Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities. - Paul Shafer; Timothy Isganitis; Golan Yona (BMC Bioinform., 2006)

Coding true arithmetic in the Medvedev and Muchnik degrees. - Paul Shafer (J. Symb. Log., 2011)

Characterizing the Join-Irreducible Medvedev Degrees. - Paul Shafer (Notre Dame J. Formal Log., 2011)

Menger's theorem in Π11-CA0. - Paul Shafer (Arch. Math. Log., 2012)

Coding true arithmetic in the Medvedev degrees of Π10 classes. - Paul Shafer (Ann. Pure Appl. Log., 2012)

Reverse mathematics, trichotomy, and dichotomy. - François G. Dorais; Jeffry L. Hirst; Paul Shafer (J. Log. Anal., 2012)

Reverse Mathematics and Algebraic Field Extensions. - François G. Dorais; Jeffry L. Hirst; Paul Shafer (Comput., 2013)

Universality, optimality, and randomness deficiency. - Rupert Hölzl 001; Paul Shafer (Ann. Pure Appl. Log., 2015)

Comparing the strength of diagonally Nonrecursive Functions in the Absence of ∑20 Induction. - François G. Dorais; Jeffry L. Hirst; Paul Shafer (J. Symb. Log., 2015)

Reverse mathematics, well-quasi-orders, and Noetherian spaces. - Emanuele Frittaion; Matthew Hendtlass; Alberto Marcone; Paul Shafer; Jeroen Van der Meeren (Arch. Math. Log., 2016)

Honest elementary degrees and degrees of relative provability without the cupping property. - Paul Shafer (Ann. Pure Appl. Log., 2017)

Randomness and Semimeasures. - Laurent Bienvenu; Rupert Hölzl 001; Christopher P. Porter; Paul Shafer (Notre Dame J. Formal Log., 2017)

Comparing the degrees of enumerability and the closed Medvedev degrees. - Paul Shafer; Andrea Sorbi (Arch. Math. Log., 2019)

The strength of compactness for countable complete linear orders. - Paul Shafer (Comput., 2020)

Randomness Notions and Reverse Mathematics. - André Nies; Paul Shafer (J. Symb. Log., 2020)

Ordinal Analysis of Partial Combinatory Algebras. - Paul Shafer; Sebastiaan A. Terwijn (J. Symb. Log., 2021)

On Cohesive powers of linear Orders. - Rumen D. Dimitrov; Valentina S. Harizanov; Andrei S. Morozov; Paul Shafer; Alexandra A. Soskova; Stefan V. Vatev (J. Symb. Log., 2023)

(Extra)ordinary Equivalences with the ascending/descending sequence Principle. - Marta Fiori-Carones; Alberto Marcone; Paul Shafer; Giovanni Soldà (J. Symb. Log., 2024)