Xiuwei Zhang

发表

Accounting for technical noise in single-cell RNA-seq experiments

Aleksandra A. Kolodziejczyk, S. Teichmann, V. Beneš, 2013, Nature Methods.

SymSim: simulating multi-faceted variability in single cell RNA sequencing

Nir Yosef, Chenling Xu, Xiuwei Zhang, 2018, bioRxiv.

Simulating multiple faceted variability in single cell RNA sequencing

Nir Yosef, Chenling Xu, Xiuwei Zhang, 2019, Nature Communications.

Evolution of protein structures and interactions from the perspective of residue contact networks.

Sarah A Teichmann, Xiuwei Zhang, S. Teichmann, 2013, Current opinion in structural biology.

Phylogenetic Transfer of Knowledge for Biological Networks

Bernard M. E. Moret, Xiuwei Zhang, Min Ye, 2014 .

Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

Sarah A. Teichmann, Berthold Göttgens, Aleksandra A. Kolodziejczyk, 2014, Cell reports.

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation

Sarah A. Teichmann, Jurij Kotar, Valentine Svensson, 2016, Genome Biology.

Single-cell RNA-sequencing resolves self-antigen expression during mTEC development

Ricardo J. Miragaia, Tomislav Ilicic, Valentine Svensson, 2018, Scientific Reports.

A new way to build cell lineages

N. Yosef, Xiuwei Zhang, 2017, eLife.

Modularity in PPI Networks : Characteristics of Existing Networks and Models of Evolution

Bernard M. E. Moret, Xiuwei Zhang, Min Ye, 2022 .

VeloSim: Simulating single cell gene-expression and RNA velocity

Xiuwei Zhang, Ziqi Zhang, 2021, bioRxiv.

CD4+ and CD8+ cytotoxic T lymphocytes may induce mesenchymal cell apoptosis in IgG4-related disease.

N. Yosef, J. Stone, Xiuwei Zhang, 2020, The Journal of allergy and clinical immunology.

scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks

Xi Chen, M. Squires, Xiuwei Zhang, 2022, bioRxiv.

Simulating multiple faceted variability in single cell RNA sequencing

N. Yosef, Chenling A. Xu, Xiuwei Zhang, 2019, Nature Communications.

scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously

Xiuwei Zhang, Ziqi Zhang, Chengkai Yang, 2021, Genome Biology.

GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks

S. Aluru, Xiuwei Zhang, Le Song, 2022, J. Comput. Biol..

TedSim: temporal dynamics simulation of single-cell RNA sequencing data and cell division history

Xiuwei Zhang, Hechen Li, Xinhai Pan, 2022, Nucleic acids research.

scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection

S. Teichmann, Vaibhav Rajan, M. Efremova, 2023, Nature Communications.

Learning latent embedding of multi-modal single cell data and cross-modality relationship simultaneously

Xiuwei Zhang, Ziqi Zhang, Chengkai Yang, 2021 .

NEMo: An Evolutionary Model With Modularity for PPI Networks

Xiuwei Zhang, Bernard M. E. Moret, Min Ye, 2016, IEEE Transactions on NanoBioscience.

Transcriptional Regulatory Networks across Species - Evolution, Inference, and Refinement

Xiuwei Zhang, Xiuwei Zhang, 2011 .

Transcriptional Regulatory Networks across Species

Xiuwei Zhang, 2011 .

Refining transcriptional regulatory networks using network evolutionary models and gene histories

Xiuwei Zhang, Bernard M. E. Moret, Xiuwei Zhang, 2010, Algorithms for Molecular Biology.

Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models

Xiuwei Zhang, Bernard M. E. Moret, Xiuwei Zhang, 2009, WABI.

Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach

Xiuwei Zhang, Bernard M. E. Moret, Xiuwei Zhang, 2008, WABI.

Using Phylogenetic Relationships to Improve the Inference of Transcriptional Regulatory Networks

Xiuwei Zhang, Bernard M. E. Moret, Maryam Zaheri, 2008, 2008 International Conference on BioMedical Engineering and Informatics.

Evolution of oligomeric state through allosteric pathways that mimic ligand binding

Sarah A. Teichmann, Jane Clarke, Nathalie Reuter, 2014, Science.

Phylogenetic Inference

Bernard M. E. Moret, Bernard M. E. Moret, Xiuwei Zhang, 2011, Encyclopedia of Parallel Computing.

Maximum Likelihood Reconstruction of Ancestral Networks by Integer Linear Programming

Xiuwei Zhang, Carl Kingsford, Vaibhav Rajan, 2019, bioRxiv.

Single-cell RNA-sequencing resolves self-antigen expression during mTEC development

Tomislav Ilicic, Valentine Svensson, R. Miragaia, 2018, Scientific Reports.

scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks

Xi Chen, M. Squires, Xiuwei Zhang, 2023, bioRxiv.

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation

Sarah A. Teichmann, Jurij Kotar, Valentine Svensson, 2016, Genome Biology.

Analysis of Coevolving Gene Families Using Mutually Exclusive Orthologous Modules

U. Gophna, M. Kupiec, T. Tuller, 2011, Genome biology and evolution.

Inference of high-resolution trajectories in single-cell RNA-seq data by using RNA velocity

Xiuwei Zhang, Ziqi Zhang, 2021, Cell reports methods.

Inference of multiple trajectories in single cell RNA-seq data from RNA velocity

Xiuwei Zhang, Ziqi Zhang, Xiuwei Zhang, 2020, bioRxiv.

Refining Regulatory Networks through Phylogenetic Transfer of Information

Xiuwei Zhang, Bernard M. E. Moret, Xiuwei Zhang, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

GRNUlar: Gene Regulatory Network reconstruction using Unrolled algorithm from Single Cell RNA-Sequencing data

Srinivas Aluru, Xiuwei Zhang, Le Song, 2020, bioRxiv.

scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data

Xiuwei Zhang, Ziqi Zhang, Peng Qiu, 2023, bioRxiv.

scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks

Xi Chen, M. Squires, Xiuwei Zhang, 2023, bioRxiv.

Erratum to: Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation

S. Teichmann, M. Kayikci, P. Cicuta, 2016, Genome Biology.

scMoMaT: Mosaic integration of single cell multi-omics data using matrix tri-factorization

S. Teichmann, Vaibhav Rajan, M. Efremova, 2022, bioRxiv.

ProPhyC: A Probabilistic Phylogenetic Model for Refining Regulatory Networks

Xiuwei Zhang, Bernard M. E. Moret, Xiuwei Zhang, 2011, ISBRA.

LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data

Xiuwei Zhang, Hechen Li, X. Pan, 2023, Research square.

LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data

Xiuwei Zhang, Hechen Li, X. Pan, 2023, bioRxiv.

LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data

Xiuwei Zhang, Hechen Li, X. Pan, 2023, Research square.

TedSim: temporal dynamics simulation of single cell RNA-sequencing data and cell division history

Xiuwei Zhang, Hechen Li, X. Pan, 2021, bioRxiv.

Hybrid Clustering of Single-Cell Gene Expression and Spatial Information via Integrated NMF and K-Means

Xiuwei Zhang, Haesun Park, Sooyoun Oh, 2021, Frontiers in Genetics.

Hybrid Clustering of single-cell gene-expression and cell spatial information via integrated NMF and k-means

Xiuwei Zhang, Haesun Park, Sooyoun Oh, 2020, bioRxiv.

CLARIFY: cell–cell interaction and gene regulatory network refinement from spatially resolved transcriptomics

Xiuwei Zhang, Hechen Li, Mihir Bafna, 2023, Bioinform..

Studying temporal dynamics of single cells: expression, lineage and regulatory networks.

Xiuwei Zhang, X. Pan, 2023, Biophysical reviews.

Inferring cell-specific gene regulatory networks from single cell gene expression data

Xiuwei Zhang, Ziqi Zhang, Leo T. Song, 2022, bioRxiv.

scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously

Xiuwei Zhang, Ziqi Zhang, Chengkai Yang, 2022, Genome Biology.