Dr. Yassene Mohammed


  • Bioinformatics
  • Computational Proteomics
  • Targeted Proteomics


Yassene is an assistant professor in bioinformatics at the Center for Proteomics and Metabolomics. He received his PhD in Medical Informatics from the University of Göttingen, Germany. His research interests are bottom-up and targeted proteomics, -omics data integration, scientific workflows, and eScience. In the past Yassene has also worked on distributed computing applications, data protection and security in grid environments, biomedical image processing, as well as multiphysics simulation and modelling.

Since July 2013 Yassene is also heading the bioinformatics activities at the Proteomics Centre of the University of Victoria, Canada focusing on targeted proteomics bioinformatics, clinical applications of proteomics and statistical approaches for MRM and PRM analyses.

Links and tools

Selected papers

  • Bhowmick P, Roome S, Borchers CH, Goodlett DR, Mohammed Y. An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community. J Proteome Res. 2021 Apr 2;20(4):2105-2115. doi: 10.1021/acs.jproteome.0c00961. Epub 2021 Mar 8. PMID: 33683131; PMCID: PMC8041396.
  • Mohammed Y, Bhowmick P, Michaud SA, Sickmann A, Borchers CH, Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays, Bioinformatics, 2021;, btab018, https://doi.org/10.1093/bioinformatics/btab018
  • Makepeace KAT*, Mohammed Y*, Rudashevskaya EL*, Petrotchenko EV, Vögtle FN, Meisinger C, Sickmann A, Borchers CH. Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker.Mol Cell Proteomics. 2020 Apr;19(4):624-639. doi: 10.1074/mcp.RA119.001839. Epub 2020 Feb 12. (* shared first authorship)
  • Tilburg, J., Michaud, S.A.,Maracle, C.X., Versteeg, H.H., Borchers, C.H., van Vlijmen, B.J.M., Mohammed, Y. Plasma Protein Signatures of a Murine Venous Thrombosis Model and Slc44a2 Knockout Mice using Quantitative Targeted Proteomics. Thrombosis and Haemostasis
  • Pirro M, Mohammed Y, van Vliet SJ, Rombouts Y, Sciacca A, de Ru AH, Janssen GMC, Tjokrodirijo RTN, Wuhrer M, van Veelen PA, Hensbergen PJ. N-Glycoproteins Have a Major Role in MGL Binding to Colorectal Cancer Cell Lines: Associations with Overall Proteome Diversity. Int J Mol Sci. 2020 Aug 1;21(15):5522. doi: 10.3390/ijms21155522.
  • Gaither C, Popp R, Mohammed Y, Borchers CH., Determination of the concentration range for 267 proteins from 21 lots of commercial human plasma using highly multiplexed multiple reaction monitoring mass spectrometry. Analyst. 2020 Apr 7. doi: 10.1039/c9an01893j. [Epub ahead of print]
  • Eshghi A, Pistawka AJ, Liu J, Chen M, Sinclair NJT, Hardie DB, Elliott M, Chen L, Newman R, Mohammed Y, Borchers CH.Concentration determination of >200 proteins in dried blood spots for biomarker discovery and validation. Molecular & Cellular Proteomics2020 Jan 2. pii: mcp.TIR119.001820. doi: 10.1074/mcp.TIR119.001820.
  • Körner A, Zhou E, Müller C, Mohammed Y, Herceg S, Bracher F, Rensen PCN, Wang Y, Mirakaj V, Giera M. Inhibition of Δ24-dehydrocholesterol reductase activates pro-resolving lipid mediator biosynthesis and inflammation resolution. Proceedings of the National Academy of Sciences of the United States of America. 2019 Oct 8;116(41):20623-20634. doi: 10.1073/pnas.1911992116. Epub 2019 Sep 23.
  • Mohammed, Y., Kootte, R.S., Kopatz, W.F., Borchers, C.H., Büller, H.R., Versteeg, H.H., Nieuwdorp, M., van Mens, T.E.The intestinal microbiome potentially affects thrombin generation in human subjects. Journal of Thrombosis and Haemostasis. 2019 Dec 6. doi: 10.1111/jth.14699.
  • 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 Clin Appl 2018, 12, (2).
  • Michaud, S. A.; Sinclair, N. J.; Petrosova, H.; Palmer, A. L.; Pistawka, A. J.; Zhang, S.; Hardie, D. B.; 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. Commun Biol 2018, 1, 78.
  • 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 1:1080-1087; doi: https://doi.org/10.1182/bloodadvances.2017007955
  • Mohammed, Y. , Palmblad, M. ,Visualizing and comparing results of different peptide identification methods. Briefings in Bioinformatics. 2016 Dec 22. pii: bbw115. doi: 10.1093/bib/bbw115.
  • 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 Sep 29. doi: 10.1002/pmic.201600210.
  • 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, August 2016, Pages 830-841, ISSN 1751-1577, http://dx.doi.org/10.1016/j.joi.2016.05.002. 
  • Percy, AJ, Mohammed, Y, Yang, J, Borchers, CH, A standardized kit for automated quantitative assessment of candidate protein biomarkers in human plasma. Bioanalysis.  2015 Dec; 7(23):2991-3004. doi: 10.4155/bio.15.222., PMID: 26626236
  • Holl, S, Mohammed, Y, Zimmermann, O, Palmblad, M., Scientific workflow optimization for improved peptide and protein identification. BMC Bioinformatics. 2015 Sep 3;16(1):284. 10.1186/s12859-015-0714-x.
  • Mohammed, Y, Borchers, CH. An Extensive Library of Surrogate Peptides for all Human Proteins, J Proteomics. 2015 Jul 28. pii: S1874-3919(15)30079-8.
  • Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH , Urbani A, Soggiu A, Yamamoto T, Archakov AI, Ponomarenko E, Lisitsa AV, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Vegvari A, Fehniger TE, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Cho JY, Paik YK, Hancock WS. A Quest for Missing Proteins: update 2015 on Chromosome-Centric Human Proteome Project. J Proteome Res. 2015 Jun 15.
  • 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, [Epub ahead of print], DOI: 10.1021/pr5010955
  • Mohammed, Y., Domanski, 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 Jun 25;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, 13 (3), pp 1537–1544 DOI: 10.1021/pr401058
  • Perl, H., Mohammed, Y. , Brenner, M., and Smith, M. Privacy/performance trade-off in private search on bio-medical data , Future Generation Computer Systems, Volume 36, July 2014, 441-452, ISSN 0167-739X
  • 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, Volume 36, July 2014, 352-362, ISSN 0167-739X
  • Holl, S., Memon, M.S., Riedel, M., Mohammed, Y. , Palmblad, M., Grimshaw, A., Enhanced Resource Management enabling Standard Parameter Sweep Jobs for Scientific Applications , 9th International Workshop on Scheduling and Resource Management for Parallel and Distributed Systems, IEEE, 2013
  • Mohammed, Y., and Palmblad, M. Simple Proteomics Data Analysis in the Object-Oriented PowerShell, in Mass Spectrometry Data Analysis in Proteomics, 2nd edition, 2013.
  • Mohammed, Y., von Voigt, G., and Smith, M., Enabling Big Data Driven Biomedicine Using Scientific Workflows and Cloud Computing, Proceedings of gmds 2012.
  • 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: 11 (10): 5101-8.
  • 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, in Computational Advances in Life Science workshop, IEEE 7th International Conference on e-Science 2011, Stockholm.
  • Mohammed, Y., Dickmann, F., Sax, U., von Voigt, G., Smith, M., and Rienhoff, O. Reaching for the Cloud: On the Lessons Learned from Grid Computing Technology Transfer Process to the Biomedical Community, Medinfo 2010, in Studies in Health Technology and Informatics, 2010. 


Leids Universitair Medisch Centrum
Gebouw 1
Kamer P-01-060

Albinusdreef 2
2333 ZA Leiden
Tel: +31 715266878

Postzone P1-P
Postbus 9600
2300 RC Leiden

E-mail: y.mohammed@lumc.nl