We consider the task of automatically extracting post-translational modification events from biomedical scientific publications. Building on the success of event extraction for phosphorylation events in the BioNLP’09 shared task, we extend the event annotation approach to four major new post-transitional modification event types. We present a new targeted corpus of 157 PubMed abstracts annotate...

PTMs (post-translational modifications) of lysine residues have proven to be major regulators of gene expression, protein-protein interactions, and protein processing and degradation. This is of particular importance in regulating the cytoskeleton, an enormously complex system of proteins responsible for cell motility, intracellular trafficking, and maintenance of cell form and structure. The c...

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Attempts to characterize cellular behaviors with static, univariate measurements cannot fully capture biological complexity and lead to an inadequate interpretation of cellular processes. Significant biological insight can be gleaned by considering the contribution of dynamic protein post-translational modifications (PTMs) utilizing systems-level quantitative analysis. High-resolution mass spec...

Type I collagen is the most abundant structural protein in vertebrates. It is a heterotrimeric molecule composed of two α1 chains and one α2 chain, forming a long uninterrupted triple helical structure with short non-triple helical telopeptides at both the N- and C-termini. During biosynthesis, collagen acquires a number of post-translational modifications, including lysine modifications, that ...

Plants have evolved multi-layered molecular defense strategies to protect against pathogens. Plant immune signaling largely relies on post-translational modifications (PTMs) to induce rapid alterations of signaling pathways to achieve a response that is appropriate to the type of pathogen and infection pressure. In host cells, dynamic PTMs have emerged as powerful regulatory mechanisms that cel...

Malaria is one of the most important human parasitic diseases in the world, affecting about 400 million people and killing about 1 million children every year. Our relationship with the malarial parasite has been a long one on the evolutionary scale, and the methods adopted by the parasite to thrive and colonize our bodies are truly fascinating. In order to control the disease, it is of fundame...

Microtubules are hollow tube-like polymeric structures composed of α,β-tubulin heterodimers. They play an important role in numerous cellular processes, including intracellular transport, cell motility and segregation of the chromosomes during cell division. Moreover, microtubule doublets or triplets form a scaffold of a cilium, centriole and basal body, respectively. To perform such diverse fu...

Development is a highly ordered process that institutes considerable changes in cell cycle structure of the different cells composing the embryo. Cell fate is decided at early stages of embryogenesis in embryonic stem cells (ESCs). These cells are derived from the inner cell mass of the primordial embryo and can give rise to all cell lineages of the 3 primary germ layers. The cell cycle of ESCs...

Circadian clocks generate 24-h rhythms that are entrained by the day/night cycle. Clock circuits include several light inputs and interlocked feedback loops, with complex dynamics. Multiple biological components can contribute to each part of the circuit in higher organisms. Mechanistic models with morning, evening and central feedback loops have provided a heuristic framework for the clock in ...