S M Ashiqul Islam

About S M Ashiqul Islam

More than eight years of experience in Python programming (), R programming (), Bash Scripting, and Next-Flow pipeline. Capable of making reproducible codes and easy-to-use Python and R packages. Routinely use NumPy, Pandas, Scikit-learn, Scipy, and many other packages for data code development and data analysis. Also, have working knowledge of Perl, HTML, CSS, and Javascript: I have been analyzing NGS datasets from TCGA, ICGC, and many other sources to define somatic mutational signatures using single nucleotide variants (SNV), copy number variants (SNV) and structural variants (SV). We use the mutational signatures to associate cancer risk factors with different types of cancer and assessment of targeted therapeutic approaches. I also have experience using different genome analysis frameworks such as GATK and Dragon Bio-IT platforms as well genome analysis tools (BWA, Samtools, FastQC) and variant callers (Mutect2, Strelka2, VarScan, MuSE): Developed tools capable of parallel computing using multiprocessors and multithreading. Also, implement a message-passing interface (MPI) in Python to use CPUs from separate nodes in a parallel fashion. Routinely implement GPU-enabled coding using PyTorch and TensorFlow frameworks: Have excellent command and understanding of supervised and unsupervised machine learning algorithms. Hands-on experience with SVM (support vector machine), Logistic regression, Random Forest, deep-learning algorithms, Non-Negative Matrix Factorization, PCA, Kmean, and Hierarchical Clustering. Also, have good knowledge of algorithms for DNA Sequencing: Comprehensive experience using Amazon Web Service (AWS). Perform large matrix operation-based data analysis in CPU, GPU, and memory-optimized instances. Quite familiar with storing, sending, and receiving data in S3 buckets. Also, routinely use other cluster/supercomputers at UC San Diego: Have comprehensive and in-depth knowledge of machine learning, next-generation sequencing (NGS), molecular biology, immunology, cancer genomics, and cell signaling pathways.

Experience

1. Assistant Professor

   University at Albany

   Aug 2024 — Present · Albany, NY, US

Education

• Baylor University

  Doctor of Philosophy - PhD, Biomedical Sciences, General

  2012 — 2018

• University of Dhaka

  Master's degree, Genetic Engineering and Biotechnology

  2009 — 2010

• University of Dhaka

  Bachelor's degree, Genetic Engineering and Biotechnology

  2005 — 2009

Skills

• Linux
• Galaxy
• Data Visualization
• R Programming
• Next Generatin Sequence Analysis (Ngs)
• Flask Framework
• Html
• Javascript
• Protein Expression in E.coli
• Data Analysis
• Data Modeling
• Web Application Development
• Transient Protein Expresion in Plant
• Protein Purification
• Protein Sequence Analysis
• Cascading Style Sheets (Css)
• Fplc
• Python
• Protein Purification Using Fplc
• Bootstrap
• Latex
• Machine Learning
• Molecular Cloning
• Mass Spectrometry