[5] One key contribution was her discovery that transfection of microRNAs into cells counter-intuitively increases the expression of some genes, due to competition for the cellular machinery that processes small RNAs.

[6] In collaboration with Alexander van Oudenaarden and Nils Bluthgen, she showed that microRNAs reduce the noise in protein expression when mRNA levels are low, reducing the likelihood of unwanted protein expression as a result of leakage at a gene's promoter.

[12] Marks and her close collaborator and husband Chris Sander have shown that this approach can also be used to predict the structures of non-coding RNAs and RNA-protein complexes,[13] to identify otherwise undetectable structured states in disordered proteins[14] and to predict the functional effects of sequence mutations.

[15] In 2016, Marks was awarded the Overton Prize by the International Society for Computational Biology.

[17] In 2022, Marks was elected as a Fellow of the International Society for Computational Biology.