Nature (2024)

Deciphering cell states and genealogies of human hematopoiesis

C Weng, F Yu, D Yang, M Poeschla, LA Liggett, MG Jones, X Qiu, L Wahlster, A Caulier, JA Hussmann, A Schnell, KE Yost, LW Koblan, JD Martin-Rufino, J Min, A Hammond, D Ssozi, R Bueno, Mallidi, A Kreso, J Escabi, WM Rideout, T Jacks, S Hormoz, P van Galen, JS Weissman & VG Sankaran

bioRxiv (2024)

scAI-SNP: a method for inferring ancestry from single-cell data

SC Hong, F Muyas, I Cortés-Ciriano, S Hormoz

Nature Biotechnology (2024)

Accurate de novo detection of somatic mutations in high-throughput single-cell profiling data sets

F Muyas, R Li, R Rahbari, TJ Mitchell, S Hormoz, I Cortes-Ciriano

Nature Microbiology (2023)

Probe-based bacterial single-cell RNA sequencing predicts toxin regulation

R McNulty*, D Sritharan*, SH Pahng, JP Meisch, S Liu, MA Brennan, G Saxer, S Hormoz#, AZ Rosenthal#
* equal contribution # co-corresponding

eLife (2022)

Paraxial mesoderm organoids model development of human somites

C Budjan, S Liu, A Ranga, S Gayen, O Pourquie, S Hormoz

Scientific Reports (2022)

A novel deep learning-based 3D cell segmentation framework for future image-based disease detection

A Wang, Q Zhang, Y Han, S Megason, S Hormoz, KR Mosaliganti, J Lam, and V Li

Experimental Hematology (2022)

Transcriptional differences between JAK2-V617F and wild-type bone marrow cells in myeloproliferative neoplasm patients

DV Egeren, B Kamaz, S Liu, M Nguyen, CR Reilly, M Kalyva, DJ DeAngelo, I Galinsky, M Wadleigh, ES Winer, MR Luskin, RM Stone, JS Garcia, GS Hobbs, F Michor, I Cortes-Ciriano#, A Mullally#, S Hormoz#
# co-corresponding

bioRxiv (2021)

Droplet-based single cell RNA sequencing of bacteria identifies known and previously unseen cellular states

R McNulty*, D Sritharan*, S Liu, S Hormoz#, AZ Rosenthal#
* equal contribution # co-corresponding

Cell Stem Cell (2021)

Reconstructing the lineage histories and differentiation trajectories of individual cancer cells in JAK2-mutant myeloproliferative neoplasms

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#
* equal contribution # co-corresponding

See also commentary: DL Paz, P Ashcroft, RC Skoda. Myeloproliferative Neoplasms: The Long Wait for JAK2-Mutant Clone Expansion. Cell Stem Cell (2021). R Norfo,A Mead. Clonal Selection of Mutant HSC in MPN:“What Do I Know?”. The Hematologist (2021).
https://hms.harvard.edu/news/original-error

Cell (2020)

An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells

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#
* equal contribution # co-corresponding

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

eLife (2018)

Metabolic interactions between dynamic bacterial subpopulations

AZ Rosenthal, Y Qi, S Hormoz, J Park, SH Li, MB Elowitz

Cell Systems (2018)

Molecular Time Sharing through Dynamic Pulsing in Single Cells

J Park, M Dies, Y Lin, S Hormoz, SE Smith-Unna, S Quinodoz, MJ Hernández-Jiménez, J Garcia-Ojalvo, JWC Locke, MB Elowitz

Nature (2017)

Synthetic recording and in situ readout of lineage information in single cells

KL Frieda*, JM Linton*, S Hormoz*, J Choi, KK Chow, ZS Singer, MW Budde, MB Elowitz#, L Cai#
* equal contribution # co-corresponding

See Also: News & Views by Lauren Beck and Arjun Raj. Molecular memoirs of a cellular family. Nature 541 (2017).

Cell Systems (2016)

Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements

S Hormoz*, ZS Singer*, JM Linton, YE Antebi, BI Shraiman#, MB Elowitz#
* equal contribution # co-corresponding

For an interactive visualization of our data visit: http://cellerie.caltech.edu/
​See Also: Commentary by Jordi Garcia-Ojalvo. Cell Lineage Trees Bear Fruit. Cell Systems (2016).

Physical Review Fluids (2016)

Potential singularity mechanism for the Euler equations

MP Brenner, S Hormoz, A Pumir

PNAS (2015)

Inferring epigenetic dynamics from kin correlations

S Hormoz, N Desprat, BI Shraiman

Bioinformatics (2015)

Inter-species inference of gene set enrichment in lung epithelial cells from large proteomic and transcriptomic data sets

S Hormoz, G Bhanot, M Biehl, E Bilal, P Meyer, R Norel, K Rhrissorrakrai, A Dayarian

Bioinformatics (2015)

Predicting protein phosphorylation from gene expression: top methods from the IMRPOVER species translation challenge

A Dayarian, R Romero, Z Wang, M Biehl, E Bilal, S Hormoz, P Meyer, R Norel, K Rhrissorrakrai, G Bhanot, F Luo, AL Tarca

Bioinformatics (2015)

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge

M Biehl, P Sadowski, G Bhanot, E Bilal, A Dayarian, P Meyer, R Norel, K Rhrissorrakrai, MD Zeller, S Hormoz

PNAS (2014)

Direct observation of Kelvin waves excited by quantized vortex reconnection

E Fonda, DP Meichle, NT Ouellette, S Hormoz, DP Lathrop

Journal of Theoretical Biology (2013)

Stem cell population asymmetry can reduce rate of replicative aging

S Hormoz

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)

Models of the hydrophobic attraction

S Hormoz, B Widom

Journal of Fluid Mechanics (2012)

Absence of singular stretching of interacting vortex filaments

S Hormoz, MP Brenner

Energy Procedia (2011)

Effect of absorption enthalpy on temperature-swing CO2 separation process performance

EA van Nierop, S Hormoz, KZ House, MJ Aziz

PNAS (2011)

Design principles for self-assembly with short-range interactions

S Hormoz, MP Brenner

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

Solid State Electronics (2010)

Limits on vanadium oxide Mott metal-insulator transition field-effect transistors

S Hormoz, S Ramanathan

Optics Express (2008)

Terahertz quantum cascade lasers with metal-metal copper waveguides operating up to 178K

MA Belkin, J Fan, S Hormoz, F Capasso, S Khanna, M Lachab, AG Davies, EH Linfield