MEDFORD: A human- and machine-readable metadata markup language.

Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a software used or iteration of a genome can easily be lost in the shuffle or perhaps not noted at all.

Characterization of sequence contexts that favor alternative end joining at Cas9-induced double-strand breaks.

Alternative end joining (alt-EJ) mechanisms, such as polymerase theta-mediated end joining, are increasingly recognized as important contributors to inaccurate double-strand break repair. We previously proposed an alt-EJ model whereby short DNA repeats near a double-strand break anneal to form secondary structures that prime limited DNA synthesis. The nascent DNA then pairs with microhomologous sequences on the other break end.

What is theory of mind? A psychometric study of theory of mind and intelligence.

Theory of mind (ToM) is an essential ability for social competence and communication, and it is necessary for understanding behaviors that differ from our own (Premack & Woodruff, 1978). Recent research suggests that tasks designed to measure ToM do not adequately capture a single ToM ability (Warnell & Redcay, 2019; Quesque & Rossetti, 2020) and, instead, might be related to tasks of general cognitive ability (Coyle, Elpers, Gonzalez, Freeman, & Baggio, 2018). This hinders the interpretation of experimental findings and puts into question the validity of the ToM construct.

Fractal Analysis of Cancer Cell Surface.

Fractal analysis of the cell surface is a rather sensitive method which has been recently introduced to characterize cell progression toward cancer. The surface of fixed and freeze-dried cells is imaged with atomic force microscopy (AFM) modality in ambient conditions. Here we describe the method to perform the fractal analysis specifically developed for the AFM images.