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Publications


publication

 

immunology online

 

immunology journal

 

 

 

Dissemination and research output

QuanTI researchers will report on their progress at network meetings and training events, and produce reports for management and host institutions when required. They will also disseminate their research results to wider audiences by giving presentations at various conferences, writing scientific articles for conference proceedings and international journals, and in the case of ESRs, producing final theses, which will be publicly available. Outreach activities will also be carried out.

 


Publications

All QuanTI related publications will reference the ITN as follows:

"The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 317040 (QuanTI)".


Fundamental properties of unperturbed haematopoiesis from stem cells in vivo
Katrin Busch, Kay Klapproth, Melania Barile, Michael Flossdorf, Tim Holland-Letz, Susan M. Schlenner, Michael Reth, Thomas Höfer & Hans-Reimer Rodewald

Nature 518, 542–546, 11 February 2015
http://dx.doi.org/10.1038/nature14242
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A pharma perspective on the systems medicine and pharmacology of inflammation
Lahoz-Beneytez, J., Schnizler, K., & Eissing, T.

Mathematical Biosciences, 260, 2-5, 1 February 2015
http://dx.doi.org/10.1016/j.mbs.2014.07.006
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Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach
Daniel J. Laydon, Charles R. M. Bangham, Becca Asquith

Philosophical Transactions B, 370 (1675), 2014.0291, 19 August 2015
http://dx.doi.org/10.1098/rstb.2014.0291
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Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments
Raya Ahmed, Liset Westera, Julia Drylewicz, Marjet Elemans, Yan Zhang, Elizabeth Kelly, Rajko Reljic, Kiki Tesselaar, Rob J. de Boer, Derek C. Macallan, José A. M. Borghans, Becca Asquith

PLoS Computational Biology, 11 (10): e1004355, 5 October 2015
http://dx.doi.org/10.1371/journal.pcbi.1004355
PDF file


HIV-1 CCR5 gene therapy will fail unless it is combined with a suicide gene
Aridaman Pandit and Rob J. de Boer

Scientific Reports, 5: 18088, 1 November 2016.
http://dx.doi.org/10.1038/srep18088
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LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins
Yaxuan Yu, Rhodri Ceredig, and Cathal Seoighe

Nucleic Acids Research 44 (4): e31, 29 February 2016
http://dx.doi.org/10.1093/nar/gkv1016
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The memory of a killer T cell: models of CD8$^+$ T cell differentiation
Bram Gerritsen and Aridaman Pandit

Immunology and Cell Biology, 94, 236-241, 1 March 2016
http://dx.doi.org/10.1038/icb.2015.118
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BIITE: A tool to determine HLA class II epitopes from T cell ELISpot data
Lies Boelen, Patrick K. O’Neill, Kathryn J. Quigley, Catherine J. Reynolds, Bernard Maillere, John H. Robinson, Ganjana Lertmemongkolchai, Daniel M. Altmann, Rosemary J. Boyton, Becca Asquith

PLoS Computational Biology, 12 (3): e1004796, 8 March 2016
http://dx.doi.org/10.1371/journal.pcbi.1004796
PDF file


Stem-cell dynamics and lineage topology from in vivo fate mapping in the hematopoietic system
Thomas Höfer, Melania Barile, Michael Flossdorf

Current Opinion in Biotechnology, 39: 150-156, 1 June 2016
http://dx.doi.org/10.1016/j.copbio.2016.04.001
http://www.sciencedirect.com/science/article/pii/S0958166916301094
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Human neutrophil kinetics: modeling of stable isotope labeling data supports short blood neutrophil half-lives
Julio Lahoz-Beneytez, Marjet Elemans, Yan Zhang, Raya Ahmed, Arafa Salam, Michael Block, Christoph Niederalt, Becca Asquith, and Derek Macallan

Blood, 2016, 127: 3431-3438, 30 June 2016
http://dx.doi.org/10.1182/blood-2016-03-700336
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RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data
Bram Gerritsen, Aridaman Pandit, Arno C. Andeweg and Rob J. de Boer

Bioinformatics, 2016, 32 (20): 3098-3106, 15 October 2016
http://dx.doi.org/10.1093/bioinformatics/btw339
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T-cell stimuli independently sum to regulate an inherited clonal division fate
J. M. Marchingo, G. Prevedello, A. Kan, S. Heinzel, P. D. Hodgkin, and K. R. Duffy

Nature Communications, 2016, 7, 13540, 21 November 2016.
http://dx.doi.org/10.1038/ncomms13540
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Stochastic descriptors to study the fate and potential of naive T cell clonotypes in the periphery
J. R. Artalejo; A. Gómez Corral; M. López García; C. Molina París

Journal of Mathematical Biology, 1 February 2017, Volume 74, Issue 3, pp 673–708
http://dx.doi.org/10.1007/s00285-016-1020-6
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A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data Yaxuan Yu, Rhodri Ceredig and Cathal Seoighe

Journal of Immunology, 1 March 2017, 198 (5) 2202-2210.
https://doi.org/10.4049/jimmunol.1601710
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Human T Cell Memory: A Dynamic View
Derek C. Macallan, José A. M. Borghans and Becca Asquith

Vaccines 2017, 5(1), 5, 1 March 2017.
http://doi:10.3390/vaccines5010005
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Physiologically Based Simulations of Deuterated Glucose for Quantifying Cell Turnover in Humans
Julio Lahoz-Beneytez, Stephan Schaller, Derek Macallan, Thomas Eissing, Christoph Niederalt and Becca Asquith

Frontiers in Immunology, 2017, 8:474, pages 1-11, 25 April 2017.
http://dx.doi.org/10.3389/fimmu.2017.00474
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A new mechanism shapes the naïve CD8+ T cell repertoire: the selection for full diversity
Pedro Gonçalves, Marco Ferrarini, Carmen Molina-Paris, Grant Lythe, Florence Vasseura, Annik Lima, Benedita Rocha, and Orly Azoguib

Molecular Immunology Volume 85, 1 May 2017, Pages 66–80
http://dx.doi.org/10.1016/j.molimm.2017.01.026
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Sampling from T Cell Receptor Repertoires
Marco Ferrarini, Carmen Molina-París, Grant Lythe

Book chapter in Modeling Cellular Systems, Volume 11 of the series Contributions in Mathematical and Computational Sciences, pp 67-79, 09 May 2017
http://dx.doi.org/10.1007/978-3-319-45833-5_3


IL-2 Stimulation of Regulatory T Cells: A Stochastic and Algorithmic Approach
Luis de la Higuera, Martín López-García, Grant Lythe, Carmen Molina-París

Book chapter in Modeling Cellular Systems, Volume 11 of the series Contributions in Mathematical and Computational Sciences, pp 81-105, 09 May 2017
http://dx.doi.org/10.1007/978-3-319-45833-5_4


The fate and lifespan of human monocyte subsets in steady state and systemic inflammation
Amit A. Patel, Yan Zhang, James N. Fullerton, Lies Boelen, Anthony Rongvaux, Alexander A. Maini, Venetia Bigley, Richard A. Flavell, Derek W. Gilroy, Becca Asquith, Derek Macallan, and Simon Yona

Journal of Experimental Medicine, 2017, 214 no. 7 1913-1923
http://dx.doi.org/10.1084/jem.20170355
PDF file

 


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Publications related to work carried out in the QuanTI network

The Branching Point in Erythro-Myeloid Differentiation
Leïla Perié, Ken R. Duffy, Lianne Kok, Rob J. de Boer, Ton N. Schumacher

Cell, 163 (7), 17 December 2015, 1655–1662


A Sigmoid Functional Response Emerges When Cytotoxic T Lymphocytes Start Killing Fresh Target Cells
Saikrishna Gadhamsetty, Athanasius F.M. Marée, Joost B. Beltman, Rob J. de Boer

Biophysical Journal Volume 112, Issue 6, 28 March 2017, Pages 1221–1235



 

 

 

Associated partners
Universidade de Vigo

QuanTI Network, 2013 | School of Maths | University of Leeds, UK | Email: quanti-admin@leeds.ac.uk | Copyright | Privacy Statement |

Last update: 11 June 2017