Publications by authors named "David A Knowles"

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Distributional genetic effects reveal context-dependent molecular regulation in human brain aging and Alzheimer's disease.
Anjing Liu, Roulan Jiang, Ruixi Li, Xuewei Cao, Zining Qi, David A Knowles

Res Sq· December 2025

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Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk.
Aline Réal, Kailash Bp, Winston H Dredge, Benjamin Z Muller, Beomjin Jang, David A Knowles

medRxiv· November 2025

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Meta-analysis of genetic regulation of RNA editing in the human brain identifies new genes underlying neurological disease.
Winston H Dredge, Kailash Bp, Aline Réal, Benjamin Z Muller, Beomjin Jang, David A Knowles

medRxiv· November 2025

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Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells.
Brielin C Brown, Alex Tokolyi, John A Morris, Tuuli Lappalainen, David A Knowles

Nat Commun· October 2025

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Leveraging functional annotations to map rare variants associated with Alzheimer disease with gruyere.
Anjali Das, Chirag Lakhani, Chloé Terwagne, Jui-Shan T Lin, Tatsuhiko Naito, David A Knowles

Am J Hum Genet· September 2025

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Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.
Isabella N Grabski, Junsuk Lee, John Blair, Carol Dalgarno, Isabella Mascio, David A Knowles

bioRxiv· September 2025

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Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning.
Alan M Moses, Jason E Stajich, Audrey P Gasch, David A Knowles

Genetics· September 2025

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Alternating hemiplegia of childhood associated mutations in Atp1a3 reveal diverse neurological alterations in mice.
Markus Terrey, Georgii Krivoshein, Scott I Adamson, Elena Arystarkhova, Laura Anderson, David A Knowles

Neurobiol Dis· August 2025

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Deriving Mendelian Randomization-Based Causal Networks of Brain Imaging Phenotypes and Bipolar Disorder.
Shane O'Connell, Brielin C Brown, Dara M Cannon, Pilib Ó Broin, Nadine Parker, David A Knowles

Biol Psychiatry Cogn Neurosci Neuroimaging· August 2025

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Perplexity as a Metric for Isoform Diversity in the Human Transcriptome.
Megan D Schertzer, Stella H Park, Jiayu Su, Gloria M Sheynkman, David A Knowles

bioRxiv· July 2025

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Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox.
Megan D Schertzer, Andrew Stirn, Keren Isaev, Laura Pereira, Stella H Park, David A Knowles

Nat Commun· July 2025

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Phenotypic complexities of rare heterozygous neurexin-1 deletions.
Michael B Fernando, Yu Fan, Yanchun Zhang, Alex Tokolyi, Aleta N Murphy, David A Knowles

Nature· June 2025

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Mosaic chromosomal alterations in blood are associated with an increased risk of Alzheimer's disease.
Tatsuhiko Naito, Kosei Hirata, Beomjin Jang, Chirag M Lakhani, Alice Buonfiglioli, David A Knowles

medRxiv· June 2025

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A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data.
Jiayu Su, Yiming Qu, Megan Schertzer, Haochen Yang, Jiahao Jiang, David A Knowles

bioRxiv· May 2025

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CONVEX APPROACHES TO ISOLATE THE SHARED AND DISTINCT GENETIC STRUCTURES OF SUBPHENOTYPES IN HETEROGENEOUS COMPLEX TRAITS.
Saikat Banerjee, Shane O'Connell, Sarah M C Colbert, Niamh Mullins, David A Knowles

medRxiv· April 2025

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Leveraging functional annotations to map rare variants associated with Alzheimer's disease with gruyere.
Anjali Das, Chirag Lakhani, Chloé Terwagne, Jui-Shan T Lin, Tatsuhiko Naito, David A Knowles

medRxiv· March 2025

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SingleBrain: A Meta-Analysis of Single-Nucleus eQTLs Linking Genetic Risk to Brain Disorders.
Beomjin Jang, Kailash Bp, Alex Tokolyi, Winston H Cuddleston, Ashvin Ravi, David A Knowles

medRxiv· March 2025

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Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries.
Daniel H Um, David A Knowles, Gail E Kaiser

Comput Biol Chem· February 2025

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Deriving Mendelian Randomization-based Causal Networks of Brain Imaging Phenotypes and Bipolar Disorder.
Shane O'Connell, Brielin C Brown, Dara M Cannon, Pilib Ó Broin, David A Knowles

medRxiv· December 2024

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Phenotypic complexities of rare heterozygous neurexin-1 deletions.
Michael B Fernando, Yu Fan, Yanchun Zhang, Alex Tokolyi, Aleta N Murphy, David A Knowles

bioRxiv· November 2024

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A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data.
Cameron Park, Shouvik Mani, Nicolas Beltran-Velez, Katie Maurer, Teddy Huang, David A Knowles

Genome Res· October 2024

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Disentangling Interpretable Factors with Supervised Independent Subspace Principal Component Analysis.
Jiayu Su, David A Knowles, Raul Rabadan

ArXiv· October 2024

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Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data.
Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, David A Knowles

Genome Biol· December 2023

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DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data.
Cameron Park, Shouvik Mani, Nicolas Beltran-Velez, Katie Maurer, Satyen Gohil, David A Knowles

bioRxiv· November 2023

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Large-scale causal discovery using interventional data sheds light on the regulatory network architecture of blood traits.
Brielin C Brown, John A Morris, Tuuli Lappalainen, David A Knowles

bioRxiv· October 2023

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