From Code
to Cure

bridging code and cure: advancing clinical impact through computational innovation

The Bioinformatics, Computational Genomics & Epigenetics Lab turns high-dimensional genomic data into biological insight, advancing vaccine and antiviral discovery.

About the Lab

The BCGE Lab blends computational and biological discovery, applying bioinformatics, genomics, and epigenetics to understand how the immune system responds to viruses and vaccines.

We integrate single-cell and multi-omic data, model systems-level immunity, and build machine-learning approaches to surface the signatures that predict protection, pushing the boundaries of biology as a programmable system to unlock new scientific and medical possibilities.

Research Areas

Computational methods applied to immunity, infection, and therapeutic discovery.

Single-Cell & Multiomics

Integrated single-nucleus RNA + ATAC (multiome), spatial, and CITE-seq analysis to map immune cell states at single-cell resolution.

Systems Immunology & Vaccines

Systems-level modeling of vaccine responses and viral reservoirs (HIV/SIV and emerging pathogens) to define correlates of protection.

Computational Genomics & Epigenetics

Chromatin accessibility, gene regulation, and the epigenetic programming of immune memory across time and tissue.

Machine Learning

Predictive models and multi-omic data integration to surface biomarkers and mechanistic hypotheses from complex datasets.

HIV: Integration, Persistence & Latency

Investigating host features that impede viral integration, persistence, and latency, to identify mechanisms of control, discover therapeutic targets for cure, and correlate biomarkers of rebound.

Host–Virus Interface, Drug Discovery & Vaccine Design

Computational analysis of host–virus interactions to identify therapeutic targets, prioritize antiviral compounds, and guide rational vaccine and immunogen design.

Integrated Multi-omics

scRNA-seq, ATAC-seq, spatial, proteomics & more

High-Performance Computing

Scalable pipelines for large-scale analysis and modeling

Translational Impact

From mechanism to intervention for improved human health

Open Science

Reproducible, transparent, and collaborative research

Genomics & epigenetics

Single-cell and multi-omic data, read at base-pair resolution.

Team

Click any portrait for a short bio.

Dr. Malika Aid-Boudries

Dr. Malika Aid-Boudries

Principal Investigator

Center for Virology and Vaccine Research · Beth Israel Deaconess Medical Center · Harvard Medical School

Computational immunologist working at the interface of bioinformatics, genomics, and epigenetics to advance vaccine and antiviral discovery. Recognized as an Influential Woman 2025.

maid@bidmc.harvard.edu

Bioinformatician Scientists

Pavan Kumar Singuru
Pavan Kumar Singuru

Bioinformatician Scientist

Shadi
Shadi

Bioinformatician Scientist

Alumni

Fatima Mostefai
Fatima Mostefai

Postdoctoral Fellow

Nazim Belbbassi
Nazim Belbbassi

Ph.D.

Milka Dawit
Milka Dawit

Intern

Esha Rakesh
Esha Rakesh

Intern

Meghana Kuppireddy
Meghana Kuppireddy

Intern

Raeed Bourai
Raeed Bourai

Intern

Arunaa Nagarajan Ganesan
Arunaa Nagarajan Ganesan

Intern

Nam Thanh Nguyen
Nam Thanh Nguyen

Intern

Valentin Boero-Teyssier
Valentin Boero-Teyssier

Intern

Pavitra Ganesan Dass
Pavitra Ganesan Dass

Intern

Michael Dong
Michael Dong

Intern

Highlighted Publications

Click any paper to see it on its own.

2,301
citations
22
h-index
33
i10-index

Selected further work

  • 2015

    ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

    S. D. Bailey et al. · Nature Communications · 246 citations

  • 2017

    Zika virus persistence in the central nervous system and lymph nodes of rhesus monkeys

    M. Aid et al. · Cell · 237 citations

  • 2018

    Initiation of antiviral B-cell immunity relies on innate signals from spatially positioned NKT cells

    M. Gaya et al. · Cell · 212 citations

  • 2024

    Mucosal boosting enhances vaccine protection against SARS-CoV-2 in macaques

    K. McMahan et al. · Nature · 105 citations

  • 2016

    Immediate dysfunction of vaccine-elicited CD8+ T cells primed in the absence of CD4+ T cells

    N. M. Provine et al. · The Journal of Immunology · 81 citations

  • 2018

    Follicular CD4 T-helper cells as a major HIV reservoir compartment: a molecular perspective

    M. Aid et al. · Frontiers in Immunology · 75 citations

News & Events

Talks, posters, symposia, and lab milestones.

Fuel Discoveries

Support the Lab

Our lab sits at the interface of computational biology and medical discovery, turning big, messy data into insights that improve human health, while training the next generation of scientists. Your support directly funds paid research opportunities, mentoring, and hands-on training, with a special focus on empowering women and girls in STEM.

Why your gift matters

We work where computational biology meets medical discovery, from algorithm design to real-world application, building tools and evidence that move ideas from code to clinic.

Invest in people

  • Paid research fellowships & summer internships: priority for women and girls in STEM
  • Mentorship and training in data science, reproducible research, and open science
  • Seed funding for high-risk, high-reward projects too early for traditional grants
  • Open-source software, datasets, and workshops for the community

Reproducible by design

Pipelines and machine learning, from raw reads to discovery.

Join the Lab

We welcome curious scientists (postdocs, students, and bioinformaticians) excited about turning data into discovery.

Get in touch

Find Us

Center for Virology & Vaccine Research · Beth Israel Deaconess Medical Center · Boston, MA

3 Blackfan Circle · Center for Life Science (CLS) · Boston, MA 02115  ·  Open in Google Maps →

Get in Touch

Questions, collaborations, or joining the lab. Reach out.

Lab Information

Laboratory

Center for Virology & Vaccine Research
Beth Israel Deaconess Medical Center
Harvard Medical School

Address

3 Blackfan Circle · Center for Life Science (CLS)
Boston, MA 02115, USA

Principal Investigator

Dr. Malika Aid-Boudries
maid@bidmc.harvard.edu

Send a Message