Home>News & Publications:Scientific Publications>Scientific Publications

Scientific Publications

Search by Keyword(s)
or use Advanced Search
Found 34 results

Filters: Author is Gnirke, A  [Clear All Filters]

Search Results

  • Showing 1-34 of 34 Results
2013
Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells.Gifford, CA, Ziller MJ, Gu H., Trapnell C., Donaghey J., Tsankov A., Shalek AK, Kelley DR, Shishkin AA, Issner R., Zhang X., Coyne M., Fostel JL, Holmes L., Meldrim J., Guttman M., Epstein C., Park H., Kohlbacher O., Rinn J., et al. Cell, 2013/05/07, (2013) Read More / View Supplemental Materials
Abstract
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.Kirby, A., Gnirke A., Jaffe DB, Barešová V., Pochet N., Blumenstiel B., Ye C., Aird D., Stevens C., Robinson JT, Cabili MN, Gat-Viks I., Kelliher E., Daza R., DeFelice M., Hůlková H., Sovová J., Vylet'al P., Antignac C., Guttman M., et al. Nature genetics, 2013/03/01, Volume 45, Issue 3, p.299-303, (2013) Read More / View Supplemental Materials
Abstract
2012
Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling.Boyle, P., Clement K., Gu H., Smith ZD, Ziller M., Fostel JL, Holmes L., Meldrim J., Kelley F., Gnirke A., and Meissner A. Genome biology, 2012/10/03, Volume 13, Issue 10, p.R92, (2012) Read More / View Supplemental Materials
Abstract
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., Blecher-Gonen R., Bornstein C., Amann-Zalcenstein D., Weiner A., Friedrich D., Meldrim J., Ram O., Cheng C., Gnirke A., Fisher S., et al. Molecular cell, 2012/09/14, Volume 47, Issue 5, p.810-22, (2012) Read More / View Supplemental Materials
Abstract
DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells.Bock, C., Beerman I., Lien WH, Smith ZD, Gu H., Boyle P., Gnirke A., Fuchs E., Rossi DJ, and Meissner A. Molecular cell, 2012/08/24, Volume 47, Issue 4, p.633-47, (2012) Read More / View Supplemental Materials
Abstract
Paired-end sequencing of Fosmid libraries by Illumina.Williams, LJ, Tabbaa DG, Li N., Berlin AM, Shea TP, Maccallum I., Lawrence MS, Drier Y., Getz G., Young SK, Jaffe DB, Nusbaum C., and Gnirke A. Genome research, 2012/07/17, (2012) Read More / View Supplemental Materials
Abstract
A unique regulatory phase of DNA methylation in the early mammalian embryo.Smith, ZD, Chan MM, Mikkelsen TS, Gu H., Gnirke A., Regev A., and Meissner A. Nature, 2012/03/28, Volume 484, Issue 7394, p.339-44, (2012) Read More / View Supplemental Materials
Abstract
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 CG Jr, Kinney JB, Kellis M., Lander E. S., and Mikkelsen TS Nature biotechnology, 2012/02/26, Volume 30, Issue 3, p.271-7, (2012) Read More / View Supplemental Materials
Abstract
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.Aird, D., Ross MG, Chen WS, Danielsson M., Fennell T., Russ C., Jaffe DB, Nusbaum C., and Gnirke A. Genome biology, 2012/01/09, Volume 12, Issue 2, p.R18, (2012) Read More / View Supplemental Materials
Abstract
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.Yassour, M., Pfiffner J., Levin JZ, Adiconis X., Gnirke A., Nusbaum C., Thompson DA, Friedman N., and Regev A. Genome biology, 2012/01/09, Volume 11, Issue 8, p.R87, (2012) Read More / View Supplemental Materials
Abstract
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.Levin, JZ, Berger MF, Adiconis X., Rogov P., Melnikov A., Fennell T., Nusbaum C., Garraway LA, and Gnirke A. Genome biology, 2012/01/09, Volume 10, Issue 10, p.R115, (2012) Read More / View Supplemental Materials
Abstract
2011
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis.Meissner, A., Gnirke A., Bell GW, Ramsahoye B., Lander E. S., and Jaenisch R. Nucleic acids research, 2011/12/08, Volume 33, Issue 18, p.5868-77, (2011) Read More / View Supplemental Materials
Abstract
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.Ziller, MJ, Müller F., Liao J., Zhang Y., Gu H., Bock C., Boyle P., Epstein CB, Bernstein BE, Lengauer T., Gnirke A., and Meissner A. PLoS genetics, 2011/12/01, Volume 7, Issue 12, p.e1002389, (2011) Read More / View Supplemental Materials
Abstract
Hybrid selection for sequencing pathogen genomes from clinical samples.Melnikov, A., Galinsky K., Rogov P., Fennell T., Van Tyne D., Russ C., Daniels R., Barnes KG, Bochicchio J., Ndiaye D., Sene PD, Wirth DF, Nusbaum C., Volkman SK, Birren BW, Gnirke A., and Neafsey DE Genome biology, 2011/08/11, Volume 12, Issue 8, p.R73, (2011) Read More / View Supplemental Materials
Abstract
Full-length transcriptome assembly from RNA-Seq data without a reference genome.Grabherr, MG, Haas BJ, Yassour M., Levin JZ, Thompson DA, Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., Di Palma F., Birren BW, Nusbaum C., Lindblad-Toh K., Friedman N., et al. Nature biotechnology, 2011/05/15, Volume 29, Issue 7, p.644-52, (2011) Read More / View Supplemental Materials
Abstract
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.Rabani, M., Levin JZ, Fan L., Adiconis X., Raychowdhury R., Garber M., Gnirke A., Nusbaum C., Hacohen N., Friedman N., Amit I., and Regev A. Nature biotechnology, 2011/05/01, Volume 29, Issue 5, p.436-42, (2011) Read More / View Supplemental Materials
Abstract
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.Gu, H., Smith ZD, Bock C., Boyle P., Gnirke A., and Meissner A. Nature protocols, 2011/04/01, Volume 6, Issue 4, p.468-81, (2011) Read More / View Supplemental Materials
Abstract
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 ZD, Ziller M., Croft GF, Amoroso MW, Oakley DH, Gnirke A., Eggan K., and Meissner A. Cell, 2011/02/04, Volume 144, Issue 3, p.439-52, (2011) Read More / View Supplemental Materials
Abstract
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.Gnerre, S., Maccallum I., Przybylski D., Ribeiro FJ, Burton JN, Walker BJ, Sharpe T., Hall G., Shea TP, Sykes S., Berlin AM, Aird D., Costello M., Daza R., Williams L., Nicol R., Gnirke A., Nusbaum C., Lander E. S., and Jaffe DB Proceedings of the National Academy of Sciences of the United States of America, 2011/01/25, Volume 108, Issue 4, p.1513-8, (2011) Read More / View Supplemental Materials
Abstract
Reprogramming factor expression initiates widespread targeted chromatin remodeling.Koche, RP, Smith ZD, Adli M., Gu H., Ku M., Gnirke A., Bernstein BE, and Meissner A. Cell stem cell, 2011/01/07, Volume 8, Issue 1, p.96-105, (2011) Read More / View Supplemental Materials
Abstract
2010
Quantitative comparison of genome-wide DNA methylation mapping technologies.Bock, C., Tomazou EM, Brinkman AB, Müller F., Simmer F., Gu H., Jäger N., Gnirke A., Stunnenberg HG, and Meissner A. Nature biotechnology, 2010/10/01, Volume 28, Issue 10, p.1106-14, (2010) Read More / View Supplemental Materials
Abstract
Comprehensive comparative analysis of strand-specific RNA sequencing methods.Levin, JZ, Yassour M., Adiconis X., Nusbaum C., Thompson DA, Friedman N., Gnirke A., and Regev A. Nature methods, 2010/09/01, Volume 7, Issue 9, p.709-15, (2010) Read More / View Supplemental Materials
Abstract
Targeted exon sequencing by in-solution hybrid selection.Blumenstiel, B., Cibulskis K., Fisher S., DeFelice M., Barry A., Fennell T., Abreu J., Minie B., Costello M., Young G., Maquire J., Kernytsky A., Melnikov A., Rogov P., Gnirke A., and Gabriel S. Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.], 2010/07/01, Volume Chapter 18, p.Unit 18.4, (2010) Read More / View Supplemental Materials
Abstract
Hi-C: a method to study the three-dimensional architecture of genomes.van Berkum, NL, Lieberman-Aiden E., Williams L., Imakaev M., Gnirke A., Mirny LA, Dekker J., and Lander E. S. Journal of visualized experiments : JoVE, 2010/05/06, Issue 39, (2010) Read More / View Supplemental Materials
Abstract
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.Guttman, M., Garber M., Levin JZ, Donaghey J., Robinson J., Adiconis X., Fan L., Koziol MJ, Gnirke A., Nusbaum C., Rinn JL, Lander E. S., and Regev A. Nature biotechnology, 2010/05/01, Volume 28, Issue 5, p.503-10, (2010) Read More / View Supplemental Materials
Abstract
Integrative analysis of the melanoma transcriptome.Berger, MF, Levin JZ, Vijayendran K., Sivachenko A., Adiconis X., Maguire J., Johnson LA, Robinson J., Verhaak RG, Sougnez C., Onofrio RC, Ziaugra L., Cibulskis K., Laine E., Barretina J., Winckler W., Fisher DE, Getz G., Meyerson M., Jaffe DB, et al. Genome research, 2010/04/01, Volume 20, Issue 4, p.413-27, (2010) Read More / View Supplemental Materials
Abstract
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.Gu, H., Bock C., Mikkelsen TS, Jäger N., Smith ZD, Tomazou E., Gnirke A., Lander E. S., and Meissner A. Nature methods, 2010/02/01, Volume 7, Issue 2, p.133-6, (2010) Read More / View Supplemental Materials
Abstract
2009
ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.Markljung, E., Jiang L., Jaffe JD, Mikkelsen TS, Wallerman O., Larhammar M., Zhang X., Wang L., Saenz-Vash V., Gnirke A., Lindroth AM, Barrés R., Yan J., Strömberg S., De S., Pontén F., Lander E. S., Carr SA, Zierath JR, Kullander K., et al. PLoS biology, 2009/12/01, Volume 7, Issue 12, p.e1000256, (2009) Read More / View Supplemental Materials
Abstract
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.Lieberman-Aiden, E., van Berkum NL, Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R., Bernstein B., Bender MA, Groudine M., Gnirke A., Stamatoyannopoulos J., Mirny LA, Lander E. S., and Dekker J. Science (New York, N.Y.), 2009/10/09, Volume 326, Issue 5950, p.289-93, (2009) Read More / View Supplemental Materials
Abstract
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.Gnirke, A., Melnikov A., Maguire J., Rogov P., LeProust EM, Brockman W., Fennell T., Giannoukos G., Fisher S., Russ C., Gabriel S., Jaffe DB, Lander E. S., and Nusbaum C. Nature biotechnology, 2009/02/01, Volume 27, Issue 2, p.182-9, (2009) Read More / View Supplemental Materials
Abstract
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.Maccallum, I., Przybylski D., Gnerre S., Burton J., Shlyakhter I., Gnirke A., Malek J., McKernan K., Ranade S., Shea TP, Williams L., Young S., Nusbaum C., and Jaffe DB Genome biology, 2009/01/01, Volume 10, Issue 10, p.R103, (2009) Read More / View Supplemental Materials
Abstract
2008
Genome-scale DNA methylation maps of pluripotent and differentiated cells.Meissner, A., Mikkelsen TS, Gu H., Wernig M., Hanna J., Sivachenko A., Zhang X., Bernstein BE, Nusbaum C., Jaffe DB, Gnirke A., Jaenisch R., and Lander E. S. Nature, 2008/08/07, Volume 454, Issue 7205, p.766-70, (2008) Read More / View Supplemental Materials
Abstract
2007
Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.Xie, X., Mikkelsen TS, Gnirke A., Lindblad-Toh K., Kellis M., and Lander E. S. Proceedings of the National Academy of Sciences of the United States of America, 2007/04/24, Volume 104, Issue 17, p.7145-50, (2007) Read More / View Supplemental Materials
Abstract
2005
DNA sequence and analysis of human chromosome 18.Nusbaum, C., Zody MC, Borowsky ML, Kamal M., Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K., FitzGerald MG, Yang X., Abouelleil A., Allen NR, Anderson S., Bloom T., Bugalter B., Butler J., Cook A., DeCaprio D., et al. Nature, 2005/09/22, Volume 437, Issue 7058, p.551-5, (2005) Read More / View Supplemental Materials
Abstract
  • Showing 1-34 of 34 Results