James P. McCusker

Learn More
We characterized the mutational landscape of melanoma, the form of skin cancer with the highest mortality rate, by sequencing the exomes of 147 melanomas. Sun-exposed melanomas had markedly more ultraviolet (UV)-like C>T somatic mutations compared to sun-shielded acral, mucosal and uveal melanomas. Among the newly identified cancer genes was PPP6C, encoding(More)
In Linked Data, the use of owl:sameAs is ubiquitous in interlinking data-sets. There is however, ongoing discussion about its use, and potential misuse, particularly with regards to interactions with inference. In fact, owl:sameAs can be viewed as encoding only one point on a scale of similarity, one that is often too strong for many of its current uses. We(More)
We report on whole-exome sequencing (WES) of 213 melanomas. Our analysis established NF1, encoding a negative regulator of RAS, as the third most frequently mutated gene in melanoma, after BRAF and NRAS. Inactivating NF1 mutations were present in 46% of melanomas expressing wild-type BRAF and RAS, occurred in older patients and showed a distinct pattern of(More)
BACKGROUND Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery. RESULTS We(More)
The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description of arbitrary (real, hypothesized, virtual, fictional) objects, processes and their attributes. SIO specifies simple design patterns to describe and(More)
1 Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA 2 Department of Cell Biology, New York University Center for Health Informatics and Bioinformatics, New York University School of Medicine and Cancer Institute, New York, NY, USA 3 Department of Surgery, Yale University School of Medicine, New Haven, CT, USA 4 Department of(More)
UNLABELLED Yale Image Finder (YIF) is a publicly accessible search engine featuring a new way of retrieving biomedical images and associated papers based on the text carried inside the images. Image queries can also be issued against the image caption, as well as words in the associated paper abstract and title. A typical search scenario using YIF is as(More)
We describe an approach to developing next generation health information portals. This prototype portal was developed to address two complementary goals (1) design and create a site where people can explore potential relationships between selected health-related behaviors, policies, and demographic data (2) explore semantic web technologies and linked data(More)
BRAF(V600E/K) is a frequent mutationally active tumor-specific kinase in melanomas that is currently targeted for therapy by the specific inhibitor PLX4032. Our studies with melanoma tumor cells that are BRAF(V600E/K) and BRAF(WT) showed that, paradoxically, while PLX4032 inhibited ERK1/2 in the highly sensitive BRAF(V600E/K), it activated the pathway in(More)
The Third Provenance Challenge (PC3) offered an opportunity for provenance researchers to evaluate the interoperability of leading provenance models with special emphasis on importing and querying workflow traces generated by others. We investigated interoperability issues related to reusing Open Provenance Model (OPM)-based workflow traces. We compiled(More)