Wasim Aftab Computational Biologist & Research Software Engineer

Professional profile

Curriculum vitae

Computational biologist and research software engineer with experience across multi-omics, proteomics, medical imaging, statistical methods, and scientific application development.

Last updated19 August 2026

01

Experience

May 2025–Present

Institute for Stroke and Dementia Research, LMU Klinikum

Postdoctoral Researcher

Developing reproducible computational methods for multimodal MRI segmentation, cell-type attribution of bulk proteomics, 3D alignment of spatial transcriptomics, and traceable neuroimaging evidence integration. The work combines statistical analysis, machine learning, scientific software, and collaboration with biomedical researchers.

January 2022–April 2025

Biomedical Center, LMU Munich

Postdoctoral Researcher / Bioinformatician

Supported chromatin research through bulk and single-cell RNA-seq analysis, interpretable visualizations, R Markdown reporting, and reproducible Snakemake workflows. Developed research applications for biomedical information retrieval and worked across R, Python, JavaScript, and web technologies.

September 2015–December 2021

Faculty of Medicine, LMU Munich

Research Assistant during PhD

Developed methods for the analysis, integration, and visualization of imaging and liquid-chromatography mass-spectrometry data. Built R command-line workflows, R Shiny interfaces, and an Electron application to make computational analyses accessible to research collaborators.

April 2012–December 2012

Icelero Technologies, Bangalore

Senior Software Engineer

Contributed to an automated software-testing pipeline using Selenium WebDriver, Python, Java, and AutoIt.

August 2009–March 2012

Jawaharlal Nehru Centre for Advanced Scientific Research

Scientific Programmer

Developed scientific C software for sparse-matrix eigensolvers, quantum-chemistry calculations, and protein-function prediction. Also contributed to numerical studies and debugging of scientific Fortran software.

February 2009–June 2009

Jawaharlal Nehru Centre for Advanced Scientific Research

Intern

Developed a C program for iterative calculation of the lowest eigenvalues and eigenvectors of large real-symmetric matrices for a bachelor’s thesis project.

02

Education

2015–2021

PhD in Computational Proteomics

Ludwig Maximilian University of Munich

2013–2015

MSc in Computer Engineering

King Abdulaziz University

2005–2009

BE in Computer Engineering

Visvesvaraya Technological University

03

Technical expertise

Programming

R, Python, MATLAB, C, JavaScript, HTML/CSS, shell scripting

Computational biology

Bulk and single-cell sequencing, spatial omics, high-throughput proteomics, imaging mass spectrometry

Methods

Medical-image segmentation, machine learning, statistical inference, knowledge graphs, information retrieval

Research software

Snakemake, Linux and HPC workflows, R Shiny, Electron, FastAPI, reproducible reporting

04

Publications

View publication list
  1. Sequence and chemical specificity define the functional landscape of intrinsically disordered regions. Nature Cell Biology. 2026 Feb;28(2):323–337. DOI
  2. Optimizing biomedical information retrieval with a keyword frequency-driven prompt enhancement strategy. Aftab W, Apostolou Z, Bouazoune K, Straub T. BMC Bioinformatics. 2024. DOI
  3. Improving SWATH-MS analysis by deep-learning. Sun B, Smialowski P, Aftab W, Schmidt A, Forne I, Straub T, Imhof A. Proteomics. 2023. DOI
  4. Discovery of Native Protein Complexes by Liquid Chromatography Followed by Quantitative Mass Spectrometry. Aftab W, Imhof A. Advances in Experimental Medicine and Biology. 2021. DOI
  5. ImShot: An Open-Source Software for Probabilistic Identification of Proteins In Situ and Visualization of Proteomics Data. Aftab W, Lahiri S, Imhof A. Molecular & Cellular Proteomics. 2022. DOI
  6. MALDI-IMS combined with shotgun proteomics identify and localize new factors in male infertility. Lahiri S, Aftab W, Walenta L, et al. Life Science Alliance. 2021. DOI
  7. Systematic functional analysis of SARS-CoV-2 proteins uncovers viral innate immune antagonists and remaining vulnerabilities. Hayn M, Hirschenberger M, Koepke L, et al. Cell Reports. 2021. DOI
  8. The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila. Lukacs A, Thomae AW, Krueger P, et al. PLoS Genetics. 2021. DOI
  9. Molecular Connectivity of Mitochondrial Gene Expression and OXPHOS Biogenesis. Singh AP, Salvatori R, Aftab W, et al. Molecular Cell. 2020. DOI
  10. Mapping protein networks in yeast mitochondria using proximity-dependent biotin identification coupled to proteomics. Salvatori R, Aftab W, Forne I, et al. STAR Protocols. 2020. DOI
  11. Molecular Wiring of a Mitochondrial Translational Feedback Loop. Salvatori R, Kehrein K, Singh AP, et al. Molecular Cell. 2020. DOI
  12. Msp1 cooperates with the proteasome for extraction of arrested mitochondrial import intermediates. Basch M, Wagner M, Rolland S, et al. Molecular Biology of the Cell. 2020. DOI
  13. A Novel Kernel for RBF Based Neural Networks. Aftab W, Moinuddin M, Shaikh MS. Abstract and Applied Analysis. 2014. DOI
  14. On Classification of PDZ Domains: A Computational Study. Aftab W, Memic A, Baleanu D. Mathematical Problems in Engineering. 2013. DOI