Rinn, John L.

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 7,314

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature

Cancer-related molecular mechanisms researchGenomics and Chromatin Dynamics

Cited by 4,098

The multilayered complexity of ceRNA crosstalk and competition

Tay, Y., Rinn, J., & Pandolfi, P. P. (2014) · Nature

Cancer-related molecular mechanisms researchMicroRNA in disease regulation

Cited by 3,910

Differential analysis of gene regulation at transcript resolution with RNA-seq

Trapnell, C., Hendrickson, D. G., Sauvageau, M., Goff, L., Rinn, J. L., & Pachter, L. (2013) · Nature Biotechnology

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 3,492

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., et al. (2009) · Proceedings of the National Academy of Sciences

Cancer-related molecular mechanisms researchGenomics and Chromatin Dynamics

Cited by 2,872

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M. J., Kenzelmann-Broz, D., Khalil, A. M., Zuk, O., Amit, I., Rabani, M., et al. (2010) · Cell

Cancer-related molecular mechanisms researchCancer-related Molecular Pathways

Cited by 2,053

Improving RNA-Seq expression estimates by correcting for fragment bias

Roberts, A., Trapnell, C., Donaghey, J., Rinn, J. L., & Pachter, L. (2011) · Genome Biology

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 1,725

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

Guttman, M., Garber, M., Levin, J. Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M. J., Gnirke, A., Nusbaum, C., et al. (2010) · Nature Biotechnology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 1,253

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

Kelley, D. R., Snoek, J., & Rinn, J. L. (2016) · Genome Research

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 1,048

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

Kelley, D., & Rinn, J. (2012) · Genome Biology

Chromosomal and Genetic VariationsCancer-related molecular mechanisms research

Cited by 531

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

Amit, I., Garber, M., Chevrier, N., Leite, A. P., Donner, Y., Eisenhaure, T., Guttman, M., Grenier, J. K., Li, W., Zuk, O., et al. (2009) · Science

Gene Regulatory Network AnalysisGenomics and Chromatin Dynamics

Cited by 488

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

Gifford, C. A., Ziller, M. J., Gu, H., Trapnell, C., Donaghey, J., Tsankov, A., Shalek, A. K., Kelley, D. R., Shishkin, A. A., Issner, R., et al. (2013) · Cell

Pluripotent Stem Cells ResearchEpigenetics and DNA Methylation

Cited by 435

Identifying Recent Adaptations in Large-Scale Genomic Data

Grossman, S. R., Andersen, K. G., Shlyakhter, I., Tabrizi, S., Winnicki, S., Yen, A., Park, D. J., Griesemer, D., Karlsson, E. K., Wong, S. H., et al. (2013) · Cell

Genetic Associations and EpidemiologyEvolution and Genetic Dynamics

Cited by 368

Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs

O'Geen, H., Squazzo, S. L., Iyengar, S., Blahnik, K., Rinn, J. L., Chang, H. Y., Green, R., & Farnham, P. J. (2007) · PLoS Genetics

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 178

DNA methylation and epigenetic control of cellular differentiation

Khavari, D. A., Sen, G. L., & Rinn, J. L. (2010) · Cell Cycle

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 135

Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage

Younger, S. T., Kenzelmann-Broz, D., Jung, H., Attardi, L. D., & Rinn, J. L. (2015) · Nucleic Acids Research

Cancer-related Molecular PathwaysGenomics and Chromatin Dynamics

Cited by 99

RNA-seq as a tool for evaluating human embryo competence

Groff, A. F., Resetkova, N., DiDomenico, F., Sakkas, D., Penzias, A., Rinn, J. L., & Eggan, K. (2019) · Genome Research

Reproductive Biology and FertilityPrenatal Screening and Diagnostics

Cited by 47

Biophysical characterization of high-confidence, small human proteins

Whited, A. M., Jungreis, I., Allen, J., Cleveland, C., Mudge, J. M., Kellis, M., Rinn, J., & Hough, L. E. (2024) · Biophysical Reports

Protein Structure and DynamicsGenomics and Phylogenetic Studies

Cited by 5

Biophysical characterization of high-confidence, small human proteins

Whited, A. M., Jungreis, I., Allen, J., Cleveland, C. L., Mudge, J. M., Kellis, M., Rinn, J. L., & Hough, L. E. (2024) · Biophysical Reports

Protein Structure and DynamicsGenomics and Phylogenetic Studies

Cited by 5