Bioinformatics Specialist · UCI MIND · Currently Active

Dr. Madhu
Sudhana Saddala

M.Sc., Ph.D  ·  Bioinformatics

Pioneering multi-omics research at UC Irvine's MIND Institute — from single-cell transcriptomics in Alzheimer's disease to spatial genomics in pancreatic cancer and beyond.

54Publications
921Citations
h:19h-index
218Impact pts
170+Papers reviewed
Ask AI about my research ↗ View publications
// experience

Professional Journey

Jul 2025 – Present
Bioinformatics Specialist
UCI MIND · University of California, Irvine
Integrated cutting-edge multi-omics approaches in both human and mouse models, significantly advancing neurodegenerative disease research.
Jun 2023 – Jun 2025
Bioinformatics Associate Specialist
UCI MIND · University of California, Irvine
Single-cell multi-omic approaches to understand molecular mechanisms of Alzheimer's disease (AD) and Fronto-temporal dementia (FTD).
Feb 2021 – Jan 2023
Postdoctoral Fellow
Wilmer Eye Institute · Johns Hopkins University School of Medicine
Transcriptomic approaches to elucidate molecular mechanisms governing tissue-specific gene regulation for improving prevention and treatment of retinal diseases.
Nov 2018 – Jan 2021
Postdoctoral Fellow
Mason Eye Institute · University of Missouri School of Medicine
Investigated transcriptome-wide gene targets and transcription factors of microglial cells in retinal degeneration disease.
Jan – Oct 2018
Postdoctoral Fellow
Wilmer Eye Institute · Johns Hopkins University School of Medicine
Transcriptome and proteome level changes in genetic ablation of placental growth factor of mouse retina under diabetic and non-diabetic conditions.
// current projects

Active Research

scTCR-seq · PDAC
Single-Cell TCR-Sequencing in Pancreatic Cancer
Integrated scTCR-seq with scRNA-seq to characterize immune heterogeneity in PDAC. Reconstructed clonotypes, quantified clonal expansion and identified tumor-associated T cell states linked to treatment response.
Spatial Transcriptomics
Stereo-seq in Pancreatic Adenocarcinoma
Resolved fine-scale spatial gene expression across treatment groups in PDAC. Integrated spatial data with scRNA-seq to reveal therapeutic mechanisms and tumor microenvironment remodeling.
Neural Repair · SCI
PCSK9-Mediated Inter-organ Regulation
Applied integrative scRNA-seq to investigate liver-derived PCSK9 signaling in spinal cord injury repair. Identified PCSK9 as key regulator via the LRP1–SPP1 axis; evaluated Alirocumab as therapeutic.
Neurodegeneration
Multi-omics in Alzheimer's & FTD
Single-cell multi-omic approaches integrating chromatin accessibility and transcriptomics to decode molecular mechanisms driving Alzheimer's disease and fronto-temporal dementia.
// technical expertise

Computational Toolkit

Single-cell & Multiomics
SeuratscRNA-seqscATAC-seqCellChatscTCR-seqStereo-seq
Programming & ML
R / BioconductorPythonMachine LearningHPC / LinuxPipeline Dev
Genomics
RNA-seqHISAT2TrinitySNP callingChIP-seqmiRNA
Drug Discovery
AutoDock VinaMODELLERPharmacophoreVirtual ScreeningMD Simulation
Proteomics
MaxQuantProteome DiscovererPEAKS Studio
Networks & Visualization
CytoscapeIGVSTRINGUCSC Browser
// selected publications

54 Publications  ·  h-index 19  ·  921 Citations

01
Advances in artificial intelligence for spatial transcriptomics in cancer: Special focus on YY1 and RKIP IF: 8.3
BBA Reviews on Cancer · 2025 · Corresponding author
02
Distinct Molecular Patterns in R6/2 HD Mouse Brain: Insights from Spatiotemporal Transcriptomics IF: 15
Neuron · 2025
03
Clonally expanded NKG7 T cells seed the aged spinal cord to disrupt myeloid-dependent wound healing IF: 15
Neuron · 2025
04
Mechanism of enhancing chemotherapy efficacy in PDAC with paricalcitol and hydroxychloroquine IF: 10.6
Cell Reports Medicine · 2025
05
Mitigating ambient RNA and doublets effects on single cell transcriptomics analysis in cancer research IF: 10.1
Cancer Letters · 2025
06
Paricalcitol plus hydroxychloroquine enhances gemcitabine activity in pancreatic adenocarcinoma: scRNA-seq analysis IF: 10.1
Cancer Letters · 2025
07
Artificial intelligence in gastrointestinal cancers: Diagnostic, prognostic, and surgical strategies IF: 10.1
Cancer Letters · 2025
08
Discovery of novel L-type voltage-gated calcium channel blockers for inflammation and angiogenesis IF: 10.1
Journal of Neuroinflammation · 2020
09
Transcriptome-wide analysis reveals core set of transcriptional key regulators of sensome and inflammation in retinal microglia IF: 3.0
Genomics · 2021
10
Identification of novel inhibitors for TNFα, TNFR1 and TNFα-TNFR1 complex using pharmacophore-based approaches IF: 7.5
Journal of Translational Medicine · 2019
11
Discovery of Small-Molecule Activators for Glucose-6-Phosphate Dehydrogenase (G6PD) Using Machine Learning IF: 4.9
International Journal of Molecular Sciences · 2020
12
Proteomics reveals ablation of PlGF increases antioxidant and neuroprotective proteins in the diabetic mouse retina IF: 3.7
Scientific Reports · 2018
13
Transcriptome wide analysis of differentially expressed genes, SNPs and SSRs in AMD human eye tissues IF: 4.3
Human Genomics · 2019
14
Small molecule tyrosine kinase inhibitors and pancreatic cancer — trials and troubles IF: 15.7
Seminars in Cancer Biology · 2018
// recognition

Awards & Honors

2025
Postdoc Portrait — The Scientist
Featured for work on systems biology & multi-omics integration
2024
Best Scientist Award
Scientific Laurels, USA — Extraordinary achievements in Bioinformatics
2024
Spotlight Associate Specialist
University of California, Irvine
2023
Outstanding Scientist Award
ScienceFather Conferences
2021
Junior Scientist Award
Dr. Reddy's Labs · ASIOA, USA
2020
Outstanding Oral Presentation
CBAT 2020 International Webinar
2020
Spotlight Postdoctoral Fellow
University of Missouri School of Medicine
2013
CSIR-NET Qualified
National level · Life Science · Rank 64/1232
// service

Editorial & Review Service

The FASEB Journal & FASEB BioAdvancesEarly Career Editorial Board
Gene & Protein in Disease (GPD)Youth Editorial Board
Discover OncologyEditorial Board Member
Bioinformatics and Biology InsightsEditorial Review Board
MDPI LifeTopic Editor
Frontiers in Bioengineering and BiotechnologyReview Editor
Journal of Bioinformatics and Systems BiologyEditorial Board Member

Total papers reviewed: 170+ · Across 30+ journals including Nature portfolio, PLOS, BMC & Frontiers

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Hello! I'm Dr. Saddala's AI assistant. I can answer questions about his research in bioinformatics, single-cell genomics, neurodegenerative diseases, retinal biology, pancreatic cancer, and drug discovery. What would you like to know?
// get in touch

Contact & Profiles

EMAILmadhubioinformatics@gmail.com WORKmsaddala@uci.edu GITHUBmadhubioinformatics SCHOLARGoogle Scholar ORCID0000-0002-6373-7080 PUBMEDPubMed Publications RGGATEResearchGate
// institution

UCI MIND

Memory Impairments and Neurological Disorders
Room 3130, Biological Science Building III
University of California, Irvine, CA-92679, USA

// society memberships
Alzheimer's Assoc. (ISTAART) Society for Neuroscience ASCA ARVO AAAS AACR Cancer Epigenetics Society