Isaac Shamie

The paper presents secRecon, a comprehensive secretory pathway reconstruction, and uses it to identify secretory differences in plasma cells and CHO cells, highlighting potential targets for improving secretion capacity.

The paper investigates lineage commitment bias in human and murine hematopoietic stem cells, finding that variation in myeloid and lymphoid engraftment is stochastic and not due to cell-intrinsic bias.

The paper identifies a relationship between protein structure and glycan structure, introducing a glycoimpact matrix to predict glycosylation patterns and validate it through disease variants and engineered antibodies.

The paper introduces a computational framework to infer the spatial code of cell-cell interactions using transcriptomic data from C. elegans, validated with experimental confirmation.

The paper revises transcription start site annotations in Chinese hamster genes using experimental data to improve gene engineering and glycosylation in CHO cells.

This study quantifies how repeated freeze-thaw cycles affect RNA-Seq reliability, showing that poly(A)-enriched samples lose reproducibility after three cycles.

StanDep improves context-specific metabolic models by using transcriptomic variability to identify core reactions, increasing inclusion of housekeeping and lowly expressed reactions.

The paper identifies replay of waking cortical activity patterns during slow-wave sleep in humans and links them to sleep features like spindles and sharp-wave ripples, supporting memory consolidation theories.