Publications by authors named "Hananeh Aliee"

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Causal machine learning for single-cell genomics.
Alejandro Tejada-Lapuerta, Paul Bertin, Stefan Bauer, Hananeh Aliee, Yoshua Bengio

Nat Genet· April 2025

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Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex.
Christina Koupourtidou, Veronika Schwarz, Hananeh Aliee, Simon Frerich, Judith Fischer-Sternjak

Nat Commun· April 2024

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Smoking increases expression of the SARS-CoV-2 spike protein-binding long ACE2 isoform in bronchial epithelium.
Simon D Pouwels, Maarten van den Berge, Gwenda F Vasse, Wim Timens, Corry-Anke Brandsma, Hananeh Aliee

Respir Res· May 2023

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TDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury.
Alessandro Zambusi, Klara Tereza Novoselc, Saskia Hutten, Sofia Kalpazidou, Christina Koupourtidou, Hananeh Aliee

Nat Neurosci· December 2022

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Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa.
Anne M van der Does, Rashad M Mahbub, Dennis K Ninaber, Senani N H Rathnayake, Wim Timens, Hananeh Aliee

Respir Res· September 2022

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Origin and function of activated fibroblast states during zebrafish heart regeneration.
Bo Hu, Sara Lelek, Bastiaan Spanjaard, Hadil El-Sammak, Mariana Guedes Simões, Hananeh Aliee

Nat Genet· August 2022

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Association of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response.
Elise M A Slob, Alen Faiz, Jos van Nijnatten, Susanne J H Vijverberg, Cristina Longo, Hananeh Aliee

Clin Transl Allergy· August 2022

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Determinants of expression of SARS-CoV-2 entry-related genes in upper and lower airways.
Hananeh Aliee, Florian Massip, Cancan Qi, Maria Stella de Biase, Jos van Nijnatten

Allergy· February 2022

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Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development.
Margaret E Magaletta, Macrina Lobo, Eric M Kernfeld, Hananeh Aliee, Jack D Huey

Nat Commun· January 2022

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Current Smoking Alters Gene Expression and DNA Methylation in the Nasal Epithelium of Patients with Asthma.
Karosham D Reddy, Andy Lan, Ilse M Boudewijn, Senani N H Rathnayake, Gerard H Koppelman, Hananeh Aliee

Am J Respir Cell Mol Biol· October 2021

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Sfaira accelerates data and model reuse in single cell genomics.
David S Fischer, Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Hananeh Aliee

Genome Biol· August 2021

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AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution.
Hananeh Aliee, Fabian J Theis

Cell Syst· July 2021

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Comparison of genome-wide gene expression profiling by RNA Sequencing microarray in bronchial biopsies of COPD patients before and after inhaled corticosteroid treatment: does it provide new insights?
Benedikt Ditz, Jeunard G Boekhoudt, Hananeh Aliee, Fabian J Theis, Martijn Nawijn

ERJ Open Res· April 2021

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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Christoph Muus, Malte D Luecken, Gökcen Eraslan, Lisa Sikkema, Avinash Waghray, Hananeh Aliee

Nat Med· March 2021

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