Kharchenko, Peter V.

RNA velocity of single cells

La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M. E., Lönnerberg, P., Furlan, A., et al. (2018) · Nature

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 4,118

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

Usoskin, D., Furlan, A., Islam, S., Abdo, H., Lönnerberg, P., Lou, D., Hjerling-Leffler, J., Haeggström, J., Kharchenko, O., Kharchenko, P. V., et al. (2015) · Nature Neuroscience

Single-cell and spatial transcriptomicsIon Channels and Receptors

Cited by 2,136

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 2,033

Bayesian approach to single-cell differential expression analysis

Kharchenko, P. V., Silberstein, L., & Scadden, D. T. (2014) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,348

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

Lake, B. B., Chen, S., Sos, B. C., Fan, J., Kaeser, G. E., Yung, Y. C., Duong, T. E., Gao, D., Chun, J., Kharchenko, P. V., et al. (2018) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 983

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., et al. (2021) · Nature

Single-cell and spatial transcriptomicsNeuroscience and Neuropharmacology Research

Cited by 812

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., et al. (2020) · Nature

Single-cell and spatial transcriptomicsNeuroscience and Neuropharmacology Research

Cited by 809

Landscape of Somatic Retrotransposition in Human Cancers

Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, L. J., Lohr, J. G., Harris, C. C., Ding, L., Wilson, R. K., et al. (2012) · Science

Chromosomal and Genetic VariationsGenomic variations and chromosomal abnormalities

Cited by 762

Spatiotemporal structure of cell fate decisions in murine neural crest

Soldatov, R., Kaucka, M., Kastriti, M. E., Petersen, J., Chontorotzea, T., Englmaier, L., Akkuratova, N., Yang, Y., Häring, M., Dyachuk, V., et al. (2019) · Science

Developmental Biology and Gene RegulationSingle-cell and spatial transcriptomics

Cited by 546

A multimodal cell census and atlas of the mammalian primary motor cortex

BRAIN Initiative Cell Census Network (BICCN), BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, Callaway, E. M., Dong, H.-W., Ecker, J. R., Hawrylycz, M. J., Huang, Z. J., Lein, E. S., Ngai, J., Osten, P., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 522

Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2

Specht, H., Emmott, E., Petelski, A. A., Huffman, R. G., Perlman, D. H., Serra, M., Kharchenko, P., Koller, A., & Slavov, N. (2021) · Genome Biology

Advanced Proteomics Techniques and ApplicationsSingle-cell and spatial transcriptomics

Cited by 493

Cell segmentation in imaging-based spatial transcriptomics

Petukhov, V., Xu, R. J., Soldatov, R. A., Cadinu, P., Khodosevich, K., Moffitt, J. R., & Kharchenko, P. V. (2022) · Nature Biotechnology

Single-cell and spatial transcriptomicsCell Image Analysis Techniques

Cited by 412

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., et al. (2021) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 398

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

Yao, Z., Liu, H., Xie, F., Fischer, S., Booeshaghi, A. S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Pinto-Duarte, A., Bartlett, A., et al. (2020) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 397

Comparative analysis of metazoan chromatin organization

Ho, J. W. K., Jung, Y. L., Liu, T., Alver, B. H., Lee, S., Ikegami, K., Sohn, K.-A., Minoda, A., Tolstorukov, M. Y., Appert, A., et al. (2014) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 390

Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin

Masuda, T., Wang, X., Maeda, M., Canver, M. C., Sher, F., Funnell, A. P. W., Fisher, C., Suciu, M., Martyn, G. E., Norton, L. J., et al. (2016) · Science

Hemoglobinopathies and Related DisordersHemoglobin structure and function

Cited by 373

The triumphs and limitations of computational methods for scRNA-seq

Kharchenko, P. V. (2021) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 321

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

Barkas, N., Petukhov, V., Nikolaeva, D., Lozinsky, Y., Demharter, S., Khodosevich, K., & Kharchenko, P. V. (2019) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 292

A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA

Lake, B. B., Codeluppi, S., Yung, Y. C., Gao, D., Chun, J., Kharchenko, P. V., Linnarsson, S., & Zhang, K. (2017) · Scientific Reports

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 271

RNA velocity—current challenges and future perspectives

Bergen, V., Soldatov, R. A., Kharchenko, P. V., & Theis, F. J. (2021) · Molecular Systems Biology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 271

Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions

Girskis, K. M., Stergachis, A. B., DeGennaro, E. M., Doan, R. N., Qian, X., Johnson, M. B., Wang, P. P., Sejourne, G. M., Nagy, M. A., Pollina, E. A., et al. (2021) · Neuron

Genomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

Cited by 193

Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer

Bersani, F., Lee, E., Kharchenko, P. V., Xu, A. W., Liu, M., Xega, K., MacKenzie, O. C., Brannigan, B. W., Wittner, B. S., Jung, H., et al. (2015) · Proceedings of the National Academy of Sciences

Chromosomal and Genetic VariationsGenomic variations and chromosomal abnormalities

Cited by 181

Influence of metabolic network structure and function on enzyme evolution

Vitkup, D., Kharchenko, P., & Wagner, A. (2006) · Genome biology

Bioinformatics and Genomic NetworksMicrobial Metabolic Engineering and Bioproduction

Cited by 175

Liver stromal cells restrict macrophage maturation and stromal IL-6 limits the differentiation of cirrhosis-linked macrophages

Buonomo, E. L., Mei, S., Guinn, S. R., Leo, I. R., Peluso, M. J., Nolan, M.-A., Schildberg, F. A., Zhao, L., Lian, C., Xu, S., et al. (2022) · Journal of Hepatology

Liver physiology and pathologyLiver Disease and Transplantation

Cited by 57