Author

Peyman Passban

Sanofi (France)ORCID 0000-0002-5901-2132Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 3 Organism:human· 3 Research Focus:trajectory inference· 3 Research Focus:benchmarking· 2 Approach:deep learning· 2 Approach:contrastive learning· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Sachin MathuriD· 3 shared Ziv Bar‐JosephiD· 2 shared Alexander KaganiD· 1 shared Amirmohammad KazemeiniiD· 1 shared Anastasios SiokisiD· 1 shared Andre Kurlovs· 1 shared Arnau Giribet· 1 shared Bryan Guan· 1 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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3 shared papersBioinformatics

Sachin MathurORCID

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Author profile →

5 papers

Recent·Most cited

From Sparse Visits to Continuous Molecular Trajectories with Flow Matching

Peyman Passban, Shikhar Gupta, Bryan Guan, Tanya G. Roosta

CohortFM reconstructs continuous molecular trajectories from sparse longitudinal data, revealing biologically meaningful progression patterns across diseases.

bioRxiv · Oct 11, 2026 · PreprintBioinformatics

AXIS: Agentic Extraction and Integration of Simulation Scenarios for Quantitative Systems Pharmacology

Amirmohammad Kazemeini, Jose Prieto, Sanjana Balaji Kuttae, Anastasios Siokis, Chelsea Gallagher, Thomas Klabunde, Gurdeep Singh, Tommaso Andreani, Peyman Passban

AXIS converts published QSP models and their companion publications into executable simulation configurations by integrating entity grounding, scenario extraction, and parameter assignment.

bioRxiv · Oct 8, 2026 · PreprintSystems Biology

Finetuning Foundation Models for Temporal Clinical Transcriptomics Data

Sachin Mathur, Alexander Kagan, Peyman Passban, Hamid Mattoo, Euxhen Hasanaj, Ziv Bar‐Joseph

The paper finetunes gene embeddings from foundation models for temporal clinical transcriptomics data, improving gene network analysis and detection of disease progression and drug response mechanisms.

Bioinformatics · Aug 27, 2026Peer-reviewedBioinformatics

Identification of Patient Trajectories in Timeseries Clinical Transcriptomics Data

Yixin Chen, Peyman Passban, Mahesh Raundhal, Lu Zhang, David M. Habiel, Sachin Mathur

The paper introduces a classification-guided autoencoder to analyze longitudinal transcriptomics data and identify patient trajectories in clinical trials.

bioRxiv · Dec 11, 2025 · PreprintBioinformatics

PyEvoCell: An LLM- Augmented Single Cell Trajectory Analysis Dashboard

Sachin Mathur, Mathieu Beauvais, Arnau Giribet, Nicolas Aragon Barrero, C. Zhang, Towsif Rahman, Seqian Wang, Jeremy Huang, Nima Nouri, Andre Kurlovs, Ziv Bar‐Joseph, Peyman Passban

PyEvoCell uses an LLM to aid in interpreting single-cell trajectory analysis by suggesting lineages, performing differential expression analysis, and validating hypotheses with PubMed citations.

Bioinformatics · Mar 29, 2025Peer-reviewedBioinformatics