Liu, X. Shirley

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 18,386

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., et al. (2018) · Nature Medicine

Cancer Immunotherapy and BiomarkersImmunotherapy and Immune Responses

Cited by 5,179

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens

Li, W., Xu, H., Xiao, T., Cong, L., Love, M. I., Zhang, F., Irizarry, R. A., Liu, J. S., Brown, M., & Liu, X. S. (2014) · Genome Biology

CRISPR and Genetic EngineeringChromatin Remodeling and Cancer

Cited by 2,684

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 2,033

A single-cell and spatially resolved atlas of human breast cancers

Wu, S. Z., Al-Eryani, G., Roden, D. L., Junankar, S., Harvey, K., Andersson, A., Thennavan, A., Wang, C., Torpy, J. R., Bartonicek, N., et al. (2021) · Nature Genetics

Single-cell and spatial transcriptomicsBreast Cancer Treatment Studies

Cited by 1,775

Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1

Carroll, J. S., Liu, X. S., Brodsky, A. S., Li, W., Meyer, C. A., Szary, A. J., Eeckhoute, J., Shao, W., Hestermann, E. V., Geistlinger, T. R., et al. (2005) · Cell

Estrogen and related hormone effectsGenomics and Chromatin Dynamics

Cited by 1,384

Transfer learning enables predictions in network biology

Theodoris, C. V., Xiao, L., Chopra, A., Chaffin, M. D., Al Sayed, Z. R., Hill, M. C., Mantineo, H., Brydon, E. M., Zeng, Z., Liu, X. S., et al. (2023) · Nature

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 1,193

A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing

Pan, D., Kobayashi, A., Jiang, P., Ferrari de Andrade, L., Tay, R. E., Luoma, A. M., Tsoucas, D., Qiu, X., Lim, K., Rao, P., et al. (2018) · Science

Cancer Immunotherapy and BiomarkersChromatin Remodeling and Cancer

Cited by 852

A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism

Feng, D., Liu, T., Sun, Z., Bugge, A., Mullican, S. E., Alenghat, T., Liu, X. S., & Lazar, M. A. (2011) · Science

Circadian rhythm and melatoninHistone Deacetylase Inhibitors Research

Cited by 701

Sequence determinants of improved CRISPR sgRNA design

Xu, H., Xiao, T., Chen, C.-H., Li, W., Meyer, C. A., Wu, Q., Wu, D., Cong, L., Zhang, F., Liu, J. S., et al. (2015) · Genome Research

CRISPR and Genetic EngineeringRNA regulation and disease

Cited by 625

Chromatin marks identify critical cell types for fine mapping complex trait variants

Trynka, G., Sandor, C., Han, B., Xu, H., Stranger, B. E., Liu, X. S., & Raychaudhuri, S. (2013) · Nature Genetics

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 580

Target analysis by integration of transcriptome and ChIP-seq data with BETA

Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang, Q., Meyer, C. A., Zhang, Y., & Liu, X. S. (2013) · Nature Protocols

Genomics and Chromatin DynamicsBioinformatics and Genomic Networks

Cited by 544

Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors

Goel, S., Wang, Q., Watt, A. C., Tolaney, S. M., Dillon, D. A., Li, W., Ramm, S., Palmer, A. C., Yuzugullu, H., Varadan, V., et al. (2016) · Cancer Cell

Advanced Breast Cancer TherapiesPI3K/AKT/mTOR signaling in cancer

Cited by 470

CEAS: cis-regulatory element annotation system

Shin, H., Liu, T., Manrai, A. K., & Liu, X. S. (2009) · Bioinformatics

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 461

Evolutionarily Conserved Multisubunit RBL2/p130 and E2F4 Protein Complex Represses Human Cell Cycle-Dependent Genes in Quiescence

Litovchick, L., Sadasivam, S., Florens, L., Zhu, X., Swanson, S. K., Velmurugan, S., Chen, R., Washburn, M. P., Liu, X. S., & DeCaprio, J. A. (2007) · Molecular Cell

Cancer-related Molecular PathwaysGenomics and Chromatin Dynamics

Cited by 396

Integrating regulatory motif discovery and genome-wide expression analysis

Conlon, E. M., Liu, X. S., Lieb, J. D., & Liu, J. S. (2003) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsFungal and yeast genetics research

Cited by 343

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., et al. (2016) · Nature Genetics

Cancer Immunotherapy and BiomarkersT-cell and B-cell Immunology

Cited by 306

Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen

Bienvenu, F., Jirawatnotai, S., Elias, J. E., Meyer, C. A., Mizeracka, K., Marson, A., Frampton, G. M., Cole, M. F., Odom, D. T., Odajima, J., et al. (2010) · Nature

Cancer-related Molecular PathwaysDevelopmental Biology and Gene Regulation

Cited by 276

Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade

Gu, S. S., Zhang, W., Wang, X., Jiang, P., Traugh, N., Li, Z., Meyer, C., Stewig, B., Xie, Y., Bu, X., et al. (2021) · Cancer Discovery

Cancer Immunotherapy and BiomarkersImmunotherapy and Immune Responses

Cited by 273

Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development

Xu, Y., Xu, C., Kato, A., Tempel, W., Abreu, J. G., Bian, C., Hu, Y., Hu, D., Zhao, B., Cerovina, T., et al. (2012) · Cell

Epigenetics and DNA MethylationDevelopmental Biology and Gene Regulation

Cited by 271

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

He, H. H., Meyer, C. A., Hu, S. S., Chen, M.-W., Zang, C., Liu, Y., Rao, P. K., Fei, T., Xu, H., Long, H., et al. (2014) · Nature Methods

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 218

An integrative ENCODE resource for cancer genomics

Zhang, J., Lee, D., Dhiman, V., Jiang, P., Xu, J., McGillivray, P., Yang, H., Liu, J., Meyerson, W., Clarke, D., et al. (2020) · Nature Communications

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 172

Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery

Boros, J., Donaldson, I. J., O'Donnell, A., Odrowaz, Z. A., Zeef, L., Lupien, M., Meyer, C. A., Liu, X. S., Brown, M., & Sharrocks, A. D. (2009) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 127

Epigenetic Regulation of Cell Type–Specific Expression Patterns in the Human Mammary Epithelium

Maruyama, R., Choudhury, S., Kowalczyk, A., Bessarabova, M., Beresford-Smith, B., Conway, T., Kaspi, A., Wu, Z., Nikolskaya, T., Merino, V. F., et al. (2011) · PLoS Genetics

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 108