Dr. D. (Dave) Speijer

Faculty of Science

Swammerdam Institute for Life Sciences

Visiting address

Science Park 904

Postal address

Postbus 1212
1000 BE Amsterdam

Contact details

dr. Dave Speijer (Mo - Wed)
020-5665134
d.speijer@amsterdamumc.nl

Publications
2023

Bruggeman, J. W., Koster, J., van Pelt, A. M. M., Speijer, D., & Hamer, G. (2023). How germline genes promote malignancy in cancer cells. BioEssays, 45(1), Article 2200112. https://doi.org/10.1002/bies.202200112

Man-Bovenkerk, S., Schipper, K., van Sorge, N. M., Speijer, D., van der Ende, A., & Pannekoek, Y. (2023). Neisseria meningitidis Sibling Small Regulatory RNAs Connect Metabolism with Colonization by Controlling Propionate Use. Journal of Bacteriology, 205(3), Article e00462-22. https://doi.org/10.1128/jb.00462-22

Speijer, D. (2023). How mitochondria showcase evolutionary mechanisms and the importance of oxygen. BioEssays, Article 2300013. Advance online publication. https://doi.org/10.1002/bies.202300013

van der Gulik, P. T. S., Hoff, W. D., & Speijer, D. (2023). Renewing Linnaean taxonomy: a proposal to restructure the highest levels of the Natural System. Biological Reviews, 98(2), 584-602. https://doi.org/10.1111/brv.12920

2022

Hammond, M., Dorrell, R. G., Speijer, D., & Lukeš, J. (2022). Eukaryotic cellular intricacies shape mitochondrial proteomic complexity. BioEssays, 44(5), Article 2100258. https://doi.org/10.1002/bies.202100258

Speijer, D. (2022). Airports: Flying in the face of science and common sense. BioEssays, 44(12), Article 2200189. https://doi.org/10.1002/bies.202200189

Speijer, D. (2022). Molecular characteristics of the multi-functional FAO enzyme ACAD9 illustrate the importance of FADH₂/NADH ratios for mitochondrial ROS formation. BioEssays, 44(8), Article 2200056. https://doi.org/10.1002/bies.202200056

Speijer, D. (2022). What are we doing, people? We have to challenge vested interests much more vigorously. BioEssays, 44(2), Article 2100251. https://doi.org/10.1002/bies.202100251

2021

Loedin, A. K., & Speijer, D. (2021). Is There a Carcinogenic Risk Attached to Vitamin B₁₂ Deficient Diets and What Should We Do About It? Reviewing the Facts. Molecular Nutrition and Food Research, 65(6), Article 2000945. https://doi.org/10.1002/mnfr.202000945

Lukeš, J., Kaur, B., & Speijer, D. (2021). RNA Editing in Mitochondria and Plastids: Weird and Widespread. Trends in Genetics, 37(2), 99-102. https://doi.org/10.1016/j.tig.2020.10.004

Speijer, D. (2021). Even The Guardian needs a guardian. BioEssays, 43(2), Article 2000328. https://doi.org/10.1002/bies.202000328

Speijer, D. (2021). Preventing the Matthew principle in science publishing. BioEssays, 43(10), Article 2100163. https://doi.org/10.1002/bies.202100163

Speijer, D. (2021). The sting of rejection. BioEssays, 43(4), Article 2100028. https://doi.org/10.1002/bies.202100028

Speijer, D. (2021). Zombie ideas about early endosymbiosis: Which entry mechanisms gave us the “endo” in different endosymbionts? BioEssays, 43(7), Article 2100069. https://doi.org/10.1002/bies.202100069

2020

Speijer, D. (2020). Debating Eukaryogenesis—Part 1: Does Eukaryogenesis Presuppose Symbiosis Before Uptake? BioEssays, 42(4), Article 1900157. https://doi.org/10.1002/bies.201900157

Speijer, D. (2020). Debating Eukaryogenesis—Part 2: How Anachronistic Reasoning Can Lure Us into Inventing Intermediates. BioEssays, 42(5), Article 1900153. https://doi.org/10.1002/bies.201900153

Speijer, D. (2020). How neoteny shapes human society: Can we escape our formative years, and fight the wrong kind of populism? BioEssays, 42(12), Article 2000230. https://doi.org/10.1002/bies.202000230

Speijer, D. (2020). Is Popperian Falsification Useful in Biology? BioEssays, 42(3), Article 2000003. https://doi.org/10.1002/bies.202000003

Speijer, D. (2020). The Future of the World Wide Web: Wikipedia or Whatsapp? BioEssays, 42(9), Article 2000186. https://doi.org/10.1002/bies.202000186

Speijer, D., Hammond, M., & Lukeš, J. (2020). Comparing early eukaryotic integration of mitochondria and chloroplasts in the light of internal ROS challenges: Timing is of the essence. MBio, 11(3), Article e00955-20. https://doi.org/10.1128/mBio.00955-20

2019

Schipper-Krom, S., Sanz, A. S., van Bodegraven, E. J., Speijer, D., Florea, B. I., Ovaa, H., & Reits, E. A. (2019). Visualizing Proteasome Activity and Intracellular Localization Using Fluorescent Proteins and Activity-Based Probes. Frontiers in Molecular Biosciences, 6, Article 56. https://doi.org/10.3389/fmolb.2019.00056

Speijer, D. (2019). Can All Major ROS Forming Sites of the Respiratory Chain Be Activated By High FADH₂/NADH Ratios? Ancient evolutionary constraints determine mitochondrial ROS formation. BioEssays, 41(1), Article 1800180. https://doi.org/10.1002/bies.201800180

Speijer, D. (2019). Dangerous Delusions about Darwinism. BioEssays, 41(11), Article 1900176. https://doi.org/10.1002/bies.201900176 [details]

Speijer, D. (2019). Let's Stop the Sloppy Use of “Lamarckian”. BioEssays, 41(2), Article 1800258. https://doi.org/10.1002/bies.201800258

Speijer, D. (2019). On the Likelihood of Life Originating. BioEssays, 41(9), Article 1900085. https://doi.org/10.1002/bies.201900085

Speijer, D. (2019). Stop the Assault on Truth. BioEssays, 41(7), Article 1900082. https://doi.org/10.1002/bies.201900082

van Montfort, T., van der Sluis, R., Darcis, G., Beaty, D., Groen, K., Pasternak, A. O., Pollakis, G., Vink, M., Westerhout, E. M., Hamdi, M., Bakker, M., van der Putten, B., Jurriaans, S., Prins, J. H., Jeeninga, R., Thomas, A. A. M., Speijer, D., & Berkhout, B. (2019). Dendritic cells potently purge latent HIV-1 beyond TCR-stimulation, activating the PI3K-Akt-mTOR pathway. eBioMedicine, 42, 97-108. https://doi.org/10.1016/j.ebiom.2019.02.014

2018

Akkerdaas, J., Totis, M., Barnett, B., Bell, E., Davis, T., Edrington, T., Glenn, K., Graser, G., Herman, R., Knulst, A., Ladics, G., McClain, S., Poulsen, L. K., Ranjan, R., Rascle, J. B., Serrano, H., Speijer, D., Wang, R., Pereira Mouriès, L., ... Van Ree, R. (2018). Protease resistance of food proteins: A mixed picture for predicting allergenicity but a useful tool for assessing exposure. Clinical and Translational Allergy, 8(1), Article 30. https://doi.org/10.1186/s13601-018-0216-9

Baardman, J., Verberk, S. G. S., Prange, K. H. M., van Weeghel, M., van der Velden, S., Ryan, D. G., Wüst, R. C. I., Neele, A. E., Speijer, D., Denis, S. W., Witte, M. E., Houtkooper, R. H., O'neill, L. A., Knatko, E. V., Dinkova-Kostova, A. T., Lutgens, E., de Winther, M. P. J., & Van den Bossche, J. (2018). A Defective Pentose Phosphate Pathway Reduces Inflammatory Macrophage Responses during Hypercholesterolemia. Cell Reports, 25(8), 2044-2052.e5. https://doi.org/10.1016/j.celrep.2018.10.092

Gillissen, M. A., Kedde, M., De Jong, G., Moiset, G., Yasuda, E., Levie, S. E., Bakker, A. Q., Claassen, Y. B., Wagner, K., Böhne, M., Hensbergen, P. J., Speijer, D., Van Helden, P. M., Beaumont, T., Spits, H., & Hazenberg, M. D. (2018). AML-specific cytotoxic antibodies in patients with durable graft-versus-leukemia responses. Blood, 131(1), 131-143. https://doi.org/10.1182/blood-2017-02-768762

Hörandl, E., & Speijer, D. (2018). How oxygen gave rise to eukaryotic sex. Proceedings of the Royal Society B: Biological Sciences, 285(1872), Article 20172706. https://doi.org/10.1098/rspb.2017.2706

Koenis, D. S., Medzikovic, L., van Loenen, P. B., van Weeghel, M., Huveneers, S., Vos, M., Evers-van Gogh, I. J., Van den Bossche, J., Speijer, D., Kim, Y., Wessels, L., Zelcer, N., Zwart, W., Kalkhoven, E., & de Vries, C. J. (2018). Nuclear Receptor Nur77 Limits the Macrophage Inflammatory Response through Transcriptional Reprogramming of Mitochondrial Metabolism. Cell Reports, 24(8), 2127-2140.e7. https://doi.org/10.1016/j.celrep.2018.07.065

Rampanelli, E., Ochodnicky, P., Vissers, J. P. C., Butter, L. M., Claessen, N., Calcagni, A., Kors, L., Gethings, L. A., Bakker, S. J. L., de Borst, M. H., Navis, G. J., Liebisch, G., Speijer, D., van den Bergh Weerman, M. A., Jung, B., Aten, J., Steenbergen, E., Schmitz, G., Ballabio, A., ... Leemans, J. C. (2018). Excessive dietary lipid intake provokes an acquired form of lysosomal lipid storage disease in the kidney. Journal of Pathology, 246(4), 470-484. https://doi.org/10.1002/path.5150

Speijer, D. (2018). Impact Factors, Reads and Real Values. BioEssays, 40(3), Article 1800014. https://doi.org/10.1002/bies.201800014

2017

Huis In 't Veld, R. A. G., Kramer, G., van der Ende, A., Speijer, D., & Pannekoek, Y. (2017). The Hfq regulon of Neisseria meningitidis. FEBS OPEN BIO, 7(6), 777-788. https://doi.org/10.1002/2211-5463.12218

Pannekoek, Y., Huis In 't Veld, R. A. G., Schipper, K., Bovenkerk, S., Kramer, G., Brouwer, M. C., van de Beek, D., Speijer, D., & van der Ende, A. (2017). Neisseria meningitidis Uses Sibling Small Regulatory RNAs To Switch from Cataplerotic to Anaplerotic Metabolism. MBio, 8(2). https://doi.org/10.1128/mBio.02293-16

Pannekoek, Y., Huis In 't Veld, R., Schipper, K., Bovenkerk, S., Kramer, G., Speijer, D., & van der Ende, A. (2017). Regulation of Neisseria meningitidis cytochrome bc1 components by NrrF, a Fur-controlled small noncoding RNA. FEBS OPEN BIO, 7(9), 1302-1315. https://doi.org/10.1002/2211-5463.12266

Speijer, D. (2017). Alternating terminal electron-acceptors at the basis of symbiogenesis: How oxygen ignited eukaryotic evolution. BioEssays, 39(2), Article 1600174. https://doi.org/10.1002/bies.201600174

Speijer, D. (2017). Evolution of peroxisomes illustrates symbiogenesis. BioEssays, 39(9), Article 1700050. https://doi.org/10.1002/bies.201700050

Wisse, L. E., Penning, R., Zaal, E. A., van Berkel, C. G. M., ter Braak, T. J., Polder, E., Kenney, J. W., Proud, C. G., Berkers, C. R., Altelaar, M. A. F., Speijer, D., van der Knaap, M. S., & Abbink, T. E. M. (2017). Proteomic and metabolomic analyses of vanishing white matter mouse astrocytes reveal deregulation of ER functions. Frontiers in Cellular Neuroscience, 11, Article 411. https://doi.org/10.3389/fncel.2017.00411

van Montfort, T., Speijer, D., & Berkhout, B. (2017). Dendritic cells as natural latency reversing agent: A wake-up call for HIV-1. Virulence, 8(8), 1494-1497. https://doi.org/10.1080/21505594.2017.1371898

van der Gulik, P. T. S., Hoff, W. D., & Speijer, D. (2017). In defence of the three-domains of life paradigm. BMC Evolutionary Biology, 17, Article 218. https://doi.org/10.1186/s12862-017-1059-z [details]
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2016

Speijer, D. (2016). Being right on Q: Shaping eukaryotic evolution. Biochemical Journal, 473(22), 4103-4127. https://doi.org/10.1042/BCJ20160647

Speijer, D. (2016). What can we infer about the origin of sex in early eukaryotes? Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1706), Article 20150530. https://doi.org/10.1098/rstb.2015.0530

Verver, D. E., Zheng, Y., Speijer, D., Hoebe, R., Dekker, H. L., Repping, S., Stap, J., & Hamer, G. (2016). Non-SMC Element 2 (NSMCE2) of the SMC5/6 Complex Helps to Resolve Topological Stress. International Journal of Molecular Sciences, 17(11), Article 1782. Advance online publication. https://doi.org/10.3390/ijms17111782 [details]
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ijms-17-01782
ijms-17-01782-s001

Verwer, R. W. H., Sluiter, A. A., Balesar, R. A., Baayen, J. C., Speijer, D., Idema, S., & Swaab, D. F. (2016). Altered Loyalties of Neuronal Markers in Cultured Slices of Resected Human Brain Tissue. Brain Pathology, 26(4), 523-532. https://doi.org/10.1111/bpa.12330

2015

Kramer, G., Woolerton, Y., van Straalen, J. P., Vissers, J. P. C., Dekker, N., Langridge, J. I., Beynon, R. J., Speijer, D., Sturk, A., & Aerts, J. M. F. G. (2015). Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards. PLoS ONE, 10(10), Article e0140097. https://doi.org/10.1371/journal.pone.0140097

Nandal, U. K., Vlietstra, W. J., Byrman, C., Jeeninga, R. E., Ringrose, J. H., van Kampen, A. H. C., Speijer, D., & Moerland, P. D. (2015). Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets. BMC Bioinformatics, 16, Article 25. https://doi.org/10.1186/s12859-015-0455-x [details]
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Candidate prioritization for low-abundant
Supplementary files
Candidate prioritization suppl. 1
Candidate prioritization suppl. 2
Candidate prioritization suppl. 3
Candidate prioritization suppl. 4
Candidate prioritization suppl. 5
Candidate prioritization suppl. 6
Candidate prioritization suppl. 7

Speijer, D. (2015). Birth of the eukaryotes by a set of reactive innovations: New insights force us to relinquish gradual models. BioEssays, 37(12), 1268-1276. https://doi.org/10.1002/bies.201500107

Speijer, D., Lukeš, J., & Eliáš, M. (2015). Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life. Proceedings of the National Academy of Sciences of the United States of America, 112(29), 8827-8834. https://doi.org/10.1073/pnas.1501725112

Stax, M. J., Mouser, E. E. I. M., van Montfort, T., Sanders, R. W., de Vries, H. J. C., Dekker, H. L., Herrera, C., Speijer, D., Pollakis, G., & Paxton, W. A. (2015). Colorectal mucus binds DC-SIGN and inhibits HIV-1 trans-infection of CD4⁺T-lymphocytes. PLoS ONE, 10(3), Article e0122020. https://doi.org/10.1371/journal.pone.0122020 [details]
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Van Der Sluis, R. M., Van Capel, T. M. M., Speijer, D., Sanders, R. W., Berkhout, B., De Jong, E. C., Jeeninga, R. E., & Van Montfort, T. (2015). Dendritic cell type-specific HIV-1 activation in effector T cells: Implications for latent HIV-1 reservoir establishment. AIDS, 29(9), 1003-1014. https://doi.org/10.1097/QAD.0000000000000637

Verwer, R. W. H., Sluiter, A. A., Balesar, R. A., Baaijen, J. C., De Witt Hamer, P. C., Speijer, D., Li, Y., & Swaab, D. F. (2015). Injury Response of Resected Human Brain Tissue in Vitro. Brain Pathology, 25(4), 454-468. https://doi.org/10.1111/bpa.12189

van der Gulik, P. T. S., & Speijer, D. (2015). How amino acids and peptides shaped the RNA world. Life, 5(1), 230-246. https://doi.org/10.3390/life5010230 [details]
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2014

Holt, I. J., Speijer, D., & Kirkwood, T. B. L. (2014). The road to rack and ruin: Selecting deleterious mitochondrial DNA variants. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1646). https://doi.org/10.1098/rstb.2013.0451

Speijer, D. (2014). How the mitochondrion was shaped by radical differences in substrates: What carnitine shuttles and uncoupling tell us about mitochondrial evolution in response to ROS Insights & Perspectives D. Speijer. BioEssays, 36(7), 634-643. https://doi.org/10.1002/bies.201400033

Speijer, D., Manjeri, G. R., & Szklarczyk, R. (2014). How to deal with oxygen radicals stemming from mitochondrial fatty acid oxidation. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1646). https://doi.org/10.1098/rstb.2013.0446

Strang, A. C., Knetsch, M. L. W., Idu, M. M., Bisoendial, R. J., Kramer, G., Speijer, D., Koole, L. H., Stroes, E. S. G., & Rotmans, J. I. (2014). Superior in vivo compatibility of hydrophilic polymer coated prosthetic vascular grafts. Journal of Vascular Access, 15(2), 95-101. Advance online publication. https://doi.org/10.5301/jva.5000166

van der Sluis, R. M., Derking, R., Breidel, S., Speijer, D., Berkhout, B., & Jeeninga, R. E. (2014). Interplay between viral Tat protein and c-Jun transcription factor in controlling LTR promoter activity in different human immunodeficiency virus type I subtypes. Journal of general virology, 95(4), 968-979. https://doi.org/10.1099/vir.0.059642-0

2013

Buhrman, H., van der Gulik, P. T. S., Klau, G. W., Schaffner, C., Speijer, D., & Stougie, L. (2013). A Realistic Model Under Which the Genetic Code is Optimal. Journal of molecular evolution, 77(4), 170-184. Advance online publication. https://doi.org/10.1007/s00239-013-9571-2 [details]

van der Sluis, R. M., van Montfort, T., Pollakis, G., Sanders, R. W., Speijer, D., Berkhout, B., & Jeeninga, R. E. (2013). Dendritic Cell-induced Activation of Latent HIV-1 Provirus in Actively Proliferating Primary T Lymphocytes. PLoS Pathogens, 9(3), Article e1003259. https://doi.org/10.1371/journal.ppat.1003259

2012

Kramer, G., Moerland, P. D., Jeeninga, R. E., Vlietstra, W. J., Ringrose, J. H., Byrman, C., Berkhout, B., & Speijer, D. (2012). Proteomic analysis of HIV-T cell interaction: an update. Frontiers in Microbiology, 3, 240. https://doi.org/10.3389/fmicb.2012.00240

2011

Dekker, N., Van Dussen, L., Hollak, C. E. M., Overkleeft, H., Scheij, S., Ghauharali, K., Van Breemen, M. J., Ferraz, M. J., Groener, J. E. M., Maas, M., Wijburg, F. A., Speijer, D., Tylki-Szymanska, A., Mistry, P. K., Boot, R. G., & Aerts, J. M. (2011). Elevated plasma glucosylsphingosine in Gaucher disease: Relation to phenotype, storage cell markers, and therapeutic response. Blood, 118(16), e118-e127. https://doi.org/10.1182/blood-2011-05-352971

Dekker, N., Voorn-Brouwer, T., Verhoek, M., Wennekes, T., Narayan, R. S., Speijer, D., Hollak, C. E. M., Overkleeft, H. S., Boot, R. G., & Aerts, J. M. F. G. (2011). The cytosolic β-glucosidase GBA3 does not influence type 1 Gaucher disease manifestation. Blood Cells, Molecules, and Diseases, 46(1), 19-26. https://doi.org/10.1016/j.bcmd.2010.07.009

Kwakman, P. H. S., Krijgsveld, J., de Boer, L., Nguyen, L. T., Boszhard, L., Vreede, J., Dekker, H. L., Speijer, D., Drijfhout, J. W., te Velde, A. A., Crielaard, W., Vogel, H. J., Vandenbroucke-Grauls, C. M. J. E., & Zaat, S. A. J. (2011). Native thrombocidin-1 and unfolded thrombocidin-1 exert antimicrobial activity via distinct structural elements. The Journal of Biological Chemistry, 286(50), 43506-43514. https://doi.org/10.1074/jbc.M111.248641 [details]

Speijer, D. (2011). Does constructive neutral evolution play an important role in the origin of cellular complexity? BioEssays, 33(5), 344-349. https://doi.org/10.1002/bies.201100010

Speijer, D. (2011). Oxygen radicals shaping evolution: Why fatty acid catabolism leads to peroxisomes while neurons do without it: FADH₂/NADH flux ratios determining mitochondrial radical formation were crucial for the eukaryotic invention of peroxisomes and catabolic tissue differentiation. BioEssays, 33(2), 88-94. https://doi.org/10.1002/bies.201000097

2010

Hopman, C. T. P., Speijer, D., van den Ende, A., & Pannekoek, Y. (2010). Identification of a novel anti-sigmaE factor in Neisseria meningitidis. BMC Microbiology, 10(1), 164. https://doi.org/10.1186/1471-2180-10-164 [details]
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Kramer, G., Sprenger, R. R., Nessen, M. A., Roseboom, W., Speijer, D., de Jong, L., Teixeira de Mattos, M. J., Back, J. W., & de Koster, C. G. (2010). Proteome-wide alterations in Escherichia coli translation rates upon anaerobiosis. Molecular & Cellular Proteomics, 9(11), 2508-2516. https://doi.org/10.1074/mcp.M110.001826

Kwakman, P. H. S., Te Velde, A. A., De Boer, L., Speijer, D., Vandenbroucke-Grauls, C. M. J. E., & Zaat, S. A. J. (2010). How honey kills bacteria. FASEB Journal, 24(7), 2576-2582. https://doi.org/10.1096/fj.09-150789

2009

Boot, R. G., van Breemen, M. J., Wegdam, W., Sprenger, R. R., de Jong, S., Speijer, D., Hollak, C. E. M., van Dussen, L., Hoefsloot, H. C. J., Smilde, A. K., de Koster, C. G., Vissers, J. P. C., & Aerts, J. M. F. G. (2009). Gaucher disease: a model disorder for biomarker discovery. Expert Review of Proteomics, 6(4), 411-419. https://doi.org/10.1586/epr.09.54 [details]

Middeldorp, J., van den Berge, S. A., Aronica, E., Speijer, D., & Hol, E. M. (2009). Specific human astrocyte subtype revealed by affinity purified GFAP⁺¹ antibody; unpurified serum cross-reacts with neurofilament-L in Alzheimer. PLoS ONE, 4(11), Article e7663. https://doi.org/10.1371/journal.pone.0007663

Pannekoek, Y., Huis In'T Veld, R., Hopman, C. T. P., Langerak, A. A. J., Speijer, D., & Van Der Ende, A. (2009). Molecular characterization and identification of proteins regulated by Hfq in neisseria meningitidis. FEMS Microbiology Letters, 294(2), 216-224. https://doi.org/10.1111/j.1574-6968.2009.01568.x

Stax, M. J., van Montfort, T., Sprenger, R. R., Melchers, M., Sanders, R. W., van Leeuwen, E., Repping, S., Pollakis, G., Speijer, D., & Paxton, W. A. (2009). Mucin 6 in seminal plasma binds DC-SIGN and potently blocks dendritic cell mediated transfer of HIV-1 to CD4⁺ T-lymphocytes. Virology, 391(2), 203-211. https://doi.org/10.1016/j.virol.2009.06.011

Van Munster, B. C., Van Breemen, M. J., Moerland, P. D., Speijer, D., De Rooij, S. E., Pfrommer, C. J., Levi, M., Hollmann, M. W., Aerts, J. M., Zwinderman, A. H., & Korevaar, J. C. (2009). Proteomic profiling of plasma and serum in elderly patients with delirium. Journal of neuropsychiatry and clinical neurosciences, 21(3), 284-291. https://doi.org/10.1176/jnp.2009.21.3.284

2008

Aerts, J. M., van Breemen, M. J., Bussink, A. P., Ghauharali, K., Sprenger, R., Boot, R. G., Groener, J. E., Hollak, C. E., Maas, M., Smit, S., Hoefsloot, H. C., Smilde, A. K., Vissers, J. P. C., de Jong, S., Speijer, D., & de Koster, C. G. (2008). Biomarkers for lysosomal storage disorders: Identification and application as exemplified by chitotriosidase in Gaucher disease. Acta Paediatrica, 97(s457), 7-14. https://doi.org/10.1111/j.1651-2227.2007.00641.x [details]

Bart, A., Van Der Heijden, H. M., Greve, S., Speijer, D., Landman, W. J., & Van Gool, T. (2008). Intragenomic variation in the internal transcribed spacer 1 region of Dientamoeba fragilis as a molecular epidemiological marker. Journal of Clinical Microbiology, 46(10), 3270-3275. https://doi.org/10.1128/JCM.00680-08

Ringrose, J., Jeeninga, R. E., Berkhout, B., & Speijer, D. (2008). Proteomic studies reveal coordinated changes in T-cell expression patterns upon infection with human immunodeficiency virus type 1. Journal of Virology, 82(9), 4320-4330. https://doi.org/10.1128/JVI.01819-07

van Breemen, M. J., Aerts, J. M. F. G., Sprenger, R. R., & Speijer, D. (2008). Potential artefacts in proteome analysis of plasma of Gaucher patients due to protease abnormalities. Clinica chimica acta, 396(1-2), 26-32. https://doi.org/10.1016/j.cca.2008.06.018

van den Bos, T., Speijer, D., Bank, R. A., Brömme, D., & Everts, V. (2008). Differences in matrix composition between calvaria and long bone in mice suggest differences in biomechanical properties and resorption: special emphasis on collagen. Bone, 43(3), 459-468. https://doi.org/10.1016/j.bone.2008.05.009 [details]

2007

Bock, V. D., Speijer, D., Hiemstra, H., & van Maarseveen, J. H. (2007). 1,2,3-Triazoles as peptide bond isosteres: synthesis and biological evaluation of cyclotetrapeptide mimics. Organic & Biomolecular Chemistry, 5(6), 971-975. [details]

Bussink, A. P., Speijer, D., Aerts, J. M. F. G., & Boot, R. G. (2007). Evolution of mammalian chitinase(-like) members of family 18 glycosyl hydrolases. Genetics, 177(2), 959-970. https://doi.org/10.1534/genetics.107.075846

Houterman, P. M., Speijer, D., Dekker, H. L., de Koster, C. G., Cornelissen, B. J. C., & Rep, M. (2007). The mixed proteome of Fusarium oxysporum-infected tomato xylem vessels. Molecular Plant Pathology, 8, 215-221. https://doi.org/10.1111/j.1364-3703.2007.00384.x [details]

van Eijk, M., Scheij, S. S., van Roomen, C. P. A. A., Speijer, D., Boot, R. G., & Aerts, J. M. F. G. (2007). TLR- and NOD2-dependent regulation of human phagocyte-specific chitotriosidase. FEBS Letters, 581(28), 5389-5395. https://doi.org/10.1016/j.febslet.2007.10.039

2006

Naarding, M. A., Dirac, A. M., Ludwig, I. S., Speijer, D., Lindquist, S., Vestman, E. L., Stax, M. J., Geijtenbeek, T. B. H., Pollakis, G., Hernell, O., & Paxton, W. A. (2006). Bile salt-stimulated lipase from human milk binds DC-SIGN and inhibits human immunodeficiency virus type 1 transfer to CD4⁺ T cells. Antimicrobial Agents and Chemotherapy, 50(10), 3367-3374. https://doi.org/10.1128/AAC.00593-06

Rep, M., van der Does, H. C., Meijer, M., Houterman, P. M., Dekker, H. L., Speijer, D., de Koster, C. G., & Cornelissen, B. J. C. (2006). Secrets of xylem colonization- The xylem sap proteome of tomato infected with Fusarium oxysporum IS-MPM1. In C. Quinto, S. Lopes-Lara Sanchez, & O. Geiger (Eds.), Biology of Plant-Microbe Interactions. (pp. 597-601) [details]

Rezaee, F., Casetta, B., Levels, J. H. M., Speijer, D., & Meijers, J. C. M. (2006). Proteomic analysis of high-density lipoprotein. Proteomics, 6(2), 721-730. https://doi.org/10.1002/pmic.200500191

Speijer, D. (2006). Is kinetoplastid pan-editing the result of an evolutionary balancing act? IUBMB LIFE, 58(2), 91-96. https://doi.org/10.1080/15216540600551355

2004

Sprenger, R. R., Speijer, D., Back, J. W., de Koster, C. G., Pannekoek, H., & Horrevoets, A. J. G. (2004). Comparative proteomics of human endothelial cell caveolae and rafts using two-dimensional gel electrophoresis and mass spectrometry. Electrophoresis, 25(1), 156-172. https://doi.org/10.1002/elps.200305675 [details]

2003

Blom, D., Speijer, D., Linthorst, G. E., Donker-Koopman, W. G., Strijland, A., & Aerts, J. M. F. G. (2003). Recombinant enzyme therapy for Fabry disease: absence of editing of human alpha-galactosidase A mRNA. American Journal of Human Genetics, 72, 23-31. https://doi.org/10.1086/345309 [details]
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2002

Meek, B., Back, J. W., Klaren, V. N. A., Speijer, D., & Peek, R. (2002). Conserved Regions of Protein Disulfide Isomerase are Targeted by Natural IgA Antibodies in Humans. International immunology, 14, 1291-1301. https://doi.org/10.1093/intimm/dxf091 [details]

Meek, B., Back, J. W., Klaren, V. N. A., Speijer, D., & Peek, R. (2002). Protein Disulfide Isomerase of Toxoplasma Gondii isTargeted by Mucosal IgA Antibodies in Humans. FEBS Letters, 522, 104-108. https://doi.org/10.1016/S0014-5793(02)02911-3 [details]

Rep, M., Dekker, H. L., Vossen, J. H., de Boer, A., Houterman, P. M., Speijer, D., Back, J. W., de Koster, C. G., & Cornelissen, B. J. C. (2002). Mass spectrometric identification of isoforms of PR proteins in xylem sap of fungus-infected tomato. Plant Physiology, 130, 904-917. https://doi.org/10.1104/pp.007427 [details]

2001

Blom, D., van den Burg, J., Breek, C. K. D., Speijer, D., Muijsers, A. O., & Benne, R. (2001). Cloning and characterization of two guide RNA-binding proteins from mitochondria of Crithidia fasciculata: gBP27, a novel protein, and gBP29, the orthologue of Trypanosoma brucei gBP21. Nucleic Acids Research, 29(14), 2950-2962. https://doi.org/10.1093/nar/29.14.2950 [details]
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2000

Spelbrink, J. N., Toivonen, J. M., Hakkaart, G. A. J., Kurkela, J. M., Cooper, H. M., Lehtinen, S. K., Lecrenier, N., Back, J. W., Speijer, D., Foury, F., & Jacobs, H. T. (2000). In vivo functional analysis of the human mitochondrial DNA polymerase POLG expressed in cultured human cells. The Journal of Biological Chemistry, 275(32), 24815-24828. [details]

1997

Speijer, D., Breek, C. K. D., Muijsers, A. O., Hartog, A. F., Berden, J. A., Albracht, S. P. J., Samyn, B., Van Beeumen, J., & Benne, R. (1997). Characterization of the respiratory chain from cultured Crithidia fasciculata. Molecular and biochemical parasitology, 85(2), 171-186. https://doi.org/10.1016/S0166-6851(96)02823-X [details]
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1996

Speijer, D., Muijsers, A. O., Dekker, H. L., Beek, C. K. D., Albracht, S. P. J., & Benne, R. (1996). Purification and characterization of cytochrome c oxidase from the insect trypanosomatid Crithidia fasciculata. Molecular and biochemical parasitology, 78, 47-59. https://doi.org/10.1016/S0166-6851(96)02603-5 [details]
2022

Speijer, D. (2022). Eukaryotes were shaped by Oxygen. Nature Ecology and Evolution, 6(9), Article 1242. https://doi.org/10.1038/s41559-022-01819-7

2020

Speijer, D. (2020). Bad Faith Reasoning, Predictable Chaos, and the Truth. BioEssays, 42(6), Article 2000040. https://doi.org/10.1002/bies.202000040

2019

Speijer, D. (2019). We Should Not Use the Term “Lamarckian” as It Is Often Used in Opposition to “Darwinian”. BioEssays, 41(9), Article 1900092. https://doi.org/10.1002/bies.201900092

Speijer, D. (2019). Why Does the Web Seem to Bring Out the Best in Science but the Worst in Politics? BioEssays, 41(10), Article 1900134. https://doi.org/10.1002/bies.201900134

2018

Speijer, D. (2018). Response to Ghiselli F et al. (2018). Philosophical Transactions of the Royal Society B: Biological Sciences, 373(1741), Article 20170278. https://doi.org/10.1098/rstb.2017.0278

2017

Speijer, D. (2017). Unmiraculous? Yes. Ancient? Probably not. (Response to DOI 10.1002/bies.201700041). BioEssays, 39(6), Article e201700048. https://doi.org/10.1002/bies.201700048

2014

Speijer, D. (2014). Reconsidering ideas regarding the evolution of peroxisomes: The case for a mitochondrial connection. Cellular and Molecular Life Sciences, 71(13), 2377-2378. https://doi.org/10.1007/s00018-013-1507-x

2012

Speijer, D. (2012). Brains have a gut feeling about fat storage: An overall inverse correlation between fat deposits and brain size in mammals is explained by neurons not burning fat. BioEssays, 34(4), 275-276. https://doi.org/10.1002/bies.201200002

Speijer, D. (2012). Penetrating insights? Frontiers in Microbiology, 3. https://doi.org/10.3389/fmicb.2012.00382

2010

Speijer, D. (2010). Constructive neutral evolution cannot explain current kinetoplastid panediting patterns. Proceedings of the National Academy of Sciences of the United States of America, 107(7), E25. https://doi.org/10.1073/pnas.0909867107

2009

Speijer, D. (2009). Defining numbers in terms of their divisors. Nature, 461(7260), 37. https://doi.org/10.1038/461037c

Stax, M. J., Pollakis, G., Sprenger, R. R., Melchers, M., van Montfort, T., Sanders, R. W., Speijer, D., & Paxton, W. A. (2009). P07-10. Natural compounds in bodily fluids which bind DC-SIGN and prevent HIV-1 capture and transfer to CD4 cells. Retrovirology, 6(SUPPL. 3), P108. Article 1742. https://doi.org/10.1186/1742-4690-6-S3-P108

2008

Speijer, D. (2008). Making sense of scrambled genomes. Science, 319(5865), 901. https://doi.org/10.1126/science.319.5865.901a
2019

van der Gulik, P. T. S. (2019). Considerations in evolutionary biochemistry. [Thesis, externally prepared, Universiteit van Amsterdam]. Institute for Logic, Language and Computation. [details]
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1997

Speijer, D. (1997). RNA editing in mitochondria of trypanosomes: studies on 'edited' and editing proteins. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
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Dr. D. (Dave) Speijer

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