Publications
My work spans deep multimodal representation learning for multi omics to building virtual cells. Here's a selection of my papers. 🧬
✨ Recent
NeurIPS 2026 · AI4DD WorkshopSpatially Informed and Direction Sensitive Representation Learning for Spatial Transcriptomics
Azim Dehghani Amirabad, Ali Khodabandeh Yalabadi, Artem Moskalev, Yun-Ching Chen, Mehdi Pirooznia, Scott Oloff, Rui Liao
NeurIPS 2026Disentangling Marginal Capacity from Geometry in Optimal-Transport Label Transfer
Ali Khodabandeh Yalabadi, Azim Dehghani Amirabad, Artem Moskalev, Yun-Ching Chen, Mehdi Pirooznia, Scott Oloff, Rui Liao
NeurIPS 2026VCLMU: Mechanism-Centric Virtual Cell World Modeling for Perturbation Response
Yuwei Miao, Azim Dehghani Amirabad, Scott Oloff, Junzhou Huang, Tianyu Cui, Rui Liao
ICML 2026PaSTel: Anchoring Histology in Spatial Transcriptomics via Multi-Scale Hierarchical Bio-Prior Contrastive Pretraining
Azim Dehghani Amirabad, Junchao Zhu, Pushpak Pati, Walid Abdelmoula, Tommaso Mansi, Rui Liao
ICML 2025Multimodal Modeling of CRISPR-Cas12 Activity Using Foundation Models and Chromatin Accessibility Data
Azim Dehghani Amirabad, Yanfei Zhang, Artem Moskalev, Sowmya Rajesh, Tommaso Mansi, Shuwei Li, Mangal Prakash, Rui Liao
📚 Earlier Work
Bioinformatics · ISMB 2019Large-scale inference of competing endogenous RNA networks with sparse partial correlation
Markus List, Azim Dehghani Amirabad, Dennis Kostka, Marcel H. Schulz
BBA Molecular Basis of Disease 2018Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis
Azim Dehghani Amirabad, Pathmanaban Ramasamy, Marina Wierz, Karl Nordström, Sonja M. Kessler, Marcel H. Schulz, Martin Simon
Genome Biology and Evolution 2018More than the Killer Trait: Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host
Katrin Grosser, Pathmanaban Ramasamy, Azim Dehghani Amirabad, Marcel H. Schulz, Gilles Gasparoni, Martin Simon, Martina Schrallhammer
Nucleic Acids Research 2016Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction
F Schmidt, N Gasparoni, G Gasparoni, K Gianmoena, C Cadenas, JK Polansky, P Ebert, KJV Nordström, M Barann, A Sinha, S Fröhler, J Xiong, A Dehghani Amirabad, F Behjati Ardakani, B Hutter, G Zipprich, B Felder, E Jürgen Eils, B Brors, W Chen, JG Hengstler, A Hamann, T Lengauer, P Rosenstiel, J Walter, MH Schulz
Immunity 2016Epigenetic reprogramming in memory formation of human CD4+ T cells
Durek P, Nordström KJV, Gasparoni G, Kressler C, Almeida M, Salhab A, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Amirabad AD, Ardakani FB, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch CD, Hutter B, Zipprich G, Tauchmann Y, Reinke S, Wassilew G, Hoffmann U, Arrigoni L, Richter AS, Sieverling L, Chang HD, Syrbe U, Manke T, Kalus U, Eils J, Brors B, Ruland J, Lengauer T, Rajewsky N, Chen W, Schulz MH, Dong J, Sawitzki B, Chung HR, Rosenstiel P, Schultze JP, Radbruch A, Walter J, Hamann A, Polansky JK
German Conference on Bioinformatics 2016Multitask regression for context-specific prioritization of miRNA targets in transcripts
Azim Dehghani Amirabad, Marcel H. Schulz
DNA Research 2015Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia
M Cheaib, A Dehghani Amirabad, KJV Nordstroem, MH Schulz, M Simon
Apoptosis 2010Attenuation of NF-kB and activation of Nrf2 signaling by 1,2,4-triazine derivatives, protects neuron-like PC12 cells against apoptosis
Tusi SK, Ansari N, Amini M, Amirabad AD, Shafiee A, Khodagholi F
Neurochemistry International 2010Inhibition of LPS-induced apoptosis in differentiated-PC12 cells by new triazine derivatives through NF-kB-mediated suppression of COX-2
Ansari N, Khodagholi F, Ramin M, Amini M, Irannejad H, Dargahi L, Amirabad AD
