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Publications

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Optimized workflow for human PBMC multiomic immunosurveillance studies

11.11.2021

Deep immune profiling is essential for understanding the human immune system in health and disease.

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A Bayesian framework for the detection of diffusive heterogeneity

05.07.2020

Cells are crowded and spatially heterogeneous, complicating the transport of organelles, proteins and other substrates. One aspect of this complex...

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A comprehensive platform for analyzing longitudinal multi-omics data

03.27.2023

Longitudinal bulk and single-cell omics data is increasingly generated for biological and clinical research but is challenging to analyze due to its...

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BarWare: efficient software tools for barcoded single-cell genomics

03.27.2022

Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies.

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CellProfiler 3.0: Next-generation image processing for biology

07.03.2018

CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we...

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A deep generative model of 3D single-cell organization

01.18.2022

We introduce a framework for end-to-end integrative modeling of 3D single-cell multi-channel fluorescent image data of diverse subcellular structures....

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Similar Odor Discrimination Behavior in Head-Restrained and Freely Moving Mice

12.18.2012

A major challenge in neuroscience is relating neuronal activity to animal behavior. In olfaction limited techniques are available for these...

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Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

04.09.2021

Single-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation,...

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Multimodal analysis for human ex vivo studies shows extensive molecular changes from delays in blood processing

04.15.2021

Multi-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms of disease. The...

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Predictive and robust gene selection for spatial transcriptomics

04.12.2023

A prominent trend in single-cell transcriptomics is providing spatial context alongside a characterization of each cell's molecular state. This...

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Measuring Consciousness in the Intensive Care Unit

04.08.2023

Early reemergence of consciousness predicts long-term functional recovery for patients with severe brain injury. However, tools to reliably detect...

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Neocortical and medial temporal seizures have distinct impacts on brain responsiveness

03.30.2023

Focal epileptic seizures are characterized by abnormal neuronal discharges that can spread to other cortical areas and interfere with brain activity,...

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Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator

03.28.2023

The ability to optically image cellular transmembrane voltages at millisecond-timescale resolutions can offer unprecedented insight into the function...

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Neural population dynamics of computing with synaptic modulations

02.23.2023

In addition to long-timescale rewiring, synapses in the brain are subject to significant modulation that occurs at faster timescales. These...

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On the Role of Theory and Modeling in Neuroscience

02.15.2023

In recent years, the field of neuroscience has gone through rapid experimental advances and a significant increase in the use of quantitative and...

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Heterogeneity in Neuronal Dynamics Is Learned by Gradient Descent for Temporal Processing Tasks

02.13.2023

Individual neurons in the brain have complex intrinsic dynamics that are highly diverse. We hypothesize that the complex dynamics produced by networks...

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Regional and cell-type-specific afferent and efferent projections of the mouse claustrum

02.11.2023

The claustrum (CLA) is a conspicuous subcortical structure interconnected with cortical and subcortical regions. Its regional anatomy and...

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Targeted anatomical and functional identification of antinociceptive and pronociceptive serotonergic neurons that project to the spinal dorsal horn

02.08.2023

Spinally-projecting serotonergic neurons play a key role in controlling pain sensitivity and can either increase or decrease nociception depending on...

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Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in a mouse model of Alzheimer’s disease

02.02.2023

Complex diseases are characterized by spatiotemporal cellular and molecular changes that may be difficult to comprehensively capture. However,...

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Acute head-fixed recordings in awake mice with multiple Neuropixels probes

02.01.2023

Multi-electrode arrays such as Neuropixels probes enable electrophysiological recordings from large populations of single neurons with high temporal...

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