My Bibliography

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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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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, 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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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. [Epub ahead of print] 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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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.

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Cheung KJ, Padmanaban V, Silvestri V, Schipper K, Cohen JD, Fairchild AN, Gorin MA, Verdone JE, Pienta KJ, Bader JS, Ewald AJ. Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters. Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):E854-63. doi: 10.1073/pnas.1508541113. Epub 2016 Feb 1. PubMed PMID: 26831077; PubMed Central PMCID: PMC4763783.

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Shen Y, Stracquadanio G, Wang Y, Yang K, Mitchell LA, Xue Y, Cai Y, Chen T, Dymond JS, Kang K, Gong J, Zeng X, Zhang Y, Li Y, Feng Q, Xu X, Wang J, Wang J, Yang H, Boeke JD, Bader JS. SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Res. 2016 Jan;26(1):36-49. doi: 10.1101/gr.193433.115. Epub 2015 Nov 13. PubMed PMID: 26566658; PubMed Central PMCID: PMC4691749.

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Beachley VZ, Wolf MT, Sadtler K, Manda SS, Jacobs H, Blatchley MR, Bader JS, Pandey A, Pardoll D, Elisseeff JH. Tissue matrix arrays for high-throughput screening and systems analysis of cell function. Nat Methods. 2015 Dec;12(12):1197-204. doi: 10.1038/nmeth.3619. Epub 2015 Oct 19. PubMed PMID: 26480475; PubMed Central PMCID: PMC4666781.

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Chu LH, Vijay CG, Annex BH, Bader JS, Popel AS. PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease. Physiol Genomics. 2015 Aug;47(8):331-43. doi: 10.1152/physiolgenomics.00125.2014. Epub 2015 Jun 9. PubMed PMID: 26058837; PubMed Central PMCID: PMC4525078.

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Sahasrabuddhe NA, Huang TC, Kumar P, Yang Y, Ghosh B, Leach SD, Chaerkady R, Pandey A. Ablation of Dicer leads to widespread perturbation of signaling pathways. Biochem Biophys Res Commun. 2015 Jul 31;463(3):389-94. doi: 10.1016/j.bbrc.2015.05.077. Epub 2015 May 30. PubMed PMID: 26032504; PubMed Central PMCID: PMC4696065.

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Subbian S, Tsenova L, Kim MJ, Wainwright HC, Visser A, Bandyopadhyay N, Bader JS, Karakousis PC, Murrmann GB, Bekker LG, Russell DG, Kaplan G. Lesion-Specific Immune Response in Granulomas of Patients with Pulmonary Tuberculosis: A Pilot Study. PLoS One. 2015;10(7):e0132249. doi: 10.1371/journal.pone.0132249. eCollection 2015. PubMed PMID: 26133981; PubMed Central PMCID: PMC4489805.

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Lin Q, Jia B, Mitchell LA, Luo J, Yang K, Zeller KI, Zhang W, Xu Z, Stracquadanio G, Bader JS, Boeke JD, Yuan YJ. RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. ACS Synth Biol. 2015 Mar 20;4(3):213-20. doi: 10.1021/sb500241e. Epub 2014 Jun 4. PubMed PMID: 24895839.

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Chuang YM, Bandyopadhyay N, Rifat D, Rubin H, Bader JS, Karakousis PC. Deficiency of the novel exopolyphosphatase Rv1026/PPX2 leads to metabolic downshift and altered cell wall permeability in Mycobacterium tuberculosis. mBio. 2015 Mar 17;6(2):e02428. doi: 10.1128/mBio.02428-14. PubMed PMID: 25784702; PubMed Central PMCID: PMC4453511.

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Cai Y, Agmon N, Choi WJ, Ubide A, Stracquadanio G, Caravelli K, Hao H, Bader JS, Boeke JD. Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):1803-8. doi: 10.1073/pnas.1424704112. Epub 2015 Jan 26. PubMed PMID: 25624482; PubMed Central PMCID: PMC4330768.

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Gupta S, Ellis SE, Ashar FN, Moes A, Bader JS, Zhan J, West AB, Arking DE. Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism. Nat Commun. 2014 Dec 10;5:5748. doi: 10.1038/ncomms6748. PubMed PMID: 25494366; PubMed Central PMCID: PMC4270294.

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Chu LH, Lee E, Bader JS, Popel AS. Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells. PLoS One. 2014;9(10):e110871. doi: 10.1371/journal.pone.0110871. eCollection 2014. PubMed PMID: 25329517; PubMed Central PMCID: PMC4199761.

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Arking DE, Pulit SL, Crotti L, van der Harst P, Munroe PB, Koopmann TT, Sotoodehnia N, Rossin EJ, Morley M, Wang X, Johnson AD, Lundby A, Gudbjartsson DF, Noseworthy PA, Eijgelsheim M, Bradford Y, Tarasov KV, Dörr M, Müller-Nurasyid M, Lahtinen AM, Nolte IM, Smith AV, Bis JC, Isaacs A, Newhouse SJ, Evans DS, Post WS, Waggott D, Lyytikäinen LP, Hicks AA, Eisele L, Ellinghaus D, Hayward C, Navarro P, Ulivi S, Tanaka T, Tester DJ, Chatel S, Gustafsson S, Kumari M, Morris RW, Naluai ÅT, Padmanabhan S, Kluttig A, Strohmer B, Panayiotou AG, Torres M, Knoflach M, Hubacek JA, Slowikowski K, Raychaudhuri S, Kumar RD, Harris TB, Launer LJ, Shuldiner AR, Alonso A, Bader JS, Ehret G, Huang H, Kao WH, Strait JB, Macfarlane PW, Brown M, Caulfield MJ, Samani NJ, Kronenberg F, Willeit J, Smith JG, Greiser KH, Meyer Zu Schwabedissen H, Werdan K, Carella M, Zelante L, Heckbert SR, Psaty BM, Rotter JI, Kolcic I, Polašek O, Wright AF, Griffin M, Daly MJ, Arnar DO, Hólm H, Thorsteinsdottir U, Denny JC, Roden DM, Zuvich RL, Emilsson V, Plump AS, Larson MG, O'Donnell CJ, Yin X, Bobbo M, D'Adamo AP, Iorio A, Sinagra G, Carracedo A, Cummings SR, Nalls MA, Jula A, Kontula KK, Marjamaa A, Oikarinen L, Perola M, Porthan K, Erbel R, Hoffmann P, Jöckel KH, Kälsch H, Nöthen MM, den Hoed M, Loos RJ, Thelle DS, Gieger C, Meitinger T, Perz S, Peters A, Prucha H, Sinner MF, Waldenberger M, de Boer RA, Franke L, van der Vleuten PA, Beckmann BM, Martens E, Bardai A, Hofman N, Wilde AA, Behr ER, Dalageorgou C, Giudicessi JR, Medeiros-Domingo A, Barc J, Kyndt F, Probst V, Ghidoni A, Insolia R, Hamilton RM, Scherer SW, Brandimarto J, Margulies K, Moravec CE, del Greco M F, Fuchsberger C, O'Connell JR, Lee WK, Watt GC, Campbell H, Wild SH, El Mokhtari NE, Frey N, Asselbergs FW, Mateo Leach I, Navis G, van den Berg MP, van Veldhuisen DJ, Kellis M, Krijthe BP, Franco OH, Hofman A, Kors JA, Uitterlinden AG, Witteman JC, Kedenko L, Lamina C, Oostra BA, Abecasis GR, Lakatta EG, Mulas A, Orrú M, Schlessinger D, Uda M, Markus MR, Völker U, Snieder H, Spector TD, Ärnlöv J, Lind L, Sundström J, Syvänen AC, Kivimaki M, Kähönen M, Mononen N, Raitakari OT, Viikari JS, Adamkova V, Kiechl S, Brion M, Nicolaides AN, Paulweber B, Haerting J, Dominiczak AF, Nyberg F, Whincup PH, Hingorani AD, Schott JJ, Bezzina CR, Ingelsson E, Ferrucci L, Gasparini P, Wilson JF, Rudan I, Franke A, Mühleisen TW, Pramstaller PP, Lehtimäki TJ, Paterson AD, Parsa A, Liu Y, van Duijn CM, Siscovick DS, Gudnason V, Jamshidi Y, Salomaa V, Felix SB, Sanna S, Ritchie MD, Stricker BH, Stefansson K, Boyer LA, Cappola TP, Olsen JV, Lage K, Schwartz PJ, Kääb S, Chakravarti A, Ackerman MJ, Pfeufer A, de Bakker PI, Newton-Cheh C. Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nat Genet. 2014 Aug;46(8):826-36. doi: 10.1038/ng.3014. Epub 2014 Jun 22. PubMed PMID: 24952745; PubMed Central PMCID: PMC4124521.

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Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CY, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S. Total synthesis of a functional designer eukaryotic chromosome. Science. 2014 Apr 4;344(6179):55-8. doi: 10.1126/science.1249252. Epub 2014 Mar 27. PubMed PMID: 24674868; PubMed Central PMCID: PMC4033833.

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Shamir ER, Pappalardo E, Jorgens DM, Coutinho K, Tsai WT, Aziz K, Auer M, Tran PT, Bader JS, Ewald AJ. Twist1-induced dissemination preserves epithelial identity and requires E-cadherin. J Cell Biol. 2014 Mar 3;204(5):839-56. doi: 10.1083/jcb.201306088. PubMed PMID: 24590176; PubMed Central PMCID: PMC3941052.

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Dutta NK, Bandyopadhyay N, Veeramani B, Lamichhane G, Karakousis PC, Bader JS. Systems biology-based identification of Mycobacterium tuberculosis persistence genes in mouse lungs. mBio. 2014 Feb 18;5(1). doi: 10.1128/mBio.01066-13. PubMed PMID: 24549847; PubMed Central PMCID: PMC3944818.

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Ellis SE, Gupta S, Ashar FN, Bader JS, West AB, Arking DE. RNA-Seq optimization with eQTL gold standards. BMC Genomics. 2013 Dec 17;14:892. doi: 10.1186/1471-2164-14-892. PubMed PMID: 24341889; PubMed Central PMCID: PMC3890578.

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Kang TH, Park Y, Bader JS, Friedmann T. The housekeeping gene hypoxanthine guanine phosphoribosyltransferase (HPRT) regulates multiple developmental and metabolic pathways of murine embryonic stem cell neuronal differentiation. PLoS One. 2013;8(10):e74967. doi: 10.1371/journal.pone.0074967. eCollection 2013. PubMed PMID: 24130677; PubMed Central PMCID: PMC3794013.

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Subbian S, Bandyopadhyay N, Tsenova L, O'Brien P, Khetani V, Kushner NL, Peixoto B, Soteropoulos P, Bader JS, Karakousis PC, Fallows D, Kaplan G. Early innate immunity determines outcome of Mycobacterium tuberculosis pulmonary infection in rabbits. Cell Commun Signal. 2013 Aug 19;11:60. doi: 10.1186/1478-811X-11-60. PubMed PMID: 23958185; PubMed Central PMCID: PMC3765177.

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Suhail Y, Kshitiz, Lee J, Walker M, Kim DH, Brennan MD, Bader JS, Levchenko A. Modeling intercellular transfer of biomolecules through tunneling nanotubes. Bull Math Biol. 2013 Aug;75(8):1400-16. doi: 10.1007/s11538-013-9819-4. Epub 2013 Feb 16. PubMed PMID: 23417627.

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Chanda P, Huang H, Arking DE, Bader JS. Fast association tests for genes with FAST. PLoS One. 2013;8(7):e68585. doi: 10.1371/journal.pone.0068585. Print 2013. PubMed PMID: 23935874; PubMed Central PMCID: PMC3720833.

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Subbian S, O'Brien P, Kushner NL, Yang G, Tsenova L, Peixoto B, Bandyopadhyay N, Bader JS, Karakousis PC, Fallows D, Kaplan G. Molecular immunologic correlates of spontaneous latency in a rabbit model of pulmonary tuberculosis. Cell Commun Signal. 2013 Feb 28;11(1):16. doi: 10.1186/1478-811X-11-16. PubMed PMID: 23448601; PubMed Central PMCID: PMC3598925.

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Chanda P, Elhaik E, Bader JS. HapZipper: sharing HapMap populations just got easier. Nucleic Acids Res. 2012 Nov 1;40(20):e159. doi: 10.1093/nar/gks709. Epub 2012 Jul 27. PubMed PMID: 22844100; PubMed Central PMCID: PMC3488212.

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Chu LH, Rivera CG, Popel AS, Bader JS. Constructing the angiome: a global angiogenesis protein interaction network. Physiol Genomics. 2012 Oct 2;44(19):915-24. doi: 10.1152/physiolgenomics.00181.2011. Epub 2012 Aug 21. PubMed PMID: 22911453; PubMed Central PMCID: PMC3472464.