Ashlyn Anderson
@ashlynganderson.bsky.social
PhD student in Cochran lab at HudsonAlpha
Neurogenomics • Gene regulation • TFs
Neurogenomics • Gene regulation • TFs
Reposted by Ashlyn Anderson
Ever wonder how the genome of human brains compares with macaque, marmoset, mouse, rat, cat, rabbit, horse, and cow? Wonder no longer! Check out a really cool pre-print from my very talented graduate student @ashlynganderson.bsky.social on multiomics across mammals: www.biorxiv.org/content/10.1...
Single Cell Multiomics Across Nine Mammals Reveals Cell Type Specific Regulatory Conservation in the Brain
Understanding the gene regulatory mechanisms underlying brain function is crucial for advancing knowledge of the genetic basis of neurologic diseases. Cis-regulatory elements (CREs) play a pivotal rol...
www.biorxiv.org
August 7, 2025 at 1:36 PM
Ever wonder how the genome of human brains compares with macaque, marmoset, mouse, rat, cat, rabbit, horse, and cow? Wonder no longer! Check out a really cool pre-print from my very talented graduate student @ashlynganderson.bsky.social on multiomics across mammals: www.biorxiv.org/content/10.1...
Reposted by Ashlyn Anderson
New @nature.com
The possibility that lithium deficiency is a driver of Alzheimer's disease. Experimental model shows Li depletion impedes amyloid clearance, and repletion in humans could be achieved with low doses
nature.com/articles/s41...
The possibility that lithium deficiency is a driver of Alzheimer's disease. Experimental model shows Li depletion impedes amyloid clearance, and repletion in humans could be achieved with low doses
nature.com/articles/s41...
Lithium deficiency and the onset of Alzheimer’s disease - Nature
Lithium has an essential role in the brain and is deficient early in Alzheimer’s disease, which can be recapitulated in mice and treated with a novel lithium salt that restores the physiological level.
nature.com
August 6, 2025 at 3:16 PM
New @nature.com
The possibility that lithium deficiency is a driver of Alzheimer's disease. Experimental model shows Li depletion impedes amyloid clearance, and repletion in humans could be achieved with low doses
nature.com/articles/s41...
The possibility that lithium deficiency is a driver of Alzheimer's disease. Experimental model shows Li depletion impedes amyloid clearance, and repletion in humans could be achieved with low doses
nature.com/articles/s41...
Reposted by Ashlyn Anderson
Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.
August 6, 2025 at 3:14 PM
Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.
Reposted by Ashlyn Anderson
Human brain vascular multi-omics elucidates disease-risk associations @cp-neuron.bsky.social www.cell.com/neuron/fullt...
Human brain vascular multi-omics elucidates disease-risk associations
Reid et al. develop MultiVINE-seq to map thousands of non-coding disease variants
to genes in human brain vascular cells. Cerebrovascular disease variants compromise
vessel integrity, whereas Alzheime...
www.cell.com
July 29, 2025 at 2:08 PM
Human brain vascular multi-omics elucidates disease-risk associations @cp-neuron.bsky.social www.cell.com/neuron/fullt...
Reposted by Ashlyn Anderson
[1/8] *New Open-Access Long Read Resource*. We sequenced 1,019 genomes from the 1000 Genomes Project sample cohort using @nanoporetech.com long-read sequencing (LRS) to median 17x coverage. Publication at go.nature.com/4ffPb8f.
@hhu.de @crg.eu @embl.org @impvienna.bsky.social
@hhu.de @crg.eu @embl.org @impvienna.bsky.social
July 24, 2025 at 9:26 AM
[1/8] *New Open-Access Long Read Resource*. We sequenced 1,019 genomes from the 1000 Genomes Project sample cohort using @nanoporetech.com long-read sequencing (LRS) to median 17x coverage. Publication at go.nature.com/4ffPb8f.
@hhu.de @crg.eu @embl.org @impvienna.bsky.social
@hhu.de @crg.eu @embl.org @impvienna.bsky.social
Reposted by Ashlyn Anderson
microRNA-206 is a reproducibly sensitive and specific plasma biomarker of amyotrophic lateral sclerosis https://www.biorxiv.org/content/10.1101/2025.06.27.662023v1
July 2, 2025 at 4:33 PM
microRNA-206 is a reproducibly sensitive and specific plasma biomarker of amyotrophic lateral sclerosis https://www.biorxiv.org/content/10.1101/2025.06.27.662023v1
Reposted by Ashlyn Anderson
Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4
arxiv.org/abs/2411.11158
arxiv.org/abs/2411.11158
Leveraging genomic deep learning models for non-coding variant effect prediction
The majority of genetic variants identified in genome-wide association studies of complex traits are non-coding, and characterizing their function remains an important challenge in human genetics. Gen...
arxiv.org
November 20, 2024 at 1:31 AM
Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4
arxiv.org/abs/2411.11158
arxiv.org/abs/2411.11158
Reposted by Ashlyn Anderson
Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Massively parallel jumping assay decodes Alu retrotransposition activity - Nature Communications
Here, the authors develop a high-throughput assay to measure the jumping potential of thousands of transposons in parallel.
www.nature.com
May 9, 2025 at 3:50 AM
Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ashlyn Anderson
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Conservation of regulatory elements with highly diverged sequences across large evolutionary distances
Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...
rdcu.be
May 27, 2025 at 12:19 PM
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Reposted by Ashlyn Anderson
New preprint alert 📣
#Cerebellum, organoid, autism & brain evolution 🧪 🧫🧠🧬
Collaboration with G. Testa; fruit of years of work by smart students, led by postdoc Davide Aprile. Organoids to understand better the developmental basis of autism (focus: CHD8) & sapiens brain evolution (focus: CADPS2) 🧵
#Cerebellum, organoid, autism & brain evolution 🧪 🧫🧠🧬
Collaboration with G. Testa; fruit of years of work by smart students, led by postdoc Davide Aprile. Organoids to understand better the developmental basis of autism (focus: CHD8) & sapiens brain evolution (focus: CADPS2) 🧵
Benchmarking cerebellar organoids to model autism spectrum disorder and human brain evolution
While cortical organoids have been used to model different facets of neurodevelopmental conditions and human brain evolution, cerebellar organoids have not yet featured so prominently in the same cont...
www.biorxiv.org
May 16, 2025 at 11:08 AM
New preprint alert 📣
#Cerebellum, organoid, autism & brain evolution 🧪 🧫🧠🧬
Collaboration with G. Testa; fruit of years of work by smart students, led by postdoc Davide Aprile. Organoids to understand better the developmental basis of autism (focus: CHD8) & sapiens brain evolution (focus: CADPS2) 🧵
#Cerebellum, organoid, autism & brain evolution 🧪 🧫🧠🧬
Collaboration with G. Testa; fruit of years of work by smart students, led by postdoc Davide Aprile. Organoids to understand better the developmental basis of autism (focus: CHD8) & sapiens brain evolution (focus: CADPS2) 🧵
Reposted by Ashlyn Anderson
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Dissecting regulatory syntax in human development with scalable multiomics and deep learning
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...
www.biorxiv.org
May 3, 2025 at 6:27 PM
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Reposted by Ashlyn Anderson
Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics.
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Programmatic design and editing of cis-regulatory elements
The development of modern genome editing tools has enabled researchers to make such edits with high precision but has left unsolved the problem of designing these edits. As a solution, we propose Ledi...
www.biorxiv.org
April 24, 2025 at 12:59 PM
Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics.
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Reposted by Ashlyn Anderson
Delighted to share our new preprint, the outcome of many years of collaborative work with Giuseppe Testa’s group, both at the bench & in front of the computer, probing human brain evolution using organoids. We tried something cool, and learned a lot 🧪🧫🧠🧬
[follow 🧵]
www.biorxiv.org/content/10.1...
[follow 🧵]
www.biorxiv.org/content/10.1...
Regulatory logic of human cortex evolution by combinatorial perturbations
Comparative genomic studies between contemporary and extinct hominins revealed key evolutionary modifications, but their number has hampered a system level investigation of their combined roles in sca...
www.biorxiv.org
May 2, 2025 at 6:51 AM
Delighted to share our new preprint, the outcome of many years of collaborative work with Giuseppe Testa’s group, both at the bench & in front of the computer, probing human brain evolution using organoids. We tried something cool, and learned a lot 🧪🧫🧠🧬
[follow 🧵]
www.biorxiv.org/content/10.1...
[follow 🧵]
www.biorxiv.org/content/10.1...
Reposted by Ashlyn Anderson
New paper out in Genome Biology! 🎉
We lay out best-practice guidelines for releasing variant effect predictors, developed through the Atlas of Variant Effects Alliance @varianteffect.bsky.social
Open, interpretable, and clinically useful VEPs are the goal.
📄 doi.org/10.1186/s130...
We lay out best-practice guidelines for releasing variant effect predictors, developed through the Atlas of Variant Effects Alliance @varianteffect.bsky.social
Open, interpretable, and clinically useful VEPs are the goal.
📄 doi.org/10.1186/s130...
Guidelines for releasing a variant effect predictor - Genome Biology
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well...
doi.org
April 15, 2025 at 12:24 PM
New paper out in Genome Biology! 🎉
We lay out best-practice guidelines for releasing variant effect predictors, developed through the Atlas of Variant Effects Alliance @varianteffect.bsky.social
Open, interpretable, and clinically useful VEPs are the goal.
📄 doi.org/10.1186/s130...
We lay out best-practice guidelines for releasing variant effect predictors, developed through the Atlas of Variant Effects Alliance @varianteffect.bsky.social
Open, interpretable, and clinically useful VEPs are the goal.
📄 doi.org/10.1186/s130...
Reposted by Ashlyn Anderson
Excited to share our MPAC preprint, a scalable ensemble of ML models for genome-wide non-coding variant effect prediction and our findings from 575M predictions across databases including @ukbiobank.bsky.social, GTEx, ClinVar, COSMIC, and @gnomad-project.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
| bioRxiv
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
https://www.biorxiv.org/content/10.1101/2025.04.16.648420v1\
April 23, 2025 at 5:28 PM
Excited to share our MPAC preprint, a scalable ensemble of ML models for genome-wide non-coding variant effect prediction and our findings from 575M predictions across databases including @ukbiobank.bsky.social, GTEx, ClinVar, COSMIC, and @gnomad-project.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ashlyn Anderson
We are so happy to share our latest paper "CHAS infers cell type-specific signatures in bulk brain acetylation studies of neurological and psychiatric disorders".
www.cell.com/cell-reports...
@ukdri.ac.uk @kingsioppn.bsky.social @imperialbrains.bsky.social
www.cell.com/cell-reports...
@ukdri.ac.uk @kingsioppn.bsky.social @imperialbrains.bsky.social
CHAS infers cell type-specific signatures in bulk brain histone acetylation studies of neurological and psychiatric disorders
Murphy et al. develop CHAS, a computational tool that uncovers cell type-specific
patterns in bulk tissue histone acetylation data. Applying CHAS to brain disorders
reveals distinct cell type targets ...
www.cell.com
April 28, 2025 at 3:20 PM
We are so happy to share our latest paper "CHAS infers cell type-specific signatures in bulk brain acetylation studies of neurological and psychiatric disorders".
www.cell.com/cell-reports...
@ukdri.ac.uk @kingsioppn.bsky.social @imperialbrains.bsky.social
www.cell.com/cell-reports...
@ukdri.ac.uk @kingsioppn.bsky.social @imperialbrains.bsky.social
Reposted by Ashlyn Anderson
Thrilled to be a part of a novel phenomics study with HudsonAlpha and Phenome Health examining how #genetics and lifestyle impact risk for #Alzheimers. www.hudsonalpha.org/hudsonalpha-...
HudsonAlpha Launches Pilot Project to Study Alzheimer’s Disease – HudsonAlpha Institute for Biotechnology
www.hudsonalpha.org
April 25, 2025 at 6:31 PM
Thrilled to be a part of a novel phenomics study with HudsonAlpha and Phenome Health examining how #genetics and lifestyle impact risk for #Alzheimers. www.hudsonalpha.org/hudsonalpha-...
Reposted by Ashlyn Anderson
Our latest work now online in Cell:
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
April 17, 2025 at 6:26 PM
Our latest work now online in Cell:
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Reposted by Ashlyn Anderson
Excited to see this NIDA supported work from lab PhD student Kasey Brida officially published! Kasey identified a marker of neurons that are responsive to the psychostimulant drug cocaine, and discovered that this marker is essential for cocaine reward.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reelin marks cocaine-activated striatal neurons, promotes neuronal excitability, and regulates cocaine reward
Reelin is a critical mechanistic link between neuronal activation and cocaine-induced behavioral adaptations.
www.science.org
March 27, 2025 at 10:08 PM
Excited to see this NIDA supported work from lab PhD student Kasey Brida officially published! Kasey identified a marker of neurons that are responsive to the psychostimulant drug cocaine, and discovered that this marker is essential for cocaine reward.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Ashlyn Anderson
geneviewer - Gene Cluster Visualizations in R. Imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. github.com/nvelden/gene... #Rstats
March 7, 2025 at 7:30 PM
geneviewer - Gene Cluster Visualizations in R. Imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. github.com/nvelden/gene... #Rstats
Reposted by Ashlyn Anderson
Nice to see this finally published!
Congratulations @jack-humphrey.bsky.social
www.nature.com/articles/s41...
(Collaborative work with Panos Roussos and his team! )
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing
Congratulations @jack-humphrey.bsky.social
www.nature.com/articles/s41...
(Collaborative work with Panos Roussos and his team! )
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing - Nature Genetics
This isoform-centric microglia genomic atlas includes 35,879 novel human microglia isoforms identified by long-read RNA sequencing. A multi-ancestry quantitative trait locus meta-analysis of known and...
www.nature.com
March 4, 2025 at 1:31 AM
Nice to see this finally published!
Congratulations @jack-humphrey.bsky.social
www.nature.com/articles/s41...
(Collaborative work with Panos Roussos and his team! )
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing
Congratulations @jack-humphrey.bsky.social
www.nature.com/articles/s41...
(Collaborative work with Panos Roussos and his team! )
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing
Reposted by Ashlyn Anderson
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Modelling and design of transcriptional enhancers - Nature Reviews Bioengineering
Enhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to unravel the rules underlying enhancer activit...
www.nature.com
February 28, 2025 at 2:45 PM
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!
@natrevbioeng.bsky.social
www.nature.com/articles/s44...
Reposted by Ashlyn Anderson
Nature research paper: Comparative characterization of human accelerated regions in neurons
https://go.nature.com/4gVRi05
https://go.nature.com/4gVRi05
Comparative characterization of human accelerated regions in neurons - Nature
The cis-regulatory functions of human accelerated regions of genomic loci and their potential contribution to human brain evolution are revealed.
go.nature.com
March 3, 2025 at 11:15 AM
Nature research paper: Comparative characterization of human accelerated regions in neurons
https://go.nature.com/4gVRi05
https://go.nature.com/4gVRi05
Reposted by Ashlyn Anderson
I talked to NIH officials, current and former, about what's been happening inside the agency since the Trump administration shut down their grantmaking pipeline in January. Their stories showed just how willing our new leaders are to break the law: www.theatlantic.com/health/archi...
Inside the Collapse at NIH
Administration officials pressured NIH to avoid clear advice from the agency’s own lawyers to restart grant funding now.
www.theatlantic.com
February 27, 2025 at 4:13 PM
I talked to NIH officials, current and former, about what's been happening inside the agency since the Trump administration shut down their grantmaking pipeline in January. Their stories showed just how willing our new leaders are to break the law: www.theatlantic.com/health/archi...
Reposted by Ashlyn Anderson
Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
February 25, 2025 at 5:38 PM
Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...