Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates

Nolan J. Hoffman, Benjamin L. Parker, Rima Chaudhuri, +15

Cell Metabolism

MechanobiologyMuscle FunctionSignal TransductionSkeletal MuscleGlobal Phosphoproteomic Analysis +9

Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

Sean J. Humphrey, Guang Yang, Pengyi Yang, +4

Cell Metabolism

Ensemble deep learning in bioinformatics

Yue Cao, Thomas A. Geddes, Jean Yang, +1

Nature Machine Intelligence

EngineeringMachine LearningData ScienceComputational BiologyEnsemble Deep Learning +3

DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis

Rajneesh Pathania, Sabarish Ramachandran, Selvakumar Elangovan, +17

Nature Communications

Csc MaintenanceEpigenetic ChangeDna MethylationCancer BiologyEpigenetics +14

Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors

Andrew J. Oldfield, Pengyi Yang, Amanda E. Conway, +4

Molecular Cell

Histone ModificationsChromatinTranscriptional RegulationChromatin StructureChromatin Remodeling +11

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

Yingxin Lin, Shila Ghazanfar, Kevin Wang, +8

Proceedings of the National Academy of Sciences

EngineeringGeneticsPresent ScmergeMultiomicsGenomics +19

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

Brad Lackford, Chun Yao, G. M. Charles, +11

The EMBO Journal

Stem Cell BiologyTranscriptional RegulationLineage PlasticityDevelopmental BiologyMedicine +7

Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance

Daniel J. Fazakerley, Rima Chaudhuri, Pengyi Yang, +21

eLife

Muscle TissueMetabolic DisorderGeneticsMetabolic RemodelingInsulin Signaling +17

Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

Pengyi Yang, Sean J. Humphrey, Senthilkumar Cinghu, +8

Cell Systems

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference

Yingxin Lin, Yue Cao, Hani Jieun Kim, +5

Molecular Systems Biology