Personal information

Biography

Assistant Professor, Department of Human Genetics, Leiden University Medical Center (Leiden, Netherlands)

Activities

Education and qualifications (2)

Delft University of Technology: Delft, Zuid-Holland, NL

2010-10-17 to 2016-06-23 | PhD (Faculty of Electrical Engineering, Mathematics, and Computer Science)
Education
Source: Self-asserted source
Ahmed Mahfouz

Nile University: Cairo, EG

2008-10-01 to 2010-07-01 | MSc (Communication and Information Technology)
Education
Source: Self-asserted source
Ahmed Mahfouz

Works (50 of 72)

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Page 1 of 2

Integration of mass cytometry and mass spectrometry imaging for spatially resolved single-cell metabolic profiling

Nature Methods
2024-10 | Journal article
Contributors: Joana B. Nunes; Marieke E. Ijsselsteijn; Tamim Abdelaal; Rick Ursem; Manon van der Ploeg; Martin Giera; Bart Everts; Ahmed Mahfouz; Bram Heijs; Noel F. C. C. de Miranda
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Crossref

gsQTL: Associating genetic risk variants with gene sets by exploiting their shared variability

2024-09-16 | Preprint
Contributors: Gerard A. Bouland; Niccolò Tesi; Ahmed Mahfouz; Marcel J.T. Reinders
Source: check_circle
Crossref

SIRV: spatial inference of RNA velocity at the single-cell resolution

NAR Genomics and Bioinformatics
2024-07-02 | Journal article
Contributors: Tamim Abdelaal; Laurens M Grossouw; R Jeroen Pasterkamp; Boudewijn P F Lelieveldt; Marcel J T Reinders; Ahmed Mahfouz
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Crossref

Predicting cell-type-specific exon inclusion in the human brain reveals more complex splicing mechanisms in neurons than glia

2024-03-18 | Preprint
Contributors: Lieke Michielsen; Justine Hsu; Anoushka Joglekar; Natan Belchikov; Marcel J.T. Reinders; Hagen Tilgner; Ahmed Mahfouz
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Crossref
grade
Preferred source (of 2)‎

An integrated single‐cell RNA‐seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptomic and functional types

Journal of Neuroendocrinology
2024-02 | Journal article
Contributors: J. B. Berkhout; D. Poormoghadam; C. Yi; A. Kalsbeek; O. C. Meijer; A. Mahfouz
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Crossref

Integrative learning of disentangled representations from single-cell RNA-sequencing datasets

2023-11-08 | Preprint
Contributors: Claudio Novella-Rausell; D.J.M Peters; Ahmed Mahfouz
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Crossref

snRNA-seq analysis in multinucleated myogenic FSHD cells identifies heterogeneous FSHD transcriptome signatures associated with embryonic-like program activation and oxidative stress-induced apoptosis

2023-10-30 | Other
Contributors: Dongxu Zheng; Annelot Wondergem; Iris Willemsen; Stephen Tapscott; Ahmed Mahfouz; Anita van den Heuvel; Silvere van der Maarel; Judit Balog; Susan Kloet
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Crossref

Integration of Mass Cytometry and Mass Spectrometry Imaging for Spatially Resolved Single Cell Metabolic Profiling

2023-08-30 | Preprint
Contributors: Joana B Nunes; Marieke E Ijsselsteijn; Tamim Abdelaal; Rick Ursem; Manon van der Ploeg; Bart Everts; Ahmed Mahfouz; Bram Heijs; Noel FCC de Miranda
Source: check_circle
Crossref

Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models

Nature Communications
2023-08-15 | Journal article
Contributors: L.G.M. Heezen; T. Abdelaal; M. van Putten; A. Aartsma-Rus; A. Mahfouz; P. Spitali
Source: check_circle
Crossref

An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and functional types

2023-07-19 | Preprint
Contributors: J.B. Berkhout; D. Poormoghadam; C. Yi; A. Kalsbeek; O.C. Meijer; A. Mahfouz
Source: check_circle
Crossref

Single-cell reference mapping to construct and extend cell-type hierarchies

NAR Genomics and Bioinformatics
2023-07-05 | Journal article
Contributors: Lieke Michielsen; Mohammad Lotfollahi; Daniel Strobl; Lisa Sikkema; Marcel J T Reinders; Fabian J Theis; Ahmed Mahfouz
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Crossref

A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery

iScience
2023-06 | Journal article
Contributors: Claudio Novella-Rausell; Magda Grudniewska; Dorien J.M. Peters; Ahmed Mahfouz
Source: check_circle
Crossref

Cell type matching across species using protein embeddings and transfer learning

Bioinformatics
2023-06-30 | Journal article
Contributors: Kirti Biharie; Lieke Michielsen; Marcel J T Reinders; Ahmed Mahfouz
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Crossref

Consequences and opportunities arising due to sparser single-cell RNA-seq datasets

Genome Biology
2023-04-21 | Journal article
Part of ISSN: 1474-760X
Contributors: Gerard A. Bouland; Ahmed Mahfouz; Marcel Reinders
Source: Self-asserted source
Ahmed Mahfouz

Benchmarking Variational AutoEncoders on cancer transcriptomics data

2023-02-10 | Preprint
Contributors: Mostafa Eltager; Tamim Abdelaal; Mohammed Charrout; Ahmed Mahfouz; Marcel J.T. Reinders; Stavros Makrodimitris
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Crossref

Cell type matching across species using protein embeddings and transfer learning

2023-02-01 | Preprint
Contributors: Kirti Biharie; Lieke Michielsen; Marcel J.T. Reinders; Ahmed Mahfouz
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Crossref

scTopoGAN: unsupervised manifold alignment of single-cell data

Bioinformatics Advances
2023-01-05 | Journal article
Contributors: Akash Singh; Kirti Biharie; Marcel J T Reinders; Ahmed Mahfouz; Tamim Abdelaal; Magnus Rattray
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Crossref

Predicting cell population-specific gene expression from genomic sequence

2022-09-08 | Preprint
Contributors: Lieke Michielsen; Marcel J.T. Reinders; Ahmed Mahfouz
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Crossref

Analyzing cell-type-specific dynamics of metabolism in kidney repair

Nature Metabolism
2022-08-25 | Journal article
Contributors: Gangqi Wang; Bram Heijs; Sarantos Kostidis; Ahmed Mahfouz; Rosalie G. J. Rietjens; Roel Bijkerk; Angela Koudijs; Loïs A. K. van der Pluijm; Cathelijne W. van den Berg; Sébastien J. Dumas et al.
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Crossref

Community-driven ELIXIR activities in single-cell omics [version 1; peer review: 2 approved with reservations]

2022-07-29 | Journal article
Part of ISSN: 2046-1402
Contributors: Paulo Czarnewski; Ahmed Mahfouz; Raffaele A. Calogero; Patricia M. Palagi; Laura Portell-Silva; Asier Gonzalez-Uriarte; Charlotte Soneson; Tony Burdett; Barbara Szomolay; Pavankumar Videm et al.
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F1000
grade
Preferred source (of 2)‎

Single-cell reference mapping to construct and extend cell-type hierarchies

2022-07-07 | Preprint
Contributors: Lieke Michielsen; Mohammad Lotfollahi; Daniel Strobl; Lisa Sikkema; Marcel J.T. Reinders; Fabian J. Theis; Ahmed Mahfouz
Source: check_circle
Crossref

A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery

2022-07-04 | Preprint
Contributors: Claudio Novella-Rausell; Magda Grudniewska; Dorien J. M. Peters; Ahmed Mahfouz
Source: check_circle
Crossref

The rise of sparser single-cell RNAseq datasets; consequences and opportunities

2022-05-21 | Preprint
Contributors: Gerard A. Bouland; Ahmed Mahfouz; Marcel J.T. Reinders
Source: check_circle
Crossref

scTopoGAN: unsupervised manifold alignment of single-cell data

2022-04-29 | Preprint
Contributors: Akash Singh; Marcel J.T. Reinders; Ahmed Mahfouz; Tamim Abdelaal
Source: check_circle
Crossref

Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models

2022-03-18 | Preprint
Contributors: L.G.M. Heezen; T. Abdelaal; M. van Putten; A. Aartsma-Rus; A. Mahfouz; P. Spitali
Source: check_circle
Crossref

Single-Cell Transcriptomics Reveals Discrete Steps in Regulatory T Cell Development in the Human Thymus

The Journal of Immunology
2022-01-15 | Journal article
Contributors: Florencia Morgana; Rianne Opstelten; Manon C. Slot; Andrew M. Scott; René A. W. van Lier; Bianca Blom; Ahmed Mahfouz; Derk Amsen
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Crossref

scMoC: single-cell multi-omics clustering

Bioinformatics Advances
2022-01-10 | Journal article
Contributors: Mostafa Eltager; Tamim Abdelaal; Ahmed Mahfouz; Marcel J T Reinders
Source: check_circle
Crossref

Transcriptional and cell type profiles of cortical brain regions showing ultradian cortisol rhythm dependent responses to emotional face stimulation

2022-01-05 | Preprint
Contributors: Philippe C Habets; Konstantinos Kalafatakis; Oleh Dzyubachyk; Steven J.A. van der Werff; Arlin Keo; Jamini Thakrar; Ahmed Mahfouz; Alberto M Pereira; Georgina M Russell; Stafford L Lightman et al.
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Crossref

Single-Cell Transcriptomics Links Loss of Human Pancreatic β-Cell Identity to ER Stress

Cells
2021-12-19 | Journal article
Contributors: Nathalie Groen; Floris Leenders; Ahmed Mahfouz; Amadeo Munoz-Garcia; Mauro J. Muraro; Natascha de Graaf; Ton. J. Rabelink; Rob Hoeben; Alexander van Oudenaarden; Arnaud Zaldumbide et al.
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Crossref
grade
Preferred source (of 2)‎

Differential analysis of binarized single-cell RNA sequencing data captures biological variation

NAR Genomics and Bioinformatics
2021-10-04 | Journal article
Contributors: Gerard A Bouland; Ahmed Mahfouz; Marcel J T Reinders
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Crossref

Intronization enhances expression of S-protein and other transgenes challenged by cryptic splicing

2021-09-15 | Other
Contributors: Kärt Tomberg; Liliana Antunes; YangYang Pan; Jacob Hepkema; Dimitrios A. Garyfallos; Ahmed Mahfouz; Allan Bradley
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Crossref

Timing and localization of myasthenia gravis‐related gene expression

European Journal of Neuroscience
2021-08 | Journal article
Contributors: Dana L. E. Vergoossen; Arlin Keo; Ahmed Mahfouz; Maartje G. Huijbers
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Crossref

SIRV: Spatial inference of RNA velocity at the single-cell resolution

2021-07-26 | Preprint
Contributors: Tamim Abdelaal; Laurens M. Grossouw; R. Jeroen Pasterkamp; Boudewijn P.F. Lelieveldt; Marcel J.T. Reinders; Ahmed Mahfouz
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Crossref

Cingulate networks associated with gray matter loss in Parkinson's disease show high expression of cholinergic genes in the healthy brain

European Journal of Neuroscience
2021-06 | Journal article
Contributors: Arlin Keo; Oleh Dzyubachyk; Jeroen van der Grond; Anne Hafkemeijer; Wilma D.J. van de Berg; Jacobus J. van Hilten; Marcel J.T. Reinders; Ahmed Mahfouz
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Crossref

Molecular characterization of the stress network in individuals at risk for schizophrenia

Neurobiology of Stress
2021-05 | Journal article
Contributors: Mandy Meijer; Arlin Keo; Judith M.C. van Leeuwen; Oleh Dzyubachyk; Onno C. Meijer; Christiaan H. Vinkers; Ahmed Mahfouz
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Crossref

Hierarchical progressive learning of cell identities in single-cell data

Nature Communications
2021-05-14 | Journal article
Contributors: Lieke Michielsen; Marcel J. T. Reinders; Ahmed Mahfouz
Source: check_circle
Crossref

scMoC: Single-Cell Multi-omics clustering

2021-02-25 | Preprint
Contributors: Mostafa Eltager; Tamim Abdelaal; Ahmed Mahfouz; Marcel J.T. Reinders
Source: check_circle
Crossref

Differential dropout analysis captures biological variation in single-cell RNA sequencing data

2021-02-02 | Preprint
Contributors: Gerard A. Bouland; Ahmed Mahfouz; Marcel J.T. Reinders
Source: check_circle
Crossref

Timing and localization of myasthenia gravis-related gene expression

2021-01-06 | Preprint
Contributors: Dana L.E. Vergoossen; Arlin Keo; Ahmed Mahfouz; Maartje G. Huijbers
Source: check_circle
Crossref

SCHNEL: scalable clustering of high dimensional single-cell data

Bioinformatics
2020-12-30 | Journal article
Contributors: Tamim Abdelaal; Paul de Raadt; Boudewijn P F Lelieveldt; Marcel J T Reinders; Ahmed Mahfouz
Source: check_circle
Crossref

Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequencing data analysis

2020-12-12 | Preprint
Contributors: Tamim Abdelaal; Jeroen Eggermont; Thomas Höllt; Ahmed Mahfouz; Marcel J.T. Reinders; Boudewijn P.F. Lelieveldt
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Crossref

SpaGE: Spatial Gene Enhancement using scRNA-seq

Nucleic Acids Research
2020-10-09 | Journal article
Contributors: Tamim Abdelaal; Soufiane Mourragui; Ahmed Mahfouz; Marcel J T Reinders
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Crossref

Untangling biological factors influencing trajectory inference from single cell data

NAR Genomics and Bioinformatics
2020-07-22 | Journal article
Contributors: Mohammed Charrout; Marcel J T Reinders; Ahmed Mahfouz
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Crossref

Transcriptomic signatures associated with regional cortical thickness changes in Parkinson’s disease

2020-06-19 | Preprint
Contributors: Arlin Keo; Oleh Dzyubachyk; Jeroen van der Grond; Jacobus J. van Hilten; Marcel J. T. Reinders; Ahmed Mahfouz
Source: check_circle
Crossref

SpaGE: Spatial Gene Enhancement using scRNA-seq

2020-05-10 | Preprint
Contributors: Tamim Abdelaal; Soufiane Mourragui; Ahmed Mahfouz; Marcel J.T. Reinders
Source: check_circle
Crossref

SCHNEL: Scalable clustering of high dimensional single-cell data

2020-03-31 | Preprint
Contributors: Tamim Abdelaal; Paul de Raadt; Boudewijn P.F. Lelieveldt; Marcel J.T. Reinders; Ahmed Mahfouz
Source: check_circle
Crossref

Hierarchical progressive learning of cell identities in single-cell data

2020-03-29 | Preprint
Contributors: Lieke Michielsen; Marcel J.T. Reinders; Ahmed Mahfouz
Source: check_circle
Crossref

Transcriptomic signatures of brain regional vulnerability to Parkinson’s disease

Communications Biology
2020-03-05 | Journal article
Contributors: Arlin Keo; Ahmed Mahfouz; Angela M. T. Ingrassia; Jean-Pascal Meneboo; Celine Villenet; Eugénie Mutez; Thomas Comptdaer; Boudewijn P. F. Lelieveldt; Martin Figeac; Marie-Christine Chartier-Harlin et al.
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Crossref

Untangling biological factors influencing trajectory inference from single cell data

2020-02-12 | Preprint
Contributors: Mohammed Charrout; Marcel J.T. Reinders; Ahmed Mahfouz
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Crossref

An educational guide for nanopore sequencing in the classroom

PLOS Computational Biology
2020-01-23 | Journal article
Contributors: Alex N. Salazar; Francis Ouellette; Franklin L. Nobrega; Christine Anyansi; Cristian Aparicio-Maldonado; Ana Rita Costa; Anna C. Haagsma; Anwar Hiralal; Ahmed Mahfouz; Rebecca E. McKenzie et al.
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Crossref
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Peer review (17 reviews for 10 publications/grants)

Review activity for Anatomy and embryology. (1)
Review activity for Cell systems. (2)
Review activity for Genome biology. (1)
Review activity for iScience. (1)
Review activity for Nature biotechnology. (2)
Review activity for Nature communications (5)
Review activity for Nature genetics. (2)
Review activity for Nature immunology. (1)
Review activity for Nature methods. (1)
Review activity for Nature protocols (1)