Bioinformatics, biocomputing and Perl - an introduction to bioinformatics computing skills and practice. - Michael J. Moorhouse; Paul Barry (Wiley, 2004)

Head First Programming - a Brain-Friendly Guide. - Paul Barry; David Griffiths (O'Reilly, 2009)

Head First Python - a Brain-Friendly Guide. - Paul Barry (O'Reilly, 2011)

Generalized Stirling Numbers, Exponential Riordan Arrays, and Toda Chain Equations. - Paul Barry (J. Integer Seq., 2014)

Constructing Exponential Riordan Arrays from Their A and Z Sequences. - Paul Barry (J. Integer Seq., 2014)

Comparing Two Matrices of Generalized Moments Defined by Continued Fraction Expansions. - Paul Barry (J. Integer Seq., 2014)

Jacobsthal Decompositions of Pascals Triangle, Ternary Trees, and Alternating Sign Matrices. - Paul Barry (J. Integer Seq., 2016)

On a Transformation of Riordan Moment Sequences. - Paul Barry (J. Integer Seq., 2018)

Classical and Semi-Classical Orthogonal Polynomials Defined by Riordan Arrays, and Their Moment Sequences. - Paul Barry; Arnauld Mesinga Mwafise (J. Integer Seq., 2018)

Deep Learning for Identification of Adverse Effect Mentions In Twitter Data. - Paul Barry; Özlem Uzuner (SMM4H@ACL, 2019)

The Central Coefficients of a Family of Pascal-like Triangles and Colored Lattice Paths. - Paul Barry (J. Integer Seq., 2019)

The γ-Vectors of Pascal-like Triangles Defined by Riordan Arrays. - Paul Barry (J. Integer Seq., 2019)

Generalized Catalan Numbers Associated with a Family of Pascal-like Triangles. - Paul Barry (J. Integer Seq., 2019)

Riordan Pseudo-Involutions, Continued Fractions and Somos-4 Sequences. - Paul Barry (J. Integer Seq., 2019)

Jointly Learning Clinical Entities and Relations with Contextual Language Models and Explicit Context. - Paul Barry; Sam Henry 001; Meliha Yetisgen; Bridget T. McInnes; Özlem Uzuner (AMIA, 2020)

Two kinds of partial Motzkin paths with air pockets. - Jean-Luc Baril; Paul Barry (Ars Math. Contemp., 2024)

Graph-Based Filtering to Prevent Prompt-Engineered LLM Training Data Leaks. - Alan Barnett; Seán Ahearne; Paul Barry; Merry Globin; Colin Duggan (SMARTCOMP, 2025)