Md. Tabassum Hossain Emon

Biography

I’m a Bioinformatics and Precision Medicine Enthusiast!

Expertise in bioinformatics analysis on Next Generation Sequencing Data, metagenomics, RNA-seq, single-cell RNA-seq.
Machine Learning (programming by using Python, R, SQL) with version control tools (git and GitHub).
Skillfulness on UNIX/Linux environment, Bash Scripting, and High-Performance Computing(HPC).
Sophisticated statistical knowledge and Basic proficiency in C++, C#, and JAVA.
Hands-on experience in the interactive web portal, ChatBot design with databases (Streamlit, Shiny, IBM Watson).
2023 Goals: Applying Scalable Technologies to Develop Efficient Deep Learning Solutions
⚡ Fun fact: I love to sing, design & arrange things, share ideas and give attention to detail!

Interests

Metagenomics
Precision Medicine
Cancer Biology

Education

B.Sc. in Biotechnology and Genetic Engineering, 2020
Mawlana Bhashani Science and Technology University

Badges

IBM & Google Cloud Skill Badges

Experience

Bioinformatics Intern(Remote)

Nucleate Biosciences LLC.

Sep 2021 – Nov 2021 1196 Preserve Cir, Golden, COLORADO 80401, USA.

Responsibilities include:

Assist in SaaS platform development.
Process and analyze single cell RNA sequencing (scRNA-seq) data Seurat in R, Scanpy in Python, and other relevant library packages.
Understand expression patterns of immune cell subtypes using diffusion pseudotime analysis.
Build and maintain quality control (QC) and analysis workflows and pipelines for large gene expression datasets.

Bioinformatics Developer & Server Admin

Bioinformatics Division

Jan 2020 – Jan 2021 National Institute of Biotechnology, Savar

Responsibilities include:

NGS Analytics
Metagenomics
Database & Functional Application Deployment
Server Administration

Skills

Language & Tools

Statistics

SQL

Projects

Click Tabs to Filter

Bash Projects

Projects Showcasing Task Automation, Data Extraction from File Dierectory, Scheduling Scripts to Run, Calculation, Build Directory Automation with Bash Scripts.

C#

Several Projects with Microsoft’s Popular Programming Language C#.

C++

Some Windows .exe File Projects with C++.

Data Driven Decision Making With Statistics

My this project repository focused on hypothesis testing involving T-test, Chi-square test, Binomial Test, ANOVA, Sample Size Determination with scipy, statmodels modules.

Deep Learning

Projects Implementing Deep Learning and Computer-Vision Methodologies.

JAVA

Java Programming Projects Focusing on OOP and Methods

Machine Learning Projects

Implementation of Linear, logistic regression, K-nearest Neighbor, Decision tree, Neural Net Algorithms with sci-kit learn.

Next Generation Sequencing Data Science

Next Generation Sequence Analytics. RNA-seq with DESeq2, Limma, scRNA-seq, CHIP-seq, INDEL analytics on Big Sequence Bulk data.

Plant Informatics

Gene Expression Exploration Profiling in Model & Other Plant Species.

Python Projects

Python Projects Focusing Data Cleaning & Visualization with Pandas, Matplotlib, Seaborn, Numpy, Scipy modules. Also Performed A/B Test Analytics, OOPs & Price Recommendation Functions.

R Projects

This Project Repository, Focused on Performing Data Tidying, Manipulation, visualization and building Machine Learning model with R.

My Very First Covid-19 Data Viz. Dashboard. Just Select a country and Slide the date bar on the top right corner. The Data History would be simplified as a visual, Displayed on the whole dashboard, scroll to view

SQL Projects

Projects on Fraud Detection, Customer Segmentation, Subscription Churn Rate, CTR Analytics, Trend Analysis with SQL.

Web Applications

Some of my Web Applications. Click the Title to dive in.

Publications

Comparative Genomic Study for Revealing the Complete Scenario of COVID-19 Pandemic in Bangladesh

In this study, we have analyzed 323 SARS-CoV-2 complete genomes sequenced in Bangladesh till October 1st, 2020. Phylogenetic analysis revealed that among the SARS-CoV-2 viruses detected in Bangladesh, the ones belonging to GH and GR clades originated in the UK, the ones in G and O clades in Italy and the ones in S and O clades originated in China. From our analyses, it was discovered that the majority of the SARS-CoV-2 found in Bangladesh belonged to the lineage B 1.1.25 of GR clade.

Mohammad Uzzal Hossain*, Ishtiaque Ahammad, Arittra Bhattacharjee, Zeshan Mahmud Chowdhury, Md Tabassum Hossain Emon, Md Golam Mosaib, Keshob Chandra Das, Chaman Ara Keya, Md Salimullah

Source Document DOI

Comparative Genomic Study for Revealing the Complete Scenario of COVID-19 Pandemic in Bangladesh

Molecular characterization and functional annotation of a hypothetical protein (SCO0618) of Streptomyces coelicolor A3(2)

This study was aimed to determine the structural and biological function of SCO0618, a hypothetical protein of this bacterium through an in-silico approach. Full work published in Genomics & Informatics.

Nadim Ferdous, Mahjerin Nasrin Reza, Md. Tabassum Hossain Emon, Md. Shariful Islam, A. K. M. Mohiuddin, Mohammad Uzzal Hossain

Source Document DOI

Molecular characterization and functional annotation of a hypothetical protein (SCO0618) of Streptomyces coelicolor A3(2)

Newly designed analogues from SARS-CoV inhibitors mimicking the druggable properties against SARS-CoV-2 and its novel variants

Our study proposed, designed and tested three novel inhibitors, UN-1, UN-2 and UN-3 against SGp and Mpro of SARS-CoV-2 and its variants. Binding of these inhibitors to the target proteins may eventually create hindrance in entering host cells and in viral replication. Full work published in RSC Advances

Nadim Ferdous, Mahjerin Nasrin Reza, Md. Tabassum Hossain Emon, Md. Shariful Islam, Mohamed A Nassan, Eman Ibrahim Ahmed, GE Batiha, A. K. M. Mohiuddin, Mohammad Uzzal Hossain

PDF Source Document DOI

Newly designed analogues from SARS-CoV inhibitors mimicking the druggable properties against SARS-CoV-2 and its novel variants

Novel Mutations in NSP1 and PLPro of SARS-CoV-2 NIB-1 Genome Mount for Effective Therapeutics

This study focused on some novel mutations in the NSP1 and NSP3 proteins of SARS-CoV-2. NSP1 is a potent virulence factor of Betacoronavirus and hence a potential target for an attenuated vaccine. PLPro of SARS-like coronavirus has appeared as suitable targets for the development of anti-SARS therapeutics. In the future, wet lab research on the mutants will accelerate research and developments regarding attenuated vaccines and antiviral drugs. Full work published in Journal of Genetic Engineering and Biotechnology.

Mohammad Uzzal Hossain, Arittra Bhattacharjee, Md Tabassum Hossain Emon, Zeshan Mahmud Chowdhury, Md Golam Mosaib, Md Moniruzzaman, Md Hadisur Rahman, Md Nazrul Islam, Irfan Ahmed, Md Ruhul Amin, Asif Rashed, Keshob Chandra Das, Chaman Ara Keya, Md Salimullah

Source Document DOI

Novel Mutations in NSP1 and PLPro of SARS-CoV-2 NIB-1 Genome Mount for Effective Therapeutics

Pathogenic Genetic Variants From Highly Connected Cancer Susceptibility Genes Confer the Loss of Structural Stability

BRCA1, ATM and TP53 protein plays a significant role as tumor suppressor in several cancer types. The present study showed that some plausible genetic variants could destabilize the protein structure and ultimately might play a critical role in altering the biological function of the respective gene. Full work published in Scientific Reports

Nadim Ferdous, Mahjerin Nasrin Reza, Md. Tabassum Hossain Emon, Md. Shariful Islam, A. K. M. Mohiuddin, Mohammad Uzzal Hossain

PDF Source Document DOI

Pathogenic Genetic Variants From Highly Connected Cancer Susceptibility Genes Confer the Loss of Structural Stability

Protein-Protein Interactions Network Model underlines the Link between Hormonal and Neurological Disorders

We have nally predicted possible relationships between the protein IGF1 and its interacting partners SOX2, SOX4 and SOX9 in diseases such as type 1 diabetes, sensorineural hearing loss and intellectual disabilities which should be investigated further for unveiling the molecular mechanisms and discovery of novel biomarkers.

Mohammad Uzzal Hossain, Ishtiaque Ahammad, Arittra Bhattacharjee, Md Tabassum Hossain Emon, Zeshan Mahmud Chowdhury, Islam Md Shariful, Tahia Anan Rahman, Taimur Md Omar, Mohammad Kamrul Hasan, Md Nazrul Islam, Omaima Nasif, Sulaiman Ali Alharbi, Gaber El-Saber Batiha, Keshob Chandra Das, Chaman Ara Keya, Md Salimullah

Source Document

Protein-Protein Interactions Network Model underlines the Link between Hormonal and Neurological Disorders

Recognition of Plausible Therapeutic Agents to Combat COVID-19: An Omics Data Based Combined Approach

This study has proposed four types of therapeutics including chimeric vaccine, potent drugs, siRNAs and ISG targets against COVID–19. We have analyzed all the genomic, host transcriptomic and proteomic data to anticipate the possible therapeutics against the recent pandemic COVID–19. Therefore, these findings might be of interest to the researchers and pharmaceuticals company to discover the novel therapeutics against the SARS-CoV–2. Full work published in Gene.

Mohammad Uzzal Hossain*, Arittra Bhattacharjee*, Md. Tabassum Hossain Emon*, Zeshan Mahmud Chowdhury*, Muntahi Mourin, Keshob Chandra Das, Chaman Ara Keya, Md Salimullah

Source Document DOI

Recognition of Plausible Therapeutic Agents to Combat COVID-19: An Omics Data Based Combined Approach

TAILORED BIOINFORMATICS & MACHINE LEARNING APPROACH FOR HACKING INTO COVID-19 MICROBIAL SYSTEM

This thesis is part of the BCSIR-NIB mNGS collaboration project, which focuses on the application of shotgun metagenomics for the characterization of the Oropharyngeal sample collected from Covid-19 patient. Click Video Button for a Quick Walkthrough.

Md. Tabassum Hossain Emon

PDF Video Source Document DOI

TAILORED BIOINFORMATICS & MACHINE LEARNING APPROACH FOR HACKING INTO COVID-19 MICROBIAL SYSTEM

Whole Genome Sequencing for Revealing the Point Mutations of SARS-CoV-2 Genome in Bangladeshi Isolates and their Structural Effects on Viral Proteins

We have performed whole genome sequencing of SARS-CoV-2 to identify genetic variations and then analyzed their impact on the structures of their corresponding proteins. We have also identified the insertions/deletions among all the sequenced Bangladeshi SARS-CoV-2 strains. The energy minimization and the drug binding analysis suggested that the identified mutations might have significant impact on structure and function of their target proteins. Full work published in RSC Advances.

Mohammad Uzzal Hossain, Ishtiaque Ahammad, Md Tabassum Hossain Emon, Arittra Bhattacharjee, Zeshan Mahmud Chowdhury, Md Golam Mosaib, Keshob Chandra Das, Chaman Ara Keya, Md Salimullah

Source Document DOI