Pappu, MAA, Alamin M*, Noman, MA, Sultana MH, Ahmed, MF, Hossain, MS, Latif, MA, Faysal, MF, Azad A, Alyami SA, Alotaibi N & Mollah MNH (2025). Multi-Transcriptome-Informed Network Pharmacology Reveals Novel Biomarkers and Therapeutic Candidates for Parkinson’s Disease. Genes, 16(12), 1459 (Q2, Index: SCIE, Scopus; IF: 2.8). https://doi.org/10.3390/genes16121459
Pappu MAA, Md. Alamin*, Sultana MH, Azad AKM, Md. Rabiul Auwul MR, Mahmud S, Ajadee A, Sarker A, Alyami SA & Mollah MNH (2025). Single nucleus RNA sequencing profile analysis to reveal cell types specific common molecular drivers of Parkinson’s Disease and therapeutic agents. Scientific Reports, 15:27086 (Q1, Index: SCIE, Scopus; IF: 3.9). https://doi.org/10.1038/s41598-025-09417-w
Pappu MAA and Md. Alamin et al. (2025). Decoding parkinson’s disease-causing biomarker genes highlighting their molecular mechanisms and therapeutic agents through transcriptomics analysis using bioinformatics approaches. (Under Review)
Labib NI, Jony IMJ, Rafi RR, Tanvir MN, Bai Renren, Alamin M*, Hossain MS (2025). Unravelling sleep deprivation on medical students: academics, social life, physical health, and depression. (Under Review)
Rokonuzzaman M, Hasan MM, Akter S, Alamin M, Hollands GJ, Hossain MS (2025). Unveiling patterns and sociodemographic characteristics of drug trafficking in Dhaka city, Bangladesh. (Under Review)
Rokonuzzaman, Hasan M, Islam MS, Hossain MS, Alamin M, Alamin Hollands GJ, Hossain MS (2025) Drug and alcohol use and related sociodemographic, psychosocial, and health characteristics: A descriptive survey of bus drivers in Bangladesh. (Under Review)
Alamin M, Sultana MH, Babarinde IA, Azad AKM, Moni MA and Xu H (2024). Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs). Briefings in Bioinformatics, 25(3), bbae230 (Q1, Index: SCIE, Scopus; IF: 6.8). https://doi.org/10.1093/bib/bbae230
Zhong Q, Wang X, Wei R, Liu F, Alamin M, Sun J, Gui L (2024). Equisetin inhibits adiposity through AMPK-dependent regulation of brown adipocyte differentiation. Heliyon, 10, e25458 (Q1, Index: SCIE, Scopus; IF: 3.4). doi.org/10.1016/j.heliyon.2024.e25458
Emelin M†, Qiu X†, Fan F†, Alamin M† et al. (2024). Identification and designed QTL breeding of reliable QTLs for milling quality and grain shape in the reciprocal introgression lines in rice. BMC Plant Biology, 24, 38 (Q1, Index: SCIE, Scopus; IF: 5.3). https://doi.org/10.1186/s12870-023-04707-9
Sultana MH†, Alamin M†, Qiu J, Fan L, Ye C (2023). Transcriptomic Profiling Reveals Candidate Allelopathic Genes in Rice Responsible for Interactions with Barnyardgrass. Frontier in Plant Sciences, 14:1104951 (Q1, Index: SCIE, Scopus; IF: 4.41). 10.3389/fpls.2023.1104951
Alamin M, Sultana MH, Wenfei J, Haiming X (2022). Dissecting complex traits using omics data: a review on the linear mixed models and their application. Plants, 11(23), 3277 (Q1, Index: SCIE, Scopus; IF: 4.0). https://doi.org/10.3390/plants11233277
Alam MS, Kong J, Tao R, Ahmed T, Alamin M, Alotaibi SS, Abdelsalam NR and Xu JH (2022). CRISPR-mediated knockout of bHLH transcription factor OsbHLH024 improves salt tolerance in rice (Oryza sativa L.). Plants, 11, 1184 (Q1, Index: SCIE, Scopus; IF: 4.0). https://doi.org/10.3390/plants11091184
Alam MJ, Alamin M, Sultana MH, Ahsan MA, Hossain MR, Islam SMI, Mollah MNH (2020). Bioinformatics studies on structures, functions, and diversifications of rolling leaf-related genes in rice (Oryza sativa). Plant Genetic Resources 18(5):382-395 (Q3, Index: SCIE, Scopus; F: 1.279). https://doi.org/10.1017/S1479262120000404
Alamin M, Sultana MH, Haiming Xu, Mollah MNH (2020). Robustification of linear regression and its application in genome-wide association studies. Frontiers in Genetics 11:549 (Q2, Index: SCIE, Scopus; IF: 2.8). http://dx.doi.org/10.3389/fpls.2023.1104951
Sultana MH, Liu F, Alamin M, Mao L, Jia L, Chen H, Wu D, Wang Y, Fu F, Wu S, Wang W, Ye C, Zhu QH, Qiu J and Fan L (2019) Gene modules co-regulated with biosynthetic gene clusters for allelopathy between rice and barnyardgrass. International Journal of Molecular Sciences 20(16):3846 (Q1, Index: SCIE, Scopus; IF: 4.9). https://doi.org/10.3390/ijms20163846
Sultana MH, Alamin M, Alam MJ, Fan L, MNH Mollah (2019) SNP Based Robust Fast-eQTL Mapping for Identification of Important Genes. International Journal of Statistical Sciences 17: 97-114. http://www.ru.ac.bd/stat/ijss-current-issue/
Zeng DD, Yang CC, Qin R, Alamin M, Yue EK, Jin XL, Shi CH (2018) A guanine insert in OsBBS1 leads to early leaf senescence and salt stress sensitivity in rice (Oryza sativa). Plant Cell Reports 37:933-946 (Q1, Index: SCIE, Scopus; IF: 5.3). https://doi.org/10.1007/s00299-018-2280-y
Alamin M, Zeng DD, Qin R, Sultana MH, Jin XL, Shi CH (2018) Rice SDSFL1 plays a critical role in the regulation of plant structure through the controlling of different phytohormones and altered cells structure. Journal of Plant Physiology 231:110-123 (Q1, Index: SCIE, Scopus; IF: 4.0). https://doi.org/10.1016/j.jplph.2018.09.005
Qin R, Zeng DD, Yang CC, Akhter D, Alamin M, Jin XL, Shi CH (2018) LTBSG1, a new allele of BRD2, regulates panicle and grain development in rice by brassinosteroid (B.R.) biosynthetic pathway. Genes 9(6):292 (Q2, Index: SCIE, Scopus; IF: 2.8). https://doi.org/10.3390/genes9060292
Yang CC, Zeng DD, Qin R, Alamin M, Jin XL, Shi CH (2018) Rice gene, BBH/Lsi1, regulates the color of rice hull by reducing the absorption and deposition of silicon and accumulating excess flavonoid. Plant Growth Regulation 85(1):133-142 (Q1, Index: SCIE, Scopus.; IF: 3.5). https://doi.org/10.1007/s10725-018-0379-3
Alamin M, Zeng DD, Qin R, Sultana MH, Jin XL, Shi CH (2018) Photosynthesis, pigment contents, cellulose contents, and ultrastructure changes in a rice mutant leading to screw flag leaf. Plant Growth Regulation 85(1):1-13 (Q1, Index: SCIE, Scopus.; IF: 3.5). https://doi.org/10.1007/s10725-018-0369-5
Akhter D, Qin R, Nath UK, Alamin M, Jin XL, Shi CH (2018) The brown midrib leaf (bml) mutation in Rice (Oryza sativa) causes premature leaf senescence and induction of defense responses. Genes 9(4):203 (Q2, Index: SCIE, Scopus; IF: 2.8). https://doi.org/10.3390/genes9040203
Alamin M, Zeng DD, Qin R, Sultana MH, Jin XL, Shi CH (2017) Characterization and fine mapping of SFL1, a gene controlling Screw Flag Leaf in rice. Plant Molecular Biology Reporter 35(5):491-503 (Q2, Index: SCIE, Scopus; IF: 1.816). https://doi:10.1007/s11105-017-1039-x
Zeng DD, Qin R, Li M, Alamin M, Jin XL, Liu Y, Shi CH (2017) The ferredoxin-dependent glutamate synthase (OsFd-GOGAT) participates in leaf senescence and the nitrogen remobilization in rice. Molecular Genetics and Genomics 292:385-395 (Q2, Index: SCIE, Scopus; IF: 2.3). https://doi.org/10.1007/s00438-016-1275-z
Qin R, Zeng DD, Liang R, Yang CC, Akhter D, Alamin M, Jin XL, Shi CH (2017) Rice gene SDL/RNRS1, encoding the small subunit of Ribonucleotide Reductase, is required for chlorophyll synthesis and plant growth development. Gene 627:351-362 (Q2, Index: SCIE, Scopus; IF: 2.6). https://doi.org/10.1016/j.gene.2017.05.059
Zeng DD, Qin R, Alamin M, Liang R, Yang CC, Jin XL, Shi CH (2016) DBOP specifies palea development by suppressing the expansion of the margin of palea in rice. Genes and Genomics 38:1095-1103 (Q3, Index: SCIE, Scopus; IF: 1.6). https:.//doi:10.1007/s13258-016-0454-y
Alam MJ, Alamin M, Sultana MH, Amanullah M, Mollah MNH (2016) Regression Based Robust QTL Analysis for F2 Rajshahi University Journal of Science & Engineering 44:95-99. doi:10.3329/rujse.v44i0.30401
Alam MJ, Alamin M, Hossain MR, Islam SMS, Mollah MNH (2016) Robust linear regression based simple interval mapping for QTL analysis with backcross population. Journal of Biological-Sciences 24:75-81. doi.org/10.3329/jbs.v24i0.37489
Purna AN, Sultana MH, Hossain MS, and Alamin M*(2025). Module-Centric Integrative Method for Gene Regulatory Network Reconstruction from scRNA-Seq Data via Control Theory. 2nd International Conference on Frontiers in Science: Innovation & Technology for Greener Industry (2nd ICFS: ITGI), 15 - 16 January 2026, Organized by: Faculty of Science, BUET, Dhaka-1000. (Accepted)
Alam MN, Ahmed KFU, and Alamin M*(2025). Integrative Single-Cell Multi-Omics with SnapATAC2 Reveals Regulatory Programs Underlying Cancer Heterogeneity. 2nd International Conference on Frontiers in Science: Innovation & Technology for Greener Industry (2nd ICFS: ITGI), 15 - 16 January 2026, Organized by: Faculty of Science, BUET, Dhaka-1000. (Accepted)
Sakib MRUD, Sultana MH, and Alamin M*(2025). Decoding Bone Marrow Lineage Architecture Through Combined Transcriptomic and Epigenomic Analysis. 2nd International Conference on Frontiers in Science: Innovation & Technology for Greener Industry (2nd ICFS: ITGI), 15 - 16 January 2026, Organized by: Faculty of Science, BUET, Dhaka-1000. (Accepted)
Purna AN, Sultana MH, and Alamin M*(2025). Single-Cell Dissection of Human Dermal Fibroblast Diversity Reveals Key Regulatory Programs Driving Tissue Remodeling. International Conference on Applied Statistics and Data Science 2025, 28 - 29 December 2025, Institute of Statistical Research and Training (ISRT), University of Dhaka, Dhaka 1000, Bangladesh. (Accepted)
Alamin M*, Sultana MH (2025). Machine Learning Powered Exploration of Single-Cell Data for Therapeutic Development. 1st International Conference on Science and Humanities for Sustainable Development (ICSHSD-2025), organized by the Faculty of Science, DUET, 23–24 October 2025, BUET, Gazipur, Bangladesh.
Purna AN, Sultana MH, Hossain MS, and Alamin M* (2025). Integrating Control theory with HDWGCNA for enhanced Identification of dynamic gene network modules. 1st International Conference on Science and Humanities for Sustainable Development (ICSHSD-2025), organized by the Faculty of Science, DUET, 23–24 October 2025, BUET, Gazipur, Bangladesh.
Sakib MRUD, Sultana MH, Khan AR, and Alamin M* (2025). Integrated Analysis Of Gene Expression And Chromatin Accessibility In PBMCS. 1st International Conference on Science and Humanities for Sustainable Development (ICSHSD-2025), organized by the Faculty of Science, DUET, 23–24 October 2025, BUET, Gazipur, Bangladesh.
Alamin M (2025). Machine Learning-Driven Analysis of Single-Cell Transcriptomics for Insights into Neurodevelopment and Neurodegenerative Disease (2025). The 19th National Statistical Conference 2025, organized by the BSA, Dhaka, Bangladesh.
Sharar S, Hrithik MIA, Dhar S, Purna AN, Ahmed MJ, Prodhan JM and Alamin M* (2025). Advancement of deep learning for accurate protein abundance predictions using single-cell data. 3rd National Mathematics Conference 2024, organized by the Department of Mathematics, 6–7 February 2025, BUET, Dhaka-1000, Bangladesh.
Purna AN, Dhar S, Ahmed MJ, Prodhan JM, Hrithik MIA, Sharar S and Alamin M* (2025). Investigating Gene Regulation and Co-Expression Patterns Using Human Fibroblasts scRNA-Seq Data. 3rd National Mathematics Conference 2024, organized by the Department of Mathematics, 6–7 February 2025, BUET, Dhaka-1000, Bangladesh.
Ahmed MR, Islam MA, Sakib A, Pranto MN, Alamin M, Rawat U, Bhattacharya P, Kumar R. Efficient Web-Based Automated Poultry Disease Detection Using Transfer Learning Models. In 2025 International Conference on Next Generation Communication & Information Processing (INCIP) 2025 Jan 23 (pp. 206-211). IEEE.
Sultana MH, Alamin M* (2024). Robust eQTL model development for Single-Cell Sequencing data. 8th International Conference in The Role of Statistics and Data Science in 4IR (ICRSDS4IR), 26-28 December 2024, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.
Hossain MA, Swarna H, Imran MA, Hossain MH, and Alamin M* (2024). Smart Health Monitoring: An IoT-Based System for Enhanced Remote Patient Care and Early Detection. 8th International Conference in The Role of Statistics and Data Science in 4IR (ICRSDS4IR), 26-28 December 2024, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.
Hrithik MIA, Ahmed MJ, Prodhan JM, Purna AN, Dhar S, and Alamin M* (2024). Advances in eQTL tools for bridging bulk and single-cell sequencing for disease risk prediction. 8th International Conference in The Role of Statistics and Data Science in 4IR (ICRSDS4IR), 26-28 December 2024, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.
Oyshi S, Peea TI, Sultana MH, Hossain MS, and Alamin M* (2024). Heart Failure Prediction Using Machine Learning Models – A Comparative Study of Multiple Algorithms. 8th International Conference in The Role of Statistics and Data Science in 4IR (ICRSDS4IR), 26-28 December 2024, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.
Pappu MAA, Alamin M, Sultana MH, Sarkar A, Mahmud S, Ajadee A, and Mollah MNH (2024). Cell-type specific gene expression changes in Parkinson's disease revealed by analyzing single-nuclei RNA-seq profiles. 8th International Conference in The Role of Statistics and Data Science in 4IR (ICRSDS4IR), 26-28 December 2024, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.
Hossen MB, Sultana MH, Pappu MAA, Mollah MNH, Alamin M* (2024). Identification of key molecular signatures and bioactive compounds modulating screw flag leaf development in rice. 8th International Conference in The Role of Statistics and Data Science in 4IR (ICRSDS4IR), 26-28 December 2024, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.
Zeng DD, Alamin M, Sultana MH, Alam MJ, Shi C, and Mollah MNH (2017). Characterization and Fine Mapping of a Defective Body of Palea, Stipulate Palea Development in Rice. Proceedings of the International Conference on Bioinformatics and Biostatistics for Agriculture, Health and Environment, 20-23 January 2017, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh.
Sultana MH, Alamin M, Alam MJ, Amanullah M, Mahmud AS, and Mollah MNH (2015). An Overview of Next Generation Sequencing Data Analysis by Statistics Methods. Second International Conference on Statistics 2015, University of Dhaka, Dhaka, Bangladesh. [Link]
Sultana MH, Alamin M, Alam MJ and Mollah MNH (2015). Robust Preprocessing of Microarray Gene Expression Data for Fast eQTL. International Conference on Biological Sciences: Food, Health and Environmental Perspectives (ICBSC), August 08, 2015, Organized & Published by Institute of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh.
Alam MJ, Alamin M, Sultana MH, Amanullah M, and Mollah MNH (2014). Robust Regression Based Interval Mapping Approach for QTL International Conference on Applied Statistics, December 27-29, 2014, Organized by ISRT, University of Dhaka, Dhaka, Bangladesh. [Link]
Sultana MH, Alamin M, Alam MJ, and Mollah MNH (2014). Robustification of Fast Map for eQTL Analysis to Find Genomic Locations Influencing Gene Expression. International Conference on Applied Statistics, December 27-29, 2014, Organized by the Institute of Statistical Research and Training (ISRT), University of Dhaka, Dhaka, Bangladesh. [Link]
Alamin M, Monir MM, Ahsan MA, Rahaman MM, Mazid MA, and Mollah MNH (2013). Regression Based QTL Analysis Using Flanking Markers. Poster presented at the Conference of the Bangladesh Society for Biochemistry and Molecular Biology, January 12 & 13, 2013, Chittagong, Bangladesh. [Link]
Mazid MA, Monir MM, Rahaman MM, Ahsan MA, Alamin M , and Mollah MNH (2013). A comparison between QTL and eQTL analysis for identification of important genes. Poster presented at the Conference of the Bangladesh Society for Biochemistry and Molecular Biology, January 12 & 13, 2013, Chittagong, Bangladesh. [Link]
Rahaman MM, Ahsan MA, Monir MM, Alamin M, Mazid MA and Mollah MNH (2013). Robust Classification for Microarray Gene Expression Data Analysis. Poster presented at the Conference of the Bangladesh Society for Biochemistry and Molecular Biology, January 12 & 13, 2013, Chittagong, Bangladesh. [Link]
Ahsan MA, Rahaman MM, Monir MM, Alamin M, Mazid MA, and Mollah MNH (2013). Factor Analysis: a unified approach for simultaneous gene clustering and identification of differential expressions. Poster presented at the Conference of the Bangladesh Society for Biochemistry and Molecular Biology, January 12 & 13, 2013, Chittagong, Bangladesh. [Link]
Monir MM, Alamin M, Ahsan MA, Rahaman MM, Mazid MA, and Mollah MNH (2013). Robust QTL Mapping for Identification of Linked and Unlinked QTLs. Poster presented at the Conference of the Bangladesh Society for Biochemistry and Molecular Biology, January 12 & 13, 2013, Chittagong, Bangladesh. [Link]
Alamin M, Hasan MM, Badsha MB, and Mollah MNH (2012). Statistical Models for Detection of Chromosomal Location Influencing Phenotypes. Presented at the Zoha Memorial Symposium on February 15, 2012. Department of Chemistry, University of Rajshahi, Rajshahi-6205, Bangladesh. [Link]
Alamin M, Hasan MM, Badsha MB, and Mollah MNH (2012). Identification of Chromosomal Locations Influencing Phenotypes. Proceeding in The 3rd BJSPSAA Symposium on Science for Society, February 24 & 25, 2012, Dhaka, Bangladesh. [Link]
Alamin M, Razzaque MA, and Mollah MNH (2012). A Robust Regression Method for QTL Analysis Using Flanking Marker. Proceedings of the International Conference on Statistical Data Mining for Bioinformatics, Health, Agriculture and Environment - 2012, University of Rajshahi, Bangladesh, pp. 112-116, ISBN-978-984-33-5876-9. (With oral presentation). [Link]
Badsha MB, Hasan MM, Alamin M, and Mollah MNH (2012). Application of Clustering Approaches for Bioinformatics. Presented at the Zoha Memorial Symposium on February 15, 2012. Department of Chemistry, University of Rajshahi, Rajshahi-6205, Bangladesh. [Link]
Hasan MM, Alamin M, Badsha MB, and Mollah MNH (2012). Identification of Differentially Expressed Genes for Bioinformatics. Presented at the Zoha Memorial Symposium on February 15, 2012. Department of Chemistry, University of Rajshahi, Rajshahi-6205, Bangladesh. [Link]
Badsha MB, Hasan MM, Alamin M, and Mollah MNH (2012). Clustering Approaches for Gene Expression Data Analysis. Proceeding in The 3rd BJSPSAA Symposium on Science for Society, February 24 & 25, 2012, Dhaka, Bangladesh. [Link]
Hasan MM, Alamin M, Badsha MB, and Mollah MNH (2012). Robust Identification of Differentially Expressed Genes Using Likelihood Ratio Test. M.M. Proceeding in The 3rd BJSPSAA Symposium on Science for Society, February 24 & 25, 2012, Dhaka, Bangladesh. [Link]
Badsha MB, Hanif MA, Hasan MM, Alamin M, and Mollah MNH (2011). Some New Robust Statistical Algorithms and Its Application in Bioinformatics. Proceedings of the Golden Jubilee 2011, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh. [Link]