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Circulating Cytokines Predict Immune-Related Toxicity in Melanoma Patients Receiving Anti-PD-1-Based Immunotherapy

Clinical cancer research, 2019-03, Vol.25 (5), p.1557-1563

2019

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Investigating higher-order interactions in single-cell data with scHOT

Nature methods, 2020-08, Vol.17 (8), p.799-806

2020

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Toward a Common Coordinate Framework for the Human Body

Cell, 2019-12, Vol.179 (7), p.1455-1467

2019

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scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

Proceedings of the National Academy of Sciences - PNAS, 2019-05, Vol.116 (20), p.9775-9784

2019

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Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation

Genome Biology, 2021-07, Vol.22 (1), p.197-197, Article 197

2021

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Single-cell expression profiling has its roots in in situ techniques

Nature reviews. Genetics, 2024-10

Ghazanfar, Shila

2024

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BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data

Nature communications, 2024-01, Vol.15 (1), p.509-509, Article 509

2024

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geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq

Genome Biology, 2021-12, Vol.22 (1), p.333-333, Article 333

2021

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Tuning of delta-protocadherin adhesion through combinatorial diversity

eLife, 2018-12, Vol.7

2018

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Systematic functional identification of cancer multi-drug resistance genes

Genome Biology, 2020-02, Vol.21 (1), p.27-27, Article 27

2020

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Evaluating stably expressed genes in single cells

Gigascience, 2019-09, Vol.8 (9)

2019

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Thinking process templates for constructing data stories with SCDNEY [version 2; peer review: 1 approved, 1 approved with reservations]

F1000 research, 2023, Vol.12, p.261-261

2023

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Clonal evolution in liver cancer at single-cell and single-variant resolution

Journal of hematology and oncology, 2021-02, Vol.14 (1), p.22-22, Article 22

2021

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Thinking process templates for constructing data stories with SCDNEY [version 1; peer review: 1 approved, 1 approved with reservations]

F1000 research, 2023, Vol.12, p.261

2023

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Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis

PloS one, 2017-06, Vol.12 (6), p.e0180378-e0180378

2017

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Genome-wide analysis in Drosophila reveals diet-by-gene interactions and uncovers diet-responsive genes

G3 : genes - genomes - genetics, 2021-10, Vol.11 (10)

2021

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Stabilized mosaic single-cell data integration using unshared features

Nature biotechnology, 2024-02, Vol.42 (2), p.284-292

2024

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Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data

Briefings in bioinformatics, 2023-05, Vol.24 (3)

2023

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MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor

Bioinformatics (Oxford, England), 2023-09, Vol.39 (9)

2023

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The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Nature (London), 2019-10, Vol.574 (7777), p.187-192

2019

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SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

Bioinformatics, 2022-05, Vol.38 (11), p.3128-3131

2022

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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Nature medicine, 2021-03, Vol.27 (3), p.546-559

2021

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Diverse Routes toward Early Somites in the Mouse Embryo

Developmental cell, 2021-01, Vol.56 (1), p.141-153.e6

2021

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Novel Mouse Model for Selective Tagging, Purification, and Manipulation of Cardiac Myofibroblasts

Circulation (New York, N.Y.), 2024-06, Vol.149 (24), p.1931-1934

2024

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Characterizing mutation–expression network relationships in multiple cancers

Computational biology and chemistry, 2016-08, Vol.63, p.73-82

2016

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Circulating Cytokines Predict Immune-Related Toxicity in Melanoma Patients Receiving Anti-PD-1-Based Immunotherapy

Investigating higher-order interactions in single-cell data with scHOT

Toward a Common Coordinate Framework for the Human Body

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation

Single-cell expression profiling has its roots in in situ techniques

BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq

Tuning of delta-protocadherin adhesion through combinatorial diversity

Systematic functional identification of cancer multi-drug resistance genes

Evaluating stably expressed genes in single cells

Thinking process templates for constructing data stories with SCDNEY [version 2; peer review: 1 approved, 1 approved with reservations]

Clonal evolution in liver cancer at single-cell and single-variant resolution

Thinking process templates for constructing data stories with SCDNEY [version 1; peer review: 1 approved, 1 approved with reservations]

Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis

Genome-wide analysis in Drosophila reveals diet-by-gene interactions and uncovers diet-responsive genes

Stabilized mosaic single-cell data integration using unshared features

Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data

MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Diverse Routes toward Early Somites in the Mouse Embryo

Novel Mouse Model for Selective Tagging, Purification, and Manipulation of Cardiac Myofibroblasts

Characterizing mutation–expression network relationships in multiple cancers

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