Director, Bioinformatics Core · Wayne State University

Aditi SinghPhD

Computational biologist & systems immunologist. I build multi-omic frameworks to decode immune cell states in cancer, reproductive biology, and human tissue health.

Detroit, MI
aditi.singh2@med.wayne.edu
github.com/aditispt
12+ Papers
4 Active Projects
8+ Trainees

Decoding immune ecosystems
through multi-omics.

I am the Director of the Bioinformatics Core and Research Scientist at Wayne State University, where I lead computational analysis across translational research programs in immunology, cancer biology, and reproductive medicine. I received my PhD in Molecular Medicine & Genetics from Wayne State in February 2025.

My research integrates single-cell transcriptomics, CITE-seq, spatial genomics, and machine learning to characterize immune cell state transitions across complex biological environments — including pregnancy, inflammation, and cancer. A central focus is macrophage and dendritic cell biology, particularly how these cells govern immune tolerance, immune evasion, and tissue remodeling.

My long-term goal is to build predictive models of immune ecosystem dynamics that inform therapeutic strategies in cancer, reproductive disease, and inflammatory disorders. I am also a committed mentor, having trained 8+ trainees ranging from high school students to resident physicians, and an advocate for DEIA in computational biology.

scRNA-seq CITE-seq Spatial transcriptomics Multi-omic integration Machine learning Tumor microenvironment Macrophage biology Reproductive immunology HPC pipelines Trajectory inference
Dr. Aditi Singh
Position Director, Bioinformatics Core
Institution Wayne State University
Location Detroit, MI
GitHub aditispt
Google Scholar View profile
Societies ASRI · AACR

Active Research Projects

Project 01 · ESC Stress Biology

Pan-Stress Forces Loss of Stemness and Drives Developmental Imbalance

Context: Early embryogenesis & miscarriage
Method: Bulk RNAseq → scRNAseq
Key Findings
  • 1
    All stressors override stemness, forcing ESCs out of their naïve (0th) lineage state
  • 2
    Stress responses segregate into two distinct lineage-imbalance trajectories
  • 3
    Identified two pan-stress marker genes that robustly predict lineage imbalance independent of stressor identity
Publications: Scientific Reports (2025) · Birth Defects Research (2024) · Patent filed April 2025
Project 02 · Reproductive Immunology

scRNA-seq Identification of Tissue-Resident Dendritic Cells in Endometrium

Context: Implantation failure & uterine biology
Method: scRNA-seq → CITE-seq
Key Findings
  • 1
    Identified 7 subsets of uDCs including progenitor cells, challenging the dogma that DCs are recruited from peripheral blood
  • 2
    Mapped the developmental trajectory of uDCs through the various stages of the endometrial cycle
  • 3
    Assigned functional roles (immune regulation & antigen presentation) to each subset based on gene expression profiles
Publication: iScience (2025)
Project 03 · Maternal–Fetal Interface

Sex-Specific Immune Regulation at the Maternal–Fetal Interface

Context: Pregnancy & miscarriage
Method: Bulk RNAseq → scRNAseq → CellChat
Key Findings
  • 1
    Sex-specific gene expression differences emerge early in normal placental development
  • 2
    Male placentas show innate inflammatory skewing; females favored adaptive immune regulation
  • 3
    Distinct immune failure pathways identified in miscarriages
Manuscript under review: 2026
Project 04 · Cancer Immunology

Cancer Cell Sialylation Fuels Immune Evasion and Stromal Remodeling in Ovarian Cancer

Context: Ovarian cancer TME
Method: CRISPR KO → Flow Cytometry → scRNAseq
Key Findings
  • 1
    Tumor cell hypersialylation drives immune-dependent ovarian cancer progression
  • 2
    ST6GAL1-mediated sialylation promotes expansion of immunosuppressive myeloid cells and suppresses cytotoxic immunity
  • 3
    Hypersialylation impairs innate danger sensing and reprograms the tumor microenvironment
  • 4
    Targeting sialylation reverses immune suppression and prevents tumor progression
Manuscript in prep · AACR 2025 abstract

Publications

2026
Fetal Sex Shapes the Immune Landscape at the Maternal–Fetal Interface During Early Human Pregnancy
Singh A, Mor G et al.
Under Review
Under Review
2025
Decoding Functional and Developmental Trajectories of Uterine Dendritic Cells
Singh A, Mor G et al.
iScience, 2025
iScience
2025
Novel Kinetic and Developmental Transcriptomic Pan-Stress Responses of Embryonic Stem Cells
Singh A, Rappolee D
Scientific Reports, 2025
Sci. Reports
2025
Prenatal Exposure to Zika Virus Shapes Offspring Neutrophil Function in a Sex-specific Manner
Ding J, Maxwell A, Singh A et al.
Nature Communications, 2025
Nat. Comms
2025
Cancer Cell Sialylation Fuels Immune Evasion and Stromal Remodeling in Ovarian Cancer
Fox A, Singh A, Mor G et al.
Manuscript in Preparation
In Prep
2025
Pan-stress marker genes — Patent filed April 2025
Singh A, Rappolee D et al.
US Patent Application, April 2025
Patent
2024
A Single Cell Transcriptomic Fingerprint of Stressed Premature, Imbalanced Differentiation of Embryonic Stem Cells
Singh A*, Marben T, Tang W, Awonuga AO, Ruden DM, Puscheck E, Feng H, Korzeniewski SJ, Rappolee DA
Birth Defects Research, 2024
Birth Defects Res.
2024
Novel high throughput screen reports that benzo(a)pyrene overrides mouse trophoblast stem cell multipotency, inducing SAPK activity, HAND1 and differentiated trophoblast giant cells
Kidder BL, Ruden X, Singh A, Marben TA, Rass L, Chakravarty A et al.
Placenta, 2024
Placenta
2023
Epigenetic Reprogramming in Mice and Humans: From Fertilization to Primordial Germ Cell Development
Singh A, Rappolee DA, Ruden DM
Cells, 12(14):1874, 2023
Cells
2023
Pathological epigenetic events and reversibility: the intersection between hallmarks of aging and developmental origin of health and disease
Ruden DM, Singh A, Rappolee DA
Epigenomics, 2023
Epigenomics
2022
Using high throughput screens to predict miscarriages with placental stem cells and long-term stress effects with embryonic stem cells
Puscheck EE, Ruden X, Singh A, Abdulhasan M, Ruden DM, Awonuga AO, Rappolee DA
Birth Defects Research, 2022 (PMID 35979652)
Birth Defects Res.
2021
Insights into the molecular mechanisms regulating mammalian hair cell regeneration
Hu Z, Singh A, Bojrab D, Sim N
Current Opinion in Otolaryngology & Head and Neck Surgery, 2021
Curr Opin
2021
Generation of a Spiral Ganglion Neuron Degeneration Mouse Model
Hu Z, Komal F, Singh A, Deng M
Frontiers in Cell and Developmental Biology, 2021
Front. Cell Dev.

Experience

Director, Bioinformatics Core & Research Scientist
Feb 2025 — Present
Wayne State University · Detroit, MI
Leading the Bioinformatics Core supporting multi-omics analysis across translational research programs in immunology, cancer biology, and reproductive medicine.
  • Lead computational analysis of large-scale single-cell and spatial-omic datasets (>100,000 cells per study)
  • Develop interpretable ML models to characterize disease-relevant cellular programs and identify therapeutic targets
  • Built scalable HPC pipelines for multi-omic integration, trajectory inference, and pathway modeling
  • Provide training and consultation to investigators on study design, single-cell analysis, and multi-omics integration
  • Contribute computational strategy to multi-disciplinary teams of clinicians, immunologists, and data scientists
Graduate Research Assistant — Computational Immunology
Aug 2021 — Feb 2025
Wayne State University · Detroit, MI
Conducted integrative computational analyses of human immune cell populations across reproductive and disease contexts using single-cell and spatial genomics.
  • Identified previously uncharacterized uterine dendritic cell subtypes using AI-driven single-cell analysis (iScience, 2025)
  • Integrated scRNA-seq, CITE-seq, and imaging data across 10 stages of the human menstrual cycle
  • Developed reproducible pipelines for QC, batch correction, clustering, and trajectory inference
  • Mentored 8+ trainees including fellows, residents, undergraduates, and high school interns
Graduate Research Assistant — Stem Cell & Epigenetics
Dec 2019 — May 2021
Wayne State University · Detroit, MI
Investigated epigenetic regulation and cellular differentiation programs in iPSCs and developmental models. Applied microscopy, immunofluorescence, and gene expression profiling to characterize differentiation states.

Education

Doctor of Philosophy
Molecular Medicine & Genetics
Wayne State University · Detroit, MI
Completed February 2025
NIH T32 predoctoral trainee. Thesis focused on single-cell and multi-omic characterization of immune cell populations.
Master of Science
Biotechnology
University of Salford · Manchester, UK
December 2018
Vice-Chancellor's Academic Excellence Scholarship recipient.
Bachelor of Technology
Biotechnology
Dr. D. Y. Patil Biotechnology Institute · Pune, India
May 2016
First position in academics. Meritorious Student of the Year award.

Active Collaborations

🔬
Ayesha Alvero, MD
Wayne State University — Dept. of Oncology
Collaborative studies on ovarian cancer tumor microenvironment remodeling, including macrophage polarization and immune suppression programs associated with differential tumor sialylation (SNAhigh vs SNAlow).
🧫
Radhika Gogoi, MD
Karmanos Cancer Institute / Wayne State University
Spatial and transcriptomic analysis of fallopian tube and endometrial cancer progression, focusing on immune niche organization and early tumor microenvironment dynamics.
🧬
Jiahui Ding, MD, PhD
Wayne State University
Collaborative work on hematopoietic stem cell differentiation and immune lineage development using transcriptomic and functional genomic approaches. Co-author on Nature Communications (2025).
🤝
Gil Mor, MD, PhD
Wayne State University
Long-standing collaboration on maternal–fetal immune interactions, including single-cell and multi-omic characterization of decidual and placental immune cell populations across multiple published studies.

Skills

Programming & Analysis

R / BioconductorExpert
PythonAdvanced
Network analysis & pathway enrichmentAdvanced
High-dimensional data visualizationExpert
HPC pipeline developmentAdvanced

Bioinformatics Tools

SeuratExpert
MonocleExpert
CellChatExpert
DESeq2 / EdgeRExpert
ML & statistical modelingAdvanced

Experimental & Translational

scRNA-seq / CITE-seqExpert
Spatial transcriptomicsAdvanced
Multiplex immunohistochemistryAdvanced
Imaging-sequencing integrationAdvanced
Cohort-level translational analysisExpert

Grants

Principal Investigator
NIH DP2 New Innovator Award
National Institutes of Health
Submitted (July & September cycles)
Principal Investigator
CLEAR RETCC Pilot Grant
Wayne State University — CLEAR RETCC
Awarded 2024 & 2025
Predoctoral Trainee
NIH T32 Training Grant
National Institutes of Health — CBI, Wayne State University
Funded third year of PhD research
Collaborator
NIH R21 — Hematopoietic Stem Cell Differentiation
National Institutes of Health
PI: Jiahui Ding, MD, PhD — provided computational analysis framework
Collaborator
NIH R01 — Ovarian Cancer TME
National Institutes of Health
PI: Ayesha Alvero, MD — computational & multi-omics analysis expertise
Collaborator
NIH R01 — Translational Immunology Studies
National Institutes of Health
PI: Gil Mor, MD, PhD — contributed to grant development

Awards & Honors

2025
Invited Panelist — Multi-omics Harmonization, NextGen Omics & Spatial Conference 2026
2025
Invited Panelist — Women in Genomics, Gen Omics Conference 2026
2024
2nd Place — Trainee Research Day Symposium, C.S. Mott Center
2024
CLEAR RETCC Pilot Grant — Principal Investigator funding, Wayne State University
2024
ASRI Travel Award — Presentation at the Annual ASRI 2024 Meeting
2023
NIH T32 Training Grant — Awarded by CBI Department, Wayne State University (3rd year PhD funding)
2023
Travel Award — Podium presentation, BDRP Annual Conference
2023
ATTRACT Award — Advanced Training Through Research And Collaborative Teamwork (summer internship funding)
2023
Hon'ble Mention — Graduate Student Research Presentation Day (GSRPD)
2021
Graduate Research Assistantship — Awarded by WSU to fund first 2 years of PhD
2018
Vice-Chancellor's Academic Excellence Scholarship — University of Salford
2016
Meritorious Student of the Year & First Position in Academics — Dr. D. Y. Patil Biotechnology Institute

Teaching & Mentorship

Courses Taught

Guest Lecture: R Programming and Bioinformatics — Wayne State University (CBI), 2025
Teaching Assistant: Stem Cell Development (Graduate level) — Wayne State University, 2023
Teaching Assistant: Embryonic Development (Graduate level) — Wayne State University, 2021

Mentees Trained

1 Graduate student (international exchange program)
2 High school students through DTC, 2025
1 Maternal-Fetal Medicine Fellow, 2024
3 Resident physicians, 2023–2024
2 High school students through DTC, 2023–2024
2 Undergraduate students from Barbers Fellowship, 2022
Peer mentoring at Chemistry Biology Interface Meeting, 2023

Service & Leadership

Organizing member, Trainee Research Day Symposium, C.S. Mott Center, 2024
Departmental Representative, CMMG at Graduate Senate, 2024
DEIA member, BDRP Society, 2023–present
Organizing member, MARTS 2023 Conference

Contact

I welcome collaborations in computational immunology, cancer biology, and reproductive medicine, as well as invitations to speak, consult on multi-omics study design, or discuss opportunities for trainees interested in bioinformatics. Feel free to reach out.