Selected Recent Publications


  1. Jiang Y, Nathanson KL, Zhang NR. CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing. 2018. Under Review.
  2. Wang X, Park J, Susztak K, Zhang NR, Li M. Bulk Tissue Cell Type Deconvolution with Multi-Subject Single-Cell Expression Reference. 2018. Under Review.
  3. Wang J, Huang M, Torre E, Dueck H,Shaffer S, Murray J, Raj A, Li M, Zhang NR. Gene expression distribution deconvolution in single-cell RNA sequencing. PNAS June 26, 2018.
  4. Huang M, Wang J, …, Li M, Zhang NR. SAVER: gene expression recovery for single-cell RNA sequencing. Nat Methods. 2018 Jun 25.
  5. Urrutia E, Chen H, Zhou Z, Zhang NR, Jiang Y. Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny. Bioinformatics. 2018 Jun 15;34(12):2126-2128.
  6. Zhang H, Zhang NR, Li M, Reilly MP. First Giant Steps Toward a Cell Atlas of Atherosclerosis. Circ Res. 2018 Jun 8; 122(12):1632-1634.
  7. Zhou Z, Wang W, Wang L, Zhang NR. Integrative DNA copy number detection and genotyping from sequencing and array-based platforms, Bioinformatics. 2018.

  8. Park J, Shrestha R, Qiu C, Kondo A, Huang S, Werth M, Li M, Barasch J, Suszták K. Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. Science. 2018 May 18;360(6390):758-763.

  9. Hu Y, Lin J, Hu J, Hu G, Wang K, Zhang H, Reilly MP, Li M. PennDiff: Detecting Differential Alternative Splicing and Transcription by RNA Sequencing. Bioinformatics. 2018 Feb 20.

  10. Xia LC, Bell JM, Wood-Bouwens C, Chen JJ, Zhang NR, Ji HP. Identification of large rearrangements in cancer genomes with barcode linked reads. Nucleic Acids Res. 2018 Feb 28;46(4):e19.


  1. Jia C, Hu Y, Kelly D, Kim J, Li M, Zhang NR. Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data. Nucleic Acids Res. 2017 Nov 2;45(19):10978-10988. 
  2. Zhang H, Xue C, Wang Y, Shi J, Zhang X, Li W, Nunez S, Foulkes AS, Lin J, Hinkle CC, Yang W, Morrisey EE, Rader DJ, Li M, Reilly MP. Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases. J Am Heart Assoc. 2017 Nov 13;6(11). pii: e007431.

  3. Jiang Y, Zhang NR, Li M. SCALE: modeling allele-specific gene expression by single-cell RNA sequencing. Genome Biol. 2017 Apr 26;18(1):74.
  4. Wang X, Chen H, Zhang NR. DNA copy number profiling using single-cell sequencing. Brief Bioinform. 2017 Feb 4.