Shaon Chakrabarti

Identifying memory gene expression from single sample scRNA-seq data using power law signatures

This paper introduces Power-Seek, an algorithm to identify memory genes from single-sample scRNA-seq data by detecting power-law signatures in covariance matrices, validated on melanoma and breast cancer data.

Transcriptional noise sets fundamental limits to decoding circadian clock phase from single-cell RNA snapshots

This study shows that transcriptional noise limits single-cell phase inference of circadian clocks, but averaging RNA levels across cells can enable accurate phase detection.

Modular to cyclic TCA governs hematopoiesis in Drosophila

The paper identifies a developmentally programmed switch in TCA cycle configuration in Drosophila lymph gland progenitors, showing modular TCA supports progenitor identity and proliferation, while cyclic TCA maintains homeostasis and differentiation.

Inheritable cell-states shape drug-persister correlations and population dynamics in cancer cells

The paper uses time-lapse microscopy to study drug-persister dynamics in cancer cells, finding that cell-state inheritance and pre-drug fate decisions shape population dynamics independent of single-cell kinetics.

Cell cycle-dependent variation in endocytosis drives phenotypic diversity in M. tuberculosis

The paper shows that host cell cycle stages influence endocytic capacity and redox states in M. tuberculosis, leading to phenotypic diversity within infected cells.

Combining lineage correlations and a small molecule inhibitor to detect circadian control of the cell cycle.

The paper uses lineage correlations and a small molecule inhibitor to detect circadian control of the cell cycle in colon cancer cells.

An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells

This paper introduces ODeGP, a Gaussian Process-based method for detecting oscillations in time series, and shows it outperforms existing methods in detecting weak and non-stationary rhythms in qPCR data.