K

Kai Zhang

University of Science and Technology of China

ORCID: 0000-0003-3454-7357

Publishes on Genomics and Chromatin Dynamics, Single-cell and spatial transcriptomics, RNA Research and Splicing. 76 papers and 7.8k citations.

76Publications
7.8kTotal Citations

Is this you? Claim your profile.

Add your photo, update your bio, and get notified when your ranking changes.

Top publicationsby citations

Representation of spatial orientation by the intrinsic dynamics of the head-direction cell ensemble: a theory
Kai Zhang|Journal of Neuroscience|1996
Cited by 1kOpen Access

The head-direction (HD) cells found in the limbic system in freely mov ing rats represent the instantaneous head direction of the animal in the horizontal plane regardless of the location of the animal. The internal direction represented by these cells uses both self-motion information for inertially based updating and familiar visual landmarks for calibration. Here, a model of the dynamics of the HD cell ensemble is presented. The stability of a localized static activity profile in the network and a dynamic shift mechanism are explained naturally by synaptic weight distribution components with even and odd symmetry, respectively. Under symmetric weights or symmetric reciprocal connections, a stable activity profile close to the known directional tuning curves will emerge. By adding a slight asymmetry to the weights, the activity profile will shift continuously without disturbances to its shape, and the shift speed can be controlled accurately by the strength of the odd-weight component. The generic formulation of the shift mechanism is determined uniquely within the current theoretical framework. The attractor dynamics of the system ensures modality-independence of the internal representation and facilitates the correction for cumulative error by the putative local-view detectors. The model offers a specific one-dimensional example of a computational mechanism in which a truly world-centered representation can be derived from observer-centered sensory inputs by integrating self-motion information.

Comprehensive analysis of single cell ATAC-seq data with SnapATAC
Rongxin Fang, Sebastian Preißl, Yang Li et al.|Nature Communications|2021
Cited by 483Open Access

Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.