arXiv · 2025
Publications
Technologies to read history. Mathematics to understand it.
Our work moves between experimental systems, inference problems, and models of control. Selected papers below trace that path.
Recent and selected
ICLR · 2025
Improving Graph Neural Networks by Learning Continuous Edge Directions
A graph neural network learns the direction of information flow directly from data.IEEE Transactions on Signal Processing · 2025
An efficient solution to Hidden Markov Models on trees with coupled branches
New mathematics for inferring hidden dynamics on branching cellular lineages.Nature · 2024
Deciphering cell states and genealogies of human hematopoiesis
Natural somatic mutations reveal the family histories of human blood cells.Nature Microbiology · 2023
Probe-based bacterial single-cell RNA sequencing predicts toxin regulation
A technology for discovering bacterial states one cell at a time.eLife · 2022
Paraxial mesoderm organoids model development of human somites
Human stem cells recapitulate a rhythmic event in embryonic development.Cell Stem Cell · 2021
Reconstructing the lineage histories of individual cancer cells
Cancer lineages reveal that driver mutations can arise decades before diagnosis.Cell · 2020
An engineered mouse line for simultaneous readout of lineage and gene expression
Cells record their histories in DNA inside a living mouse.Foundations
Ideas that shaped the lab
Recording history
Synthetic recording and in situ readout of lineage information in single cells
Nature · 2017Inferring dynamics
Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements
Cell Systems · 2016Hidden states
Inferring epigenetic dynamics from kin correlations
PNAS · 2015High-dimensional geometry
Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds
PNAS · 2021Natural recorders
Accurate de novo detection of somatic mutations in high-throughput single-cell profiling data sets
Nature Biotechnology · 2024Complete archive
All publications
Peer-reviewed research, methods, perspectives, conference papers, and preprints, listed in reverse chronological order.
2026
Relationship between the distribution of LEDGF along genes and positions of HIV-1 DNA integration
R Pathak, C Esnault, R Radhakrishnan, PK Singh, H Zhang, R Dale, A Anand, A Mitra, GJ Bedwell, AN Engelman, A Rabi, S Hormoz, P Singh, R John, and HL Levin
mBio 17:e00090-262025
An efficient solution to Hidden Markov Models on trees with coupled branches
F Vafa and S Hormoz
IEEE Transactions on Signal Processing 73:4183–4192scAI-SNP: a method for inferring ancestry from single-cell data
SC Hong, F Muyas, I Cortés-Ciriano, and S Hormoz
BMC Methods 2:1–17Evolution of myeloproliferative neoplasms from normal blood stem cells
S Hormoz, VG Sankaran, and A Mullally
Haematologica 110:840–849Improving Graph Neural Networks by Learning Continuous Edge Directions
SH Pahng and S Hormoz
International Conference on Learning Representations (ICLR)DiffeoMorph: Learning to Morph 3D Shapes Using Differentiable Agent-Based Simulations
SH Pahng, G Guan, B Fefferman, and S Hormoz
arXiv:2512.17129Cooperative short- and long-range interactions enable robust symmetry breaking and axis formation
G Guan, S Wang, TG Shields, SH Pahng, CX Shao, J Ye, C Budjan, and S Hormoz
bioRxiv 2025.09.27.678924Discovery of a small molecule non-IMiD degrader of ZBTB7A for the treatment of β-hemoglobinopathies
J Liu, Z Shen, S-Y Park, Y Dong, N Yu, J Zeng, H Lee, B Pate, S Adamia, K Vanuytsel, J Zhang, S-C Wu, A Herman, S Moein, W Li, M Liu, C Gao, X Tian, Z Liu, J Kwon, K Qin, C Budjan, P-S Ko, C Shao, C Jaladanki, J Li, E Lee, B-H Liu, S Stowell, JP Manis, D Justus, GA Blobel, HR Luo, R Belizaire, Y Zheng, S Hormoz, S Nikiforow, JA Cancelas, H Fan, DE Bauer, D Tenen, and L Chai
bioRxiv 2025.09.17.676148Robustness of Selection and Timing Inference under Model Variation in Population Genetics
J Escabi and S Hormoz
bioRxiv 2025.01.08.6319742024
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, and I Cortés-Ciriano
Nature Biotechnology 42:758–767Deciphering cell states and genealogies of human haematopoiesis
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, S Mallidi, A Kreso, J Escabi, WM Rideout III, T Jacks, S Hormoz, P van Galen, JS Weissman, and VG Sankaran
Nature 627:389–398Mutation-Specific Differences in the Relationship between Obesity and Clonal Hematopoiesis, with a Focus on JAK2V617F and MPN Prevention
B Rolles, A Sekar, L Serrano-Ron, NF Ameerul Faiz, A Perry, AC Hillerbrandt, J Hem, J Jutzi, AE Marneth, A Niroula, AG Bick, CJ Gibson, GK Griffin, MM Uddin, P Natarajan, BL Ebert, P van Galen, F Al-Shahrour, S Hormoz, and A Mullally
Blood 144:872ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets
P Samanta, SF Cooke, R McNulty, S Hormoz, and A Rosenthal
Nature Protocols2023
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, and AZ Rosenthal
Nature MicrobiologyAn improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells
S Sahay, S Adhikari, S Hormoz, and S Chakrabarti
Bioinformatics 39:btad6022022
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 Cortés-Ciriano, A Mullally, and S Hormoz
Experimental Hematology 107:14–19A 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, JC Lam, and VO Li
Scientific Reports 12:342Paraxial mesoderm organoids model development of human somites
C Budjan, S Liu, A Ranga, S Gayen, O Pourquié, and S Hormoz
eLife 11:e68925Collective polymerase dynamics emerge from DNA supercoiling during transcription
S Sevier and S Hormoz
Biophysical Journal 121:4153–41652021
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, I Galinsky, M Wadleigh, ES Winer, MR Luskin, RM Stone, JS Garcia, GS Hobbs, FD Camargo, F Michor, A Mullally, I Cortés-Ciriano, and S Hormoz
Cell Stem Cell 28:514–523Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry
D Sritharan, S Wang, and S Hormoz
PNAS 118:e2100473118Integrating readout of somatic mutations in individual cells with single-cell transcriptional profiling
S Liu, M Nguyen, and S Hormoz
STAR Protocols 2:1006732020
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, and FD Camargo
Cell 181:1410–1422Evaluation of Arai et al.: What Can Differences across Daughter Cells Tell Us about Stem Cell Renewal?
S Hormoz
Cell Systems 11:547–5492018
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, and MB Elowitz
Cell Systems 6:1–14Metabolic interactions between dynamic bacterial subpopulations
AZ Rosenthal, Y Qi, S Hormoz, J Park, SH Li, and MB Elowitz
eLife 7:e330992017
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, and L Cai
Nature 541:107–1112016
Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements
S Hormoz, ZS Singer, JM Linton, YE Antebi, BI Shraiman, and MB Elowitz
Cell Systems 3:419–433Potential singularity mechanism for the Euler equations
MP Brenner, S Hormoz, and A Pumir
Physical Review Fluids 1:0845032015
Inferring epigenetic dynamics from kin correlations
S Hormoz, N Desprat, and BI Shraiman
PNAS 112:E2281–E2289Inter-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, and S Hormoz
Bioinformatics 31:453–461Predicting protein phosphorylation from gene expression: top methods from the IMPROVER 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, and AL Tarca
Bioinformatics 31:462–470Inter-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, and A Dayarian
Bioinformatics 31:492–5002014
Direct observation of Kelvin waves excited by quantized vortex reconnection
E Fonda, DP Meichle, NT Ouellette, S Hormoz, and DP Lathrop
PNAS 111:4707–47102013
Amino acid composition of proteins reduces deleterious impact of mutations
S Hormoz
Scientific Reports 3:2919Stem cell population asymmetry can reduce rate of replicative aging
S Hormoz
Journal of Theoretical Biology 331:19–27Quantum collapse and the second law of thermodynamics
S Hormoz
Physical Review E 87:022129Cross talk and interference enhance information capacity of a signaling pathway
S Hormoz
Biophysical Journal 104:1170–1180Non-universal and non-singular asymptotics of interacting vortex filaments
S Hormoz and MP Brenner
Procedia IUTAM 7:97–1062012
Absence of singular stretching of interacting vortex filaments
S Hormoz and MP Brenner
Journal of Fluid Mechanics 707:191–204Models of the hydrophobic attraction
S Hormoz and B Widom
Proceedings of the International School of Physics ‘Enrico Fermi,’ Course CLXXVI2011
Design principles for self-assembly with short-range interactions
S Hormoz and MP Brenner
PNAS 108:5193–5198Effect of absorption enthalpy on temperature-swing CO2 separation process performance
EA van Nierop, S Hormoz, KZ House, and MJ Aziz
Energy Procedia 4:1783–17902010
Limits on vanadium oxide Mott metal-insulator transition field-effect transistors
S Hormoz and S Ramanathan
Solid-State Electronics 54:6542008
Terahertz quantum cascade lasers with metal-metal copper waveguides operating up to 178 K
MA Belkin, J Fan, S Hormoz, F Capasso, S Khanna, M Lachab, AG Davies, and EH Linfield
Optics Express 16:3242