X. Shirley Liu

Research interests

Publications

• Transfer learning enables predictions in network biology

  Nature · 2023 · https://doi.org/10.1038/s41586-023-06139-9

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

  Nature Genetics · 2021 · https://doi.org/10.1038/s41588-021-00911-1

• An integrative ENCODE resource for cancer genomics

  Nature Communications · 2020 · https://doi.org/10.1038/s41467-020-14743-w

• TIMER2.0 for analysis of tumor-infiltrating immune cells

  Nucleic Acids Research · 2020 · https://doi.org/10.1093/nar/gkaa407

• Large-scale public data reuse to model immunotherapy response and resistance

  Genome Medicine · 2020 · https://doi.org/10.1186/s13073-020-0721-z

• Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale

  Nature Genetics · 2020 · https://doi.org/10.1038/s41588-020-0676-4

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

  Science · 2018 · 10.1126/science.aao1710

• Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

  Nucleic Acids Research · 2018 · 10.1093/nar/gky1094

• Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

  Nature Medicine · 2018 · https://doi.org/10.1038/s41591-018-0136-1

• TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells

  Cancer Research · 2017 · https://doi.org/10.1158/0008-5472.can-17-0307

• Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

  Nucleic Acids Research · 2016 · 10.1093/nar/gkw983

• Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

  Genome biology · 2016 · 10.1186/s13059-016-1028-7

• Sequence determinants of improved CRISPR sgRNA design

  Genome Research · 2015 · 10.1101/gr.191452.115

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

  Genome biology · 2014 · https://doi.org/10.1186/s13059-014-0554-4

• XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway

  Nature · 2014 · 10.1038/nature13119

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

  Nature Genetics · 2012 · 10.1038/ng.2504

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

  Genome Research · 2012 · 10.1101/gr.136184.111

• EZH2 Oncogenic Activity in Castration-Resistant Prostate Cancer Cells Is Polycomb-Independent

  Science · 2012 · https://doi.org/10.1126/science.1227604

• Cistrome: an integrative platform for transcriptional regulation studies

  Genome biology · 2011 · 10.1186/gb-2011-12-8-r83

• A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism

  Science · 2011 · 10.1126/science.1198125

• The JAK2/STAT3 signaling pathway is required for growth of CD44+CD24– stem cell–like breast cancer cells in human tumors

  Journal of Clinical Investigation · 2011 · https://doi.org/10.1172/jci44745

• Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer

  Cell · 2009 · 10.1016/j.cell.2009.04.056

• Differential chromatin marking of introns and expressed exons by H3K36me3

  Nature Genetics · 2009 · 10.1038/ng.322

• Model-based Analysis of ChIP-Seq (MACS)

  Genome biology · 2008 · https://doi.org/10.1186/gb-2008-9-9-r137

• A Hierarchical Network of Transcription Factors Governs Androgen Receptor-Dependent Prostate Cancer Growth

  Molecular Cell · 2007 · 10.1016/j.molcel.2007.05.041

• Genome-wide analysis of estrogen receptor binding sites

  Nature Genetics · 2006 · https://doi.org/10.1038/ng1901

• Model-based analysis of tiling-arrays for ChIP-chip

  Proceedings of the National Academy of Sciences · 2006 · https://doi.org/10.1073/pnas.0601180103

• Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1

  Cell · 2005 · https://doi.org/10.1016/j.cell.2005.05.008

Current projects

No projects listed.