A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery
Biology
Cancer
Genomics
Immunology
R&D
Technology
Alex K. Shalek
Vitrification preserves murine ovarian follicular cell transcriptome in a 3D encapsulated in vitro follicle growth system
BiologyGenomicsImmunologyR&DTechnology
Riley Drake
Daniela RussoAlex K. Shalek
Brittany Goods
Compressed phenotypic screens for complex multicellular models and high-content assays
BiologyCancer
Chemistry
Computational MethodsGenomicsR&D
StatisticsTechnology
Ben Mead
Conner Kummerlowe
Ivy Liu
Walaa Kattan
Thomas Nok Hin Cheng
Peter WinterAlex K. Shalek
Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation
BiologyComputational MethodsGenomicsImmunology
MedicineR&DTechnologyBen Mead
Marko VukovicConner Kummerlowe
José Ordovas-MontañesAlex K. Shalek
Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity
Biology
Cell AtlasComputational MethodsGenomicsImmunology
Infectious DiseaseR&DTechnology
Alex Genshaft
Mike VilmeRiley Drake
Ira Fleming
Nancy Tran
Constantine Tzouanas
Jasmin Joseph-ChazanAlex K. Shalek
Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip
BiologyGenomicsImmunologyInfectious DiseaseMedicineR&DTechnology
Vincent Miao
Andrew Navia
Carly ZieglerJosé Ordovas-MontañesAlex K. Shalek
Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice
BiologyCancerGenomicsImmunology
PhysicsR&DTechnology
Nolawit MulugetaAlex K. Shalek
Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes
GenomicsR&DTechnologyAlex GenshaftCarly ZieglerConstantine TzouanasBen MeadAndrew NaviaAlex K. Shalek
Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
BiologyCell AtlasChemistryGenomicsImmunologyR&DTechnology
Travis Hughes
Marc Wadsworth IIJosé Ordovas-MontañesAlex K. Shalek
High-throughput organoid screening enables engineering of intestinal epithelial composition
BiologyGenomicsMedicineR&DTechnologyBen MeadMarko VukovicJosé Ordovas-MontañesAlex K. Shalek
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
Computational MethodsGenomicsR&DTechnologyTravis HughesMarc Wadsworth II
Shaina CarrollAlex K. Shalek
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
BiologyCancerChemistryGenomicsR&DTechnologyAlex GenshaftCarly ZieglerConstantine TzouanasBen MeadAndrew NaviaAlex K. Shalek
TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
BiologyCell AtlasGenomicsImmunologyR&DTechnologyAlex K. Shalek
Voices in methods development
Computational MethodsGenomicsR&DTechnologyAlex K. Shalek
Highly efficient, massively-parallel single-cell RNA-Seq reveals cellular states and molecular features of human skin pathology
BiologyGenomicsImmunologyR&DTechnologyTravis HughesMarc Wadsworth IIJosé Ordovas-MontañesAlex K. ShalekSeq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing
R&DTechnology
Toby AicherShaina CarrollMarc Wadsworth IITravis HughesAlex K. Shalek
Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
Marc Wadsworth IITravis HughesAlex K. Shalek
Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer
BiologyCancerComputational MethodsR&DTechnology
Jay PrakadanAndrew NaviaPeter WinterRiley Drake
Alejandro GuptaAlex K. Shalek
Linking single-cell measurements of mass, growth rate, and gene expression
BiologyCancerGenomicsPhysicsR&DTechnologyJay PrakadanAlejandro GuptaRiley DrakeAlex K. Shalek
Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
Ben MeadJosé Ordovas-MontañesTravis HughesMarc Wadsworth IIAlex K. Shalek
Linking single-cell measurements of mass, growth rate, and gene expression
ChemistryGenomicsTechnologyJay PrakadanAlejandro GuptaRiley DrakeAlex K. Shalek
Scaling by shrinking: empowering single-cell ‘omics’ with microfluidic devices
GenomicsTechnologyJay PrakadanAlex K. Shalek
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
ChemistryGenomicsR&DTechnology
TravelMarc Wadsworth IITravis HughesAlex K. Shalek
Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
BiologyChemistryGenomicsR&DTechnologyAlex GenshaftJay PrakadanCarly ZieglerAlex K. Shalek
Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM
ChemistryGenomicsTechnology
Sam Kazer
Aleth GaillardAlex K. Shalek
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
BiologyGenomicsImmunologyR&DTechnologyAlex GenshaftSam KazerAlex K. Shalek
Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics
GenomicsR&DTechnologyMarc Wadsworth IITravis HughesAlex K. Shalek
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
GenomicsR&DTechnologyAlex K. Shalek
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing
R&DTechnologyAlex K. Shalek
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
BiologyGenomicsImmunologyAlex K. Shalek
Probing Enzymatic Activity inside Living Cells Using a Nanowire−Cell “Sandwich” Assay
BiologyChemistryImmunologyTechnologyAlex K. Shalek
Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia
CancerGenomicsR&DTechnologyAlex K. Shalek
Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits
BiologyChemistryTechnologyAlex K. Shalek
Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells
ChemistryGenomicsPhysicsR&DTechnologyAlex K. Shalek
Photoinduced Interfacial Charging and “Explosion” of Monolayer Pentacene Islands
ChemistryPhysicsR&DTechnologyAlex K. Shalek