bioengineering

Su1295: Chemically defined peptide-based matrices enabling the development of colorectal organoid models for therapeutic applications and disease modeling

Year: 2025 Venue: Gastroenterology Authors: Dana Alhattab, Duna Barakeh, Basma Khoja, Ahmad Elhadi, Jameel Miro, Saleh A. Alessy, Ahmed Alharbi, Manal Bokhary, May Alzahrani, Saga Ali, Wadha Almohamdi, Lama Hefni, Manola Moretti, Abeer Abdullah, Waleed Alomaim, Robert Hoehndorf, Charlotte Hauser, Saleh A. Alqahtani DOI: 10.1016/s0016-5085(25)02643-5 Topics Bioengineering · Drug mechanisms

Sa1216: Development of colorectal cancer and matched healthy organoids from Saudi patients: a case study

Year: 2025 Venue: Gastroenterology Authors: Dana Alhattab, Duna Barakeh, Basma Khoja, Ahmad Elhadi, Jameel Miro, Saleh A. Alessy, Ahmed Alharbi, Manal Bokhary, May Alzahrani, Saga Ali, Wadha Almohamdi, Lama Hefni, Manola Moretti, Yang Liu, Marwa Abdelhakim, Abeer Abdullah, Waleed Alomaim, Robert Hoehndorf, Charlotte Hauser, Saleh A. Alqahtani DOI: 10.1016/s0016-5085(25)01866-9 Topics Bioengineering · Biomedical informatics

Nanodesigner: resolving the complex-CDR interdependency with iterative refinement

Year: 2025 Venue: Journal of Cheminformatics Authors: Melissa Maria Rios Zertuche, Senay Kafkas, Dominik Renn, Magnus Rueping, Robert Hoehndorf DOI: 10.1186/s13321-025-01069-2 Abstract Abstract Camelid heavy-chain only antibodies consist of two heavy chains and single variable domains (VHHs), which retain antigen-binding functionality even when isolated. The term “nanobody” is now more generally used for describing small, single-domain antibodies. Several antibody generative models have been developed for the sequence and structure co-design of the complementarity-determining regions (CDRs)

Age-related differences in gene expression and pathway activation following heatstroke

Year: 2025 Venue: Physiological Genomics Authors: Maria Gomez, Saeed Al Mahri, Mashan Abdullah, Shuja Shafi Malik, Saber Yezli, Yara Yassin, Anas Khan, Cynthia Lehe, Sameer Mohammad, Robert Hoehndorf, Abderrezak Bouchama DOI: 10.1152/physiolgenomics.00053.2024 Abstract This study investigates the molecular responses to heatstroke in young and old patients by comparing whole-genome transcriptomes between age groups. We analyzed transcriptomic profiles from patients categorized into two age-defined cohorts: young (mean age = 44.9 ± 6 yr) and old (mean age = 66.1 ± 4 yr). Control subjects

Molecular basis and cellular effects of Janus-class–driven cytoplasmic PYK2 coacervates

Year: 2026 Venue: Communications Biology Authors: Giovanni Colombo, Israa Salem, Kacper Szczepski, Piao Yu, Shaden Alfaiyz, Francisco Javier Guzman-Vega, Ahmed Abogosh, Maxat Kulmanov, Samah Al-Harthi, Gress Kadare, Robert Hoehndorf, Jean-Antoine Girault, Łukasz Jaremko, Afaque A. Momin, Stefan T. Arold DOI: 10.1038/s42003-025-09463-0 Abstract Kinase activity is increasingly linked to biomolecular phase separation. Focal adhesion kinase (FAK) forms membrane-associated condensates with paxillin to promote adhesion. Here we show that its paralogue, proline-rich tyrosine kinase 2 (PYK2)

Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke

Year: 2025 Venue: Journal of Applied Physiology Authors: Abderrezak Bouchama, Maria Gomez, Mashan L. Abdullah, Saeed Al Mahri, Shuja Shafi Malik, Saber Yezli, Sameer Mohammad, Cynthia Lehe, Bisher Abuyassin, Robert Hoehndorf DOI: 10.1152/japplphysiol.00001.2025 Abstract Heat-related mortality remains health challenges exacerbated by climate change, with sex-based differences in outcomes, yet underlying mechanisms remain poorly understood. This study examined transcriptomic responses to heat exposure in peripheral blood mononuclear cells from 19 patients with heat stroke (HS; 8 males, mean age

The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds

Year: 2023 Venue: ACS Nano Authors: Sherin Abdelrahman, Rui Ge, Hepi H. Susapto, Yang Liu, Faris Samkari, Manola Moretti, Xinzhi Liu, Robert Hoehndorf, Abdul-Hamid Emwas, Mariusz Jaremko, Ranim H. Rawas, Charlotte A. E. Hauser DOI: 10.1021/acsnano.3c01176 Abstract Cells' interactions with their microenvironment influence their morphological features and regulate crucial cellular functions including proliferation, differentiation, metabolism, and gene expression. Most biological data available are based on in vitro two-dimensional (2D) cellular models, which fail to recapitulate the

Bioengineering

Bioengineering at the interface between materials, cells, and computation requires the careful pairing of wet-lab experimentation with omics-scale analysis. Our contribution here is computational and analytic: we partner with synthetic biology, biomaterials, and clinical teams to interpret transcriptomic, metabolomic, and structural data from engineered biological systems, patient-derived models, and human studies. The distinctive angle is to bring the same ontology-aware, multi-omics integration that underpins our diagnostic and functional-genomics work to bear on bioengineered constructs and

Sawsan Al Boeisa

Sawsan Al Boeisa completed her MSc in Bioengineering at KAUST in 2025 under the supervision of Robert Hoehndorf, with co-supervision and laboratory hosting from the Merzaban lab. She defended her thesis on 17 November 2025 and the final document was archived in the KAUST repository in December 2025. Her thesis, Differential Effects of p38 MAPK Inhibition on Chemoresistance in Patients with Colorectal Cancer, is a wet-lab pilot study in translational cancer biology. It investigates whether pharmacological inhibition of p38 MAPK can reverse or modulate chemoresistance in patient-derived

Melissa Rios Zertuche

Melissa Maria Rios Zertuche completed her MSc in Bioscience at KAUST in 2024 under the supervision of Robert Hoehndorf. Her thesis project was carried out in collaboration with the Eppinger lab and developed a computational pipeline for the rational design and optimisation of nanobodies. Her thesis, Establishment and Evaluation of a Computational Workflow for the Design and Optimization of Nanobodies, addresses the lack of comprehensive end-to-end computational tools tailored to the design of single-domain antibodies. Nanobodies (VHHs) are roughly one-tenth the size of conventional antibodies

Amal Alhelal

Amal Alhelal completed her MSc in Bioengineering at KAUST in 2024 under the supervision of Robert Hoehndorf. She was a student in the Bioinformatics and Machine Learning track of the Bioengineering programme, based at the Computational Bioscience Research Center (CBRC), and defended her thesis in May 2024. Her thesis, titled Protein functional domain identification methodology (defended under the working title Exploring the association between protein functional domains and pathogenicity information derived from AI tools), investigated computational approaches to delineate functional domains

Foundations of Bioengineering (2021)

Year: 2021 Code: BioE 200 Program: Bioengineering Institution: KAUST Role: Co-Instructor Topics: Bioengineering

Foundations of Bioengineering (2024)

Year: 2024 Code: BioE 200 Program: Bioengineering Institution: KAUST Role: Co-Instructor Topics: Bioengineering

Foundations of Bioengineering (2025)

Year: 2025 Code: BioE 200 Program: Bioengineering Institution: KAUST Role: Co-Instructor Topics: Bioengineering

Modelling and Simulation of Biological Systems - 2022-11-28

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B2 L5 R5209

Biological systems are distinguished by their enormous complexity and variability. That is why mathematical modelling and computational simulation of those systems is very difficult, in particular thinking of detailed models which are based on first principles. The difficulties start with geometric modelling which needs to extract basic structures from highly complex and variable phenotypes, on the other hand also has to take the statistic variability into account.

Coronavirus testing made quick and easy

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New diagnostic technique could help contain the spread of COVID-19 and other viral outbreaks.

Zainab A. Homoud

M.S. Student, Bioengineering
Research Interest Studying : Brain time series, fMRI, EEG, Signal Processing and Machine Learning for better Mental Disease Diagnosis and Consciousness Study. Previous Education Undergraduate study (B.S) in Biomedical Engineering and Health Science at the Joint program of North Carolina State University and UNC Chapel Hill.

Veerappan Mani

Research Scientist, Sensors
Dr. Veerappan Mani is currently a Research Scientist at the Sensors Lab, in the Electrical Engineering Department, CEMSE, King Abdullah University of Science and Technology (KAUST). He is one of the world’s top 2% scientists since 2020. Education and Early Career Dr. Veerappan Mani received his Ph.D. from the Department of Chemical Engineering and Biotechnology, National Taipei University of Technology (NTUT), Taiwan in 2014. He worked as a research assistant professor at the Institute of Biochemical and Biomedical Engineering, Taipei Tech, Taiwan, from 2016 to 2019. He was a research visiting

Krishnakumar Sivakumar

Research Interests ​Environmental Microbiology and Bioengineering, Biofilm Engineering and Biofilm-based Bioprocesses, Anaerobic Microbiology, Antibiotic resistance in the environment, Microbial Ecology Education Profile Ph.D. (Sustainable Earth – Biofilm Engineering, Nanyang Technological University, Singapore) Masters (Environmental Engineering & Management, Indian Institute of Technology Delhi, India) Bachelors (Civil Engineering, Kerala University)​

Khalil Moussi

Postdoctoral Research Fellow, Electrical and Computer Engineering
Selected ​Publications K. Moussi and J. Kosel, "3-D Printed Biocompatible Micro-Bellows Membranes," Journal of Microelectromechanical Systems, vol. 27, no. 3, pp. 472-478, June 2018. K. Moussi, A. Bukhamsin, and J. Kosel, "Implantable 3D Printed Drug Delivery System," IEEE Transducers/EUROSENSORS, June 2019. K. Moussi, M. AlDajani, and J. Kosel, "Miniaturized Drug Delivery System for Biomedical Applications," IEEE NEMS Conference, April 2019. K. Moussi, S. Naifar, O. Kanoun, S. Bradai. “Analytical Model of Magnetostrictive/Piezoelectric Laminate Composites”, 5th IMEKO TC19 SYMPOSIUM, pp. 51-55