- Ma, Yitong; Budde, Mark W.; et el. (2023) Tuning
Methylation-Dependent Silencing Dynamics by Synthetic Modulation of CpG
Density; ACS Synthetic Biology; Vol. 12; No. 9; 2536-2545; 10.1021/acssynbio.3c00078
- Horns, Felix; Martinez, Joe A.; et el. (2023) Engineering
RNA export for measurement and manipulation of living cells; Cell;
Vol. 186; No. 17; 3642-3658.e32; PMCID PMC10528933; 10.1016/j.cell.2023.06.013
- Zhu, Ronghui; Santat, Leah A.; et el. (2023) Reconstitution
of morphogen shuttling circuits; Science Advances; Vol. 9; No. 28;
eadf9336; PMCID PMC10337948; 10.1126/sciadv.adf9336
- Kong, Qing; Xia, Shiyu; et el. (2023) Alternative
splicing of GSDMB modulates killer lymphocyte-triggered pyroptosis;
Science Immunology; Vol. 8; No. 82; Art. No. eadg3196; PMCID
PMC10338320; 10.1126/sciimmunol.adg3196
- Cabrera, Alan; Edelstein, Hailey I.; et el. (2022) The
sound of silence: Transgene silencing in mammalian cell engineering;
Cell Systems; Vol. 13; No. 12; 950-973; PMCID PMC9880859; 10.1016/j.cels.2022.11.005
- Wang, Sheng; Garcia-Ojalvo, Jordi; et el. (2022) Periodic
spatial patterning with a single morphogen; Cell Systems; Vol. 13;
No. 12; 1033-1047.e7; 10.1016/j.cels.2022.11.001
- Amadei, Gianluca; Handford, Charlotte E.; et el. (2022) Embryo model
completes gastrulation to neurulation and organogenesis; Nature;
Vol. 610; No. 7930; 143-153; PMCID PMC9534772; 10.1038/s41586-022-05246-3
- Ding, Fangyuan; Su, Christina J.; et el. (2022) Dynamics
and functional roles of splicing factor autoregulation; Cell
Reports; Vol. 39; No. 12; Art. No. 110985; PMCID PMC9262138; 10.1016/j.celrep.2022.110985
- Su, Christina J.; Murugan, Arvind; et el. (2022) Ligand-receptor
promiscuity enables cellular addressing; Cell Systems; Vol. 13;
No. 5; 408-425; 10.1016/j.cels.2022.03.001
- Klumpe, Heidi E.; Langley, Matthew A.; et el. (2022) The
context-dependent, combinatorial logic of BMP signaling; Cell
Systems; Vol. 13; No. 5; 388-407; PMCID PMC9127470; 10.1016/j.cels.2022.03.002
- Ma, Yitong; Budde, Mark W.; et el. (2022) Synthetic
mammalian signaling circuits for robust cell population control;
Cell; Vol. 185; No. 6; 967-979; PMCID PMC8995209; 10.1016/j.cell.2022.01.026
- Vlahos, Alexander E.; Kang, Jeewoo; et el. (2022) Protease-controlled
secretion and display of intercellular signals; Nature
Communications; Vol. 13; Art. No. 912; PMCID PMC8854555; 10.1038/s41467-022-28623-y
- Zhu, Ronghui; del Rio-Salgado, Jesus M.; et el. (2022) Synthetic
multistability in mammalian cells; Science; Vol. 375; No. 6578; Art.
No. eabg9765; 10.1126/science.abg9765
- Cable, Jennifer; Elowitz, Michael B.; et el. (2021) Single
cell biology—a Keystone Symposia report; Annals of the New York
Academy of Sciences; Vol. 1506; 74-97; 10.1111/nyas.14692
- Gong, Wuming; Granados, Alejandro A.; et el. (2021) Benchmarked
approaches for reconstruction of in vitro cell lineages and in silico
models of C. elegans and M. musculus developmental trees; Cell
Systems; Vol. 12; No. 8; 810-826; 10.1016/j.cels.2021.05.008
- Chen, Zibo and Elowitz, Michael B. (2021) Programmable
protein circuit design; Cell; Vol. 184; No. 9; 2284-2301; PMCID
PMC8087657; 10.1016/j.cell.2021.03.007
- Chow, Ke-Huan K.; Budde, Mark W.; et el. (2021) Imaging
cell lineage with a synthetic digital recording system; Science;
Vol. 372; No. 6538; Art. No. eabb3099; 10.1126/science.abb3099
- Askary, Amjad; Sánchez-Guardado, Luis; et el. (2020) In
situ readout of DNA barcodes and single base edits facilitated by in
vitro transcription; Nature Biotechnology; Vol. 38; No. 1; 66-75;
PMCID PMC6954335; 10.1038/s41587-019-0299-4
- Li, Pulin and Elowitz, Michael B. (2019) Communication
codes in developmental signaling pathways; Development; Vol. 146;
No. 12; Art. No. dev170977; PMCID PMC6602343; 10.1242/dev.170977
- Ding, Fangyuan and Elowitz, Michael B. (2019) Constitutive
splicing and economies of scale in gene expression; Nature
Structural & Molecular Biology; Vol. 26; No. 6; 424-432; PMCID
PMC6663491; 10.1038/s41594-019-0226-x
- Nandagopal, Nagarajan; Santat, Leah A.; et el. (2019) Cis-activation
in the Notch signaling pathway; eLife; Vol. 8; Art. No. e37880;
PMCID PMC6345567; 10.7554/eLife.37880
- Ng, Kenneth K. N.; Yui, Mary A.; et el. (2018) A
stochastic epigenetic switch controls the dynamics of T-cell lineage
commitment; eLife; Vol. 7; Art. No. e37851; PMCID PMC6245732; 10.7554/eLife.37851
- Martinez-Corral, Rosa; Raimundez, Elba; et el. (2018) Self-Amplifying
Pulsatile Protein Dynamics without Positive Feedback; Cell Systems;
Vol. 7; No. 4; 453-462; 10.1016/j.cels.2018.08.012
- Siddique, Hifzur; Zheng, Mengmei; et el. (2018) Novel
NOTCH-Binding Protein Directs Self-Renewal of Tumor-Initiating Stem-like
Cells and HCC Development through Cell Fate Reprogramming;
Hepatology; Vol. 68; No. S1; Art. No. 1365; 10.1002/hep.30257
- Gao, Xiaojing J.; Chong, Lucy S.; et el. (2018) Programmable
protein circuits in living cells; Science; Vol. 361; No. 6408;
1252-1258; PMCID PMC7176481; 10.1126/science.aat5062
- Siddique, H. R.; Zheng, M.; et el. (2018) Cell
fate and metabolic reprogramming of tumor-initiating stem-like
cells; Alcoholism: Clinical and Experimental Research; Vol. 42;
No. S2; Art. No. 427; 10.1111/acer.13834
- Rosenthal, Adam Z.; Qi, Yutao; et el. (2018) Metabolic
interactions between dynamic bacterial subpopulations; eLife; Vol.
7; Art. No. e33099; PMCID PMC6025961; 10.7554/eLife.33099
- Li, Pulin; Markson, Joseph S.; et el. (2018) Morphogen
gradient reconstitution reveals Hedgehog pathway design principles;
Science; Vol. 360; No. 6388; 543-548; PMCID PMC6516753; 10.1126/science.aao0645
- Park, Jin; Dies, Marta; et el. (2018) Molecular
Time Sharing through Dynamic Pulsing in Single Cells; Cell Systems;
Vol. 6; No. 2; 216-229; PMCID PMC6070344; 10.1016/j.cels.2018.01.011
- Nandagopal, Nagarajan; Santat, Leah A.; et el. (2018) Dynamic
Ligand Discrimination in the Notch Signaling Pathway; Cell; Vol.
172; No. 4; 869-880; PMCID PMC6414217; 10.1016/j.cell.2018.01.002
- Tycko, Josh; Van, Mike V.; et el. (2017) Advancing
towards a global mammalian gene regulation model through single-cell
analysis and synthetic biology; Current Opinion in Biomedical
Engineering; Vol. 4; 174-193; 10.1016/j.cobme.2017.10.011
- Antebi, Yaron E.; Linton, James M.; et el. (2017) Combinatorial
Signal Perception in the BMP Pathway; Cell; Vol. 170; No. 6;
1184-1196; PMCID PMC5612783; 10.1016/j.cell.2017.08.015
- Yuan, Guo-Cheng; Cai, Long; et el. (2017) Challenges
and emerging directions in single-cell analysis; Genome Biology;
Vol. 18; No. 1; Art. No. 84; PMCID PMC5421338; 10.1186/s13059-017-1218-y
- Clevers, Hans; Rafelski, Susanne; et el. (2017) What
Is Your Conceptual Definition of “Cell Type” in the Context of a Mature
Organism?; Cell Systems; Vol. 4; No. 3; 255-259; 10.1016/j.cels.2017.03.006
- Antebi, Yaron E.; Nandagopal, Nagarajan; et el. (2017) An
operational view of intercellular signaling pathways; Current
Opinion in Systems Biology; Vol. 1; 16-24; PMCID PMC5665397; 10.1016/j.coisb.2016.12.003
- Frieda, Kirsten L.; Linton, James M.; et el. (2017) Synthetic
recording and in situ readout of lineage information in single
cells; Nature; Vol. 541; No. 7635; 107-111; PMCID PMC6487260; 10.1038/nature20777
- Hormoz, Sahand; Singer, Zakary S.; et el. (2016) Inferring
Cell-State Transition Dynamics from Lineage Trees and Endpoint
Single-Cell Measurements; Cell Systems; Vol. 3; No. 5; 419-433;
PMCID PMC5142829; 10.1016/j.cels.2016.10.015
- Gao, Xiaojing J. and Elowitz, Michael B. (2016) Synthetic
biology: Precision timing in a cell; Nature; Vol. 538; No. 7626;
462-463; 10.1038/nature19478
- Kueh, Hao Yuan; Yui, Mary A.; et el. (2016) Asynchronous
combinatorial action of four regulatory factors activates Bcl11b for T
cell commitment; Nature Immunology; Vol. 17; No. 8; 956-965; PMCID
PMC4955789; 10.1038/ni.3514
- Rothenberg, E.; Kueh, H. Y.; et el. (2016) Dissecting
the transcriptional regulatory network for early T-cell commitment;
European Journal of Immunology; Vol. 46; No. S1; 797; 10.1002/eji.201670200
- Lin, Yihan and Elowitz, Michael B. (2016) Central
Dogma Goes Digital; Molecular Cell; Vol. 61; No. 6; 791-792; 10.1016/j.molcel.2016.03.005
- Bintu, Lacramioara; Yong, John; et el. (2016) Dynamics
of epigenetic regulation at the single-cell level; Science; Vol.
351; No. 6274; 720-724; PMCID PMC5108652; 10.1126/science.aab2956
- Lin, Yihan; Sohn, Chang Ho; et el. (2015) Combinatorial
gene regulation by modulation of relative pulse timing; Nature; Vol.
527; No. 7576; 54-58; PMCID PMC4870307; 10.1038/nature15710
- Kim, Daniel H.; Marinov, Georgi K.; et el. (2015) Single-Cell
Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression
during Reprogramming; Cell Stem Cell; Vol. 16; No. 1; 88-101; PMCID
PMC4291542; 10.1016/j.stem.2014.11.005
- Markson, Joseph S. and Elowitz, Michael B. (2014) Synthetic
Biology of Multicellular Systems: New Platforms and Applications for
Animal Cells and Organisms; ACS Synthetic Biology; Vol. 3; No. 12;
875-876; PMCID PMC4476972; 10.1021/sb500358y
- Sanghez, Valentina; Kee, Dustin; et el. (2014) HoxA3
Controls Notch Pathway to Repress Blood Development; Blood; Vol.
124; No. 21
- Levine, Joe H. and Elowitz, Michael B. (2014) Polyphasic
feedback enables tunable cellular timers; Current Biology; Vol. 24;
No. 20; R994-R995; PMCID PMC4451454; 10.1016/j.cub.2014.08.030
- LeBon, Lauren; Lee, Tom V.; et el. (2014) Fringe
proteins modulate Notch-ligand cis and trans interactions to specify
signaling states; eLife; Vol. 3; Art. No. e02950; PMCID PMC4174579;
10.7554/eLife.02950
- Dalal, Chiraj K.; Cai, Long; et el. (2014) Pulsatile
Dynamics in the Yeast Proteome; Current Biology; Vol. 24; No. 18;
2189-2194; PMCID PMC4203654; 10.1016/j.cub.2014.07.076
- Kueh, Hao Yuan; Elowitz, Michael B.; et el. (2014) Macrophage
and T-cell fate control: Insights from tracking transcription factor
dynamics in single cells; Experimental Hematology; Vol. 42; No. 8;
S16; 10.1016/j.exphem.2014.07.054
- Singer, Zakary S.; Yong, John; et el. (2014) Dynamic
Heterogeneity and DNA Methylation in Embryonic Stem Cells; Molecular
Cell; Vol. 55; No. 2; 319-331; PMCID PMC4104113; 10.1016/j.molcel.2014.06.029
- Tan, Frederick E. and Elowitz, Michael B. (2014) Brf1
posttranscriptionally regulates pluripotency and differentiation
responses downstream of Erk MAP kinase; Proceedings of the National
Academy of Sciences of the United States of America; Vol. 111; No. 17;
E1740-E1748; PMCID PMC4035916; 10.1073/pnas.1320873111
- Church, George M.; Elowitz, Michael B.; et el. (2014) Realizing
the potential of synthetic biology; Nature Reviews. Molecular Cell
Biology; Vol. 15; No. 4; 289-294; PMCID PMC9645560; 10.1038/nrm3767
- Levine, Joe H.; Lin, Yihan; et el. (2013) Functional
Roles of Pulsing in Genetic Circuits; Science; Vol. 342; No. 6163;
1193-1200; PMCID PMC4100686; 10.1126/science.1239999
- Kueh, Hao Yuan; Champhekhar, Ameya; et el. (2013) Positive
Feedback Between PU.1 and the Cell Cycle Controls Myeloid
Differentiation; Science; Vol. 341; No. 6146; 670-673; PMCID
PMC3913367; 10.1126/science.1240831
- Young, Jonathan W.; Locke, James C. W.; et el. (2013) Rate
of environmental change determines stress response specificity;
Proceedings of the National Academy of Sciences of the United States of
America; Vol. 110; No. 10; 4140-4145; PMCID PMC3593889; 10.1073/pnas.1213060110
- Rosenthal, Adam Z. and Elowitz, Michael B. (2012) Following
evolution of bacterial antibiotic resistance in real time; Nature
Genetics; Vol. 44; No. 1; 11-13; 10.1038/ng.1048
- Young, Jonathan W.; Locke, James C. W.; et el. (2012) Measuring
single-cell gene expression dynamics in bacteria using fluorescence
time-lapse microscopy; Nature Protocols; Vol. 7; No. 1; 80-88; PMCID
PMC4161363; 10.1038/nprot.2011.432
- Levine, Joe H.; Fontes, Michael E.; et el. (2012) Pulsed
Feedback Defers Cellular Differentiation; PLoS Biology; Vol. 10;
No. 1; e1001252; PMCID PMC3269414; 10.1371/journal.pbio.1001252
- Locke, James C. W.; Young, Jonathan W.; et el. (2011) Stochastic
Pulse Regulation in Bacterial Stress Response; Science; Vol. 334;
No. 6054; 366-369; PMCID PMC4100694; 10.1126/science.1208144
- Zheng, Guoan; Lee, Seung Ah; et el. (2011) The
ePetri dish, an on-chip cell imaging platform based on subpixel
perspective sweeping microscopy (SPSM); Proceedings of the National
Academy of Sciences of the United States of America; Vol. 108; No. 41;
16889-16894; PMCID PMC3193234; 10.1073/pnas.1110681108
- Sen, Shaunak; Garcia-Ojalvo, Jordi; et el. (2011) Dynamical
Consequences of Bandpass Feedback Loops in a Bacterial Phosphorelay;
PLoS ONE; Vol. 6; No. 9; Art. No. e25102; PMCID PMC3182994; 10.1371/journal.pone.0025102
- Nandagopal, Nagarajan and Elowitz, Michael B. (2011) Synthetic
Biology: Integrated Gene Circuits; Science; Vol. 333; No. 6047;
1244-1248; PMCID PMC4117316; 10.1126/science.1207084
- Sprinzak, David; Lakhanpal, Amit; et el. (2011) Mutual
Inactivation of Notch Receptors and Ligands Facilitates Developmental
Patterning; PLoS Computational Biology; Vol. 7; No. 6; Art.
No. e1002069; PMCID PMC3111533; 10.1371/journal.pcbi.1002069
- Young, Jonathan W. and Elowitz, Michael B. (2011) Mixed
Messages: How Bacteria Resolve Conflicting Signals; Molecular Cell;
Vol. 42; No. 4; 405-406; PMCID PMC4117311; 10.1016/j.molcel.2011.05.005
- Elowitz, Michael B. and Lim, Wendell A. (2010) Build
life to understand it; Nature; Vol. 468; 889-890; PMCID PMC3068207;
10.1038/468889a
- Acar, Murat; Pando, Bernardo F.; et el. (2010) A
General Mechanism for Network-Dosage Compensation in Gene Circuits;
Science; Vol. 329; No. 5999; 1656-1660; PMCID PMC3138731; 10.1126/science.1190544
- Eldar, Avigdor and Elowitz, Michael B. (2010) Functional
roles for noise in genetic circuits; Nature; Vol. 467; No. 7312;
167-173; PMCID PMC4100692; 10.1038/nature09326
- Cox, Robert Sidney, III; Dunlop, Mary J.; et el. (2010) A
synthetic three-color scaffold for monitoring genetic regulation and
noise; Journal of Biological Engineering; Vol. 4; Art. No. 10; PMCID
PMC2918530; 10.1186/1754-1611-4-10
- Sprinzak, David; Lakhanpal, Amit; et el. (2010) Cis-interactions
between Notch and Delta generate mutually exclusive signalling
states; Nature; Vol. 465; No. 7294; 86-91; PMCID PMC2886601; 10.1038/nature08959
- Çağatay, Tolga; Turcotte, Marc; et el. (2009) Architecture-Dependent
Noise Discriminates Functionally Analogous Differentiation Circuits;
Cell; Vol. 139; No. 3; 512-522; 10.1016/j.cell.2009.07.046
- Eldar, Avigdor; Chary, Vasant K.; et el. (2009) Partial
penetrance facilitates developmental evolution in bacteria; Nature;
Vol. 460; No. 7254; 510-514; PMCID PMC2716064; 10.1038/nature08150
- Locke, James C. W. and Elowitz, Michael B. (2009) Using
movies to analyse gene circuit dynamics in single cells; Nature
Reviews Microbiology; Vol. 7; No. 5; 383-392; PMCID PMC2853934; 10.1038/nrmicro2056
- Dunlop, Mary J.; Cox, Robert Sidney, III; et el. (2008) Regulatory
activity revealed by dynamic correlations in gene expression noise;
Nature Genetics; Vol. 40; No. 12; 1493-1498; PMCID PMC2829635; 10.1038/ng.281
- Cai, Long; Dalal, Chiraj K.; et el. (2008) Frequency-modulated
nuclear localization bursts coordinate gene regulation; Nature; Vol.
455; No. 7212; 485-491; PMCID PMC2695983; 10.1038/nature07292
- Presser, Aviva; Elowitz, Michael B.; et el. (2008) The
evolutionary dynamics of the Saccharomyces cerevisiae protein
interaction network after duplication; Proceedings of the National
Academy of Sciences of the United States of America; Vol. 105; No. 3;
950-954; PMCID PMC2242688; 10.1073/pnas.0707293105
- Rosenfeld, Nitzan; Young, Jonathan W.; et el. (2007) Accurate
prediction of gene feedback circuit behavior from component
properties; Molecular Systems Biology; Vol. 3; Art. No. 143; PMCID
PMC2132446; 10.1038/msb4100185
- Cox, Robert Sidney, III; Surette, Michael G.; et el. (2007) Programming
gene expression with combinatorial promoters; Molecular Systems
Biology; Vol. 3; Art. No. 145; PMCID PMC2132448; 10.1038/msb4100187
- Süel, Gürol M.; Kulkarni, Rajan P.; et el. (2007) Tunability
and Noise Dependence in Differentiation Dynamics; Science; Vol. 315;
No. 5819; 1716-1719; 10.1126/science.1137455
- Rosenfeld, Nitzan; Perkins, Theodore J.; et el. (2006) A
Fluctuation Method to Quantify In Vivo Fluorescence Data;
Biophysical Journal; Vol. 91; No. 2; 759-766; PMCID PMC1483091; 10.1529/biophysj.105.073098
- Süel, Gürol M.; Garcia-Ojalvo, Jordi; et el. (2006) An
excitable gene regulatory circuit induces transient cellular
differentiation; Nature; Vol. 440; No. 7083; 545-550; 10.1038/nature04588
- Sprinzak, David and Elowitz, Michael B. (2005) Reconstruction
of genetic circuits; Nature; Vol. 438; No. 7067; 443-448; 10.1038/nature04335
- Eldar, Avigdor and Elowitz, Michael (2005) Systems
biology: Deviations in mating; Nature; Vol. 437; No. 7059; 631-632;
10.1038/437631a
- Rosenfeld, Nitzan; Young, Jonathan W.; et el. (2005) Gene
Regulation at the Single-Cell Level; Science; Vol. 307; No. 5717;
1962-1965; 10.1126/science.1106914
- Garcia-Ojalvo, Jordi; Elowitz, Michael B.; et el. (2004) Modeling a
synthetic multicellular clock: Repressilators coupled by quorum
sensing; Proceedings of the National Academy of Sciences of the
United States of America; Vol. 101; No. 30; 10955-10960; PMCID
PMC503725; 10.1073/pnas.0307095101
- Lahav, Galit; Rosenfeld, Nitzan; et el. (2004) Dynamics
of the p53-Mdm2 feedback loop in individual cells; Nature Genetics;
Vol. 36; No. 2; 147-150; 10.1038/ng1293
- Overholtzer, Michael; Rao, Pulivarthi H.; et el. (2003) The
presence of p53 mutations in human osteosarcomas correlates with high
levels of genomic instability; Proceedings of the National Academy
of Sciences of the United States of America; Vol. 100; No. 20;
11547-11552; PMCID PMC208795; 10.1073/pnas.1934852100
- Rosenfeld, Nitzan; Elowitz, Michael B.; et el. (2002) Negative
Autoregulation Speeds the Response Times of Transcription Networks;
Journal of Molecular Biology; Vol. 323; No. 5; 785-793; 10.1016/s0022-2836(02)00994-4
- Swain, Peter S.; Elowitz, Michael B.; et el. (2002) Intrinsic
and extrinsic contributions to stochasticity in gene expression;
Proceedings of the National Academy of Sciences of the United States of
America; Vol. 99; No. 20; 12795-12800; PMCID PMC130539; 10.1073/pnas.162041399
- Elowitz, Michael B.; Levine, Arnold J.; et el. (2002) Stochastic
Gene Expression in a Single Cell; Science; Vol. 297; No. 5584;
1183-1186; 10.1126/science.1070919
- Elowitz, Michael B. and Leibler, Stanislas (2000) A
synthetic oscillatory network of transcriptional regulators; Nature;
Vol. 403; No. 6767; 335-338; 10.1038/35002125
- Elowitz, Michael B.; Surette, Michael G.; et el. (1999) Protein
Mobility in the Cytoplasm of Escherichia coli; Journal of
Bacteriology; Vol. 181; No. 1; 197-203; PMCID PMC103549
- Surrey, Thomas; Elowitz, Michael B.; et el. (1998) Chromophore-assisted
light inactivation and self-organization of microtubules and motors;
Proceedings of the National Academy of Sciences of the United States of
America; Vol. 95; No. 8; 4293-4298; PMCID PMC22482
- Elowitz, Michael B.; Surette, Michael G.; et el. (1997) Photoactivation
turns green fluorescent protein red; Current Biology; Vol. 7;
No. 10; 809-812; 10.1016/s0960-9822(06)00342-3
- Bourdieu, L.; Duke, T.; et el. (1995) Spiral
Defects in Motility Assays: A Measure of Motor Protein Force;
Physical Review Letters; Vol. 75; No. 1; 176-179; 10.1103/PhysRevLett.75.176