Epigenetics and Bioinformatics Research Laboratory

Department of Genetic Engineering and Biotechnology, University of Dhaka

About Us

The Human Genome Project was initiated with the goal of unraveling our genetic makeup to better understand the underlying mechanisms of diseases like cancer, diabetes, and arthritis. While this project laid the groundwork, we've since learned that DNA alone doesn't hold all the answers. Genetic processes are further regulated by the "epigenome," which operates as a separate coding system. Unlike DNA, the epigenome's code is adaptable and reversible. It can respond to environmental cues, altering its pattern and subsequently influencing gene expression.

Bioinformatics plays a crucial role in interpreting the vast amounts of genetic data from humans, animals, and plants worldwide. This knowledge can be leveraged to deepen our understanding of disease mechanisms, improve diagnosis, and aid in the development of drugs and vaccines.

Recent advances in high-throughput technologies have enabled more systematic exploration of epigenetic mechanisms. Bioinformatics expertise has become indispensable for extracting meaningful insights from the enormous data sets. Epigenetic defects are increasingly recognized as key players in complex diseases, such as cancer, presenting new opportunities for enhanced diagnosis and treatment.

Furthermore, emerging infectious diseases continue to pose significant risks to global health. Gaining a deeper understanding of disease mechanisms and host-pathogen interactions is critical for developing effective drugs and vaccines. These areas of research offer rich possibilities for bioinformatics analysis. We utilize bioinformatics and experimental biological techniques, along with high-throughput data—both publicly available and generated in our own laboratory—to tackle biological mysteries.

Our Research Interests

Medical Biotechnology

(Genomics & Molecular Biology of Diseases)

Epigenetic & Genetic mechanisms of human diseases, specially cancer, arthritis, diabetes and metabolic disorders; and emerging infectious diseases. Epigenetic drug target and drug discovery. Mechanism and drug/vaccine discovery against infectious disease, specially viruses

Bioinformatics, Computational & System Biology

Optimization, analysis and management of Next Generation (NGS)/Third generation sequence data (whole genome sequencing, exonm seq, ATAC-seq, ChIPseq, RNAseq, Single Cell RNAseq, CITE-seq, MethylomeSeq etc), HiC, microarray, Chip-on-chip, ChIP-tiling and other high-throughput genomic and proteomic data; In Silico/computer aided drug design (CADD); Vaccine design. Data integration, mining and visualization; bioinformatic study of Epigenetic mechanisms in cancer; drug target identification, biological PPIN/GRN/PCN/metabolic network; MALDI/NMR etc proteomic data analysis for marker identification for cancer diagnosis; prediction of structure based regulatory elements in genomics and proteomic data; Metagenomics

Our Aims

Cancer Genomics & Epigenetics

Arthritis, Diabetes Molecular Mechanisms

mRNA Vaccine Designing & Immunoinformatics

Host-Pathogen Interaction

Biology of non-coding RNAs

NGS, Whole Genome Analysis & Metagenomics

Epigenetics of Disease & Development

Drug Designing Biosimilar & Biologics

Selected Publications

Coronavirus Research

Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2.

Abul B.M.M.K. Islam*, Md. Abdullah-Al-Kamran Khan, Rasel Ahmed, Md. Sabbir Hossain, Shah Md. Tamim Kabir, Md. Shahidul Islam, A.M.A.M. Zonaed Siddiki. (*Corresponding). (2021). Journal of Translational Medicine. (Impact Factor: 4.541)

SARS-CoV-2 proteins exploit host’s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology

Md. Abdullah-Al-Kamran Khan and Abul Bashar Mir Md. Khademul Islam. (2021). Frontiers in Molecular Biosciences. (Impact Factor: 4.188)

Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy.

Abul Bashar Mir Md. Khademul Islam and Md. Abdullah-Al-Kamran Khan (2020). Scientific Report. (Impact Factor: 3.998)

Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis.

Refat Sharmin and Abul B.M.M.K. Islam. (2016). Source Code in Biology & Medicine.

Cancer Research

Coregulation of Histone-modifying Enzymes in Cancer.

Abul B.M.M.K. Islam, Richter WF, Jacobs LA, Lopez-Bigas N and Benevolenskaya EV. (2011). PLoS One. (Impact Factor: 4.61)

Cell autonomous versus systemic Akt isoform deletions uncovered new roles for Akt1 and Akt2 in breast cancer.

Xinyu Chen, Majd Ariss, Gopalkrishnan Ramakrishnan, Veronique Nogueira, Cathreine Blahah, Wiliam Putzbach, Abul BMMK Islam, Maxim V Frolov, and Nissim Hay. (2020). Molecular Cell. (Impact Factor: 15.584).

DNA methylation and hormone receptor status in breast cancer.

Elizaveta Benevolenskaya, Abul B.M.M.K. Islam, Habibul Ahsan, Muhammad G. Kibriya, Farzana Jasmine, Ben Wolff, Umaima Al-Alem, Elizabeth Wiley, Andre Kajdacsy-Balla, Virgilia Macias, Garth H. Rauscher. (2016). Clinical Epigenetics. (Impact Factor: 4.543)

Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells.

Renáta Váraljai*, Abul B.M.M.K. Islam*, Michael L. Beshiri, Jalees Rehman, Nuria Lopez-Bigas and Elizaveta V. Benevolenskaya. (2015). (*equal contribution). Genes and Development. (Impact Factor:12.64)

Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2.

Lluís Millán-Ariño, Abul B.M.M.K. Islam, Andrea Izquierdo-Bouldstridge, Regina Mayor, Jean-Michel Terme, Neus Luque, Mónica Sancho, Núria López-Bigas and Albert Jordan (2014). Nucleic Acids Research. (Impact Factor: 8.278)

Chromatin-Bound IκBα Regulates a Subset of Polycomb Target Genes in Differentiation and Cancer.

Mulero C, Ferres-Marco D, Abul B.M.M.K. Islam, Pecoraro M , Charneco C, Bellora N, Toll A, Gallardo F, Asensio E, López-Arribillaga E, Rodilla V, Iglesias M, Shih V, Alba M, Di Croce L, Hoffmann A, Villà-Freixa J, López-Bigas N, Keyes B, Domínguez M, Bigas A and Espinosa L. (2013). Cancer Cell. (Impact Factor: 28.2)

miRNA epigenetics Research

A switch in bidirectional histone mark leads to differential modulation of lincRNAs involved in neuronal and hematopoietic cell differentiation from their progenitors.

Wahid Murad, Md. Abdullah-Al-Kamran Khan, Md. Sajedul Islam, and Abul BMMK Islam. Journal of Cellular Biochemistry. (Impact Factor: 3.448)

Intronic miRNA miR-3666 is a potential modulator of its host gene FOXP2 functions in neurodevelopment and may contribute to the pathogenesis of neurological disorders schizophrenia and autism.

Salwa Mohd. Mostafa, Md. Wahid Murad, Eusra Mohammad and Abul B.M.M.K. Islam. (2017). Journal of Applied Biotechnology & Bioengineering.

In silico analysis revealed Zika virus miRNAs associated with viral pathogenesis through alteration of host genes involved in immune response and neurological functions.

Md Sajedul Islam, Md Abdullah-Al-Kamran Khan, Md Wahid Murad, Marwah Karim, and Abul BMMK Islam. (2019). Journal of Medical Virology. (Impact Factor: 2.094)

Biosimilar and Biologics Research

Computational engineering the binding affinity of Adalimumab monoclonal antibody for designing potential biosimilar candidate

Md. Abdullah-Al-Kamran Khan, Rafeed Rahman Turjya, Rabi Us Sany, and Abul BMMK Islam. (2021). Journal of Molecular Graphics and Modelling. (Impact Factor: 2.079)

Immunoinformatics Research

An in silico approach predicted potential therapeutics that can confer protection from maximum pathogenic Hantaviruses.

Salwa Mohd. Mostafa and Abul B.M.M.K. Islam. (2016). Future Virology. (Impact Factor: 1.011)

A highly conserved YPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design.

Refat Sharmin and Abul B.M.M.K. Islam. BMC Bioinformatics. (Impact Factor: 3.02)

Arthritis research

Mandar Dave*, Abul B.M.M.K. Islam*, Roderick V. Jensen, Agueda Rostagno, Jorge Ghiso, Ashok R. Amin.

Proteomic Analysis Shows Constitutive Secretion of MIF and p53-associated Activity of COX-2-/- Lung Fibroblasts. (2017). Genomics, Proteomics & Bioinformatics. (*equal contribution). (Impact Factor: 7.051).

Genomic, Lipidomic and Metabolomic Analysis of Cyclooxygenase-null Cells: Eicosanoid Storm, Cross Talk, and Compensation by COX-1.

Abul Islam, Mandar Dave, Sonia Amin; Roderick Jensen, Ashok Amin. (2016). Genomics, Proteomics & Bioinformatics. (Impact Factor: 7.051)

Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression.

Lorenzo de la Rica, José M Urquiza, David Gómez-Cabrero, Abul B. M. M. K. Islam, Nuria López-Bigas, Jesper Tegnér, René E.M. Toes, and Esteban Ballestar. (2013). Journal of Autoimmunity. (Impact Factor: 7.37)

Single Cell Research

Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer.

Alexandre Aissa, Abul BMMK Islam, Majd Ariss, Cammille Go, Alexandra Rader, Ryan Conrardy, Alexa Gajda, Carlota Rubio-Perez, Klara Valyi-Nagy, Mary Pasquinelli, Lawrence Feldman, Stefan Green, Nuria Lopez-Bigas, Maxim Frolov, and Elizaveta Benevolenskaya. (2021). Nature Communication. (Impact Factor: 12.121).

Single cell RNA-sequencing identifies a metabolic aspect of apoptosis in Rbf mutant.

Majd M Ariss, Abul BMMK Islam, Meg Critcher, Maria Paula Zappia, and Maxim V Frolov. (2018). Nature Communications. (Impact Factor: 12.353).

A cell atlas of the adult muscle precursors uncovers early events in fiber-type divergence in Drosophila.

Maria Paula Zappia, Majd Ariss, Lucia De Castro, Abul BMMK Islam, and Maxim V Frolov. (2020). EMBO Reports. (Impact Factor: 4.95).

Cell autonomous versus systemic Akt isoform deletions uncovered new roles for Akt1 and Akt2 in breast cancer.

Amalgam regulates the receptor tyrosine kinase pathway through Sprouty in glial cell development in the Drosophila larval brain.

Majd M. Ariss, Alexander R. Terry, Abul B. M. M. K. Islam, Nissim Hay and Maxim V. Frolov. (2020). Journal of Cell Science. (Impact Factor: 4.573).

Transcriptional repression by FoxM1 suppresses tumor differentiation and promotes metastasis of breast cancer.

Dragana Kopanja, Vaibhav Chand, Eilidh O'Brien, Nishit Mukhopadhyay, Maria Zappia, Abul Islam, Maxim Frolov, Bradley Merrill, and Pradip Raychaudhuri. (2022). Cancer Research (Impact Factor: 12.843)

COVID-19 Research

Clinical management of COVID-19 is still complicated due to the lack of therapeutic interventions to reduce the breathing problems, respiratory complications and acute lung injury - which are the major complications of most of the mild to critically affected patients and the molecular mechanisms behind these clinical features are still largely unknown.

The SARS-CoV-2 genome, initially reported on January 12, has been studied extensively with the hope of uncovering useful information about COVID-19. The novel Coronavirus that has created so much havoc in several countries but was unable to do so in some other countries. One very important question is, why is it so? Also, some are severely affected while others even remain asymptomatic. The genomes, transcriptomes and immunome of SARS-CoV-2 hold many answers to questions scientists are searching for at a feverish pace. Our group is working on this area to understand the COVID-19 disease mechanism, find drug targets and drug design.

Our five research articles have been published already and some other projects are going on.

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