Publications

2025:5

1. Adv Materials Techno

   Thermal Annealing Enhances Piezoelectricity and Regenerative Potential of PVDF‐TrFE Nanofiber Scaffolds

   Krutko Maksym, Poling Holly M., Sheth Maulee, Kongsomros Supasek, Bryan Andrew E., Sharma Manju, Singh Akaljot, Reza Hasan A., Wikenheiser‐Brokamp Kathryn A., Takebe Takanori, Helmrath Michael A., Harris Greg M., Esfandiari Leyla

   Adv Materials Technologies 2025

   Abstract DOI

   Abstract This study investigates bioelectric stimulation’s role in tissue regeneration by enhancing the piezoelectric properties of tissue‐engineered grafts using annealed poly(vinylidene fluoride‐trifluoroethylene) (PVDF‐TrFE) scaffolds. Annealing at temperatures of 80, 100, 120, and 140 °C is assessed for its impact on material properties and physiological utility. Analytical techniques such as Differential Scanning Calorimetry (DSC), Fourier‐Transform Infrared Spectroscopy (FTIR), and X‐ray Diffraction (XRD) reveal increased crystallinity with higher annealing temperatures, peaking in β‐phase content and crystallinity at 140 °C. Scanning Electron Microscopy (SEM) shows that 140 °C annealed scaffolds have enhanced lamellar structures, increased porosity, and maximum piezoelectric response. Mechanical tests indicate that 140 °C annealing improved elastic modulus, tensile strength, and substrate stiffness, aligning these properties with physiological soft tissues. In vitro assessments in Schwann cells demonstrate favorable responses, with increased cell proliferation, contraction, and extracellular matrix attachment. Additionally, genes linked to extracellular matrix production, vascularization, and calcium signaling are upregulated. The foreign body response in C57BL/6 mice, evaluated through Hematoxylin and Eosin (H&E) and Picrosirius Red staining, shows no differences between scaffold groups, supporting the potential for future functional evaluation of the annealed group in tissue repair.

2. Journal of Hepatolog

   Modeling Immune Lineage Co-Development in Human Pluripotent Stem Cell-derived Liver Organoids

   Rezvani Milad, Quach Susanna, Lewis Kyle, Saiki Norikazu, Xue Chuqing, Kimura Masaki, Iwasawa Kentaro, Weihs Julian, Elzobair Tahlil, Al Reza Hasan

   Journal of Hepatology 2025
3. bioRxiv

   Decoding lymphangioleiomyomatosis (LAM) niche environment via integrative analysis of single cell multiomics and spatial transcriptomics

   Chen Ken, Zhao Shuyang, Guo Minzhe, Reza Hasan, Wagner Andrew, Cakar Adnan Cihan, Jiang Cheng, Zhang Erik, Green Jenna, Martin Emily

   bioRxiv 2025
4. bioRxiv

   Primitive Hepatoblasts Driving Early Liver Development

   Iwasawa Kentaro, Koike Hiroyuki, Al Reza Hasan, Milton Yuka, Kishimoto Keishi, Thorner Konrad, Granitto Marissa, Saiki Norikazu, Santangelo Connie, Glaser Kathryn

   bioRxiv 2025
5. Nature

   Multi-zonal liver organoids from human pluripotent stem cells

   Reza Hasan Al, Santangelo Connie, Iwasawa Kentaro, Reza Abid Al, Sekiya Sachiko, Glaser Kathryn, Bondoc Alexander, Merola Jonathan, Takebe Takanori

   Nature 2025

2024:7

1. US Patent App

   Liver organoid model for hyperbilirubinemia and methods of making and using same

   Takebe Takanori, Al Reza Hasan

   2024
2. Genom. Inform.

   A computational approach for structural and functional analyses of disease-associated mutations in the human CYLD gene

   Roy Arpita Singha, Feroz Tasmiah, Islam Md. Kobirul, Munim Md. Adnan, Supti Dilara Akhter, Antora Nusrat Jahan, Al Reza Hasan, Gosh Supriya, Bahadur Newaz Mohammed, Alam Mohammad Rahanur, Hossain Md Shahadat

   Genom. Inform. 2024

   Abstract DOI

   Abstract Tumor suppressor cylindromatosis protein (CYLD) regulates NF-κB and JNK signaling pathways by cleaving K63-linked poly-ubiquitin chain from its substrate molecules and thus preventing the progression of tumorigenesis and metastasis of the cancer cells. Mutations in CYLD can cause aberrant structure and abnormal functionality leading to tumor formation. In this study, we utilized several computational tools such as PANTHER, PROVEAN, PredictSNP, PolyPhen-2, PhD-SNP, PON-P2, and SIFT to find out deleterious nsSNPs. We also highlighted the damaging impact of those deleterious nsSNPs on the structure and function of the CYLD utilizing ConSurf, I-Mutant, SDM, Phyre2, HOPE, Swiss-PdbViewer, and Mutation 3D. We shortlisted 18 high-risk nsSNPs from a total of 446 nsSNPs recorded in the NCBI database. Based on the conservation profile, stability status, and structural impact analysis, we finalized 13 nsSNPs. Molecular docking analysis and molecular dynamic simulation concluded the study with the findings of two significant nsSNPs (R830K, H827R) which have a remarkable impact on binding affinity, RMSD, RMSF, radius of gyration, and hydrogen bond formation during CYLD-ubiquitin interaction. The principal component analysis compared native and two mutants R830K and H827R of CYLD that signify structural and energy profile fluctuations during molecular dynamic (MD) simulation. Finally, the protein–protein interaction network showed CYLD interacts with 20 proteins involved in several biological pathways that mutations can impair. Considering all these in silico analyses, our study recommended conducting large-scale association studies of nsSNPs of CYLD with cancer as well as designing precise medications against diseases associated with these polymorphisms.

3. APL bioengineering

   Three-dimensional matrix stiffness modulates mechanosensitive and phenotypic alterations in oral squamous cell carcinoma spheroids

   Sheth Maulee, Sharma Manju, Lehn Maria, Reza HasanAl, Takebe Takanori, Takiar Vinita, Wise-Draper Trisha, Esfandiari Leyla

   APL bioengineering 2024
4. bioRxiv

   Fetal Liver-like Organoids Recapitulate Blood-Liver Niche Development and Multipotent Hematopoiesis from Human Pluripotent Stem Cells

   Rezvani Milad, Lewis Kyle, Quach Susanna, Iwasawa Kentaro, Weihs Julian, Reza Hasan Al, Cai Yuqi, Kimura Masaki, Zhang RanRan, Milton Yuka

   bioRxiv 2024
5. bioRxiv

   Self-Assembled Generation of Multi-zonal Liver Organoids from Human Pluripotent Stem Cells

   Al Reza Hasan, Santangelo Connie, Al Reza Abid, Iwasawa Kentaro, Sachiko Sachiko, Glaser Kathryn, Bondoc Alexander, Merola Jonathan, Takebe Takanori

   bioRxiv 2024
6. bioRxiv

   Enhanced piezoelectric performance of PVDF-TRFE nanofibers through annealing for tissue engineering applications

   Krutko Maksym, Poling Holly M., Bryan Andrew E., Sharma Manju, Singh Akaljot, Reza Hasan A., Wikenheiser-Brokamp Kathryn A., Takebe Takanori, Helmrath Michael A., Harris Greg M.

   bioRxiv 2024
7. Heliyon

   Meta-analysis investigating the impact of the LEPR rs1137101 (A\textgreater G) polymorphism on obesity risk in Asian and Caucasian ethnicities

   Supti Dilara Akhter, Akter Farzana, Rahman Md Imranur, Munim Md Adnan, Tonmoy Mahafujul Islam Quadery, Tarin Rabia Jahan, Afroz Sumaiya, Al Reza Hasan, Yeasmin Roksana, Alam Mohammad Rahanur

   Heliyon 2024

2023:3

1. Stem Cell Reports

   Synthetic augmentation of bilirubin metabolism in human pluripotent stem cell-derived liver organoids

   Al Reza Hasan, Farooqui Zishaan, Al Reza Abid, Conroy Callen, Iwasawa Kentaro, Ogura Yasuhiro, Okita Keisuke, Osafune Kenji, Takebe Takanori

   Stem Cell Reports 2023
2. American Journal of

   FOXF1 regulates alveolar epithelial morphogenesis through transcriptional activation of mesenchymal WNT5A

   Reza Abid A., Kohram Fatemeh, Reza Hasan A., Kalin Timothy R., Kannan Paranthaman S., Zacharias William J., Kalinichenko Vladimir V.

   American Journal of Respiratory Cell and Molecular Biology 2023
3. Human Gene

   Association of an intronic SNP rs9939609 in FTO gene with type 2 diabetes mellitus among Bangladeshi population: A case–control study combined with updated meta-analysis

   Kar Kumkum, Munim Md Adnan, Fariha Atqiya, Roy Arpita Singha, Rahman Md Imranur, Akter Shahana, Tonmoy Mahafujul Islam Quadery, Alam Mohammad Rahanur, Raunak Ahmed Ifrad Bin, Selim Shahjada

   Human Gene 2023

2022:3

1. Infection, Genetics

   Identification of novel inhibitors of high affinity iron permease (FTR1) through implementing pharmacokinetics index to fight against black fungus: An in silico approach

   Tonmoy Mahafujul Islam Quadery, Ahmed Sk Faisal, Hami Ithmam, Shakil Md Shahriar Kabir, Verma Abhishek Kumar, Hasan Mahmudul, Al Reza Hasan, Bahadur Newaz Mohammed, Rahaman Md Mizanur, Hossain Md Shahadat

   Infection, Genetics and Evolution 2022
2. Heliyon

   Cell cycle associated miRNAs as target and therapeutics in lung cancer treatment

   Fariha Atqiya, Hami Ithmam, Tonmoy Mahafujul Islam Quadery, Akter Shahana, Al Reza Hasan, Bahadur Newaz Mohammed, Rahaman Md Mizanur, Hossain Md Shahadat

   Heliyon 2022
3. Scientific Reports

   Computational epigenetic landscape analysis reveals association of CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1 lncRNAs in prostate cancer progression through aberrant methylation

   Tonmoy Mahafujul Islam Quadery, Fariha Atqiya, Hami Ithmam, Kar Kumkum, Reza Hasan Al, Bahadur Newaz Mohammed, Hossain Md Shahadat

   Scientific Reports 2022

2021:5

1. Transpl Int

   Organoid transplant approaches for the liver

   Reza Hasan Al, Okabe Ryo, Takebe Takanori

   Transpl Int 2021

   DOI
2. Heliyon

   MicroRNAs expression analysis shows key affirmation of Synaptopodin-2 as a novel prognostic and therapeutic biomarker for colorectal and cervical cancers

   Hossain Md Shahadat, Tonmoy Mahafujul Islam Quadery, Islam Md Nur, Islam Md Sajedul, Afif Ibrahim Khalil, Roy Arpita Singha, Fariha Atqiya, Al Reza Hasan, Bahadur Newaz Mohammed, Rahaman Md Mizanur

   Heliyon 2021
3. Informatics in Medic

   Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning

   Hossain Md Shahadat, Pathan AQM Sala Uddin, Islam Md Nur, Tonmoy Mahafujul Islam Quadery, Rakib Mahmudul Islam, Munim Md Adnan, Saha Otun, Fariha Atqiya, Al Reza Hasan, Roy Maitreyee

   Informatics in Medicine Unlocked 2021
4. Informatics in Medic

   In silico identification of potential inhibitors with higher potency than bumetanide targeting NKCC1: An important ion co-transporter to treat neurological disorders

   Roy Arpita Singha, Sawrav Md Sad Salabi, Hossain Md Shahadat, Johura Fatema Tuz, Ahmed Sk Faisal, Hami Ithmam, Islam Md Kobirul, Al Reza Hasan, Bhuiyan Mohammad Iqbal H., Bahadur Newaz Mohammed

   Informatics in Medicine Unlocked 2021
5. Informatics in Medic

   Prediction of novel miRNA biomarker candidates for diagnostic and prognostic analysis of STAD and LIHC: An integrated in silico approach

   Kar Kumkum, Fariha Atqiya, Hossain Md Shahadat, Tonmoy Mahafujul Islam Quadery, Hami Ithmam, Roy Arpita Singha, Shakil Md Shahriar Kabir, Al Reza Hasan, Bahadur Newaz Mohammed, Rahaman Md Mizanur

   Informatics in Medicine Unlocked 2021

2020:2

1. The Korean Journal o

   A cohort study on the association of MDM2 SNP309 with lung cancer risk in Bangladeshi population

   Al Reza Hasan, Anamika Wardatul Jannat, Chowdhury Md Miraj Kobad, Mostafa Mohammad Golam, Uddin M. Aftab

   The Korean Journal of Internal Medicine 2020
2. Mymensingh Med J

   MDM2 SNP 285 is associated with reduced lung cancer risk in bangladeshi population

   Reza H. A., Anamika W. J., Mostafa M. G., Chowdhury M. K., Uddin M. A.

   Mymensingh Med J 2020

2019:1

1. J Adv Microbiol

   Immunoinformatics approach identified two highly conserved B and T cell epitopes, LEASKRWAF and DSPLEASKRWAFRTG, for effective vaccine design against Ebola and Marburg viruses

   Hossain Md Shahadat, Reza Hasan Al, Hossain Mohammad Shahnoor

   J Adv Microbiol 2019

2018:2

1. FishTaxa

   Molecular characterization of Channa species from Bangladesh based on Cytochrome c Oxidase Subunit I (COI) gene

   AHMED Md Sagir, DINA Sabrina Rahman, NAHAR Luthfun, ISLAM Nafisa Nawal, Al REZA Hasan

   FishTaxa 2018
2. IJ Fauna Bio Stud

   Molecular characterization of hilsa shads in Bangladesh using Cytochrome C oxidase subunit 1 (CO1) gene

   Rahman ASMS, Begum M. H., Reza H. A., Ahsan M. N., Ahmed M. S.

   IJ Fauna Bio Stud 2018

2016:1

1. IOSR Journal of Phar

   Efficiency of different DNA extraction methods for fish tissues: a comparative analysis

   Chowdhury Mohammad Mamun, Rahman A. S., Nahar Luthfun, Rahman Monzillur, Al Reza Hasan, Ahmed Md Sagir

   IOSR Journal of Pharmacy and Biological Sciences 2016