Alam Ahmad Hidayat

Alam Ahmad Hidayat

PhD Student

Summary

A highly independent and fast-learning junior researcher with multidisciplinary research experiences in computational-based studies using machine learning, biomolecular modelling, and molecular dynamics simulations to obtain structural and mechanistic insights into biomolecular systems.

Education

2016 – 2018
Master of Science in Physics
Universität Bonn
Thesis: Bayesian Study of the Pion Charge Radius
Graduation date: November 2018

2010 – 2014
Bachelor of Science in Physics
Institut Teknologi Bandung
Thesis: The Penrose Inequality in Higher Dimensional Spherically Symmetric Spacetime
Graduation date: July 2014

Work Experiences

Since 2023
Junior Faculty Member
Mathematics Department, School of Computer Science, Bina Nusantara University

  • Involved in teaching activities for undergraduate students by teaching courses such as “Scientific Computing”, “Computational Biology”, and “Discrete Mathematics”
  • Designing assignments and their grading scheme as well as exam corrections.
     

2019 – Now
Research Assistant
Bionformatics and Data Science Research Center (BDSRC), Bina Nusantara University

  • Involved in research activities with BDSRC’ industry partners such as PT Genetics Indonesia and PT Mega Medica Pharmaceuticals (MMP)
  • A data analysist and a bioinformatician in collaborative research projects (genome-wide associarion studies) between BDSRC with Indonesian Heart Association (PERKI) and Faculty of Medicine, Hasanuddin University
  • Partcipated in internal research projects involving machine learning applications
  • Mentoring an d training in basic statistics, Python programming and academic writing for junior research assistants in BDSRC
     

2020 – 2021
Teaching Assistant
“Research Methodology” Course, Binus Graduate Program, Bina Nusantara University

  • Gave a tutorial in R programming lab for data analysis and statistics for a graduate students enrolled in “Research Methodology” course
  • Created and corrected the lab assignments and the their gradin g scheme scheme

2015 – 2016
Research Assistant
Theoretical Physic Physics Laboratory, Institut Teknologi Bandung

  • Participated in theoretical physics research with a topic of mathematical general relativity
  • Wrote and dissem inated a scientific article about t he research output

 

Relevant Research Experiences

Since 2023
Independent Research Project in Computational Prediction of Mutation Effects on Disease-related Proteins at Mathematics Department, School of Computer Science, Bina Nusantara University

  • Computational approach for variant effect predictions of BRCA1 protein mutations using sequence features from a large protein language model (e.g., Evolutionary Scale Modelling).
  • Computational analysis of mutations in BRCT domains of BRCA1 protein using structural features derived from thermodynamic stability and molecular dynamics (MD) simulations.
  • Ongoing MD study of mutational effects on oncogenic RAS proteins in active conformational states using advanced enhanced sampling techniques simulated using parallel computing.


Since 2022
Research Project under Riset dan Inovasi untuk Indonesia Maju (RIIM)
Scheme Funded by National Research and Innovation Agency (BRIN) Indonesia

  • A bioinformatician in the research project for exploring potential DAEases of bacteria collected from hot springs in Indonesia.
  • Conducted protein modelling and MD simulations of thermostable enzyme structures to assess their potential stability.

2021 – 2022
Research Project in Identifying Risk Factors of Stunting in Serdang Bedagai, Indonesia
Bioinformatics and Data Science Research Center (BDSRC), Bina Nusantara University

  • A data analyst and statistician for the research project collaboration between BDSRC, Local Health Office (Dinkes) of Serdang Bedagai and Mega Medica Pharmaceuticals
  • Yearly Research Projects in Polygenic Risk Scoring (PRS) at Bioinformatics and Data Science Research Center, Bina Nusantara University
  • A data analyst in the genetic testing applications using PRS with a partner industry PT Genetics Indonesia.
  • Involved with the development of Python-based pipeline for genetic testing module development for several phenotypes: cancer, cardiovascular diseases and skin health.


2019 – 2022
Research Assistance in Artificial Intelligence R&D Centre, Bina Nusantara University

  • Collaborative research with Student Advisory Center, Bina Nusantara University on deep learning implementation for analyzing student’s academic performance.
  • Independent research project on convolutional neural networks for scops owl sound recordings via spectrogram conversion.
  • Independent research projects on opic modelling of biomedical corpora.using BERT-based approach.


2017 – 2018
Research Internship in Helmholtz-Institut für Strahlen- und Kernphysik, Universität Bonn

  • Formulate a phenomenological model to extract a quantity called pion charge radius that is of utmost importance in low-energy particle physics.
  • Estimate the model hyperparameters using Bayesian analysis with a Python-based Markov Chain Monte Carlo algorithm on experimental hadron physics data.


2015 – 2016
Research Assistance in Laboratory of Theoretical High Energy Physics, Department of Physics, Institut Teknologi Bandung

  • An further exploration of mathematical approach to improve the work from the bachelor’s thesis project.

Relevant Skills

Language Skills

  • Bahasa Indonesia (Mother’s Tongue)
  • English: IELTS 6.5 (CEFR Level B2)

Operating System

  • Windows, Linux

Programming Language

  • Python, Unix shell scripting/bash, R

Data Science and Visualizations

  • Python: numpy, pandas, matplotlib, seaborn, statsmodel
  • R: dpylr, ggplot, glm, stats, nlme

Machine Learning and Probabilistic Modelling

  • Python: keras, pytorch, scikit-learn, emcee, pomegranate

Genomic Data Analysis

  • PLINK, vcftools, bcftools, adegenet (R package), biopython (Python package)

Protein Modeling and Molecular Dynamics Simulations

  • Rosetta and PyRosetta, Modeller, SWISS-MODEL, Pymol, Gromacs, PLUMED, VMD

Certification

Google Data Analytics Professional Certificate
Ongoing

NVIDIA Deep Learning Institute: Fundamentals of Deep Learning for Computer Vision
2019

Workshops and conferences attended

  • The 8th International Conference on Biological Sciences, Yogyakarta, Indonesia
    October 2023
  • The 8th International Conference on Computer Science and Computational Intelligence, Indonesia
    August 2023
  • International Conference on Informatics, Multimedia, Cyber, and Information System 2022, Indonesia
    November 2022
  • The 3rd International Conference of Biospheric Harmony Advanced Research 2021, Indonesia
    June 2021
  • The 5th International Conference on Computer Science and Computational Intelligence, Indonesia
    August 2020
  • GOJEK Upscale 2.0: Hands-on Experiences with GOJEK Data Science Team, Indonesia
    July 2019
  • Hadron Physics Summer School Jülich 2018, Germany
    September 2018
  • International Conference on Mathematics and Natural Sciences 2014, Bandung, Indonesia
    November 2014

Teaching Experiences

Since 2023
Taught undergraduate courses:
“Scientific Computing”, “Computational Biology”, “Computational Physics”
“Discrete Mathematics” in the odd and even semesters of 2023
For students in School of Computer Science, Bina Nusantara University.

2020 – 201
Teaching assistant for Research Methodology course
Master program of Information Technology, Bina Nusantara University

2013 – 2014
Teaching assistant for Elementary Physics I and II courses
Department of Physics, Institut Teknologi Bandung

 

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