Pellegrini, Matteo

Detecting Protein Function and Protein-Protein Interactions from Genome Sequences

Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W., Yeates, T. O., & Eisenberg, D. (1999) · Science

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 1,670

Conservation and divergence of methylation patterning in plants and animals

Feng, S., Cokus, S. J., Zhang, X., Chen, P.-Y., Bostick, M., Goll, M. G., Hetzel, J., Jain, J., Strauss, S. H., Halpern, M. E., et al. (2010) · Proceedings of the National Academy of Sciences

Epigenetics and DNA MethylationChromosomal and Genetic Variations

Cited by 1,285

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

Soufi, A., Garcia, M. F., Jaroszewicz, A., Osman, N., Pellegrini, M., & Zaret, K. S. (2015) · Cell

Genomics and Chromatin DynamicsPluripotent Stem Cells Research

Cited by 780

Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis

Zhang, X., Clarenz, O., Cokus, S., Bernatavichute, Y. V., Pellegrini, M., Goodrich, J., & Jacobsen, S. E. (2007) · PLoS Biology

Epigenetics and DNA MethylationPlant Molecular Biology Research

Cited by 767

Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Grasso, C. S., Giannakis, M., Wells, D. K., Hamada, T., Mu, X. J., Quist, M., Nowak, J. A., Nishihara, R., Qian, Z. R., Inamura, K., et al. (2018) · Cancer Discovery

Genetic factors in colorectal cancerCancer Immunotherapy and Biomarkers

Cited by 535

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality

Clark, R. I., Salazar, A., Yamada, R., Fitz-Gibbon, S., Morselli, M., Alcaraz, J., Rana, A., Rera, M., Pellegrini, M., Ja, W. W., et al. (2015) · Cell Reports

Genetics, Aging, and Longevity in Model OrganismsGut microbiota and health

Cited by 510

The IntAct database: efficient access to fine-grained molecular interaction data

del Toro, N., Shrivastava, A., Ragueneau, E., Meldal, B., Combe, C., Barrera, E., Perfetto, L., How, K., Ratan, P., Shirodkar, G., et al. (2022) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 405

A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas

Soragni, A., Janzen, D. M., Johnson, L. M., Lindgren, A. G., Thai-Quynh Nguyen, A., Tiourin, E., Soriaga, A. B., Lu, J., Jiang, L., Faull, K. F., et al. (2016) · Cancer Cell

Cancer-related Molecular PathwaysOvarian cancer diagnosis and treatment

Cited by 341

Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana

Bernatavichute, Y. V., Zhang, X., Cokus, S., Pellegrini, M., & Jacobsen, S. E. (2008) · PLoS ONE

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 333

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

Denholtz, M., Bonora, G., Chronis, C., Splinter, E., de Laat, W., Ernst, J., Pellegrini, M., & Plath, K. (2013) · Cell Stem Cell

Genomics and Chromatin DynamicsPluripotent Stem Cells Research

Cited by 274

ACTINN: automated identification of cell types in single cell RNA sequencing

Ma, F., & Pellegrini, M. (2020) · Bioinformatics

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 252

Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency

Sridharan, R., Gonzales-Cope, M., Chronis, C., Bonora, G., McKee, R., Huang, C., Patel, S., Lopez, D., Mishra, N., Pellegrini, M., et al. (2013) · Nature Cell Biology

Pluripotent Stem Cells ResearchEpigenetics and DNA Methylation

Cited by 220

CRISPR/Cas9-Mediated Correction of the Sickle Mutation in Human CD34+ cells

Hoban, M. D., Lumaquin, D., Kuo, C. Y., Romero, Z., Long, J., Ho, M., Young, C. S., Mojadidi, M., Fitz-Gibbon, S., Cooper, A. R., et al. (2016) · Molecular Therapy

CRISPR and Genetic EngineeringHemoglobinopathies and Related Disorders

Cited by 220

A multi-tissue full lifespan epigenetic clock for mice

Thompson, M. J., Chwiałkowska, K., Rubbi, L., Lusis, A. J., Davis, R. C., Srivastava, A., Korstanje, R., Churchill, G. A., Horvath, S., & Pellegrini, M. (2018) · Aging

Epigenetics and DNA MethylationGenetics, Aging, and Longevity in Model Organisms

Cited by 203

CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data

Guo, W., Zhu, P., Pellegrini, M., Zhang, M. Q., Wang, X., & Ni, Z. (2018) · Bioinformatics

Epigenetics and DNA MethylationGenomics and Phylogenetic Studies

Cited by 198

Glucose inhibits cardiac muscle maturation through nucleotide biosynthesis

Nakano, H., Minami, I., Braas, D., Pappoe, H., Wu, X., Sagadevan, A., Vergnes, L., Fu, K., Morselli, M., Dunham, C., et al. (2017) · eLife

Congenital heart defects researchPluripotent Stem Cells Research

Cited by 195

Stage-Specific Roles for Tet1 and Tet2 in DNA Demethylation in Primordial Germ Cells

Vincent, J. J., Huang, Y., Chen, P.-Y., Feng, S., Calvopiña, J. H., Nee, K., Lee, S. A., Le, T., Yoon, A. J., Faull, K., et al. (2013) · Cell Stem Cell

Epigenetics and DNA MethylationPluripotent Stem Cells Research

Cited by 169

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse

Morselli, M., Pastor, W. A., Montanini, B., Nee, K., Ferrari, R., Fu, K., Bonora, G., Rubbi, L., Clark, A. T., Ottonello, S., et al. (2015) · eLife

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 167

Scl Represses Cardiomyogenesis in Prospective Hemogenic Endothelium and Endocardium

Van Handel, B., Montel-Hagen, A., Sasidharan, R., Nakano, H., Ferrari, R., Boogerd, C. J., Schredelseker, J., Wang, Y., Hunter, S., Org, T., et al. (2012) · Cell

Congenital heart defects researchDevelopmental Biology and Gene Regulation

Cited by 154

Functional reprogramming of regulatory T cells in the absence of Foxp3

Charbonnier, L.-M., Cui, Y., Stephen-Victor, E., Harb, H., Lopez, D., Bleesing, J. J., Garcia-Lloret, M. I., Chen, K., Ozen, A., Carmeliet, P., et al. (2019) · Nature Immunology

T-cell and B-cell ImmunologyPsoriasis: Treatment and Pathogenesis

Cited by 145

TREM2 macrophages induced by human lipids drive inflammation in acne lesions

Do, T. H., Ma, F., Andrade, P. R., Teles, R., de Andrade Silva, B. J., Hu, C., Espinoza, A., Hsu, J.-E., Cho, C.-S., Kim, M., et al. (2022) · Science Immunology

Acne and Rosacea Treatments and EffectsDermatology and Skin Diseases

Cited by 139

DNA methylation networks underlying mammalian traits

Haghani, A., Li, C. Z., Robeck, T. R., Zhang, J., Lu, A. T., Ablaeva, J., Acosta-Rodríguez, V. A., Adams, D. M., Alagaili, A. N., Almunia, J., et al. (2023) · Science

Epigenetics and DNA MethylationGenetic Syndromes and Imprinting

Cited by 128

The effects of perinatal testosterone exposure on the DNA methylome of the mouse brain are late-emerging

Ghahramani, N. M., Ngun, T. C., Chen, P.-Y., Tian, Y., Krishnan, S., Muir, S., Rubbi, L., Arnold, A. P., de Vries, G. J., Forger, N. G., et al. (2014) · Biology of Sex Differences

Sexual Differentiation and DisordersEpigenetics and DNA Methylation

Cited by 121

let-7 miRNAs Can Act through Notch to Regulate Human Gliogenesis

Patterson, M., Gaeta, X., Loo, K., Edwards, M., Smale, S., Cinkornpumin, J., Xie, Y., Listgarten, J., Azghadi, S., Douglass, S. M., et al. (2014) · Stem Cell Reports

Neurogenesis and neuroplasticity mechanismsDevelopmental Biology and Gene Regulation

Cited by 103