Phylogenetic profiling involves the comparison of phylogenetic data across gene families. It is possible to construct phylogenetic trees, or related data structures, for specific gene families using a wide variety of tools and approaches. Phylogenetic profiling involves the comparison of this data to determine which families have correlated or coupled evolution. The underlying assumption is tha...

Identifying viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. We describe a high-throughput approach to quantify the selection that monoclonal antibodies exert on all single amino-acid mutations to a viral protein. This approach, mutational antigenic profiling, involves creating all replication-competent protein v...

Molecular interactions that underlie pathophysiological states are being elucidated using techniques that profile proteomic endpoints in cellular systems. Within the field of cancer research, protein interaction networks play pivotal roles in the establishment and maintenance of the hallmarks of malignancy, including cell division, invasion, and migration. Multiple complementary tools enable a ...

This study aimed to detect protein changes that can assist to understand the underlying biology of bladder cancer. The data showed forty five proteins were found to be differentially expressed comparing tumors vs non-tumor tissues, of which EGFR and cdc2p34 were correlated with muscle invasion and histological grade. Ten proteins (ß-catenin, HSP70, autotaxin, Notch4, PSTPIP1, DPYD, ODC, cyclinB...

With the postgenome era rapidly approaching, new strategies for the functional analysis of proteins are needed. To date, proteomics efforts have primarily been confined to recording variations in protein level rather than activity. The ability to profile classes of proteins on the basis of changes in their activity would greatly accelerate both the assignment of protein function and the identif...

Proteome profiling techniques rely on the separation of proteins or peptides and their subsequent quantification. The reliability of this technique is still limited because a proteome profiling result does not necessarily represent the true protein composition of the analysed sample, thus seriously hampering proper data interpretation. Many experimentally observed proteome alterations are biolo...

Abstract Proteins are ubiquitously modified with glycans of varied chemical structures through distinct glycosidic linkages, making the landscape protein glycosylation challenging to map. Profiling intact glycopeptides mass spectrometry (MS) has recently emerged as a powerful tool for revealing matched information sites and attached (i.e., glycosites), but is largely limited individual types. H...

The regulation of protein function through posttranslational modification, local environment, and protein-protein interaction is critical to cellular function. The ability to analyze on a genome-wide scale protein functional activity rather than changes in protein abundance or structure would provide important new insights into complex biological processes. Herein, we report the application of ...

Profile Hidden Markov Models (PHMMs) are recognized as powerful computational vehicles for homology search of protein sequences. Extant PHMM training approaches either use completely unaligned or aligned sequences. The PHMMs resulting from these two training approaches present contrasting tradeoffs w.r.t. alignment information and the accuracy of the search outcome. This paper describes a PHMM ...

The abundance of cellular proteins is determined largely by the rate of transcription and translation coupled with the stability of individual proteins. Although we know a great deal about global transcript abundance, little is known about global protein stability. We present a highly parallel multiplexing strategy to monitor protein turnover on a global scale by coupling flow cytometry with mi...