Research outputs
2025
Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets
Prakash, A., Collins, A., Vilmovsky, L., Fexova, S., Jones, A. R., & Vizcaino, J. A. (2025). Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets. Journal of Proteome Research. doi:10.1021/acs.jproteome.4c00788
2024
Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues.
Wang, S., Collins, A., Prakash, A., Fexova, S., Papatheodorou, I., Jones, A. R., & Vizcaíno, J. A. (2024). Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues.. Journal of proteome research. doi:10.1021/acs.jproteome.3c00741
2023
Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets
Camacho, O. M., Ramsbottom, K. A., Collins, A., & Jones, A. R. (2023). Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets. JOURNAL OF PROTEOME RESEARCH, 22(6), 1828-1842. doi:10.1021/acs.jproteome.2c00823
Integrated View of Baseline Protein Expression in Human Tissues
Prakash, A., Garcia-Seisdedos, D., Wang, S., Kundu, D. J., Collins, A., George, N., . . . Vizcaino, J. A. (2023). Integrated View of Baseline Protein Expression in Human Tissues. JOURNAL OF PROTEOME RESEARCH, 22(3), 729-742. doi:10.1021/acs.jproteome.2c00406
2022
Assessing multiple evidence streams to decide on confidence for identification of post-translational modifications, within and across data sets
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues
Wang, S., Garcia-Seisdedos, D. R., Prakash, A., Kundu, D. J., Collins, A., George, N., . . . Vizcaino, J. A. (2022). Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues. PLOS COMPUTATIONAL BIOLOGY, 18(6). doi:10.1371/journal.pcbi.1010174
2021
2019
Proteomics Standards Initiative Extended FASTA Format
Binz, P. -A., Shofstahl, J., Vizcaino, J. A., Barsnes, H., Chalkley, R. J., Menschaert, G., . . . Deutsch, E. W. (2019). Proteomics Standards Initiative Extended FASTA Format. JOURNAL OF PROTEOME RESEARCH, 18(6), 2686-2692. doi:10.1021/acs.jproteome.9b00064
Proteomics Standards Initiative Extended FASTA Format (PEFF)
2018
phpMs: A PHP-Based Mass Spectrometry Utilities Library
Collins, A., & Jones, A. R. (2018). phpMs: A PHP-Based Mass Spectrometry Utilities Library. JOURNAL OF PROTEOME RESEARCH, 17(3), 1309-1313. doi:10.1021/acs.jproteome.7b00783
2014
ProteoAnnotator – Open source proteogenomics annotation software supporting PSI standards
Ghali, F., Krishna, R., Perkins, S., Collins, A., Xia, D., Wastling, J., & Jones, A. R. (2014). ProteoAnnotator – Open source proteogenomics annotation software supporting PSI standards. Proteomics, 14(23-24), 2731-2741. doi:10.1002/pmic.201400265
2013
Distributed Navigation
Collins, A. (2013). Distributed Navigation. (PhD Thesis, University of Liverpool).
Optimal patrolling of fragmented boundaries
Collins, A., Czyzowicz, J., Gasieniec, L., Kosowski, A., Kranakis, E., Krizanc, D., . . . Morales Ponce, O. (2013). Optimal patrolling of fragmented boundaries. In Proceedings of the twenty-fifth annual ACM symposium on Parallelism in algorithms and architectures (pp. 241-250). ACM. doi:10.1145/2486159.2486176
2011
Synchronous Rendezvous for Location-Aware Agents
Collins, A., Czyzowicz, J., Gasieniec, L., Kosowski, A., & Martin, R. (2011). Synchronous Rendezvous for Location-Aware Agents. In DISTRIBUTED COMPUTING Vol. 6950 (pp. 447-+). Retrieved from https://www.webofscience.com/
2010
Tell Me Where I Am So I Can Meet You Sooner
Collins, A., Czyzowicz, J., Gąsieniec, L., & Labourel, A. (2010). Tell Me Where I Am So I Can Meet You Sooner. In Unknown Conference (pp. 502-514). Springer Berlin Heidelberg. doi:10.1007/978-3-642-14162-1_42
2009
2D Graph Exploration Using Irrational Numbers
Collins, A. (2009). 2D Graph Exploration Using Irrational Numbers. (Master's Thesis, University of Liverpool).