| Year |
Citation |
Score |
| 2024 |
Kim MS, Bhargava HK, Shavey GE, Lim WA, El-Samad H, Ng AH. Degron-based bioPROTACs for controlling signaling in CAR T cells. Biorxiv : the Preprint Server For Biology. PMID 38405763 DOI: 10.1101/2024.02.16.580396 |
0.562 |
|
| 2024 |
Weinberg ZY, Soliman SS, Kim MS, Chen IP, Ott M, El-Samad H. -designed minibinders expand the synthetic biology sensing repertoire. Biorxiv : the Preprint Server For Biology. PMID 38293112 DOI: 10.1101/2024.01.12.575267 |
0.717 |
|
| 2022 |
Allen GM, Frankel NW, Reddy NR, Bhargava HK, Yoshida MA, Stark SR, Purl M, Lee J, Yee JL, Yu W, Li AW, Garcia KC, El-Samad H, Roybal KT, Spitzer MH, et al. Synthetic cytokine circuits that drive T cells into immune-excluded tumors. Science (New York, N.Y.). 378: eaba1624. PMID 36520915 DOI: 10.1126/science.aba1624 |
0.715 |
|
| 2021 |
Woodall NB, Weinberg Z, Park J, Busch F, Johnson RS, Feldbauer MJ, Murphy M, Ahlrichs M, Yousif I, MacCoss MJ, Wysocki VH, El-Samad H, Baker D. De novo design of tyrosine and serine kinase-driven protein switches. Nature Structural & Molecular Biology. 28: 762-770. PMID 34518698 DOI: 10.1038/s41594-021-00649-8 |
0.713 |
|
| 2021 |
Weinberg ZY, Hilburger CE, Kim M, Cao L, Khalid M, Elmes S, Diwanji D, Hernandez E, Lopez J, Schaefer K, Smith AM, Zhou F, Renuka Kumar G, Ott M, ... ... El-Samad H, et al. Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein. Biorxiv : the Preprint Server For Biology. PMID 33907743 DOI: 10.1101/2021.04.20.440678 |
0.729 |
|
| 2020 |
Chen SY, Osimiri LC, Chevalier M, Bugaj LJ, Nguyen TH, Greenstein RA, Ng AH, Stewart-Ornstein J, Neves LT, El-Samad H. Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics. Cell Systems. PMID 32898473 DOI: 10.1016/J.Cels.2020.08.009 |
0.327 |
|
| 2020 |
Chen Z, Kibler RD, Hunt A, Busch F, Pearl J, Jia M, VanAernum ZL, Wicky BIM, Dods G, Liao H, Wilken MS, Ciarlo C, Green S, El-Samad H, Stamatoyannopoulos J, et al. De novo design of protein logic gates. Science (New York, N.Y.). 368: 78-84. PMID 32241946 DOI: 10.1126/Science.Aay2790 |
0.352 |
|
| 2020 |
Mace K, Krakowiak J, El-Samad H, Pincus D. Multi-kinase control of environmental stress responsive transcription. Plos One. 15: e0230246. PMID 32160258 DOI: 10.1371/Journal.Pone.0230246 |
0.571 |
|
| 2019 |
Dalal CK, Zuleta IA, Lohse MB, Zordan RE, El-Samad H, Johnson AD. A population shift between two heritable cell types of the pathogen is based both on switching and selective proliferation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31822605 DOI: 10.1073/Pnas.1908986116 |
0.31 |
|
| 2019 |
Langan RA, Boyken SE, Ng AH, Samson JA, Dods G, Westbrook AM, Nguyen TH, Lajoie MJ, Chen Z, Berger S, Mulligan VK, Dueber JE, Novak WRP, El-Samad H, Baker D. De novo design of bioactive protein switches. Nature. PMID 31341284 DOI: 10.1038/S41586-019-1432-8 |
0.331 |
|
| 2019 |
Ng AH, Nguyen TH, Gómez-Schiavon M, Dods G, Langan RA, Boyken SE, Samson JA, Waldburger LM, Dueber JE, Baker D, El-Samad H. Modular and tunable biological feedback control using a de novo protein switch. Nature. PMID 31341280 DOI: 10.1038/S41586-019-1425-7 |
0.375 |
|
| 2018 |
Harrigan P, Madhani HD, El-Samad H. Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control. Cell. 175: 877-886.e10. PMID 30340045 DOI: 10.1016/J.Cell.2018.09.044 |
0.359 |
|
| 2017 |
Stewart-Ornstein J, Chen S, Bhatnagar R, Weissman JS, El-Samad H. Model-guided optogenetic study of PKA signaling in budding yeast. Molecular Biology of the Cell. 28: 221-227. PMID 28035051 DOI: 10.1091/Mbc.E16-06-0354 |
0.358 |
|
| 2016 |
Aranda-Diaz A, Mace K, Zuleta I, Harrigan P, El-Samad H. Robust synthetic circuits for two-dimensional control of gene expression in yeast. Acs Synthetic Biology. PMID 27930885 DOI: 10.1021/Acssynbio.6B00251 |
0.352 |
|
| 2016 |
Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad H, Johnson AD. Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. Elife. 5. PMID 27614020 DOI: 10.7554/Elife.18981 |
0.33 |
|
| 2016 |
Heimberg G, Bhatnagar R, El-Samad H, Thomson M. Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. Cell Systems. 2: 239-50. PMID 27135536 DOI: 10.1016/J.Cels.2016.04.001 |
0.301 |
|
| 2016 |
Bhatnagar R, El-Samad H. Tradeoffs in adapting biological systems European Journal of Control. DOI: 10.1016/J.Ejcon.2016.04.010 |
0.333 |
|
| 2015 |
Chevalier M, Venturelli O, El-Samad H. The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks. Plos Computational Biology. 11: e1004462. PMID 26484538 DOI: 10.1371/Journal.Pcbi.1004462 |
0.329 |
|
| 2015 |
Yang J, McCormick MA, Zheng J, Xie Z, Tsuchiya M, Tsuchiyama S, El-Samad H, Ouyang Q, Kaeberlein M, Kennedy BK, Li H. Systematic analysis of asymmetric partitioning of yeast proteome between mother and daughter cells reveals "aging factors" and mechanism of lifespan asymmetry. Proceedings of the National Academy of Sciences of the United States of America. 112: 11977-82. PMID 26351681 DOI: 10.1073/Pnas.1506054112 |
0.318 |
|
| 2015 |
Lipinski-Kruszka J, Stewart-Ornstein J, Chevalier MW, El-Samad H. Using dynamic noise propagation to infer causal regulatory relationships in biochemical networks. Acs Synthetic Biology. 4: 258-64. PMID 24967515 DOI: 10.1021/Sb5000059 |
0.709 |
|
| 2014 |
Pincus D, Aranda-Díaz A, Zuleta IA, Walter P, El-Samad H. Delayed Ras/PKA signaling augments the unfolded protein response. Proceedings of the National Academy of Sciences of the United States of America. 111: 14800-5. PMID 25275008 DOI: 10.1073/Pnas.1409588111 |
0.638 |
|
| 2014 |
Zuleta IA, Aranda-Díaz A, Li H, El-Samad H. Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nature Methods. 11: 443-8. PMID 24608180 DOI: 10.1038/Nmeth.2879 |
0.325 |
|
| 2014 |
Bhatnagar R, El-Samad H. Sensitivity Analysis and Model Reduction Applied to Adapting Biological Systems Biophysical Journal. 106: 3-7. DOI: 10.1016/J.Bpj.2013.11.2136 |
0.312 |
|
| 2013 |
Stewart-Ornstein J, Nelson C, DeRisi J, Weissman JS, El-Samad H. Msn2 coordinates a stoichiometric gene expression program. Current Biology : Cb. 23: 2336-45. PMID 24210615 DOI: 10.1016/J.Cub.2013.09.043 |
0.323 |
|
| 2013 |
Chen S, Harrigan P, Heineike B, Stewart-Ornstein J, El-Samad H. Building robust functionality in synthetic circuits using engineered feedback regulation. Current Opinion in Biotechnology. 24: 790-6. PMID 23566378 DOI: 10.1016/J.Copbio.2013.02.025 |
0.331 |
|
| 2013 |
Vidal SE, Pincus D, Stewart-Ornstein J, El-Samad H. Formation of subnuclear foci is a unique spatial behavior of mating MAPKs during hyperosmotic stress. Cell Reports. 3: 328-34. PMID 23416049 DOI: 10.1016/J.Celrep.2013.01.022 |
0.548 |
|
| 2012 |
Venturelli OS, El-Samad H, Murray RM. Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response. Proceedings of the National Academy of Sciences of the United States of America. 109: E3324-33. PMID 23150580 DOI: 10.1073/Pnas.1211902109 |
0.37 |
|
| 2012 |
Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL. Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses. Proceedings of the National Academy of Sciences of the United States of America. 109: E3084-93. PMID 23054834 DOI: 10.1073/Pnas.1212457109 |
0.611 |
|
| 2012 |
Stewart-Ornstein J, El-Samad H. Stochastic modeling of cellular networks. Methods in Cell Biology. 110: 111-37. PMID 22482947 DOI: 10.1016/B978-0-12-388403-9.00005-9 |
0.378 |
|
| 2012 |
Stewart-Ornstein J, Weissman JS, El-Samad H. Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae. Molecular Cell. 45: 483-93. PMID 22365828 DOI: 10.1016/J.Molcel.2011.11.035 |
0.4 |
|
| 2012 |
Paluch E, El-Samad H. Modeling and simulation of cellular functions Molecular Biology of the Cell. 23: 972. DOI: 10.1091/Mbc.E11-12-0968 |
0.361 |
|
| 2011 |
El-Samad H, Weissman JS. Genetics: Noise rules. Nature. 480: 188-9. PMID 22158239 DOI: 10.1038/480188A |
0.301 |
|
| 2011 |
Chevalier MW, El-Samad H. A data-integrated method for analyzing stochastic biochemical networks. The Journal of Chemical Physics. 135: 214110. PMID 22149782 DOI: 10.1063/1.3664126 |
0.321 |
|
| 2011 |
Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J. In silico feedback for in vivo regulation of a gene expression circuit. Nature Biotechnology. 29: 1114-6. PMID 22057053 DOI: 10.1038/Nbt.2018 |
0.667 |
|
| 2011 |
Rubio C, Pincus D, Korennykh A, Schuck S, El-Samad H, Walter P. Homeostatic adaptation to endoplasmic reticulum stress depends on Ire1 kinase activity. The Journal of Cell Biology. 193: 171-84. PMID 21444684 DOI: 10.1083/Jcb.201007077 |
0.644 |
|
| 2011 |
El-Samad H. Homeostatic Regulation of the Unfolded Protein Response Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.1153 |
0.371 |
|
| 2010 |
McCullagh E, Seshan A, El-Samad H, Madhani HD. Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway. Nature Cell Biology. 12: 954-62. PMID 20852627 DOI: 10.1038/Ncb2097 |
0.4 |
|
| 2010 |
Pincus D, Chevalier MW, Aragón T, van Anken E, Vidal SE, El-Samad H, Walter P. BiP binding to the ER-stress sensor Ire1 tunes the homeostatic behavior of the unfolded protein response. Plos Biology. 8: e1000415. PMID 20625545 DOI: 10.1371/Journal.Pbio.1000415 |
0.63 |
|
| 2010 |
El-Samad H, Khammash M. Modelling and analysis of gene regulatory network using feedback control theory International Journal of Systems Science. 41: 17-33. DOI: 10.1080/00207720903144545 |
0.58 |
|
| 2009 |
Arkin A, Berry D, Church G, Arnold F, Boldt J, Müller O, Ellington AD, Endy D, Fussenegger M, Gold ER, Greenwood J, Lee SY, Lim W, Minshull J, Murray TH, ... ... El-Samad H, et al. What's in a name? Nature Biotechnology. 27: 1071-1073. PMID 20010573 DOI: 10.1038/nbt1209-1071 |
0.422 |
|
| 2009 |
McCullagh E, Farlow J, Fuller C, Girard J, Lipinski-Kruszka J, Lu D, Noriega T, Rollins G, Spitzer R, Todhunter M, El-Samad H. Not all quiet on the noise front. Nature Chemical Biology. 5: 699-704. PMID 19763097 DOI: 10.1038/Nchembio.222 |
0.705 |
|
| 2009 |
Ma W, Trusina A, El-Samad H, Lim WA, Tang C. Defining network topologies that can achieve biochemical adaptation. Cell. 138: 760-73. PMID 19703401 DOI: 10.1016/J.Cell.2009.06.013 |
0.565 |
|
| 2009 |
Chevalier MW, El-Samad H. A rigorous framework for multiscale simulation of stochastic cellular networks. The Journal of Chemical Physics. 131: 054102. PMID 19673546 DOI: 10.1063/1.3190327 |
0.323 |
|
| 2009 |
Justman QA, Serber Z, Ferrell JE, El-Samad H, Shokat KM. Tuning the activation threshold of a kinase network by nested feedback loops. Science (New York, N.Y.). 324: 509-12. PMID 19390045 DOI: 10.1126/Science.1169498 |
0.344 |
|
| 2006 |
Kurata H, El-Samad H, Iwasaki R, Ohtake H, Doyle JC, Grigorova I, Gross CA, Khammash M. Module-based analysis of robustness tradeoffs in the heat shock response system. Plos Computational Biology. 2: e59. PMID 16863396 DOI: 10.1371/Journal.Pcbi.0020059 |
0.556 |
|
| 2006 |
El-Samad H, Khammash M. Regulated degradation is a mechanism for suppressing stochastic fluctuations in gene regulatory networks. Biophysical Journal. 90: 3749-61. PMID 16500958 DOI: 10.1529/Biophysj.105.060491 |
0.626 |
|
| 2006 |
El-Samad H, Prajna S, Papachristodoulou A, Doyle J, Khammash M. Advanced methods and algorithms for biological networks analysis Proceedings of the Ieee. 94: 832-852. DOI: 10.1109/JPROC.2006.871776 |
0.462 |
|
| 2006 |
El-Samad H, Khammash M. Coherence resonance: A mechanism for noise induced stable oscillations in gene regulatory networks Proceedings of the Ieee Conference On Decision and Control. 2382-2387. |
0.55 |
|
| 2005 |
El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M. Surviving heat shock: control strategies for robustness and performance. Proceedings of the National Academy of Sciences of the United States of America. 102: 2736-41. PMID 15668395 DOI: 10.1073/Pnas.0403510102 |
0.583 |
|
| 2004 |
Khammash M, El-Samad H. Systems biology: From physiology to gene regulation Ieee Control Systems Magazine. 24: 62-76. DOI: 10.1109/Mcs.2004.1316654 |
0.564 |
|
| 2004 |
El-Samad H, Khammash M. Intrinsic noise rejection in gene networks by regulation of stability International Symposium On Control, Communications and Signal Processing, Isccsp. 187-190. |
0.571 |
|
| 2003 |
El-Samad H, Prajna S, Papachristodoulou A, Khammash M, Doyle JC. Model Validation and Robust Stability Analysis of the Bacterial Heat Shock Response Using SOSTOOLS Proceedings of the Ieee Conference On Decision and Control. 4: 3766-3771. |
0.453 |
|
| 2002 |
El-Samad H, Goff JP, Khammash M. Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective. Journal of Theoretical Biology. 214: 17-29. PMID 11786029 DOI: 10.1006/Jtbi.2001.2422 |
0.521 |
|
| 2002 |
El-Samad H, Khammash M, Kurata H, Doyle J. Robustness analysis of the heat shock response in E. coli Proceedings of the American Control Conference. 3: 1742-1747. |
0.497 |
|
| 2001 |
Kurata i, El-Samad H, Yi TM, Khammash M, Doyle J. Feedback regulation of the heat shock response in E. coli Proceedings of the Ieee Conference On Decision and Control. 1: 837-842. |
0.508 |
|
| 2000 |
El-Samad H, Khammash M. Feedback analysis of calcium homeostasis and parturient paresis Proceedings - Ieee International Symposium On Bio-Informatics and Biomedical Engineering, Bibe 2000. 365-369. DOI: 10.1109/BIBE.2000.889629 |
0.436 |
|
| 2000 |
El-Samad H, Khammash M, Goff J. Calcium homeostasis: a feedback control point of view Proceedings of the American Control Conference. 5: 2962-2966. |
0.465 |
|
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