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

Geoffrey Schiebinger, Jian Shu, Marcin Tabaka, +15

Cell

Cell LineageDevelopmental BiologyOptimal-transport AnalysisEngineeringSingle Cell Sequencing +11

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

Charles P. Fulco, Mathias Munschauer, Rockwell Anyoha, +7

Science

BioinformaticsTranscriptional RegulationTranscription FactorsSystems BiologySystematic Mapping +13

Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion

Chris J. Frangieh, Johannes C. Melms, Pratiksha I. Thakore, +18

Nature Genetics

Tumor BiologyImmune EvasionCancer Immune EvasionOncologyCancer Immunosurveillance +9

High resolution time series reveals cohesive but short-lived communities in coastal plankton

Antonio M. Martín‐Platero, Brian Cleary, Kathryn M. Kauffman, +4

Nature Communications

EngineeringOceanographyEarth ScienceMarine EnvironmentMicrobial Ecology +14

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

Brian Cleary, Ilana Brito, Katherine Huang, +4

Nature Biotechnology

Microbial DiversityMetagenomic DatasetsLow-abundance Bacterial StrainsEigengenome PartitioningMicrobial Ecology +9

Efficient Generation of Transcriptomic Profiles by Random Composite Measurements

Brian Cleary, Le Cong, Anthea Cheung, +2

Cell

Functional GenomicsEngineeringRandom Composite MeasurementsGeneticsComputational Genomics +8

Scalable genetic screening for regulatory circuits using compressed Perturb-seq

Douglas Yao, Loïc Binan, Jon Bezney, +8

Nature Biotechnology

Convergence of coronary artery disease genes onto endothelial cell programs

Gavin R. Schnitzler, Helen Kang, Shi Fang, +24

Nature

AngiogenesisCardiovascular DiseaseNatural SciencesVascular AdaptationGene Expression +9

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

Kerstin U. Ludwig, Ricarda Maria Schmithausen, David Li, +37

Nature Biotechnology

Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming

Geoffrey Schiebinger, Jian Shu, Marcin Tabaka, +14

EngineeringDevelopmental LandscapesCell SpecializationOptimal TransportTrajectory Analysis +17