Jasper van Bemmelen, Davida S. Smyth, Jasmijn A. Baaijens (2024), Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes, In BMC Bioinformatics Volume 25.

Steven G. Sutcliffe, Susanne A. Kraemer, Isaac Ellmen, Jennifer J. Knapp, Alyssa K. Overton, Delaney Nash, Jozef I. Nissimov, Jasmijn A. Baaijens, B. Jesse Shapiro, More Authors (2024), Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data, In Microbial Genomics Volume 10.

Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén (2022), Computational graph pangenomics: A tutorial on data structures and their applications, In Natural Computing Volume 21 p.81-108.

Jasmijn A. Baaijens, Alessandro Zulli, Isabel M. Ott, Ioanna Nika, Mart J. van der Lugt, Mary E. Petrone, Tara Alpert, Joseph R. Fauver, Chaney C. Kalinich, More Authors (2022), Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques, In Genome biology Volume 23.