Gnirke, Andreas

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 8,898

A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis

Feder, J. N., Gnirke, A., Thomas, W., Tsuchihashi, Z., Ruddy, D. A., Basava, A., Dormishian, F., Domingo, R., Ellis, M. C., Fullan, A., et al. (1996) · Nature Genetics

Iron Metabolism and DisordersNeurological diseases and metabolism

Cited by 3,664

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 2,536

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,730

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., et al. (2009) · Nature Biotechnology

Genomics and Phylogenetic StudiesGenomics and Rare Diseases

Cited by 1,433

Charting a dynamic DNA methylation landscape of the human genome

Ziller, M. J., Gu, H., Müller, F., Donaghey, J., Tsai, L. T.-Y., Kohlbacher, O., De Jager, P. L., Rosen, E. D., Bennett, D. A., Bernstein, B. E., et al. (2013) · Nature

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 1,357

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

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Shalek, A. K., Satija, R., Adiconis, X., Gertner, R. S., Gaublomme, J. T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., et al. (2013) · Nature

Single-cell and spatial transcriptomicsRNA Research and Splicing

Cited by 1,190

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Aird, D., Ross, M. G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D. B., Nusbaum, C., & Gnirke, A. (2011) · Genome Biology

Genomics and Phylogenetic StudiesMolecular Biology Techniques and Applications

Cited by 1,174

Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines

Bock, C., Kiskinis, E., Verstappen, G., Gu, H., Boulting, G., Smith, Z. D., Ziller, M., Croft, G. F., Amoroso, M. W., Oakley, D. H., et al. (2011) · Cell

Pluripotent Stem Cells ResearchEpigenetics and DNA Methylation

Cited by 1,009

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

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Melnikov, A., Murugan, A., Zhang, X., Tesileanu, T., Wang, L., Rogov, P., Feizi, S., Gnirke, A., Callan, C. G., Kinney, J. B., et al. (2012) · Nature Biotechnology

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 711

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

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

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

Brinkman, A. B., Gu, H., Bartels, S. J. J., Zhang, Y., Matarese, F., Simmer, F., Marks, H., Bock, C., Gnirke, A., Meissner, A., et al. (2012) · Genome Research

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 413

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

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Grubaugh, N. D., Ladner, J. T., Kraemer, M. U. G., Dudas, G., Tan, A. L., Gangavarapu, K., Wiley, M. R., White, S., Thézé, J., Magnani, D. M., et al. (2017) · Nature

Mosquito-borne diseases and controlViral Infections and Vectors

Cited by 353

Integrative analysis of the melanoma transcriptome

Berger, M. F., Levin, J. Z., Vijayendran, K., Sivachenko, A., Adiconis, X., Maguire, J., Johnson, L. A., Robinson, J., Verhaak, R. G., Sougnez, C., et al. (2010) · Genome Research

Cancer Genomics and DiagnosticsCutaneous Melanoma Detection and Management

Cited by 305

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

Xie, X., Mikkelsen, T. S., Gnirke, A., Lindblad-Toh, K., Kellis, M., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 305

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

Gaiti, F., Chaligne, R., Gu, H., Brand, R. M., Kothen-Hill, S., Schulman, R. C., Grigorev, K., Risso, D., Kim, K.-T., Pastore, A., et al. (2019) · Nature

Chronic Lymphocytic Leukemia ResearchEpigenetics and DNA Methylation

Cited by 262

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

Smith, Z. D., Shi, J., Gu, H., Donaghey, J., Clement, K., Cacchiarelli, D., Gnirke, A., Michor, F., & Meissner, A. (2017) · Nature

Epigenetics and DNA MethylationGenetic Syndromes and Imprinting

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