51cg

People

Dr Louie Van de Lagemaat

Dr Louie Van de Lagemaat
Dr Louie Van de Lagemaat
Dr Louie Van de Lagemaat

Bioinformatician

51cg
Office Address
2.26 Institute of Medical Sciences
Foresterhill Campus
Ashgrove Road West
AB25 2ZD

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School/Department
School of Medicine, Medical Sciences and Nutrition

Biography

Louie van de Lagemaat joined the Centre for Genome-Enabled Biology and Medicine as a bioinformatician in October 2021. He completed his PhD in Genetics at the University of British Columbia, Canada in 2006. Subsequent positions focused on diverse subjects, including molecular neuroscience of the mammalian excitatory synapse and developmental and malignant haematopoiesis. He has used varied analytical methods such as linear and mixed effects models and has broad experience with short-read sequencing technologies including ChIP-seq, bulk and low-cell-count RNA-seq, mRNA splicing, ribosomal profiling (Ribo-seq), transcript methylation (meRIP-seq), poly-A tail length (tail-seq) and transcript half-life (SLAM-seq). He has also performed analysis of survival and loss of HLA allele heterozygosity in cancers.

Research

Research Specialisms

  • Genomics
  • Behavioural Biology
  • Bioinformatics

Our research specialisms are based on the Higher Education Classification of Subjects (HECoS) which is , published under the licence.

Publications

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  • Mannose metabolism inhibition sensitizes acute myeloid leukaemia cells to therapy by driving ferroptotic cell death.

    Woodley, K., Dillingh, L., Giotopoulos, G., Madrigal, P., Rattigan, K., Philippe, C., Dembitz, V., Magee, A., Asby, R., van de Lagemaat, L. N., Mapperley, C., James, S., Prehn, J., Tzelepis, K., Rouault-Pierre, K., Vassiliou, G., Kranc, K., Helgason, G. V., Huntly, B., Gallipoli, P.
    Nature Communications, vol. 14, 2132
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [OPEN ACCESS]
    • [ONLINE]

  • Intrinsic function of the peptidylarginine deiminase PADI4 is dispensable for normal haematopoiesis

    Young, C., Russell, J. R., van de Lagemaat, L. N., Lawson, H., Mapperley, C., Kranc, K. R., Christophorou, M. A.
    Open Biology, vol. 11, no. 6, bio059143
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [OPEN ACCESS]

  • CITED2 coordinates key hematopoietic regulatory pathways to maintain the HSC pool in both steady-state hematopoiesis and transplantation

    Lawson, H., van de Lagemaat, L. N., Barile, M., Tavosanis, A., Durko, J., Villacreces, A., Bellani, A., Mapperley, C., Georges, E., Martins-Costa, C., Sepulveda, C., Allen, L., Campos, J., Campbell, K. J., O'Carroll, D., Göttgens, B., Cory, S., Rodrigues, N. P., Guitart, A. V., Kranc, K. R.
    Stem Cell Reports, vol. 16, no. 11, pp. 2784-2797
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [OPEN ACCESS]

  • NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cells

    Codino, A., Turowski, T., van de Lagemaat, L. N., Ivanova, I., Tavosanis, A., Much, C., Auchynnikava, T., Vasiliauskaitė, L., Morgan, M., Rappsilber, J., Allshire, R. C., Kranc, K. R., Tollervey, D., O'Carroll, D.
    iScience, vol. 24, no. 7, pp. 102762
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [OPEN ACCESS]

  • The mRNA m6A reader YTHDF2 suppresses proinflammatory pathways and sustains hematopoietic stem cell function

    Mapperley, C., van de Lagemaat, L. N., Lawson, H., Tavosanis, A., Paris, J., Campos, J., Wotherspoon, D., Durko, J., Sarapuu, A., Choe, J., Ivanova, I., Krause, D. S., von Kriegsheim, A., Much, C., Morgan, M., Gregory, R. I., Mead, A. J., O'Carroll, D., Kranc, K. R.
    Journal of Experimental Medicine, vol. 218, no. 3, e20200829
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [OPEN ACCESS]

  • JMJD6 promotes self-renewal and regenerative capacity of hematopoietic stem cells

    Lawson, H., Sepulveda, C., van de Lagemaat, L. N., Durko, J., Barile, M., Tavosanis, A., Georges, E., Shmakova, A., Timms, P., Carter, R. N., Allen, L., Campos, J., Vukovic, M., Guitart, A. V., Giles, P., O'Shea, M., Vernimmen, D., Morton, N. M., Rodrigues, N. P., Göttgens, B., Schofield, C. J., Lengeling, A., O'Carroll, D., Kranc, K. R.
    Blood Advances, vol. 5, no. 3, pp. 889-899
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Targeting the RNA m6A Reader YTHDF2 Selectively Compromises Cancer Stem Cells in Acute Myeloid Leukemia

    Paris, J., Morgan, M., Campos, J., Spencer, G. J., Shmakova, A., Ivanova, I., Mapperley, C., Lawson, H., Wotherspoon, D. A., Sepulveda, C., Vukovic, M., Allen, L., Sarapuu, A., Tavosanis, A., Guitart, A. V., Villacreces, A., Much, C., Choe, J., Azar, A., van de Lagemaat, L. N., Vernimmen, D., Nehme, A., Mazurier, F., Somervaille, T. C. P., Gregory, R. I., O'Carroll, D., Kranc, K. R.
    Cell stem cell, vol. 25, no. 1, pp. 137-148, e1-.e6
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [OPEN ACCESS]
    • [ONLINE]

  • CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands.

    van de Lagemaat, L. N., Flenley, M., Lynch, M., David, G., Tomlinson, S., Kranc, K., Vernimmen, D.
    Epigenetics & Chromatin, vol. 11, 59
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [OPEN ACCESS]
    • [ONLINE]

  • A combinatorial postsynaptic molecular mechanism converts patterns of nerve impulses into the behavioral repertoire

    Kopanitsa, M. V., van de Lagemaat, L. N., Afinowi, N. O., Strathdee, D. J., Strathdee, K. E., Fricker, D. G., Tuck, E. J., Elsegood, K. A., Croning, M. D. R., Komiyama, N. H., Grant, S. G. N.
    Working Papers: Preprint Papers
    • [ONLINE]
    • [ONLINE] DOI:

  • Synaptic combinatorial molecular mechanisms generate repertoires of innate and learned behavior

    Komiyama, N. H., van de Lagemaat, L. N., Stanford, L. E., Pettit, C. M., Strathdee, D. J., Strathdee, K. E., Fricker, D. G., Tuck, E. J., Elsegood, K. A., Ryan, T. J., Nithianantharajah, J., Skene, N. G., Croning, M. D. R., Grant, S. G. N.
    Working Papers: Preprint Papers
    • [ONLINE]
    • [ONLINE] DOI:

  • Standardized experiments in mutant mice reveal behavioural similarity on 129S5 and C57BL/6J backgrounds

    van de Lagemaat, L. N., Stanford, L. E., Pettit, C. M., Strathdee, D. J., Strathdee, K. E., Elsegood, K. A., Fricker, D. G., Croning, M. D. R., Komiyama, N. H., Grant, S. G. N.
    Genes, Brain, and Behavior, vol. 16, no. 4, pp. 409-418
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Fumarate hydratase is a critical metabolic regulator of hematopoietic stem cell functions

    Guitart, A. V., Panagopoulou, T. I., Villacreces, A., Vukovic, M., Sepulveda, C., Allen, L., Carter, R. N., van de Lagemaat, L. N., Morgan, M., Giles, P., Sas, Z., Gonzalez, M. V., Lawson, H., Paris, J., Edwards-Hicks, J., Schaak, K., Subramani, C., Gezer, D., Armesilla-Diaz, A., Wills, J., Easterbrook, A., Coman, D., So, C. W. E., O'Carroll, D., Vernimmen, D., Rodrigues, N. P., Pollard, P. J., Morton, N. M., Finch, A., Kranc, K. R.
    Journal of Experimental Medicine, vol. 214, no. 3, pp. 719-735
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Psychometric precision in phenotype definition is a useful step in molecular genetic investigation of psychiatric disorders

    Xu, M. K., Gaysina, D., Barnett, J. H., Scoriels, L., van de Lagemaat, L. N., Wong, A., Richards, M., Croudace, T. J., Jones, P. B., LHA Genetics Group
    Translational Psychiatry, vol. 5, no. 6, pp. e593
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Age-related decreased inhibitory vs. excitatory gene expression in the adult autistic brain.

    van de Lagemaat, L. N., Nijhof, B., Bosch, D. G. M., Kohansal-Nodehi, M., Keerthikumar, S., Heimel, J. A.
    Frontiers in Neuroscience, vol. 8, 394
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [ONLINE]

  • Human post-mortem synapse proteome integrity screening for proteomic studies of postsynaptic complexes

    Bayés, ?., Collins, M. O., Galtrey, C. M., Simonnet, C., Roy, M., Croning, M. D. R., Gou, G., van de Lagemaat, L. N., Milward, D., Whittle, I. R., Smith, C., Choudhary, J. S., Grant, S. G. N.
    Molecular brain, vol. 7, 88
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Human cognitive ability is influenced by genetic variation in components of postsynaptic signalling complexes assembled by NMDA receptors and MAGUK proteins

    Hill, W. D., Davies, G., Van De Lagemaat, L. N., Christoforou, A., Marioni, R. E., Fernandes, C. P. D., Liewald, D. C., Croning, M. D. R., Payton, A., Craig, L. C. A., Whalley, L. J., Horan, M., Ollier, W., Hansell, N. K., Wright, M. J., Martin, N. G., Montgomery, G. W., Steen, V. M., Le Hellard, S., Espeseth, T., Lundervold, A. J., Reinvang, I., Starr, J. M., Pendleton, N., Grant, S. G. N., Bates, T. C., Deary, I. J.
    Translational Psychiatry, vol. 4, pp. 1-8
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [ONLINE]
    • [ONLINE]

  • Synaptic scaffold evolution generated components of vertebrate cognitive complexity

    Nithianantharajah, J., Komiyama, N. H., McKechanie, A., Johnstone, M., Blackwood, D. H., Clair, D. S., Emes, R. D., Van De Lagemaat, L. N., Saksida, L. M., Bussey, T. J., Grant, S. G.
    Nature Neuroscience, vol. 16, no. 1, pp. 16-24
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [ONLINE]

  • Comparative study of human and mouse postsynaptic proteomes finds high compositional conservation and abundance differences for key synaptic proteins

    Bayés, A., Collins, M. O., Croning, M. D. R., van de Lagemaat, L. N., Choudhary, J. S., Grant, S. G. N.
    PloS ONE, vol. 7, no. 10, e46683
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • An anatomically comprehensive atlas of the adult human brain transcriptome.

    Hawrylycz, M., Lein, E., Guillozet-Bongaarts, A., Shen, E., Ng, L., Miller, J., van de Lagemaat, L., Smith, K., Ebbert, A., Riley, Z., Abajian, C., Beckmann, C. F., Bernard, A., Bertagnolli, D., Boe, A., Cartagena, P., Chakravarty, M., Chapin, M., Chong, J., Dalley, R., David, D. B., Dang, C., Datta, S., Dee, N., Dolbeare, T., Faber, V., Feng, D., Fowler, D., Goldy, J., Gregor, B., Haradon, Z., Haynor, D., Hohmann, J., Horvath, S., Howard, R., Jeromin, A., Jochim, J., Kinnunen, M., Lau, C., Lazarz, E., Lee, C., Lemon, T., Li, L., Li, Y., Morris, J., Overly, C., Parker, P., Parry, S., Reding, M., Royall, J., Schulkin, J.
    Nature, vol. 489, pp. 391-399
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [ONLINE]

  • De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.

    Kirov, G., Pocklington, A., Holmans, P., Ivanov, D., Ikeda, M., Ruderfer, D. M., Moran, J., Chambert, K., Toncheva, D., Georgieva, L., Grozeva, D., Fjodorova, M., Wollerton, R., Rees, E., Nikolov, I., van de Lagemaat, L., Bayés, ?., Fernandez, E., Olason, P., Böttcher, Y., Komiyama, N., Collins, M. O., choudhary, j., Stefansson, K., Stefansson, H., Grant, S., Purcell, S., Sklar, P., O'Donovan, M. C., Owen, M.
    Molecular Psychiatry, vol. 17, pp. 142-153
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [ONLINE]

  • Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder

    Frank, R. A. W., McRae, A. F., Pocklington, A. J., van de Lagemaat, L. N., Navarro, P., Croning, M. D. R., Komiyama, N. H., Bradley, S. J., Challiss, R. A. J., Armstrong, J. D., Finn, R. D., Malloy, M. P., MacLean, A. W., Harris, S. E., Starr, J. M., Bhaskar, S. S., Howard, E. K., Hunt, S. E., Coffey, A. J., Ranganath, V., Deloukas, P., Rogers, J., Muir, W. J., Deary, I. J., Blackwood, D. H., Visscher, P. M., Grant, S. G. N.
    PloS ONE, vol. 6, no. 4, e19011
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Characterization of the proteome, diseases and evolution of the human postsynaptic density.

    Bayés, ?., van de Lagemaat, L., Collins, M. O., Croning, M., Whittle, I., choudhary, j., Grant, S.
    Nature Neuroscience, vol. 14, pp. 19-21
    Contributions to Journals: Articles
    • [ONLINE] DOI:
    • [ONLINE]

  • Genome variation and complexity in the autism spectrum

    van de Lagemaat, L. N., Grant, S. G. N.
    Neuron, vol. 67, no. 1, pp. 8-10
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Confirmed rare copy number variants implicate novel genes in schizophrenia

    Tam, G. W. C., van de Lagemaat, L. N., Redon, R., Strathdee, K. E., Croning, M. D. R., Malloy, M. P., Muir, W. J., Pickard, B. S., Deary, I. J., Blackwood, D. H. R., Carter, N. P., Grant, S. G. N.
    Biochemical Society Transactions, vol. 38, no. 2, pp. 445-451
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements

    Zhang, Y., Maksakova, I. A., Gagnier, L., van de Lagemaat, L. N., Mager, D. L.
    PLoS Genetics, vol. 4, no. 2, pp. e1000007
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution

    Romanish, M. T., Lock, W. M., van de Lagemaat, L. N., Dunn, C. A., Mager, D. L.
    PLoS Genetics, vol. 3, no. 1, pp. e10
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Transcription of two human genes from a bidirectional endogenous retrovirus promoter

    Dunn, C. A., Romanish, M. T., Gutierrez, L. E., van de Lagemaat, L. N., Mager, D. L.
    Gene, vol. 366, no. 2, pp. 335-342
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line

    Maksakova, I. A., Romanish, M. T., Gagnier, L., Dunn, C. A., van de Lagemaat, L. N., Mager, D. L.
    PLoS Genetics, vol. 2, no. 1, pp. e2
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Multiple effects govern endogenous retrovirus survival patterns in human gene introns

    van de Lagemaat, L. N., Medstrand, P., Mager, D. L.
    Genome Biology, vol. 7, no. 9, pp. R86
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Endogenous retrovirus long terminal repeats as ready-to-use mobile promoters: the case of primate beta3GAL-T5

    Dunn, C. A., van de Lagemaat, L. N., Baillie, G. J., Mager, D. L.
    Gene, vol. 364, pp. 2-12
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates

    van de Lagemaat, L. N., Gagnier, L., Medstrand, P., Mager, D. L.
    Genome Research, vol. 15, no. 9, pp. 1243-1249
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Impact of transposable elements on the evolution of mammalian gene regulation

    Medstrand, P., van de Lagemaat, L. N., Dunn, C. A., Landry, J., Svenback, D., Mager, D. L.
    Cytogenetic and Genome Research, vol. 110, no. 1-4, pp. 342-52
    Contributions to Journals: Review articles
    • [ONLINE] DOI:

  • Multiple groups of endogenous betaretroviruses in mice, rats, and other mammals

    Baillie, G. J., van de Lagemaat, L. N., Baust, C., Mager, D. L.
    Journal of Virology, vol. 78, no. 11, pp. 5784-5798
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions

    van de Lagemaat, L. N., Landry, J., Mager, D. L., Medstrand, P.
    Trends in Genetics, vol. 19, no. 10, pp. 530-536
    Contributions to Journals: Articles
    • [ONLINE] DOI:

  • Retroelement distributions in the human genome: variations associated with age and proximity to genes

    Medstrand, P., van de Lagemaat, L. N., Mager, D. L.
    Genome Research, vol. 12, no. 10, pp. 1483-1495
    Contributions to Journals: Articles
    • [ONLINE] DOI:

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