Publications by authors named "Kasper D Hansen"

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nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes.
Lukas M Weber, Arkajyoti Saha, Abhirup Datta, Kasper D Hansen, Stephanie C Hicks

Nat Commun· July 2023

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Linear models enable powerful differential activity analysis in massively parallel reporter assays.
Leslie Myint, Dimitrios G Avramopoulos, Loyal A Goff, Kasper D Hansen

BMC Genomics· March 2019

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Orchestrating Spatial Transcriptomics Analysis with Bioconductor.
Helena L Crowell, Yixing Dong, Ilaria Billato, Peiying Cai, Martin Emons, Kasper D Hansen

bioRxiv· November 2025

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Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks.
Prashanthi Ravichandran, Princy Parsana, Rebecca Keener, Kasper D Hansen, Alexis Battle

Genome Res· September 2025

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Single-cell spatial transcriptomics reveals immunotherapy-driven bone marrow niche remodeling in AML.
Gege Gui, Molly A Bingham, Julius R Herzog, Abigail Wong-Rolle, Laura W Dillon, Kasper D Hansen

Sci Adv· July 2025

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mNSF: multi-sample non-negative spatial factorization.
Yi Wang, Kyla Woyshner, Chaichontat Sriworarat, Genevieve Stein-O'Brien, Loyal A Goff, Kasper D Hansen

Genome Biol· June 2025

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Correction: Comprehensive DNA Methylation Analysis Indicates That Pancreatic Intraepithelial Neoplasia Lesions Are Acinar-Derived and Epigenetically Primed for Carcinogenesis.
Emily K W Lo, Brian M Mears, H Carlo Maurer, Adrian Idrizi, Kasper D Hansen

Cancer Res· April 2025

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Newborn blood DNA methylation and childhood asthma: findings from the ECHO program.
Yijun Li, Krystin Jones, Carole Ober, Anne P Starling, William A Gower, Kasper D Hansen

Int J Epidemiol· April 2025

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Multi-sample non-negative spatial factorization.
Yi Wang, Kyla Woyshner, Chaichontat Sriworarat, Genevieve Stein-O'Brien, Loyal A Goff, Kasper D Hansen

bioRxiv· November 2024

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Large-scale genotype prediction from RNA sequence data necessitates a new ethical and policy framework.
Mary A Majumder, Jeffrey T Leek, Kasper D Hansen, Afrooz Razi, Amy L McGuire

Nat Genet· August 2024

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Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data.
Albert Kuo, Kasper D Hansen, Stephanie C Hicks

Biostatistics· July 2024

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Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice.
Leandros Boukas, Teresa Romeo Luperchio, Afrooz Razi, Kasper D Hansen, Hans T Bjornsson

Genome Res· June 2024

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Growth deficiency in a mouse model of Kabuki syndrome 2 bears mechanistic similarities to Kabuki syndrome 1.
Christine W Gao, WanYing Lin, Ryan C Riddle, Sheetal Chopra, Jiyoung Kim, Kasper D Hansen

PLoS Genet· June 2024

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Genotype prediction of 336,463 samples from public expression data.
Afrooz Razi, Christopher C Lo, Siruo Wang, Jeffrey T Leek, Kasper D Hansen

bioRxiv· March 2024

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Removing unwanted variation between samples in Hi-C experiments.
Kipper Fletez-Brant, Yunjiang Qiu, David U Gorkin, Ming Hu, Kasper D Hansen

Brief Bioinform· March 2024

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A mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition.
Christine W Gao, WanYing Lin, Ryan C Riddle, Priyanka Kushwaha, Leandros Boukas, Kasper D Hansen

JCI Insight· January 2024

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Precision pharmacological reversal of strain-specific diet-induced metabolic syndrome in mice informed by epigenetic and transcriptional regulation.
Phillip Wulfridge, Adam Davidovich, Anna C Salvador, Gabrielle C Manno, Rakel Tryggvadottir, Kasper D Hansen

PLoS Genet· October 2023

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Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates.
Shijie C Zheng, Genevieve Stein-O'Brien, Leandros Boukas, Loyal A Goff, Kasper D Hansen

Genome Biol· October 2023

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Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice.
Leandros Boukas, Teresa Romeo Luperchio, Afrooz Razi, Kasper D Hansen, Hans T Bjornsson

bioRxiv· August 2023

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Comprehensive DNA Methylation Analysis Indicates That Pancreatic Intraepithelial Neoplasia Lesions Are Acinar-Derived and Epigenetically Primed for Carcinogenesis.
Emily K W Lo, Brian M Mears, H Carlo Maurer, Adrian Idrizi, Kasper D Hansen

Cancer Res· June 2023

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Novel mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition.
Christine W Gao, WanYing Lin, Ryan C Riddle, Priyanka Kushwaha, Leandros Boukas, Kasper D Hansen

bioRxiv· June 2023

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Precision pharmacological reversal of genotype-specific diet-induced metabolic syndrome in mice informed by transcriptional regulation.
Phillip Wulfridge, Adam Davidovich, Anna C Salvador, Gabrielle C Manno, Rakel Tryggvadottir, Kasper D Hansen

bioRxiv· April 2023

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recountmethylation enables flexible analysis of public blood DNA methylation array data.
Sean K Maden, Brian Walsh, Kyle Ellrott, Kasper D Hansen, Reid F Thompson

Bioinform Adv· February 2023

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Addressing the mean-correlation relationship in co-expression analysis.
Yi Wang, Stephanie C Hicks, Kasper D Hansen

PLoS Comput Biol· March 2022

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A mammalian methylation array for profiling methylation levels at conserved sequences.
Adriana Arneson, Amin Haghani, Michael J Thompson, Matteo Pellegrini, Soo Bin Kwon, Kasper D Hansen

Nat Commun· February 2022

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Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space.
Michael C Schatz, Anthony A Philippakis, Enis Afgan, Eric Banks, Vincent J Carey, Kasper D Hansen

Cell Genom· January 2022

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