• 1207 Citations
  • 14 h-Index
20122019
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Research Output 2012 2019

  • 1207 Citations
  • 14 h-Index
  • 19 Article
  • 2 Letter
  • 1 Comment/debate
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Article
2019

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

Haas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N. & Regev, A., Oct 21 2019, In : Genome Biology. 20, 1, 213.

Research output: Contribution to journalArticle

Open Access
accuracy assessment
cancer
Transcriptome
neoplasms
RNA
7 Citations (Scopus)

Landscape of B cell immunity and related immune evasion in human cancers

Hu, X., Zhang, J., Wang, J., Fu, J., Li, T., Zheng, X., Wang, B., Gu, S., Jiang, P., Fan, J., Ying, X., Zhang, J., Carroll, M. C., Wucherpfennig, K. W., Hacohen, N., Zhang, F., Zhang, P., Liu, J. S., Li, B. & Liu, X. S., Jan 1 2019, In : Nature Genetics.

Research output: Contribution to journalArticle

Immune Evasion
Immunity
B-Lymphocytes
Neoplasms
Complementarity Determining Regions
2018
21 Citations (Scopus)

Analysis of PD1, PDL1, PDL2 expression and T cells infiltration in 1014 gastric cancer patients

Xing, X., Guo, J., Wen, X., Ding, G., Li, B., Dong, B., Feng, Q., Li, S., Zhang, J., Cheng, X., Guo, T., Du, H., Hu, Y., Wang, X., Li, L., Li, Q., Xie, M., Li, L., Gao, X., Shan, F. & 5 others, Li, Z., Ying, X., Zhou, T., Wang, J. & Ji, J., Mar 4 2018, In : OncoImmunology. 7, 3, e1356144.

Research output: Contribution to journalArticle

Stomach Neoplasms
T-Lymphocytes
Proliferating Cell Nuclear Antigen
Neoplasms
Epstein-Barr Virus Infections
1 Citation (Scopus)

Evaluation of immune repertoire inference methods from RNA-seq data

Hu, X., Zhang, J., Liu, J. S., Li, B. & Liu, X. S., Nov 9 2018, In : Nature Biotechnology. 36, 11, 1 p.

Research output: Contribution to journalArticle

RNA
67 Citations (Scopus)

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

Jiang, P., Gu, S., Pan, D., Fu, J., Sahu, A., Hu, X., Li, Z., Traugh, N., Bu, X., Li, B., Liu, J., Freeman, G. J., Brown, M. A., Wucherpfennig, K. W. & Liu, X. S., Oct 1 2018, In : Nature Medicine. 24, 10, p. 1550-1558 9 p.

Research output: Contribution to journalArticle

T-cells
Immunotherapy
Tumors
T-Lymphocytes
Infiltration
6 Citations (Scopus)

Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration

Wang, Z., Cao, S., Morris, J. S., Ahn, J., Liu, R., Tyekucheva, S., Gao, F., Li, B., Lu, W., Tang, X., Wistuba, I. I., Bowden, M., Mucci, L., Loda, M., Parmigiani, G., Holmes, C. C. & Wang, W., Nov 30 2018, In : Food Science and Human Wellness. 9, p. 451-460 10 p.

Research output: Contribution to journalArticle

Open Access
Transcriptome
transcriptome
transcriptomics
neoplasms
Neoplasms
15 Citations (Scopus)

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Cornwell, M. I., Vangala, M., Taing, L., Herbert, Z., Köster, J., Li, B., Sun, H., Li, T., Zhang, J., Qiu, X., Pun, M., Jeselsohn, R., Brown, M., Liu, X. S. & Long, H. W., Apr 12 2018, In : BMC Bioinformatics. 19, 1, 135.

Research output: Contribution to journalArticle

Workflow
RNA
Work Flow
Visualization
Pipelines
2017
13 Citations (Scopus)

Cistrome cancer: A web resource for integrative gene regulation modeling in cancer

Mei, S., Meyer, C. A., Zheng, R., Qin, Q., Wu, Q., Jiang, P., Li, B., Shi, X., Wang, B., Fan, J., Shih, C., Brown, M., Zang, C. & Liu, X. S., Nov 1 2017, In : Cancer Research. 77, 21, p. e19-e22

Research output: Contribution to journalArticle

Genes
Neoplasms
Atlases
Chromatin
Genome
7 Citations (Scopus)

Clonality analysis of synchronous gastro-oesophageal junction carcinoma and distal gastric cancer by whole-exome sequencing

Xing, X., Jia, S., Wu, J., Feng, Q., Dong, B., Li, B., Jia, Y., Shan, F., Li, Y., Zhang, Y., Hu, Y., Wang, X., Liu, X., Yu, W., Zhang, L., Bu, Z., Wu, A., Li, Z. & Ji, J., Oct 1 2017, In : Journal of Pathology. 243, 2, p. 165-175 11 p.

Research output: Contribution to journalArticle

Exome
Stomach Neoplasms
Carcinoma
Neoplasms
CD274 Antigen
115 Citations (Scopus)

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

Sade-Feldman, M., Jiao, Y. J., Chen, J. H., Rooney, M. S., Barzily-Rokni, M., Eliane, J. P., Bjorgaard, S. L., Hammond, M. R., Vitzthum, H., Blackmon, S. M., Frederick, D. T., Hazar-Rethinam, M., Nadres, B. A., Van Seventer, E. E., Shukla, S. A., Yizhak, K., Ray, J. P., Rosebrock, D., Livitz, D., Adalsteinsson, V. & 11 others, Getz, G., Duncan, L. M., Li, B., Corcoran, R. B., Lawrence, D. P., Stemmer-Rachamimov, A., Boland, G. M., Landau, D. A., Flaherty, K. T., Sullivan, R. J. & Hacohen, N., Dec 1 2017, In : Nature Communications. 8, 1, 1136.

Research output: Contribution to journalArticle

beta 2-Microglobulin
Antigen Presentation
antigens
deactivation
therapy
110 Citations (Scopus)

TIMER: A web server for comprehensive analysis of tumor-infiltrating immune cells

Li, T., Fan, J., Wang, B., Traugh, N., Chen, Q., Liu, J. S., Li, B. & Liu, X. S., Nov 1 2017, In : Cancer Research. 77, 21, p. e108-e110

Research output: Contribution to journalArticle

Neoplasms
Antigen-Antibody Complex
Immunotherapy
Immune System
Research Personnel
2016
191 Citations (Scopus)

Comprehensive analyses of tumor immunity: Implications for cancer immunotherapy

Li, B., Severson, E., Pignon, J. C., Zhao, H., Li, T., Novak, J., Jiang, P., Shen, H., Aster, J. C., Rodig, S., Signoretti, S., Liu, J. S. & Liu, X. S., Aug 22 2016, In : Genome Biology. 17, 1, 174.

Research output: Contribution to journalArticle

immunotherapy
immunity
tumor
Immunotherapy
Immunity
15 Citations (Scopus)

High-dimensional genomic data bias correction and data integration using MANCIE

Zang, C., Wang, T., Deng, K., Li, B., Hu, S., Qin, Q., Xiao, T., Zhang, S., Meyer, C. A., He, H. H., Brown, M., Liu, J. S., Xie, Y. & Liu, X. S., Apr 13 2016, In : Nature Communications. 7, 11305.

Research output: Contribution to journalArticle

data integration
Data integration
cancer
Encyclopedias
augmentation
99 Citations (Scopus)

Landscape of tumor-infiltrating T cell repertoire of human cancers

Li, B., Li, T., Pignon, J. C., Wang, B., Wang, J., Shukla, S. A., Dou, R., Chen, Q., Hodi, F. S., Choueiri, T. K., Wu, C., Hacohen, N., Signoretti, S., Liu, J. S. & Liu, X. S., Jul 1 2016, In : Nature Genetics. 48, 7, p. 725-732 8 p.

Research output: Contribution to journalArticle

Complementarity Determining Regions
T-Lymphocytes
Neoplasms
Mutation
Kidney Neoplasms
2015
20 Citations (Scopus)

Network analysis of gene essentiality in functional genomics experiments

Jiang, P., Wang, H., Li, W., Zang, C., Li, B., Wong, Y. J., Meyer, C., Liu, J. S., Aster, J. C. & Liu, X. S., Oct 30 2015, In : Genome Biology. 16, 1, 239.

Research output: Contribution to journalArticle

Gene Regulatory Networks
network analysis
Genomics
Clustered Regularly Interspaced Short Palindromic Repeats
genomics
2014
29 Citations (Scopus)

A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data

Li, B. & Li, J. Z., Jan 1 2014, In : Genome Biology. 15, 9, 1 p.

Research output: Contribution to journalArticle

DNA Sequence Analysis
tumor
Single Nucleotide Polymorphism
sequence analysis
DNA
329 Citations (Scopus)

Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

Theriot, C. M., Koenigsknecht, M. J., Carlson, P. E., Hatton, G. E., Nelson, A. M., Li, B., Huffnagle, G. B., Li, J. Z. & Young, V. B., Jan 20 2014, In : Nature Communications. 5, 3114.

Research output: Contribution to journalArticle

Clostridium
Clostridium Infections
Metabolome
Clostridium difficile
antibiotics
112 Citations (Scopus)

Integrated genomic sequencing reveals mutational landscape of T-cell prolymphocytic leukemia

Kiel, M. J., Velusamy, T., Rolland, D., Sahasrabuddhe, A. A., Chung, F., Bailey, N. G., Schrader, A., Li, B., Li, J. Z., Ozel, A. B., Betz, B. L., Miranda, R. N., Medeiros, L. J., Zhao, L., Herling, M., Lim, M. S. & Elenitoba-Johnson, K. S. J., Aug 28 2014, In : Blood. 124, 9, p. 1460-1472 13 p.

Research output: Contribution to journalArticle

T-Cell Prolymphocytic Leukemia
T-cells
Leukemia
T-Lymphocytes
Exome
2012
19 Citations (Scopus)

Genomic estimates of aneuploid content in glioblastoma multiforme and improved classification

Li, B., Senbabaoglu, Y., Peng, W., Yang, M. L., Xu, J. & Li, J. Z., Oct 15 2012, In : Clinical Cancer Research. 18, 20, p. 5595-5605 11 p.

Research output: Contribution to journalArticle

Aneuploidy
Glioblastoma
Methylation
Neoplasms
CpG Islands