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1.

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions.

Zhao, Yu; Coelho, Camila; Hughes, Amanda L; Lazar-Stefanita, Luciana; Yang, Sandy; Brooks, Aaron N; Walker, Roy S K; Zhang, Weimin; Lauer, Stephanie; Hernandez, Cindy; Cai, Jitong; Mitchell, Leslie A; Agmon, Neta; Shen, Yue; Sall, Joseph; Fanfani, Viola; Jalan, Anavi; Rivera, Jordan; Liang, Feng-Xia; Bader, Joel S; Stracquadanio, Giovanni; Steinmetz, Lars M; Cai, Yizhi; Boeke, Jef D.

Cell; 186(24): 5220-5236.e16, 2023 11 22.

Artículo en Inglés | MEDLINE | ID: mdl-37944511

2.

An expanded universe of cancer targets.

Hahn, William C; Bader, Joel S; Braun, Theodore P; Califano, Andrea; Clemons, Paul A; Druker, Brian J; Ewald, Andrew J; Fu, Haian; Jagu, Subhashini; Kemp, Christopher J; Kim, William; Kuo, Calvin J; McManus, Michael; B Mills, Gordon; Mo, Xiulei; Sahni, Nidhi; Schreiber, Stuart L; Talamas, Jessica A; Tamayo, Pablo; Tyner, Jeffrey W; Wagner, Bridget K; Weiss, William A; Gerhard, Daniela S.

Cell; 184(5): 1142-1155, 2021 03 04.

Artículo en Inglés | MEDLINE | ID: mdl-33667368

3.

Synthetic Genomes.

Zhang, Weimin; Mitchell, Leslie A; Bader, Joel S; Boeke, Jef D.

Annu Rev Biochem; 89: 77-101, 2020 06 20.

Artículo en Inglés | MEDLINE | ID: mdl-32569517

4.

Manipulating the 3D organization of the largest synthetic yeast chromosome.

Zhang, Weimin; Lazar-Stefanita, Luciana; Yamashita, Hitoyoshi; Shen, Michael J; Mitchell, Leslie A; Kurasawa, Hikaru; Lobzaev, Evgenii; Fanfani, Viola; Haase, Max A B; Sun, Xiaoji; Jiang, Qingwen; Goldberg, Gregory W; Ichikawa, David M; Lauer, Stephanie L; McCulloch, Laura H; Easo, Nicole; Lin, S Jiaming; Camellato, Brendan R; Zhu, Yinan; Cai, Jitong; Xu, Zhuwei; Zhao, Yu; Sacasa, Maya; Noyes, Marcus B; Bader, Joel S; Deutsch, Samuel; Stracquadanio, Giovanni; Aizawa, Yasunori; Dai, Junbiao; Boeke, Jef D.

Mol Cell; 83(23): 4424-4437.e5, 2023 Dec 07.

Artículo en Inglés | MEDLINE | ID: mdl-37944526

5.

Pervasive RNA folding is crucial for narnavirus genome maintenance.

Fukuda, Makiha; Cai, Jitong; Bader, Joel S; Boeke, Jef D.

Proc Natl Acad Sci U S A; 120(26): e2304082120, 2023 06 27.

Artículo en Inglés | MEDLINE | ID: mdl-37339222

6.

E-cadherin is required for metastasis in multiple models of breast cancer.

Padmanaban, Veena; Krol, Ilona; Suhail, Yasir; Szczerba, Barbara M; Aceto, Nicola; Bader, Joel S; Ewald, Andrew J.

Nature; 573(7774): 439-444, 2019 09.

Artículo en Inglés | MEDLINE | ID: mdl-31485072

7.

Priors, population sizes, and power in genome-wide hypothesis tests.

Cai, Jitong; Zhan, Jianan; Arking, Dan E; Bader, Joel S.

BMC Bioinformatics; 24(1): 170, 2023 Apr 26.

Artículo en Inglés | MEDLINE | ID: mdl-37101120

8.

Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants.

Dai, Junbiao; Hyland, Edel M; Yuan, Daniel S; Huang, Hailiang; Bader, Joel S; Boeke, Jef D.

Cell; 134(6): 1066-78, 2008 Sep 19.

Artículo en Inglés | MEDLINE | ID: mdl-18805098

9.

Myocardial Gene Expression Signatures in Human Heart Failure With Preserved Ejection Fraction.

Hahn, Virginia S; Knutsdottir, Hildur; Luo, Xin; Bedi, Kenneth; Margulies, Kenneth B; Haldar, Saptarsi M; Stolina, Marina; Yin, Jun; Khakoo, Aarif Y; Vaishnav, Joban; Bader, Joel S; Kass, David A; Sharma, Kavita.

Circulation; 143(2): 120-134, 2021 01 12.

Artículo en Inglés | MEDLINE | ID: mdl-33118835

10.

OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics.

Hasnain, Zaki; Fraser, Andrew K; Georgess, Dan; Choi, Alex; Macklin, Paul; Bader, Joel S; Peyton, Shelly R; Ewald, Andrew J; Newton, Paul K.

Bioinformatics; 36(10): 3292-3294, 2020 05 01.

Artículo en Inglés | MEDLINE | ID: mdl-32091578

11.

Between-tumor and within-tumor heterogeneity in invasive potential.

Padmanaban, Veena; Tsehay, Yohannes; Cheung, Kevin J; Ewald, Andrew J; Bader, Joel S.

PLoS Comput Biol; 16(1): e1007464, 2020 01.

Artículo en Inglés | MEDLINE | ID: mdl-31961880

12.

Schizophrenia risk alleles often affect the expression of many genes and each gene may have a different effect on the risk: A mediation analysis.

Peng, Xi; Bader, Joel S; Avramopoulos, Dimitrios.

Am J Med Genet B Neuropsychiatr Genet; 186(4): 251-258, 2021 06.

Artículo en Inglés | MEDLINE | ID: mdl-33683021

13.

Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae.

Agmon, Neta; Tang, Zuojian; Yang, Kun; Sutter, Ben; Ikushima, Shigehito; Cai, Yizhi; Caravelli, Katrina; Martin, James A; Sun, Xiaoji; Choi, Woo Jin; Zhang, Allen; Stracquadanio, Giovanni; Hao, Haiping; Tu, Benjamin P; Fenyo, David; Bader, Joel S; Boeke, Jef D.

Proc Natl Acad Sci U S A; 114(8): E1470-E1479, 2017 02 21.

Artículo en Inglés | MEDLINE | ID: mdl-28174266

14.

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.

Shen, Yue; Stracquadanio, Giovanni; Wang, Yun; Yang, Kun; Mitchell, Leslie A; Xue, Yaxin; Cai, Yizhi; Chen, Tai; Dymond, Jessica S; Kang, Kang; Gong, Jianhui; Zeng, Xiaofan; Zhang, Yongfen; Li, Yingrui; Feng, Qiang; Xu, Xun; Wang, Jun; Wang, Jian; Yang, Huanming; Boeke, Jef D; Bader, Joel S.

Genome Res; 26(1): 36-49, 2016 Jan.

Artículo en Inglés | MEDLINE | ID: mdl-26566658

15.

Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters.

Cheung, Kevin J; Padmanaban, Veena; Silvestri, Vanesa; Schipper, Koen; Cohen, Joshua D; Fairchild, Amanda N; Gorin, Michael A; Verdone, James E; Pienta, Kenneth J; Bader, Joel S; Ewald, Andrew J.

Proc Natl Acad Sci U S A; 113(7): E854-63, 2016 Feb 16.

Artículo en Inglés | MEDLINE | ID: mdl-26831077

16.

Tissue matrix arrays for high-throughput screening and systems analysis of cell function.

Beachley, Vince Z; Wolf, Matthew T; Sadtler, Kaitlyn; Manda, Srikanth S; Jacobs, Heather; Blatchley, Michael R; Bader, Joel S; Pandey, Akhilesh; Pardoll, Drew; Elisseeff, Jennifer H.

Nat Methods; 12(12): 1197-204, 2015 Dec.

Artículo en Inglés | MEDLINE | ID: mdl-26480475

17.

Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.

Lin, Yu-yi; Kiihl, Samara; Suhail, Yasir; Liu, Shang-Yun; Chou, Yi-hsuan; Kuang, Zheng; Lu, Jin-ying; Khor, Chin Ni; Lin, Chi-Long; Bader, Joel S; Irizarry, Rafael; Boeke, Jef D.

Nature; 482(7384): 251-5, 2012 Feb 08.

Artículo en Inglés | MEDLINE | ID: mdl-22318606

18.

Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes.

Cai, Yizhi; Agmon, Neta; Choi, Woo Jin; Ubide, Alba; Stracquadanio, Giovanni; Caravelli, Katrina; Hao, Haiping; Bader, Joel S; Boeke, Jef D.

Proc Natl Acad Sci U S A; 112(6): 1803-8, 2015 Feb 10.

Artículo en Inglés | MEDLINE | ID: mdl-25624482

19.

Hypoxia Sensing and Persistence Genes Are Expressed during the Intragranulomatous Survival of Mycobacterium tuberculosis.

Hudock, Teresa A; Foreman, Taylor W; Bandyopadhyay, Nirmalya; Gautam, Uma S; Veatch, Ashley V; LoBato, Denae N; Gentry, Kaylee M; Golden, Nadia A; Cavigli, Amy; Mueller, Michelle; Hwang, Shen-An; Hunter, Robert L; Alvarez, Xavier; Lackner, Andrew A; Bader, Joel S; Mehra, Smriti; Kaushal, Deepak.

Am J Respir Cell Mol Biol; 56(5): 637-647, 2017 05.

Artículo en Inglés | MEDLINE | ID: mdl-28135421

20.

BioPartsDB: a synthetic biology workflow web-application for education and research.

Stracquadanio, Giovanni; Yang, Kun; Boeke, Jef D; Bader, Joel S.

Bioinformatics; 32(22): 3519-3521, 2016 11 15.

Artículo en Inglés | MEDLINE | ID: mdl-27412090

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