Bioinformatics,Computational Biology,Artificial Intelligence,Genomics

Shamima Akter

Email: *******@***.*** Cell: 540-***-****

Google scholar: https://scholar.google.com/citations?user=X7Mf04MAAAAJ&hl=en

• Career Goal

I want to secure a responsible position in industry utilizing my academic knowledge and industry experience in the fields of genomics, bioinformatics, and computational biology. I am interested in identifying genetic and genomic alterations that may be responsible for inherited and acquired diseases or conditions. I have extensive experience in Artificial Intelligence (AI), computational modeling, and pipeline development regarding genomics data analysis such as RNA-seq, Single-cell RNA-seq or Microarrays.

• Legal Status

Permanent Resident (no visa sponsorship is required)

• Education

• PhD candidate: Bioinformatics and Computational Biology, George Mason University (GMU), Virginia, USA, expected graduation by July 2024,

Dissertation: Computational Modeling of Calcium dynamics involving different calcium channels in Alzheimer’s disease

• MS: Bioinformatics and Genomics, Virginia Tech (VT), December 2017 Thesis: Development of RNA-Seq pipeline to identify common and unique stress responsive genes in Arabidopsis Thaliana

• MS: Biochemistry & Molecular Biology (BMB), University of Dhaka, Bangladesh Thesis: Identifying Biochemical test parameters in different Liver diseases

• BS: Biochemistry & Molecular Biology, University of Dhaka, Bangladesh

• Programming Skills

• Artificial Intelligence (Machine learning and Deep learning) in heterogeneous biological data set

(gene expression, clinical and cancer) using Python

• Expertise in visualization (line plot, barplot, scatterplot, boxplot, histogram, AUC curve) using Python

• Computational modeling of calcium signaling and receptors in ER and plasma membrane through simulation in Fortran and Linux server to find out disease pathology and response

• Biostatistical analysis (t-test, different statistical analysis) using R

• Genomics Analysis (RNA-seq, Single Cell RNA-Seq, Microarray) using R

• Bash Coding (Linux) for RNA-seq

• Next-Generation sequence analysis tools (STAR, featureCounts,DESeq2 etc.)

• In Silico analysis of SNPs of several genes (TP63, IFNAR2)

• Lab Skills

• Molecular biological procedures: Transformation, electrophoresis, cloning, restriction digestion, and PCR

• Microbiological techniques: Media preparation, bacteria culture

• Biochemical techniques: spectrophotometry, High Performance Liquid Chromatography (HPLC) and ELISA

• Plasmid DNA & plant DNA isolation, plant tissue culture, and q-RT PCR

• Experimental Work (Cell culture)

• Performed in cell splitting, cell seeding, and infection with virus and plaque assay to get the virus titer after infection

• Worked for growth curve analysis of different viruses in various cell lines

• Employment History

• Graduate Research Assistant, George Mason University (GMU) Aug 2019 - present

• Computational analysis of calcium dynamics in neurological disorder, currently working for Alzheimer’s disease

• Computational modeling of neuron cell along with calcium channels i.e., IP3 receptor, RyR, Mitochondria through simulation

• Application of machine learning (Naïve Bayes, logistic regression, Linear Regression, Random Forest, CART, DecisionTree)

• Application of deep learning models (ANN, RNN, MLP, LSTM, GRU) in kidney, liver, and Alzheimer disease

• Development of hybrid deep learning models for classification and prediction of CKD

• Genomics and data analysis (RNA-seq, Single Cell RNA-seq, Micro-array, phylogenetic tree),

• Biostatistical analysis (t-test, Wilcoxon test, regression, k-means, and hierarchical clustering) ANOVA, parametric and non-parametric analysis, normal distribution) with disease data set

• Instructor, Cell Biology (BIOL 213), GMU

• Research Associate, Biomedical Sciences and Pathobiology, VT July 2016- Aug 2019

• Worked rigorously in R for different data parsing, preparation from simple to complex type

• Analyzed microbial transcriptome data in Linux and R

• Performed visualization of gene expression data in R

• Performed network analysis (Bayesian statistical method; ‘bnlearn’ package) in R for the gene expression data

• Performed python programming for data parsing and preparation

• Assistant Manager, Quality Assurance and Research Jan 2004- Dec 2010 Ambee Pharmaceutical Ltd, Dhaka, Bangladesh

• Conducted complex biochemical analysis of oral & injectable drugs using spectrophotometry, mass spectroscopy, HPLC, electrophoresis, and immunoassay

• Identified the underlying principles of information by breaking down information or data into separate parts.

Shamima Akter

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