Biology subjects

Tarhan, L.

Publications and source records attributed to Tarhan, L..

4 recordsLinked to original sources

bioRxiv2023

Single Cell Portal: an interactive home for single-cell genomics data

Single-cell omics research has the power to leave a deep impact on modern healthcare. Sharing data widely and freely advances this progress in both the academic and clinical spheres. We developed the Single Cell Portal (SCP) to maximize the impact of this work. SCP enables data sharing, supports dynamic results visualization, and facilitates scientific exploration across a large repository of single-cell datasets. SCPs data contributors maintain full control over how their data are shared and presented, without requiring web development expertise. Finally, SCP supports the entire lifecycle of a research project, from sparking an idea, to fine-tuning the data with collaborators, to sharing results in an accessible and interactive way. This paper highlights the most valuable ways in which SCP helps to advance single-cell research.

scientific communication and education↗

bioRxiv2021

Behavioral and Neural Representations en route to Intuitive Action Understanding

When we observe another persons actions, we process many kinds of information - from how their body moves to the intention behind their movements. What kinds of information underlie our intuitive understanding about how similar actions are to each other? To address this question, we measured the intuitive similarities among a large set of everyday action videos using multi-arrangement experiments, then used a modeling approach to predict this intuitive similarity space along three hypothesized properties. We found that similarity in the actors inferred goals predicted the intuitive similarity judgments the best, followed by similarity in the actors movements, with little contribution from the videos visual appearance. In opportunistic fMRI analyses assessing brain-behavior correlations, we found suggestive evidence for an action processing hierarchy, in which these three kinds of action similarities are reflected in the structure of brain responses along a posterior-to-anterior gradient on the lateral surface of the visual cortex. Altogether, this work joins existing literature suggesting that humans are naturally tuned to process others intentions, and that the visuo-motor cortex computes the perceptual precursors of the higher-level representations over which intuitive action perception operates.

neuroscience↗

bioRxiv2019

Reliability-Based Voxel Selection

While functional magnetic resonance imaging (fMRI) studies typically measure responses across the whole brain, not all regions are likely to be informative for a given study. Which voxels should be considered? Here we propose a method for voxel selection based on the reliability of the data. This method isolates voxels that respond consistently across imaging runs while maximizing the reliability of multi-voxel patterns across the selected voxels. We estimate that it is suitable for designs with at least 15 conditions. In two example datasets, we found that this proposed method defines a smaller set of voxels than another common method, activity-based voxel selection. Broadly, this method eliminates the need to define regions or statistical thresholds a priori and puts the focus on data reliability as the first step in analyzing fMRI data.

neuroscience↗

bioRxiv2019

Sociality and Interaction Envelope Organize Visual Action Representations

Humans observe a wide range of actions in their surroundings. How is the visual cortex organized to process this diverse input? Using functional neuroimaging, we measured brain responses while participants viewed short videos of everyday actions, then probed the structure in these responses using voxel-wise encoding modeling. Responses were well fit by feature spaces that capture the body parts involved in an action and the actions targets (i.e. whether the action was directed at an object, another person, the actor, and space). Clustering analyses revealed five large-scale networks that summarized the voxel tuning: one related to social aspects of an action, and four related to the scale of the interaction envelope, ranging from fine-scale manipulations directed at objects, to large-scale whole-body movements directed at distant locations. We propose that these networks reveal the major representational joints in how actions are processed by visual regions of the brain. Significance StatementHow does the brain perceive other peoples actions? Prior work has established that much of the visual cortex is active when observing others actions. However, this activity reflects a wide range of processes, from identifying a movements direction to recognizing its social content. We investigated how these diverse processes are organized within the visual cortex. We found that five networks respond during action observation: one that is involved in processing actions social content, and four that are involved in processing agent-object interactions and the scale of the effect that these actions have on the world (its "interaction envelope"). Based on these findings, we propose that sociality and interaction envelope size are two of the major features that organize action perception in the visual cortex.

neuroscience↗