Prestige centrality-based functional outlier detection in gene expression analysis (2009)
Torkamani, Ali, Schork, Nicholas J.
Motivation: Traditional gene expression analysis techniques capture an average gene expression state across sample replicates. However, the average signal across replicates will not capture activated...
Identification of rare cancer driver mutations by network reconstruction (2009)
Torkamani, Ali, Schork, Nicholas J.
Recent large-scale tumor resequencing studies have identified a number of mutations that might be involved in tumorigenesis. Analysis of the frequency of specific mutations across different tumors...
Ali Torkamani, Nicholas J. Schork, Prof Martin Bishop
Motivation: Contemporary, high-throughput sequencing efforts have identified a rich source of naturally occurring single nucleotide polymorphisms (SNPs), a subset of which occur in the coding region...
Accurate prediction of deleterious protein kinase polymorphisms (2007)
Torkamani, Ali, Schork, Nicholas J.
Motivation: Contemporary, high-throughput sequencing efforts have identified a rich source of naturally occurring single nucleotide polymorphisms (SNPs), a subset of which occur in the coding region...
Congenital disease SNPs target lineage specific structural elements in protein kinases
Torkamani, Ali, Kannan, Natarajan, Taylor, Susan S., Schork, Nicholas J.
The catalytic domain of protein kinases harbors a large number of disease-causing single nucleotide polymorphisms (SNPs) and common or neutral SNPs that are not known or hypothesized to be associated...
Predicting functional regulatory polymorphisms
Torkamani, Ali, Schork, Nicholas J.
Motivation: Limited availability of data has hindered the development of algorithms that can identify functionally meaningful regulatory single nucleotide polymorphisms (rSNPs). Given the large...
Sequence and Structure Signatures of Cancer Mutation Hotspots in Protein Kinases
Dixit, Anshuman, Yi, Lin, Gowthaman, Ragul, Torkamani, Ali, Schork, Nicholas J., Verkhivker, Gennady M.
Protein kinases are the most common protein domains implicated in cancer, where somatically acquired mutations are known to be functionally linked to a variety of cancers. Resequencing studies of...