID: PMC6994152.

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Padmanaban V, Tsehay Y, Cheung K, Ewald A, Bader J. Between-tumor and within-tumor heterogeneity in invasive potential. PLOS Computational Biology. 2020-1-; 16(1):e1007464-. doi: 10.1371/journal.pcbi.1007464.

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Ostrov N, Beal J, Ellis T, Gordon DB, Karas BJ, Lee HH, Lenaghan SC, Schloss JA, Stracquadanio G, Trefzer A, Bader JS, Church GM, Coelho CM, Efcavitch JW, Güell M, Mitchell LA, Nielsen AAK, Peck B, Smith AC, Stewart CN Jr, Tekotte H. Technological challenges and milestones for writing genomes. Science. 2019 Oct 18;366(6463):310-312. doi: 10.1126/science.aay0339. PubMed PMID: 31624201.

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Padmanaban V, Krol I, Suhail Y, Szczerba BM, Aceto N, Bader JS, Ewald AJ. E-cadherin is required for metastasis in multiple models of breast cancer. Nature. 2019 Sep;573(7774):439-444. doi: 10.1038/s41586-019-1526-3. Epub 2019 Sep 4. PubMed PMID: 31485072; PubMed Central PMCID: PMC7365572.

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Cai J, Zhan J, Arking D, Bader J. Priors, population sizes, and power in genome-wide hypothesis tests. [preprint]. 2019 August. doi: 10.1101/737676.

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Dutta NK, Klinkenberg LG, Vazquez MJ, Segura-Carro D, Colmenarejo G, Ramon F, Rodriguez-Miquel B, Mata-Cantero L, Porras-De Francisco E, Chuang YM, Rubin H, Lee JJ, Eoh H, Bader JS, Perez-Herran E, Mendoza-Losana A, Karakousis PC. Inhibiting the stringent response blocks Mycobacterium tuberculosis entry into quiescence and reduces persistence. Sci Adv. 2019 Mar;5(3):eaav2104. doi: 10.1126/sciadv.aav2104. eCollection 2019 Mar. PubMed PMID: 30906866; PubMed Central PMCID: PMC6426458.

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Li L, Knutsdottir H, Hui K, Weiss MJ, He J, Philosophe B, Cameron AM, Wolfgang CL, Pawlik TM, Ghiaur G, Ewald AJ, Mezey E, Bader JS, Selaru FM. Human primary liver cancer organoids reveal intratumor and interpatient drug response heterogeneity. JCI Insight. 2019 Jan 24;4(2). doi: 10.1172/jci.insight.121490. PubMed PMID: 30674722; PubMed Central PMCID: PMC6413833.

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Matern WM, Bader JS, Karakousis PC. Genome analysis of Mycobacterium avium subspecies hominissuis strain 109. Sci Data. 2018 Dec 4;5:180277. doi: 10.1038/sdata.2018.277. PubMed PMID: 30512015; PubMed Central PMCID: PMC6278689.

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Matern W, Bader J, Karakousis P. Genome analysis of Mycobacterium avium subspecies hominissuis strain 109. Scientific Data. 2018 December; 5(1):-. doi: 10.1038/sdata.2018.277.

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van Setten J, Brody JA, Jamshidi Y, Swenson BR, Butler AM, Campbell H, Del Greco FM, Evans DS, Gibson Q, Gudbjartsson DF, Kerr KF, Krijthe BP, Lyytikäinen LP, Müller C, Müller-Nurasyid M, Nolte IM, Padmanabhan S, Ritchie MD, Robino A, Smith AV, Steri M, Tanaka T, Teumer A, Trompet S, Ulivi S, Verweij N, Yin X, Arnar DO, Asselbergs FW, Bader JS, Barnard J, Bis J, Blankenberg S, Boerwinkle E, Bradford Y, Buckley BM, Chung MK, Crawford D, den Hoed M, Denny JC, Dominiczak AF, Ehret GB, Eijgelsheim M, Ellinor PT, Felix SB, Franco OH, Franke L, Harris TB, Holm H, Ilaria G, Iorio A, Kähönen M, Kolcic I, Kors JA, Lakatta EG, Launer LJ, Lin H, Lin HJ, Loos RJF, Lubitz SA, Macfarlane PW, Magnani JW, Leach IM, Meitinger T, Mitchell BD, Munzel T, Papanicolaou GJ, Peters A, Pfeufer A, Pramstaller PP, Raitakari OT, Rotter JI, Rudan I, Samani NJ, Schlessinger D, Silva Aldana CT, Sinner MF, Smith JD, Snieder H, Soliman EZ, Spector TD, Stott DJ, Strauch K, Tarasov KV, Thorsteinsdottir U, Uitterlinden AG, Van Wagoner DR, Völker U, Völzke H, Waldenberger M, Jan Westra H, Wild PS, Zeller T, Alonso A, Avery CL, Bandinelli S, Benjamin EJ, Cucca F, Dörr M, Ferrucci L, Gasparini P, Gudnason V, Hayward C, Heckbert SR, Hicks AA, Jukema JW, Kääb S, Lehtimäki T, Liu Y, Munroe PB, Parsa A, Polasek O, Psaty BM, Roden DM, Schnabel RB, Sinagra G, Stefansson K, Stricker BH, van der Harst P, van Duijn CM, Wilson JF, Gharib SA, de Bakker PIW, Isaacs A, Arking DE, Sotoodehnia N. PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity. Nat Commun. 2018 Jul 25;9(1):2904. doi: 10.1038/s41467-018-04766-9. PubMed PMID: 30046033; PubMed Central PMCID: PMC6060178.

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Shen MJ, Wu Y, Yang K, Li Y, Xu H, Zhang H, Li BZ, Li X, Xiao WH, Zhou X, Mitchell LA, Bader JS, Yuan Y, Boeke JD. Heterozygous diploid and interspecies SCRaMbLEing. Nat Commun. 2018 May 22;9(1):1934. doi: 10.1038/s41467-018-04157-0. PubMed PMID: 29789590; PubMed Central PMCID: PMC5964232.

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Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nat Methods. 2018 May;15(5):330-338. doi: 10.1038/nmeth.4632. Epub 2018 Mar 19. PubMed PMID: 29638227; PubMed Central PMCID: PMC6063793.

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Matern WM, Rifat D, Bader JS, Karakousis PC. Gene Enrichment Analysis Reveals Major Regulators of Mycobacterium tuberculosis Gene Expression in Two Models of Antibiotic Tolerance. Front Microbiol. 2018;9:610. doi: 10.3389/fmicb.2018.00610. eCollection 2018. PubMed PMID: 29670589; PubMed Central PMCID: PMC5893760.

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Weiner DJ, Wigdor EM, Ripke S, Walters RK, Kosmicki JA, Grove J, Samocha KE, Goldstein JI, Okbay A, Bybjerg-Grauholm J, Werge T, Hougaard DM, Taylor J, Skuse D, Devlin B, Anney R, Sanders SJ, Bishop S, Mortensen PB, Børglum AD, Smith GD, Daly MJ, Robinson EB. Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders. Nat Genet. 2017 Jul;49(7):978-985. doi: 10.1038/ng.3863. Epub 2017 May 15. PubMed PMID: 28504703; PubMed Central PMCID: PMC5552240.

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Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia. Mol Autism. 2017;8:21. doi: 10.1186/s13229-017-0137-9. eCollection 2017. PubMed PMID: 28540026; PubMed Central PMCID: PMC5441062.

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Hudock TA, Foreman TW, Bandyopadhyay N, Gautam US, Veatch AV, LoBato DN, Gentry KM, Golden NA, Cavigli A, Mueller M, Hwang SA, Hunter RL, Alvarez X, Lackner AA, Bader JS, Mehra S, Kaushal D. Hypoxia Sensing and Persistence Genes Are Expressed during the Intragranulomatous Survival of Mycobacterium tuberculosis. Am J Respir Cell Mol Biol. 2017 May;56(5):637-647. doi: 10.1165/rcmb.2016-0239OC. PubMed PMID: 28135421; PubMed Central PMCID: PMC5449490.

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Yang JP, Anderson AE, McCartney A, Ory X, Ma G, Pappalardo E, Bader J, Elisseeff JH. Metabolically Active Three-Dimensional Brown Adipose Tissue Engineered from White Adipose-Derived Stem Cells. Tissue Eng Part A. 2017 Apr;23(7-8):253-262. doi: 10.1089/ten.TEA.2016.0399. Epub 2016 Feb 21. PubMed PMID: 28073315; PubMed Central PMCID: PMC5397238.

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Zhang W, Zhao G, Luo Z, Lin Y, Wang L, Guo Y, Wang A, Jiang S, Jiang Q, Gong J, Wang Y, Hou S, Huang J, Li T, Qin Y, Dong J, Qin Q, Zhang J, Zou X, He X, Zhao L, Xiao Y, Xu M, Cheng E, Huang N, Zhou T, Shen Y, Walker R, Luo Y, Kuang Z, Mitchell LA, Yang K, Richardson SM, Wu Y, Li BZ, Yuan YJ, Yang H, Lin J, Chen GQ, Wu Q, Bader JS, Cai Y, Boeke JD, Dai J. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf3981. PubMed PMID: 28280149.

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Mitchell LA, Wang A, Stracquadanio G, Kuang Z, Wang X, Yang K, Richardson S, Martin JA, Zhao Y, Walker R, Luo Y, Dai H, Dong K, Tang Z, Yang Y, Cai Y, Heguy A, Ueberheide B, Fenyö D, Dai J, Bader JS, Boeke JD. Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf4831. PubMed PMID: 28280154.

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Shen Y, Wang Y, Chen T, Gao F, Gong J, Abramczyk D, Walker R, Zhao H, Chen S, Liu W, Luo Y, Müller CA, Paul-Dubois-Taine A, Alver B, Stracquadanio G, Mitchell LA, Luo Z, Fan Y, Zhou B, Wen B, Tan F, Wang Y, Zi J, Xie Z, Li B, Yang K, Richardson SM, Jiang H, French CE, Nieduszynski CA, Koszul R, Marston AL, Yuan Y, Wang J, Bader JS, Dai J, Boeke JD, Xu X, Cai Y, Yang H. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf4791. PubMed PMID: 28280153; PubMed Central PMCID: PMC5390853.

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Wu Y, Li BZ, Zhao M, Mitchell LA, Xie ZX, Lin QH, Wang X, Xiao WH, Wang Y, Zhou X, Liu H, Li X, Ding MZ, Liu D, Zhang L, Liu BL, Wu XL, Li FF, Dong XT, Jia B, Zhang WZ, Jiang GZ, Liu Y, Bai X, Song TQ, Chen Y, Zhou SJ, Zhu RY, Gao F, Kuang Z, Wang X, Shen M, Yang K, Stracquadanio G, Richardson SM, Lin Y, Wang L, Walker R, Luo Y, Ma PS, Yang H, Cai Y, Dai J, Bader JS, Boeke JD, Yuan YJ. Bug mapping and fitness testing of chemically synthesized chromosome X. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf4706. PubMed PMID: 28280152; PubMed Central PMCID: PMC5679077.

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Richardson SM, Mitchell LA, Stracquadanio G, Yang K, Dymond JS, DiCarlo JE, Lee D, Huang CL, Chandrasegaran S, Cai Y, Boeke JD, Bader JS. Design of a synthetic yeast genome. Science. 2017 Mar 10;355(6329):1040-1044. doi: 10.1126/science.aaf4557. PubMed PMID: 28280199.

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Xie ZX, Li BZ, Mitchell LA, Wu Y, Qi X, Jin Z, Jia B, Wang X, Zeng BX, Liu HM, Wu XL, Feng Q, Zhang WZ, Liu W, Ding MZ, Li X, Zhao GR, Qiao JJ, Cheng JS, Zhao M, Kuang Z, Wang X, Martin JA, Stracquadanio G, Yang K, Bai X, Zhao J, Hu ML, Lin QH, Zhang WQ, Shen MH, Chen S, Su W, Wang EX, Guo R, Zhai F, Guo XJ, Du HX, Zhu JQ, Song TQ, Dai JJ, Li FF, Jiang GZ, Han SL, Liu SY, Yu ZC, Yang XN, Chen K, Hu C, Li DS, Jia N, Liu Y, Wang LT, Wang S, Wei XT, Fu MQ, Qu LM, Xin SY, Liu T, Tian KR, Li XN, Zhang JH, Song LX, Liu JG, Lv JF, Xu H, Tao R, Wang Y, Zhang TT, Deng YX, Wang YR, Li T, Ye GX, Xu XR, Xia ZB, Zhang W, Yang SL, Liu YL, Ding WQ, Liu ZN, Zhu JQ, Liu NZ, Walker R, Luo Y, Wang Y, Shen Y, Yang H, Cai Y, Ma PS, Zhang CT, Bader JS, Boeke JD, Yuan YJ. "Perfect" designer chromosome V and behavior of a ring derivative. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf4704. PubMed PMID: 28280151.

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Mercy G, Mozziconacci J, Scolari VF, Yang K, Zhao G, Thierry A, Luo Y, Mitchell LA, Shen M, Shen Y, Walker R, Zhang W, Wu Y, Xie ZX, Luo Z, Cai Y, Dai J, Yang H, Yuan YJ, Boeke JD, Bader JS, Muller H, Koszul R. 3D organization of synthetic and scrambled chromosomes. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf4597. PubMed PMID: 28280150; PubMed Central PMCID: PMC5679085.

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Agmon N, Tang Z, Yang K, Sutter B, Ikushima S, Cai Y, Caravelli K, Martin JA, Sun X, Choi WJ, Zhang A, Stracquadanio G, Hao H, Tu BP, Fenyo D, Bader JS, Boeke JD. Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1470-E1479. doi: 10.1073/pnas.1621250114. Epub 2017 Feb 7. PubMed PMID: 28174266; PubMed Central PMCID: PMC5338387.

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Stracquadanio G, Yang K, Boeke JD, Bader JS. BioPartsDB: a synthetic biology workflow web-application for education and research. Bioinformatics. 2016 Nov 15;32(22):3519-3521. doi: 10.1093/bioinformatics/btw394. Epub 2016 Jul 13. PubMed PMID: 27412090; PubMed Central PMCID: PMC5181553.

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Blackshaw S, Venkataraman A, Irizarry J, Yang K, Anderson S, Campbell E, Gatlin CL, Freeman NL, Basavappa R, Stewart R, Loss MA, Pino I, Zhu H, Bader JS. The NIH Protein Capture Reagents Program (PCRP): a standardized protein affinity reagent toolbox. Nat Methods. 2016 Sep 29;13(10):805-6. doi: 10.1038/nmeth.4013. PubMed PMID: 27684578; PubMed Central PMCID: PMC5886368.

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Zhu M, Monroe JG, Suhail Y, Villiers F, Mullen J, Pater D, Hauser F, Jeon BW, Bader JS, Kwak JM, Schroeder JI, McKay JK, Assmann SM. Molecular and systems approaches towards drought-tolerant canola crops. New Phytol. 2016 Jun;210(4):1169-89. doi: 10.1111/nph.13866. Epub 2016 Feb 16. Review. PubMed PMID: 26879345.

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Pienaar E, Matern WM, Linderman JJ, Bader JS, Kirschner DE. Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions. Infect Immun. 2016 May;84(5):1650-1669. doi: 10.1128/IAI.01438-15. Print 2016 May. PubMed PMID: 26975995; PubMed Central PMCID: PMC4862722.

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Yang K, Stracquadanio G, Luo J, Boeke JD, Bader JS. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. Bioinformatics. 2016 Mar 15;32(6):937-9. doi: 10.1093/bioinformatics/btv664. Epub 2015 Nov 14. PubMed PMID: 26568632; PubMed Central PMCID: PMC4803390.