LAB LOGA page on LabLog, a review site (not the lab's official page)
Standley Lab
Machine-translated · View original
The lab uses computation to explore how the immune system works, starting from sequences and structures.
AboutAbout the lab
Decoding the immune system computationally
The Standley Lab (Department of Genome Informatics) studies the immune system through both collaboration with experimental researchers and development of bioinformatics software.
The lab analyzes the immune repertoire, the collection of receptors carried by B cells and T cells, searching for signatures specific to diseases such as cancer, with the aim of using them for diagnosis.
The lab has continued to develop MAFFT, multiple sequence alignment software that aligns and compares biological sequences, since its release in 2002.
The lab also studies how biomolecules function based on their structures, in collaboration with experimental researchers.
Key terms
- Immune repertoire
- The collection of receptors carried by B cells and T cells
- Multiple sequence alignment
- An analysis that aligns multiple sequences to compare the regions that are similar and different
- Coarse-grained molecular dynamics simulation
- A method that simplifies a molecular system so that large-scale motions and interactions can be studied over long timescales
ResearchResearch themes
To understand in detail how the immune system works, the lab pursues both collaboration with experimental researchers and development of bioinformatics software. It puts particular emphasis on B-cell and T-cell repertoires and on protein–nucleic acid interactions, and both rely heavily on multiple sequence alignment, structural modeling, and machine learning.
*Illustrative imageReading immunity and disease computationally
The lab combines coarse-grained molecular dynamics simulation, analysis of immune repertoires and gene expression, machine learning, and structural modeling of biomacromolecules. In the analysis of immune repertoires and gene expression, it searches for disease-specific signatures and uses them to shape diagnostic approaches.
*Illustrative imageMAFFT and annotation of immune genes
The lab has added to MAFFT a function for interactively selecting the sequences used in phylogenetic tree inference, parallel processing, and options for virus genomes including SARS-CoV-2. It also works on annotating immune receptor genes in the genomes of eutherian mammals.
*Illustrative imageProtein–nucleic acid interactions
The lab developed aaRNA, a tool that predicts the RNA-binding sites of RNA-binding proteins, and extended it to aaDNA, which predicts DNA-binding sites. Multiple studies have shown that the predicted binding sites agree well with experiments.
MembersFaculty
The members of the Standley Lab are faculty, visiting researchers, postdoctoral researchers, doctoral and master's students, research students, non-degree course students, and administrative assistants.As of 2025
- ProfessorDaron M. Standley
- Associate ProfessorSongling Li
- Assistant ProfessorArthur Millius
- Project Assistant ProfessorHendra Saputra Ismanto
VoicesStudent voices
Ratings and reviews reflect the experiences of individual current or former students, not the lab's official views. Whether a lab has reviews, or how many, says nothing about the lab itself.
Students who take part in an interview may receive a thank-you gift worth ¥1,000, regardless of what they say.
Student ratings (0 students)
--
--
--
--
--
--
Student voices answer questions like these
- What's great about this lab?
- What did you learn after joining?
- What's the vibe, and what is the professor like?
- Who is this lab for?
- Where do graduates go?
Your experience can help younger students choose their lab. Your name won't be shown.
Write a lab reviewAnonymous · Your draft is saved if you stopRelatedLabs similar to Standley Lab
Ito LabResearch Institute for Microbial Diseases, Bioinformatics CenterDevelopment of bioinformatics technologies using viral genom…
Nakatani LabResearch Institute for Microbial Diseases, Bioinformatics CenterGenome data analysis, multi-omics analysis, and algorithm de…
Nakamura LabResearch Institute for Microbial Diseases, Bioinformatics CenterUnderstanding pathogens and infectious diseases through geno…
Yamazaki LabResearch Institute for Microbial Diseases, Bioinformatics CenterUnderstanding and application of gene expression regulation …The information on this page is compiled by the LabLog team from the lab's public information and interviews. For corrections or removal requests, please contact LabLog, not the lab.
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: “PDB 1scs EBI” Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute / Public domain (cropped)
- Reading immunity and disease computationally: “PDB 2rcj EBI” Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute / Public domain (cropped)
- MAFFT and annotation of immune genes: “Coronavirus. SARS-CoV-2” Alexey Solodovnikov (Idea, Producer, CG, Editor), Valeria Arkhipova (Scientific Сonsultant) / CC BY-SA 4.0 (cropped)
- Protein–nucleic acid interactions: “Double-stranded RNA-binding protein Staufen homolog 1” Smoniodes / CC BY-SA 4.0 (cropped)
- Related lab (Ito Lab): “Potyvirus genome and virion” Jiri Sochor, Petr Babula, Vojtech Adam, Boris Krska, and Rene Kizek / CC BY 3.0 (cropped)
- Related lab (Nakatani Lab): “Medaka (Oryzias latipes) egg, day 0” Ethmostigmus / CC BY-SA 4.0 (cropped)
- Related lab (Nakamura Lab): “370A automated DNA sequencer” Giac83 / CC BY-SA 2.5 (cropped)
- Related lab (Yamazaki Lab): “RNA pol” 作者不詳 / Public domain (cropped)
About LabLog
LabLog is a lab review app for students only. Student members at each university interview students in labs and publish what they say. Student voices can only be read by students who sign up with a university email address. Operated by bestiee Inc.
Learn more about LabLog ↗Search engines and AI may reference the basic lab info and rating summaries on this page and the description of LabLog. Student voices are for student members only. Automated collection by programs (scraping, or input to or training of AI) is prohibited under Article 8 of the Terms of Service. If you need data for research or analysis, please contact us.