Syed Danish Ali, Ph.D.

Research Associate, Biological Systems Engineering
Madison, US.

About

A highly accomplished Research Associate with a Ph.D. in Engineering, specializing in the application of advanced machine learning and deep learning techniques to complex problems in biological systems engineering, bioinformatics, and computational biology. Proven expertise in developing predictive models for biomass conversion efficiency, identifying disease-related genetic markers, and optimizing industrial processes, backed by 14 peer-reviewed journal publications and significant grant funding. Seeking to leverage strong analytical, modeling, and research skills to drive innovation in a leading R&D or academic institution.

Work

University of Wisconsin-Madison and USDA Forest Products Laboratory
|

Research Associate

Madison, WI, US

Summary

Deploys machine learning algorithms to predict biomass handling properties and conversion efficiencies, develops models for biomass characteristics, and optimizes cellulose nanomaterial production.

Highlights

Deployed advanced machine learning algorithms to accurately predict biomass handling properties and conversion efficiencies.

Developed sophisticated machine learning models to analyze biomass characteristics, handling techniques, pretreatment processes, and fuel conversion, enhancing process understanding.

Leveraged experimental data and hyperspectral images from forest and crop residues to validate and refine predictive models.

Optimized and scaled up the analysis of cellulose nanomaterial production through advanced machine learning models.

Jeonbuk National University
|

Research Assistant

Jeonju, South Korea, Korea (Republic of)

Summary

Developed computational models for bioinformatics and computational biology using deep and machine learning techniques, focusing on disease identification and genetic marker analysis.

Highlights

Developed advanced computational models for bioinformatics and computational biology, leveraging deep and machine learning techniques to address complex biological problems.

Participated in identifying genes associated with neurodegenerative diseases and disorders by applying artificial intelligence tools and techniques.

Assisted in developing deep learning models to accurately identify cancer-associated DNA methylation markers, contributing to early detection research.

The University of Azad Jammu and Kashmir (UAJK)
|

Lab Engineer/Instructor

Muzaffarabad, Pakistan, Pakistan

Summary

Conducted undergraduate lab sessions and designed lab manuals for electrical engineering courses, ensuring compliance with Higher Education Commission (HEC) guidelines.

Highlights

Conducted undergraduate lab sessions for 7 diverse electrical engineering courses, including Data Structures, Digital Signal Processing, and Electronic Circuit Design.

Designed and updated lab manuals for all assigned courses, ensuring alignment with Higher Education Commission (HEC) guidelines and enhancing student learning outcomes.

Participated in Pakistan Engineering Council accreditation visits, maintaining and improving standard operating procedures (SOPs) for departmental labs.

Sprintech Packaging Pvt. Ltd.
|

Assistant Manager Electrical

Lahore, Pakistan, Pakistan

Summary

Contributed to automating a seven-color rotogravure printing machine and oversaw the installation, commissioning, and maintenance of electrical and production units.

Highlights

Contributed to the automation of a seven-color rotogravure printing machine, significantly enhancing operational efficiency and output.

Oversaw the successful installation, commissioning, and troubleshooting of PLC and HMI interfaces.

Led the installation and commissioning of advanced bag-making machines, optimizing production capabilities.

Managed shifts for operation and maintenance (OM), utilities, and production units, ensuring seamless workflow and minimizing downtime.

AJK Power Development Organization
|

Assistant Engineer Electrical

Muzaffarabad, Pakistan, Pakistan

Summary

Supervised shift operations and oversaw the installation and maintenance of electromechanical equipment for hydropower plants.

Highlights

Supervised shift operations for the 3.0 MW Qadirabad Hydel Power Station, ensuring efficient load management, synchronization, monitoring, and maintenance of electromechanical equipment using SCADA.

Oversaw the installation of electromechanical equipment at the 3.2 MW Rehra Hydropower Plant, contributing to project completion and operational readiness.

Education

Jeonbuk National University
Jeonju, South Korea, Korea (Republic of)

Doctor of Philosophy

Electronics and Information Engineering

Abasyn University Islamabad Campus
Islamabad, Pakistan, Pakistan

Master of Science

Electrical Engineering

Ghulam Ishaq Khan Institute of Science and Technology
Swabi, Pakistan, Pakistan

Bachelor of Science

Electronic Engineering

Awards

USDA-DOE Cooperative Agreement Support

Awarded By

U.S. Department of Agriculture Forest Service and Department of Energy

Secured funding under Cooperative Agreement No. 22-CO-11111137-017 and DOE Award No. DE-EE0008911 for collaborative research with the University of Georgia and University of Wisconsin.

Forestry Nanotechnology Research Grant

Awarded By

U.S. Endowment for Forestry and Communities, Inc., and P3Nano

Awarded for Project No. 21-00288, supporting research in forestry nanotechnology.

AFRI Competitive Research Grant

Awarded By

USDA National Institute of Food and Agriculture

Received grant funding under Grant No. 2020-68012-31881 for competitive research.

Brain Korea (BK-21) Scholarship

Awarded By

National Research Foundation of Korea

Awarded for doctoral studies in Engineering, supporting research under Grant Numbers: 2017M3C7A1044816 and 2020R1A2C2005612.

Publications

Integrating deep learning and machine learning models to simulate soil heterotrophic respiration and rhizosphere priming effect in Duke Forest

Published by

Bioresource Technology

Summary

(To be submitted; Internal review)

Near-infrared hyperspectral imaging-driven machine learning models for predicting southern pine residue thermochemical conversion efficiency

Published by

Energy and AI

Summary

(To be submitted; Internal review)

Advancing Biomass Handling and Logistics: Machine Learning Models for Predicting Corn Stover Bulk Flow Properties.

Published by

ASABE Annual International Meeting

Summary

Oral Presentation at Sheraton Centre Toronto Hotel, Toronto, Ontario.

Application of machine learning to predict the products yield of lignocellulosic biomass fast pyrolysis process

Published by

Bioresource Technology

Summary

(To be submitted; Internal review)

Machine learning for predicting and optimizing corn stover hydrolysis conversion efficiency

Published by

Applied Energy

Summary

(Submitted)

Deep learning enabled process design and decision-making for lignocellulosic biomass slow pyrolysis

Published by

Renewable and Sustainable Energy Reviews

Summary

(Submitted)

Stacking based ensemble learning framework for identification of nitrotyrosine sites

Published by

Computers in Biology and Medicine

Summary

Volume 183, 109200. (Co-first author)

Utilization of synthetic near-infrared spectra via generative adversarial network to improve wood stiffness prediction

Published by

Sensors

Summary

Volume 24, no. 6, 1992. (Editor's Choice Article)

Fiber quality prediction using NIR spectral data: tree-based ensemble learning vs. deep neural networks

Published by

Wood and Fiber Science

Summary

Volume 55, no. 1, 100-115.

Model interpretability vs model complexity: comparing partial least squares and artificial neural network wood property near infrared spectroscopy models.

Published by

International Union of Forest Research Organizations (IUFRO) Division 5 Conference

Summary

Oral Presentation in Cairns, Queensland, Australia.

Identification of piRNA disease associations using deep learning

Published by

Computational and Structural Biotechnology Journal

Summary

Volume 20, 1208-1217.

Interpretable machine learning identification of arginine methylation sites

Published by

Computers in Biology and Medicine

Summary

Volume 147, 105767.

Identification of functional piRNAs using a convolutional neural network

Published by

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Summary

Volume 19, 1661-1669.

Prediction of RNA 5-Hydroxymethylcytosine modifications using deep learning

Published by

IEEE Access

Summary

Volume 9, 8491-8496.

Identification of Human Promoter using Convolutional Neural Network.

Published by

2021 International Conference on Artificial Intelligence (ICAI)

Summary

pp. 213-216. IEEE.

A CNN-based RNA N6-methyladenosine site predictor for multiple species using heterogeneous features representation

Published by

IEEE Access

Summary

Volume 8, 138203-138209. (Co-first author)

iIM-CNN: Intelligent identifier of 6mA sites on different species by using convolution neural network

Published by

IEEE Access

Summary

Volume 7, 178577-178583. (Co-first author)

Identification of protein-ligand binding residue having variable length sequences using deep learning.

Published by

2019 Korean Electrical Society on Information and Control Conference (CICS)

Summary

pp. 266-267.

Languages

English

Skills

Machine Learning Frameworks

Tensorflow, Scikit-Learn, Biopython.

Programming Languages

Python, Matlab, C.

Data Analysis & Modeling

Machine Learning, Deep Learning, Bioinformatics, Computational Biology, Hyperspectral Imaging, Predictive Modeling, Statistical Analysis.

Engineering & Systems

Biological Systems Engineering, Electrical Engineering, Electronic Engineering, SCADA, PLC, HMI Interfaces, Electromechanical Equipment, Biomass Conversion, Cellulose Nanomaterials.

Research & Development

Experimental Design, Data Interpretation, Grant Writing, Publication, Academic Mentoring, Peer Review.

Projects

Machine Learning Framework for Biomass Handling and Conversion

Summary

Developing a machine learning-based modeling framework to relate biomass tissue properties with handling and conversion performances.

P3Nano: Advancing Commercialization of Cellulosic Nanomaterials

Summary

A project focused on advancing the commercialization of cellulosic nanomaterials.

Mid-Atlantic Sustainable Biomass Consortium for Value-Added Products

Summary

Developing value-added products from biomass within the Mid-Atlantic region.

AI-driven Modeling of Microbial Environment Interactions

Summary

Utilizing AI for modeling microbial environment interactions to support sustainable biomass ecosystems.

AI-driven Gene Identification for Neurological Diseases

Summary

Identification of genes causing natural intelligence and brain diseases using artificial intelligence.

Deep Learning Model for Cancer-causing DNA Methylation

Summary

Development of a deep learning model to identify cancer-causing DNA methylation markers.