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List of works by Aviv Regev

142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis

scientific article published on August 2016

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

article

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia

scientific article published on 23 May 2019

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

scientific article published on September 2016

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

scientific article published in November 2017

A Distinct Transcriptional Program in Human CAR T Cells Bearing the 4-1BB Signaling Domain Revealed by scRNA-Seq

scientific article published on 25 July 2020

A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians

scientific article published in December 2015

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks ⬇️

scientific article published on 16 July 2015

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

scientific article

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

scientific article

A Switch in p53 Dynamics Marks Cells That Escape from DSB-Induced Cell Cycle Arrest

scientific article published on 01 August 2020

A Switch in p53 Dynamics Marks Cells That Escape from DSB-Induced Cell Cycle Arrest

scientific article published on 01 November 2020

A Synthesis Concerning Conservation and Divergence of Cell Types across Epithelia

scientific article published on 02 March 2020

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

scientific article

A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies

scientific article published on 30 October 2020

A cellular and spatial map of the choroid plexus across brain ventricles and ages

scientific article published on 30 April 2021

A comprehensive fitness landscape model reveals the evolutionary history and future evolvability of eukaryotic cis-regulatory DNA sequences

scientific article

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

scientific article published on January 2012

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

scientific article published on 30 August 2012

A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response

scientific journal article

A module map showing conditional activity of expression modules in cancer

scientific article

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

article

A multimodal cell census and atlas of the mammalian primary motor cortex

scientific article

A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection

scientific article

A quantitative framework for characterizing the evolutionary history of mammalian gene expression

article

A quantitative model for characterizing the evolutionary history of mammalian gene expression

article

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

scientific article published in Nature

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

scientific article published on 11 May 2020

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

article published in 2021

A single-cell atlas of human and mouse white adipose tissue

A single-cell landscape of high-grade serous ovarian cancer

scientific article published on 22 June 2020

A single-cell survey of the small intestinal epithelium

scientific article published on 8 November 2017

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

scientific article

A transcriptomic atlas of the mouse cerebellum reveals regional specializations and novel cell types

scientific article

A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation

scientific article published on 20 September 2012

A unique regulatory phase of DNA methylation in the early mammalian embryo ⬇️

scientific article published on March 28, 2012

AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia

scientific article published on 26 June 2017

ATIM-32. PERSONALIZED NEOANTIGEN-TARGETING VACCINE GENERATES ROBUST SYSTEMIC AND INTRATUMORAL T CELL RESPONSES IN GLIOBLASTOMA (GBM) PATIENTS

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

scientific article

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

scientific article (publication date: May 2010)

Abstract SY12-04: Multicellular spatial community featuring a novel neuronal-like malignant phenotype is enriched in pancreatic cancer after neoadjuvant chemotherapy and radiotherapy

scientific article published in 2022

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

scientific article published on 21 October 2019

Acquired FGFR and FGF alterations confer resistance to estrogen receptor (ER) targeted therapy in ER+ metastatic breast cancer

scientific article published on 28 July 2020

Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to estrogen receptor-directed therapies

scientific article published on 10 December 2018

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

scientific article

Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing

scientific article published on 01 December 2020

An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets

scientific article published on 01 November 2020

An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling

scientific article

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

scientific article published on 18 July 2019

An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

scientific article

Anatomically and Functionally Distinct Lung Mesenchymal Populations Marked by Lgr5 and Lgr6.

scientific article published on September 2017

Antigen dominance hierarchies shape TCF1+ progenitor CD8 T cell phenotypes in tumors

scientific article published on 16 September 2021

Application of a stochastic name-passing calculus to representation and simulation of molecular processes

article

Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

scientific article

Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

scientific article published on 25 June 2020

Author Correction: Comprehensive comparative analysis of 5'-end RNA-sequencing methods

scientific article published on 01 December 2018

Author Correction: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

scientific article published on 13 August 2020

Author Correction: Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

scientific article published on 19 June 2020

Author Correction: Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

scientific article published on 02 November 2020

Author Correction: Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

scientific article published on 27 April 2020

Automatic genome-wide reconstruction of phylogenetic gene trees

scientific article published in July 2007

B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV

scientific article published on 24 April 2021

BRNI: Modular analysis of transcriptional regulatory programs

scientific article

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization.

scientific article published on 3 July 2018

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

scientific article published on 06 April 2020

BioAmbients: an abstraction for biological compartments

article

Blood and immune development in human fetal bone marrow and Down syndrome

scientific article published on 29 September 2021

Building a high-quality Human Cell Atlas ⬇️

journal article from 'Nature Biotechnology' published in 2021

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

scientific article

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity

scientific article

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq

scientific article published on 28 April 2016

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets ⬇️

journal article from 'Nature' published in 2021

Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses

scientific article published on 08 October 2019

Cell Atlas of The Human Fovea and Peripheral Retina

scientific article published on 17 June 2020

Cell Atlases as Roadmaps in Health and Disease

scientific article published on 01 January 2020

Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis

scientific article published on 27 April 2020

Cell type ontologies of the Human Cell Atlas

peer-reviewed article published in November 2021

Cell types and ontologies of the Human Cell Atlas ⬇️

journal article published in 2021

Cells as computation

scientific article published on September 2002

Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver

scientific article

Checkpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1-CD8+ Tumor-Infiltrating T Cells

scientific article published on 08 January 2019

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

scientific article published on 20 October 2020

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.

scientific article

Chromatin signature of embryonic pluripotency is established during genome activation

scientific article published on 24 March 2010

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

scientific article (publication date: 12 March 2009)

Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing

scientific article published on 27 January 2022

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

scientific article published in December 2011

Combinatorial prediction of marker panels from single-cell transcriptomic data

scientific article published on 01 October 2019

Common genetic variants modulate pathogen-sensing responses in human dendritic cells

scientific article

Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis

scientific article

Comparative analysis of RNA sequencing methods for degraded or low-input samples

scientific article

Comparative analysis of gene regulatory networks: from network reconstruction to evolution

scientific article published on 03 September 2015

Comparative cellular analysis of motor cortex in human, marmoset and mouse

scientific article published on 06 October 2021

Comparative functional genomics of the fission yeasts

scientific article

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

scientific article

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

scientific article published on August 2016

Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq

scientific article published on 9 March 2018

Comprehensive comparative analysis of 5'-end RNA-sequencing methods

scholarly article by Xian Adiconis published in July 2018

Comprehensive comparative analysis of strand-specific RNA sequencing methods

scientific article

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

scientific article published on 4 February 2013

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast

scientific article

Convergent Evolution of Calcineurin Pathway Roles in Thermotolerance and Virulence in Candida glabrata

scientific article

Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML

scientific article published on April 2016

Correction: Evolutionary principles of modular gene regulation in yeasts

scientific article published on 2 July 2013

Corrigendum: Landscape of X chromosome inactivation across human tissues

scientific article published in Nature

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system

scientific article

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.

scientific article published on 6 February 2017

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

scientific article published on 27 July 2020

DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data

scientific article published in 2022

DIPG-03. EXCITATORY SYNAPSES BETWEEN PRESYNAPTIC NEURONS AND POSTSYNAPTIC GLIOMA CELLS PROMOTE DIPG PROGRESSION

scientific article published on 22 June 2018

DIPG-06. REDEFINING THE CELLULAR ARCHITECTURE OF DIFFUSE MIDLINE GLIOMAS WITH H3 K27M MUTATIONS THROUGH LARGE-SCALE SINGLE-CELL ANALYSES.

scientific article

DIPG-21. ELECTRICAL INTEGRATION OF GLIOMA INTO NEURAL CIRCUITRY

scientific article published on 23 April 2019

DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction

scientific article published on 20 June 2019

DNA methylation dynamics of the human preimplantation embryo

scientific article

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

scientific article (publication date: August 2013)

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

scientific article published on 02 December 2019

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli

scientific article published on 17 March 2013

Decoding human fetal liver haematopoiesis

scientific article published on 09 October 2019

Deconstructing transcriptional heterogeneity in pluripotent stem cells

scientific article published on December 2014

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.

scientific article published on March 2017

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces ⬇️

journal article from 'bioRxiv' published in 2019

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces

scientific article

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

scientific article published on 28 October 2021

Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram ⬇️

webpage

Densely interconnected transcriptional circuits control cell states in human hematopoiesis

scientific article

Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations

scientific article published on 15 July 2010

Development and evaluation of RNA-seq methods

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

scientific article published in April 2018

Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps

scientific article published on 14 December 2021

Digital transcriptome profiling from attomole-level RNA samples

scientific article

Disease-associated astrocytes in Alzheimer's disease and aging

scientific article published on 27 April 2020

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

scientific article published on April 2016

Dissecting timing variability in yeast meiosis

scientific article published in November 2007

Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1

scientific article published on 26 August 2019

Distinct physiological states of Plasmodium falciparum in malaria-infected patients

scientific article

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

scientific article

Dynamic regulatory network controlling TH17 cell differentiation

scientific article published on 6 March 2013

Dynamic single-cell imaging of direct reprogramming reveals an early specifying event

scientific article

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

scientific article published on 18 February 2016

Efficient Generation of Transcriptomic Profiles by Random Composite Measurements

scientific article

Efficient prevalence estimation and infected sample identification with group testing for SARS-CoV-2

scientific article published on 06 May 2020

Electrical and synaptic integration of glioma into neural circuits

scientific article published on 18 September 2019

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution

scientific article published on 08 July 2020

Endogenous Glucocorticoid Signaling Regulates CD8+ T Cell Differentiation and Development of Dysfunction in the Tumor Microenvironment

scientific article published on 01 September 2020

Enforcement of developmental lineage specificity by transcription factor Oct1.

scientific article

Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma

scientific article published on 07 July 2020

Erratum: Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

scholarly article published in Nature Biotechnology

Erratum: Deconstructing transcriptional heterogeneity in pluripotent stem cells

scientific article published in Nature

Erratum: The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation

scientific article published on 15 November 2017

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

scientific article published in April 2020

Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

scientific article published on 2 February 2016

Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

scientific article

Evolutionary principles of modular gene regulation in yeasts ⬇️

scientific article published on June 18, 2013

Extracellular Vesicle Isolation and Analysis by Western Blotting

scientific article published in January 2017

Fas Promotes T Helper 17 Cell Differentiation and Inhibits T Helper 1 Cell Development by Binding and Sequestering Transcription Factor STAT1

scientific article published on 01 March 2018

From elements to modules: regulatory evolution in Ascomycota fungi

scientific article published on 29 October 2009

From signatures to models: understanding cancer using microarrays

scientific article

Full-length transcriptome assembly from RNA-Seq data without a reference genome

scientific article

Fungal regulatory evolution: cis and trans in the balance

scientific article

GeNets: a unified web platform for network-based genomic analyses.

scientific article

Gene duplication and the evolution of ribosomal protein gene regulation in yeast

scientific article

Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing.

scientific article

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of transcripts under balancing selection

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

scientific article published on 09 July 2018

Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation.

scientific article published on 25 May 2018

Genome-wide identification and characterization of replication origins by deep sequencing

scientific article

Geometry-dependent functional changes in iPSC-derived cardiomyocytes probed by functional imaging and RNA sequencing

scientific article

Germline copy number variation associated with Mendelian inheritance of CLL in two families

scientific article published on 7 February 2012

HG-110SINGLE-CELL TRANSCRIPTOME ANALYSIS IN PEDIATRIC HEMISPHERIC AND MIDLINE HIGH-GRADE GLIOMAS.

scientific article published on 30 May 2016

Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli Are Altered with Age

scientific article published on 01 December 2018

High-definition spatial transcriptomics for in situ tissue profiling

scientific article published on 09 September 2019

High-resolution interrogation of functional elements in the noncoding genome

scientific article

High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis

scientific article

High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

scientific article

High-resolution view of the yeast meiotic program revealed by ribosome profiling

scientific article

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

scientific article

Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells

scientific article published on 22 January 2020

IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment

scientific article

IL-33 Signaling Alters Regulatory T Cell Diversity in Support of Tumor Development

scientific article published on 01 December 2019

ISMB 2003 BioPathways SIG and 5th BioPathways Meeting

scientific article

Identification of transcriptional regulators in the mouse immune system

scientific article

Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics

scientific article

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics

scientific article published on 29 September 2022

Imaging of Isolated Extracellular Vesicles Using Fluorescence Microscopy

scientific article published in January 2017

ImmVar project: Insights and design considerations for future studies of "healthy" immune variation

scientific article published on February 2015

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens

scientific article published on 12 February 2015

Impulse Control: Temporal Dynamics in Gene Transcription ⬇️

scientific article published on March 18, 2011

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

scientific article published on 01 November 2020

In vivo profiles in malaria are consistent with a novel physiological state

scientific article published in July 2009

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

scientific article published on 05 June 2019

Induction and molecular signature of pathogenic TH17 cells

scientific article

Induction and transcriptional regulation of the co-inhibitory gene module in T cells

scientific article published in Nature

Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1

scientific journal article

Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies

scientific article published on May 2017

Inferring quantitative models of regulatory networks from expression data

scientific article

Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers

scientific article published on 25 March 2019

Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells

scientific article published on 14 October 2020

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

scientific article published on 15 February 2021

Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma

scientific article published on 01 September 2020

Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes

scientific article published on 13 April 2020

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

scientific article (publication date: 15 September 2011)

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

scientific article published on 18 January 2016

Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia

scientific article published on 23 May 2012

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

scientific article published on 02 December 2019

Intersection of population variation and autoimmunity genetics in human T cell activation

scientific article published on September 2014

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

scientific article published on 01 July 2019

Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair-Deficient Colorectal Cancer

scientific article published on 19 June 2019

Joint single-cell measurements of nuclear proteins and RNA in vivo

scientific article published on 04 October 2021

Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet

scientific article published on 01 August 2019

Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics: Supplemental Tables

LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding

scientific article published on 29 June 2021

LAMP-Seq: Population-Scale COVID-19 Diagnostics Using a Compressed Barcode Space

scientific article published on 08 April 2020

LGG-05. SINGLE CELL RNA SEQUENCING REVEALS MITOGENIC AND PROGENITOR GENE PROGRAMS IN BRAF-REARRANGED PILOCYTIC ASTROCYTOMAS

scientific article published on 23 April 2019

LGG-13. RESOLVING TRANSCRIPTIONAL PROFILES IN BRAF-REARRANGED PILOCYTIC ASTROCYTOMA USING SINGLE CELL RNA SEQUENCING

scientific article published on 22 June 2018

Landscape of X chromosome inactivation across human tissues

scientific article published on October 2017

Landscape of X chromosome inactivation across human tissues

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

scientific article published on 28 February 2019

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

scientific article

Longitudinal single cell profiling of regulatory T cells identifies IL-33 as a driver of tumor immunosuppression

MAUDE: Inferring expression changes in sorting-based CRISPR screens

scientific article

MAUDE: inferring expression changes in sorting-based CRISPR screens

scientific article published on 03 June 2020

MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

scientific article published on 25 November 2021

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

scientific article

Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins

scientific article published on 19 December 2015

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

scientific article published on 12 August 2020

Massively parallel single-nucleus RNA-seq with DroNc-seq

scientific article published on 28 August 2017

MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis

scientific article (publication date: 31 January 2012)

Metabolic Network Analysis Demystified

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

scientific article

Minreg: inferring an active regulator set.

scientific article

Mitochondrial dysfunction remodels one-carbon metabolism in human cells

scientific article

Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells

scientific article published on 19 August 2019

Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina

scientific article published on 31 January 2019

Molecular analysis of transitional cell carcinoma using cDNA microarray

scientific article

Molecular logic of cellular diversification in the mouse cerebral cortex

scientific article published on 23 June 2021

Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region

scientific article published in Science

Mouse ooplasm confers context-specific reprogramming capacity

scientific article

Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

scientific article published on 27 August 2020

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

scientific article

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

scientific article

Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia

scientific article published on 3 December 2012

Natural history and evolutionary principles of gene duplication in fungi

scientific article

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

scientific article published on 19 December 2018

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

scientific article published on 02 July 2019

Nucleic acid detection with CRISPR-Cas13a/C2c2

scientific article

Oct1 and OCA-B are selectively required for CD4 memory T cell function

scientific article

Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma

scientific article published on 25 January 2021

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

scientific article published on 31 January 2019

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

scientific article published on 01 March 2019

PDTM-04. REDEFINING THE CELLULAR ARCHITECTURE OF DIFFUSE MIDLINE GLIOMAS WITH H3 K27M MUTATIONS THROUGH LARGE-SCALE SINGLE-CELL ANALYSES

PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes

scientific article published on 12 June 2017

PTPS-06SINGLE-CELL TRANSCRIPTOME ANALYSIS IN PEDIATRIC HIGH-GRADE GLIOMA.

scientific article

Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity

scientific article published on 30 October 2020

Parsing the Interferon Transcriptional Network and Its Disease Associations

scientific article published on January 2016

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

scientific article

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

article

Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites

scientific article

Physical Module Networks: an integrative approach for reconstructing transcription regulation

scientific article published on July 2011

Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion

scientific article published on 12 January 2015

Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes

scientific article published on May 2014

Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing

scientific article

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

scientific article published on 06 March 2020

Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity.

scientific article published on 26 September 2016

Proto-genes and de novo gene birth

scientific article

Purifying Selection against Pathogenic Mitochondrial DNA in Human T Cells

scientific article published on 12 August 2020

Purine synthesis promotes maintenance of brain tumor initiating cells in glioma.

scientific article published on 27 March 2017

QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis

scientific article published on 01 January 2021

RBPJ Controls Development of Pathogenic Th17 Cells by Regulating IL-23 Receptor Expression

scientific article published on 22 June 2016

RNA targeting with CRISPR-Cas13.

scientific article published on 4 October 2017

RNA-Seq methods for imperfect samples: development, evaluation and applications

scientific article published on 19 September 2011

Rapid CLIP dissociation from MHC II promotes an unusual antigen presentation pathway in autoimmunity

scientific article published on 05 September 2018

Reconstructing Gene Histories in Ascomycota Fungi

scientific article published on January 1, 2010

Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells

scientific article published on 10 April 2014

Regenerative potential of prostate luminal cells revealed by single-cell analysis

scientific article published on 01 May 2020

Regulation of Cellular Heterogeneity and Rates of Symmetric and Asymmetric Divisions in Triple-Negative Breast Cancer

scientific article published on 01 September 2018

Regulation of X-linked gene expression during early mouse development by Rlim

scientific article published on 19 September 2016

Regulatory network controlling tumor-promoting inflammation in human cancers

scientific article

Reply to "Do genome-scale models need exact solvers or clearer standards?".

scientific article published on 14 October 2015

Resolving medulloblastoma cellular architecture by single-cell genomics

scientific article published on 24 July 2019

Revealing targeted therapy for human cancer by gene module maps.

scientific article

Revealing the vectors of cellular identity with single-cell genomics

scientific article published on November 2016

Revisiting the Saccharomyces cerevisiae predicted ORFeome

scientific article

Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis

scientific article published on 9 March 2018

Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs

scientific article published on 22 May 2013

SM-Omics is an automated platform for high-throughput spatial multi-omics

scientific article published on 10 February 2022

SM-Omics: An automated platform for high-throughput spatial multi-omics

scientific article

SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas ⬇️

scientific article

STEM-22LARGE-SCALE SINGLE-CELL RNA-seq REVEALS A DEVELOPMENTAL CELLULAR HIERARCHY IN HUMAN OLIGODENDROGLIOMA.

scientific article

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

scientific article published on 03 June 2021

Scaling single-cell genomics from phenomenology to mechanism

scientific article published on January 2017

Semiconductor-based DNA sequencing of histone modification states

scientific article published on January 2013

Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression

scientific article

Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer's disease

scientific article published on 30 November 2020

Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation

scientific article published on 29 November 2019

Single cell profiling of immature human postnatal thymocytes resolves the complexity of intra-thymic lineage differentiation and thymus seeding precursors ⬇️

journal article from 'bioRxiv' published in 2020

Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations

scientific article published on 31 May 2019

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

scientific article

Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes

scientific article published on 26 November 2019

Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma

scientific article published on 01 July 2020

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

scientific article

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

scientific article

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

scientific article

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

scientific article

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

scientific article

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

scientific article published on 2 November 2016

Single-cell multimodal profiling of proteins and chromatin accessibility using PHAGE-ATAC

scientific article

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

scientific article

Single-cell transcriptomic profiling of the aging mouse brain

scientific article published on 24 September 2019

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

scientific article (publication date: 13 June 2013)

Single-cell transcriptomics to explore the immune system in health and disease

scientific article

Skin-resident innate lymphoid cells converge on a pathogenic effector state

scientific article published on 03 February 2021

Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate

scientific article published on 29 November 2018

Small-molecule RORγt antagonists inhibit T helper 17 cell transcriptional network by divergent mechanisms

scientific article

Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL.

scientific article

Spatial components of molecular tissue biology

scientific article published on 07 February 2022

Spatial reconstruction of single-cell gene expression data

scientific article

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

scientific article

Strategies to discover regulatory circuits of the mammalian immune system

scientific article

Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells

scientific article published on 21 February 2019

Structure and function of a transcriptional network activated by the MAPK Hog1.

scientific article published on 19 October 2008

Systematic benchmarking of single-cell ATAC-sequencing protocols

scientific article published in 2023

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

scientific article published on 06 April 2020

Systematic discovery of TLR signaling components delineates viral-sensing circuits

scientific article

Systematic dissection of roles for chromatin regulators in a yeast stress response

scientific article

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

scientific article published on 22 November 2011

T Follicular Regulatory Cell-Derived Fibrinogen-like Protein 2 Regulates Production of Autoantibodies and Induction of Systemic Autoimmunity

scientific article published on 09 November 2020

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation

scientific article published on 01 November 2018

TIM-3 restrains anti-tumour immunity by regulating inflammasome activation

scientific article published on 09 June 2021

TMIC-09. EXCITATORY SYNAPSES BETWEEN PRESYNAPTIC NEURONS AND POSTSYNAPTIC GLIOMA CELLS PROMOTE GLIOMA PROGRESSION

scientific article published on 5 November 2018

Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution

scientific article published on October 2017

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

scientific article published on November 2017

The Human Cell Atlas

scientific article

The Human Cell Atlas

The Human Cell Atlas White Paper ⬇️

journal article from 'arXiv:1810.05192 [q-bio]' published in 2018

The Human Cell Atlas: from vision to reality

scientific article published in October 2017

The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease

scientific article published on 01 July 2019

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

scientific article published on 01 April 2020

The Human and Mouse Enteric Nervous System at Single-Cell Resolution

scientific article published on 21 August 2020

The MicroRNA-132 and MicroRNA-212 Cluster Regulates Hematopoietic Stem Cell Maintenance and Survival with Age by Buffering FOXO3 Expression

scientific article published on June 2015

The Organoid Cell Atlas

scientific article

The Organoid Cell Atlas: A Rosetta Stone for Biomedical Discovery and Regenerative Therapy ⬇️

journal article published in 2020

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution

scientific article published on 28 March 2019

The Taste Receptor TAS1R3 Regulates Small Intestinal Tuft Cell Homeostasis

scientific article published on 24 January 2020

The evolution of drug resistance in clinical isolates of Candida albicans

scientific article

The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism

scientific article

The microbiota regulate neuronal function and fear extinction learning

scientific article published on 23 October 2019

The network effect: studying COVID-19 pathology with the Human Cell Atlas

scientific article published on 30 June 2020

The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation.

scientific article published on 13 September 2017

The role of nucleosome positioning in the evolution of gene regulation

scientific article

The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells

scientific article published on 02 March 2014

The transcriptional landscape of αβ T cell differentiation

scientific article

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

scientific article

Toward a Common Coordinate Framework for the Human Body

scientific article published on 01 December 2019

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses

scientific article published on 01 October 2019

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis

scientific article published on 01 June 2019

Transcriptional mediators of treatment resistance in lethal prostate cancer

scientific article published on 04 March 2021

Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters

scientific article

Transcriptional regulatory circuits: predicting numbers from alphabets

scientific article

Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells

scientific article published on 15 August 2013

Transcriptome-scale RNase-footprinting of RNA-protein complexes

scientific article published on 22 February 2016

Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.

scientific article

Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses

scientific article

Voices of biotech

scientific article published on March 2016

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

scientific article

YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

scientific article

lincRNAs act in the circuitry controlling pluripotency and differentiation

scientific article (publication date: 28 August 2011)

scSVA: an interactive tool for big data visualization and exploration in single-cell omics

scholarly article published 6 January 2019

snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis

scientific article published on 28 October 2020

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