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2026
  • 3' BRB-seq, BRB-seq

Cell-cycle inhibition preserves robust development but rebalances lineages in mouse gastruloids.

Maxine Leonardi, Yves Paychère, Felix Naef.
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2025
  • FLASH-seq, Single-cell FLASH-seq

Local niche-derived immunosuppressive CXCR2+ cells impair antiviral immunity.

Akisawa Satomi, Riho Saito, Tadahaya Mizuno, Hiroki Sugishita, Hideki Ukai, Shigeyuki Shichino, Masashi Yanagisawa, Kouji Matsushima, Yukiko Gotoh, Tomohiko Okazaki.
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2025
  • FLASH-seq, Single-cell FLASH-seq

Molecular determinants of brain-resident CD8+ T cell formation and function. 

Tarek Elmzzahi, Chun-Hsi Su, Mehrnoush Hadaddzadeh Shakiba, Doaa Hamada, DaryaMalko, Maren Koehne, Aleksej Frolov, Teisha Mason, Yuanfang Li, Rebekka Scholz, Collins Osei-Sarpong, Leonie Heyden, Jonas Schulte-Schrepping, Lorenzo Bonaguro, Kristian Haendler, Vassiliki Boussiotis, Annett Halle, Elena De Domenico, Daniel HDGray, Martin Fuhrmann, Zeinab Abdullah, Axel Kallies, Kevin Man, Marc D. Beyer.
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2025
  • Blood BRB-seq, BRB-seq

BioSkel – Towards a Framework for OMICS Applications.

Valentin Beauvais, Clémence Couton Nicolò Tonci, Sébastien, Limet, Lucile Mollet,  Thierry Prazuck and Sophie Robert.
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2025
  • 3' BRB-seq, BRB-seq

MTCH2 modulates CPT1 activity to regulate lipid metabolism of adipocytes.

Wu, C., Wang, T., Ghosh, A. et al.
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2025
  • 3' BRB-seq, BRB-seq

Spermidine Reproduces the Anti-Inflammatory Effects of Intermittent Fasting and Prevents Urate and Calcium Pyrophosphate Crystal-Induced Inflammation.

Pham, C.N., Castelli, F., Finet, F., Leroy, C., Chollet, C., Chirayath, T.W., Moitra, S., Zarka, M., Ostertag, A., Brial, F., Combes, C., Latourte, A., Bardin, T., Fenaille, F., Richette, P. and Ea, H.K.
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2025
  • DRUG-seq, Spheroid DRUG-seq

In Vitro Evaluation of the Safety and Efficacy of Cibisatamab Using Adult Stem Cell-Derived Organoids and Colorectal Cancer Spheroids.

Anstett, V.; Heinzelmann, E.; Piraino, F.; Roch, A.; Chrisnandy, A.; Norkin, M.; Garnier, V.; Homicsko, K.; Hoehnel-Ka, S.; Brandenberg, N.
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2025
  • 3' BRB-seq, BRB-seq

Targeting stemness pathways modulates macrophage polarization and reprograms the tumor microenvironment.

Austeja Butkute, Marius Baltramonaitis, Simona Malmige, Adas Darinskas, Vita Pasukoniene, Agata Mlynska.
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2024
  • 3' DRUG-seq, DRUG-seq

CRIPTO’s multifaceted role in driving aggressive prostate cancer unveiled by in vivo, organoid, and patient data.

Rodrigues Sousa, E., de Brot, S., Zoni, E. et al.
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2024
  • 3' BRB-seq, BRB-seq

Transcriptomic profiling of the response to excess iodide in Keap1 hypomorphic mice reveals new gene-environment interactions in thyroid homeostasis.

Panos G. Ziros, Dionysios V. Chartoumpekis, Ilias Georgakopoulos-Soares, Georgios Psarias, Gerasimos P. Sykiotis.
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2024

Radiana Ferrero, Pernille Yde Rainer, Marie Rumpler, Julie Russeil, Magda Zachara, Joern Pezoldt, Guido van Mierlo, Vincent Gardeux, Wouter Saelens, Daniel Alpern, Lucie Favre, Nathalie Vionnet, Styliani Mantziari, Tobias Zingg, Nelly Pitteloud, Michel Suter, Maurice Matter, Kai-Uwe Schlaudraff, Carles Canto, and Bart Deplancke. A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion.

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2024

Radiana Ferrero, Pernille Yde Rainer, Marie Rumpler, Julie Russeil, Magda Zachara, Joern Pezoldt, Guido van Mierlo, Vincent Gardeux, Wouter Saelens, Daniel Alpern, Lucie Favre, Nathalie Vionnet, Styliani Mantziari, Tobias Zingg, Nelly Pitteloud, Michel Suter, Maurice Matter, Kai-Uwe Schlaudraff, Carles Canto, and Bart Deplancke. A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion.

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2024

Katarina Pinjusic, Giovanna Ambrosini, Joao Lourenco, Nadine Fournier, Christian Iseli, Nicolas Guex, Olga Egorova, Sina Nassiri and Daniel B. Constam. Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING.

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2024
  • 3' BRB-seq, BRB-seq

Sustained Vascular Inflammatory Effects of SARS‑CoV‑2 Spike Protein on Human Endothelial Cells.

Mitra Gultom, Lin Lin,  Camilla Blunk Brandt, Anastasia Milusev,  Alain Despont, Jane Shaw, Yvonne Döring, Yonglun Luo, Robert Rieben.
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2024
  • 3' BRB-seq, BRB-seq

Transcriptional landscape of human keratinocyte models exposed to 60-GHz millimeter-waves.

Catherine Martin, Bertrand Evrard, Frédéric Percevault, Kate Ryder, Thomas Darde, Aurélie Lardenois, Maxim Zhadobov, Ronan Sauleau, Frédéric Chalmel, Yves Le Dréan, Denis Habauzit.
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2024
  • 3' BRB-seq, BRB-seq

Multi‐well plate lid for single‐step pooling of 96 samples for high‐throughput barcode‐based sequencing.

Stéphanie Boder‐Pasche, Mustafa Demir, Sarah Heub, Manon Garzuel, Réal Ischer, Daniel Migliozzi,  Siegfried Graf, Noa Schmid, H. Baris Atakan, Daria Gudkova, Daniel Alpern,  Riccardo Dainese, Bart Deplancke, Gilles Weder
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2023
  • 3' BRB-seq, BRB-seq

CRISPR‑Cas9 genetic screen leads to the discovery of L‑Moses, a KAT2B inhibitor that attenuates Tunicamycin‑mediated neuronal cell death.

Sofa Pavlou, Stefanie Foskolou, Nikolaos Patikas, Sarah F. Field, Evangelia K. Papachristou, Clive D’ Santos, Abigail R. Edwards, Kamal Kishore, Rizwan Ansari, Sandeep S. Rajan, Hugo J. R. Fernandes, Emmanouil Metzakopian.
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2023
  • 3' BRB-seq, BRB-seq

Multiscale physiological responses to nitrogen supplementation of maize hybrids.

Sheng Ying, Brandon Webster, Lina Gomez-Cano, Kiran-Kumar Shivaiah, Qianjie Wang, Linsey Newton, Erich Grotewold, Addie Thompson and Peter K. Lundquist.
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2022
  • 3' BRB-seq, BRB-seq

Imipridones affect tumor bioenergetics and promote cell lineage differentiation in diffuse midline gliomas.

Przystal, J. M., Cianciolo Cosentino, C., Yadavilli, S., Zhang, J., Laternser, S., Bonner, E. R., Prasad, R., Dawood, A. A., Lobeto, N., Chin Chong, W., Biery, M. C., Myers, C., Olson, J. M., Panditharatna, E., Kritzer, B., Mourabit, S., Vitanza, N. A., Filbin, M. G., de Iuliis, G. N., Dun, M. D., Koschmann, C., Cain, J. E., Grotzer, M. A., Waszak, S. M., Mueller, S., & Nazarian, J.
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2022
  • FLASH-seq, Single-cell FLASH-seq

Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.

Hahaut, V., Pavlinic, D., Carbone, W et al.,
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2022
  • 3' BRB-seq, BRB-seq

Time-resolved characterization of the innate immune response in the respiratory epithelium of human, porcine, and bovine during influenza virus infection.

Laloli, L., Licheri, M. F., Probst, L., Licheri, M., Gultom, M., Holwerda, M., V’kovski, P., & Dijkman, R.
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2022
  • 3' BRB-seq, BRB-seq

Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells.

Mouri, K., Guo, M. H., de Boer, C. G., Lissner, M. M., Harten, I. A., Newby, G. A., DeBerg, H. A., Platt, W. F., Gentili, M., Liu, D. R., Campbell, D. J., Hacohen, N., Tewhey, R., & Ray, J. P.
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2022
  • 3' BRB-seq, BRB-seq

Distinct Gene Set Enrichment Profiles in Eosinophilic and Non-Eosinophilic Chronic Rhinosinusitis with Nasal Polyps by Bulk RNA Barcoding and Sequencing.

Ishino, T., Takeno, S., Takemoto, K., Yamato, K., Oda, T., Nishida, M., Horibe, Y., Chikuie, N., Kono, T., Taruya, T., Hamamoto, T., & Ueda, T.
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2022
  • BRB-seq

Profiling the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq.

Hu, T., Todberg, T., Andersen, D., Danneskiold-Samsøe, N. B., Hansen, S. B. N., Kristiansen, K., Ewald, D. A., Brix, S., Rosa, J. C. d., Hoof, I., Skov, L., & Litman, T.
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2022
  • 3' BRB-seq, BRB-seq

Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant.

Hirai, S., Tomimatsu, K., Miyawaki-Kuwakado, A., Takizawa, Y., Komatsu, T., Tachibana, T., Fukushima, Y., Takeda, Y., Negishi, L., Kujirai, T., Koyama, M., Ohkawa, Y., & Kurumizaka, H.
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2022
  • 3' BRB-seq, BRB-seq

Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes.

Lalli, M., Yen, A., Thopte, U., Dong, F., Moudgil, A., Chen, X., Milbrandt, J., Dougherty, Joseph D., & Mitra, Robi D.
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2021
  • 3' BRB-seq, BRB-seq

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression.

Kaya-Çopur, A., Marchiano, F., Hein, M. Y., Alpern, D., Russeil, J., Luis, N. M., Mann, M., Deplancke, B., Habermann, B. H., & Schnorrer, F.
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2021
  • 3' BRB-seq, BRB-seq

Cooperative Blockade of CK2 and ATM Kinases Drives Apoptosis in VHL-Deficient Renal Carcinoma Cells through ROS Overproduction.

Giacosa, S., Pillet, C., Séraudie, I., Guyon, L., Wallez, Y., Roelants, C., Battail, C., Evrard, B., Chalmel, F., Barette, C., Soleilhac, E., Fauvarque, M.-O., Franquet, Q., Sarrazin, C., Peilleron, N., Fiard, G., Long, J.-A., Descotes, J.-L., Cochet, C., & Filhol, O.
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2021
  • 3' BRB-seq, BRB-seq

LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis.

Bast-Habersbrunner, A., Kiefer, C., Weber, P., Fromme, T., Schießl, A., Schwalie, P. C., Deplancke, B., Li, Y., & Klingenspor, M.
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2021
  • 3' BRB-seq, BRB-seq

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

Litovchenko, M., Meireles-Filho, A. C. A., Frochaux, M. V., Bevers, R. P. J., Prunotto, A., Anduaga, A. M., Hollis, B., Gardeux, V., Braman, V. S., Russeil, J. M. C., Kadener, S., dal Peraro, M., & Deplancke, B.
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2021
  • 3' BRB-seq, BRB-seq

Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma.

Christian, W. T., Tiphaine, O.-M., Nava, E., Christian, H., Federico, A. S., Jonathan, N., Dominique, C., Cécile, G., Laurence, M., Sophia, S. W., Shehnaz, K. H., Ioannis, T., Matthias, C., Andri, R., Manuel, B., Matthias, H., Patrick, S., Enos, B., Huldrych, F. G., Pejman, M., Paul, J. M., Charles, S. R., Caroline, B., & Jacques, F.
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2020
  • 3' BRB-seq, BRB-seq

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo.

Liu, J., Frochaux, M., Gardeux, V., Deplancke, B., & Robinson-Rechavi, M.
View Publication
2020
  • 3' BRB-seq, BRB-seq

Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress.

Weger, M., Alpern, D., Cherix, A., Ghosal, S., Grosse, J., Russeil, J., Gruetter, R., de Kloet, E. R., Deplancke, B., & Sandi, C.
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2020
  • 3' BRB-seq, BRB-seq

Classification of four distinct osteoarthritis subtypes with a knee joint tissue transcriptome atlas.

Yuan, C., Pan, Z., Zhao, K., Li, J., Sheng, Z., Yao, X., Liu, H., Zhang, X., Yang, Y., Yu, D., Zhang, Y., Xu, Y., Zhang, Z.-Y., Huang, T., Liu, W., & Ouyang, H.
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2020
  • 3' BRB-seq, BRB-seq

Cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel.

Frochaux, M. V., Bou Sleiman, M., Gardeux, V., Dainese, R., Hollis, B., Litovchenko, M., Braman, V. S., Andreani, T., Osman, D., & Deplancke, B.
View Publication
2019
  • 3' BRB-seq, BRB-seq

Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel.

Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., Hollis, B., & Deplancke, B.
View Publication
2019

Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning.

Li, Y., Schwalie, P. C., Bast-Habersbrunner, A., Mocek, S., Russeil, J., Fromme, T., Deplancke, B., & Klingenspor, M.
View Publication
2019
  • 3' BRB-seq, BRB-seq

Sex-dependent and sex-independent regulatory systems of size variation in natural populations.

Okada, H., Yagi, R., Gardeux, V., Deplancke, B., & Hafen, E.
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2019
  • 3' BRB-seq, BRB-seq

Commensal Gut Bacteria Buffer the Impact of Host Genetic Variants on Drosophila Developmental Traits under Nutritional Stress.

Ma, D., Bou-Sleiman, M., Joncour, P., Indelicato, C.-E., Frochaux, M., Braman, V., Litovchenko, M., Storelli, G., Deplancke, B., & Leulier, F.
View Publication
2018

A stromal cell population that inhibits adipogenesis in mammalian fat depots.

Schwalie, P. C., Dong, H., Zachara, M., Russeil, J., Alpern, D., Akchiche, N., Caprara, C., Sun, W., Schlaudraff, K.-U., Soldati, G., Wolfrum, C., & Deplancke, B.
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