Behaviours of complex biomolecular systems are often irreducible to the elementary
properties of their individual components. Explanatory and predictive mathematical models …

The logical (or logic) formalism is increasingly used to model regulatory and signaling
networks. Complementing these applications, several groups contributed various methods …

Reconstruction of the molecular pathways controlling organ development has been
hampered by a lack of methods to resolve embryonic progenitor cells. Here we describe a …

Single-cell omics is transforming our understanding of cell biology and disease, yet the
systems-level analysis and interpretation of single-cell data faces many challenges. In this …

Blood cells are derived from a common set of hematopoietic stem cells, which differentiate
into more specific progenitors of the myeloid and lymphoid lineages, ultimately leading to …

We present new applications of parity inversion and time reversal to the emergence of
complex behavior from simple dynamical rules in stochastic discrete models. Our parity …

Adult blood contains a mixture of mature cell types, each with specialized functions. Single
hematopoietic stem cells (HSCs) have been functionally shown to generate all mature cell …

Background Reconstruction of executable mechanistic models from single-cell gene
expression data represents a powerful approach to understanding developmental and …

Background Rapid technological innovation for the generation of single-cell genomics data
presents new challenges and opportunities for bioinformatics analysis. One such area lies in …

Hematopoietic stem cells (HSCs) are characterized by their ability to execute a wide range
of cell fate choices, including self-renewal, quiescence, and differentiation into the many …