We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! github.com/bluenote-157...
www.biorxiv.org/content/10.1...
1/5
www.biorxiv.org/content/10.1...
1/5
devider: long-read reconstruction of many diverse haplotypes
Reconstructing haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling se-quencing erro...
www.biorxiv.org
December 17, 2024 at 11:32 PM
We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! github.com/bluenote-157...
www.biorxiv.org/content/10.1...
1/5
www.biorxiv.org/content/10.1...
1/5
I don't got whatever clade of gay haplotypes that makes you wanna fuck your dad so I can't say I'm feeling shaved head George costanza
July 7, 2026 at 10:56 PM
I don't got whatever clade of gay haplotypes that makes you wanna fuck your dad so I can't say I'm feeling shaved head George costanza
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
December 16, 2025 at 4:06 PM
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
This is finally out.
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections
Snell et al. develop sequencing methodology to identify full-length spike haplotypes
and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence,
accelerating viral evolution an...
www.cell.com
February 2, 2026 at 4:09 PM
This is finally out.
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
A new preprint on indexing pangenome graphs using an FM-index of the haplotypes and a tag array. Joint work with Parsa Eskandar and @benedictpaten.bsky.social.
Lossless Pangenome Indexing Using Tag Arrays
Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due t...
www.biorxiv.org
May 15, 2025 at 8:22 PM
A new preprint on indexing pangenome graphs using an FM-index of the haplotypes and a tag array. Joint work with Parsa Eskandar and @benedictpaten.bsky.social.
Makes it extremely clear what their concern actually is, and it's got nothing to do with rare haplotypes.
February 3, 2026 at 4:13 PM
Makes it extremely clear what their concern actually is, and it's got nothing to do with rare haplotypes.
BLink-seq is out! Linked-read sequencing that brings phased whole-genome data to non-model species at population scale. We show it phases haplotypes and detects SVs, revealing previously undocumented structural complexity in an adaptive Atlantic silverside inversion.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
BLink-seq delivers population-scale haplotypes without long reads: a scalable framework for non-model genomics
Information about segregating haplotypes and structural variation (SV) can be extremely rich for a variety of applications in population genomics but remains largely inaccessible for many non-model sp...
www.biorxiv.org
August 8, 2026 at 12:40 PM
BLink-seq is out! Linked-read sequencing that brings phased whole-genome data to non-model species at population scale. We show it phases haplotypes and detects SVs, revealing previously undocumented structural complexity in an adaptive Atlantic silverside inversion.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Need haplotypes, but have lots of hets in your vcf? Gotta phase when the Data tells you to.
May 8, 2026 at 5:33 PM
Need haplotypes, but have lots of hets in your vcf? Gotta phase when the Data tells you to.
1. This adds weight to a point I've been making for years, namely, that the important differential at the population level between now and the Spanish Flu of 1918-1920 is the considerably higher percentage of the global population who are immunocompromised.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections
Evolution of SARS-CoV-2 in long-term persistent infections is hypothesised to be a major source of variants of concern (VOC). However, the linkage of intra-host variants into haplotypes that reflect v...
www.biorxiv.org
April 24, 2025 at 9:47 AM
1. This adds weight to a point I've been making for years, namely, that the important differential at the population level between now and the Spanish Flu of 1918-1920 is the considerably higher percentage of the global population who are immunocompromised.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
🚨 New preprint out!
We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation.
This reveals intensified assortment in recent generations.
www.biorxiv.org/content/10.1...
We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation.
This reveals intensified assortment in recent generations.
www.biorxiv.org/content/10.1...
September 26, 2025 at 5:10 PM
🚨 New preprint out!
We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation.
This reveals intensified assortment in recent generations.
www.biorxiv.org/content/10.1...
We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation.
This reveals intensified assortment in recent generations.
www.biorxiv.org/content/10.1...
New preprint from Luke Snell from GSTT, Suzanne Pickering in my lab and Rui Galao, my colleague at KCL.
Here we examine in detail the evolution of the SARS CoV-2 spike in persistent infections, and essentially catch a potential variant in the act of developing. 1/n
www.biorxiv.org/content/10.1...
Here we examine in detail the evolution of the SARS CoV-2 spike in persistent infections, and essentially catch a potential variant in the act of developing. 1/n
www.biorxiv.org/content/10.1...
Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections
Evolution of SARS-CoV-2 in long-term persistent infections is hypothesised to be a major source of variants of concern (VOC). However, the linkage of intra-host variants into haplotypes that reflect v...
www.biorxiv.org
April 23, 2025 at 6:42 AM
New preprint from Luke Snell from GSTT, Suzanne Pickering in my lab and Rui Galao, my colleague at KCL.
Here we examine in detail the evolution of the SARS CoV-2 spike in persistent infections, and essentially catch a potential variant in the act of developing. 1/n
www.biorxiv.org/content/10.1...
Here we examine in detail the evolution of the SARS CoV-2 spike in persistent infections, and essentially catch a potential variant in the act of developing. 1/n
www.biorxiv.org/content/10.1...
A forest is more than its trees: haplotypes and inferred ARGs https://www.biorxiv.org/content/10.1101/2024.11.30.626138v1
A forest is more than its trees: haplotypes and inferred ARGs https://www.biorxiv.org/content/10.1101/2024.11.30.626138v1
Foreshadowing haplotype-based methods of the genomics era, it is an old observation that the ``junct
www.biorxiv.org
December 2, 2024 at 8:33 AM
A forest is more than its trees: haplotypes and inferred ARGs https://www.biorxiv.org/content/10.1101/2024.11.30.626138v1
Gap-free telomere-to-telomere haplotypes assembly of the hybrid grouper 'Yushuban' (Cromileptes altivelis female x Epinephelus fuscoguttatus male) https://www.biorxiv.org/content/10.64898/2026.09.20.752973v1
September 25, 2026 at 5:30 PM
Gap-free telomere-to-telomere haplotypes assembly of the hybrid grouper 'Yushuban' (Cromileptes altivelis female x Epinephelus fuscoguttatus male) https://www.biorxiv.org/content/10.64898/2026.09.20.752973v1
Direct Inference of Haplotypes from Sequencing Data. #Haplotypes #SequencingData #Bioinformatics #Genomics
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
August 31, 2025 at 10:31 AM
Direct Inference of Haplotypes from Sequencing Data. #Haplotypes #SequencingData #Bioinformatics #Genomics
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Fewer genetic studies have been completed on Central & S. American pumas than N. American pumas. However, mtDNA sequencing has shown that Central & S. American pumas form distinct groups and that N. American pumas are genetically homogenous. #2025MMM doi.org/10.3109/1940...
March 28, 2025 at 12:30 AM
Fewer genetic studies have been completed on Central & S. American pumas than N. American pumas. However, mtDNA sequencing has shown that Central & S. American pumas form distinct groups and that N. American pumas are genetically homogenous. #2025MMM doi.org/10.3109/1940...
2. Mendel didn't observe linkage between traits that are actually linked. Sometimes genes physically located close together will always travel together, rather than segregating independently.
Mendel somehow found genes that were 40% linked had NO linkage.
Mendel somehow found genes that were 40% linked had NO linkage.
November 22, 2023 at 2:11 PM
2. Mendel didn't observe linkage between traits that are actually linked. Sometimes genes physically located close together will always travel together, rather than segregating independently.
Mendel somehow found genes that were 40% linked had NO linkage.
Mendel somehow found genes that were 40% linked had NO linkage.
Sharing our new paper, "Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts". Genomics & evolution of a mating type system involving two morphs with alternating sexes in walnut relatives www.cell.com/current-biol...
Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts
In most species within the walnut family, two genetically determined morphs alternate
between male and female flowering phases in time. Groh et al. identify a distinct
locus for this dimorphism in two...
www.cell.com
October 16, 2025 at 3:43 PM
Sharing our new paper, "Distinct haplotypes and reversed dominance at a single-gene balanced polymorphism controlling heterodichogamy in two genera of wingnuts". Genomics & evolution of a mating type system involving two morphs with alternating sexes in walnut relatives www.cell.com/current-biol...
"tell me about your haplotypes! I am very normal!"
has anyone noticed that TERFs always talk like aliens
November 26, 2025 at 8:01 PM
"tell me about your haplotypes! I am very normal!"
debugging some slim code, and these flashing haplotypes are mostly gratuitous, but the closest I'll ever get to the matrix I think
August 22, 2025 at 3:58 AM
debugging some slim code, and these flashing haplotypes are mostly gratuitous, but the closest I'll ever get to the matrix I think
Our new study shows that island populations of grey long-eared #bats have distinct DNA haplotypes compared to mainland populations, reflecting long-term isolation & independent evolutionary trajectories: link.springer.com/article/10.1... @iccs.bsky.social @jesusoxford.bsky.social @biology.ox.ac.uk
November 10, 2025 at 8:59 PM
Our new study shows that island populations of grey long-eared #bats have distinct DNA haplotypes compared to mainland populations, reflecting long-term isolation & independent evolutionary trajectories: link.springer.com/article/10.1... @iccs.bsky.social @jesusoxford.bsky.social @biology.ox.ac.uk
Some people talk about sexual and subcultural aesthetics like they're haplotypes. Assigned bottom at birth. No wonder everyone has horoscope shit and Myers-Briggs types in their cool progressive queer dating apps.
May 7, 2026 at 3:41 PM
Some people talk about sexual and subcultural aesthetics like they're haplotypes. Assigned bottom at birth. No wonder everyone has horoscope shit and Myers-Briggs types in their cool progressive queer dating apps.
"HPRC2 contributes 460 haplotypes that together capture over 99% of common variation observed in the All of Us Research Program v8 cohort"
Also, coordinate system, transcriptomes,..
Also, coordinate system, transcriptomes,..
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1
July 22, 2026 at 8:42 AM
"HPRC2 contributes 460 haplotypes that together capture over 99% of common variation observed in the All of Us Research Program v8 cohort"
Also, coordinate system, transcriptomes,..
Also, coordinate system, transcriptomes,..
Only ~300 Addax remain in the wild & ~1000 in ex-situ groups. The latter are vital for preventing extinction, but genetic data show wild Addax hold more diversity than all ex-situ combined. Enhancing genetic management in captivity is crucial to preserve the species. #2025MMM doi.org/10.1111/eva....
March 28, 2025 at 12:28 AM
Only ~300 Addax remain in the wild & ~1000 in ex-situ groups. The latter are vital for preventing extinction, but genetic data show wild Addax hold more diversity than all ex-situ combined. Enhancing genetic management in captivity is crucial to preserve the species. #2025MMM doi.org/10.1111/eva....
New issue alert👉https://cell.com/cell/current
On the cover: The Telomere-to-Telomere Consortium has finished the complete, diploid genome of a person. The cover is inspired by a karyotype of the chromosomes in metaphase, representing the two haplotypes as different colors.
On the cover: The Telomere-to-Telomere Consortium has finished the complete, diploid genome of a person. The cover is inspired by a karyotype of the chromosomes in metaphase, representing the two haplotypes as different colors.
August 6, 2026 at 3:35 PM
New issue alert👉https://cell.com/cell/current
On the cover: The Telomere-to-Telomere Consortium has finished the complete, diploid genome of a person. The cover is inspired by a karyotype of the chromosomes in metaphase, representing the two haplotypes as different colors.
On the cover: The Telomere-to-Telomere Consortium has finished the complete, diploid genome of a person. The cover is inspired by a karyotype of the chromosomes in metaphase, representing the two haplotypes as different colors.