| Year |
Citation |
Score |
| 2023 |
Williams TC, Kroukamp H, Xu X, Wightman ELI, Llorente B, Borneman AR, Carpenter AC, Van Wyk N, Meier F, Collier TRV, Espinosa MI, Daniel EL, Walker RSK, Cai Y, Nevalainen HKM, ... ... Bader JS, et al. Parallel laboratory evolution and rational debugging reveal genomic plasticity to synthetic chromosome XIV defects. Cell Genomics. 3: 100379. PMID 38020977 DOI: 10.1016/j.xgen.2023.100379 |
0.733 |
|
| 2023 |
McCulloch LH, Sambasivam V, Hughes AL, Annaluru N, Ramalingam S, Fanfani V, Lobzaev E, Mitchell LA, Cai J, Jiang H, LaCava J, Taylor MS, Bishai WR, Stracquadanio G, Steinmetz LM, ... Bader JS, et al. Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast strains. Cell Genomics. 3: 100419. PMID 38020974 DOI: 10.1016/j.xgen.2023.100419 |
0.712 |
|
| 2023 |
Blount BA, Lu X, Driessen MRM, Jovicevic D, Sanchez MI, Ciurkot K, Zhao Y, Lauer S, McKiernan RM, Gowers GF, Sweeney F, Fanfani V, Lobzaev E, Palacios-Flores K, Walker RSK, ... ... Bader JS, et al. Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics. Cell Genomics. 3: 100418. PMID 38020971 DOI: 10.1016/j.xgen.2023.100418 |
0.731 |
|
| 2023 |
Foo JL, Kitano S, Susanto AV, Jin Z, Lin Y, Luo Z, Huang L, Liang Z, Mitchell LA, Yang K, Wong A, Cai Y, Cai J, Stracquadanio G, Bader JS, et al. Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration. Cell Genomics. 3: 100435. PMID 38020970 DOI: 10.1016/j.xgen.2023.100435 |
0.715 |
|
| 2023 |
Lauer S, Luo J, Lazar-Stefanita L, Zhang W, McCulloch LH, Fanfani V, Lobzaev E, Haase MAB, Easo N, Zhao Y, Yu F, Cai J, Bader JS, Stracquadanio G, Boeke JD. Context-dependent neocentromere activity in synthetic yeast chromosome . Cell Genomics. 3: 100437. PMID 38020969 DOI: 10.1016/j.xgen.2023.100437 |
0.727 |
|
| 2023 |
Shen Y, Gao F, Wang Y, Wang Y, Zheng J, Gong J, Zhang J, Luo Z, Schindler D, Deng Y, Ding W, Lin T, Swidah R, Zhao H, Jiang S, ... ... Bader JS, et al. Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast. Cell Genomics. 3: 100364. PMID 38020968 DOI: 10.1016/j.xgen.2023.100364 |
0.506 |
|
| 2023 |
Luo J, Vale-Silva LA, Raghavan AR, Mercy G, Heldrich J, Sun X, Li MK, Zhang W, Agmon N, Yang K, Cai J, Stracquadanio G, Thierry A, Zhao Y, Coelho C, ... ... Bader JS, et al. Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function. Cell Genomics. 3: 100439. PMID 38020967 DOI: 10.1016/j.xgen.2023.100439 |
0.718 |
|
| 2023 |
Zhang W, Lazar-Stefanita L, Yamashita H, Shen MJ, Mitchell LA, Kurasawa H, Lobzaev E, Fanfani V, Haase MAB, Sun X, Jiang Q, Goldberg GW, Ichikawa DM, Lauer SL, McCulloch LH, ... ... Bader JS, et al. Manipulating the 3D organization of the largest synthetic yeast chromosome. Molecular Cell. PMID 37944526 DOI: 10.1016/j.molcel.2023.10.015 |
0.734 |
|
| 2023 |
Zhao Y, Coelho C, Hughes AL, Lazar-Stefanita L, Yang S, Brooks AN, Walker RSK, Zhang W, Lauer S, Hernandez C, Cai J, Mitchell LA, Agmon N, Shen Y, Sall J, ... ... Bader JS, et al. Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions. Cell. PMID 37944511 DOI: 10.1016/j.cell.2023.09.025 |
0.735 |
|
| 2023 |
Fukuda M, Cai J, Bader JS, Boeke JD. Pervasive RNA folding is crucial for narnavirus genome maintenance. Proceedings of the National Academy of Sciences of the United States of America. 120: e2304082120. PMID 37339222 DOI: 10.1073/pnas.2304082120 |
0.399 |
|
| 2020 |
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, ... ... Bader JS, et al. Genetic interaction mapping informs integrative structure determination of protein complexes. Science (New York, N.Y.). 370. PMID 33303586 DOI: 10.1126/science.aaz4910 |
0.438 |
|
| 2020 |
Zhang W, Mitchell LA, Bader JS, Boeke JD. Synthetic Genomes. Annual Review of Biochemistry. 89: 77-101. PMID 32569517 DOI: 10.1146/annurev-biochem-013118-110704 |
0.506 |
|
| 2020 |
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. Nature Structural & Molecular Biology. 27: 179-191. PMID 32042152 DOI: 10.1038/S41594-020-0374-Z |
0.471 |
|
| 2020 |
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. Scientific Reports. 10: 1095. PMID 31974396 DOI: 10.1038/S41598-020-57845-7 |
0.344 |
|
| 2019 |
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, et al. Technological challenges and milestones for writing genomes. Science (New York, N.Y.). 366: 310-312. PMID 31624201 DOI: 10.1126/Science.Aay0339 |
0.636 |
|
| 2018 |
Matern WM, Bader JS, Karakousis PC. Genome analysis of Mycobacterium avium subspecies hominissuis strain 109. Scientific Data. 5: 180277. PMID 30512015 DOI: 10.1038/Sdata.2018.277 |
0.394 |
|
| 2018 |
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. Nature Communications. 9: 1934. PMID 29789590 DOI: 10.1038/S41467-018-04157-0 |
0.546 |
|
| 2018 |
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, ... ... Bader JS, et al. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nature Methods. PMID 29638227 DOI: 10.1038/Nmeth.4632 |
0.478 |
|
| 2017 |
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 (New York, N.Y.). 355: 1040-1044. PMID 28280199 DOI: 10.1126/Science.Aaf4557 |
0.739 |
|
| 2017 |
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, ... ... Bader JS, et al. Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science (New York, N.Y.). 355. PMID 28280154 DOI: 10.1126/Science.Aaf4831 |
0.741 |
|
| 2017 |
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, ... ... Bader JS, et al. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science (New York, N.Y.). 355. PMID 28280153 DOI: 10.1126/Science.Aaf4791 |
0.739 |
|
| 2017 |
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, ... ... Bader JS, et al. Bug mapping and fitness testing of chemically synthesized chromosome X. Science (New York, N.Y.). 355. PMID 28280152 DOI: 10.1126/Science.Aaf4706 |
0.737 |
|
| 2017 |
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, ... ... Bader JS, et al. "Perfect" designer chromosome V and behavior of a ring derivative. Science (New York, N.Y.). 355. PMID 28280151 DOI: 10.1126/Science.Aaf4704 |
0.737 |
|
| 2017 |
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, ... ... Bader JS, et al. 3D organization of synthetic and scrambled chromosomes. Science (New York, N.Y.). 355. PMID 28280150 DOI: 10.1126/Science.Aaf4597 |
0.591 |
|
| 2017 |
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, ... ... Bader JS, et al. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science (New York, N.Y.). 355. PMID 28280149 DOI: 10.1126/Science.Aaf3981 |
0.587 |
|
| 2017 |
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, et al. Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. PMID 28174266 DOI: 10.1073/Pnas.1621250114 |
0.702 |
|
| 2016 |
Stracquadanio G, Yang K, Boeke JD, Bader JS. BioPartsDB: a synthetic biology workflow web-application for education and research. Bioinformatics (Oxford, England). PMID 27412090 DOI: 10.1093/Bioinformatics/Btw394 |
0.689 |
|
| 2015 |
Yang K, Stracquadanio G, Luo J, Boeke JD, Bader JS. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. Bioinformatics (Oxford, England). PMID 26568632 DOI: 10.1093/Bioinformatics/Btv664 |
0.703 |
|
| 2015 |
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, ... ... Bader JS, et al. SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Research. PMID 26566658 DOI: 10.1101/Gr.193433.115 |
0.748 |
|
| 2015 |
Chu LH, Vijay CG, Annex BH, Bader JS, Popel AS. PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease. Physiological Genomics. 47: 331-43. PMID 26058837 DOI: 10.1152/Physiolgenomics.00125.2014 |
0.316 |
|
| 2015 |
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. Proceedings of the National Academy of Sciences of the United States of America. 112: 1803-8. PMID 25624482 DOI: 10.1073/Pnas.1424704112 |
0.709 |
|
| 2015 |
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 Synthetic Biology. 4: 213-20. PMID 24895839 DOI: 10.1021/Sb500241E |
0.722 |
|
| 2015 |
Park Y, Bader JS. Dynamic network models of protein complexes Systems Genetics: Linking Genotypes and Phenotypes. 191-213. DOI: 10.1017/CBO9781139012751.010 |
0.505 |
|
| 2014 |
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, ... ... Bader JS, et al. Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nature Genetics. 46: 826-36. PMID 24952745 DOI: 10.1038/Ng.3014 |
0.632 |
|
| 2014 |
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, ... ... Bader JS, et al. Total synthesis of a functional designer eukaryotic chromosome. Science (New York, N.Y.). 344: 55-8. PMID 24674868 DOI: 10.1126/Science.1249252 |
0.751 |
|
| 2014 |
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. 5. PMID 24549847 DOI: 10.1128/Mbio.01066-13 |
0.759 |
|
| 2014 |
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, ... ... Bader JS, et al. Total synthesis of a functional designer eukaryotic chromosome (Science (2014) 344, 6179 (55-58)) Science. 344. DOI: 10.1126/Science.1254596 |
0.714 |
|
| 2013 |
Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z, Lu JY, Khor CN, Lin CL, Bader JS, Irizarry R, Boeke JD. Retraction: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK Nature. 503: 146-146. PMID 24201285 DOI: 10.1038/Nature12727 |
0.436 |
|
| 2013 |
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. 8: e74967. PMID 24130677 DOI: 10.1371/Journal.Pone.0074967 |
0.571 |
|
| 2013 |
Chanda P, Huang H, Arking DE, Bader JS. Fast association tests for genes with FAST. Plos One. 8: e68585. PMID 23935874 DOI: 10.1371/Journal.Pone.0068585 |
0.517 |
|
| 2013 |
Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. XErratum: A DNA integrity network in the yeast Saccharomyces cerevisiae (Cell (2006) 124 (1069-1081)) Cell. 153. DOI: 10.1016/J.Cell.2013.04.054 |
0.491 |
|
| 2012 |
Chu LH, Rivera CG, Popel AS, Bader JS. Constructing the angiome: a global angiogenesis protein interaction network. Physiological Genomics. 44: 915-24. PMID 22911453 DOI: 10.1152/Physiolgenomics.00181.2011 |
0.301 |
|
| 2012 |
Park Y, Bader JS. How networks change with time. Bioinformatics (Oxford, England). 28: i40-8. PMID 22689777 DOI: 10.1093/Bioinformatics/Bts211 |
0.556 |
|
| 2012 |
Chanda P, Yuhki N, Li M, Bader JS, Hartz A, Boerwinkle E, Kao WH, Arking DE. Comprehensive evaluation of imputation performance in African Americans. Journal of Human Genetics. 57: 411-21. PMID 22648186 DOI: 10.1038/Jhg.2012.43 |
0.305 |
|
| 2012 |
Cooper EM, Müller H, Chandrasegaran S, Bader JS, Boeke JD. The Build-a-Genome course. Methods in Molecular Biology (Clifton, N.J.). 852: 273-83. PMID 22328440 DOI: 10.1007/978-1-61779-564-0_20 |
0.48 |
|
| 2012 |
Richardson SM, Liu S, Boeke JD, Bader JS. Design-A-Gene with GeneDesign. Methods in Molecular Biology (Clifton, N.J.). 852: 235-47. PMID 22328438 DOI: 10.1007/978-1-61779-564-0_18 |
0.495 |
|
| 2012 |
Muller H, Annaluru N, Schwerzmann JW, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S. Assembling large DNA segments in yeast. Methods in Molecular Biology (Clifton, N.J.). 852: 133-50. PMID 22328431 DOI: 10.1007/978-1-61779-564-0_11 |
0.545 |
|
| 2012 |
Annaluru N, Muller H, Ramalingam S, Kandavelou K, London V, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S. Assembling DNA fragments by USER fusion. Methods in Molecular Biology (Clifton, N.J.). 852: 77-95. PMID 22328427 DOI: 10.1007/978-1-61779-564-0_7 |
0.505 |
|
| 2012 |
Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z, Lu JY, Khor CN, Lin CL, Bader JS, Irizarry R, Boeke JD. Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 482: 251-5. PMID 22318606 DOI: 10.1038/Nature10804 |
0.51 |
|
| 2011 |
Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. 477: 471-6. PMID 21918511 DOI: 10.1038/Nature10403 |
0.61 |
|
| 2011 |
Huang H, Chanda P, Alonso A, Bader JS, Arking DE. Gene-based tests of association. Plos Genetics. 7: e1002177. PMID 21829371 DOI: 10.1371/Journal.Pgen.1002177 |
0.545 |
|
| 2011 |
Bader JS. Grand network convergence. Genome Biology. 12: 306. PMID 21682935 DOI: 10.1186/Gb-2011-12-6-306 |
0.351 |
|
| 2011 |
Park Y, Bader JS. Resolving the structure of interactomes with hierarchical agglomerative clustering. Bmc Bioinformatics. 12: S44. PMID 21342576 DOI: 10.1186/1471-2105-12-S1-S44 |
0.541 |
|
| 2010 |
Zhong J, Krawczyk SA, Chaerkady R, Huang H, Goel R, Bader JS, Wong GW, Corkey BE, Pandey A. Temporal profiling of the secretome during adipogenesis in humans. Journal of Proteome Research. 9: 5228-38. PMID 20707391 DOI: 10.1021/Pr100521C |
0.495 |
|
| 2010 |
Veeramani B, Bader JS. Predicting functional associations from metabolism using bi-partite network algorithms. Bmc Systems Biology. 4: 95. PMID 20630077 DOI: 10.1186/1752-0509-4-95 |
0.746 |
|
| 2010 |
Lee PA, Dymond JS, Scheifele LZ, Richardson SM, Foelber KJ, Boeke JD, Bader JS. CLONEQC: lightweight sequence verification for synthetic biology. Nucleic Acids Research. 38: 2617-23. PMID 20211841 DOI: 10.1093/Nar/Gkq093 |
0.493 |
|
| 2010 |
Richardson SM, Nunley PW, Yarrington RM, Boeke JD, Bader JS. GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic Acids Research. 38: 2603-6. PMID 20211837 DOI: 10.1093/Nar/Gkq143 |
0.447 |
|
| 2010 |
Park Y, Moore C, Bader JS. Dynamic networks from hierarchical bayesian graph clustering. Plos One. 5: e8118. PMID 20084108 DOI: 10.1371/Journal.Pone.0008118 |
0.576 |
|
| 2010 |
Richardson SM, Olson BS, Dymond JS, Burns R, Chandrasegaran S, Boeke JD, Shehu A, Bader JS. Automated design of assemblable, modular, synthetic chromosomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6068: 280-289. DOI: 10.1007/978-3-642-14403-5_30 |
0.479 |
|
| 2009 |
Huang H, Maertens AM, Hyland EM, Dai J, Norris A, Boeke JD, Bader JS. HistoneHits: a database for histone mutations and their phenotypes. Genome Research. 19: 674-81. PMID 19218532 DOI: 10.1101/Gr.083402.108 |
0.609 |
|
| 2009 |
Veeramani B, Bader JS. Metabolic flux correlations, genetic interactions, and disease. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 291-302. PMID 19193147 DOI: 10.1089/Cmb.2008.14Tt |
0.758 |
|
| 2009 |
Czar MJ, Anderson JC, Bader JS, Peccoud J. Gene synthesis demystified. Trends in Biotechnology. 27: 63-72. PMID 19111926 DOI: 10.1016/J.Tibtech.2008.10.007 |
0.317 |
|
| 2009 |
Huang H, Bader JS. Precision and recall estimates for two-hybrid screens. Bioinformatics (Oxford, England). 25: 372-8. PMID 19091773 DOI: 10.1093/Bioinformatics/Btn640 |
0.501 |
|
| 2009 |
Dymond JS, Scheifele LZ, Richardson S, Lee P, Chandrasegaran S, Bader JS, Boeke JD. Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course. Genetics. 181: 13-21. PMID 19015540 DOI: 10.1534/Genetics.108.096784 |
0.559 |
|
| 2008 |
Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS. Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Research. 18: 1991-2004. PMID 18832443 DOI: 10.1101/Gr.077693.108 |
0.488 |
|
| 2008 |
Dai J, Hyland EM, Yuan DS, Huang H, Bader JS, Boeke JD. Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants. Cell. 134: 1066-78. PMID 18805098 DOI: 10.1016/J.Cell.2008.07.019 |
0.628 |
|
| 2008 |
Lin YY, Qi Y, Lu JY, Pan X, Yuan DS, Zhao Y, Bader JS, Boeke JD. A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes & Development. 22: 2062-74. PMID 18676811 DOI: 10.1101/Gad.1679508 |
0.51 |
|
| 2008 |
Bader JS. Systems approaches for pharmacogenetics and pharmacogenomics. Pharmacogenomics. 9: 257-62. PMID 18303961 DOI: 10.2217/14622416.9.3.257 |
0.366 |
|
| 2008 |
Pan X, Yuan D, Ye P, Bader J, Boeke JD. Response to Dr Stephen Cooper's 'On the use of metaphor to understand, explain, or rationalize redundant genes in yeast' Fems Yeast Research. 8: 349-350. DOI: 10.1111/J.1567-1364.2008.00357.X |
0.475 |
|
| 2007 |
Huang H, Jedynak BM, Bader JS. Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. Plos Computational Biology. 3: e214. PMID 18039026 DOI: 10.1371/Journal.Pcbi.0030214 |
0.522 |
|
| 2007 |
Stuart LM, Boulais J, Charriere GM, Hennessy EJ, Brunet S, Jutras I, Goyette G, Rondeau C, Letarte S, Huang H, Ye P, Morales F, Kocks C, Bader JS, Desjardins M, et al. A systems biology analysis of the Drosophila phagosome. Nature. 445: 95-101. PMID 17151602 DOI: 10.1038/Nature05380 |
0.513 |
|
| 2006 |
Liu LA, Bader JS. Decoding transcriptional regulatory interactions. Physica D. Nonlinear Phenomena. 224: 174-181. PMID 17364011 DOI: 10.1016/J.Physd.2006.09.022 |
0.336 |
|
| 2006 |
Dorer MS, Kirton D, Bader JS, Isberg RR. RNA interference analysis of Legionella in Drosophila cells: exploitation of early secretory apparatus dynamics. Plos Pathogens. 2: e34. PMID 16652170 DOI: 10.1371/Journal.Ppat.0020034 |
0.306 |
|
| 2006 |
Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, ... ... Bader JS, et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 38: 285-93. PMID 16501559 DOI: 10.1038/Ng1747 |
0.505 |
|
| 2006 |
Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell. 124: 1069-81. PMID 16487579 DOI: 10.1016/J.Cell.2005.12.036 |
0.532 |
|
| 2006 |
Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD. Global synthetic-lethality analysis and yeast functional profiling. Trends in Genetics : Tig. 22: 56-63. PMID 16309778 DOI: 10.1016/J.Tig.2005.11.003 |
0.536 |
|
| 2005 |
Ye P, Peyser BD, Pan X, Boeke JD, Spencer FA, Bader JS. Gene function prediction from congruent synthetic lethal interactions in yeast. Molecular Systems Biology. 1: 2005.0026. PMID 16729061 DOI: 10.1038/Msb4100034 |
0.535 |
|
| 2005 |
Qi Y, Ye P, Bader JS. Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethality. Bmc Bioinformatics. 6: 288. PMID 16332255 DOI: 10.1186/1471-2105-6-288 |
0.329 |
|
| 2005 |
Ye P, Peyser BD, Spencer FA, Bader JS. Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast. Bmc Bioinformatics. 6: 270. PMID 16283923 DOI: 10.1186/1471-2105-6-270 |
0.324 |
|
| 2005 |
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 437: 376-80. PMID 16056220 DOI: 10.1038/Nature03959 |
0.32 |
|
| 2004 |
Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, Bader JS, Hieter P, Spencer F, Boeke JD. A robust toolkit for functional profiling of the yeast genome. Molecular Cell. 16: 487-96. PMID 15525520 DOI: 10.1016/J.Molcel.2004.09.035 |
0.571 |
|
| 2004 |
Bader JS, Chaudhuri A, Rothberg JM, Chant J. Gaining confidence in high-throughput protein interaction networks. Nature Biotechnology. 22: 78-85. PMID 14704708 DOI: 10.1038/Nbt924 |
0.351 |
|
| 2003 |
Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, et al. A protein interaction map of Drosophila melanogaster. Science (New York, N.Y.). 302: 1727-36. PMID 14605208 DOI: 10.1126/Science.1090289 |
0.324 |
|
| 2003 |
Bader JS. Greedily building protein networks with confidence. Bioinformatics (Oxford, England). 19: 1869-74. PMID 14555618 DOI: 10.1093/Bioinformatics/Btg358 |
0.333 |
|
| 2002 |
Bader JS, Deem MW, Hammond RW, Henck SA, Simpson JW, Rothberg JM. A Brownian-ratchet DNA pump with applications to single-nucleotide polymorphism genotyping Applied Physics a: Materials Science and Processing. 75: 275-278. DOI: 10.1007/S003390201330 |
0.526 |
|
| 2000 |
Hammond RW, Bader JS, Henck SA, Deem MW, McDermott GA, Bustillo JM, Rothberg JM. Differential transport of DNA by a rectified Brownian motion device. Electrophoresis. 21: 74-80. PMID 10634472 DOI: 10.1002/(Sici)1522-2683(20000101)21:1<74::Aid-Elps74>3.0.Co;2-K |
0.532 |
|
| 1999 |
Bader JS, Hammond RW, Henck SA, Deem MW, McDermott GA, Bustillo JM, Simpson JW, Mulhern GT, Rothberg JM. DNA transport by a micromachined Brownian ratchet device. Proceedings of the National Academy of Sciences of the United States of America. 96: 13165-9. PMID 10557291 DOI: 10.1073/Pnas.96.23.13165 |
0.53 |
|
| 1996 |
Deem MW, Bader JS. A configurational bias Monte Carlo method for linear and cyclic peptides Molecular Physics. 87: 1245-1260. DOI: 10.1080/00268979600100841 |
0.507 |
|
| 1992 |
Bader JS, Chandler D. Computer simulation study of the mean forces between ferrous and ferric ions in water The Journal of Physical Chemistry. 96: 6423-6427. DOI: 10.1021/J100194A059 |
0.408 |
|
| 1990 |
Bader JS, Kuharski RA, Chandler D. Role of nuclear tunneling in aqueous ferrous–ferric electron transfer Journal of Chemical Physics. 93: 230-236. DOI: 10.1063/1.459596 |
0.418 |
|
| 1989 |
Bader JS, Chandler D. Computer simulation of photochemically induced electron transfer Chemical Physics Letters. 157: 501-504. DOI: 10.1016/S0009-2614(89)87399-3 |
0.405 |
|
| 1988 |
Kuharski RA, Bader JS, Chandler D, Sprik M, Klein ML, Impey RW. Molecular model for aqueous ferrous–ferric electron transfer Journal of Chemical Physics. 89: 3248-3257. DOI: 10.1063/1.454929 |
0.421 |
|
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