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27/11/2023

Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer

Journal Pubmed

28/9/2023

Learning single-cell perturbation responses using neural optimal transport

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28/8/2023

DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites

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27/7/2023

Cellular state landscape and herpes simplex virus type 1 infection progression are connected

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10/7/2023

OME-Zarr: a cloud-optimized bioimaging file format with international community support

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5/7/2023

Iterative Indirect Immunofluorescence Imaging (4i) on Adherent Cells and Tissue Sections

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16/6/2023

scROSHI: robust supervised hierarchical identification of single cells

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29/5/2023

Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps

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8/5/2023

Multimodal spatiotemporal phenotyping of human retinal organoid development

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4/4/2023

ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma

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5/8/2022

Multimodal perception links cellular state to decision-making in single cells

Kramer BA, Sarabia Del Castillo J, Pelkmans L.Multimodal perception links cellular state to decision-making in single cells. Science, 377(6606):642-648 (2022)

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31/5/2022

Mechanisms of cellular mRNA transcript homeostasis

Berry S, Pelkmans L. Mechanisms of cellular mRNA transcript homeostasis. Trends in Cell Biology, 32(8):655-668 (2022)

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24/5/2022

Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells

Berry S, Müller M, Rai A, Pelkmans L. Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells. Cell Systems, 3(6):454-470.e15 (2022)

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1/4/2022

Erratum: Publisher Correction: Non-specific adhesive forces between filaments and membraneless organelles

Böddeker TJ, Rosowski KA, Berchtold D, Emmanouilidis L, Han Y, Allain FHT, Style RW, Pelkmans L, Dufresne ER. Erratum: Publisher Correction: Non-specific adhesive forces between filaments and membraneless organelles. Nature Physics, 18, page 601 (2022)

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24/3/2022

Non-specific adhesive forces between filaments and membraneless organelles

Böddeker TJ, Rosowski KA, Berchtold D, Emmanouilidis L, Han Y, Allain FHT, Style RW, Pelkmans L, Dufresne ER. Non-specific adhesive forces between filaments and membraneless organelles. Nature Physics, 18, 571–578 (2022)

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28/1/2022

Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging

John Darby Cole, Jacobo Sarabia del Castillo, Gabriele Gut, Daniel Gonzalez-Bohorquez, Lucas Pelkmans, Sebastian Jessberger. Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging. Elife, 11:e68000 (2022)

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26/8/2021

Establishing standardized immune phenotyping of metastatic melanoma by digital pathology

Bettina Sobottka, Marta Nowak, Anja Laura Frei, Martina Haberecker, Samuel Merki, Tumor Profiler consortium, Mitchell P. Levesque, Reinhard Dummer, Holger Moch & Viktor Hendrik Koelzer. Establishing standardized immune phenotyping of metastatic melanoma by digital pathology. Laboratory Investigation, 101, pages 1561–1570 (2021)

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28/6/2021

High content genome-wide siRNA screen to investigate the coordination of cell size and RNA production

Micha Müller, Merve Avar, Daniel Heinzer, Marc Emmenegger, Adriano Aguzzi, Lucas Pelkmans & Scott Berry. High content genome-wide siRNA screen to investigate the coordination of cell size and RNA production. Scientific Data, 8(1):313 (2021)

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21/1/2021

The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support

Irmisch A, Bonilla X, Chevrier S, Lehmann KV, Singer F, Toussaint NC, Esposito C, Mena J, Milani ES, Casanova R, Stekhoven DJ, Wegmann R, Jacob F, Sobottka B, Goetze S, Kuipers J, Sarabia Del Castillo J, Prummer M, Tuncel MA, Menzel U, Jacobs A, Engler S, Sivapatham S, Frei AL, Gut G, Ficek J, Miglino N; Tumor Profiler Consortium, Aebersold R, Bacac M, Beerenwinkel N, Beisel C, Bodenmiller B, Dummer R, Heinzelmann-Schwarz V, Koelzer VH, Manz MG, Moch H, Pelkmans L, Snijder B, Theocharides APA, Tolnay M, Wicki A, Wollscheid B, Rätsch G, Levesque MP. The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. Cancer Cell, 39(3):288-293 (2021)

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13/3/2020

Liquid droplets in the skin

Rai, Arpan; Pelkmans, Lucas. Liquid droplets in the skin. Science, 367(6483):1193-1194 (2020).

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24/11/2018

A Systems-Level Study Reveals Regulators of Membrane-less Organelles in Human Cells

Berchtold D, Battich N, Pelkmans L. A Systems-Level Study Reveals Regulators of Membrane-less Organelles in Human Cells. Mol Cell 72(6):1035-1049 (2018)

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17/10/2018

Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells

Popovic D, Koch B, Kueblbeck M, Ellenberg J, Pelkmans L. Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells. Cell Syst. 7(4):398-411 (2018)

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3/8/2018

Multiplexed protein maps link subcellular organization to cellular states

Gut G, Herrmann MH, Pelkmans L. Multiplexed protein maps link subcellular organization to cellular states. Science 361, eaar7042 (2018)

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24/7/2018

Hypertonic Stress Causes Cytoplasmic Translocation of Neuronal, but Not Astrocytic, FUS due to Impaired Transportin Function

Hock EM, Maniecka Z, Hruska-Plochan M, Reber S, Laferrière F, Sahadevan M K S, Ederle H, Gittings L, Pelkmans L, Dupuis L, Lashley T, Ruepp MD, Dormann D, Polymenidou M. Hypertonic Stress Causes Cytoplasmic Translocation of Neuronal, but Not Astrocytic, FUS due to Impaired Transportin Function. Cell Rep. 24(4):987-1000 (2018)

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4/7/2018

Kinase-controlled phase transition of membraneless organelles in mitosis

Rai, A. K., Chen, J.-X., Selbach, M. & Pelkmans, L. Kinase-controlled phase transition of membraneless organelles in mitosis. Nature (2018). doi:10.1038/s41586-018-0279-8

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23/1/2018

Large‐scale image‐based profiling of single‐cell phenotypes in arrayed CRISPR‐Cas9 gene perturbation screens

de Groot, R., Lüthi, J., Lindsay, H., Holtackers, R. & Pelkmans, L. Large‐scale image‐based profiling of single‐cell phenotypes in arrayed CRISPR‐Cas9 gene perturbation screens. Mol Syst Biol 14, (2018).

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19/5/2017

Modifiers of prion protein biogenesis and recycling identified by a highly parallel endocytosis kinetics assay.

Ballmer, BA. Moos, R. Liberali, P. Pelkmans, L. Hornemann, S. Aguzzi, A. Modifiers of prion protein biogenesis and recycling identified by a highly parallel endocytosis kinetics assay. J Bio Chem, 292, 8356-8368 (2017)

 

 

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1/10/2016

Post-transcriptional control of executioner caspases by RNA-binding proteins.

Subasic, D. Stoeger, T. Eisenring, S. Matia-González, AM.  Imig, J. Zheng, X. Xiong, L. Gisler, P. Eberhard, R. Holtackers, R. Gerber, AP. Pelkmans, L. Hengartner, MO. Post-transcriptional control of executioner caspases by RNA-binding proteins. Genes Dev. 30, 2213 – 2230 (2016).

 

 

 

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13/7/2016

A Systems Survey of Progressive Host-Cell Reorganization during Rotavirus Infection

Green, V. A. & Pelkmans, L. A Systems Survey of Progressive Host-Cell Reorganization during Rotavirus Infection. Cell Host & Microbe 20, 107–120 (2016).

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10/3/2016

Passive Noise Filtering by Cellular Compartmentalization

Stoeger, T., Battich, N. & Pelkmans, L. Passive Noise Filtering by Cellular Compartmentalization. Cell 164, 1151–1161 (2016).

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17/12/2015

Control of Transcript Variability in Single Mammalian Cells

Battich, N., Stoeger, T. & Pelkmans, L. Control of Transcript Variability in Single Mammalian Cells. Cell 163, 1596–1610 (2015).

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24/8/2015

Trajectories of cell-cycle progression from fixed cell populations

Gut, G., Tadmor, M. D., Pe’er, D., Pelkmans, L. & Liberali, P. Trajectories of cell-cycle progression from fixed cell populations. Nature Methods 12, 951–954 (2015).

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17/6/2015

Sumoylation regulates EXO1 stability and processing of DNA damage

Bologna, S. et al. Sumoylation regulates EXO1 stability and processing of DNA damage. Cell Cycle 14, 2439–2450 (2015).

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25/5/2015

Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour

Frechin, M. et al. Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour. Nature (2015). doi:10.1038/nature14429

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23/5/2015

Computer vision for image-based transcriptomics

Stoeger, T., Battich, N., Herrmann, M. D., Yakimovich, Y. & Pelkmans, L. Computer vision for image-based transcriptomics. Methods 85, 44–53 (2015).

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7/4/2015

Wnt directs the endosomal flux of LDL-derived cholesterol and lipid droplet homeostasis

Scott, C. C. et al. Wnt directs the endosomal flux of LDL-derived cholesterol and lipid droplet homeostasis. EMBO reports 16, 741–752 (2015).

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22/12/2014

Simultaneous analysis of large-scale RNAi screens for pathogen entry

Rämö, P. et al. Simultaneous analysis of large-scale RNAi screens for pathogen entry. BMC genomics 15, 1 (2014).

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2/12/2014

Single-cell and multivariate approaches in genetic perturbation screens

Liberali, P., Snijder, B. & Pelkmans, L. Single-cell and multivariate approaches in genetic perturbation screens. Nature Reviews Genetics (2014). doi:10.1038/nrg3768

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6/11/2014

Coronavirus Cell Entry Occurs through the Endo-/Lysosomal Pathway in a Proteolysis-Dependent Manner

Burkard, C. et al. Coronavirus Cell Entry Occurs through the Endo-/Lysosomal Pathway in a Proteolysis-Dependent Manner. PLoS Pathogens 10,e1004502 (2014).

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5/6/2014

A Hierarchical Map of Regulatory Genetic Interactions in Membrane Trafficking

Liberali, P., Snijder, B. & Pelkmans, L. A Hierarchical Map of Regulatory Genetic Interactions in Membrane Trafficking. Cell 157, 1473–1487 (2014).

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29/5/2014

Large Scale RNAi Reveals the Requirement of Nuclear Envelope Breakdown for Nuclear Import of Human Papillomaviruses

Aydin, I. et al. Large Scale RNAi Reveals the Requirement of Nuclear Envelope Breakdown for Nuclear Import of Human Papillomaviruses. PLoS Pathogens 10, e1004162 (2014).

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25/3/2014

Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens

Franceschini, A. et al. Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proceedings of the National Academy of Sciences 111, 4548–4553 (2014).

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6/10/2013

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

Battich, N., Stoeger, T. & Pelkmans, L. Image-based transcriptomics in thousands of single human cells at single-molecule resolution. Nature Methods10, 1127–1133 (2013).

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6/10/2013

Predicting functional gene interactions with the hierarchical interaction score

Snijder, B., Liberali, P., Frechin, M., Stoeger, T. & Pelkmans, L. Predicting functional gene interactions with the hierarchical interaction score. Nature Methods 10, 1089–1092 (2013).

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14/2/2013

Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling

Wippich, F. et al. Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling. Cell 152, 791–805 (2013).

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7/2/2013

Integrin-Mediated Signaling Induced by Simian Virus 40 Leads to Transient Uncoupling of Cortical Actin and the Plasma Membrane

Stergiou, L. et al. Integrin-Mediated Signaling Induced by Simian Virus 40 Leads to Transient Uncoupling of Cortical Actin and the Plasma Membrane. PLoS ONE 8, e55799 (2013).

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1/12/2012

Towards quantitative cell biology

Liberali, P. & Pelkmans, L. Towards quantitative cell biology. Nature cell biology 14, 1233–1233 (2012).

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25/10/2012

RNAi Screening Reveals Proteasome- and Cullin3-Dependent Stages in Vaccinia Virus Infection

Mercer, J. et al. RNAi Screening Reveals Proteasome- and Cullin3-Dependent Stages in Vaccinia Virus Infection. Cell Reports 2, 1036–1047 (2012).

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24/4/2012

Single-cell analysis of population context advances RNAi screening at multiple levels

Snijder, B. et al. Single-cell analysis of population context advances RNAi screening at multiple levels. Molecular Systems Biology 8, (2012).

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29/3/2012

Using Cell-to-Cell Variability—A New Era in Molecular Biology

Pelkmans, L. Using Cell-to-Cell Variability—A New Era in Molecular Biology. Science 336, 425–426 (2012).

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15/3/2011

RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42

Misselwitz, B. et al. RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42. Molecular Systems Biology 7, (2011).

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12/1/2011

Origins of regulated cell-to-cell variability

Snijder, B. & Pelkmans, L. Origins of regulated cell-to-cell variability. Nature Reviews Molecular Cell Biology 12, 119–125 (2011).

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13/5/2010

Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images

Ruusuvuori, P. et al. Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC bioinformatics 11, 248 (2010).

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24/9/2009

Population context determines cell-to-cell variability in endocytosis and virus infection

Snijder, B. et al. Population context determines cell-to-cell variability in endocytosis and virus infection. Nature 461, 520–523 (2009).

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2/9/2009

CellClassifier: supervised learning of cellular phenotypes

Ramo, P., Sacher, R., Snijder, B., Begemann, B. & Pelkmans, L. CellClassifier: supervised learning of cellular phenotypes. Bioinformatics 25, 3028–3030 (2009).

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22/7/2009

Systems biology of virus infection in mammalian cells

Pelkmans, L. Systems biology of virus infection in mammalian cells. Current Opinion in Microbiology 12, 429–431 (2009).

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15/6/2009

Lucas Pelkmans: Taking it from the top

Short, B. Lucas Pelkmans: Taking it from the top. J Cell Biol 185, 932–933 (2009).

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1/2/2009

Report on EU–USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008)

Aebersold, R. et al. Report on EU–USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008). Molecular Oncology 3,9–17 (2009).

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11/7/2008

Lessons from genetics: interpreting complex phenotypes in RNAi screens

Sacher, R., Stergiou, L. & Pelkmans, L. Lessons from genetics: interpreting complex phenotypes in RNAi screens. Current Opinion in Cell Biology 20,483–489 (2008).

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3/7/2008

Protein Kinases: Starting a Molecular Systems View of Endocytosis

Liberali, P., Rämö, P. & Pelkmans, L. Protein Kinases: Starting a Molecular Systems View of Endocytosis. Annual Review of Cell and Developmental Biology 24, 501–523 (2008).

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13/6/2008

Ameobal Pathogen Mimivirus Infects Macrophages through Phagocytosis

Ghigo, E. et al. Ameobal Pathogen Mimivirus Infects Macrophages through Phagocytosis. PLoS Pathogens 4, e1000087 (2008).

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1/11/2007

Simian Virus 40 Depends on ER Protein Folding and Quality Control Factors for Entry into Host Cells

Schelhaas, M. et al. Simian Virus 40 Depends on ER Protein Folding and Quality Control Factors for Entry into Host Cells. Cell 131, 516–529 (2007).

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12/9/2006

A new paradigm for membrane-organizing and -shaping scaffolds

Bauer, M. & Pelkmans, L. A new paradigm for membrane-organizing and -shaping scaffolds. FEBS Letters 580, 5559–5564 (2006).

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27/6/2006

Systems biology of virus entry in mammalian cells

Damm, E.-M. & Pelkmans, L. Systems biology of virus entry in mammalian cells. Cellular Microbiology 8, 1219–1227 (2006).

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29/8/2005

Assembly and trafficking of caveolar domains in the cell: caveolae as stable, cargo-triggered, vesicular transporters

Tagawa, A. Assembly and trafficking of caveolar domains in the cell: caveolae as stable, cargo-triggered, vesicular transporters. The Journal of Cell Biology 170, 769–779 (2005).

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7/7/2005

Kinase-regulated quantal assemblies and kiss-and-run recycling of caveolae

Pelkmans, L. & Zerial, M. Kinase-regulated quantal assemblies and kiss-and-run recycling of caveolae. Nature 436, 128–133 (2005).

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7/7/2005

Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis

Pelkmans, L. et al. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 436, 78–86 (2005).

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5/7/2005

Secrets of caveolae- and lipid raft-mediated endocytosis revealed by mammalian viruses

Pelkmans, L. Secrets of caveolae- and lipid raft-mediated endocytosis revealed by mammalian viruses. Biochimica et Biophysica Acta (BBA) – Molecular Cell Research 1746, 295–304 (2005).

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5/5/2005

Viruses as probes for systems analysis of cellular signalling, cytoskeleton reorganization and endocytosis

Pelkmans, L. Viruses as probes for systems analysis of cellular signalling, cytoskeleton reorganization and endocytosis. Current Opinion in Microbiology 8, 331–337 (2005).

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24/1/2005

Clathrin- and caveolin-1-independent endocytosis: entry of simian virus 40 into cells devoid of caveolae

Damm, E.-M. Clathrin- and caveolin-1-independent endocytosis: entry of simian virus 40 into cells devoid of caveolae. The Journal of Cell Biology 168,477–488 (2005).

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17/9/2004

Caveolin-stabilized membrane domains as multifunctional transport and sorting devices in endocytic membrane traffic

Pelkmans, L., Bürli, T., Zerial, M. & Helenius, A. Caveolin-stabilized membrane domains as multifunctional transport and sorting devices in endocytic membrane traffic. Cell 118, 767–780 (2004).

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8/9/2004

Echovirus 1 endocytosis into caveosomes requires lipid rafts, dynamin II, and signaling events

Pietiäinen, V. et al. Echovirus 1 endocytosis into caveosomes requires lipid rafts, dynamin II, and signaling events. Molecular biology of the cell 15,4911–4925 (2004).

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19/6/2004

Not just a sink: endosomes in control of signal transduction

Miaczynska, M., Pelkmans, L. & Zerial, M. Not just a sink: endosomes in control of signal transduction. Current Opinion in Cell Biology 16, 400–406 (2004).

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4/8/2003

Insider information: what viruses tell us about endocytosis

Pelkmans, L. & Helenius, A. Insider information: what viruses tell us about endocytosis. Current Opinion in Cell Biology 15, 414–422 (2003).

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19/4/2002

Local Actin Polymerization and Dynamin Recruitment in SV40-Induced Internalization of Caveolae

Pelkmans, L. Local Actin Polymerization and Dynamin Recruitment in SV40-Induced Internalization of Caveolae. Science 296, 535–539 (2002).

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18/4/2001

Caveolar endocytosis of simian virus 40 reveals a new two-step vesicular-transport pathway to the ER

Pelkmans, L., Kartenbeck, J. & Helenius, A. Caveolar endocytosis of simian virus 40 reveals a new two-step vesicular-transport pathway to the ER. Nature cell biology 3, 473–483 (2001).

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15/3/2000

Rabaptin4, a novel effector of the small GTPase rab4a, is recruited to perinuclear recycling vesicles

Nagelkerken, B. et al. Rabaptin4, a novel effector of the small GTPase rab4a, is recruited to perinuclear recycling vesicles. Biochem. J 346, 593–601 (2000).

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24/2/1999

Expression of antibody interferes with disulfide bond formation and intracellular transport of antigen in the secretory pathway

Pelkmans, L. & Helenius, A. Expression of antibody interferes with disulfide bond formation and intracellular transport of antigen in the secretory pathway. Journal of Biological Chemistry 274, 14495–14499 (1999).

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