One common problem in applying formal methods to the analysis of realistic industrial-size systems is that these methods often do not scale well. In order to overcome such difficulty, formal languages and tools supporting modularization and compositionality must be realized and used. Under this respect, this thesis addresses the problem of designing techniques and tools to support the formal sp...

The Trio project at Stanford [35] for managing data, uncertainty, and lineage is developed on top of a conventional DBMS. Uncertain data with lineage is encoded in relational tables, and Trio queries are translated to SQL queries on the encoding. Such a layered approach reaps significant benefits in terms of architectural simplicity, and the ability to use an off-the-shelf query processing engi...

We begin with studying closure properties of language classes. Informally, a closure property of a languages class C states that a certain type of transformation applied to languages in C always yields languages that belong to C as well. Examples for such transformations are: (i) Homomorphisms α : X∗ → Y ∗. They transform a language L ⊆ X∗ into the language α(L) = {α(w) | w ∈ L}. (ii) Inverse h...

UNLABELLED We have recently identified a metastasis suppressor gene for colorectal cancer: AES/Aes, which encodes an endogenous inhibitor of NOTCH signaling. When Aes is knocked out in the adenomatous epithelium of intestinal polyposis mice, their tumors become malignant, showing marked submucosal invasion and intravasation. Here, we show that one of the genes induced by NOTCH signaling in colo...

Endothelial cell-cell junctions maintain a restrictive barrier that is tightly regulated to allow dynamic responses to permeability-inducing angiogenic factors, as well as to inflammatory agents and adherent leukocytes. The ability of these stimuli to transiently remodel adherens junctions depends on Rho-GTPase-controlled cytoskeletal rearrangements. How the activity of Rho-GTPases is spatio-te...

Defects in neuronal connectivity of the brain are well documented among schizophrenia patients. Although the schizophrenia susceptibility gene Disrupted-in-Schizophrenia 1 (DISC1) has been implicated in various neurodevelopmental processes, its role in regulating axonal connections remains elusive. Here, a heterologous DISC1 transgenic system in the relatively simple and well-characterized Caen...

Embryogenesis is an intricate process involving multiple genes and pathways. Some of the key transcription factors controlling specific cell types are the Sox trio, namely, Sox5, Sox6, and Sox9, which play crucial roles in organogenesis working in a concerted manner. Much however still needs to be learned about their combinatorial roles during this process. A developmental genomics and systems ...

BACKGROUND Phagocytosis of cells undergoing apoptosis is essential during development, cellular turnover, and wound healing. Failure to promptly clear apoptotic cells has been linked to autoimmune disorders. C. elegans CED-12 and mammalian ELMO are evolutionarily conserved scaffolding proteins that play a critical role in engulfment from worm to human. ELMO functions together with Dock180 (a gu...