Mark Thompson

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Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene(More)
There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that(More)
Daedalus is a system-level design flow for the design of multiprocessor system-on-chip (MP-SoC) based embedded multimedia systems. It offers a fully integrated tool-flow in which design space exploration (DSE), system-level synthesis, application mapping, and system prototyping of MP-SoCs are highly automated. In this paper, we describe our first industrial(More)
High-level performance modeling and simulation have become a key ingredient of system-level design as they facilitate early architectural design space exploration. An important precondition for such highlevel modeling and simulation methods is that they should yield trustworthy performance estimations. This requires validation (if possible) and calibration(More)
System-level simulation and design space exploration (DSE) are key ingredients for the design of multiprocessor system-on-chip (MP-SoC) based embedded systems. The efforts in this area, however, typically use ad-hoc software infrastructures to facilitate and support the system-level DSE experiments. In this paper, we present a new, generic system-level(More)
The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource ( http://fantom.gsc.riken.jp/5/ ).(More)
In fracture and bone defect healing, MSCs largely drive tissue regeneration. MSCs have been shown to promote angiogenesis both in vivo and in vitro. Angiogenesis is a prerequisite to large tissue reconstitution. The present study investigated how mechanical loading of MSCs influences their proangiogenic capacity. The results show a significant enhancement(More)
The high complexity of modern embedded systems impels designers of such systems to model and simulate system components and their interactions in the early design stages. It is therefore essential to develop good tools for exploring a wide range of design choices at these early stages, where the design space is very large. This paper provides an overview of(More)
In this paper, we present the Daedalus framework, which allows for traversing the path from sequential application specification to a working MP-SoC prototype in FPGA technology with the (parallelized) application mapped onto it in only a matter of hours. During this traversal, which offers a high degree of automation, guidance is provided by Daedalus'(More)