A5036701994- Bioinformatics and Genomic Networks
- vaccines and immunoinformatics approaches
- Monoclonal and Polyclonal Antibodies Research
- Allergic Rhinitis and Sensitization
- Asthma and respiratory diseases
- Machine Learning in Bioinformatics
- Tuberculosis Research and Epidemiology
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Food Allergy and Anaphylaxis Research
- Immune Cell Function and Interaction
- Computational Drug Discovery Methods
- Metabolomics and Mass Spectrometry Studies
- T-cell and B-cell Immunology
- Immunotherapy and Immune Responses
- Genomics and Phylogenetic Studies
- Mycobacterium research and diagnosis
- Ubiquitin and proteasome pathways
- Adenosine and Purinergic Signaling
- Antibiotic Resistance in Bacteria
- interferon and immune responses
- Gene expression and cancer classification
- Pulmonary Hypertension Research and Treatments
- Respiratory viral infections research
Bose Institute
2016-2025
Dhaka Shishu Hospital
2022
Chattogram Veterinary and Animal Sciences University
2019
Case Western Reserve University
2010-2013
University School
2012
Center for Systems Biology
2008
Indiana University – Purdue University Indianapolis
2008
Institute of Microbial Technology
2004-2007
Indian Veterinary Research Institute
2003
B-cell epitopes play a vital role in the development of peptide vaccines, diagnosis diseases, and also for allergy research. Experimental methods used characterizing are time consuming demand large resources. The availability epitope prediction method(s) can rapidly aid experimenters simplifying this problem. standard feed-forward (FNN) recurrent neural network (RNN) have been study predicting an antigenic sequence. networks trained tested on clean data set, which consists 700 non-redundant...
In this study a systematic attempt has been made to integrate various approaches in order predict allergenic proteins with high accuracy. The dataset used for testing and training consists of 578 allergens 700 non-allergens obtained from A. K. Bjorklund, D. Soeria-Atmadja, Zorzet, U. Hammerling M. G. Gustafsson (2005) Bioinformatics , 21 39–50. First, we developed methods based on support vector machine using amino acid dipeptide composition achieved an accuracy 85.02 84.00%, respectively....
Abstract Background Bcipep is a database of experimentally determined linear B-cell epitopes varying immunogenicity collected from literature and other publicly available databases. Results The current version contains 3031 entries that include 763 immunodominant, 1797 immunogenic 471 null-immunogenic epitopes. It covers wide range pathogenic organisms like viruses, bacteria, protozoa, fungi. provides set tools for the analysis extraction data includes keyword search, peptide mapping BLAST...
Abstract In this study, an attempt has been made to predict the major functions of gram-negative bacterial proteins from their amino acid sequences. The dataset used for training and testing consists 670 non-redundant (255 cellular process, 60 information molecules, 285 metabolism, 70 virulence factors). First we developed SVM-based method using dipeptide composition achieved overall accuracy 52.39% 47.01%, respectively. We introduced a new concept classification based on tetrapeptides, in...
Abstract Background In past number of methods have been developed for predicting subcellular location eukaryotic, prokaryotic (Gram-negative and Gram-positive bacteria) human proteins but no method has mycobacterial which may represent repertoire potent immunogens this dreaded pathogen. study, attempt made to develop proteins. Results The models were trained tested on 852 evaluated using five-fold cross-validation technique. First SVM (Support Vector Machine) model was amino acid composition...
Viral-host protein-protein interaction plays a vital role in pathogenesis, since it defines viral infection of the host and regulation proteins. Identification key viral-host interactions (PPIs) has great implication for therapeutics.In this study, systematic attempt been made to predict PPIs by integrating different features, including domain-domain association, network topology sequence information using from VirusMINT. The three well-known supervised machine learning methods, such as SVM,...
Protein-protein interactions (PPIs) are important for the study of protein functions and pathways involved in different biological processes, as well understanding cause progression diseases. Several high-throughput experimental techniques have been employed identification PPIs a few model organisms, but still, there is huge gap identifying all possible binary an organism. Therefore, PPI prediction using machine-learning algorithms has used conjunction with methods discovery novel...
Abstract Tuberculosis treatment includes broad-spectrum antibiotics such as rifampicin, streptomycin and fluoroquinolones, which are also used against other pathogenic bacteria. We developed Drug Resistance Associated Genes database (DRAGdb), a manually curated repository of mutational data drug resistance associated genes (DRAGs) across ESKAPE (i.e. Enterococcus faecium , Staphylococcus aureus Klebsiella pneumonia e, Acinetobacter baumannii Pseudomonas aeruginosa Enterobacter spp.)...
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides, which show evidence of pervasive transcription and participate in a plethora cellular regulatory processes. Although several have been functionally annotated as lncRNAs within the genome, not all proven to fulfill criteria for functional regulator further analyses be done order include them cohort. LncRNAs being classified reclassified an ongoing annotation process, challenge is fraught with ambiguity, newer evidences...
PIWI-interacting RNA (piRNA) is a novel and emerging class of small non-coding (sncRNA). Ranging in length from 26-32 nucleotides, this sncRNA potent player guiding the vital regulatory processes within cellular system. Inspite having such wide role systems, piRNAs are not well organized classified, so that researcher can pool out biologically relevant information concerning class. Here we present piRNAQuest- unified comprehensive database 41749 human, 890078 mouse 66758 rat obtained NCBI...
Post-translational modification pathways such as SUMOylation are integral to all cellular processes and tissue homeostasis. We investigated the possible involvement of in epithelial signalling Crohn's disease (CD) ulcerative colitis (UC), two major forms inflammatory bowel (IBD). Initially a murine model IBD, induced by dextran-sulfate-sodium (DSS mice), we observed inflammation accompanied lowering global colonic epithelium. The alteration was due decrease sole SUMO E2 enzyme (Ubc9)....
This paper describes a method developed for predicting bacterial toxins from their amino acid sequences. All the modules, in this study, were trained and tested on non-redundant dataset of 150 that included 77 exotoxins 73 endotoxins. Firstly, support vector machines (SVM) based modules using acids dipeptides composition achieved an accuracy 96.07% 92.50%, respectively. Secondly, SVM discriminating entotoxins exotoxins, 95.71% 92.86%, In addition, have been classifying (e.g. activate...
Comprehensive knowledge of host-pathogen interactions is central to understand the life cycle a pathogen and devise specific therapeutic strategies. Protein-protein (PPIs) are key mediators interactions. Hepatitis E virus (HEV) major cause viral hepatitis in humans. Recent reports also demonstrate its extrahepatic manifestations brain. Toward understanding molecular details HEV cycle, we screened human liver fetal brain cDNA libraries identify host interaction partners proteins encoded by...
Abstract Cancer stem cells (CSCs) are a small heterogeneous population present within the tumor exhibiting self-renewal properties. CSCs have been demonstrated to elicit an important role in cancer recurrence, metastasis and drug resistance. distinguished from cell populations based on their molecular profiling or expression of distinct CSC biomarker(s). Recently, huge amount omics data generated for characterization CSCs, which enables distinguishing different cancers. Here, we report...
We have developed a method NTXpred for predicting neurotoxins and classifying them based on their function origin. The dataset used in this study consists of 582 non-redundant, experimentally annotated obtained from Swiss-Prot. A number modules been using residue composition feed-forwarded neural network (FNN), recurrent (RNN), support vector machine (SVM) achieved maximum accuracy 84.19%, 92.75%, 97.72% respectively. In addition, SVM source (e.g., eubacteria, cnidarians, molluscs,...
The emergence of drug-resistant strains Mycobacterium tuberculosis makes identification and validation newer drug targets a global priority. Phosphoserine phosphatase (PSP), key essential metabolic enzyme involved in conversion O-phospho-l-serine to l-serine, was characterized this study. M. genome harbors all enzymes l-serine biosynthesis including two PSP homologs: Rv0505c (SerB1) Rv3042c (SerB2). In the present study, we have biochemically SerB2 developed malachite green-based high...
Bacterial Rieske-type aromatic ring-hydroxylating oxygenases (RHOs) constitute a large family of enzymes, primarily involved in bioremediation diverse compounds the environment. In present study, we have designed manually curated database, Ring-Hydroxylating Oxygenase database (RHObase), which provides comprehensive information on all biochemically characterized bacterial RHOs. It consists ∼ 1000 entries including 196 oxygenase α-subunits, 153 β-subunits, 92 ferredoxins and 110 reductases,...
Paired two-component systems (TCSs), having a sensor kinase (SK) and cognate response regulator (RR), enable the human pathogen Mycobacterium tuberculosis to respond external environment persist within its host. Here, we inactivated SK gene of TCS MtrAB, mtrB, generating strain ΔmtrB. We show that mtrB loss reduces bacterium's ability survive in macrophages increases association with autophagosomes autolysosomes. Notably, ΔmtrB was markedly defective establishing lung infection mice, no...