Zijian Ni

发表

SKiM - A generalized literature-based discovery system for uncovering novel biomedical knowledge from PubMed

John W. Steill, R. Stewart, M. Livny, 2020, bioRxiv.

An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells

R. Stewart, Rhonda Bacher, Li-Fang Chu, 2019, Cell reports.

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

C. Kendziorski, Zijian Ni, Shuyang Chen, 2020, Genome Biology.

SpotClean adjusts for spot swapping in spatial transcriptomics data

C. Kendziorski, Zijian Ni, R. Halberg, 2021, Nature Communications.

Normalization by distributional resampling of high throughput single-cell RNA-sequencing data

Christina Kendziorski, Rhonda Bacher, Zijian Ni, 2020, bioRxiv.

SpatialCorr: Identifying Gene Sets with Spatially Varying Correlation Structure

R. Stewart, C. Kendziorski, Zijian Ni, 2022, bioRxiv.

CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets

Ron M. Stewart, Christina Kendziorski, Matthew N. Bernstein, 2021, BMC Bioinform..

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

C. Kendziorski, Zijian Ni, Shuyang Chen, 2020, Genome Biology.

CB2 distinguishes cells from background barcodes in 10x Genomics data

Shuyang Chen, Christina Kendziorski, Zijian Ni, 2019, bioRxiv.

The Anna Karenina Model of β-Cell Maturation in Development and Their Dedifferentiation in Type 1 and Type 2 Diabetes

C. Kendziorski, Zijian Ni, B. Blum, 2021, Diabetes.

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments

R. Stewart, Li-Fang Chu, Ning Leng, 2018, BMC Bioinformatics.

Genomic Analysis of Human Brain Metastases Treated with Stereotactic Radiosurgery Under the Phase-II Clinical Trial (NCT03398694) Reveals DNA Damage Repair at the Peripheral Tumor Edge

Atique U. Ahmed, C. Kendziorski, Zijian Ni, 2023, medRxiv.

Rare penetrant mutations confer severe risk of common diseases

Dylan M. Cable, T. Marquès-Bonet, H. Rehm, 2023, medRxiv.

CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets

Christina Kendziorski, Ron Stewart, Matthew N. Bernstein, 2020, BMC Bioinformatics.

Rare penetrant mutations confer severe risk of common diseases

Dylan M. Cable, H. Rehm, Tobias Hamp, 2023, Science.

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments

Ning Leng, James A. Thomson, Christina Kendziorski, 2018, BMC Bioinformatics.

Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response

S. Varambally, C. Kendziorski, Zijian Ni, 2023, bioRxiv.

Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models

John W. Steill, R. Stewart, M. Livny, 2023, BMC Bioinformatics.