Wei Shi
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Wei Shicomputer-science Degrees
Computer Science
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Machine Learning
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Artificial Intelligence
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Computer Science
Wei Shi's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science Stanford University
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Why Is Wei Shi Influential?
(Suggest an Edit or Addition)Wei Shi's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- limma powers differential expression analyses for RNA-sequencing and microarray studies (2015) (20115)
- featureCounts: an efficient general purpose program for assigning sequence reads to genomic features (2013) (12280)
- voom: precision weights unlock linear model analysis tools for RNA-seq read counts (2014) (4030)
- The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote (2013) (2078)
- The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads (2018) (1182)
- A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium (2014) (799)
- Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes (2016) (642)
- The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells (2011) (520)
- The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue–resident regulatory T cells (2015) (424)
- The transcription factor IRF4 is essential for TCR affinity–mediated metabolic programming and clonal expansion of T cells (2013) (332)
- Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells (2015) (295)
- Blimp-1 controls plasma cell function through regulation of immunoglobulin secretion and the unfolded protein response (2015) (258)
- Transcription Factor IRF4 Promotes CD8+ T Cell Exhaustion and Limits the Development of Memory‐like T Cells during Chronic Infection (2017) (257)
- CIS is a potent checkpoint in NK cell–mediated tumor immunity (2016) (250)
- Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips (2010) (221)
- Blocking IL-6 trans-signaling prevents high-fat diet-induced adipose tissue macrophage recruitment but does not improve insulin resistance. (2015) (202)
- Targeting Antigen to Mouse Dendritic Cells via Clec9A Induces Potent CD4 T Cell Responses Biased toward a Follicular Helper Phenotype (2011) (199)
- Complementarity and redundancy of IL-22-producing innate lymphoid cells (2015) (198)
- HDAC inhibitors induce tumor-cell-selective pro-apoptotic transcriptional responses (2013) (146)
- A molecular threshold for effector CD8+ T cell differentiation controlled by transcription factors Blimp-1 and T-bet (2016) (138)
- Global changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2. (2013) (119)
- Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures (2014) (118)
- The transcription factors IRF8 and PU.1 negatively regulate plasma cell differentiation (2014) (116)
- Gata-3 Negatively Regulates the Tumor-Initiating Capacity of Mammary Luminal Progenitor Cells and Targets the Putative Tumor Suppressor Caspase-14 (2011) (110)
- Early precursor T cells establish and propagate T cell exhaustion in chronic infection (2020) (107)
- Sex-specific adipose tissue imprinting of regulatory T cells (2020) (107)
- Deciphering the Innate Lymphoid Cell Transcriptional Program. (2016) (107)
- Transcription Factor IRF4 Regulates Germinal Center Cell Formation through a B Cell–Intrinsic Mechanism (2014) (107)
- c-Maf-dependent Treg cell control of intestinal TH17 cells and IgA establishes host–microbiota homeostasis (2019) (98)
- The TNF Receptor Superfamily-NF-κB Axis Is Critical to Maintain Effector Regulatory T Cells in Lymphoid and Non-lymphoid Tissues. (2017) (91)
- The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity (2014) (90)
- The Helix-Loop-Helix Protein ID2 Governs NK Cell Fate by Tuning Their Sensitivity to Interleukin-15. (2016) (86)
- Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia (2013) (83)
- Transforming growth factor–β and Notch ligands act as opposing environmental cues in regulating the plasticity of type 3 innate lymphoid cells (2016) (72)
- Effector Regulatory T Cell Differentiation and Immune Homeostasis Depend on the Transcription Factor Myb (2017) (71)
- Germline-activating mutations in PIK3CD compromise B cell development and function (2018) (64)
- Requirement for Lyl1 in a model of Lmo2-driven early T-cell precursor ALL. (2013) (62)
- Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB (2017) (62)
- Peripheral natural killer cell maturation depends on the transcription factor Aiolos (2014) (61)
- Blockade of the co-inhibitory molecule PD-1 unleashes ILC2-dependent anti-tumor immunity in melanoma (2021) (60)
- Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (2021) (55)
- A lineage of diploid platelet-forming cells precedes polyploid megakaryocyte formation in the mouse embryo. (2014) (51)
- Dynamic changes in Id3 and E-protein activity orchestrate germinal center and plasma cell development (2016) (48)
- Attenuation of TCR-induced transcription by Bach2 controls regulatory T cell differentiation and homeostasis (2020) (47)
- Transforming growth factor-β-regulated mTOR activity preserves cellular metabolism to maintain long-term T cell responses in chronic infection. (2021) (45)
- featureCounts: an efficient general-purpose read summarization program (2013) (44)
- Linear Models for Microarray Data User's Guide (Now Including RNA-Seq Data Analysis) (2013) (43)
- Linear Models for Microarray and RNA-Seq Data User's Guide (2015) (42)
- IRF4 Activity Is Required in Established Plasma Cells to Regulate Gene Transcription and Mitochondrial Homeostasis. (2019) (40)
- Erratum: The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue–resident regulatory T cells (2015) (39)
- TCF-1 limits the formation of Tc17 cells via repression of the MAF–RORγt axis (2019) (38)
- A crucial role for the homeodomain transcription factor Hhex in lymphopoiesis. (2015) (36)
- Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits (2015) (34)
- An update on using CRISPR/Cas9 in the one-cell stage mouse embryo for generating complex mutant alleles (2017) (31)
- The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells (2015) (31)
- Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression of Cdkn2a (2016) (28)
- Transcription Factor T-bet in B Cells Modulates Germinal Center Polarization and Antibody Affinity Maturation in Response to Malaria. (2019) (28)
- IMiDs prime myeloma cells for daratumumab-mediated cytotoxicity through loss of Ikaros and Aiolos. (2018) (27)
- Estimating the proportion of microarray probes expressed in an RNA sample (2010) (26)
- Illumina WG-6 BeadChip strips should be normalized separately (2009) (25)
- Oct2 and Obf1 as Facilitators of B:T Cell Collaboration during a Humoral Immune Response (2014) (25)
- MYB orchestrates T cell exhaustion and response to checkpoint inhibition (2022) (25)
- Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart (2011) (24)
- Hhex Regulates Hematopoietic Stem Cell Self‐Renewal and Stress Hematopoiesis via Repression of Cdkn2a (2017) (18)
- Blimp1 controls plasma cell function through regulation of immunoglobulin secretion and the unfolded protein response (2016) (16)
- Tailored NEOadjuvant epirubicin, cyclophosphamide and Nanoparticle Albumin-Bound paclitaxel for breast cancer: The phase II NEONAB trial—Clinical outcomes and molecular determinants of response (2019) (16)
- The transcription factor IRF4 represses proapoptotic BMF and BIM to licence multiple myeloma survival (2020) (13)
- The NUP98-HOXD13 fusion oncogene induces thymocyte self-renewal via Lmo2/Lyl1 (2018) (13)
- Mining the Plasma Cell Transcriptome for Novel Cell Surface Proteins (2018) (12)
- MiR-506 suppresses papillary thyroid carcinoma cell proliferation and metastasis via targeting IL17RD. (2019) (12)
- Pax 5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia (2014) (12)
- Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction (2020) (11)
- Plasmacytoid dendritic cell heterogeneity is defined by CXCL10 expression following TLR7 stimulation (2018) (11)
- Quantitative proteomic profiling reveals novel region‐specific markers in the adult mouse brain (2014) (10)
- Read trimming is not required for mapping and quantification of RNA-seq reads at the gene level (2020) (10)
- A point mutation in the Ncr1 signal peptide impairs the development of innate lymphoid cell subsets (2018) (9)
- miR-125b suppresses cell proliferation and metastasis by targeting HAX-1 in esophageal squamous cell carcinoma. (2019) (8)
- Therapeutic inhibition of the SRC-kinase HCK facilitates T cell tumor infiltration and improves response to immunotherapy (2022) (8)
- Acute lymphoblastic leukemia The NUP 98-HOXD 13 fusion oncogene induces thymocyte self-renewal via Lmo 2 / Lyl 1 (2019) (5)
- Subread/Rsubread Users Guide (2016) (4)
- An effective non-parametric method for globally clustering genes from expression profiles (2007) (4)
- Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells (2014) (4)
- Identifying cis-regulatory elements by statistical analysis and phylogenetic footprinting and analyzing their coexistence and related gene ontology. (2007) (4)
- Read trimming is not required for mapping and quantification of RNA-seq reads (2019) (4)
- voom: precision weights unlock linear model analysis tools for RNA-seq read counts (2014) (2)
- Erratum: Blocking IL-6 trans-signaling prevents high-fat diet-induced adipose tissue macrophage recruitment but does not improve insulin resistance (Cell Metabolism (2015) 21 (403-416)) (2016) (2)
- Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria (2022) (2)
- Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB (2017) (1)
- Author Correction: Sex-specific adipose tissue imprinting of regulatory T cells (2021) (1)
- Attenuation of TCR-induced transcription by Bach2 controls regulatory T cell differentiation and homeostasis (2020) (1)
- Loss of IRF4 Results in Multiple Myeloma Cell Apoptosis through the Transcriptional up-Regulation of the BH3-Only Proteins Bmf and BIM (2019) (1)
- Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits (2015) (1)
- Erratum: The transcription factor IRF4 is essential for TCR affinity-mediated metabolic programming and clonal expansion of T cells (Nature Immunology (2013) 14 (1155-1165 )) (2014) (1)
- Impact of gene annotation choice on the quantification of RNA-seq data (2021) (1)
- LMO2-INDUCED MURINE T-CELL ACUTE LYMPHOBLASTIC LEUKEMIA FREQUENTLY EVOLVES TO ONCOGENE INDEPENDENCE (2019) (0)
- Transcription Factor IRF 4 Promotes CD 8 + T Cell Exhaustion and Limits the Development of Memory-like T Cells during Chronic Infection Graphical (2019) (0)
- Epithelial de-differentiation triggered by co-ordinate epigenetic inactivation of the EHF and CDX1 transcription factors drives colorectal cancer progression (2022) (0)
- Integrated systems immunology approach identifies impaired effector T cell memory responses as a feature of progression to severe dengue fever (2023) (0)
- Sex-specific adipose tissue imprinting of regulatory T cells (2020) (0)
- c-Maf-dependent Treg cell control of intestinal TH17 cells and IgA establishes host–microbiota homeostasis (2019) (0)
- Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection (2018) (0)
- RNA-seq Data Employed in The Sequencing Quality Control ( SEQC ) Project (2016) (0)
- Identification of diploid platelet-forming cells prior to the emergence of polyploidy megakaryocyte in the mouse embryo (2014) (0)
- Mechanisms of tumour-selective apoptosis induced by the histone deacetylase inhibitor vorinostat (2008) (0)
- PS925 LMO2-INDUCED MURINE T-CELL ACUTE LYMPHOBLASTIC LEUKEMIA FREQUENTLY EVOLVES TO ONCOGENE INDEPENDENCE (2019) (0)
- Author Correction: Sex-specific adipose tissue imprinting of regulatory T cells (2021) (0)
- The Cell Polarity and Scaffolding Protein, PAR3, Acts as A Tumour Suppressor in Acute Myeloid Leukemia Through Regulation of the Hippo Pathway (2018) (0)
- The Immunomodulatory Drugs, through Loss of Ikaros and Aiolos, Derepress CD38 and Functionally Synergise with Daratumumab (2017) (0)
- Bach2 attenuates T cell receptor-dependent transcription to fine-tune regulatory T cell differentiation (2019) (0)
- TCR induced transcription factors RelA and IRF4 co-operatively regulate the differentiation of effector T-reg cells (2016) (0)
- CTL differentiation and function (WS-108) Chairpersons: Hideo Yagita, Laurence Boumsell (2010) (0)
- Correction: Corrigendum: The transcription factor IRF4 is essential for TCR affinity–mediated metabolic programming and clonal expansion of T cells (2014) (0)
- CD137L and CD4 T cells limit BCL6‐expressing pre‐germinal center B cell expansion and BCL6‐driven B cell malignancy (2022) (0)
- MYB orchestrates T cell exhaustion and response to checkpoint inhibition (2022) (0)
- Molecular control of tissue resident memory T cell generation in the liver (2016) (0)
- Genome-wide in vivo CRISPR screens identify GATOR1 as a TP53 induced tumour suppressor (2022) (0)
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