@BioConorWalker

Bioinformatics Scientist. Formerly postdoc at @nygenome/@Columbia and PhD @emblebi/@Cambridge_Uni.

 New York, NY
conorwalker.net
Joined March 2017
  • Tweets56
  • Following678
  • Followers146
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Super excited to share my lab's latest work on quantifying the private information leakage from single cell count matrices. Led by very first postdoc in the g2lab, brilliant @BioConorWalker, we showed that individuals can be reidentified 1/n cell.com/cell/fulltext/S0092…

Private information leakage from single-cell count matrices

This study demonstrates that single-cell RNA sequencing count matrices, although valuable for biological research, can inadvertently reveal private information about individuals.

cell.com
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Conor Walker retweeted
Anoushka@noush_joglekar
9 Apr 2024
If you were looking for evidence that isoforms are cool, all-pervasive in the 🧠, and everybody should study them at the single cell level, our work on mouse development and brain-region variability from the @hagentilgner lab is now live @NatureNeuro! 1/ nature.com/articles/s41593-0…

Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing...

Nature Neuroscience - RNA alternative splicing is involved in determining cell identity, but a comprehensive molecular map is missing. Here, the authors provide a human and mouse brain atlas of...

nature.com
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A few months ago we posted a pre-print regarding a new approach to likelihood-based phylogenetics at short divergence scales (e.g. genomic epidemiology). I have now further optimized the code and updated the preprint doi.org/10.1101/2022.03.22.4…
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We've made a draft human pangenome! 47 haplotype-resolved assemblies, two reference genomes, and five pangenome graphs!
Structural haplotypes of HLA-A in the PGGB HPRCy1 graph

ALT Structural haplotypes of HLA-A in the PGGB HPRCy1 graph

bioRxiv@biorxivpreprint
10 Jul 2022
A Draft Human Pangenome Reference biorxiv.org/cgi/content/shor… #bioRxiv
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Shai Carmi@ShaiCarmi
27 May 2022
This is a brilliant preprint. It describes an experimental method for separately sequencing the paternal and maternal genomes. This goes beyond the standard "experimental phasing" - the method can also tell which chr is maternal and which is paternal. biorxiv.org/content/10.1101/…

Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation...

Hundreds of loci in human genomes have alleles that are methylated differentially according to their parent of origin. These imprinted loci generally show little variation across tissues, individua...

biorxiv.org
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We've known for a long time that a large fraction of noncoding GWAS hits are not currently explained by eQTLs. Why?? I'm excited to share our new preprint on this! Take home: GWAS and eQTL assays maximize power for different types of variants. (1/n) biorxiv.org/content/10.1101/…

Limited overlap of eQTLs and GWAS hits due to systematic differences in discovery

Most signals in genome-wide association studies (GWAS) of complex traits point to noncoding genetic variants with putative gene regulatory effects. However, currently identified expression quantita...

biorxiv.org
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Zamin Iqbal@ZaminIqbal
23 Mar 2022
Groundbreaking work from @Nicola_De_Maio @EBIgoldman and colleagues "we rewrite the classical Felsenstein pruning algorithm so that we can infer phylogenetic trees on at least 10 times larger datasets with higher accuracy than existing maximum likelihood methods. "
bioRxiv Bioinfo@biorxiv_bioinfo
23 Mar 2022
Maximum likelihood pandemic-scale phylogenetics biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Conor Walker retweeted
Mat Legut, PhD@MatLegut
16 Mar 2022
Really chuffed to share our latest work from Sanjana Lab out in @nature today (nature.com/articles/s41586-0…). We tested >12,000 genes to find positive regulators of T cell proliferation to be used for next-gen #immunotherapies. A thread...
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Looking forward to starting my new position with @gamzeandgursoy at @nygenome! I will be working on developing methods for genomic #privacy. g2lab.org/people/
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A huge thank you to @Nick_Goldman, @aylwyn_scally, @Nicola_De_Maio, and members of @EBIgoldman for their supervision and support during my #PhD.
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Simulating pandemic-scale genome sequencing datasets, e.g to benchmark your new analysis methods? Try phastSim, now updated to include indels (biorxiv.org/content/10.1101/…) [1/2]
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Conor Walker retweeted
josé@zga_aaa
13 Aug 2021
Glad to see this out. Here, we track ~700 clones across >300 individuals over ~13 years to unravel key aspects of clonal haematopoiesis (when there are genetically-defined subpopulations of haematopoietic stem cells in your bone marrow).
bioRxiv@biorxivpreprint
13 Aug 2021
The longitudinal dynamics and natural history of clonal haematopoiesis biorxiv.org/cgi/content/shor… #bioRxiv
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Conor Walker retweeted
EvolCompGen@EvolComp
6 Aug 2021
Congrats to the 2021 @EvolComp Talk & Poster awardees for #ismbeccb2021 Best talk - Elise Parey (@CamLBerthelot lab) Best poster - Vignesh Sridhar (@Vigs_24, @JRaviLab) Honorable mentions Talks - @punto_c @BioConorWalker @matteodelabre Posters - @elliotmajlessi
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Conor Walker retweeted
Goldman Group@EBIgoldman
3 Aug 2021
We are still looking to hire a postdoc bioinformatician on this fascinating project. Please read/RT/pass on to anyone who might be interested: nitter.cf/emblebi/status/1422516…
EMBL-EBI@emblebi
3 Aug 2021
🎉 Congratulations on recent @EU_Commission @HorizonEU funding awarded to researchers at @IITalk, @uni_lu, @CNRS, @UniPadova and EMBL-EBI’s @EBIgoldman and colleagues. Find out more 👇 ebi.ac.uk/about/news/press-r…

Using ultrafast technology for protein sequencing

Funding from the European Union's Horizon 2020 has been awarded to a consortium of researchers developing a new method for protein sequencing

ebi.ac.uk
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We are re-advertising this position! Please check-out 👇 the original thread 👇, pass to anyone you think might be interested, share with colleagues, RT ... nitter.cf/EBIgoldman/status/1384…
Goldman Group@EBIgoldman
20 Apr 2021
Postdoc position in @EBIgoldman Group at @emblebi, to join new multinatl collab project creating proof-of-principle high-throughput nanopore device for determining amino acid sequence and identity of proteins Full details at embl.org/jobs/position/EBI01… <1/2>
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The impressively huge scale of SARS-CoV-2 sequencing has really stretched our ability to do phylogenetics, and is leading to some fantastic advances in methods. Here's one that @Nicola_De_Maio from the @EBIgoldman group at @emblebi contributed to. nitter.cf/emblebi/status/1392006…
EMBL-EBI@emblebi
11 May 2021
#SARSCoV2 is spreading through human populations & evolving. Ultrafast Sample placement on Existing tRees (UShER) is a game-changing new tool which can be used to track this evolution in real time & reconstruct the source of new cases. @NatureGenet @ucsc nature.com/articles/s41588-0…
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Conor Walker retweeted
Goldman Group@EBIgoldman
7 May 2021
Last call; closing date on Monday. Please apply! If you don't apply, at least promise me you'll RT or pass to a friend. nitter.cf/EBIgoldman/status/1384…
Goldman Group@EBIgoldman
20 Apr 2021
Postdoc position in @EBIgoldman Group at @emblebi, to join new multinatl collab project creating proof-of-principle high-throughput nanopore device for determining amino acid sequence and identity of proteins Full details at embl.org/jobs/position/EBI01… <1/2>
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Postdoc position in @EBIgoldman Group at @emblebi, to join new multinatl collab project creating proof-of-principle high-throughput nanopore device for determining amino acid sequence and identity of proteins Full details at embl.org/jobs/position/EBI01… <1/2>
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For those of you who love to explain complex mutation clusters parsimoniously (who doesn't?), the final version of @BioConorWalker's paper is now out at journals.plos.org/plosgeneti… - also feat. @aylwyn_scally and @Nicola_De_Maio. And me. Cool figures too: this 👇 is part of S.Fig 10
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We developed a new method (phastSim) to simulate sequence evolution along huge phylogenies, in particular pandemic-scale ones like in SARS-CoV-2 doi.org/10.1101/2021.03.15.4… with @EBIgoldman @RussCorbett @BioConorWalker @weilgunyl @yatishturakhia
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