Antibody Language Models. Taking the biology seriously makes models better
A Matas Gil, A Tiffeau-Mayer
eLife (2026)

Popular article summarising and contextualising Erick Matsen et al’s work on Separating selection from mutation in antibody language models

Fluctuating environments are sufficient to drive substantial variability in species abundance across locations
J Henderson, A Tiffeau-Mayer
arXiv (2026)

Evolution of T cell responses in the tuberculin skin test reveals generalisable Mtb-reactive T cell metaclones
CT Turner*, A Tiffeau-Mayer*, J Rosenheim, A Chandran, R Saxena, P Zhang, J Jiang, M Berkeley, F Pang, I Uddin, G Nageswaran, S Byrne, A Karthikeyan, W Smidt, P Ogongo, R Byng-Maddick, S Capocci, M Lipman, H Kunst, S Lozewicz, V Rasmussen, G Pollara, JC Knight, A Leslie, BM Chain, M Noursadeghi
Nature Communications (2026)

How different are self and nonself?
A Tiffeau-Mayer*, JA Levine*, CJ Russo, Q Marcou, W Bialek, BD Greenbaum
PRX Life (2026)

Unifying Theories in High-Dimensional Biology. Approaches, Challenges and Opportunities
M Bauer, A Goyal, S Goyal, G Reddy, S Chakrabarti, MM Desai, W Gilpin, J Grilli, K Husain, S Jain, M Kumar Jolly, K Kawaguchi, A Koseska, M Lin, L Narlikar, S Pigolotti, A Raju, K Shrinivas, R Siddarthan, GJ Stephens, A Tiffeau-Mayer, S Vaikuntanathan
npj Systems Biology and Applications (2026)

Temporal Dynamics of Antigen-Specific T Cell Expansion in Primary SARS-CoV-2 Infection
AGT Pyo, A Chan, J Rosenheim, C Thakker, L Bell, G Nageswaran, S Byrne, B Killingley, D Scobie, M Kalinova, A Boyers, A Catchpole, A Mann, RGH Lindeboom, MZ Nikolic, SA Teichmann, H Wagstaffe, M Noursadeghi, C Chiu, CG Callan Jr., A Tiffeau-Mayer, NS Wingreen, B Chain
bioRxiv preprint (2025)

Exploiting TCR Repertoire Analysis to Select Therapeutic TCRs for Cancer Immunotherapy
U Demael, T Rirkkrai, FZ Okus, A Tiffeau-Mayer, H Stauss
Cells (2025)

Data-driven Discovery of Biophysical T Cell Receptor Co-specificity Rules
AGT Pyo, Y Nagano, M Milighetti, J Henderson, CG Callan Jr., B Chain, NS Wingreen, A Tiffeau-Mayer
PRX Life (2025)

Video of Andreas presenting this work (slide 29-31)

Deep profiling of human T cells defines compartmentalized clones and phenotypic trajectories across blood and tonsils
S Sureshchandra, J Henderson, E Levendosky, S Bhattacharyya, JM Kastenschmidt, AM Sorn, M Tabassum Mitul, A Benchorin, K Batucal, A Daugherty, SJH Murphy, C Thakur, D Trask, G Ahuja, Q Zhong, A Moisan, A Tiffeau-Mayer**, N Saligrama**, LE Wagar**
Immunity (2025)

Video of Suhas presenting this work | UC Irvine press release

Contrastive learning of T cell receptor representations
Y Nagano, A Pyo, M Milighetti, J Henderson, J Shawe-Taylor, B Chain*, A Tiffeau-Mayer*
Cell Systems (2025)

Video of Andreas presenting this work at ICTS

Lessons learned from the IMMREP23 TCR-epitope prediction challenge
M Nielsen, A Eugster, MF Jensen, M Goel, A Tiffeau-Mayer, A Pelissier, S Valkiers, M Rodriguez Martinez, B Meynard-Piganeau, V Greiff, T Mora, AM Walczak, G Croce, DL Moreno, D Gfeller, P Meysman, J Barton
Immunoinformatics (2024)

Link to Kaggle competition page

Intra-and inter-chain contacts determine TCR specificity: applying protein co-evolution methods to TCRab pairing
M Milighetti, Y Nagano, J Henderson, U Hershberg, A Tiffeau-Mayer, A-F Bitbol, B Chain
bioRxiv preprint (2024)

Lightning-fast adaptive immune receptor similarity search by symmetric deletion lookup
T Chotisorayuth, A Tiffeau-Mayer
arXiv preprint (2024)

Limits on Inferring T cell Specificity from Partial Information
J Henderson, Y Nagano, M Milighetti, A Tiffeau-Mayer
PNAS (2024)

Popular summary on Kudos

Unbiased estimation of sampling variance for Simpson’s diversity index
A Tiffeau-Mayer
Physical Review E (2024)

Human SARS-CoV-2 challenge uncovers local and systemic response dynamics
RGH Lindeboom*, KB Worlock*, LM Dratva, M Yoshida, D Scobie, HR Wagstaffe, …, M Noursadeghi, B Chain, A Mayer, KB Meyer, C Chiu, MZ Nikolic**, SA Teichmann**
Nature (2024)

Featured by Nature News & Views, the Guardian and others.

Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease
P Mehta*, B Sanz-Magallón Duque de Estrada*, EK Denneny*, K Foster, CT Turner, A Mayer, M Milighetti, M Platé, KB Worlock, M Yoshida, JS Brown, MZ Nikolić, A Nair, BM Chain, M Noursadeghi, RC Chambers**, JC Porter**, GS Tomlinson**
Frontiers in Immunology (2024)

Defining and Studying B Cell Receptor and TCR Interactions
CG Rapazzo, ML Fernandez Quintero, A Mayer, NC Wu, V Greiff, JJ Guthmiller
Journal of Immunology (2023)

Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection
M Milighetti*, Y Peng*, C Tan*, M Mark*, G Nageswaran, S Byrne, T Ronel, T Peacock, A Mayer, A Chandran, J Rosenheim, …, COVIDsortium Investigators, M Noursadeghi, B Chain
iScience (2023)

Featured in news-medical.net

Measures of epitope binding degeneracy from T cell receptor repertoires
A Mayer, CG Callan Jr.
PNAS (2023)

Video of Andreas presenting this work in the iReceptor+ Seminar Series and in Banff

A scaling law in CRISPR repertoire sizes arises from avoidance of autoimmunity
H Chen*, A Mayer*, V Balasubramanian
Current Biology (2022)

Featured in UPenn Today and Genetic Engineering & Biotechnology News. Video of Vijay presenting this work at ICTP-SAIFR

Optimal immune specificity at the intersection of host life history and parasite epidemiology
AE Downie, A Mayer, CJE Metcalf, AL Graham
PloS Comp Bio (2021)

Tregs self-organize into a “computing ecosystem” and implement a sophisticated optimization algorithm for mediating immune response
R Marsland, O Howell, A Mayer, P Mehta
PNAS (2021)

Early life imprints the hierarchy of T cell clone sizes
MG Gaimann, M Nguyen, J Desponds, A Mayer
eLife (2020)

Video of Andreas presenting this work in Oaxaca

Regulation of T cell expansion by antigen presentation dynamics
A Mayer, Y Zhang, AS Perelson, NS Wingreen
PNAS (2019)

Featured in Princeton discovery blog and MedicalXpress. Video of Andreas presenting this work at the Human immunome project webinar

Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex
S Mayer*, J Chen*, D Velmeshev, A Mayer, UZ Eze, A Bhaduri, CE Cunha, D Jung,A Arjun, E Li, B Alvarado, S Wang, N Lovegren, ML Gonzales, L Szpankowski, A Leyrat, JAA West, G Panagiotakos, A Alvarez-Buylla, MF Paredes, TJ Nowakowski, AA Pollen, AR Kriegstein
Neuron (2019)

Featured in Brainpost blog · F1000 recommended

How a well-adapting immune system remembers
A Mayer, V Balasubramanian, AM Walczak**, T Mora**
PNAS (2019)

Video of Aleksandra presenting this work in Bordeaux

Receptor crosstalk improves concentration sensing of multiple ligands
M Carballo-Pacheco*, J Desponds*, T Gavrilchenko*, A Mayer*, R Prizak*, G Reddy*, I Nemenman**, T Mora**
PRE (2019)

Complex restitution behavior and reentry in a cardiac tissue model for neonatal mice
A Mayer, P Bittihn, S Luther
Physiol Rep (2017)

Optimal immune systems. A resource allocation and information processing view of immune defense
A Mayer
PhD thesis (2017)

Transitions in optimal adaptive strategies for populations in fluctuating environments
A Mayer, T Mora, O Rivoire, and AM Walczak
PRE (2017)

Selected as an Editor’s suggestion.

Noisyopt. A Python library for optimizing noisy functions
A Mayer
Journal of Open Source Software (2017)

Population dynamics of immune repertoires
J Desponds, A Mayer, T Mora, and AM Walczak
Book chapter in Mathematical, Computational and Experimental T Cell Immunology (Springer), first appeared as arXiv preprint arXiv:1703.00226 (2017)

Diversity of immune strategies explained by adaptation to pathogen statistics
A Mayer, T Mora, O Rivoire, and AM Walczak
PNAS (2016)

French résumé of this work published in Med Sci (2017) · F1000 recommended · Video of Aleksandra presenting this work @ KITP (from slide 15)

How a well-adapted immune system is organized
A Mayer, V Balasubramanian, T Mora, and AM Walczak
PNAS (2015)

Featured in phys.org medicalxpress · Videos of Aleksandra presenting this work @ ENS (from 38 min 10 s) and @ KITP (to slide 15) · Video of Vijay presenting this work @ ICTS

X-ray standing wave study of Si clusters on a decagonal Al-Co-Ni quasicrystal surface
DP Woodruff, J Ledieu, KRJ Lovelock, RG Jones, A Deyko, LH Wearing, R McGrath, A Chaudhuri, HI Li, SY Su, A Mayer, NA Stanisha, and RD Diehl
PRB (2015)

Quantitative adsorbate structure determination for quasicrystals using X-ray standing waves
RD Diehl, HI Li, SY Su, A Mayer, NA Stanisha, J Ledieu, KRJ Lovelock, RG Jones, A Deyko, LH Wearing, R McGrath, A Chaudhuri, and DP Woodruff
PRL (2014)

A novel method for the extraction of intensity–energy spectra from low-energy electron diffraction patterns
A Mayer, H Salopaasi, K Pussi, and RD Diehl
Comput Phys Commun (2012)

* equal first author contribution, ** equal last author contribution