TY - JOUR AU - Hayflick, L. PY - 1965 DA - 1965// TI - The limited in vitro lifetime of human diploid cell strains JO - Exp Cell Res VL - 37 UR - https://doi.org/10.1016/0014-4827(65)90211-9 DO - 10.1016/0014-4827(65)90211-9 ID - Hayflick1965 ER - TY - JOUR AU - Wagner, W. AU - Horn, P. AU - Castoldi, M. AU - Diehlmann, A. AU - Bork, S. AU - Saffrich, R. PY - 2008 DA - 2008// TI - Replicative senescence of mesenchymal stem cells - a continuous and organized process JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0002213 DO - 10.1371/journal.pone.0002213 ID - Wagner2008 ER - TY - JOUR AU - Schellenberg, A. AU - Stiehl, T. AU - Horn, P. AU - Joussen, S. AU - Pallua, N. AU - Ho, A. PY - 2012 DA - 2012// TI - Population dynamics of mesenchymal stromal cells during culture expansion JO - Cytotherapy VL - 14 UR - https://doi.org/10.3109/14653249.2011.640669 DO - 10.3109/14653249.2011.640669 ID - Schellenberg2012 ER - TY - JOUR AU - Lansdorp, P. M. PY - 2008 DA - 2008// TI - Telomeres, stem cells, and hematology JO - Blood VL - 111 UR - https://doi.org/10.1182/blood-2007-09-084913 DO - 10.1182/blood-2007-09-084913 ID - Lansdorp2008 ER - TY - JOUR AU - Drummond, M. W. AU - Balabanov, S. AU - Holyoake, T. L. AU - Brummendorf, T. H. PY - 2007 DA - 2007// TI - Concise review: telomere biology in normal and leukemic hematopoietic stem cells JO - Stem Cells VL - 25 UR - https://doi.org/10.1634/stemcells.2007-0057 DO - 10.1634/stemcells.2007-0057 ID - Drummond2007 ER - TY - JOUR AU - Narita, M. AU - Nunez, S. AU - Heard, E. AU - Narita, M. AU - Lin, A. W. AU - Hearn, S. A. PY - 2003 DA - 2003// TI - Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence JO - Cell VL - 113 UR - https://doi.org/10.1016/S0092-8674(03)00401-X DO - 10.1016/S0092-8674(03)00401-X ID - Narita2003 ER - TY - JOUR AU - D‘Adda Di, F. F. AU - Reaper, P. M. AU - Clay-Farrace, L. AU - Fiegler, H. AU - Carr, P. AU - Von, Z. T. PY - 2003 DA - 2003// TI - A DNA damage checkpoint response in telomere-initiated senescence JO - Nature VL - 426 UR - https://doi.org/10.1038/nature02118 DO - 10.1038/nature02118 ID - D‘Adda Di2003 ER - TY - JOUR AU - Capell, B. C. AU - Collins, F. S. PY - 2006 DA - 2006// TI - Human laminopathies: nuclei gone genetically awry JO - Nat Rev Genet VL - 7 UR - https://doi.org/10.1038/nrg1906 DO - 10.1038/nrg1906 ID - Capell2006 ER - TY - JOUR AU - Fraser, P. AU - Bickmore, W. PY - 2007 DA - 2007// TI - Nuclear organization of the genome and the potential for gene regulation JO - Nature VL - 447 UR - https://doi.org/10.1038/nature05916 DO - 10.1038/nature05916 ID - Fraser2007 ER - TY - JOUR AU - Cremer, T. AU - Cremer, M. AU - Dietzel, S. AU - Muller, S. AU - Solovei, I. AU - Fakan, S. PY - 2006 DA - 2006// TI - Chromosome territories - a functional nuclear landscape JO - Curr Opin Cell Biol VL - 18 UR - https://doi.org/10.1016/j.ceb.2006.04.007 DO - 10.1016/j.ceb.2006.04.007 ID - Cremer2006 ER - TY - JOUR AU - Puckelwartz, M. J. AU - Depreux, F. F. AU - McNally, E. M. PY - 2011 DA - 2011// TI - Gene expression, chromosome position and lamin A/C mutations JO - Nucleus VL - 2 UR - https://doi.org/10.4161/nucl.2.3.16003 DO - 10.4161/nucl.2.3.16003 ID - Puckelwartz2011 ER - TY - JOUR AU - Bork, S. AU - Pfister, S. AU - Witt, H. AU - Horn, P. AU - Korn, B. AU - Ho, A. D. PY - 2010 DA - 2010// TI - DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells JO - Aging Cell VL - 9 UR - https://doi.org/10.1111/j.1474-9726.2009.00535.x DO - 10.1111/j.1474-9726.2009.00535.x ID - Bork2010 ER - TY - JOUR AU - Schellenberg, A. AU - Lin, Q. AU - Schueler, H. AU - Koch, C. AU - Joussen, S. AU - Denecke, B. PY - 2011 DA - 2011// TI - Replicative senescence of mesenchymal stem cells causes DNA-methylation changes which correlate with repressive histone marks JO - Aging (Albany NY) VL - 3 ID - Schellenberg2011 ER - TY - JOUR AU - Koch, C. M. AU - Joussen, S. AU - Schellenberg, A. AU - Lin, Q. AU - Zenke, M. AU - Wagner, W. PY - 2012 DA - 2012// TI - Monitoring of cellular senescence by DNA-methylation at specific CpG sites JO - Aging Cell VL - 11 UR - https://doi.org/10.1111/j.1474-9726.2011.00784.x DO - 10.1111/j.1474-9726.2011.00784.x ID - Koch2012 ER - TY - JOUR AU - Koch, C. AU - Suschek, C. V. AU - Lin, Q. AU - Bork, S. AU - Goergens, M. AU - Joussen, S. PY - 2011 DA - 2011// TI - Specific age-associated DNA methylation changes in human dermal fibroblasts JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0016679 DO - 10.1371/journal.pone.0016679 ID - Koch2011 ER - TY - JOUR AU - Horwitz, E. M. AU - Blanc, K. AU - Dominici, M. AU - Mueller, I. AU - Slaper-Cortenbach, I. AU - Marini, F. C. PY - 2005 DA - 2005// TI - Clarification of the nomenclature for MSC: The International Society for Cellular Therapy position statement JO - Cytotherapy VL - 7 UR - https://doi.org/10.1080/14653240500319234 DO - 10.1080/14653240500319234 ID - Horwitz2005 ER - TY - JOUR AU - Cruickshanks, H. A. AU - McBryan, T. AU - Nelson, D. M. AU - Vanderkraats, N. D. AU - Shah, P. P. AU - van, T. J. PY - 2013 DA - 2013// TI - Senescent cells harbour features of the cancer epigenome JO - Nat Cell Biol VL - 15 UR - https://doi.org/10.1038/ncb2879 DO - 10.1038/ncb2879 ID - Cruickshanks2013 ER - TY - JOUR AU - Teschendorff, A. E. AU - Menon, U. AU - Gentry-Maharaj, A. AU - Ramus, S. J. AU - Weisenberger, D. J. AU - Shen, H. PY - 2010 DA - 2010// TI - Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.103606.109 DO - 10.1101/gr.103606.109 ID - Teschendorff2010 ER - TY - JOUR AU - Koch, C. M. AU - Reck, K. AU - Shao, K. AU - Lin, Q. AU - Joussen, S. AU - Ziegler, P. PY - 2013 DA - 2013// TI - Pluripotent stem cells escape from senescence-associated DNA methylation changes JO - Genome Res VL - 23 UR - https://doi.org/10.1101/gr.141945.112 DO - 10.1101/gr.141945.112 ID - Koch2013 ER - TY - JOUR AU - Rakyan, V. K. AU - Down, T. A. AU - Maslau, S. AU - Andrew, T. AU - Yang, T. P. AU - Beyan, H. PY - 2010 DA - 2010// TI - Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.103101.109 DO - 10.1101/gr.103101.109 ID - Rakyan2010 ER - TY - JOUR AU - Hannum, G. AU - Guinney, J. AU - Zhao, L. AU - Zhang, L. AU - Hughes, G. AU - Sadda, S. PY - 2013 DA - 2013// TI - Genome-wide methylation profiles reveal quantitative views of human aging rates JO - Mol Cell VL - 49 UR - https://doi.org/10.1016/j.molcel.2012.10.016 DO - 10.1016/j.molcel.2012.10.016 ID - Hannum2013 ER - TY - JOUR AU - Teschendorff, A. E. AU - West, J. AU - Beck, S. PY - 2013 DA - 2013// TI - Age-associated epigenetic drift: implications, and a case of epigenetic thrift? JO - Hum Mol Genet VL - 22 UR - https://doi.org/10.1093/hmg/ddt375 DO - 10.1093/hmg/ddt375 ID - Teschendorff2013 ER - TY - JOUR AU - Crabbe, L. AU - Cesare, A. J. AU - Kasuboski, J. M. AU - Fitzpatrick, J. A. AU - Karlseder, J. PY - 2012 DA - 2012// TI - Human telomeres are tethered to the nuclear envelope during postmitotic nuclear assembly JO - Cell Rep VL - 2 UR - https://doi.org/10.1016/j.celrep.2012.11.019 DO - 10.1016/j.celrep.2012.11.019 ID - Crabbe2012 ER - TY - JOUR AU - Brinkman, A. B. AU - Simmer, F. AU - Ma, K. AU - Kaan, A. AU - Zhu, J. AU - Stunnenberg, H. G. PY - 2010 DA - 2010// TI - Whole-genome DNA methylation profiling using MethylCap-seq JO - Methods VL - 52 UR - https://doi.org/10.1016/j.ymeth.2010.06.012 DO - 10.1016/j.ymeth.2010.06.012 ID - Brinkman2010 ER - TY - JOUR AU - Bernstein, B. E. AU - Stamatoyannopoulos, J. A. AU - Costello, J. F. AU - Ren, B. AU - Milosavljevic, A. AU - Meissner, A. PY - 2010 DA - 2010// TI - The NIH Roadmap Epigenomics Mapping Consortium JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt1010-1045 DO - 10.1038/nbt1010-1045 ID - Bernstein2010 ER - TY - JOUR AU - Guelen, L. AU - Pagie, L. AU - Brasset, E. AU - Meuleman, W. AU - Faza, M. B. AU - Talhout, W. PY - 2008 DA - 2008// TI - Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions JO - Nature VL - 453 UR - https://doi.org/10.1038/nature06947 DO - 10.1038/nature06947 ID - Guelen2008 ER - TY - JOUR AU - Zhu, J. AU - Adli, M. AU - Zou, J. Y. AU - Verstappen, G. AU - Coyne, M. AU - Zhang, X. PY - 2013 DA - 2013// TI - Genome-wide chromatin state transitions associated with developmental and environmental cues JO - Cell VL - 152 UR - https://doi.org/10.1016/j.cell.2012.12.033 DO - 10.1016/j.cell.2012.12.033 ID - Zhu2013 ER - TY - JOUR AU - Gonzalez-Suarez, I. AU - Redwood, A. B. AU - Perkins, S. M. AU - Vermolen, B. AU - Lichtensztejin, D. AU - Grotsky, D. A. PY - 2009 DA - 2009// TI - Novel roles for A-type lamins in telomere biology and the DNA damage response pathway JO - EMBO J VL - 28 UR - https://doi.org/10.1038/emboj.2009.196 DO - 10.1038/emboj.2009.196 ID - Gonzalez-Suarez2009 ER - TY - JOUR AU - Raz, V. AU - Vermolen, B. J. AU - Garini, Y. AU - Onderwater, J. J. AU - Mommaas-Kienhuis, M. A. AU - Koster, A. J. PY - 2008 DA - 2008// TI - The nuclear lamina promotes telomere aggregation and centromere peripheral localization during senescence of human mesenchymal stem cells JO - J Cell Sci VL - 121 UR - https://doi.org/10.1242/jcs.034876 DO - 10.1242/jcs.034876 ID - Raz2008 ER - TY - JOUR AU - Koch, C. M. AU - Wagner, W. PY - 2013 DA - 2013// TI - Epigenetic biomarker to determine replicative senescence of cultured cells JO - Methods Mol Biol VL - 1048 UR - https://doi.org/10.1007/978-1-62703-556-9_20 DO - 10.1007/978-1-62703-556-9_20 ID - Koch2013 ER - TY - JOUR AU - Schellenberg, A. AU - Mauen, S. AU - Koch, C. M. AU - Wagner, W. AU - Jans, R. AU - De, W. P. PY - 2014 DA - 2014// TI - Proof of principle: quality control of therapeutic cell preparations using senescence-associated DNA-methylation changes JO - BMC Res Notes VL - 7 UR - https://doi.org/10.1186/1756-0500-7-254 DO - 10.1186/1756-0500-7-254 ID - Schellenberg2014 ER - TY - JOUR AU - Serre, D. AU - Lee, B. H. AU - Ting, A. H. PY - 2010 DA - 2010// TI - MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp992 DO - 10.1093/nar/gkp992 ID - Serre2010 ER - TY - JOUR AU - Robinson, M. D. AU - Stirzaker, C. AU - Statham, A. L. AU - Coolen, M. W. AU - Song, J. Z. AU - Nair, S. S. PY - 2010 DA - 2010// TI - Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.110601.110 DO - 10.1101/gr.110601.110 ID - Robinson2010 ER - TY - JOUR AU - Weidner, C. I. AU - Lin, Q. AU - Koch, C. M. AU - Eisele, L. AU - Beier, F. AU - Ziegler, P. PY - 2014 DA - 2014// TI - Aging of blood can be tracked by DNA methylation changes at just three CpG sites JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/gb-2014-15-2-r24 DO - 10.1186/gb-2014-15-2-r24 ID - Weidner2014 ER - TY - JOUR AU - Horvath, S. PY - 2013 DA - 2013// TI - DNA methylation age of human tissues and cell types JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-10-r115 DO - 10.1186/gb-2013-14-10-r115 ID - Horvath2013 ER - TY - JOUR AU - McClay, J. L. AU - Aberg, K. A. AU - Clark, S. L. AU - Nerella, S. AU - Kumar, G. AU - Xie, L. Y. PY - 2014 DA - 2014// TI - A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects JO - Hum Mol Genet VL - 23 UR - https://doi.org/10.1093/hmg/ddt511 DO - 10.1093/hmg/ddt511 ID - McClay2014 ER - TY - JOUR AU - Maegawa, S. AU - Hinkal, G. AU - Kim, H. S. AU - Shen, L. AU - Zhang, L. AU - Zhang, J. PY - 2010 DA - 2010// TI - Widespread and tissue specific age-related DNA methylation changes in mice JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.096826.109 DO - 10.1101/gr.096826.109 ID - Maegawa2010 ER - TY - JOUR AU - Bocker, M. T. AU - Hellwig, I. AU - Breiling, A. AU - Eckstein, V. AU - Ho, A. D. AU - Lyko, F. PY - 2011 DA - 2011// TI - Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging JO - Blood VL - 117 UR - https://doi.org/10.1182/blood-2011-01-331926 DO - 10.1182/blood-2011-01-331926 ID - Bocker2011 ER - TY - STD TI - Fernandez AF, Bayon GF, Urdinguio RG, Torano EG, Garcia MG, Carella A, et al. H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells. Genome Res. in press. ID - ref39 ER - TY - JOUR AU - Weidner, C. I. AU - Wagner, W. PY - 2014 DA - 2014// TI - The epigenetic tracks of aging JO - Biol Chem VL - 395 UR - https://doi.org/10.1515/hsz-2014-0180 DO - 10.1515/hsz-2014-0180 ID - Weidner2014 ER - TY - JOUR AU - Aebi, U. AU - Cohn, J. AU - Buhle, L. AU - Gerace, L. PY - 1986 DA - 1986// TI - The nuclear lamina is a meshwork of intermediate-type filaments JO - Nature VL - 323 UR - https://doi.org/10.1038/323560a0 DO - 10.1038/323560a0 ID - Aebi1986 ER - TY - JOUR AU - Lund, E. AU - Oldenburg, A. R. AU - Delbarre, E. AU - Freberg, C. T. AU - Duband-Goulet, I. AU - Eskeland, R. PY - 2013 DA - 2013// TI - Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes JO - Genome Res VL - 23 UR - https://doi.org/10.1101/gr.159400.113 DO - 10.1101/gr.159400.113 ID - Lund2013 ER - TY - JOUR AU - Collas, P. AU - Lund, E. G. AU - Oldenburg, A. R. PY - 2014 DA - 2014// TI - Closing the (nuclear) envelope on the genome: how nuclear lamins interact with promoters and modulate gene expression JO - Bioessays VL - 36 UR - https://doi.org/10.1002/bies.201300138 DO - 10.1002/bies.201300138 ID - Collas2014 ER - TY - JOUR AU - Mewborn, S. K. AU - Puckelwartz, M. J. AU - Abuisneineh, F. AU - Fahrenbach, J. P. AU - Zhang, Y. AU - MacLeod, H. PY - 2010 DA - 2010// TI - Altered chromosomal positioning, compaction, and gene expression with a lamin A/C gene mutation JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0014342 DO - 10.1371/journal.pone.0014342 ID - Mewborn2010 ER - TY - JOUR AU - Freund, A. AU - Laberge, R. M. AU - Demaria, M. AU - Campisi, J. PY - 2012 DA - 2012// TI - Lamin B1 loss is a senescence-associated biomarker JO - Mol Biol Cell VL - 23 UR - https://doi.org/10.1091/mbc.E11-10-0884 DO - 10.1091/mbc.E11-10-0884 ID - Freund2012 ER - TY - JOUR AU - Shimi, T. AU - Butin-Israeli, V. AU - Adam, S. A. AU - Hamanaka, R. B. AU - Goldman, A. E. AU - Lucas, C. A. PY - 2011 DA - 2011// TI - The role of nuclear lamin B1 in cell proliferation and senescence JO - Genes Dev VL - 25 UR - https://doi.org/10.1101/gad.179515.111 DO - 10.1101/gad.179515.111 ID - Shimi2011 ER - TY - JOUR AU - Shah, P. P. AU - Donahue, G. AU - Otte, G. L. AU - Capell, B. C. AU - Nelson, D. M. AU - Cao, K. PY - 2013 DA - 2013// TI - Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape JO - Genes Dev VL - 27 UR - https://doi.org/10.1101/gad.223834.113 DO - 10.1101/gad.223834.113 ID - Shah2013 ER - TY - JOUR AU - Guarda, A. AU - Bolognese, F. AU - Bonapace, I. M. AU - Badaracco, G. PY - 2009 DA - 2009// TI - Interaction between the inner nuclear membrane lamin B receptor and the heterochromatic methyl binding protein, MeCP2 JO - Exp Cell Res VL - 315 UR - https://doi.org/10.1016/j.yexcr.2009.01.019 DO - 10.1016/j.yexcr.2009.01.019 ID - Guarda2009 ER - TY - JOUR AU - Reddy, K. L. AU - Zullo, J. M. AU - Bertolino, E. AU - Singh, H. PY - 2008 DA - 2008// TI - Transcriptional repression mediated by repositioning of genes to the nuclear lamina JO - Nature VL - 452 UR - https://doi.org/10.1038/nature06727 DO - 10.1038/nature06727 ID - Reddy2008 ER - TY - JOUR AU - Peric-Hupkes, D. AU - Meuleman, W. AU - Pagie, L. AU - Bruggeman, S. W. AU - Solovei, I. AU - Brugman, W. PY - 2010 DA - 2010// TI - Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation JO - Mol Cell VL - 38 UR - https://doi.org/10.1016/j.molcel.2010.03.016 DO - 10.1016/j.molcel.2010.03.016 ID - Peric-Hupkes2010 ER - TY - JOUR AU - Zimmerman, S. M. AU - Kim, S. K. PY - 2014 DA - 2014// TI - The GATA transcription factor/MTA-1 homolog egr-1 promotes longevity and stress resistance in Caenorhabditis elegans JO - Aging Cell VL - 13 UR - https://doi.org/10.1111/acel.12179 DO - 10.1111/acel.12179 ID - Zimmerman2014 ER - TY - JOUR AU - Pardo, P. S. AU - Boriek, A. M. PY - 2012 DA - 2012// TI - An autoregulatory loop reverts the mechanosensitive Sirt1 induction by EGR1 in skeletal muscle cells JO - Aging (Albany NY) VL - 4 ID - Pardo2012 ER - TY - JOUR AU - Krones-Herzig, A. AU - Adamson, E. AU - Mercola, D. PY - 2003 DA - 2003// TI - Early growth response 1 protein, an upstream gatekeeper of the p53 tumor suppressor, controls replicative senescence JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.2628034100 DO - 10.1073/pnas.2628034100 ID - Krones-Herzig2003 ER - TY - JOUR AU - Ohtani, N. AU - Zebedee, Z. AU - Huot, T. J. AU - Stinson, J. A. AU - Sugimoto, M. AU - Ohashi, Y. PY - 2001 DA - 2001// TI - Opposing effects of Ets and Id proteins on p16INK4a expression during cellular senescence JO - Nature VL - 409 UR - https://doi.org/10.1038/35059131 DO - 10.1038/35059131 ID - Ohtani2001 ER - TY - JOUR AU - Keane, M. AU - Magalhaes, J. P. PY - 2013 DA - 2013// TI - MYCN/LIN28B/Let-7/HMGA2 pathway implicated by meta-analysis of GWAS in suppression of post-natal proliferation thereby potentially contributing to aging JO - Mech Ageing Dev VL - 134 UR - https://doi.org/10.1016/j.mad.2013.04.006 DO - 10.1016/j.mad.2013.04.006 ID - Keane2013 ER - TY - JOUR AU - Tian, Y. PY - 2009 DA - 2009// TI - Ah receptor and NF-kappaB interplay on the stage of epigenome JO - Biochem Pharmacol VL - 77 UR - https://doi.org/10.1016/j.bcp.2008.10.023 DO - 10.1016/j.bcp.2008.10.023 ID - Tian2009 ER - TY - JOUR AU - Lohmann, M. AU - Walenda, G. AU - Hemeda, H. AU - Joussen, S. AU - Drescher, W. AU - Jockenhoevel, S. PY - 2012 DA - 2012// TI - Donor age of human platelet lysate affects proliferation and differentiation of mesenchymal stem cells JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0037839 DO - 10.1371/journal.pone.0037839 ID - Lohmann2012 ER - TY - JOUR AU - Varela, E. AU - Schneider, R. P. AU - Ortega, S. AU - Blasco, M. A. PY - 2011 DA - 2011// TI - Different telomere-length dynamics at the inner cell mass versus established embryonic stem (ES) cells JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1105414108 DO - 10.1073/pnas.1105414108 ID - Varela2011 ER - TY - JOUR AU - Beier, F. AU - Foronda, M. AU - Martinez, P. AU - Blasco, M. A. PY - 2012 DA - 2012// TI - Conditional TRF1 knockout in the hematopoietic compartment leads to bone marrow failure and recapitulates clinical features of dyskeratosis congenita JO - Blood VL - 120 UR - https://doi.org/10.1182/blood-2012-03-418038 DO - 10.1182/blood-2012-03-418038 ID - Beier2012 ER - TY - JOUR AU - Dodt, M. AU - Roehr, J. AU - Ahmad, R. AU - Dieterich, C. PY - 2012 DA - 2012// TI - FLEXBAR - flexible barcode and adapter processing for next-generation sequencing platforms JO - Biology VL - 1 UR - https://doi.org/10.3390/biology1030895 DO - 10.3390/biology1030895 ID - Dodt2012 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with Burrows-Wheeler transform JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - JOUR AU - Zhang, Y. AU - Liu, T. AU - Meyer, C. A. AU - Eeckhoute, J. AU - Johnson, D. S. AU - Bernstein, B. E. PY - 2008 DA - 2008// TI - Model-based analysis of ChIP-Seq (MACS) JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-9-r137 DO - 10.1186/gb-2008-9-9-r137 ID - Zhang2008 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Kim, D. AU - Pertea, G. AU - Trapnell, C. AU - Pimentel, H. AU - Kelley, R. AU - Salzberg, S. L. PY - 2013 DA - 2013// TI - TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-4-r36 DO - 10.1186/gb-2013-14-4-r36 ID - Kim2013 ER - TY - JOUR AU - Anders, S. AU - Pyl, P. T. AU - Huber, W. PY - 2015 DA - 2015// TI - HTSeq A Python framework to work with high-throughput sequencing data JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btu638 DO - 10.1093/bioinformatics/btu638 ID - Anders2015 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - JOUR AU - Favorov, A. AU - Mularoni, L. AU - Cope, L. M. AU - Medvedeva, Y. AU - Mironov, A. A. AU - Makeev, V. J. PY - 2012 DA - 2012// TI - Exploring massive, genome scale datasets with the GenometriCorr package JO - PLoS Comput Biol VL - 8 UR - https://doi.org/10.1371/journal.pcbi.1002529 DO - 10.1371/journal.pcbi.1002529 ID - Favorov2012 ER - TY - JOUR AU - Wilczynski, B. AU - Dojer, N. AU - Patelak, M. AU - Tiuryn, J. PY - 2009 DA - 2009// TI - Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs JO - BMC Bioinf VL - 10 UR - https://doi.org/10.1186/1471-2105-10-82 DO - 10.1186/1471-2105-10-82 ID - Wilczynski2009 ER - TY - JOUR AU - Newburger, D. E. AU - Bulyk, M. L. PY - 2009 DA - 2009// TI - UniPROBE: an online database of protein binding microarray data on protein-DNA interactions JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn660 DO - 10.1093/nar/gkn660 ID - Newburger2009 ER - TY - JOUR AU - Bryne, J. C. AU - Valen, E. AU - Tang, M. H. AU - Marstrand, T. AU - Winther, O. PY - 2008 DA - 2008// TI - da P, et al. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm955 DO - 10.1093/nar/gkm955 ID - Bryne2008 ER - TY - JOUR AU - Hochberg, Y. AU - Benjamini, Y. PY - 2009 DA - 2009// TI - Controlling the false discovery rate: a practical and powerful approach to multiple testing JO - J R Stat Soc VL - 57 ID - Hochberg2009 ER -