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European Network linking informatics and genomics of helper T cells

Deliverables

Midterm review meeting

Compulsory deliverable

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Publications

Cellular Stress in the Context of an Inflammatory Environment Supports TGF-β-Independent T Helper-17 Differentiation

Author(s): Verena Brucklacher-Waldert, Cristina Ferreira, Marisa Stebegg, Olivier Fesneau, Silvia Innocentin, Julien C. Marie, Marc Veldhoen
Published in: Cell Reports, Issue 19/11, 2017, Page(s) 2357-2370, ISSN 2211-1247
DOI: 10.1016/j.celrep.2017.05.052

ROTS: An R package for reproducibility-optimized statistical testing

Author(s): Tomi Suomi, Fatemeh Seyednasrollah, Maria K. Jaakkola, Thomas Faux, Laura L. Elo
Published in: PLOS Computational Biology, Issue 13/5, 2017, Page(s) e1005562, ISSN 1553-7358
DOI: 10.1371/journal.pcbi.1005562

Follicular T Helper Cells: A New Marker of Type 1 Diabetes Risk?

Author(s): Frank Heuts, Natalie M. Edner, Lucy S.K. Walker
Published in: Diabetes, Issue 66/2, 2017, Page(s) 258-260, ISSN 0012-1797
DOI: 10.2337/dbi16-0062

Regulation of the Germinal Center Response

Author(s): Marisa Stebegg, Saumya D. Kumar, Alyssa Silva-Cayetano, Valter R. Fonseca, Michelle A. Linterman, Luis Graca
Published in: Frontiers in Immunology, Issue 9, 2018, ISSN 1664-3224
DOI: 10.3389/fimmu.2018.02469

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation

Author(s): Ricardo J. Miragaia, Tomás Gomes, Agnieszka Chomka, Laura Jardine, Angela Riedel, Ahmed N. Hegazy, Natasha Whibley, Andrea Tucci, Xi Chen, Ida Lindeman, Guy Emerton, Thomas Krausgruber, Jacqueline Shields, Muzlifah Haniffa, Fiona Powrie, Sarah A. Teichmann
Published in: Immunity, Issue 50/2, 2019, Page(s) 493-504.e7, ISSN 1074-7613
DOI: 10.1016/j.immuni.2019.01.001

Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation

Author(s): Jhuma Pramanik, Xi Chen, Gozde Kar, Johan Henriksson, Tomás Gomes, Jong-Eun Park, Kedar Natarajan, Kerstin B. Meyer, Zhichao Miao, Andrew N. J. McKenzie, Bidesh Mahata, Sarah A. Teichmann
Published in: Genome Medicine, Issue 10/1, 2018, ISSN 1756-994X
DOI: 10.1186/s13073-018-0589-3

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation

Author(s): Johan Henriksson, Xi Chen, Tomás Gomes, Ubaid Ullah, Kerstin B. Meyer, Ricardo Miragaia, Graham Duddy, Jhuma Pramanik, Kosuke Yusa, Riitta Lahesmaa, Sarah A. Teichmann
Published in: Cell, Issue 176/4, 2019, Page(s) 882-896.e18, ISSN 0092-8674
DOI: 10.1016/j.cell.2018.11.044

CTLA-4–mediated transendocytosis of costimulatory molecules primarily targets migratory dendritic cells

Author(s): Vitalijs Ovcinnikovs, Ellen M. Ross, Lina Petersone, Natalie M. Edner, Frank Heuts, Elisavet Ntavli, Alexandros Kogimtzis, Alan Kennedy, Chun Jing Wang, Clare L. Bennett, David M. Sansom, Lucy S. K. Walker
Published in: Science Immunology, Issue 4/35, 2019, Page(s) eaaw0902, ISSN 2470-9468
DOI: 10.1126/sciimmunol.aaw0902

T Cell/B Cell Collaboration and Autoimmunity: An Intimate Relationship

Author(s): Lina Petersone, Natalie M. Edner, Vitalijs Ovcinnikovs, Frank Heuts, Ellen M. Ross, Elisavet Ntavli, Chun J. Wang, Lucy S. K. Walker
Published in: Frontiers in Immunology, Issue 9, 2018, ISSN 1664-3224
DOI: 10.3389/fimmu.2018.01941

Heterochronic faecal transplantation boosts gut germinal centres in aged mice

Author(s): Marisa Stebegg, Alyssa Silva-Cayetano, Silvia Innocentin, Timothy P. Jenkins, Cinzia Cantacessi, Colin Gilbert, Michelle A. Linterman
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-10430-7

RepViz: a replicate-driven R tool for visualizing genomic regions

Author(s): Thomas Faux, Kalle T. Rytkönen, Asta Laiho, Laura L. Elo
Published in: BMC Research Notes, Issue 12/1, 2019, ISSN 1756-0500
DOI: 10.1186/s13104-019-4473-z

Molecular Markers Distinguishing T Cell Subtypes With TSDR Strand-Bias Methylation

Author(s): Ekaterina Minskaia, Barbara C. Saraiva, Maria M. V. Soares, Rita I. Azevedo, Ruy M. Ribeiro, Saumya D. Kumar, Ana I. S. Vieira, João F. Lacerda
Published in: Frontiers in Immunology, Issue 9, 2018, ISSN 1664-3224
DOI: 10.3389/fimmu.2018.02540

Immune Cell Dynamics Unfolded by Single-Cell Technologies

Author(s): Daniel J. Kunz, Tomás Gomes, Kylie R. James
Published in: Frontiers in Immunology, Issue 9, 2018, ISSN 1664-3224
DOI: 10.3389/fimmu.2018.01435

Immunology Driven by Large-Scale Single-Cell Sequencing

Author(s): Tomás Gomes, Sarah A. Teichmann, Carlos Talavera-López
Published in: Trends in Immunology, Issue 40/11, 2019, Page(s) 1011-1021, ISSN 1471-4906
DOI: 10.1016/j.it.2019.09.004

Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation

Author(s): Yi-Ling Chen, Tomas Gomes, Clare S. Hardman, Felipe A. Vieira Braga, Danuta Gutowska-Owsiak, Maryam Salimi, Nicki Gray, David A. Duncan, Gary Reynolds, David Johnson, Mariolina Salio, Vincenzo Cerundolo, Jillian L. Barlow, Andrew N.J. McKenzie, Sarah A. Teichmann, Muzlifah Haniffa, Graham Ogg
Published in: The Journal of Experimental Medicine, Issue 217/3, 2020, ISSN 0022-1007
DOI: 10.1084/jem.20190811

Metabolic pathways in T cell activation and lineage differentiation

Author(s): Luís Almeida, Matthias Lochner, Luciana Berod, Tim Sparwasser
Published in: Seminars in Immunology, Issue 28/5, 2016, Page(s) 514-524, ISSN 1044-5323
DOI: 10.1016/j.smim.2016.10.009