Hemberg, Martin

Widespread transcription at neuronal activity-regulated enhancers

Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature

Genomics and Chromatin DynamicsCancer-related molecular mechanisms research

Cited by 2,450

SC3: consensus clustering of single-cell RNA-seq data

Kiselev, V. Y., Kirschner, K., Schaub, M. T., Andrews, T., Yiu, A., Chandra, T., Natarajan, K. N., Reik, W., Barahona, M., Green, A. R., et al. (2017) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,500

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

Mathys, H., Adaikkan, C., Gao, F., Young, J. Z., Manet, E., Hemberg, M., De Jager, P. L., Ransohoff, R. M., Regev, A., & Tsai, L.-H. (2017) · Cell Reports

Neuroinflammation and Neurodegeneration MechanismsSingle-cell and spatial transcriptomics

Cited by 740

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

Gabel, H. W., Kinde, B., Stroud, H., Gilbert, C. S., Harmin, D. A., Kastan, N. R., Hemberg, M., Ebert, D. H., & Greenberg, M. E. (2015) · Nature

Genetics and Neurodevelopmental DisordersEpigenetics and DNA Methylation

Cited by 569

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

Heaton, H., Talman, A. M., Knights, A., Imaz, M., Gaffney, D. J., Durbin, R., Hemberg, M., & Lawniczak, M. K. N. (2020) · Nature Methods

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 506

Tau promotes neurodegeneration through global chromatin relaxation

Frost, B., Hemberg, M., Lewis, J., & Feany, M. B. (2014) · Nature Neuroscience

Alzheimer's disease research and treatmentsGenomics and Chromatin Dynamics

Cited by 495

Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

Bayraktar, O. A., Bartels, T., Holmqvist, S., Kleshchevnikov, V., Martirosyan, A., Polioudakis, D., Ben Haim, L., Young, A. M. H., Batiuk, M. Y., Prakash, K., et al. (2020) · Nature Neuroscience

Single-cell and spatial transcriptomicsNeurogenesis and neuroplasticity mechanisms

Cited by 489

Genome-Wide Analysis of MEF2 Transcriptional Program Reveals Synaptic Target Genes and Neuronal Activity-Dependent Polyadenylation Site Selection

Flavell, S. W., Kim, T.-K., Gray, J. M., Harmin, D. A., Hemberg, M., Hong, E. J., Markenscoff-Papadimitriou, E., Bear, D. M., & Greenberg, M. E. (2008) · Neuron

Genetics and Neurodevelopmental DisordersNeuroscience and Neuropharmacology Research

Cited by 440

Genome-Wide Activity-Dependent MeCP2 Phosphorylation Regulates Nervous System Development and Function

Cohen, S., Gabel, H. W., Hemberg, M., Hutchinson, A. N., Sadacca, L. A., Ebert, D. H., Harmin, D. A., Greenberg, R. S., Verdine, V. K., Zhou, Z., et al. (2011) · Neuron

Genetics and Neurodevelopmental DisordersNeuroscience and Neuropharmacology Research

Cited by 298

High-throughput functional comparison of promoter and enhancer activities

Nguyen, T. A., Jones, R. D., Snavely, A. R., Pfenning, A. R., Kirchner, R., Hemberg, M., & Gray, J. M. (2016) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 146

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

Georgakopoulos-Soares, I., Morganella, S., Jain, N., Hemberg, M., & Nik-Zainal, S. (2018) · Genome Research

Cancer Genomics and DiagnosticsDNA and Nucleic Acid Chemistry

Cited by 146

False signals induced by single-cell imputation

Andrews, T. S., & Hemberg, M. (2018) · F1000Research

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 142

Bhlhb5 and Prdm8 form a repressor complex involved in neuronal circuit assembly

Ross, S. E., McCord, A. E., Jung, C., Atan, D., Mok, S. I., Hemberg, M., Kim, T.-K., Salogiannis, J., Hu, L., Cohen, S., et al. (2012) · Neuron

Neurogenesis and neuroplasticity mechanismsDevelopmental Biology and Gene Regulation

Cited by 137

Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data

Delmans, M., & Hemberg, M. (2016) · BMC Bioinformatics

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 111

Discrete Distributional Differential Expression (D 3 E) - A Tool for Gene Expression Analysis of Single-cell RNA-seq Data

Delmans, M., & Hemberg, M. (2015) · BMC Bioinformatics

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 111

Extensive remodeling of the extracellular matrix during aging contributes to age-dependent impairments of muscle stem cell functionality

Schüler, S. C., Kirkpatrick, J. M., Schmidt, M., Santinha, D., Koch, P., Di Sanzo, S., Cirri, E., Hemberg, M., Ori, A., & von Maltzahn, J. (2021) · Cell Reports

Muscle Physiology and DisordersMuscle metabolism and nutrition

Cited by 106

Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench

Chazarra-Gil, R., van Dongen, S., Kiselev, V. Y., & Hemberg, M. (2021) · Nucleic Acids Research

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 93

Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Neavin, D., Senabouth, A., Arora, H., Lee, J. T. H., Ripoll-Cladellas, A., sc-eQTLGen Consortium, Franke, L., Prabhakar, S., Ye, C. J., McCarthy, D. J., et al. (2024) · Genome Biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 90

Demuxafy : Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Neavin, D., Senabouth, A., Hang Lee, J. T., Ripoll, A., sc-eQTLGen Consortium, Franke, L., Prabhakar, S., Ye, C. J., McCarthy, D. J., Melé, M., et al. (2022) · Genome biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 90