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Sanja Vickovic

Assistant professor of biomedical engineering (in the Herbert and Florence Irving Institute for Cancer Dynamics) Core Faculty and Director of Technology Innovation at the New York Genome Center

351 Engineering Terrace
Mail Code: 8904
United States

Tel(212) 854-44460
Email[email protected]

Research Interests

SPATIAL TRANSCRIPTOMICS, COMPUTATIONAL BIOLOGY, MACHINE LEARNING, GENOMICS, CANCER BIOLOGY, AGING

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Sanja Vicković, PhD, is a Core Faculty Member and Director, Technology Innovation Lab, at the New York Genome Center. She holds joint appointments as an Assistant Professor at the Fu Foundation School of Engineering and Applied Science and the Herbert and Florence Irving Institute for Cancer Dynamics at Columbia University, and as a Wallenberg Academy Fellow of the Royal Swedish Academy of Sciences and the Royal Swedish Academy of Engineering Sciences at Uppsala University.

Dr. Vicković is an experienced and accomplished engineer and an inventor of the spatial transcriptomic technology called “Visium” and now commercialized by 10x Genomics. In addition to being a skilled technologist, Dr. Vicković also has training and experience in mathematics and biological sciences. Prior to joining the NYGC in 2022, Dr. Vicković had already collaborated with the NYGC, playing a crucial role in the first demonstration of the application of spatial transcriptomics to a disease model in collaboration with researchers at the NYGC’s Center for Genomics of Neurodegenerative Disease.

Dr. Vicković joined the NYGC from the Broad Institute of MIT and Harvard, where she was a Wallenberg Fellow in Aviv Regev’s lab. She obtained her PhD in Gene Technology from the KTH Royal Institute of Technology, Stockholm.

Research experience
  • Wallenberg Fellow at the Broad Institute of MIT and Harvard, 2017-2022
  • Postdoctoral Fellow, KTH Royal Institute of Technology, 2016-2017

Professional experience
  • Assistant Professor of Biomedical Engineering, Columbia University, 2022-
  • Herbert & Florence Irving Assistant Professor of Cancer Data Research, Irving Institute for Cancer Dynamics, 2022-
  • Wallenberg Academy Fellow at Uppsala University, 2022-

Professional affiliations
  • Wallenberg Academy Fellow with the Royal Academy of Sciences and Royal Academy of Engineering

Honors & awards
  • Wallenberg Academy Fellow,  2022-
  • Wallenberg Fellow for distinguished young Swedish researchers to the Broad Institute of MIT and Harvard, 2017-2022

Selected publications
  • Vickovic S*, Schapiro D, Carlberg K, Lötstedt B, Larsson L, Korotkova M, Hensvold SH, Catrina AI, Sorger PK, Malmström V, Regev A, Ståhl PL. Three-dimensional spatial transcriptomics uncovers cell type dynamics in the human rheumatoid arthritis synovium, Nat. Commun. Bio. 5: 129(2021), doi: https://doi.org/10.1038/s42003-022-03050-3 *Corresponding author
  • Vickovic S*, Lötstedt B, Klughammer J, Segerstolpe Å, Rozenblatt-Rosen O, Regev A. SM-Omics is an automated platform for high-throughput spatial multi-omics, Nat. Commun. 13: 795 (2021), doi: https://doi.org/10.1038/s41467-022-28445-y *Corresponding author
  • Vickovic S*, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL. High-definition spatial transcriptomics arrays for in situ tissue profiling. Nat. Methods. 16: 987-990 (2019), doi: https://doi.org/10.1038/s41592-019-0548-y *Corresponding author
  • Biancalani T, Scalia G, Buffoni L, Avasthi R, Lu Z, Sanger A, Tokcan N, Vanderburg CR, Segerstolpe Å, Zhang M, Avraham-Davidi I, Vickovic S, Nitzan M, Ma S, Subramanian A, Lipinski M, Buenrostro J, Brown NB, Fanelli D, Zhuang X, Macosko EZ, Regev A. Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram. Nat. Methods. 18: 1352-62 (2021), doi: https://doi.org/10.1038/s41592-021-01264-7
  • Maniatis S*, Äijö T*, Vickovic S*, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivová Ž, Saarenpää S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J, Bonneau R, Phatnani H. Spatiotemporal Dynamics of Molecular Pathology in Amyotrophic Lateral Sclerosis, Science. 364, 89-93 (2019), doi: https://doi.org/10.1126/science.aav9776 *Equal contribution
  • Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, Herbst RH, Rogel N, Slyper M, Waldman J, Sud M, Andrews E, Velonias G, Haber AL, Jagadeesh K, Vickovic S, Yao J, Stevens C, Dionne D, Nguyen LT, Villani AC, Hofree M, Creasey EA, Huang H, Rozenblatt-Rosen O, Garber JJ, Khalili H, Desch AN, Daly MJ, Ananthakrishnan AN, Shalek AK, Xavier RJ, Regev A. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. Intra-and inter-cellular rewiring of the human colon during ulcerative colitis, Cell 178, 714-730 (2019), doi: https://doi.org/10.1016/j.cell.2019.06.029
  • Salmén F, Ståhl PL, Mollbrink A, Navarro JF, Vickovic S, Frisén J, Lundeberg J. Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections. Nat. Protoc. 13, 2501–2534 (2018), doi: https://doi.org/10.1038/s41596-018-0045-2
  • Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, Tarish F, Tanoglidi A, Vickovic S, Larsson L, Salmén F, Ogris C, Wallenborg K, Lagergren J, Ståhl P, Sonnhammer E, Helleday T, Lundeberg J.Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nat. Commun. 9, 2419 (2018), doi: https://doi.org/10.1038/s41467-018-04724-5
  • Asp M, Salmén F*, Ståhl PL*, Vickovic S*, Felldin U, Löfling M, Fernandez Navarro J, Maaskola J, Eriksson MJ, Persson B, Corbascio M, Persson H, Linde C, Lundeberg J. Spatial detection of fetal marker genes expressed at low level in adult human heart tissue. Sci. Rep. 7, 12941 (2017), doi: https://doi.org/10.1038/s41598-017-13462-5 *Equal contribution
  • Giacomello S, Salmén F, Terebieniec BK, Vickovic S, Navarro JF, Alexeyenko A, Reimegård J, McKee LS, Mannapperuma C, Bulone V, Ståhl PL, Sundström JF, Street NR, Lundeberg J. Spatially resolved transcriptome profiling in model plant species. Nat. Plants. 3, 17061 (2017), doi: https://doi.org/10.1038/nplants.2017.61
  • Vickovic S, Ståhl PL, Salmén F, Giatrellis S, Westholm JO, Mollbrink A, Navarro JF, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J. Massive and parallel expression profiling using microarrayed single-cell sequencing. Nat. Commun. 7, 13182 (2016), doi: https://doi.org/10.1038/ncomms13182
  • Ståhl PL*, Salmén F*, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 353, 78–82 (2016), doi: https://doi.org/10.1126/science.aaf2403 *Equal contribution
  • Kvastad L, Werne Solnestam B, Johansson E, Nygren AO, Laddach N, Sahlén P, Vickovic S, Bendigtsen SC, Aaserud M, Floer L, Borgen E, Schwind C, Himmelreich R, Latta D, Lundeberg J. Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring. Sci. rep. 5: 1-12 (2015), doi: https://doi.org/10.1038/srep16519
  • Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J, Toward Rare Blood Cell Preservation for RNA Sequencing. J. Mol. Diagn. 17, 352–359 (2015), doi: https://doi.org/10.1016/j.jmoldx.2015.03.009
  • Dezfouli M, Vickovic S, Iglesias MJ, Schwenk JM, Ahmadian A, Parallel barcoding of antibodies for DNA-assisted proteomics. Proteomics. 14, 2432–2436 (2014), doi: https://doi.org/10.1002/pmic.201400215
  • Dezfouli M*, Vickovic S*, Iglesias MJ, Nilsson P, Schwenk JM, Ahmadian A. Magnetic bead assisted labeling of antibodies at nanogram scale. Magnetic bead assisted labeling of antibodies at nanogram scale. Proteomics. 14, 14–18 (2014), doi: https://doi.org/10.1002/pmic.201300283 *Equal contribution
  • Gršković B, Zrnec D, Vicković S, Popović M, Mršić G, DNA methylation: the future of crime scene investigation? Mol. Biol. Rep. 40, 4349–4360 (2013), doi: https://doi.org/10.1007/s11033-013-2525-3

Pre-prints

  • Baker E, Schapiro D*, Dumitrascu B, Vickovic S*, Regev A*. Power analysis for spatial omics. bioRxiv (2022), doi: https://doi.org/10.1101/2022.01.26.477748 *Corresponding author
  • Äijö T*, Maniatis S*, Vickovic S*, Kang K, Cuevas M, Braine C, Phatnani H, Lundeberg J, Bonneau R. Splotch: Robust estimation of aligned spatial temporal gene expression data, bioRxiv (2019), doi: https://doi.org/10.1101/757096 *Equal contribution
  • Salmén F*, Vickovic S*, Larsson L, Stenbeck L, Vallon-Christersson J, Ehinger A, Häkkinen J, Borg Å, Frisén J, Ståhl PL, Lundeberg J. Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors. bioRxiv (2018), doi: https://doi.org/10.1101/358937 *Equal contribution