Nick Borcherding
@thehumanborch.bsky.social
Assistant Professor @wusm_pathology | TCRs 🤝 HLA | MD/PhD Pathologist using computers and ML for immunology and oncology | Former Marine Corp Sgt
Reposted by Nick Borcherding
Renewing my yearly bet on Cooper/Miller for the Nobels.
One might think that I would learn after being wrong so many times, but one would be mistaken.
laskerfoundation.org/winners/b-an...
One might think that I would learn after being wrong so many times, but one would be mistaken.
laskerfoundation.org/winners/b-an...
B and T cells—the organizing principle of the adaptive immune system - Lasker Foundation
For their discovery of the two distinct classes of lymphocytes, B and T cells – a monumental achievement that provided the organizing principle of the adaptive immune system and launched the course of...
laskerfoundation.org
October 4, 2025 at 1:43 PM
Renewing my yearly bet on Cooper/Miller for the Nobels.
One might think that I would learn after being wrong so many times, but one would be mistaken.
laskerfoundation.org/winners/b-an...
One might think that I would learn after being wrong so many times, but one would be mistaken.
laskerfoundation.org/winners/b-an...
Excited to present at the ASHI Annual Meeting next week on Predicting TCR Specificity in the Age of Single-Cell Sequencing. See you on Monday!
ashiannualmeeting2025.eventscribe.net/agenda.asp?p...
ashiannualmeeting2025.eventscribe.net/agenda.asp?p...
October 3, 2025 at 1:56 PM
Excited to present at the ASHI Annual Meeting next week on Predicting TCR Specificity in the Age of Single-Cell Sequencing. See you on Monday!
ashiannualmeeting2025.eventscribe.net/agenda.asp?p...
ashiannualmeeting2025.eventscribe.net/agenda.asp?p...
Excited to announce ImmReferent - A one stop shop for getting and handling IMGT immune receptor and HLA sequences in R.
github.com/BorchLab/imm...
github.com/BorchLab/imm...
GitHub - BorchLab/immReferent: An Interface for Immune Receptor and HLA Gene IMGT Reference Data
An Interface for Immune Receptor and HLA Gene IMGT Reference Data - BorchLab/immReferent
github.com
August 20, 2025 at 3:41 PM
Excited to announce ImmReferent - A one stop shop for getting and handling IMGT immune receptor and HLA sequences in R.
github.com/BorchLab/imm...
github.com/BorchLab/imm...
Anyone interested in medical/laboratory information systems and language models - Check out the 2025 ADLM Data Science Challenge:
github.com/myADLM/ADLM-...
github.com/myADLM/ADLM-...
GitHub - myADLM/ADLM-2025-Data-Challenge: Build an AI Tool for Extracting Information from Laboratory Documentation
Build an AI Tool for Extracting Information from Laboratory Documentation - myADLM/ADLM-2025-Data-Challenge
github.com
July 28, 2025 at 1:31 PM
Anyone interested in medical/laboratory information systems and language models - Check out the 2025 ADLM Data Science Challenge:
github.com/myADLM/ADLM-...
github.com/myADLM/ADLM-...
Researching at the intersection of HLA and viral infections - check out the special issue from Viruses.
www.mdpi.com/journal/viru...
www.mdpi.com/journal/viru...
July 18, 2025 at 9:49 AM
Researching at the intersection of HLA and viral infections - check out the special issue from Viruses.
www.mdpi.com/journal/viru...
www.mdpi.com/journal/viru...
scRepertoire now supports exporting clones directly into the immunarch workflow. Removing barriers like it's an anti-PD1.
vignette: www.borch.dev/uploads/scre...
vignette: www.borch.dev/uploads/scre...
July 17, 2025 at 7:44 PM
scRepertoire now supports exporting clones directly into the immunarch workflow. Removing barriers like it's an anti-PD1.
vignette: www.borch.dev/uploads/scre...
vignette: www.borch.dev/uploads/scre...
Reposted by Nick Borcherding
dandelionR: Single-cell immune repertoire trajectory analysis in R is out! www.sciencedirect.com/science/arti...
Checkout our package at github.com/tuonglab/dan... and on Bioconductor 3.21 onwards!
Thanks to everyone involved! @thehumanborch.bsky.social
Checkout our package at github.com/tuonglab/dan... and on Bioconductor 3.21 onwards!
Thanks to everyone involved! @thehumanborch.bsky.social
dandelionR: Single-cell immune repertoire trajectory analysis in R
Integration of single-cell RNA-sequencing (scRNA-seq) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) is extremely powerful in studying lymp…
www.sciencedirect.com
July 1, 2025 at 12:19 AM
dandelionR: Single-cell immune repertoire trajectory analysis in R is out! www.sciencedirect.com/science/arti...
Checkout our package at github.com/tuonglab/dan... and on Bioconductor 3.21 onwards!
Thanks to everyone involved! @thehumanborch.bsky.social
Checkout our package at github.com/tuonglab/dan... and on Bioconductor 3.21 onwards!
Thanks to everyone involved! @thehumanborch.bsky.social
Reposted by Nick Borcherding
❗How can a cancer exploit its environment and still resist treatment?
✅The answer: co-existing malignant subclones.
Let me walk you through our latest study investigating how divergent evolution drives adaptability, aggressiveness, and drug resistance of T cell cancer. 1/🧵
doi.org/10.1158/2159...
✅The answer: co-existing malignant subclones.
Let me walk you through our latest study investigating how divergent evolution drives adaptability, aggressiveness, and drug resistance of T cell cancer. 1/🧵
doi.org/10.1158/2159...
June 19, 2025 at 11:31 AM
❗How can a cancer exploit its environment and still resist treatment?
✅The answer: co-existing malignant subclones.
Let me walk you through our latest study investigating how divergent evolution drives adaptability, aggressiveness, and drug resistance of T cell cancer. 1/🧵
doi.org/10.1158/2159...
✅The answer: co-existing malignant subclones.
Let me walk you through our latest study investigating how divergent evolution drives adaptability, aggressiveness, and drug resistance of T cell cancer. 1/🧵
doi.org/10.1158/2159...
Just resubmited the scRepertoire manuscript. Favorite part of the reviewer suggestions was benchmarking - scRepertoire v2 (yellow) can assign > 1 million TCR clonotypes in 30 seconds! Let's not talk about scRepertoire v1 (green line).
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
April 20, 2025 at 8:54 PM
Just resubmited the scRepertoire manuscript. Favorite part of the reviewer suggestions was benchmarking - scRepertoire v2 (yellow) can assign > 1 million TCR clonotypes in 30 seconds! Let's not talk about scRepertoire v1 (green line).
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
Ibex update!
Our single-cell BCR deep learning package just got a major overhaul!
✅ Now supports CDR3 & full CDR1/2/3 embeddings
✅ Human & mouse models available
✅ Trained on 2–10M unique sequences for high accuracy
Check it out! github.com/BorchLab/Ibex
Our single-cell BCR deep learning package just got a major overhaul!
✅ Now supports CDR3 & full CDR1/2/3 embeddings
✅ Human & mouse models available
✅ Trained on 2–10M unique sequences for high accuracy
Check it out! github.com/BorchLab/Ibex
GitHub - BorchLab/Ibex: Using BCR and expression for sequence embedding
Using BCR and expression for sequence embedding . Contribute to BorchLab/Ibex development by creating an account on GitHub.
github.com
February 15, 2025 at 11:43 AM
Ibex update!
Our single-cell BCR deep learning package just got a major overhaul!
✅ Now supports CDR3 & full CDR1/2/3 embeddings
✅ Human & mouse models available
✅ Trained on 2–10M unique sequences for high accuracy
Check it out! github.com/BorchLab/Ibex
Our single-cell BCR deep learning package just got a major overhaul!
✅ Now supports CDR3 & full CDR1/2/3 embeddings
✅ Human & mouse models available
✅ Trained on 2–10M unique sequences for high accuracy
Check it out! github.com/BorchLab/Ibex
If you are interested in HLA, adaptive immunity, or viral infections, please see the special issue I am guest editor for: www.mdpi.com/journal/viru...
Human Leukocyte Antigen (HLA) in Viral Infections
Special Issue in journal Viruses: Human Leukocyte Antigen (HLA) in Viral Infections
www.mdpi.com
January 15, 2025 at 4:58 PM
If you are interested in HLA, adaptive immunity, or viral infections, please see the special issue I am guest editor for: www.mdpi.com/journal/viru...
Reposted by Nick Borcherding
1/2 Every #rstats user, interested in #reproducible analysis should try the new version of #rix. It's much more robust than just using renv. With this update rix allows to use date specific versions and improves using github packages.
bsky.app/profile/brod...
bsky.app/profile/brod...
rix v0.14.3 is on CRAN with many new features and improvements!
cran.r-project.org/web/packages...
Thanks to the many contributors for this release (credited in the DESCRIPTION file)
Here is a sneak peak of what awaits you:
1/4
cran.r-project.org/web/packages...
Thanks to the many contributors for this release (credited in the DESCRIPTION file)
Here is a sneak peak of what awaits you:
1/4
NEWS
cran.r-project.org
January 10, 2025 at 10:03 PM
1/2 Every #rstats user, interested in #reproducible analysis should try the new version of #rix. It's much more robust than just using renv. With this update rix allows to use date specific versions and improves using github packages.
bsky.app/profile/brod...
bsky.app/profile/brod...
scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 31, 2024 at 8:11 PM
scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nick Borcherding
There's a really interesting new paper out in Science for people who care about immunity to flu (which should be everyone because flu is a VERY big problem):
www.science.org/doi/10.1126/...
Here's my thread explaining this work🧵
www.science.org/doi/10.1126/...
Here's my thread explaining this work🧵
Coupling antigens from multiple subtypes of influenza can broaden antibody and T cell responses
The seasonal influenza vaccine contains strains of viruses from distinct subtypes that are grown independently and then combined. However, most individuals exhibit a more robust response to one of the...
www.science.org
December 20, 2024 at 4:57 PM
There's a really interesting new paper out in Science for people who care about immunity to flu (which should be everyone because flu is a VERY big problem):
www.science.org/doi/10.1126/...
Here's my thread explaining this work🧵
www.science.org/doi/10.1126/...
Here's my thread explaining this work🧵
Reposted by Nick Borcherding
Exciting news from Palleon Pharma. Engineered sialidases remove glyco-immune checkpoint ligands from B cells, thereby potentiating antibody-mediated B cell depletion for treatment of autoimmune disease. Clinical studies gearing up in partnership with Henlius Biotech #glycotime
Palleon Pharmaceuticals and Henlius Collaborate to Advance Glycan Editing as a Treatment for Autoimmune Diseases
Palleon Pharmaceuticals, a company pioneering glyco-immunology drug development to treat autoimmune diseases and cancer, today announced a collaborati
www.businesswire.com
December 19, 2024 at 3:17 PM
Exciting news from Palleon Pharma. Engineered sialidases remove glyco-immune checkpoint ligands from B cells, thereby potentiating antibody-mediated B cell depletion for treatment of autoimmune disease. Clinical studies gearing up in partnership with Henlius Biotech #glycotime
Reposted by Nick Borcherding
Our paper has now been published @elife.bsky.social 🎉🎉🎉
Check it out, especially if you are interested in the TCR repertoire and T cell development in the thymus
doi.org/10.7554/eLif...
Check it out, especially if you are interested in the TCR repertoire and T cell development in the thymus
doi.org/10.7554/eLif...
Distinct T-cell receptor (TCR) gene segment usage and MHC-restriction between foetal and adult thymus
The foetal thymic T-cell receptor (TCR) repertoire is distinct from adult, and it is less governed by MHC-restriction, more closely encoded by genomic sequence with distinct gene-segment usage includi...
doi.org
December 6, 2024 at 1:56 PM
Our paper has now been published @elife.bsky.social 🎉🎉🎉
Check it out, especially if you are interested in the TCR repertoire and T cell development in the thymus
doi.org/10.7554/eLif...
Check it out, especially if you are interested in the TCR repertoire and T cell development in the thymus
doi.org/10.7554/eLif...
Reposted by Nick Borcherding
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
www.nature.com
December 6, 2024 at 8:52 PM
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
Reposted by Nick Borcherding
Our massive effort to recontextualize #single #T-cell data is now out in Science Advances! We developed a new system, STEGO, to do a TCR-first analysis, and reanalyzed 12 studies and more than 500 000 individual T-cells.
Supported by @cziscience.bsky.social !
doi.org/10.1126/scia...
Supported by @cziscience.bsky.social !
doi.org/10.1126/scia...
T cell receptor–centric perspective to multimodal single-cell data analysis
T cell receptor–centric perspective improves single-cell analysis.
doi.org
December 2, 2024 at 8:30 AM
Our massive effort to recontextualize #single #T-cell data is now out in Science Advances! We developed a new system, STEGO, to do a TCR-first analysis, and reanalyzed 12 studies and more than 500 000 individual T-cells.
Supported by @cziscience.bsky.social !
doi.org/10.1126/scia...
Supported by @cziscience.bsky.social !
doi.org/10.1126/scia...
Reposted by Nick Borcherding
Rather than immune suppression, CD206+ TAMs recruit a tumor-reactive network of CD8 T cells, cDC1s, and NK cells
doi.org/10.1084/jem....
@maxkrummel.bsky.social @jexpmed.bsky.social
doi.org/10.1084/jem....
@maxkrummel.bsky.social @jexpmed.bsky.social
November 28, 2024 at 12:04 PM
Rather than immune suppression, CD206+ TAMs recruit a tumor-reactive network of CD8 T cells, cDC1s, and NK cells
doi.org/10.1084/jem....
@maxkrummel.bsky.social @jexpmed.bsky.social
doi.org/10.1084/jem....
@maxkrummel.bsky.social @jexpmed.bsky.social
Reposted by Nick Borcherding
I had zero luck with grants. People really didn’t get why what I did was important and never figured out how to explain it to them.
November 26, 2024 at 5:57 PM
I had zero luck with grants. People really didn’t get why what I did was important and never figured out how to explain it to them.
Reposted by Nick Borcherding
Cool preprint by Dustin and coworkers on how various T cell engager formats, w/varying geometries/rigidities, impact synapse structure and potency
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Solution structure and synaptic analyses reveal determinants of bispecific T cell engager potency
Bispecific T-cell engagers (TcEs) link T cell receptors to tumor-associated antigens on cancer cells, forming cytotoxic immunological synapses (IS). Close membrane-to-membrane contact (≤13 nm) has bee...
www.biorxiv.org
November 27, 2024 at 5:47 PM
Cool preprint by Dustin and coworkers on how various T cell engager formats, w/varying geometries/rigidities, impact synapse structure and potency
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nick Borcherding
We keep improving TIRTL-seq, see the updated preprint (www.biorxiv.org/content/10.1...)! New additions include: a manual 96-well protocol, code and raw data now available, and successful in vitro validation of EBV and SARS-CoV-2 TCRs.
TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing
α/β T cells are key players in adaptive immunity. The specificity of T cells is determined by the sequences of the hypervariable T cell receptor (TCR) α and β chains. Although bulk TCR sequencing offe...
www.biorxiv.org
November 26, 2024 at 7:42 PM
We keep improving TIRTL-seq, see the updated preprint (www.biorxiv.org/content/10.1...)! New additions include: a manual 96-well protocol, code and raw data now available, and successful in vitro validation of EBV and SARS-CoV-2 TCRs.
Reposted by Nick Borcherding
🎨 In case anyone need…
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
November 23, 2024 at 3:50 PM
🎨 In case anyone need…
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
Reposted by Nick Borcherding
This #glycotime work by @virusesimmunity.bsky.social is intriguing; terminal GlcNAc is a viral epitope recognized by Abs that keep endogenous retroviruses at bay. Must be something about the context of that GlcNAc, would love to see some followup structural biology.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
A B cell screen against endogenous retroviruses identifies glycan-reactive IgM that recognizes a broad array of enveloped viruses
Profiling of ERV-reactive B-1 cells in mice reveals natural antibodies against terminal N-acetylglucosamine on multiple viral envelope proteins.
www.science.org
November 22, 2024 at 4:55 PM
This #glycotime work by @virusesimmunity.bsky.social is intriguing; terminal GlcNAc is a viral epitope recognized by Abs that keep endogenous retroviruses at bay. Must be something about the context of that GlcNAc, would love to see some followup structural biology.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
VDJ space-based trajectory analysis for single-cell immune profiling is coming to R!
Check the dandelionR package (in progress): github.com/tuonglab/dan...
Original Publication: www.nature.com/articles/s41...
Check the dandelionR package (in progress): github.com/tuonglab/dan...
Original Publication: www.nature.com/articles/s41...
November 20, 2024 at 8:41 PM
VDJ space-based trajectory analysis for single-cell immune profiling is coming to R!
Check the dandelionR package (in progress): github.com/tuonglab/dan...
Original Publication: www.nature.com/articles/s41...
Check the dandelionR package (in progress): github.com/tuonglab/dan...
Original Publication: www.nature.com/articles/s41...