The Stem Cell Reports paper linked in the question is open-access, so anyone can download it freely. Unfortunately the Nature paper is not.
There are two different abbreviation conventions being used in the open paper – MyoD+/MyoD- and MyoD+/MyoD-. The italicized version indicates the genotype of the cell, tissue, or individual being referenced, so for example MyoD- indicates the MyoD knockout they made. This convention is very widely used to refer to genes or mRNA.
Examples where the gene name is not italicized refer to the protein product of that particular gene and its presence or absence. So, MyoD+ cells express the wild-type protein, while MyoD- cells do not. This convention is also very widely used to refer to the presence or absence of the indicated protein.