Eric D. Siggia

This paper introduces a computational framework to reconstruct developmental landscapes from single-cell data, revealing morphogen-dependent cell fate transitions in neural progenitors.

The paper proposes a geometrical model of cell fate specification in the mouse blastocyst using a heteroclinic flip bifurcation to explain lineage decisions.

The paper shows how floorplate organiser forms autonomously in neural tube organoids through BMP-mediated cluster competition and FOXA2 dynamics.

The paper identifies EOMES as a key mediator of WNT priming in human embryonic stem cells, enabling subsequent Activin-induced mesendodermal differentiation.

This paper describes an in vitro method to self-organize a human neural tube using geometric constraints, showing that neural and epidermal tissues are sufficient for morphogenesis.

The paper constructs a Waddington landscape model to predict cell fate decisions during C. elegans mesoendoderm differentiation based on Wnt dynamics and mutant penetrance data.

The paper shows that NOGGIN and BMP4 are secreted into opposite extracellular spaces in human epiblasts, with NOGGIN inhibiting BMP4 through apical-to-basal transcytosis.

The paper quantifies cell fate transitions during differentiation and identifies two mechanisms for binary cell fate decisions using a statistical model and experimental data.

The paper models primitive streak formation in human embryonic stem cells using a WNT signaling system and shows that DKK1 controls patterning extent and duration.

The paper uses human gastruloids to create a partial fate map of the human primitive streak by analyzing cell migrations and subpopulation organization under different signaling conditions.

The paper shows that WNT signaling memory enables ACTIVIN to act as a morphogen in human gastruloids by allowing graded responses to ACTIVIN without altering SMAD2 dynamics.

The paper generates a 3D human epiblast model to study axial symmetry breaking, showing BMP4 induces symmetry breaking through WNT3 and DKK1.

The paper shows that WNT and ACTIVIN signals can induce a functional human organizer in hESCs, characterized by PS formation and EMT markers, and demonstrate its ability to contribute to a secondary axis in chick embryos.

The paper develops a mouse pluripotent stem cell micropattern system to study regionalized fate specification and patterning, revealing how signals direct distinct identities and spatial organization.