Article-Journal

ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets

CITE-seq enables paired measurement of surface protein and mRNA expression in single cells using antibodies conjugated to …

Zheng Y , Caron D, Kim J, Jun S, Tian Y, Florian M, Stuart K, Sims P, Gottardo R

Total whole-arm chromosome losses predict malignancy in human cancer

Aneuploidy is observed as gains or losses of whole chromosomes or chromosome arms and is a common hallmark of cancer. Whereas models …

Zheng Y , Ahmad K, Henikoff S

Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion

Chimeric antigen receptor-modified T cell (CAR-T) immunotherapy has revolutionised blood cancer treatment. Parsing the genetic …

Fiorenza S, Zheng Y , Purushe J, Bock T, Sarthy J, Janssens D, Sheih A, Kimble E, Kirchmeier D, Phi T, Gauthier J, Hirayama A, Riddell S, Wu Q, Gottardo R, Maloney D, Yang J, Henikoff S, Turtle C

Histone Methylation Mark Analyses Distinguish Carts Manufactured from Distinct Sources and Uncover Novel Transcription Factors Associated with In Vivo Function of Carts after Infusion into DLBCL Patients That Are Not Identified By RNA-Seq

Chimeric antigen receptor-modified T cell (CART) therapy has heralded a revolution in cancer immunotherapy. Yet, understanding the …

Fiorenza S, Zheng Y , Sarthy J, Sheih A, Kimble E, Kirchmeier D, Janssens D, Phi T, Gauthier J, Hirayama A, Wu Q, Gottardo R, Riddell S, Maloney D, Henikoff S, Turtle C

Defining cellular population dynamics at single cell resolution during prostate cancer progression

Advanced prostate malignancies are a leading cause of cancer-related deaths in men, in large part due to our incomplete understanding …

Germanos AA, Arora S, Zheng Y , Goddard ET, Coleman IM, Ku AT, Wilkinson S, Amezquita RA, Zager M, Long A, Yang YC, Bielas J, Gottardo R, Ghajar C, Nelson P, Sowalsky A, Setty M, Hsieh A

Cellular profiling of leukapheresis and infusion products of patients enrolled in CD19 CAR T cell therapy identifies biomarkers associated with clinical outcomes

CD19 CAR T cell therapy has emerged as a promising therapy in the treatment of B cell malignancies, such as B cell acute lymphoblastic …

Chour T, Hirayama A, Zheng Y , Sheih A, Zhuang S, Wilson A, Wu V, Gottardo R, Turtle C, Gardner R, Newell E

Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary and enhancer elements in B cells

The Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes with shared functions within the …

Cheng J, Clayton J, Acemel R, Zheng Y , Taylor R, Keles S, Harley J, Quail E, Gómez-Skarmeta J, Ulgiati D

scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data

Quantitative tools are needed to leverage the unprecedented resolution of single-cell high-throughput chromatin conformation (scHi-C) …

Shen S, Zheng Y , Keles S

Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D

Single-cell high-throughput chromatin conformation capture methodologies (scHi-C) enable profiling of long-range genomic interactions. …

Zheng Y , Shen S, Keles S

Long-Term Follow-up and Single-Cell Multiomics Characteristics of Infusion Products in Patients with Chronic Lymphocytic Leukemia Treated with CD19 CAR-T Cells

Lymphodepletion chemotherapy followed by infusion of autologous T cells engineered to express a CD19-targeted chimeric antigen receptor …

Hirayama AV, Zheng Y , Dowling MR, Sheih A, Phi TD, Kirchmeier DR, Chucka AW, Gauthier J, Maloney DG, Gottardo R, Turtle CJ