The following is a list of selected papers from the recent years

Mohammed, Y., Palmblad, M., Visualization and application of amino acid retention coefficients obtained from modeling of peptide retention, Journal of
Separation Science 2018. 10.1002/jssc.201800488.

Michaud, S. A., Sinclair, N. J., Pětrošová, H., Palmer, A. L., Pistawka, A. J., Zhang, S., Hardie, D., Mohammed, Y., Eshghi, A., Richard, V.R., Sickmann, A., Borchers, C.H. Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays, Nature Communications Biology, 2018. DOI: 10.1038/s42003-018-0087-6.

Bhowmick, P.#, Mohammed, Y.#,*, Borchers, C.H.*, MRMAssayDB: an integrated resource for validated targeted proteomics assays, Bioinformatics 2018. DOI: 10.1093/bioinformatics/bty385. (# shared first authorship, * corresponding authors)

Mohammed, Y., Pan, J., Zhang, S., Han, J., Borchers, C.H. ExSTA: External Standard Addition Method for Accurate High-throughput Quantitation in Targeted Proteomics Experiments. Proteomics Clinical Applications 2018. doi: 10.1002/prca.201600180.

Mohammed, Y., van Vlijmen, B.J., Yang, J., Percy, A.J., Palmblad, M., Borchers, C.H., Rosendaal, F.R., Multiplexed targeted proteomic assay to assess coagulation factor concentrations and thrombosis-associated cancer. Blood Advances 2017. doi: https://doi.org/10.1182/bloodadvances.2017007955.

Mohammed, Y., Palmblad, M., Visualizing and comparing results of different peptide identification methods. Briefings in Bioinformatics, Volume 19, Issue 2, 2018. https://doi.org/10.1093/bib/bbw115.

Popp, R., Li, H., LeBlanc, A., Mohammed, Y., Aguilar-Mahecha, A., Chambers, A.G., Lan, C., Poetz, O., Basik, M., Batist, G., Borchers, C.H. Immuno-Matrix-Assisted Laser Desorption/Ionization Assays for Quantifying AKT1 and AKT2 in Breast and Colorectal Cancer Cell Lines and Tumors. Analytical Chemistry. 2017. DOI: 10.1021/acs.analchem.7b02934.

Mohammed, Y.Bhowmick, P., Smith, D.S., Domanski, D., Jackson, A.M., Michaud, S.A., Malchow, S., Percy, A.J., Chambers, A.G., Palmer, A., Zhang, S., Sickmann, A., Borchers, C.H., PeptideTracker: A knowledgebase for collecting and storing information on protein concentrations in biological tissues. Proteomics 2016. doi: 10.1002/pmic.201600210.

Percy, A.J., Michaud, S.A., Jardim, A., Sinclair, N.J., Zhang, S., Mohammed, Y., Palmer, A.L., Hardie, D.B., Yang, J., LeBlanc, A.M., Borchers, C.H., Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue, Proteomics. 2016. DOI: 10.1002/pmic.201600097.

Percy, A.J., Hardie, D.B., Jardim, A., Yang, J., Elliott, M.H., Zhang, S., Mohammed, Y., Borchers, C.H.,Multiplexed panel of precisely quantified salivary proteins for biomarker assessment, Proteomics. 2016. DOI: 10.1002/pmic.201600230.

Guler, AT, Waaijer, C., Mohammed, Y., Palmblad, M., Automating Bibliometric Analyses using Taverna Scientific Workflows: A Tutorial on Integrating Web Services. Journal of Informetrics, Volume 10, Issue 3, 2016, http://dx.doi.org/10.1016/j.joi.2016.05.002.

Mohammed, Y., Borchers, C.H. An Extensive Library of Surrogate Peptides for all Human Proteins, Journal of Proteomics 2015. pii: S1874-3919(15)30079-8.

Mohammed, Y., Percy, A.J., Chambers, A.G., Borchers, C.H., Qualis-SIS: Automated Standard Curve Generation and Quality Assessment for Multiplexed Targeted Quantitative Proteomic Experiments with Labeled Standards, Journal of Proteome Research 2015, DOI: 10.1021/pr5010955.

Percy, A.J., Mohammed, Y., Yang, J., Borchers, C.H., A standardized kit for automated quantitative assessment of candidate protein biomarkers in human plasma. Bioanalysis, 2015. DOI: 10.4155/bio.15.222.

Holl, S., Mohammed, Y., Zimmermann, O., Palmblad, M., Scientific workflow optimization for improved peptide and protein identification. BMC Bioinformatics. 2015. DOI: 10.1186/s12859-015-0714-x.

Horvatovich, P., Lundberg, E.K., Chen, Y.J., Sung, T.Y., He, F., Nice, E.C., Goode, R.J., Yu, S., Ranganathan, S., Baker, M.S., Domont, G.B., Velasquez, E., Li, D., Liu, S., Wang Q., He, Q.Y., Menon, R., Guan, Y., Corrales, F.J., Segura, V., Casal, J.I., Pascual-Montano, A., Albar, J.P., Fuentes, M., Gonzalez-Gonzalez, M., Diez, P., Ibarrola, N., Degano, R.M., Mohammed, Y., Borchers, C.H. , Urbani, A., Soggiu, A., Yamamoto, T., Archakov, A.I., Ponomarenko, E., Lisitsa, A.V., Lichti, C.F., Mostovenko, E., Kroes, R.A., Rezeli, M., Vegvari, A., Fehniger, T.E., Bischoff, R., Vizcaíno, J.A., Deutsch, E.W., Lane, L., Nilsson, C.L., Marko-Varga, G., Omenn, G.S., Jeong, S.K., Cho, J.Y., Paik, Y.K., Hancock, W.S. A Quest for Missing Proteins: update 2015 on Chromosome-Centric Human Proteome Project. Journal of Proteome Research. 2015. DOI: 10.1021/pr5013009

Mohammed, Y., Domański, D., Jackson, A.M., Smith, D.S., Deelder, A.M., Palmblad, M., Borchers, C.H. PeptidePicker: a Scientific Workflow with Web Interface for Selecting Appropriate Peptides for Targeted Proteomics Experiments, Journal of Proteomics 2014. 106:151-61. doi: 10.1016.

van der Plas-Duivesteijn, S., Mohammed, Y.. Dalebout, H., Meijer, A., Botermans, A., Hoogendijk, J., Henneman, A., Deelder, A., Spaink, H., Palmblad, M. Identifying Proteins in Zebrafish Embryos Using Spectral Libraries Generated from Dissected Adult Organs and Tissues. Journal of Proteome Research, 2014. DOI: 10.1021/pr4010585

Perl, H., Mohammed, Y., Brenner, M., and Smith, M. Privacy/performance trade-off in private search on bio-medical data, Future Generation Computer Systems, 2014. https://doi.org/10.1016/j.future.2013.12.006

Holl, S., Zimmermann, O., Palmblad, M., Mohammed, Y., and Hofmann-Apitius, M. A New Optimization Phase for Scientific Workflow Management Systems, Future Generation Computer Systems, 2014. DOI: 10.1016/j.future.2013.09.005

Holl, S., Memon, M.S., Riedel, M., Mohammed, Y., Palmblad, M., Grimshaw, A., Enhanced Resource Management enabling Standard Parameter Sweep Jobs for Scientific Applications, Proceeding of 9th International Workshop on Scheduling and Resource Management for Parallel and Distributed Systems, 2013. DOI: 10.1109/ICPP.2013.92

Mohammed, Y., Mostovenko, E., Henneman, A.A., Marissen, R.J., Deelder, A.M., and Palmblad, M. Cloud parallel processing of tandem mass spectrometry based proteomics data, Journal of Proteome Research 2012. DOI: 10.1021/pr300561q

Perl, H., Mohammed, Y., Brenner, and M., Smith, M. Fast Confidential Search for Bio-Medical Data Using Bloom Filters and Homomorphic Cryptography, Proceedings of the 8th IEEE International Conference on eScience, 2012. DOI: 10.1109/eScience.2012.6404484

Mohammed, Y., von Voigt, G., and Smith, M., Enabling Big Data Driven Biomedicine Using Scientific Workflows and Cloud Computing, Proceedings of 57 Congress of the German Society for Medical Informatics, Biometry and Epidemiology, 2012. DOI: 10.3205/12gmds044

Mohammed, Y., Shahand, S., Korkhov, V., Luyf, A.C.M., van Schaik, B.D.C.,  Caan, M.W.A., van Kampen, A.H.C., Palmblad, M., and Olabarriaga, S.D. Data Decomposition in Biomedical e-Science Applications, proceeding of IEEE 7th International Conference on e-Science, 2011. DOI: 10.1109/eScienceW.2011.7



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