BLUEPRINT papers in Cell and Cell Press journals

BLUEPRINT scientists release a collection of 26 publications in Cell, Cell Press-associated and other high-impact journals.
Of these 26 publications, 14 are being released in Cell and Cell Press-associated journals, and an additional 12 papers have been published or will soon be published in other high-impact journals.

Cell

Editorial: The Cell editorial team: A Cornucopia of Advances in Human Epigenomics. Cell 167 (5): 1139

Essay
: Hendrik G. Stunnenberg, The International Human Epigenome Consortium, Martin Hirst. (2016).
          The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and
          Discovery. Cell 167 (5): 1145-1149 

  1. Astle, W.J., Elding, H., Jiang, T., Allen, D., Ruklisa, D., Mann, A.L., Mead, D., Bouman, H., Riveros-Mckay, F., Kostadima, M.A., et al. (2016). The allelic landscape of human blood cell trait variation and links to common complex disease. Cell 167 (5): 1415-1429.e19
  2. Chen, L., Ge, B., Casale, F.P., Vasquez, L., Kwan, T., Garrido-Martín, D., Watt, S., Yang, Y., Kundu, K., Ecker, S., et al. (2016). Genetic drivers of epigenetic and transcriptional variation in human immune cells. Cell 167 (5): 1398-1414.e24
  3. Javierre, B.M., Burren, O.S., Wilder, S.P., Kreuzhuber , R., Hill, S.M., Sewitz, S., Cairns, J., Wingett, S.W., Várnai, C., Thiecke, M.J., et al. (2016). Lineage-specific genome architecture links diseasevariants to target genes. Cell 167 (5): 1369-1384.e19
  4. Novakovic, B., Habibi, E., Wang, S.-Y., Arts, R.J.W., Davar, R., Megchelenbrink, W., Kim, B., Kuznetsova, T., Kox, M., Zwaag, J., et al. (2016). ß-glucan reverses the epigenetic state of LPS induced immunological tolerance. Cell 167 (5): 1354-1368.e14


Cell Stem Cell

  1. Farlik, M., Halbritter, F., Müller, F., Choudry, F.A., Ebert, P., Klughammer, J., Farrow, S., Santoro, A., Ciaurro, V., Mathur, A., et al. (2016). DNA methylation dynamics of human hematopoietic stem cell differentiation. Cell Stem Cell 19. (http://dx.doi.org/10.1016/j.stem.2016.10.019).


Cell Metabolism

  1. Arts, R.J.W., Novakovic, B., ter Horst, R., Carvalho, A., Bekkering, S., Lachmandas, E., Rodrigues, F., Silvestre, R., Cheng, S.-H., Wang, S.-Y., et al. (2016). Glutaminolysis and fumarate accumulation integrate immunometabolic and epigenetic programs in trained immunity. Cell Metab. 24.


Immunity

  1. De Simone, M., Arrigoni, A., Rossetti, G., Gruarin, P., Ranzani, V., Politano, C., Bonnal, R.J.P., Provasi, E., Sarnicola, M.L., Panzeri, I., Moro, M., et al. (2016). Transcriptional landscape of human tissue lymphocytes unveils uniqueness of tumorinfiltrating T regulatory cells. Immunity 45 (5), 1135-1147.


Cell Systems

  1. Fernandez, J.M., de la Torre, V., Richardson, D., Royo, R., Puiggros, M., Moncunill, V., Fragkogianni, S., Clarke, L., Flicek, P., Rico, D., et al.; BLUEPRINT consortium (2016). EPICO platform: a reference cyber-infrastructure for comparative epigenomics. The BLUEPRINT Data Analysis Portal as a practical case. Cell Syst. 3.


Cell Reports

  1. Breeze, C.E., Paul, D.S., van Dongen, J., Butcher, L.M., Ambrose, J.C., Barrett, J.E., Lowe, R., Rakyan, V.K., Iotchkova, V., Frontini, M., et al. (2016). eFORGE: a tool for identifying cell typespecific signal in epigenomic data. Cell Rep. 17 (8), 2137-2150.
  2. Galindo-Albarrán, A.O., López-Portales, O.H., Gutiérrez-Reyna, D.Y., Rodríguez-Jorge, O., Sánchez-Villanueva, J.A., Ramırez-Pliego, O., Bergon, A., Lorio, B., Holota, H., Imbert, J., et al. (2016). CD8+ T cells from human neonates are biased towards an innate immune response. Cell Rep. 17 (8) 2151-2160.
  3. Juan, D., Perner, J., Carrillo de Santa Pau, E., Marsili, S., Ochoa, D., Chung, H.R., Vingron, M., Rico, D., and Valencia, A. (2016). Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs. Cell Rep. 14 (5), 1246–1257.
  4. Mandoli, A., Singh, A.A., Prange, K.H.M., Tijchon, E., Oerlemans, M., Dirks, R., Ter Huurne, M., Wierenga, A.T.J., Janssen-Megens, E.M., Berentsen, K., et al. (2016). The hematopoietic transcription factors RUNX1 and ERG prevent AML1-ETO oncogene overexpression and onset of the apoptosis program in t(8;21) AMLs. Cell Rep. 17 (8), 2087-2100
  5. Schuyler, R.P., Merkel, A., Raineri, E., Altucci, L., Vellenga, E., Martens, J.H.A., Pourfarzad, F., Kuijpers, T.W., Burden, F., Farrow, S., et al. (2016). Distinct trends of DNA methylation patterning in the innate and adaptive immune systems. Cell Rep. 17 (8), 2101-2111.

    Cancer Cell
  1. Queirós, A.C., Beekman, R., Vilarrasa-Blasi, R., Duran-Ferrer, M., Clot, G., Merkel, A., Raineri, E., Russinol, N., Castellano, G., Beà, S., et al. (2016). Decoding the DNA methylome of mantle cell lymphoma in the light of the entire B-cell lineage. Cancer Cell 30 (5), 806-821.



Publications in other journals

  1. Albrecht, F., List, M., Bock, C. and Lengauer, T. (2016). DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. Nucleic Acids Res. 44(W1), W581–W586.
  2. Bock, C., Halbritter, F., Carmona, F.J., Tierling, S., Datlinger, P., Assenov, Y., Berdasco, M., Bergmann, A.K., Booher, K., Busato, F., et al.; BLUEPRINT consortium (2016). Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat. Biotechnol. 34, 726–737.
  3. Franci, G., Sarno, F., Nebbioso, A., and Altucci, L. (2016). Identification and characterization of PKF118-310 as a KDM4A inhibitor. Epigenetics, 0. Published online October 21, 2016.
  4. Holland, M.L., Lowe, R., Caton, P.W., Gemma, C., Carbajosa, G., Danson, A.F., Carpenter, A.A., Loche, E., Ozanne, S.E., and Rakyan, V.K. (2016). Early-life nutrition modulates the epigenetic state of specific rDNA genetic variants in mice. Science 353, 495–498.
  5. Nebbioso, A., Carafa, V., Conte,M., Tambaro, F.P., Abbondanza, C., Martens, J.H., Nees, M., Benedetti, R., Pallavicini, I., Minucci, S., et al. (2016). c-Myc modulation & acetylation is a key HDAC inhibitor target in cancer. Clin. Cancer Res. online October 6, 2016.
  6. Pancaldi, V., Carrillo-de-Santa-Pau, E., Javierre, B.M., Juan, D., Fraser, P., Spivakov, M., Valencia, A., and Rico, D. (2016). Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity. Genome Biol. 17, 152. http://dx.doi.org/10.1186/s13059-016-1003-3.
  7. Libertini, E., Heath, S.C., Hamoudi, R.A., Gut, M., Ziller, M.J., Czyz, A., Ruotti, V., Stunnenberg, H.G., Frontini, M., Ouwehand, W.H., et al. (2016). Information recovery from low coverage whole-genome bisulfite sequencing. Nat. Commun. 7 article 11306, online June 27, 2016.
  8. Libertini, E., Heath, S.C., Hamoudi, R.A., Gut, M., Ziller, M.J., Herrero, J., Czyz, A., Ruotti, V., Stunnenberg, H.G., Frontini, M., et al. (2016). Saturation analysis for whole-genome bisulfite sequencing data. Nat. Biotechnol. online June 27, 2016. http://dx.doi.org/10.1038/nbt.3524.
  9. Paul, D.S., Teschendorff, A. E., Dang, M. A. N., Lowe, R., Hawa, M. I., Ecker, S., Cunningham, S., Fouts, A. R., Ramelius, A., Burden, F., Farrow, S., Rowlston, S., Rehnstrom, K., Frontini, M., Downes, K., Busche, S., Cheung, W., Bing Ge, Simon, M.-M., Bujold, D., Kwan, T., Bourque, G., Datta, A., Lowy, E., Clarke, L., Flicek, P., Libertini, E., Heath, S., Gut, M., Gut, I. G., Ouwehand, W. H., Pastinen, T., Soranzo, N., Hofer, S. E., Karges, B., Meissner, T., Boehm, B. O., Cilio, C., Elding Larsson, H., Lernmark, Å., Steck, A. K., Rakyan, V. K., Beck S., and Leslie, R. D. (2016). Increased DNA methylation variability in type 1 diabetes across three immune effector cell types. Nature Commun., in press
  10. Rendeiro, A.F., Schmidl, C., Strefford, J.C., Walewska, R., Davis, Z., Farlik, M., Oscier, D., and Bock, C. (2016). Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtypespecific epigenome signatures and transcription regulatory networks. Nat. Commun. 7, 11938, online June 27, 2016.
  11. Stricker, S.H., Köferle, A., and Beck, S. (2016). From profiles to function in epigenomics. Nature Reviews Genetics. online November 21, 2016
  12. Weiner, A., Lara-Astiaso, D., Krupalnik, V., Gafni, O., David, E., Winter, D.R., Hanna, J.H., and Amit, I. (2016). Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution. Nat. Biotechnol. 34, online July 25, 2016



For all BLUEPRINT publications over the last 5 years.