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profileMichael Johannes Ziller, Ph.D.

TitleFellow, Dept/Prog (Stip) (EXT)
InstitutionFaculty of Arts & Sciences
DepartmentStem Cell and Regenerative Biology
AddressMeissner Lab
Bauer Laboratory, 2nd Floor
7 Divinity Ave
Cambridge MA 02138
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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Hoffmann A, Sportelli V, Ziller M, Spengler D. Epigenomics of Major Depressive Disorders and Schizophrenia: Early Life Decides. Int J Mol Sci. 2017 Aug 04; 18(8). PMID: 28777307.
    View in: PubMed
  2. Yu VW, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells. Cell. 2017 Feb 23; 168(5):944-945. PMID: 28235203.
    View in: PubMed
  3. Ziller MJ, Stamenova EK, Gu H, Gnirke A, Meissner A. Targeted bisulfite sequencing of the dynamic DNA methylome. Epigenetics Chromatin. 2016; 9:55. PMID: 27980681.
    View in: PubMed
  4. Hoffmann A, Ziller M, Spengler D. The Future is The Past: Methylation QTLs in Schizophrenia. Genes (Basel). 2016 Nov 24; 7(12). PMID: 27886132.
    View in: PubMed
  5. Yu VW, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells. Cell. 2016 11 17; 167(5):1310-1322.e17. PMID: 27863245.
    View in: PubMed
  6. Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S. Information recovery from low coverage whole-genome bisulfite sequencing. Nat Commun. 2016 Jun 27; 7:11306. PMID: 27346250; PMCID: PMC4931220.
  7. Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Herrero J, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S. Saturation analysis for whole-genome bisulfite sequencing data. Nat Biotechnol. 2016 Jun 27. PMID: 27347755.
    View in: PubMed
  8. Shea JM, Serra RW, Carone BR, Shulha HP, Kucukural A, Ziller MJ, Vallaster MP, Gu H, Tapper AR, Gardner PD, Meissner A, Garber M, Rando OJ. Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome. Dev Cell. 2015 Dec 21; 35(6):750-8. PMID: 26702833; PMCID: PMC4691283 [Available on 12/21/16].
  9. Galonska C, Ziller MJ, Karnik R, Meissner A. Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding before Global Epigenetic Reprogramming. Cell Stem Cell. 2015 Oct 01; 17(4):462-70. PMID: 26235340; PMCID: PMC4592414 [Available on 10/01/16].
  10. Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell. 2015 Jul 16; 162(2):412-424. PMID: 26186193; PMCID: PMC4511597.
  11. Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet. 2015 May; 47(5):469-78. PMID: 25822089; PMCID: PMC4414868.
  12. Edri R, Yaffe Y, Ziller MJ, Mutukula N, Volkman R, David E, Jacob-Hirsch J, Malcov H, Levy C, Rechavi G, Gat-Viks I, Meissner A, Elkabetz Y. Analysing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors. Nat Commun. 2015 Mar 23; 6:6500. PMID: 25799239; PMCID: PMC4383005.
  13. Tsankov AM, Gu H, Akopian V, Ziller MJ, Donaghey J, Amit I, Gnirke A, Meissner A. Transcription factor binding dynamics during human ES cell differentiation. Nature. 2015 Feb 19; 518(7539):344-9. PMID: 25693565; PMCID: PMC4499331.
  14. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563; PMCID: PMC4530010.
  15. Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 2015 Feb 19; 518(7539):355-359. PMID: 25533951; PMCID: PMC4336237.
  16. Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell. 2014 Dec 08; 26(6):813-25. PMID: 25490447; PMCID: PMC4302418 [Available on 12/08/15].
  17. Ziller MJ, Hansen KD, Meissner A, Aryee MJ. Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nat Methods. 2015 Mar; 12(3):230-2, 1 p following 232. PMID: 25362363; PMCID: PMC4344394.
  18. Ichida JK, Tcw J, Williams LA, Carter AC, Shi Y, Moura MT, Ziller M, Singh S, Amabile G, Bock C, Umezawa A, Rubin LL, Bradner JE, Akutsu H, Meissner A, Eggan K. Notch inhibition allows oncogene-independent generation of iPS cells. Nat Chem Biol. 2014 Aug; 10(8):632-639. PMID: 24952596; PMCID: PMC4310751.
  19. Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K. Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1. Cell Stem Cell. 2014 Jun 05; 14(6):781-95. PMID: 24704492; PMCID: PMC4653065.
  20. Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A. Charting a dynamic DNA methylation landscape of the human genome. Nature. 2013 Aug 22; 500(7463):477-81. PMID: 23925113; PMCID: PMC3821869.
  21. Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A. The systems biology simulation core algorithm. BMC Syst Biol. 2013 Jul 05; 7:55. PMID: 23826941; PMCID: PMC3707837.
  22. Kearns NA, Genga RM, Ziller M, Kapinas K, Peters H, Brehm MA, Meissner A, Maehr R. Generation of organized anterior foregut epithelia from pluripotent stem cells using small molecules. Stem Cell Res. 2013 Nov; 11(3):1003-12. PMID: 23917481.
    View in: PubMed
  23. 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, Gnirke A, Lander ES, Bernstein BE, Meissner A. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013 May 23; 153(5):1149-63. PMID: 23664763; PMCID: PMC3709577.
  24. Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol. 2012 Oct 03; 13(10):R92. PMID: 23034176; PMCID: PMC3491420.
  25. Akopian V, Chan MM, Clement K, Galonska C, Gifford CA, Lehtola E, Liao J, Samavarchi-Tehrani P, Sindhu C, Smith ZD, Tsankov AM, Webster J, Zhang Y, Ziller MJ, Meissner A. Epigenomics and chromatin dynamics. Genome Biol. 2012 Feb 24; 13(2):313. PMID: 22364154; PMCID: PMC3334565.
  26. Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 2011 Dec; 7(12):e1002389. PMID: 22174693; PMCID: PMC3234221.
  27. Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, Gnirke A, Eggan K, Meissner A. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell. 2011 Feb 04; 144(3):439-52. PMID: 21295703; PMCID: PMC3063454.
  28. Zhang F, Weggler S, Ziller MJ, Ianeselli L, Heck BS, Hildebrandt A, Kohlbacher O, Skoda MW, Jacobs RM, Schreiber F. Universality of protein reentrant condensation in solution induced by multivalent metal ions. Proteins. 2010 Dec; 78(16):3450-7. PMID: 20872851.
    View in: PubMed
  29. Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, Oldiges M, Kohlbacher O, Zell A. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst Biol. 2009 Jan 14; 3:5. PMID: 19144170; PMCID: PMC2661887.
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