Fadhl M. Alakwaa, PhD — Computational Kidney Disease Researcher

Research Program

My research bridges computational biology and clinical nephrology, using multi-omics data integration to advance precision medicine for kidney disease.

🧬

Multi-Omics Data Integration for CKD

Developing and applying complementary data integration methods (MOFA, DIABLO) to combine transcriptomics, proteomics, and metabolomics for mechanistic insights into chronic kidney disease progression.

JCI Insight · NEPTUNE · KPMP

🐁

Cross-Species Molecular Mapping

Building computational frameworks (Mouse Map App) to translate between mouse model and human kidney disease signatures, enabling drug target validation and preclinical-to-clinical translation.

RPC2 · 6 Pharma Partners

🤖

Machine Learning for Kidney Cell Typing

Applying machine learning algorithms to identify kidney cell types in single-cell and single-nucleus RNA-seq data, improving resolution of disease-specific cellular changes across kidney compartments.

Heliyon · scRNA-seq · snRNA-seq

💊

Computational Drug Repurposing

Using single-cell transcriptomics and network pharmacology to identify repurposing opportunities, including SGLT2 inhibitor mechanisms in diabetic kidney disease and tamoxifen resistance in breast cancer.

Patent Pending · mSystems

Software & Data Tools

Open-source computational tools for the research community.

R Package

Lilikoi

Personalized pathway-based classification modeling using metabolomics data. Enables deep learning and traditional ML for disease subtyping.

Published: GigaScience (2018) · PMID: 30535020

R Package

proRate

Infer gene transcription elongation rates with a novel least sum of squares method from Pol II profiling data.

Published: NAR Genomics & Bioinformatics (2025) · PMID: 40918071

Web Application

Mouse Map App

Cross-species molecular mapping tool for translating mouse CKD model signatures to human kidney disease. Used by RPC2 pharma partners for target validation.

Presented at RPC2 across 5 countries

Pipeline

MetabolonR

Reproducible Jupyter-notebook and R Shiny workflow for analyzing Metabolon metabolomics data. Used in NEPTUNE and ALS research.

Presented at MANA & Dept. of Internal Medicine

Selected Publications

39 peer-reviewed articles including 3 in J Clin Invest, 2 in Nature Communications, and publications in Kidney International, JCI Insight, and CJASN.

2026

Metabolic surgery mitigates early kidney injury in obese youth with diabetes by suppressing mTORC1/JAK-STAT signaling

Journal of Clinical Investigation

Naik AS*, Alakwaa FM*, Nair V, McCown PJ, Schaub JA, et al.

Co-First

2025

Leveraging complementary multi-omics data integration methods for mechanistic insights in kidney diseases

JCI Insight

Alakwaa F, Das V, Majumdar A, Nair V, Fermin D, et al.

First Author

2025

proRate: an R package to infer gene transcription rates with a novel least sum of squares method

NAR Genomics and Bioinformatics

Liu Y, Alakwaa F**

Corresponding

2024

Identification of kidney cell types in scRNA-seq and snRNA-seq data using machine learning algorithms

Heliyon

Tisch A, Madapoosi S, Blough S, ..., Mahfouz A, Alakwaa F**

Senior Author

2023

SGLT2 inhibitors mitigate kidney tubular metabolic and mTORC1 perturbations in youth-onset type 2 diabetes

Journal of Clinical Investigation

Schaub JA, AlAkwaa FM*, McCown PJ*, Naik AS*, Nair V, et al.

Co-First

2023

Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis

Kidney International

Mariani LH, Eddy S, AlAkwaa FM, McCown PJ, et al.

Key Author

2020

Repurposing didanosine as a potential treatment for COVID-19 using single-cell RNA sequencing data

mSystems

Alakwaa FM** (sole author)

Sole Author

2018

Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data

GigaScience

Al-Akwaa FM, Yunits B, Huang S, Alhajaji H, Garmire LX

First Author

View all 39 publications on PubMed →

Training & Workshops

I organize and lead hands-on data training workshops for clinicians, wet lab researchers, and industry scientists across three continents.

🌏 International — Tokyo, Japan

WCN Big Data Lab 2026

Hands-on training for clinicians and scientists on cellxgene, KPMP Kidney Cell Atlas, and Nephroseq tools at the World Congress of Nephrology.

2026 · World Congress of Nephrology

🌎 International — Buenos Aires, Argentina

WCN Big Data Lab 2024

Trained clinicians and scientists on cellxgene, KPMP Kidney Cell Atlas, and Nephroseq tools for kidney disease research.

2024 · World Congress of Nephrology

🇺🇸 National — Houston, TX

KPMP Industry Roundtable

Hands-on training for industry scientists on KPMP data tools for kidney research at ASN Kidney Week 2025.

November 2025 · ASN Kidney Week

🇺🇸 National — Consortium

KPMP Data Training Workshop

Two-day hands-on training for KPMP consortium investigators on cellxgene, Explorer, Spatial Viewer, DAVE Repository, and Study Participant Atlas.

March 10–11, 2026 · KPMP Consortium

🏛️ Institutional — Ann Arbor, MI

Pizza & Pixels: Xenium Explorer

Organized hands-on workshop for wet lab researchers on subcellular gene expression visualization using 10x Xenium Explorer 3.2.0.

September 2025 · MiKTMC

🏛️ Ongoing

cellxgene VIP Training

Teaching clinical scientists to use cellxgene VIP for data analysis and visualization of scRNA-seq data since 2020.

2020–Present · University of Michigan

Get in Touch

I'm always interested in collaborations on computational kidney disease research, multi-omics integration, and precision nephrology.

Department of Internal Medicine — Nephrology
University of Michigan Medical School
Ann Arbor, MI 48109

✉ alakwaaf@umich.edu 📚 PubMed Profile 🆔 ORCID: 0000-0001-5349