Miles, John, Watkins, Thomas, Darko, Sam, Wijaya, Kuatrinnus, Cooper, Martha, Ransier, Amy, Waardenberg, Ashley, Amante, Fiona, Mccarthy, James, Price, David, Burrows, Scott, Doolan, Denise, Field, Matt, and Douek, Daniel (2022) T cell differentiation and lineage choice are determined by the TCR. FASEB Journal, 36 (S1).

Müller, Johannes, Betzin, Julia, Santos-Tejedor, Jorge, Mayer, Annika, Oprişoreanu, Ana Maria, Engholm-Keller, Kasper, Paulußen, Isabelle, Gulakova, Polina, McGovern, Terrence Daniel, Gschossman, Lena Johanna, Schönhense, Eva, Wark, Jesse R., Lamprecht, Alf, Becker, Albert J., Waardenberg, Ashley J., Graham, Mark E., Dietrich, Dirk, and Schoch, Susanne (2022) A presynaptic phosphosignaling hub for lasting homeostatic plasticity. Cell Reports, 39 (3). 110696.

Buitrago, Geraldine, Pickering, Darren, Ruscher, Roland, Cobos Caceres, Claudia, Jones, Linda, Cooper, Martha, Van Waardenberg, Ashley, Ryan, Stephanie, Miles, Kim, Field, Matthew, Dredge, Keith, Daly, Norelle L., Giacomin, Paul R., and Loukas, Alex (2021) A netrin domain-containing protein secreted by the human hookworm Necator americanus protects against CD4 T cell transfer colitis. Translational Research, 232. pp. 88-102.

Browne, Daniel J., Brady, Jamie L., Van Waardenberg, Ashley J., Loiseau, Claire, and Doolan, Denise L. (2020) An analytically and diagnostically sensitive RNA extraction and RT-qPCR protocol for peripheral blood mononuclear cells. Frontiers in Immunology, 11. 402.

Muruganandah, Visai, Sathkumara, Harindra D., Pai, Saparna, Rush, Catherine M., Brosch, Roland, Waardenberg, Ashley J., and Kupz, Andreas (2020) A systematic approach to simultaneously evaluate safety, immunogenicity, and efficacy of novel tuberculosis vaccination strategies. Science Advances, 6 (10).

Waardenberg, Ashley J., and Field, Matthew A. (2019) consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction. PeerJ, 7. e8206. pp. 1-16.

Engholm-Keller, Kasper, Waardenberg, Ashley J., Müller, Johannes A., Wark, Jesse R., Fernando, Rowena N., Arthur, Jonathan W., Robinson, Phillip J., Dietrich, Dirk, Schoch, Susanne, Graham, Mark E., UNSPECIFIED, and UNSPECIFIED (2019) The temporal profile of activity-dependent presynaptic phospho-signalling reveals long-lasting patterns of poststimulus regulation. PLoS Biology, 17 (3). e3000170.

Ramialison, Mirana, Waardenberg, Ashley J., Schonrock, Nicole, Doan, Tram, de Jong, Danielle, Bouveret, Romaric, and Harvey, Richard P. (2017) Analysis of steric effects in DamID profiling of transcription factor target genes. Genomics, 109 (2). pp. 75-82.

Bottje, Walter, Kong, Byung-Whi, Reverter, Antonio, Waardenberg, Ashley J., Lassiter, Kentu, and Hudson, Nicholas J. (2017) Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency. BMC Systems Biology, 11. 29.

Van Waardenberg, Ashley J. (2017) Statistical Analysis of ATM-Dependent Signaling in Quantitative Mass Spectrometry Phosphoproteomics. In: Kozlov, Sergei V., (ed.) ATM Kinase. Methods in Molecular Biology, 1599 . Springer, New York, NY, USA, pp. 229-244.

Waardenberg, Ashley J., Homan, Bernou, Mohamed, Stephanie, Harvey, Richard P., and Bouveret, Romaric (2016) Prediction and validation of protein–protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. Open Biology, 6. 160183.

Waardenberg, Ashley J., Bassett, Samuel D., Bouveret, Romaric, and Harvey, Richard P. (2015) CompGO: an R package for comparing and visualizing gene ontology enrichment differences between DNA binding experiments. BMC Bioinformatics, 16. 275.

Cannon, Leah, Yu, Ze-Yan, Marciniec, Tadeusz, Waardenberg, Ashley J., Iismaa, Siiri E., Nikolova-Krstevski, Vesna, Neist, Elysia, Ohanian, Monique, Qiu, Min Ru, Rainer, Stephen, Harvey, Richard P., Feneley, Michael P., Graham, Robert M., and Fatkin, Diane (2015) Irreversible triggers for hypertrophic cardiomyopathy are established in the early postnatal period. Journal of the American College of Cardiology, 65 (6). pp. 560-569.

Bouveret, Romaric, Waardenberg, Ashley J., Schonrock, Nicole, Ramialison, Mirana, Doan, Tram, de Jong, Danielle, Bondue, Antoine, Kaur, Gurpreet, Mohamed, Stephanie, Fonoudi, Hananeh, Chen, Chiann-mun, Wouters, Merridee A., Bhattacharya, Shoumo, Plachta, Nicolas, Dunwoodie, Sally L., Chapman, Gavin, Blanpain, Cédric, and Harvey, Richard P. (2015) NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets. eLife, 4. e06942.

Kozlov, Sergei V., Waardenberg, Ashley J., Engholm-Keller, Kasper, Arthur, Jonathan W., Graham, Mark E., and Lavin, Martin (2015) Reactive oxygen species (ROS)-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large-scale phosphoproteomics screen. Molecular and Cellular Proteomics, 15 (3). pp. 1032-1047.

Sun, Wei, Hudson, Nicholas J., Reverter, Antonio, Waardenberg, Ashley, Tellam, Ross L, Vuocolo, Tony, Byrne, Keren, and Dalrymple, Brian P (2012) An always correlated gene expression landscape for ovine skeletal muscle, lessons learnt from comparison with an “equivalent” bovine landscape. BMC Research Notes, 5. 632.

Waardenberg, Ashley J., Bernardo, Bianca C., Ng, Dominic C. H., Shepherd, Peter R., Cemerlang, Nelly, Sbroggiò, Mauro, Wells, Christine A., Dalrymple, Brian P., Brancaccio, Mara, Lin, Ruby C. Y., McMullen, Julie R., and UNSPECIFIED (2011) Phosphoinositide 3-Kinase (PI3K(p110α)) directly regulates key components of the Z-disc and cardiac structure. Journal of Biological Chemistry, 286 (35). pp. 30837-30846.

The Bovine Genome Sequencing and Analysis Consortium, , Elsik, Christine G., Tellam, Ross L., and Worley, Kim C. (2009) The genome sequence of Taurine cattle: a window to ruminant biology and evolution. Science, 324 (5926). pp. 522-528.

Waardenberg, Ashley J., Reverter, Antonio, Wells, Christine A., and Dalrymple, Brian P. (2008) Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle. BMC Systems Biology, 2. 88.