All Publications

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Preprints

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

Gerard Bouland, Niccolo Tesi, Ahmed Mahfouz*, Marcel J.T. Reinders*
bioRxiv | preprint | software

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

Lieke Michielsen, Justine Hsu, Anoushka Joglekar, Natan Belchikov, Marcel J.T. Reinders, Hagen Tilgner*, Ahmed Mahfouz*
bioRxiv | preprint | code

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

Claudio Novella-Rausell, D.J.M Peters, Ahmed Mahfouz
bioRxiv | preprint | code

Single-cell RNA sequencing data reveals rewiring of transcriptional relationships in Alzheimer’s Disease associated with risk variants

Gerard A. Bouland, Kevin I. Marinus, Ronald E. van Kesteren, August B. Smit, Ahmed Mahfouz*, Marcel J.T. Reinders*
medRxiv | preprint

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

Kärt Tomberg, Liliana Antunes, YangYang Pan, Jacob Hepkema, Dimitrios A. Garyfallos, Ahmed Mahfouz, Allan Bradley
bioRxiv | preprint | code

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

Tamim Abdelaal, Jeroen Eggermont, Thomas Höllt, Ahmed Mahfouz, Marcel J.T. Reinders, Boudewijn P.F. Lelieveldt
bioRxiv | preprint | software

Preprints | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014

2024

Combined plasma protein and memory T cell profiling discern IBD-patient-immunotypes related to intestinal disease and treatment outcomes

Maud Heredia*, Mohammed Charrout*, Renz C.W. Klomberg, Martine A. Aardoom, Maria M.E. Jongsma, Polychronis Kemos, Danielle H. Hulleman-van Haaften, Bastiaan Tuk, Lisette A. van Berkel, Brenda Bley Folly, Beatriz Calado, Sandrine Nugteren, Ytje Simons-Oosterhuis, Michail Doukas, Mathijs A. Sanders, Gregory van Beek, Frank M. Ruemmele, Nicholas M. Croft, Ahmed Mahfouz, Marcel J.T. Reinders, Johanna C. Escher, Lissy de Ridder, Janneke N. Samsom
Mucosal Immunology | journal | data

Identification of kidney cell types in scRNA-seq and snRNA-seq data using machine learning algorithms

Adam Tisch, Siddharth Madapoosi, Stephen Blough, Jan Rosa, Sean Eddy, Laura Mariani, Abhijit Naik, Christine Limonte, Philip McCown, Rajasree Menon, Sylvia E. Rosas, Chirag R. Parikh, Matthias Kretzler, Ahmed Mahfouz, Fadhl Alakwaa, Kidney Precision Medicine Project (KPMP)
Heliyon | journal | code

Activated CD27+PD-1+ CD8 T cells and CD4 Tregs dominate the tumor microenvironment in Refractory Celiac Disease type II

Tessa Dieckman, Mette Schreurs, Ciska Lindelauf, Ahmed Mahfouz, Caroline R. Meijer, Louise Pigeaud, Vincent van Unen, Gerd Bouma, Frits Koning
Gastro Hep Advances | journal

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

Joana B Nunes, Marieke Erica Ijsselsteijn, Tamim Abdelaal, Rick Ursem, Manon van der Ploeg, Martin Giera, Bart Everts, Ahmed Mahfouz, Bram Heijs, Noel de Miranda
Nature Methods | journal | data & code

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

Tamim Abdelaal, Boudewijn Lelieveldt, Marcel Reinders, Ahmed Mahfouz
NAR Genomics and Bioinformatics | journal | code

Predicting cell population-specific gene expression from genomic sequence

Lieke Michielsen, Marcel J.T. Reinders, Ahmed Mahfouz
Front. Bioinform. | journal | code

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

Jari B. Berkhout*, Delaram Poormoghadam*, Chun-Xia Yi, Andries Kalsbeek, Onno C. Meijer*, Ahmed Mahfouz*
Journal of Neuroendocrinology | journal | code | data

Preprints | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014

2023

scTopoGAN: unsupervised manifold alignment of single-cell data

Akash Singh, Kirti Biharie, Marcel J.T. Reinders, Ahmed Mahfouz, Tamim Abdelaal
Bioinformatics Advances | journal | code

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

Dongxu Zheng, Annelot Wondergem, Susan Kloet, Iris Willemsen, Judit Balog, Stephen J Tapscott, Ahmed Mahfouz, Anita van den Heuvel, Silvère M van der Maarel
Human Molecular Genetics, ddad186 | journal

Benchmarking Variational AutoEncoders on cancer transcriptomics data

Mostafa Eltager, Tamim Abdelaal, Mohammed Charrout, Ahmed Mahfouz, Marcel J.T. Reinders, Stavros Makrodimitris
PLoS ONE 18(10): e0292126 | journal | code

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

Laura G.M. Heezen, Tamim Abdelaal, Maaike van Putten, Annemieke Aartsma-Rus, Ahmed Mahfouz, Pietro Spitali
Nat Commun 14, 4909 (2023) | journal | code | data

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

Lieke Michielsen*, Mohammad Lotfollahi*, Daniel Strobl, Lisa Sikkema, Marcel J.T. Reinders, Fabian J. Theis*, Ahmed Mahfouz*
NAR Genomics and Bioinformatics, Volume 5, Issue 3, September 2023, lqad070 | journal | code | tutorials

Cell type matching across species using protein embeddings and transfer learning

Kirti Biharie, Lieke Michielsen, Marcel J.T. Reinders, Ahmed Mahfouz
Bioinformatics (ISMB) Volume 39, 2023, Pages i404–i412 | journal | code

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

Claudio Novella-Rausell, Magda Grudniewska, Dorien J. M. Peters, Ahmed Mahfouz
iScience May 18;26(6):106877 (2023) | journal | code | software

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

Gerard Bouland, Ahmed Mahfouz*, Marcel J.T. Reinders*
Genome Biology 24, 86 (2023) | journal | code

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

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, Onno C Meijer
Neurobiology of Stress, Volume 22, January 2023 | journal | code

Preprints | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014

2022

Spatial dynamic metabolomics identifies metabolic cell fate trajectories in human kidney differentiation

Gangqi Wang, Bram Heijs, Sarantos Kostidis, Rosalie G.J. Rietjens, Marije Koning, Lushun Yuan, Gesa L. Tiemeier, Ahmed Mahfouz, Sébastien J. Dumas, Martin Giera, Jesper Kers, Susana M. Chuva de Sousa Lopes, Cathelijne W. van den Berg, Bernard M. van den Berg, Ton J.Rabelink
Cell Stem Cell Volume 29, Issue 11 (2022) | journal | data | code

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

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, Peter Carmeliet, Martin Giera, Bernard M. van den Berg, Ton J. Rabelink
Nature Metabolism (2022) | journal | data | code

Identification of a Disease-Associated Network of Intestinal Immune Cells in Treatment-Naive Inflammatory Bowel Disease

Vincent van Unen*, Laura F. Ouboter*, Na Li, Mette Schreurs, Tamim Abdelaal, Yvonne Kooy-Winkelaar, Guillaume Beyrend, Thomas Höllt, P. W. Jeroen Maljaars, M. Luisa Mearin, Ahmed Mahfouz, Anne M. C. Witte, Cornelis H. M. Clemens, Sunje Abraham, Johanna C. Escher, Boudewijn P. F. Lelieveldt, M. Fernanda Pascutti, Andrea E. van der Meulen – de Jong, Frits Koning
Front. Immunol., 23 June 2022 | journal | data | code

Community-driven ELIXIR activities in single-cell omics

Paulo Czarnewski, Ahmed Mahfouz, Raffaele A. Calogero, Patricia M. Palagi, Laura Portell-Silva, Asier Gonzalez-Uriarte, Charlotte Soneson, Tony Burdett, Barbara Szomolay, Pavankumar Videm, Hans-Rudolf Hotz, Irene Papatheodorou, John M. Hancock, Björn Grüning, Wilfried Haerty, Roland Krause, Salvador Capella-Gutierrez, Brane Leskošek, Luca Alessandri, Maddalena Arigoni, Tadeja Rezen, Alexander Botzki, Polonca Ferk, Jessica Lindvall, Katharina F Heil, Naveed Ishaque, Eija Korpelainen
F1000Research 2022, 11(ELIXIR):869 [awaiting peer review] | link

Single-cell analysis of Refractory Celiac Disease demonstrates inter- and intra-patient aberrant cell heterogeneity

Tessa Dieckman, Mette Schreurs, Ahmed Mahfouz, Yvonne Kooy-Winkelaar, Andra Neefjes-Borst, Gerd Bouma, Frits Koning
Cellular and Molecular Gastroenterology and Hepatology, March 2022 | journal

scMoC: Single-Cell Multi-omics clustering

Mostafa Eltager, Tamim Abdelaal, Ahmed Mahfouz, Marcel Reinders
Bioinformatics Advances, vbac011 | journal | code

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

Florencia Morgana, Rianne Opstelten, Manon C. Slot, Andrew M. Scott, René A. W. van Lier, Bianca Blom, Ahmed Mahfouz, Derk Amsen
J Immunol January 15, 2022, 208 (2) 384-395 | journal | data

Correcting differential gene expression analysis for cyto-architectural alterations in substantia nigra of Parkinson's disease patients reveals known and potential novel disease-associated genes and pathways

Federico Ferraro, Christina Fevga, Vincenzo Bonifati, Wim Mandemakers, Ahmed Mahfouz, Marcel Reinders
Cells 2022, 11(2), 198 | journal | code

Cell type specificity of glucocorticoid signaling in the adult mouse hippocampus

Eva M.G. Viho, Jacobus C. Buurstede, Jari B. Berkhout, Ahmed Mahfouz*, Onno C. Meijer*
J Neuroendocrinol. 2022 Feb;34(2):e13072 | journal | code

The Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease

Arno R Bourgonje, Shixian Hu*, Lieke M Spekhorst, Daria V Zhernakova, Arnau Vich Vila, et al.
Journal of Crohn's and Colitis, Volume 16, Issue 3 | journal | code | data

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2021

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

Gerard A. Bouland, Ahmed Mahfouz*, Marcel J.T. Reinders*
NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab118 | journal | code | software | data

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

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, Marcel J. T. Reinders, Eelco J. P. de Koning, Françoise Carlotti
Cells 2021, 10(12), 3585 | journal

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

Arlin Keo, Oleh Dzyubachyk, Jeroen van der Grond, Jacobus J. van Hilten, Marcel Reinders, and Ahmed Mahfouz
Front. Neurosci. 2021 | journal | code

Timing and localization of myasthenia gravis-related gene expression

Dana L.E. Vergoossen, Arlin Keo, Ahmed Mahfouz*, Maartje G. Huijbers*
Eur J Neurosci. 2021 Aug;54(4):5574-5585 | journal

Potential associations between immune signaling genes, deactivated microglia, and oligodendrocytes and cortical grey matter loss in patients with long-term remitted Cushing’s Disease

Stephanie Bauduin, IJsbrand den Rooijen, Mandy Meijer, Steven van der Werff, Arlin Keo, Oleh Dzyubachyk, Alberto Pereira, Erik Giltaya, Nik van der Wee, Onno Meijer, and Ahmed Mahfouz
Psychoneuroendocrinology. 2021 Jun 18;132:105334 | journal

Hierarchical progressive learning of cell identities in single-cell data

Lieke Michielsen, Marcel Reinders, and Ahmed Mahfouz
Nat Commun 12, 2799 (2021) | journal | code

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

Arlin Keo, Oleh Dzyubachyk, Jeroen van der Grond, Anne Hafkemeijer, Wilma D.J. van de Berg, Jacobus J. van Hilten, Marcel Rreinders, and Ahmed Mahfouz
Eur J Neurosci. 2021; 53: 3727– 3739 | journal | code

CBA: Cluster-guided batch alignment for single cell RNA-seq

Wenbo Yu, Ahmed Mahfouz*, and Marcel Reinders*
Front Genet 2021 Apr 13;12:644211 | journal | code

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

Mandy Meijer, Arlin Keo, Judith M.C. van Leeuwen, Oleh Dzyubachyk, Onno Meijer, Christiaan H. Vinkers*, and Ahmed Mahfouz*
Neurobiol Stress Feb 10;14:100307 | journal

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

Anoushka Joglekar, Andrey Prjibelski, Ahmed Mahfouz, Paul Collier, Susan Lin, Anna Katharina Schlusche, Jordan Marrocco, Stephen R. Williams, Bettina Haase, Ashley Hayes, Jennifer G. Chew, Neil I. Weisenfeld, Man Ying Wong, Alexander N. Stein, Simon A. Hardwick, Toby Hunt, Qi Wang, Christoph Dieterich, Zachary Bent, Olivier Fedrigo, Steven A. Sloan, Davide Risso, Erich D. Jarvis, Paul Flicek, Wenjie Luo, Geoffrey S. Pitt, Adam Frankish, August B. Smit, M. Elizabeth Ross & Hagen U. Tilgner
Nat Commun 12, 463 (2021) | journal | code | data

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2020

SCHNEL: Scalable clustering of high dimensional single-cell data

Tamim Abdelaal, Paul de Raadt, Lelieveldt, Marcel Reinders, and Ahmed Mahfouz
Bioinformatics, Volume 36, Issue Supplement_2, December 2020, Pages i849–i856 | journal | code

SpaGE: Spatial Gene Enhancement using scRNA-seq

Tamim Abdelaal, Soufiane Mourragui, Ahmed Mahfouz*, and Marcel Reinders*
Nucleic Acids Research, Volume 48, Issue 18, 09 October 2020, Page e107 | journal | code | data

Identification and characterization of two consistent osteoarthritis subtypes by transcriptome and clinical data integration

Rodrigo Coutinho de Almeida, Ahmed Mahfouz, Hailiang Mei, Evelyn Houtman, Wouter den Hollander, Jamie Soul, Eka Suchiman, Nico Lakenberg, Jennifer Meessen, Kasper Huetink, Rob G H H Nelissen, Yolande F M Ramos, Marcel Reinders, Ingrid Meulenbelt
Rheumatology, keaa391 | journal

Untangling biological factors influencing trajectory inference from single cell data

Mohammed Charrout, Marcel Reinders, and Ahmed Mahfouz
NAR Genomics and Bioinformatics, Volume 2, Issue 3, September 2020, lqaa053 | journal | code

Unravelling the complexity of the cancer microenvironment with multidimensional genomic and cytometric technologies

Natasja L. de Vries, Ahmed Mahfouz, Frits Koning, and Noel F. de Miranda
Front. Oncol., 23 July 2020 | journal

The single-cell eQTLGen consortium

Monique G.P. van der Wijst*, Dylan H. de Vries*, Hilde E. Groot, Gosia Trynka, Chung-Chau Hon, Marc Jan Bonder, Oliver Stegle, Martijn C Nawijn, Youssef Idaghdour, Pim van der Harst, Chun Jimmie Ye, Joseph Powell, Fabian J Theis, Ahmed Mahfouz, Matthias Heinig, Lude Franke
eLife 2020;9:e52155 | journal | website

Transcriptomic signatures of brain regional vulnerability to Parkinson’s disease

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*, Wilma D. J. van de Berg*, Jacobus J. van Hilten* & Marcel J. T. Reinders*
Commun Biol 3, 101 (2020) | journal | code

Eleven Grand challenges in single-cell data science

David Laehnemann, Johannes Köster​, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, et al.
Genome Biol 21, 31 (2020) | journal

An educational guide for nanopore sequencing in the classroom

Alex N. Salazar, Franklin L. Nobrega, Christine Anyansi, Cristian Aparicio-Maldonado, Ana Rita Costa, Anna C. Haagsma, Anwar Hiralal, Ahmed Mahfouz, Rebecca E. McKenzie, Teunke van Rossum, Stan J. J. Brouns, Thomas Abeel
PLoS Comput Biol 16(1): e1007314 | journal | code

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2019

A comparison of automatic cell identification methods for single-cell RNA-sequencing data

Tamim Abdelaal*, Lieke Michielsen*, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel Reinders, and Ahmed Mahfouz
Genome Biol 20, 194 (2019) | journal | code | data

Conserved Cell Types With Divergent Features in Human Versus Mouse Cortex

Rebecca D Hodge*, Trygve E Bakken*, Jeremy A Miller, Kimberly A Smith, Eliza R Barkan, et al.
Nature 573, 61–68 (2019) | journal | software | data

Early-Life Compartmentalization of Immune Cells in Human Fetal Tissues Revealed by High-Dimensional Mass Cytometry

Na Li, Vincent van Unen, Nannan Guo, Tamim Abdelaal, Antonis Somarakis, Jeroen Eggermont, Ahmed Mahfouz, Susana Chuva de Sousa Lopes, Boudewijn Lelieveldt, and Frits Koning
Front. Immunol., 14 August 2019 | journal | data

High-Dimensional Cytometric Analysis of Colorectal Cancer Reveals Novel Mediators of Antitumour Immunity

Natasja L de Vries, Vincent van Unen, Marieke E Ijsselsteijn, Tamim Abdelaal, Ruud van der Breggen, Arantza Farina Sarasqueta, Ahmed Mahfouz, Koen C M J Peeters, Thomas Höllt, Boudewijn P F Lelieveldt, Frits Koning, Noel F C C de Miranda
Gut 2020;69:691-703 | journal

Corticosteroid action in the brain: the potential of selective receptor modulation

Eva M.G. Viho, Jacobus C. Buurstede, Ahmed Mahfouz, Lisa L. Koorneef, Lisa T.C.M van Weert, René Houtman, Hazel J. Hunt, Jan Kroon, and Onno Meijer
Neuroendocrinology 2019;109:266–276 | journal

Functional genomics analysis of Phelan-McDermid syndrome 22q13 region during human neurodevelopment

Catherine A. Ziats, Luke P. Grosvenor, Sara M. Sarasua, Audrey E. Thurm, Susan E. Swedo, Ahmed Mahfouz, Owen M. Rennert, and Mark N. Ziats
PLoS ONE 14(3): e0213921 | journal

CyTOFmerge: Integrating mass cytometry data across multiple panels

Tamim Abdelaal, Thomas Höllt, Vincent van Unen, Boudewijn Lelieveldt, Frits Koning, Marcel Reinders, and Ahmed Mahfouz
Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4063–4071 | journal | code

Predicting cell populations in single cell mass cytometry data

Tamim Abdelaal, Vincent van Unen, Thomas Höllt, Frits Koning, Marcel Reinders, and Ahmed Mahfouz
Cytometry, 95: 769-781 | journal | code

RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage

Rodrigo Coutinho de Almeida*, Yolande F M Ramos*, Ahmed Mahfouz, Wouter den Hollander, Nico Lakenberg, Evelyn Houtman1, Marcella van Hoolwerff, H Eka D Suchiman, Alejandro Rodríguez Ruiz, P Eline Slagboom, Hailiang Mei, Szymon M Kiełbasa, Rob G H H Nelissen, Marcel Reinders, Ingrid Meulenbelt
Annals of the Rheumatic Diseases 2019;78:270-277 | journal | code | data

Single-cell RNA sequencing in facioscapulohumeral muscular dystrophy disease etiology and development

Anita van den Heuvel, Ahmed Mahfouz, Susan L Kloet, Judit Balog, Baziel G M van Engelen, Rabi Tawil, Stephen J Tapscott, Silvère M van der Maarel
Human Molecular Genetics, Volume 28, Issue 7, 1 April 2019, Pages 1064–1075 | journal | data

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2018

Natriuretic Peptides in Post-mortem Brain Tissue and Cerebrospinal Fluid of Non-demented Humans and Alzheimer’s Disease Patients

Simin Mahinrad, Marjolein Bulk, Isabelle van der Velpen, Ahmed Mahfouz, Willeke van Roon-Mom, Neal Fedarko, Sevil Yasar, Behnam Sabayan, Diana van Heemst, and Louise van der Weerd
Front. Neurosci., 26 November 2018 | journal

A structural equation model for imaging genetics using spatial transcriptomics

Sjoerd Huisman, Ahmed Mahfouz, Nematollah K. Batmanghelich, Boudewijn Lelieveldt, and Marcel Reinders
Brain Inf. 5, 13 (2018) | journal

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

Ishaan Gupta*, Paul G Collier*, Bettina Haase, Ahmed Mahfouz, Anoushka Joglekar, Taylor Floyd, Frank Koopmans, Ben Barres, August B Smit, Steven A Sloan, Wenjie Luo, Olivier Fedrigo, M Elizabeth Ross & Hagen U Tilgner
Nat Biotechnol 36, 1197–1202 (2018) | journal | data | raw data

How Metabolic State May Regulate Fear: Presence of Metabolic Receptors in the Fear Circuitry

Lisa Koorneef, Marit Bogaards, Marcel Reinders, Onno Meijer, and Ahmed Mahfouz
Front. Neurosci., 27 August 2018 | journal

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2017

Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington’s Disease

Arlin Keo, N. Ahmad Aziz, Oleh Dzyubachyk, Jeroen van der Grond, Willeke M. C. van Roon-Mom, Boudewijn Lelieveldt, Marcel Reinders, and Ahmed Mahfouz
Front. Mol. Neurosci., 30 November 2017 | journal | code

Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy

Nathalie Doorenweerd*, Ahmed Mahfouz*, Maaike van Putten, Rajaram Kaliyaperumal, Peter-Bram 't Hoen, Jos G. M. Hendriksen, Annemieke M. Aartsma-Rus, Jan J. G. M. Verschuuren, Erik H. Niks, Marcel J. T. Reinders, Hermien E. Kan & Boudewijn P. F. Lelieveldt
Sci Rep 7, 12575 (2017) | journal | code | author correction

BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome

Sjoerd Huisman, Baldur van Lew, Ahmed Mahfouz, Nicola Pezzotti, Thomas Höllt, Lieke Michielsen, Anna Vilanova, Marcel Reinders, and Boudewijn Lelieveldt
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e83 | journal | software

NeuroD factors discriminate mineralocorticoid from glucocorticoid receptor DNA binding in the male rat brain

Lisa van Weert, Jacobus C. Buurstede, Ahmed Mahfouz, Pamela S.M. Braakhuis, J. Annelies E. Polman, Hetty C.M. Sips, Benno Roozendaal, Judit Balog, E. Ronald de Kloet, Nicole A. Datson, Onno C. Meijer
Endocrinology, Volume 158, Issue 5, 1 May 2017, Pages 1511–1522 | journal | data

Cortical spreading depression causes unique dysregulation of inflammatory pathways in a transgenic mouse model of migraine

Else Eising, Reinald Shyti, Peter-Bram 't Hoen, Lisanne S. Vijfhuizen, Sjoerd Huisman, Ludo A. M. Broos, Ahmed Mahfouz, Marcel J. T. Reinders, Michel D. Ferrari, Else A. Tolner, Boukje de Vries & Arn M. J. M. van den Maagdenberg
Mol Neurobiol 54, 2986–2996 (2017) | journal

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2016

Brain Transcriptome Atlases: A Computational Perspective

Ahmed Mahfouz, Sjoerd Huisman, Boudewijn Lelieveldt, and Marcel Reinders
Brain Struct Funct 222, 1557–1580 (2017) | journal

Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics

Erdogan Taskesen, Sjoerd Huisman, Ahmed Mahfouz, Jesse H. Krijthe, Jeroen de Ridder, Anja van de Stolpe, Erik van den Akker, Wim Verheagh, and Marcel Reinders
Sci Rep 6, 24949 (2016) | journal | software | code

Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas

Else Eising*, Sjoerd Huisman*, Ahmed Mahfouz, Lisanne S Vijfhuizen, Verneri Anttila, et al.
Hum Genet 135, 425–439 (2016) | journal

Genome-wide coexpression of steroid receptors in the mouse brain: Identifying signaling pathways and functionally coordinated regions

Ahmed Mahfouz, Boudewijn Lelieveldt, Aldo Grefhorst, Lisa TCM van Weert, Isabel M. Mol, Hetty C. M. Sips, José K. van den Heuvel, Nicole A. Datson, Jenny A. Visser, Marcel J. T. Reinders, and Onno C. Meijer
Proceedings of the National Academy of Sciences Mar 2016, 113 (10) 2738-2743 | journal | code | commentary

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2015

Shared Pathways Among Autism Candidate Genes Determined by Co-expression Network Analysis of the Developing Human Brain Transcriptome

Ahmed Mahfouz*, Mark N Ziats*, Owen M Rennert, Boudewijn Lelieveldt, and Marcel Reinders
J Mol Neurosci 57, 580–594 (2015) | journal | code

Hi-C chromatin interaction networks predict co-expression in the mouse cortex

Sepideh Babaei, Ahmed Mahfouz, Marc Hulsman, Boudewijn PF Lelieveldt, Jeroen de Ridder, Marcel Reinders
PLoS Comput Biol 11 (5), e1004221 | journal 

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2014

Genomic connectivity networks based on the BrainSpan atlas of the developing human brain

Ahmend Mahfouz*, Mark N Ziats*, Owen M Rennert, Boudewijn PF Lelieveldt, Marcel JT Reinders
Proceedings Volume 9034, Medical Imaging 2014: Image Processing; 90344G (2014) | proceedings | code

Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings

Ahmed Mahfouz*, Martijn van de Giessen*, Laurens van der Maaten, Sjoerd Huisman, Marcel Reinders, Michael J.Hawrylycz, Boudewijn P.F.Lelieveldt
Methods 73, 79–89 | journal | code