Contrastive learning of T cell receptor representations
Y Nagano, A Pyo, M Milighetti, J Henderson, J Shaw-Taylor, B Chain*, A Tiffeau-Mayer*
arXiv preprint (2024)

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)

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

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

Unbiased estimation of sampling variance for Simpson’s diversity index
A Tiffeau-Mayer
arXiv preprint (2023)

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

Human SARS-CoV-2 challenge resolves 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**
medRxiv preprint (2023)

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)

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

How different are self and nonself?
A Mayer, CJ Russo, Q Marcou, W Bialek, BD Greenbaum
arXiv preprint (2022)

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 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