Xiuwei Zhang

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Sarah A. TeichmannUniversity of CambridgeVerified email at cam.ac.uk
Ziqi ZhangPhD student, Georgia Institute of TechnologyVerified email at gatech.edu
Valentina ProserpioUniversity of TurinVerified email at unito.it
Aleksandra A KolodziejczykInternational Institute of Molecular and Cell BiologyVerified email at iimcb.gov.pl
Bernard M.E. MoretISCB Fellow, Professor emeritus, Computer & Communication Sciences, EPFLVerified email at epfl.ch
Liora Haim VilmovskyEMBL EBIVerified email at ebi.ac.uk
Nir YosefAssociate Professor, Department of Systems Immunology, Weizmann Institute of ScienceVerified email at berkeley.edu
Tapio LönnbergUniversity of TurkuVerified email at utu.fi
Vaibhav RajanResearch Scientist, Google DeepMindVerified email at google.com
Tina PericaUniversity of ZurichVerified email at bioc.uzh.ch
Bidesh MahataResearch Group Leader, Division of Immunology, Department of Pathology, University of CambridgeVerified email at cam.ac.uk
Xinhai PanGeorgia institute of TechnologyVerified email at gatech.edu
Chenling Xu AntelopeLawrence Livermore National LabVerified email at llnl.gov
Mario NicodemiProfessor of Theoretical Physics, Università di Napoli "Federico II"Verified email at na.infn.it
Mihir BafnaMassachusetts Institute of TechnologyVerified email at mit.edu
Haesun ParkRegents' Professor of Computational Science and Engineering, Georgia Institute of TechnologyVerified email at cc.gatech.edu
Tamir Tuller (תמיר טולר)Tel Aviv UniversityVerified email at post.tau.ac.il
Zhidong DengProfessor of Computer Science, Tsinghua UniversityVerified email at tsinghua.edu.cn
Xi ChenDepartment of Biology, Southern University of Science and TechnologyVerified email at sustech.edu.cn
Shiv S PillaiProfessor of Medicine, Harvard Medical SchoolVerified email at helix.mgh.harvard.edu

Xiuwei Zhang

Georgia Institute of Technology

Verified email at gatech.edu - Homepage

Computational biology Algorithms


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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	1088	2013
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	233	2014
Simulating multiple faceted variability in single cell RNA sequencing X Zhang, C Xu, N Yosef Nature communications 10 (1), 2611, 2019	135	2019
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	83	2021
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	77	2014
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	69	2016
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	64*	2022
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	50	2018
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	49	2013
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	39*	2021
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	27	2023
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	27	2022
Refining transcriptional regulatory networks using network evolutionary models and gene histories X Zhang, BME Moret Algorithms for Molecular Biology 5 (1), 1, 2010	24	2010
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	16	2023
VeloSim: Simulating single cell gene-expression and RNA velocity Z Zhang, X Zhang bioRxiv, 2021.01. 11.426277, 2021	15	2021
Boosting the performance of inference algorithms for transcriptional regulatory networks using a phylogenetic approach X Zhang, B Moret Algorithms in Bioinformatics, 245-258, 2008	15	2008
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, rs. 3. rs-2675530, 2023	14	2023
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	14	2020
TedSim: temporal dynamics simulation of single-cell RNA sequencing data and cell division history X Pan, H Li, X Zhang Nucleic acids research 50 (8), 4272-4288, 2022	11	2022
Refining regulatory networks through phylogenetic transfer of information X Zhang, BME Moret IEEE/ACM transactions on computational biology and bioinformatics 9 (4 …, 2012	11	2012

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