Friedman, Nir

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., et al. (2013) · Nature Protocols

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 8,464

Bayesian network classifiers

Friedman, N., Geiger, D., & Goldszmidt, M. (1997) · Machine Learning

Bayesian Modeling and Causal InferenceData Mining and Machine Learning Applications

Cited by 4,742

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

Dixit, A., Parnas, O., Li, B., Chen, J., Fulco, C. P., Jerby-Arnon, L., Marjanovic, N. D., Dionne, D., Burks, T., Raychowdhury, R., et al. (2016) · Cell

Single-cell and spatial transcriptomicsCRISPR and Genetic Engineering

Cited by 1,863

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Shalek, A. K., Satija, R., Shuga, J., Trombetta, J. J., Gennert, D., Lu, D., Chen, P., Gertner, R. S., Gaublomme, J. T., Yosef, N., et al. (2014) · Nature

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 1,000

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., Habib, N., Yosef, N., Chang, C. Y., Shay, T., et al. (2011) · Cell

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 942

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

Hsieh, T.-H. S., Weiner, A., Lajoie, B., Dekker, J., Friedman, N., & Rando, O. J. (2015) · Cell

Genomics and Chromatin DynamicsNuclear Structure and Function

Cited by 788

Chromatin state dynamics during blood formation

Lara-Astiaso, D., Weiner, A., Lorenzo-Vivas, E., Zaretsky, I., Jaitin, D. A., David, E., Keren-Shaul, H., Mildner, A., Winter, D., Jung, S., et al. (2014) · Science

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 776

Comprehensive comparative analysis of strand-specific RNA sequencing methods

Levin, J. Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D. A., Friedman, N., Gnirke, A., & Regev, A. (2010) · Nature Methods

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 753

A module map showing conditional activity of expression modules in cancer

Segal, E., Friedman, N., Koller, D., & Regev, A. (2004) · Nature Genetics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 685

Natural history and evolutionary principles of gene duplication in fungi

Wapinski, I., Pfeffer, A., Friedman, N., & Regev, A. (2007) · Nature

Fungal and yeast genetics researchChromosomal and Genetic Variations

Cited by 614

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

Rabani, M., Levin, J. Z., Fan, L., Adiconis, X., Raychowdhury, R., Garber, M., Gnirke, A., Nusbaum, C., Hacohen, N., Friedman, N., et al. (2011) · Nature Biotechnology

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 583

Dynamics of Replication-Independent Histone Turnover in Budding Yeast

Dion, M. F., Kaplan, T., Kim, M., Buratowski, S., Friedman, N., & Rando, O. J. (2007) · Science

Genomics and Chromatin DynamicsNuclear Structure and Function

Cited by 556

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

Brar, G. A., Yassour, M., Friedman, N., Regev, A., Ingolia, N. T., & Weissman, J. S. (2012) · Science

RNA and protein synthesis mechanismsFungal and yeast genetics research

Cited by 533

Comparative functional genomics of the fission yeasts

Rhind, N., Chen, Z., Yassour, M., Thompson, D. A., Haas, B. J., Habib, N., Wapinski, I., Roy, S., Lin, M. F., Heiman, D. I., et al. (2011) · Science

Fungal and yeast genetics researchGenomics and Phylogenetic Studies

Cited by 484

Identifying novel constrained elements by exploiting biased substitution patterns

Garber, M., Guttman, M., Clamp, M., Zody, M. C., Friedman, N., & Xie, X. (2009) · Bioinformatics

Genomics and Phylogenetic StudiesGenomics and Chromatin Dynamics

Cited by 370

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

Garber, M., Yosef, N., Goren, A., Raychowdhury, R., Thielke, A., Guttman, M., Robinson, J., Minie, B., Chevrier, N., Itzhaki, Z., et al. (2012) · Molecular Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 369

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

de Boer, C. G., Vaishnav, E. D., Sadeh, R., Abeyta, E. L., Friedman, N., & Regev, A. (2020) · Nature Biotechnology

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 283

Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors

Segman, R. H., Shefi, N., Goltser-Dubner, T., Friedman, N., Kaminski, N., & Shalev, A. Y. (2005) · Molecular Psychiatry

Posttraumatic Stress Disorder ResearchStress Responses and Cortisol

Cited by 281

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

Rabani, M., Raychowdhury, R., Jovanovic, M., Rooney, M., Stumpo, D. J., Pauli, A., Hacohen, N., Schier, A. F., Blackshear, P. J., Friedman, N., et al. (2014) · Cell

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 226

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

Habib, N., Wapinski, I., Margalit, H., Regev, A., & Friedman, N. (2012) · Molecular Systems Biology

Fungal and yeast genetics researchGene Regulatory Network Analysis

Cited by 50

Modularity and directionality in genetic interaction maps

Jaimovich, A., Rinott, R., Schuldiner, M., Margalit, H., & Friedman, N. (2010) · Bioinformatics

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 32