28. S Liu, M Nguyen, S Hormoz.
Integrating readout of somatic mutations in individual cells with single-cell transcriptional profiling.
Cell STAR Protocols 2 (3), 100673 (2021).

27. C Budjan, S Liu, A Ranga, S Gayen, O Pourquie, S Hormoz.
Paraxial mesoderm organoids model development of human somites.
bioRxiv 2021.03.22.436471 (2021); doi:

26. R McNulty*, D Sritharan*, S Liu,  S Hormoz#,  AZ Rosenthal#.
Droplet-based single cell RNA sequencing of bacteria identifies known and previously unseen cellular states.
bioRxiv 2021.03.10.434868 (2021); doi:
* equal contribution  # co-corresponding authors

25. D Sritharan*, S Wang*, S Hormoz.
Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry.
PNAS 118 (29) e2100473118 (2021);
* equal contribution

24. DV Egeren*, J Escabi*, M Nguyen*, S Liu, CR Reilly, S Patel, B Kamaz, M Kalyva, DJ DeAngelo, Ilene Galinsky, Martha Wadleigh, ES Winer, MR Luskin, RM Stone, JS Garcia, GS Hobbs, FD Camargo, F Michor, A Mullally#, I Cortes-Ciriano#, S Hormoz#.
Reconstructing the lineage histories and differentiation trajectories of individual cancer cells in JAK2-mutant myeloproliferative neoplasms.
Cell Stem Cell 28 (3):514-523 (2021).
* equal contribution # co-corresponding authors

See also commentary: DL Paz, P Ashcroft, RC Skoda. Myeloproliferative Neoplasms: The Long Wait for JAK2-Mutant Clone Expansion. Cell Stem Cell 28(3):359-61 (2021). R Norfo,A Mead. Clonal Selection of Mutant HSC in MPN:“What Do I Know?”. The Hematologist  1;18(1) (2021).

23. S Hormoz
Evaluation of Arai et al.: What Can Differences across Daughter Cells Tell Us about Stem Cell Renewal?.
Cell Systems 11(6):547-549 (2020).

22. S Bowling*, D Sritharan*, FG Osorio, M Nguyen, P Cheung, A Rodriguez-Fraticelli, S Patel, WC Yuan, Y Fujiwara, BE Li, SH Orkin, S Hormoz#, FD Camargo#.
An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells.
Cell 181 (6):1410-1422 (2020).
* equal contribution # co-corresponding authors

See also commentary: DJ Burgess. A mouse with history. Nature Reviews Genetics 21(7):388 (2020).

21. AZ Rosenthal, Y Qi, S Hormoz, J Park, SH Li, MB Elowitz.
Metabolic interactions between dynamic bacterial subpopulations.
eLife 7:e33099 (2018). 

20. J Park, M Dies, Y Lin, S Hormoz, SE Smith-Unna, S Quinodoz, MJ Hernández-Jiménez, J Garcia-Ojalvo, JWC Locke, MB Elowitz.
Molecular Time Sharing through Dynamic Pulsing in Single Cells.
Cell Systems 6 (2): 1-14 (2018). Featured on the cover.

19. KL Frieda*, JM Linton*, S Hormoz*, J Choi, KK Chow, ZS Singer, MW Budde, MB Elowitz, L Cai.
Synthetic recording and in situ readout of lineage information in single cells.
Nature 541 (7635): 107-111 (2017).
* equal contribution

See Also: News & Views by Lauren Beck and Arjun Raj, "Systems biology: Molecular memoirs of a cellular family." Nature 541 (7635): 38-39 (2017).

18. S Hormoz*, ZS Singer*, JM Linton, YE Antebi, BI Shraiman,  MB Elowitz.
Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements.
Cell Systems 3 (5): 419-433 (2016). Featured on the cover.
* equal contribution.

For an interactive visualization of our data visit:

See Also: Commentary by Jordi Garcia-Ojalvo, "Cell Lineage Trees Bear Fruit." Cell Systems 3 (6): 511-513 (2016).

17. MP Brenner, S Hormoz, A Pumir.
Potential singularity mechanism for the Euler equations.
Physical Review Fluids 1 (8): 084503 (2016).

16. S Hormoz, N Desprat, BI Shraiman.
Inferring epigenetic dynamics from kin correlations.
PNAS 112, (18) E2281-E2289 (2015).

15. S Hormoz, G Bhanot, M Biehl, E Bilal, P Meyer, R Norel, K Rhrissorrakrai, A Dayarian.
Inter-species inference of gene set enrichment in lung epithelial cells from large proteomic and transcriptomic data sets.
Bioinformatics 31 (4): 492-500 (2015).

14. A Dayarian, R Romero, Z Wang, M Biehl, E Bilal, S Hormoz, P Meyer, R Norel, K Rhrissorrakrai, G Bhanot, F Luo, AL Tarca.
Predicting protein phosphorylation from gene expression: top methods from the IMRPOVER species translation challenge.
Bioinformatics 31 (4): 462-470 (2015).

13. M Biehl, P Sadowski, G Bhanot, E Bilal, A Dayarian, P Meyer, R Norel, K Rhrissorrakrai, MD Zeller, S Hormoz.
Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge.
Bioinformatics 31 (4): 453-461 (2015).

12. E Fonda, DP Meichle, NT Ouellette, S Hormoz, DP Lathrop.
Direct observation of Kelvin waves excited by quantized vortex reconnection.
PNAS 111, 4707-4710 (2014). Featured on the cover.

11. S Hormoz.
Amino acid composition of proteins reduces deleterious impact of mutations.
Scientific Reports 3, 2919 (2013).

10. S Hormoz.
Stem cell population asymmetry can reduce rate of replicative aging.
Journal of Theoretical Biology 331, 19-27 (2013).

9. S Hormoz.
Quantum collapse and the second law of thermodynamics.
Physical Review E 87 (2), 022129 (2013).

8. S Hormoz.
Cross talk and interference enhance information capacity of a signaling pathway.
Biophysical Journal 104 (5), 1170-1180 (2013). Featured on the cover.

7. S Hormoz, MP Brenner.
Non-universal and non-singular asymptotics of interacting vortex filaments.
Procedia IUTAM 7, 97-106 (2013).

6. S Hormoz, B Widom.
Models of the hydrophobic attraction.
Proceedings of the International School of Physics  "Enrico Fermi" Course CLXXVI "Complex Materials in Physics and Biology" ed. by F Mallamace and HE Stanley (IOS, Amsterdam; SIF, Bologna) (2012).

5. S Hormoz, MP Brenner.
Absence of singular stretching of interacting vortex filaments.
Journal of Fluid Mechanics 707, 191-204 (2012).

4. EA van Nierop, S Hormoz, KZ House, MJ Aziz.
Effect of absorption enthalpy on temperature-swing CO2 separation process performance.
Energy Procedia 4, 1783-1790 (2011).

3. S Hormoz, MP Brenner.
Design principles for self-assembly with short-range interactions.
PNAS 108, 5193-5198 (2011).

See Also: News and Views, D Frenkel, DJ Wales. Nature Materials 10, 410-411 (2011).

2. S Hormoz, S Ramanathan.
Limits on vanadium oxide Mott metal-insulator transition field-effect transistors.
Solid State Electronics 54, 654 (2010).

1. MA Belkin, J Fan, S Hormoz, F Capasso, S Khanna, M Lachab, AG Davies, EH Linfield.
Terahertz quantum cascade lasers with metal-metal copper waveguides operating up to 178K.
Optics Express 16, 3242 (2008).



1. L Cai, MB Elowitz, JD Linton, CH Joonhyuk, KL Frieda, S Hormoz, and KK Chow.
Recording and mapping lineage information and molecular events in individual cells.
U.S. Patent Application 14/620,133, filed February 11, 2015.