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Systems Immunology Lab
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The lab investigates how the immune system works through computational analysis of sequences and structures.
AboutAbout the lab
Reading the immune system through data and computation.
The Systems Immunology Lab studies how the immune system works through computational analysis.
It analyzes immune repertoires, the collections of receptor sequences carried by T cells and B cells, to investigate the characteristics of diseases such as cancer.
The lab has continued to develop MAFFT, software for comparing biological sequences, since its first release.
It also collaborates with experimental researchers on studies that explore how biological macromolecules function from their three-dimensional structures.
Key terms
- immune repertoire
- The collection of receptor sequences carried by the T cells and B cells in the body
- multiple sequence alignment
- The task of lining up several DNA or protein sequences so that similar regions match, in order to compare them
- coarse-grained molecular dynamics simulation
- A computational method that simplifies the fine details of molecules so that large-scale motions and interactions between molecules can be studied over long timescales
ResearchResearch themes
This lab uses computational analysis of sequence data and three-dimensional structures to study how the immune system works. It pursues collaborative research with experimental researchers alongside the development of analysis software.
Computational Biology and Bioinformatics
By combining coarse-grained molecular dynamics simulation, immune repertoire analysis, gene expression analysis, machine learning, and structural modeling of biological macromolecules, the lab investigates the dynamics of the immune system and the characteristics of diseases.
Development of the MAFFT Sequence Alignment Software
The lab has added several features to MAFFT, a multiple sequence alignment program: interactive selection of the sequences used to build phylogenetic trees, parallel processing, and options for viral genomes including SARS-CoV-2. It also works on annotating immune receptor genes in the genomes of eutherian mammals.
*Illustrative imageProtein–DNA and Protein–RNA Interactions
The binding of proteins to DNA and RNA is essential for regulating immune responses and for detecting and eliminating viral infections. The lab developed aaRNA, which predicts RNA-binding sites, extended it to DNA-binding site prediction (aaDNA), and is incorporating it into docking simulations.
MembersFaculty
The Systems Immunology Lab's members are faculty, visiting researchers, project researchers, doctoral and master's students, research students, auditing students, and administrative assistants.As of 2025
- ProfessorDaron M. Standley
- Associate ProfessorSongling Li
- Assistant ProfessorArthur Millius
- Project Assistant ProfessorHendra Saputra Ismanto
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “1FYT T-cell receptor and HLA class II complex” Takuma-sa / CC0 (cropped)
- Protein–DNA and Protein–RNA Interactions: “Streptococcus pyogenes Cas9-DNA-RNA complex PDB 4OO8” Deposition authors: Nishimasu, H., Ishitani, R., Nureki, O.; Visualization author: Synpath / CC0 (cropped)
- Related lab (Statistical Immunology Lab): “Preparing genotyping arrays” Daniel Sone (Photographer) / Public domain (cropped)
- Related lab (Molecular Immunology Lab): “T Lymphocyte, also known as a T cell (yellow color)” NIAID / CC BY 2.0 (cropped)
- Related lab (Seymour Lab): “Stuttering-brain-scan-neurosciennews” DanaAlmutawaaa / CC BY-SA 4.0 (cropped)
- Related lab (Malaria Immunology Lab): “Malaria falciparum ring forms” Dr Graham Beards / CC BY-SA 4.0 (cropped)
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