Publications

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2026

Lama Alabdi, Abdullah Sezer, Fatema Alzahrani, Sebiha Cevik, Zanyar Demir, Nor Linda Abdullah, Özlem Durukan, Efe Dallı, Mais O Hashem, Omar Abuyousef, Bayan Aljamal, Rana Helaby, Mona Radwan, Amal Jaafar, Tarfa Alshidi, Israa Salem, Halima Hamid, Bader Alhaddad, Khadijah Bakur, Elifcan Taşdelen, Mustafa Kılıç, Mohammed Al-Owain, Amal Alhashem, Eirik Bratland, Julie Paulsen, Gunnar Houge Douzgos, Anya Revah Politi, Kevin Uguen, Emmanuelle Masson, Severine Audebert, Talal AlAnzi, Stefan T Arold, Bora Ergin, Leena A Ibrahim, Oktay I Kaplan, Fowzan S Alkuraya. Bi-allelic variants in OLA1 cause a neurodevelopmental disorder with joint hypermobility. American Journal of Human Genetics March 2026 10.1016/j.ajhg.2026.03.001

Idoia Blanco-Luquin, Xabier Martínez-de-Morentin, Amaia Vilas-Zornoza, Daniel Mouzo, Alejandro Lumbreras Lopez, Mónica Macías, Diego Alignani, Alberto Maillo, Ana Cecilia Gonzalez Alvarez, Leena Ali Ibrahim, Vincenzo Lagani, Natalia Ramírez, Jesper Tegner, Felipe Prósper, Maite Mendioroz, David Gomez-Cabrero. Human neuronal differentiation under Aβ exposure: a single-cell transcriptomic and epigenomic dataset. Scientific Data March 2026 https://doi.org/10.1038/s41597-026-06971-4.

2025

Mansour Alyahyay, Dimitri Dumontier, Deyl S. Djama, Morris Jackson, Abdullah Lugtum, Edenia Da Cunha Menezes, Haojie Ye, Jun Chen Qian, Giulia Sansone, Mohammed Soheib, Andrea M.C. Mirow, Leena Ali Ibrahim#, Gabrielle Pouchelon#. Context-dependent presynaptic inhibition of somatostatin interneuron inputs to Layer 1 of the visual cortex. Biorxiv, Sept 2025 https://doi.org/10.1101/2025.09.25.678558

Vincenzo Lagani, Lela Chitadze, Ana Cecilia Gonzalez Alvarez, Teimuraz Bokuchava, Giulia Sansone, Veriko Bokuchava, Lia Tsverava, Aragorn Jones, Steven Lisgo, Xabier Martinez De Morentin,  Robert Lehmann, Jesper Tegner, Leena Ali Ibrahim, Brian J. McCabe, Zaza Khuchua, David Gomez Cabrero, Revaz Solomonia. Charting the single cell transcriptional landscape governing visual imprinting. Biorxiv, June 2025. https://doi.org/10.1101/2025.06.23.660422

Lama Alabdi, Norah Altuwaijri, Jun-yi Zhu, Stephanie Efthymiou, Hangnoh Lee, Jianli Duan, Israa Salem, Piao Yu, Nor Linda Abdullah, Fatema Alzahrani, Qing Xu, Mashael M Felemban, ………. Stefan T Arold, Leena A Ibrahim, Zhe Han, Fowzan S Alkuraya. SLK is mutated in individuals with a neurodevelopmental disorder. EBiomedicine June 2025 10.1016/j.ebiom.2025.105725

Elisabetta Furlanis, Min Dai, Brenda Leyva Garcia, Thien Tran, Josselyn Vergara, Ana Pereira, Bram L. Gorissen, Sara Wills, Anna Vlachos, Ariel Hairston, Deepanjali Dwivedi, Sarah Du, Justin McMahon, Shuhan Huang, Annunziato Morabito, Arenski Vazquez, Soyoun Kim, Anthony T. Lee, EdwardF. Chang, Taha Razzaq, Ahmed Qazi, Geoffrey Vargish, Xiaoqing Yuan, Adam Caccavano, Steven Hunt, Ramesh Chittajallu, Nadiya McLean, Lauren Hewitt, Emily Paranzino, Haley Rice, Alex C. Cummins, Anya Plotnikova, Arya Mohanty, Anne Claire Tangen, Jung Hoon Shin, Reza Azadi, Mark A.G. Eldridge, Veronica A. Alvarez, Bruno B. Averbeck, Mansour Alyahyay, Tania Reyes Vallejo, Mohammed Soheib, Lucas G. Vattino, Cathryn P. MacGregor, Carolina Piletti Chatain, Emmie Banks, Viktor Janos Olah, Shovan Naskar, Sophie Hill, Sophie Liebergall, Rohan Badiani, Lili Hyde, Ella Hanley, Qing Xu, Kathryn C. Allaway, Ethan M. Goldberg, Matthew J.M. Rowan, Tomasz J. Nowakowski, Soohyun Lee, Emilia Favuzzi, Pascal S. Kaeser, Lucas Sjulson, Renata Batista-Brito, Anne E. Takesian, Leena A. Ibrahim, Asim Iqbal, Kenneth A. Pelkey, Chris J. McBain, Jordane Dimidschstein, Gord Fishell, Yating Wang. An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes. Neuron May 2025 10.1016/j.neuron.2025.05.002 

Sarbojit Roy, Malik Shahid Sultan, Tania Reyes Vallejo, Leena Ali Ibrahim, Hernando Ombao. Classification of High-dimensional Time Series in Spectral Domain Using Explainable Features with Applications to Neuroimaging Data. The 28th International Conference on Artificial Intelligence and Statistics

2024

Mara Sherlin D Talento, Sarbojit Roy, Tania Reyes Vallejo, Leena A Ibrahim, Hernando C Ombao. Kencoh: A ranked-based canonical coherence. arxiv Dec 2024 https://doi.org/10.48550/arXiv.2412.10521.

Shuhan Huang, Daniella Rizzo, Sherry Jingjing Wu, Qing Xu, Leena Ziane, Norah Alghamdi, David A Stafford, Tanya L Daigle, Bosiljka Tasic, Hongkui Zeng, Leena Ali Ibrahim#, Gord Fishell#. Neurogliaform Cells Exhibit Laminar-specific Responses in the Visual Cortex and Modulate Behavioral State-dependent Cortical Activity. bioRxiv June 8, 2024 https://doi.org/10.1101/2024.06.05.597539

Timothy J Burbridge, Jacob M Ratliff, Deepanjali Dwivedi, Uma Vrudhula, Francisco Alvarado-Huerta, Lucas Sjulson, Leena Ali Ibrahim, Lucas Cheadle, Gordon Fishell, Renata Batista-Brito. Disruption of Cholinergic Retinal Waves Alters Visual Cortex Development and Function. bioRxiv April 15, 2024 https://doi.org/10.1101/2024.04.05.588143

Shuhan Huang, Sherry Jingjing Wu, Giulia Sansone, Leena Ali Ibrahim#, Gord Fishell#. Layer 1 neocortex: Gating and integrating multidimensional signals. Neuron Jan 17, 2024 https://doi.org/10.1016/j.neuron.2023.09.041

2023

Leena Ali Ibrahim#,  Brie Wamsley,  Norah Alghamdi,  Nusrath Yusuf,  Elaine Sevier,  Ariel Hairston,  Mia Sherer,  Xavier Hubert Jaglin,  Qing Xu,  Lihua Guo,  Alireza Khodadadi-Jamayran,  Emilia Favuzzi,  Yuan Yuan,  Jordane Dimidschstein,  Robert B Darnell,  Gordon Fishell#. Nova proteins direct synaptic integration of somatostatin interneurons through activity-dependent alternative splicing. eLife Jun 22, 2023 https://doi.org/10.7554/eLife.86842

2022 and prior to joining KAUST!

Lorenzo Gesuita, Anna Cavaccini, Ali Özgür Argunsah, Emilia Favuzzi, Leena Ali Ibrahim, Tevye Jason Stachniak, Martina De Gennaro, Sebastian Utz, Melanie Greter, Theofanis Karayannis. Microglia contribute to the postnatal development of cortical somatostatin-positive inhibitory cells and to whisker-evoked cortical activity. Cell Reports, Volume 40, Issue 7, 2022, 111209, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2022.111209.

Leena A. Ibrahim, Shuhan Huang, Marian Fernandez-Otero, Mia Sherer, Spurti Vemuri, Robert Machold, Bernardo Rudy, Gord Fishell. Bottom-up inputs are required for the establishment of top-down connectivity onto cortical layer 1 neurogliaform cells. Neuron, Volume 109, Issue 21, 3 November 2021, Pages 3473-3485.e5, https://doi.org/10.1016/j.neuron.2021.08.004

Emilia Favuzzi, Shuhan Huang, Giuseppe A. Saldi, Loïc Binan, Leena A. Ibrahim, Marian Fernández-Otero, Yuqing Cao, Ayman Zeine, Adwoa Sefah, Karen Zheng, Qing Xu, Elizaveta Khlestova, Samouil L. Farhi, Richard Bonneau, Sandeep Robert Datta, Beth Stevens, Gord Fishell. GABA-receptive microglia selectively sculpt developing inhibitory circuits. Cell, Volume 184, Issue 15, 2021, Pages 4048-4063.e32, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2021.06.018.

Ibrahim LA, Schuman B, Bandler R, Rudy B, Fishell G. Mining the jewels of the cortex’s crowning mystery. Curr Opin Neurobiol. 2020 Aug; 63:154-161. doi: 10.1016/j.conb.2020.04.005. Epub 2020 May 29. PMID: 32480351 Review.

Vormstein-Schneider D, Lin JD, Pelkey KA, Chittajallu R, Guo B, Arias-Garcia MA, Allaway K, Sakopoulos S, Schneider G, Stevenson O, Vergara J, Sharma J, Zhang Q, Franken TP, Smith J, Ibrahim LA, M Astro KJ, Sabri E, Huang S, Favuzzi E, Burbridge T, Xu Q, Guo L, Vogel I, Sanchez V, Saldi GA, Gorissen BL, Yuan X, Zaghloul KA, Devinsky O, Sabatini BL, Batista-Brito R, Reynolds J, Feng G, Fu Z, McBain CJ, Fishell G, Dimidschstein J. Viral manipulation of functionally distinct neurons from mice to humans. Nature Neuroscience, Aug 2020. doi: 10.1038/s41593- 020-0692-9. PMID: 32807948

Ibrahim LA, Huang JJ, Wang SZ, Kim YJ, Zhang LI, Tao HW. Sparse Labeling and Neural Tracing in Brain Circuits by STARS Strategy: Revealing Morphological Development of Type II Spiral Ganglion Neurons. Cereb Cortex. 2018 Jul 6. doi: 10.1093/cercor/bhy154. PMID: 29982390.

Ibrahim LA, Mesik L, Ji X.Y, Fang Q, Li HF, Li Y.T, Zingg B, Zhang LI, Tao HW. Cross Modality Sharpening of Visual Cortical Processing through Layer-1 mediated inhibition and disinhibition. Neuron. 2016 Mar 2;89(5):1031-45. doi: 10.1016/j.neuron.2016.01.027. Epub 2016 Feb 18. PMID: 26898778.

Li YT, Ibrahim LA, Liu BH, Zhang LI, Tao HW. Linear transformation of thalamocortical input by intracortical excitation. Nat Neurosci. 2013 Sep;16(9):1324-30. doi: 10.1038/nn.3494. Epub 2013 Aug 11. PubMed PMID: 23933750; PubMed Central PMCID: PMC3855439.

Kim YJ, Ibrahim LA, Wang SZ, Yuan W, Evgrafov OV, Knowles JA, Wang K, Tao HW, Zhang LI. EphA7 regulates spiral ganglion innervation of cochlear hair cells. Dev Neurobiol. 2016 Apr;76(4):452-69. doi: 10.1002/dneu.22326. Epub 2015 Jul 27 PubMed PMID: 26178595.

Wang SZ, Ibrahim LA, Kim YJ, Gibson DA, Leung HC, Yuan W, Zhang KK, Tao HW, Ma L, Zhang LI. Slit/Robo signaling mediates spatial positioning of spiral ganglion neurons during development of cochlear innervation. J Neurosci. 2013 Jul 24;33(30):12242-54. PMID:23884932.

Mesik L, Ma WP, Li LY, Ibrahim LA, Huang ZJ, Zhang LI, Tao HW. Functional response properties of VIP-expressing inhibitory neurons in mouse visual and auditory cortex. Front Neural Circuits. 2015 May 22;9:22. doi: 10.3389/fncir.2015.00022. eCollection 2015. PMID:26106301.

Xiong XR, Liang F, Zingg B, Ji XY, Ibrahim LA, Tao HW, Zhang LI. Auditory cortex controls sound-driven innate defense behaviour through corticofugal projections to inferior colliculus. Nat Commun. 2015 Jun 11;6:7224. doi: 10.1038/ncomms8224. PMID:26068082.

Li LY, Xiong XR, Ibrahim LA, Yuan W, Tao HW, Zhang LI. Differential Receptive Field Properties of Parvalbumin and Somatostatin Inhibitory Neurons in Mouse Auditory Cortex. Cereb Cortex. 2015 Jul;25(7):1782-91. doi: 10.1093/cercor/bht417. Epub 2014 Jan 14. PMID:24425250.

Sun YJ, Kim YJ, Ibrahim LA, Tao HW, Zhang LI. Synaptic mechanisms underlying functional dichotomy between intrinsic-bursting and regular-spiking neurons in auditory cortical layer 5. J Neurosci. 2013 Mar 20;33(12):5326-39. doi: 10.1523/JNEUROSCI.4810-12.2013. PMID:23516297.

Li YT, Ma WP, Li LY, Ibrahim LA, Wang SZ, Tao HW. Broadening of inhibitory tuning underlies contrast-dependent sharpening of orientation selectivity in mouse visual cortex. J Neurosci. 2012 Nov 14;32(46):16466-77. doi: 10.1523/JNEUROSCI.3221-12.2012. PMID:23152629.