Omid Arhami
@omidarhami.bsky.social
#Bioinformatics PhD & #Statistics MS student @universityofga. RA @ Rohani Lab @CIDER_UGA. EE & MBA@ Sharif.
#Compbio, Modeling, #ML
(opinions R mine)
#Compbio, Modeling, #ML
(opinions R mine)
Please download version 2 from GitHub to use the new function Euclidify until September, when CRAN resumes publishing updates.
github.com/omid-arhami/...
github.com/omid-arhami/...
GitHub - omid-arhami/topolow: A physics-inspired R package for robust Euclidean embedding of sparse, non-metric dissimilarity data. Particularly powerful for antigenic cartography and viral evolution ...
A physics-inspired R package for robust Euclidean embedding of sparse, non-metric dissimilarity data. Particularly powerful for antigenic cartography and viral evolution tracking, but applicable to...
github.com
August 6, 2025 at 1:47 AM
Please download version 2 from GitHub to use the new function Euclidify until September, when CRAN resumes publishing updates.
github.com/omid-arhami/...
github.com/omid-arhami/...
(7/7) So, it's not just about the linkage type (α2,6 vs α2,3).
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Avian influenza A viruses exhibit plasticity in sialylglycoconjugate receptor usage in human lung cells | Journal of Virology
It is well known that influenza A viruses (IAV) initiate host cell infection by binding
to sialic acid, a sugar molecule present at the ends of various sugar chains called
glycoconjugates. These sugar...
journals.asm.org
April 14, 2025 at 4:39 AM
(7/7) So, it's not just about the linkage type (α2,6 vs α2,3).
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
(6/7) efficiently, revealing they could use alternative, less common glycoconjugates like sialyl Tn and sialyl T antigens.
This adaptability in receptor usage may explain why avian influenza viruses can more readily jump between species.
This adaptability in receptor usage may explain why avian influenza viruses can more readily jump between species.
April 14, 2025 at 4:39 AM
(6/7) efficiently, revealing they could use alternative, less common glycoconjugates like sialyl Tn and sialyl T antigens.
This adaptability in receptor usage may explain why avian influenza viruses can more readily jump between species.
This adaptability in receptor usage may explain why avian influenza viruses can more readily jump between species.
(5/7) C1GALT1, and UGCG
The most striking discovery was that when all three glycoconjugate types were truncated:
1.Human IAV strains showed a dramatic 1-3 log decrease in replication, suggesting they require at least one of these major glycoconjugate types.
2.Avian IAV strains continued replicating
The most striking discovery was that when all three glycoconjugate types were truncated:
1.Human IAV strains showed a dramatic 1-3 log decrease in replication, suggesting they require at least one of these major glycoconjugate types.
2.Avian IAV strains continued replicating
April 14, 2025 at 4:37 AM
(5/7) C1GALT1, and UGCG
The most striking discovery was that when all three glycoconjugate types were truncated:
1.Human IAV strains showed a dramatic 1-3 log decrease in replication, suggesting they require at least one of these major glycoconjugate types.
2.Avian IAV strains continued replicating
The most striking discovery was that when all three glycoconjugate types were truncated:
1.Human IAV strains showed a dramatic 1-3 log decrease in replication, suggesting they require at least one of these major glycoconjugate types.
2.Avian IAV strains continued replicating
(4/7) The researchers used #CRISPR #gene editing on human lung cells, naturally expressing both α2,6-linked and α2,3-linked sialic acids distributed across all three glycoconjugate types, to create lung cells lacking different combinations of glycoconjugate types by knocking out key enzymes: MGAT1,
April 14, 2025 at 4:36 AM
(3/7) The paper examines how #sialic acids can be attached to three different types of molecules on cell surfaces (#glycoconjugates):
1- N-glycans
2- O-glycans
3- Glycolipids
No one had systematically tested how different IAV strains might differ in their use of these three glycoconjugate types.
1- N-glycans
2- O-glycans
3- Glycolipids
No one had systematically tested how different IAV strains might differ in their use of these three glycoconjugate types.
April 14, 2025 at 4:35 AM
(3/7) The paper examines how #sialic acids can be attached to three different types of molecules on cell surfaces (#glycoconjugates):
1- N-glycans
2- O-glycans
3- Glycolipids
No one had systematically tested how different IAV strains might differ in their use of these three glycoconjugate types.
1- N-glycans
2- O-glycans
3- Glycolipids
No one had systematically tested how different IAV strains might differ in their use of these three glycoconjugate types.
(2/7)
- Human IAVs prefer sialic acids with α2,6 linkages
- Avian IAVs prefer sialic acids with α2,3 linkages
But this collaboration by researchers from University of Iowa, U. of Georgia, U. of Chicago, U. at Buffalo, and UCSD reveals that the story is more complex than just the type of linkage.
- Human IAVs prefer sialic acids with α2,6 linkages
- Avian IAVs prefer sialic acids with α2,3 linkages
But this collaboration by researchers from University of Iowa, U. of Georgia, U. of Chicago, U. at Buffalo, and UCSD reveals that the story is more complex than just the type of linkage.
April 14, 2025 at 4:35 AM
(2/7)
- Human IAVs prefer sialic acids with α2,6 linkages
- Avian IAVs prefer sialic acids with α2,3 linkages
But this collaboration by researchers from University of Iowa, U. of Georgia, U. of Chicago, U. at Buffalo, and UCSD reveals that the story is more complex than just the type of linkage.
- Human IAVs prefer sialic acids with α2,6 linkages
- Avian IAVs prefer sialic acids with α2,3 linkages
But this collaboration by researchers from University of Iowa, U. of Georgia, U. of Chicago, U. at Buffalo, and UCSD reveals that the story is more complex than just the type of linkage.
Right. But one example doesn't negate a whole concept; It shows that peer review isn't 100% error-proof. But it's still way better than no control.
February 12, 2025 at 5:23 PM
Right. But one example doesn't negate a whole concept; It shows that peer review isn't 100% error-proof. But it's still way better than no control.
Peer-reviewed journals are like municipal courts. They cost money but we can't get rid of them and let people on streets decide who is a criminal and who is not. I think the solution is to regulate the profit journals demand with something like fare-trade rules.
January 26, 2025 at 11:50 PM
Peer-reviewed journals are like municipal courts. They cost money but we can't get rid of them and let people on streets decide who is a criminal and who is not. I think the solution is to regulate the profit journals demand with something like fare-trade rules.