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Lab members in bold.
† equal contribution.
* corresponding author.
In Press and In Review
Ultra-scalable differential testing for spatial omics
Mason K†, Jiang Y†, Klötzer KA, Zhang NR*
Nature Biotechnology (in press)
Dissecting the coordinated progression of cell states in spatial transcriptomics with CoPro
Miao Z, Qu Y, Huang S, Laux L, Peters S, Aristel A, Zhang Z, Zhang NR*
bioRxiv
Deciphering cell fate and clonal dynamics via integrative single-cell lineage modeling
Fu Y, Mathew D, Wang M, Chen XE, Lin KZ, Schaff D, Shaffer SM, Pardoll DM, Jackson C, Zhang NR*
bioRxiv
A measure of transcriptional dyscoordination for quantifying aging in single cells
Yang Y, Hess PR, Huang S, Teneche MG, Wang H, Miller KN, Davis AE, Miciano C, Li KY, Mamde S, Yip K, Ren B, Yang Q, Smoot E, Wang A, Johnson B, Wilson P, Adams PD, Zhang NR*
bioRxiv
Mitochondrial clone tracing within spatially intact human tissues
Bracht SA, Rong J, Gier RA, DeMarshall M, Golden H, Dhakal D, Zhang NR*, Shaffer SM*
bioRxiv
Dual checkpoint blockade of glioblastoma with anti-PD-1 and anti-LAG-3 promotes expansion of tumor-reactive T cell clones along a unique pathway of differentiation
Wang M, Fu Y, Bom S, Ning Y, Matthews D, Zhang M, Lucas CH, Choi J, Zhang NR, Jackson CM*
bioRxiv
Targeting interferon-driven inflammatory memory prevents epigenetic evolution of cancer immunotherapy resistance
Qiu J, Ye D, Chen XE, Dangle N, Yoshor B, Zhang T, Shao Y, Zhang NR, Minn AJ*
bioRxiv
Intestinal immune dysregulation fuels islet autoimmunity in type 1 diabetes
Bartolo L, Afroze S, Lin Y, Ansari A, Pan Y-G, Liu C, Zhang NR, Naji A, Su LF*
In review
Temporal and clonal resolution of cellular evolution under stress
Chen XE†, Lin KZ†, Schaff D†, Vander Velde R, Cote C, Huang S, Minn AJ, Shaffer SM*, Zhang NR*
In review
2026
Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus
Enninful A†, Zhang Z†, Klymyshyn D, Ingalls M, Yang M, Zong H, …, Zhang NR, …, Xu ML*, Ma Z*, Fan R*
Nature Methods 23, 1827–1839 (2026)
Pre-existing cell states predict resistance to multiple treatments
Schaff DL, White PE, Cote CJ, Watterson GE, Lin KZ, Fasse AJ, Zhang NR, Shaffer SM*
Cell Genomics 6, 101191 (2026)
Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq
Lin Y, Wang H, Wilson PC*, Zhang NR*
Nature Communications 17 (2026)
2025
Cancer subclone detection based on DNA copy number in single-cell and spatial omic sequencing data
Wu C-Y, Rong J, Sathe A, Hess PR, Lau BT, Grimes SM, Huang S, Ji HP*, Zhang NR*
Nature Methods 22, 1846–1856 (2025)
Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas
Klötzer KA, Abedini A, Li S, Balzer MS, Liang X, Levinsohn J, …, Halmos B, Zhang NR*, Susztak K*
Nature Genetics 57, 1922–1934 (2025)
Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring
Yu W, Biyik-Sit R, Uzun Y, Chen C-H, Thadi A, Sussman JH, …, Zhang NR, Maris JM, Tan K*
Nature Genetics 57, 1142–1154 (2025)
Improving gene isoform quantification with miniQuant
Li H, Wang D, Gao Q, Tan P, Wang Y, Cai X, Li A, Zhao Y, Thurman AL, Malekpour SA, Zhang Y, Sala R, Cipriano A, Wei C-L, Sebastiano V, Song C, Zhang NR, Au KF*
Nature Biotechnology 44, 477–489 (2025)
Single cell and spatial alternative splicing analysis with Nanopore long read sequencing
Fu Y*, Kim H, Roy S, Huang S, Adams JI, Grimes SM, Lau BT, Sathe A, Ji HP*, Zhang NR*
Nature Communications 16, 6654 (2025)
Clonal cell states link gastroesophageal junction tissues with metaplasia and cancer
Gier RA, Bracht SA, Rong J, Reyes Hueros RLA, Wahlsten ML, Cote C, …, Falk GW, Zhang NR, Shaffer SM*
Nature Communications 16, 10952 (2025)
2024
Recovery of biological signals lost in single-cell batch integration with CellANOVA
Zhang Z, Mathew D, Lim TL, Mason K, Martinez CM, Huang S, Wherry EJ, Susztak K, Minn AJ, Ma Z*, Zhang NR*
Nature Biotechnology 43, 1861–1877 (2024)
A multiomic atlas identifies a treatment-resistant, bone marrow progenitor-like cell population in T cell acute lymphoblastic leukemia
Xu J†, Chen C†, Sussman JH, Yoshimura S, Vincent T, Pölönen P, …, Zhang NR, …, Mullighan CG, Tan K*, Teachey DT*
Nature Cancer 6, 102–122 (2024)
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
Mason K, Sathe A, Hess PR, Rong J, Wu C-Y, Furth E, Susztak K, Levinsohn J, Ji HP, Zhang NR*
Genome Biology 25, 14 (2024)
Combined JAK inhibition and PD-1 immunotherapy for non-small cell lung cancer patients
Mathew D, Marmarelis ME, Foley C, Bauml JM, Ye D, Ghinnagow R, Ngiow SF, Klapholz M, Jun S, Zhang Z, Zorc R, Diehn M, Hwang W-T, Zhang NR, Langer CJ, Wherry EJ, Minn AJ*
Science 384, eadf1329 (2024)
A comparative study of structural variant calling in WGS from Alzheimer's disease families
Malamon JS†, Farrell JJ†, Xia LC, Dombroski BA, Das RG, Way J, …, Zhang NR, …, Schellenberg GD, Lee WP†*, Vardarajan BN†*
Life Science Alliance 7, e202302181 (2024)
2023
Integration of spatial and single-cell data across modalities with weakly linked features
Chen S†, Zhu B†, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR*, Ma Z*
Nature Biotechnology 42, 1096–1106 (2023)
Quantifying common and distinct information in single-cell multimodal data with tilted canonical correlation analysis
Lin KZ, Zhang NR*
PNAS 120, e2303647120 (2023)
Organization of the human intestine at single-cell resolution
Hickey JW, Becker WR, Nevins SA, Horning A, Perez AE, Zhu C, …, Zhang NR, …, Nolan GP*, Greenleaf WJ*, Snyder M*
Nature 619, 572–584 (2023)
2022
Systematic single-cell pathway analysis to characterize early T cell activation
Bibby JA, Agarwal D, Freiwald T, Kunz N, Merle NS, West EE, Singh P, Larochelle A, Chinian F, Mukherjee S, Afzali B, Kemper C*, Zhang NR*
Cell Reports 41, 111697 (2022)
Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions
Jiang Y, Harigaya Y, Zhang Z, Zhang H, Zang C, Zhang NR*
Cell Systems 13, 737–751.e4 (2022)
The interferon-stimulated gene RIPK1 regulates cancer cell intrinsic and extrinsic resistance to immune checkpoint blockade
Cucolo L, Chen Q, Qiu J, Yu Y, Klapholz M, Budinich KA, Zhang Z, Shao Y, Brodsky IE, Jordan MS, Gilliland DG, Zhang NR, Shi J, Minn AJ*
Immunity 55, 671–685.e10 (2022)
Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor-associated SPP1+ macrophages and fibroblasts
Sathe A, Mason K, Grimes SM, Zhou Z, Lau BT, Bai X, Su A, Tan X, Lee H, Suarez CJ, Nguyen Q, Poultsides G, Zhang NR, Ji HP*
Clinical Cancer Research 29, 244–260 (2022)
2021
Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer
Wu C-Y, Lau BT, Kim HS, Sathe A, Grimes SM, Ji HP, Zhang NR*
Nature Biotechnology 39, 1259–1269 (2021)
New frontiers in single-cell genomics
Navin NE, Rozenblatt-Rosen O, Zhang NR
Genome Research 31, ix–x (2021)
Causal inference for heritable phenotypic risk factors using heterogeneous genetic instruments
Wang J, Zhao Q, Bowden J, Hemani G, Davey Smith G, Small DS, Zhang NR
PLoS Genetics 17, e1009575 (2021)
A Mendelian randomization study of the role of lipoprotein subfractions in coronary artery disease
Zhao Q*, Wang J, Miao Z, Zhang NR, Hennessy S, Small DS, Rader DJ
eLife 10, e58361 (2021)
2020
DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing
Zhou Z, Xu B, Minn AJ, Zhang NR*
Genome Biology 21, 10 (2020)
Surface protein imputation from single cell transcriptomes by deep neural networks
Zhou Z, Ye C, Wang J, Zhang NR*
Nature Communications 11, 651 (2020)
Data denoising and post-denoising corrections in single cell RNA sequencing
Agarwal D, Wang J, Zhang NR*
Statistical Science 35, 112–128 (2020)
Distribution-free multisample tests based on optimal matchings with applications to single cell genomics
Mukherjee S, Agarwal D, Zhang NR, Bhattacharya BB
Journal of the American Statistical Association 117, 627–638 (2020)
The Human Tumor Atlas Network: charting tumor transitions across space and time at single-cell resolution
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, …, Zhang NR, … (Human Tumor Atlas Network)
Cell 181, 236–249 (2020)
2019
Bulk tissue cell type deconvolution with multi-subject single-cell expression reference
Wang X, Park J, Susztak K, Zhang NR*, Li M*
Nature Communications 10, 380 (2019)
Data denoising with transfer learning in single-cell transcriptomics
Wang J, Agarwal D, Huang M, Hu G, Zhou Z, Ye C, Zhang NR*
Nature Methods 16, 875–878 (2019)
Opposing functions of interferon coordinate adaptive and innate immune responses to cancer immune checkpoint blockade
Benci JL, Johnson LR, Choa R, Xu Y, Qiu J, Zhou Z, …, Zhang NR, …, Wolchok JD, Kambayashi T, Minn AJ*
Cell 178, 933–948.e14 (2019)
Elite control of HIV is associated with distinct functional and transcriptional signatures in lymphoid tissue CD8+ T cells
Nguyen S, Deleage C, Darko S, Ransier A, Truong DP, Agarwal D, …, Zhang NR, …, Deeks SG, Buggert M, Betts MR*
Science Translational Medicine 11, eaax4077 (2019)
Cell-type-specific complement expression in the healthy and diseased retina
Pauly D, Agarwal D, Dana N, Schäfer N, Biber J, Wunderlich KA, …, Zhang NR, …, Stambolian D, Li M, Grosche A*
Cell Reports 29, 2835–2848.e4 (2019)
Semblance: an empirical similarity kernel on probability spaces
Agarwal D, Zhang NR*
Science Advances 5, eaau9630 (2019)
2018
SAVER: gene expression recovery for single-cell RNA sequencing
Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR*
Nature Methods 15, 539–542 (2018)
Gene expression distribution deconvolution in single-cell RNA sequencing
Wang J, Huang M, Torre E, Dueck H, Shaffer S, Murray JI, Raj A, Li M, Zhang NR*
PNAS 115, E6437–E6446 (2018)
CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing
Jiang Y*, Wang R, Urrutia E, Anastopoulos IN, Nathanson KL, Zhang NR*
Genome Biology 19, 202 (2018)
Integrative DNA copy number detection and genotyping from sequencing and array-based platforms
Zhou Z, Wang W, Wang L-S, Zhang NR*
Bioinformatics 34, 2349–2355 (2018)
Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny
Urrutia E, Chen H, Zhou Z, Zhang NR*, Jiang Y*
Bioinformatics 34, 2126–2128 (2018)
Sensitivity analysis and power for instrumental variable studies
Wang X, Jiang Y, Zhang NR, Small DS
Biometrics 74, 1150–1160 (2018)
First giant steps toward a cell atlas of atherosclerosis
Zhang H, Zhang NR, Li M, Reilly MP*
Circulation Research 122, 1632–1634 (2018)
2017
SCALE: modeling allele-specific gene expression by single-cell RNA sequencing
Jiang Y, Zhang NR*, Li M*
Genome Biology 18, 74 (2017)
Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data
Jia C, Hu Y, Kelly D, Kim J, Li M*, Zhang NR*
Nucleic Acids Research 45, 10978–10988 (2017)
Allele-specific copy number estimation by whole exome sequencing
Chen H, Jiang Y, Maxwell KN, Nathanson KL, Zhang NR*
Annals of Applied Statistics 11, 1169–1192 (2017)
Identification of large rearrangements in cancer genomes with barcode linked reads
Xia LC, Bell JM, Wood-Bouwens C, Chen JJ, Zhang NR*, Ji HP*
Nucleic Acids Research 46, e19 (2017)
BRCA locus-specific loss of heterozygosity in germline BRCA1 and BRCA2 carriers
Maxwell KN, Wubbenhorst B, Wenz BM, De Sloover D, Pluta J, Emery L, …, Zhang NR, …, Feldman M, Domchek SM, Nathanson KL*
Nature Communications 8, 319 (2017)
Genetic and genomic characterization of 462 melanoma patient-derived xenografts, tumor biopsies, and cell lines
Garman B, Anastopoulos IN, Krepler C, Brafford P, Sproesser K, Jiang Y, …, Zhang NR, Davies MA, Herlyn M, Nathanson KL*
Cell Reports 21, 1936–1952 (2017)
DNA copy number profiling using single-cell sequencing
Wang X, Chen H, Zhang NR
Briefings in Bioinformatics 19, 731–736 (2017)
2016
Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing
Jiang Y, Qiu Y, Minn AJ, Zhang NR*
PNAS 113, E5528–E5537 (2016)
A genome-wide approach for detecting novel insertion-deletion variants of mid-range size
Xia LC, Sakshuwong S, Hopmans ES, Bell JM, Grimes SM, Siegmund DO, Ji HP*, Zhang NR*
Nucleic Acids Research 44, e126 (2016)
Scan statistics on Poisson random fields with applications in genomics
Zhang NR, Yakir B, Xia LC, Siegmund DO
Annals of Applied Statistics 10, 726–755 (2016)
Global copy number profiling of cancer genomes
Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang NR, Powers RS, Krauthammer M*
Bioinformatics 32, 926–928 (2016)
2015
Graph-based change-point detection
Chen H, Zhang NR
Annals of Statistics 43, 139–176 (2015)
Allele-specific copy number profiling by next-generation DNA sequencing
Chen H, Bell JM, Zavala NA, Ji HP, Zhang NR*
Nucleic Acids Research 43, e23 (2015)
CODEX: a normalization and copy number variation detection method for whole exome sequencing
Jiang Y, Oldridge DA, Diskin SJ, Zhang NR*
Nucleic Acids Research 43, e39 (2015)
Emergence of hemagglutinin mutations during the course of influenza infection
Cushing A, Kamali A, Winters M, Hopmans ES, Bell JM, Grimes SM, Xia LC, Zhang NR, Moss RB, Holodniy M, Ji HP*
Scientific Reports 5, 16178 (2015)
Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression
Peixoto LL, Wimmer ME, Poplawski SG, Tudor JC, Kenworthy CA, Liu S, Mizuno K, Garcia BA, Zhang NR, Giese KP, Abel T*
BMC Genomics 16, S5 (2015)
Allelic variation contributes to bacterial host specificity
Yue M, Han X, De Masi L, Zhu C, Ma X, Zhang J, …, Zhang NR, Rankin SC, Schifferli DM*
Nature Communications 6, 8754 (2015)
2014
Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer
Nadauld LD, Garcia S, Natsoulis G, Bell JM, Miotke L, Hopmans ES, …, Zhang NR, Ford JM, Kuo CJ*, Ji HP*
Genome Biology 15, 428 (2014)
2013
Graph-based tests for two-sample comparisons of categorical data
Chen H, Zhang NR
Statistica Sinica 23, 1479–1503 (2013)
Identification of insertion deletion mutations from deep targeted resequencing
Natsoulis G†, Zhang NR†, Welch K, Bell JM, Ji HP*
Journal of Data Mining in Genomics & Proteomics 4, 132 (2013)
2012
A cross-sample statistical model for SNP detection in short-read sequencing data
Muralidharan O, Natsoulis G, Bell JM, Newburger D, Xu H, Kela I, Ji HP, Zhang NR*
Nucleic Acids Research 40, e5 (2012)
Ultrasensitive detection of rare mutations using next-generation targeted resequencing
Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell JM, Brown S, Holodniy M, Zhang NR, Ji HP*
Nucleic Acids Research 40, e2 (2012)
Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing
Shen JJ, Zhang NR*
Annals of Applied Statistics 6, 476–496 (2012)
Detecting mutations in mixed sample sequencing data using empirical Bayes
Muralidharan O, Natsoulis G, Bell JM, Ji HP, Zhang NR*
Annals of Applied Statistics 6, 1047–1067 (2012)
Model selection for high-dimensional, multi-sequence change-point problems
Zhang NR, Siegmund DO
Statistica Sinica 22, 1507–1538 (2012)
Multiple hypothesis testing adjusted for latent variables, with an application to the AGEMAP gene expression data
Sun Y, Zhang NR, Owen AB
Annals of Applied Statistics 6, 1664–1688 (2012)
2011
Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays
Chen H, Xing H, Zhang NR*
PLoS Computational Biology 7, e1001060 (2011)
Detecting simultaneous variant intervals in aligned sequences
Siegmund DO, Yakir B, Zhang NR
Annals of Applied Statistics 5, 645–668 (2011)
False discovery rates and copy number variation
Efron B, Zhang NR
Biometrika 98, 251–271 (2011)
A flexible approach for highly multiplexed candidate gene targeted resequencing
Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang NR, Ji HP*
PLoS ONE 6, e21088 (2011)
False discovery rate for scanning statistics
Siegmund DO, Zhang NR, Yakir B
Biometrika 98, 979–985 (2011)
For the complete list including work before 2011, see
Google Scholar.