SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis

Kavli Affiliate: Jean Fan | Authors: Gohta Aihara, Kalen Clifton, Mayling Chen, Lyla Atta, Brendan F. Miller and Jean Fan | Summary: Motivation Spatial omics data demand computational analysis but many analysis tools have computational resource requirements that increase with the number of cells analyzed. This presents scalability challenges as researchers use spatial omics technologies […]


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A TBX5-dependent compartment boundary patterns the cardiac interventricular septum

Kavli Affiliate: Denis Wirtz | Authors: Irfan S Kathiriya, Martin H Dominguez, Kavitha S Rao, Jonathan M. Muncie-Vasic, W. Patrick Devine, Kevin M. Hu, Swetansu K Hota, Bayardo I Garay, Diego Quintero, Piyush Goyal, Megan N Matthews, Reuben Thomas, Tatyana Sukonnik, Dario Miguel-Perez, Sarah Winchester, Emily F Brower, AndrĂ© Forjaz, Pei-Hsun Wu, Denis Wirtz, Ashley […]


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Neural substrates underlying the expectation of rewards resulting from effortful exertion

Kavli Affiliate: Vikram Chib | Authors: Aram Kim and Vikram S. Chib | Summary: Expectations as a reference point shape our decisions to motivate effortful activity. Despite the important role of reference points in human performance, little is known about how the brain processes expectations to guide motivated exertion. Participants completed a reward-based effort task […]


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Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies

Kavli Affiliate: Brian Caffo Keri Martinowich | Authors: Jianing Yao, Jinglun Yu, Brian Caffo, Stephanie Cerceo Page, Keri Martinowich and Stephanie C Hicks | Summary: Recent advances in spatially-resolved single-omics and multi-omics technologies have led to the emergence of computational tools to detect or predict spatial domains. Additionally, histological images and immunofluorescence (IF) staining of […]


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When no answer is better than a wrong answer: a causal perspective on batch effects

Kavli Affiliate: Brian Caffo Joshua Vogelstein | Authors: Eric W. Bridgeford, Michael Powell, Gregory Kiar, Stephanie Noble, Jaewon Chung, Sambit Panda, Ross Lawrence, Ting Xu, Michael Milham, Brian Caffo and Joshua T. Vogelstein | Summary: Abstract Batch effects, undesirable sources of variability across multiple experiments, present significant challenges for scientific and clinical discoveries. Batch effects […]


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Multiplexing of temporal and spatial information in the lateral entorhinal cortex

Kavli Affiliate: James Knierim | Authors: Cheng Wang, Heekyung Lee, Geeta Rao and James J Knierim | Summary: Abstract Episodic memory involves the processing of spatial and temporal aspects of personal experiences. The lateral entorhinal cortex (LEC) plays an essential role in subserving memory. However, the specific mechanism by which LEC integrates spatial and temporal […]


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Structurally-informed human interactome reveals proteome-wide perturbations by disease mutations

Kavli Affiliate: Jin Kang | Authors: Dapeng Xiong, Yunguang Qiu, Junfei Zhao, Yadi Zhou, Dongjin Lee, Shobhita Gupta, Mateo Torres, Weiqiang Lu, Siqi Liang, Jin Joo Kang, Charis Eng, Joseph Loscalzo, Feixiong Cheng and Haiyuan Yu | Summary: Abstract Human genome sequencing studies have identified numerous loci associated with complex diseases. However, translating human genetic […]


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Multi-day Neuron Tracking in High Density Electrophysiology Recordings using EMD

Kavli Affiliate: Adam S. Charles | Authors: Augustine Xiaoran Yuan, Jennifer I Colonell, Anna Lebedeva, Michael Okun, Adam Charles and Timothy D Harris | Summary: Accurate tracking of the same neurons across multiple days is crucial for studying changes in neuronal activity during learning and adaptation. New advances in high density extracellular electrophysiology recording probes, […]


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Moving Beyond Processing and Analysis-Related Variation in Neuroscience

Kavli Affiliate: Joshua Vogelstein | Authors: Xinhui Li, Nathalia Bianchini Esper, Lei Ai, Steve Giavasis, Hecheng Jin, Eric Feczko, Ting Xu, Jon Clucas, Alexandre Franco, Anibal Solon Heinsfeld, Azeez Adebimpe, Joshua T. Vogelstein, Chao-Gan Yan, Oscar Esteban, Russell A. Poldrack, Cameron Craddock, Damien Fair, Theodore Satterthwaite, Gregory Kiar and Michael P. Milham | Summary: Abstract […]


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The lateral habenula integrates age and experience to promote social transitions in developing rats

Kavli Affiliate: Maya Opendak | Authors: Dana E Cobb-Lewis, Anne George, Shannon Hu, Katherine Packard, Mingyuan Song, Oliver Nguyen-Lopez, Emily Ikematsu Tesone, Jhanay Rowden, Julie Wang and Maya Opendak | Summary: Social behavior deficits are an early-emerging marker of psychopathology and are linked with early caregiving quality. However, the infant neural substrates linking early care […]


Continue.. The lateral habenula integrates age and experience to promote social transitions in developing rats