Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.8
4.5
Journals
Biomedicines
Special Issues
Selected Papers from the Tanawwo Workshop on Clinical Research in...
share announcement

Selected Papers from the Tanawwo Workshop on Clinical Research in Precision Medicine, Rare Diseases, and Pharmacogenomics (Doha, Qatar, 2025)

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Neurobiology and Clinical Neuroscience".

Deadline for manuscript submissions: closed (30 April 2026) | Viewed by 3102

Editors

Prof. Dr. Felipe Fregni

E-Mail Website
Guest Editor
1. Neuromodulation Center and Center for Clinical Research Learning, Spaulding Rehabilitation Hospital and Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
2. Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
Interests: neuromodulation; pain perception modulation; neurophysiology; neuroplasticity
Special Issues, Collections and Topics in MDPI journals
Dr. Radja Messai Badji

E-Mail Website
Guest Editor
Qatar Precision Health Institute (QPHI), Doha, Qatar
Interests: precision public health; genomics; pharmacogenomics; clinical research; translational science; implementation science

Special Issue Information

Dear Colleagues,

This Special Issue of Biomedicines is dedicated to selected papers from the Tanawwo Workshop on Clinical Research in Precision Medicine, Rare Diseases, and Pharmacogenomics, held on December 8–11, 2025 at Qatar University, Doha, Qatar.

Organized by the Qatar Precision Health Institute (QPHI) in partnership with the Principles and Practice of Clinical Research Program (ECE department, Harvard TH Chan School of Public Health) and Qatar University, this four-day workshop provided a unique platform for multidisciplinary training and discussion at the intersection of genomics, clinical research, and innovation.

The program addressed methodological foundations and cutting-edge advances in the following areas:

  1. Clinical trial design in precision medicine and rare diseases;
  2. Pharmacogenomics and individualized therapy;
  3. Multi-omics and big data integration in clinical research;
  4. Artificial intelligence and digital health applications in trial methodology;
  5. Patient registries, adaptive and platform trials;
  6. Global perspectives on ethics, regulation, and governance (including WHO frameworks);
  7. Translational pipelines from bench to bedside in precision medicine.

This Special Issue seeks to capture the advances, methodologies, and innovations presented and discussed during the workshop. All participants are encouraged to submit extended full manuscripts for peer-reviewed publication in this Special Issue (with a 20% discount on the publication fee). All submissions will undergo MDPI’s standard peer review procedure. In addition, submissions from others that are not associated with this conference but with themes focusing on related topics are also welcome.

We look forward to receiving your contributions and thank you for supporting this important initiative at the intersection of precision health, genomics, and clinical research.

Prof. Dr. Felipe Fregni
Dr. Radja Messai Badji
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • precision medicine
  • rare diseases
  • pharmacogenomics
  • adaptive and platform trials
  • multi-omics integration
  • artificial intelligence in clinical research
  • big data and digital health
  • translational medicine

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

31 pages, 2776 KB  
Article
A Multimodal Biomedical Transformer Fusion Network for Disease-Level Rare-Disease-Inheritance Classification Using Ontology-Enriched Text, Metadata, and Gene Associations
by Mahmood A. Mahmood and Khalaf Alsalem
Biomedicines 2026, 14(7), 1439; https://doi.org/10.3390/biomedicines14071439 - 25 Jun 2026
Viewed by 304
Abstract
Background/Objectives: Inheritance classification in rare diseases remains challenging because curated knowledge is incomplete, heterogeneous, and imbalanced across inheritance categories. Disease-level inheritance modeling can support knowledge organization, annotation review, and hypothesis generation in rare-disease resources. This paper introduces RareFusion-Net, a multimodal benchmark framework for [...] Read more.
Background/Objectives: Inheritance classification in rare diseases remains challenging because curated knowledge is incomplete, heterogeneous, and imbalanced across inheritance categories. Disease-level inheritance modeling can support knowledge organization, annotation review, and hypothesis generation in rare-disease resources. This paper introduces RareFusion-Net, a multimodal benchmark framework for disease-level inheritance classification, and evaluates whether integrating ontology-enriched disease text, structured epidemiological metadata, and gene-association information improves prediction in curated rare-disease knowledge bases. RareFusion-Net is intended for knowledge modeling, not individual patient diagnosis. Methods: We developed RareFusionBalanced, a gated multimodal fusion model that combines biomedical disease descriptions, structured metadata, and gene-related information using auxiliary supervision. Ontology-enriched disease text was treated as the dominant semantic modality, while tabular and gene modalities were incorporated as complementary evidence when available. Robustness was improved using balanced regularization, selective transformer fine-tuning, dropout, weight decay, label smoothing, early stopping, and prediction aggregation across random seeds. Evaluation included accuracy, macro-F1, micro-F1, macro-AUC, mean average precision, calibration metrics, class-wise analysis, statistical testing, and ablation experiments. Results: RareFusionBalanced achieved 0.7382 test accuracy, 0.6284 macro-F1, 0.7382 micro-F1, 0.9183 macro-AUC, and 0.6686 mean average precision. Calibration was favorable, with an expected calibration error of 0.0395 and a Brier-OVR of 0.0528. The multimodal model slightly outperformed TextOnly-TransformerBalanced, but improvement over the best TF-IDF baseline was not statistically significant. Ablation showed ontology-enriched text as the strongest modality, with gene associations adding complementary value. Conclusions: RareFusion-Net provides a practical benchmark for ontology-aware rare-disease inheritance modeling. Results suggest selective multimodal benefit while highlighting minority-class difficulty, limited statistical superiority, need for external validation, and improved biological interpretability. Full article
(This article belongs to the Special Issue Selected Papers from the Tanawwo Workshop on Clinical Research in Precision Medicine, Rare Diseases, and Pharmacogenomics (Doha, Qatar, 2025))
►▼ Show Figures

Figure 1

12 pages, 618 KB  
Article
Toward Personalized Anticoagulation: Clinical Predictors of Early Warfarin Response in Heart Valve Replacement Patients
by Rania Abdel-latif, Shaban Mohammed, Tamer Abdalghafoor, Rana Mekkawi, Cornelia Sonia Carr, Abdulaziz M. Alkhulaifi, Ali Kindawi, Mohd Lateef Wani, Samim Azizi, Mohamad El-Kahlout, Sankar Balasubramanian, Hatem Sarhan, Samy Hanoura, Sameh Aboulnaga, Yasser Shouman, Abdulwahid Al Mulla, Radja Badji, Wadha Al-Muftah and Amr Salah Omar
Biomedicines 2026, 14(2), 446; https://doi.org/10.3390/biomedicines14020446 - 17 Feb 2026
Cited by 1 | Viewed by 963
Abstract
Background/Objective: Warfarin is the standard anticoagulant for patients with mechanical heart valve replacement (HVR). However, its narrow therapeutic index and interpatient variability complicate early postoperative management. Evidence on how valve position influences warfarin sensitivity is limited. This study evaluated the impact of [...] Read more.
Background/Objective: Warfarin is the standard anticoagulant for patients with mechanical heart valve replacement (HVR). However, its narrow therapeutic index and interpatient variability complicate early postoperative management. Evidence on how valve position influences warfarin sensitivity is limited. This study evaluated the impact of prosthetic valve position and clinical factors on early warfarin response and developed a prediction model to guide initial warfarin dosing in HVR patients. Methods: A retrospective study was conducted on 310 adults who underwent mechanical aortic, mitral, or double valve replacement at Hamad Medical Corporation (2015–2022). Warfarin was initiated within 24 h postoperatively, and patients were monitored for three days. Outcomes included daily warfarin dose, international normalized ratio (INR) levels, attainment of therapeutic INR, INR overshoot (≥4), and the warfarin dose index on day 3 (WDI3). Predictors of WDI3 were analyzed using multivariable regression, and a LASSO model was applied to a dose prediction algorithm for the day 1 dose. Results: Mitral valve recipients required lower doses than aortic or double valve groups (p = 0.008) but had higher INR overshoot rates (18.75% vs. 16.05% and 4.55%; p = 0.033). Female sex and a higher baseline INR were associated with greater sensitivity (p < 0.01), whereas mitral/double valve position predicted reduced sensitivity (p = 0.010). Only half of the cohort reached therapeutic INR by day 3. The prediction model explained ~28% of dose variance with moderate performance. Conclusions: Valve position, sex, and baseline INR significantly influence early postoperative warfarin response. Incorporating these clinical factors into dosing algorithms may optimize initial warfarin management in HVR patients. Full article
(This article belongs to the Special Issue Selected Papers from the Tanawwo Workshop on Clinical Research in Precision Medicine, Rare Diseases, and Pharmacogenomics (Doha, Qatar, 2025))
►▼ Show Figures

Figure 1

Review

Jump to: Research

13 pages, 1258 KB  
Review
BRAF Mutations in Myeloid Neoplasms: Prevalence, Co-Mutation Landscape, and Clinical Outcomes—A Comprehensive Review
by Shehab F. Mohamed, Ali Mohamed, Mohamed Fawzi Mudarres, Azza E. A. Abdalla, Abdulrahman F. Al-Mashdali, Mohammed Abdulgayoom, Rowan Mesilhy, Tareq Abuasab, Honar Cherif and Gautam Borthakur
Biomedicines 2026, 14(3), 672; https://doi.org/10.3390/biomedicines14030672 - 15 Mar 2026
Viewed by 1144
Abstract
Background: BRAF is a core component of the RAS–MAPK signaling pathway and an established oncogenic driver in several solid tumors and selected hematologic malignancies. In myeloid neoplasms, BRAF mutations are rare, and their prevalence, molecular context, and clinical significance remain incompletely defined. Available [...] Read more.
Background: BRAF is a core component of the RAS–MAPK signaling pathway and an established oncogenic driver in several solid tumors and selected hematologic malignancies. In myeloid neoplasms, BRAF mutations are rare, and their prevalence, molecular context, and clinical significance remain incompletely defined. Available evidence is scattered across heterogeneous reports involving acute myeloid leukemia, myelodysplastic syndromes, myeloproliferative neoplasms, and overlap myelodysplastic/myeloproliferative neoplasms, with variable descriptions of mutation subtypes, co-mutational profiles, cytogenetic associations, therapeutic approaches, and clinical outcomes. To address these gaps, this review synthesizes data from the published literature up to 2025, summarizing the distribution, genetic landscape, and clinical impact of molecularly confirmed BRAF mutations across the spectrum of myeloid neoplasms. Results: Across published cohorts, BRAF mutations occurred in less than 1% of unselected myeloid neoplasms, with enrichment in chronic myelomonocytic leukemia and therapy-related or secondary acute myeloid leukemia. Both V600E and non-V600E variants were observed, typically within a complex genomic background involving ASXL1, TET2, DNMT3A, SRSF2, and RAS-pathway mutations. Acute myeloid leukemia cases showed poor prognosis, with median overall survival measured in months, whereas myelodysplastic syndromes and chronic myelomonocytic leukemia demonstrated relatively longer survival. Targeted MAPK inhibition produced hematologic responses in selected cases but rarely resulted in durable molecular clearance. Conclusions: BRAF mutations in myeloid neoplasms are rare, heterogeneous, and usually represent secondary events in clonal evolution. Although mutation clearance appears prognostically relevant, current targeted approaches provide limited durability, underscoring the need for prospective studies in this setting. Full article
(This article belongs to the Special Issue Selected Papers from the Tanawwo Workshop on Clinical Research in Precision Medicine, Rare Diseases, and Pharmacogenomics (Doha, Qatar, 2025))
►▼ Show Figures

Graphical abstract

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-3
Back to TopTop