High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer

A Python library for probabilistic analysis of single-cell omics data

(2022) Adam Gayoso et al.   NATURE BIOTECHNOLOGY

The Good, the Bad, and the Ugly: Neutrophils, Angiogenesis, and Cancer

(2022) Irem Ozel et al.   Cancers

Intratumoral plasma cells predict outcomes to PD-L1 blockade in non-small cell lung cancer

(2022) Namrata S. Patil et al.   CANCER CELL

B cells and tertiary lymphoid structures as determinants of tumour immune contexture and clinical outcome

(2022) Wolf H. Fridman et al.   Nature Reviews Clinical Oncology

Tumor-derived Jagged1 promotes cancer progression through immune evasion

(2022) Jingjing Meng et al.   Cell Reports

Single-cell RNA-seq analysis reveals BHLHE40-driven pro-tumour neutrophils with hyperactivated glycolysis in pancreatic tumour microenvironment

(2022) Liwen Wang et al.   GUT

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

(2021) Chenling Xu et al.   Molecular Systems Biology

SCISSOR: a framework for identifying structural changes in RNA transcripts

(2021) Hyo Young Choi et al.   Nature Communications

Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

(2021) Hyuna Sung et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers

(2021) Christoph H Mayr et al.   EMBO Molecular Medicine

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Knockdown of RIPK2 Inhibits Proliferation and Migration, and Induces Apoptosis via the NF-κB Signaling Pathway in Gastric Cancer

(2021) Qian Yang et al.   Frontiers in Genetics

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis

(2021) Dénes Türei et al.   Molecular Systems Biology

Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non-small cell lung cancer

(2021) Fengying Wu et al.   Nature Communications

Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung

(2021) Jonas C. Schupp et al.   CIRCULATION

Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma

(2021) Giacomo Oliveira et al.   NATURE

Mapping single-cell data to reference atlases by transfer learning

(2021) Mohammad Lotfollahi et al.   NATURE BIOTECHNOLOGY

FcγR engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity

(2021) Vijayashree Mysore et al.   Nature Communications

The Correlation Between SPP1 and Immune Escape of EGFR Mutant Lung Adenocarcinoma Was Explored by Bioinformatics Analysis

(2021) Yi Zheng et al.   Frontiers in Oncology

Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification

(2021) Andrew M. Leader et al.   CANCER CELL

Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data

(2021) Duanchen Sun et al.   NATURE BIOTECHNOLOGY

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

(2021) Luz Garcia-Alonso et al.   NATURE GENETICS

Benchmarking atlas-level data integration in single-cell genomics

(2021) Malte D. Luecken et al.   NATURE METHODS

Systematic investigation of cytokine signaling activity at the tissue and single-cell levels

(2021) Peng Jiang et al.   NATURE METHODS

scCODA is a Bayesian model for compositional single-cell data analysis

(2021) M. Büttner et al.   Nature Communications

Confronting false discoveries in single-cell differential expression

(2021) Jordan W. Squair et al.   Nature Communications

Inflammation causes remodeling of mitochondrial cytochrome c oxidase mediated by the bifunctional gene C15orf48

(2021) Sally A. Clayton et al.   Science Advances

An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates

(2020) Jermaine Goveia et al.   CANCER CELL

The role of B lymphocytes in the immuno-biology of non-small-cell lung cancer

(2020) Akshay J. Patel et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

Regenerative lineages and immune-mediated pruning in lung cancer metastasis

(2020) Ashley M. Laughney et al.   NATURE MEDICINE

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

A conserved dendritic-cell regulatory program limits antitumour immunity

(2020) Barbara Maier et al.   NATURE

Vimentin prevents a miR-dependent negative regulation of tissue factor mRNA during epithelial–mesenchymal transitions and facilitates early metastasis

(2020) Marie-Emilie Francart et al.   ONCOGENE

Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma

(2020) Nayoung Kim et al.   Nature Communications

Androgen receptor affects the response to immune checkpoint therapy by suppressing PD-L1 in hepatocellular carcinoma

(2020) Guangyi Jiang et al.   Aging-US

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

(2020) Jonas Schulte-Schrepping et al.   CELL

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning

(2020) Nicholas J. Bernstein et al.   Cell Systems

Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis

(2020) Taylor S. Adams et al.   Science Advances

Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

(2020) Arun C. Habermann et al.   Science Advances

Co-option of Neutrophil Fates by Tissue Environments

(2020) Iván Ballesteros et al.   CELL

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

(2020) Ashley Maynard et al.   CELL

Good cops turn bad: The contribution of neutrophils to immune-checkpoint inhibitor treatment failures in cancer

(2020) Huajia Zhang et al.   PHARMACOLOGY & THERAPEUTICS

TICAM2-related pathway mediates neutrophil exhaustion

(2020) RuiCi Lin et al.   Scientific Reports

Targeting MARCO and IL-37R on immunosuppressive macrophages in lung cancer blocks regulatory T cells and supports cytotoxic lymphocyte function

(2020) Linnéa La Fleur et al.   CANCER RESEARCH

A molecular cell atlas of the human lung from single-cell RNA sequencing

(2020) Kyle J. Travaglini et al.   NATURE

Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data

(2020) Nan Miles Xi et al.   Cell Systems

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

(2019) Gregor Sturm et al.   BIOINFORMATICS

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

A cellular census of human lungs identifies novel cell states in health and in asthma

(2019) Felipe A. Vieira Braga et al.   NATURE MEDICINE

Tumour-associated neutrophils in patients with cancer

(2019) Merav E. Shaul et al.   Nature Reviews Clinical Oncology

CD83: Activation Marker for Antigen Presenting Cells and Its Therapeutic Potential

(2019) Ziduo Li et al.   Frontiers in Immunology

KRAS-Driven Lung Adenocarcinoma and B Cell Infiltration: Novel Insights for Immunotherapy

(2019) Pinto et al.   Cancers

lncRNA NEAT1 competes against let-7a to contribute to non-small cell lung cancer proliferation and metastasis

(2018) Li Qi et al.   BIOMEDICINE & PHARMACOTHERAPY

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

TP53,STK11andEGFRMutations Predict Tumor Immune Profile and the Response to anti-PD-1 in Lung Adenocarcinoma

(2018) Jerome Biton et al.   CLINICAL CANCER RESEARCH

CD97 Promotes Tumor Aggressiveness through the Traditional G Protein-Coupled Receptor-mediated signaling in Hepatocellular Carcinoma

(2018) Yin Yin et al.   HEPATOLOGY

Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions

(2018) Maximilien Evrard et al.   IMMUNITY

Cancer-Cell-Intrinsic Mechanisms Shaping the Tumor Immune Landscape

(2018) Max D. Wellenstein et al.   IMMUNITY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

(2018) Paul A Reyfman et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Plasminogen Activator Inhibitor-1 Promotes the Recruitment and Polarization of Macrophages in Cancer

(2018) Marta Helena Kubala et al.   Cell Reports

Atezolizumab versus docetaxel in patients with previously treated non-small-cell lung cancer (OAK): a phase 3, open-label, multicentre randomised controlled trial

(2017) Achim Rittmeyer et al.   LANCET

Mesothelin promotes epithelial-to-mesenchymal transition and tumorigenicity of human lung cancer and mesothelioma cells

(2017) Xiaoqing He et al.   Molecular Cancer

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Neutrophils dominate the immune cell composition in non-small cell lung cancer

(2017) Julia Kargl et al.   Nature Communications

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

(2017) Pornpimol Charoentong et al.   Cell Reports

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

(2017) Julien Racle et al.   eLife

Interleukin-4 Supports the Suppressive Immune Responses Elicited by Regulatory T Cells

(2017) Wei-Cheng Yang et al.   Frontiers in Immunology

EGFR mutation correlates with uninflamed phenotype and weak immunogenicity, causing impaired response to PD-1 blockade in non-small cell lung cancer

(2017) Zhong-Yi Dong et al.   OncoImmunology

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

Tumor-Associated Neutrophils Show Phenotypic and Functional Divergence in Human Lung Cancer

(2016) Shilpi Saha et al.   CANCER CELL

CXCR2 Inhibition Profoundly Suppresses Metastases and Augments Immunotherapy in Pancreatic Ductal Adenocarcinoma

(2016) Colin W. Steele et al.   CANCER CELL

Atezolizumab versus docetaxel for patients with previously treated non-small-cell lung cancer (POPLAR): a multicentre, open-label, phase 2 randomised controlled trial

(2016) Louis Fehrenbacher et al.   LANCET

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

(2016) Nikolaos Ignatiadis et al.   NATURE METHODS

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Neutrophil ageing is regulated by the microbiome

(2015) Dachuan Zhang et al.   NATURE

Non-redundant requirement for CXCR3 signalling during tumoricidal T-cell trafficking across tumour vascular checkpoints

(2015) M. E. Mikucki et al.   Nature Communications

Tumor-associated neutrophils stimulate T cell responses in early-stage human lung cancer

(2014) Evgeniy B. Eruslanov et al.   JOURNAL OF CLINICAL INVESTIGATION

Prognostic Role of Neutrophil-to-Lymphocyte Ratio in Solid Tumors: A Systematic Review and Meta-Analysis

(2014) Arnoud J. Templeton et al.   JNCI-Journal of the National Cancer Institute

Lectin-Like Oxidized LDL Receptor-1 Is an Enhancer of Tumor Angiogenesis in Human Prostate Cancer Cells

(2014) Iván González-Chavarría et al.   PLoS One

Proteome profiling of human neutrophil granule subsets, secretory vesicles, and cell membrane: correlation with transcriptome profiling of neutrophil precursors

(2013) Sara Rørvig et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

LTB4 Is a Signal-Relay Molecule during Neutrophil Chemotaxis

(2012) Philippe V. Afonso et al.   DEVELOPMENTAL CELL

Osteopontin induces growth of metastatic tumors in a preclinical model of non-small lung cancer

(2012) Farbod Shojaei et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

PAD4 mediated histone hypercitrullination induces heterochromatin decondensation and chromatin unfolding to form neutrophil extracellular trap-like structures

(2012) Marc Leshner et al.   Frontiers in Immunology

Foxo in the immune system

(2008) S L Peng   ONCOGENE