Lucas Miranda

I am a postdoctoral researcher at EPFL MLBio, directed by Maria Brbić. Previously, I was a postdoctoral researcher at the Max Planck Institute of Biochemistry (MLSB, Karsten Borgwardt). I obtained my PhD in 2024 from the Technical University of Munich (TUM), under the supervision of Bertram Müller-Myhsok. My research focuses on the development of machine learning methods for biochemical and medical informatics problems.

Publications

Single-cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue architecture

C Weiss, LA Brown, L Miranda, P Pellizzoni, S Steigerwald, K Remmert, J Hernandez, K Borgwardt, DE Kleiner, S Ben-Moshe, FA Rosenberger, N Porat-Shliom, M Mann
Nature Metabolism, 2026

Paper

Conformal Prediction with Knowledge Graphs for Reliable Antimicrobial Resistance Detection with MALDI-TOF Mass Spectra

N Corvelo Benz‡, L Miranda‡, D Chen, J Sattler, K Borgwardt
Journal of Computational Biology, 2026

Paper Code

Loss of noradrenergic Fkbp5 disrupts social behavior and norepinephrine dynamics in the basolateral amygdala

J Bordes, L Stont, T Bajaj, S Chang, T Ebert, L Miranda, P Schlegel, M Reinhardt, M Pöhlmann, Y Mecdad, L van Doeselaar, H Yang, V Kovarova, S Mitra, M De Angelis, B Müller-Myhsok, JM Deussing, A Beyeler, NC Gassen, MV Schmidt
bioRxiv, 2025

arXiv

Classification of social behavioral responses in stress and non-stress adult male mice with high precision

JM Restrepo-Lozano, M Teixeira, G Hernandez, L Miranda, A Mahmud, MV Schmidt, C Flores
NPP—Digital Psychiatry and Neuroscience, 2025

Paper

Early detection of ampicillin susceptibility in Enterococcus faecium with MALDI-TOF MS and machine learning

T Pichl, L Miranda, N Wantia, K Borgwardt, J Sattler
bioRxiv, 2025

arXiv

Detecting antimicrobial resistance through MALDI-TOF mass spectrometry with statistical guarantees using conformal prediction

N Corvelo Benz‡, L Miranda‡, D Chen, J Sattler, K Borgwardt
RECOMB, 2025

Page Paper Code

Sex-specific fear acquisition following early life stress is linked to amygdala and hippocampal purine and glutamate metabolism

J Bordes, T Bajaj, L Miranda, L van Doeselaar, L Brix, S Narayan, S Mitra, V Kovarova, MV Schmidt, M Springer, K Kleigrewe, B Müller-Myhsok, N Gassen, MV Schmidt
Communications biology, 2024

Paper

Deep clustering of animal motion tracking data: software development and applications to psychiatric preclinical research

L Miranda
Doctoral thesis, Technical University of Munich (TUM), 2024

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Early life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus

A Kos‡, JP Lopez‡, J Bordes, C de Donno, J Dine, E Brivio, S Karamilhalev, S Gasperoni, A Dick, L Miranda, M Büttner, R Stoffel, C Flachskamm, F Theis, MV Schmidt, A Chen
Science Advances, 2023

Paper

Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information

G Visonà‡, D Duroux‡, L Miranda, E Sukei, Y Li, K Borgwardt, C Oliver
Bioinformatics, 2023

Paper Code

Advancing social behavioral neuroscience by integrating ethology and comparative psychology methods through machine learning

J Bordes, L Miranda, B Müller-Myhsok, MV Schmidt
Neuroscience & Biobehavioral Reviews, 2023

Paper

Automatically annotated motion tracking identifies a distinct social behavioral profile following chronic social defeat stress

J Bordes‡, L Miranda‡, M Reinhardt, S Narayan, J Hartmann, E Newman, LM Brix, L van Doeselaar, C Engelhardt, L Dillmann, S Mitra, K Ressler, B Pütz, F Agakov, B Müller-Myhsok, MV Schmidt
Nature Communications, 2023

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DeepOF: A Python package for supervised and unsupervised pattern recognition in mice motion tracking data

L Miranda, J Bordes, B Pütz, MV Schmidt, B Müller-Myhsok
Journal of Open Source Software, 2023

Page Paper Code

miRNAs associated with endoplasmic reticulum stress and unfolded protein response during decidualization

E Soczewski, JM Murrieta-Coxca, L Miranda, P Fuentes-Zacarías, R Gutiérrez-Samudio, E Grasso, M Martí, C Pérez Leirós, D Morales-Prieto, R Ramhorst
Reproductive BioMedicine Online, 2023

Paper

Increasing resolution in stress neurobiology: from single cells to complex group behaviors

L Miranda‡, J Bordes‡, S Gasperoni, JP Lopez
Stress, 2023

Paper

Systematic review of functional MRI applications for psychiatric disease subtyping

L Miranda, R Paul, B Pütz, N Koutsouleris, B Müller-Myhsok
Frontiers in Psychiatry, 2021

Paper

Comprehensive identification of pathogenic gene variants in patients with neuroendocrine disorders

SA Vishnopolska, MF Mercogliano, MA Camilletti, AH Mortensen, D Braslavsky, A Kaselman, I Bergadá, F Olivieri, L Miranda, R Marino, P Ramírez, N Pérez Garrido, H Patiño Mejia, M Ciaccio, MI Di Palma, A Belgorosky, MA Martí, JO Kitzman, SA Camper, MI Perez-Millán
The Journal of Clinical Endocrinology & Metabolism, 2021

Paper

The transcription factor NF-kB mediates thyrotropin-stimulated expression of thyroid differentiation markers

RC Geyesis, V peyret, M Martín, M Nazar, C Reale, CE Bernal Barquero, L Miranda, MA Martí, P Vito, AM Masini-Repiso, JP Nicola
Thyroid, 2021

Paper