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Xiuwei Zhang
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Accounting for technical noise in single-cell RNA-seq experiments
P Brennecke, S Anders, JK Kim, AA Kołodziejczyk, X Zhang, V Proserpio, ...
Nature methods 10 (11), 1093-1095, 2013
10412013
Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis
B Mahata, X Zhang, AA Kolodziejczyk, V Proserpio, L Haim-Vilmovsky, ...
Cell reports 7 (4), 1130-1142, 2014
2232014
Simulating multiple faceted variability in single cell RNA sequencing
X Zhang, C Xu, N Yosef
Nature communications 10 (1), 2611, 2019
1222019
Evolution of oligomeric state through allosteric pathways that mimic ligand binding
T Perica, Y Kondo, SP Tiwari, SH McLaughlin, KR Kemplen, X Zhang, ...
Science 346, 2014
762014
Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation
V Proserpio, A Piccolo, L Haim-Vilmovsky, G Kar, T Lönnberg, ...
Genome Biology 17 (1), 103, 2016
682016
CD4+ and CD8+ cytotoxic T lymphocytes may induce mesenchymal cell apoptosis in IgG4-related disease
CA Perugino, N Kaneko, T Maehara, H Mattoo, J Kers, H Allard-Chamard, ...
Journal of Allergy and Clinical Immunology 147 (1), 368-382, 2021
642021
Single-cell RNA-sequencing resolves self-antigen expression during mTEC development
RJ Miragaia, X Zhang, T Gomes, V Svensson, T Ilicic, J Henriksson, G Kar, ...
Scientific Reports 8, 685, 2018
492018
Evolution of protein structures and interactions from the perspective of residue contact networks
X Zhang, T Perica, SA Teichmann
Current opinion in structural biology 23 (6), 954-963, 2013
482013
scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously
Z Zhang, C Yang, X Zhang
Genome biology 23 (1), 139, 2022
45*2022
Inference of high-resolution trajectories in single-cell RNA-seq data by using RNA velocity
Z Zhang, X Zhang
Cell Reports Methods 1 (6), 2021
33*2021
Refining transcriptional regulatory networks using network evolutionary models and gene histories
X Zhang, BME Moret
Algorithms for Molecular Biology 5 (1), 1, 2010
252010
GRNUlar: a deep learning framework for recovering single-cell gene regulatory networks
H Shrivastava, X Zhang, L Song, S Aluru
Journal of Computational Biology 29 (1), 27-44, 2022
212022
Boosting the performance of inference algorithms for transcriptional regulatory networks using a phylogenetic approach
X Zhang, B Moret
Algorithms in Bioinformatics, 245-258, 2008
152008
VeloSim: Simulating single cell gene-expression and RNA velocity
Z Zhang, X Zhang
bioRxiv, 2021.01. 11.426277, 2021
132021
scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection
Z Zhang, H Sun, R Mariappan, X Chen, X Chen, MS Jain, M Efremova, ...
Nature Communications 14 (1), 384, 2023
122023
Grnular: gene regulatory network reconstruction using unrolled algorithm from single cell rna-sequencing data
H Shrivastava, X Zhang, S Aluru, L Song
bioRxiv, 2020.04. 23.058149, 2020
122020
Refining regulatory networks through phylogenetic transfer of information
X Zhang, BME Moret
IEEE/ACM transactions on computational biology and bioinformatics 9 (4 …, 2012
112012
Bioinformatics research and applications
X Zhang, BME Moret
102011
CLARIFY: cell–cell interaction and gene regulatory network refinement from spatially resolved transcriptomics
M Bafna, H Li, X Zhang
Bioinformatics 39 (Supplement_1), i484-i493, 2023
92023
scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks
H Li, Z Zhang, M Squires, X Chen, X Zhang
Research Square, 2022
82022
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