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Michael Johannes Ziller, Ph.D.

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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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Genga RMJ, Kernfeld EM, Parsi KM, Parsons TJ, Ziller MJ, Maehr R. Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development. Cell Rep. 2019 Apr 16; 27(3):708-718.e10. PMID: 30995470.
    Citations:    
  2. Giulitti S, Pellegrini M, Zorzan I, Martini P, Gagliano O, Mutarelli M, Ziller MJ, Cacchiarelli D, Romualdi C, Elvassore N, Martello G. Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics. Nat Cell Biol. 2019 02; 21(2):275-286. PMID: 30598530.
    Citations:    Fields:    
  3. Hoffmann A, Ziller M, Spengler D. Childhood-Onset Schizophrenia: Insights from Induced Pluripotent Stem Cells. Int J Mol Sci. 2018 Nov 30; 19(12). PMID: 30513688.
    Citations:    Fields:    
  4. Sheng C, Jungverdorben J, Wiethoff H, Lin Q, Flitsch LJ, Eckert D, Hebisch M, Fischer J, Kesavan J, Weykopf B, Schneider L, Holtkamp D, Beck H, Till A, Wüllner U, Ziller MJ, Wagner W, Peitz M, Brüstle O. A stably self-renewing adult blood-derived induced neural stem cell exhibiting patternability and epigenetic rejuvenation. Nat Commun. 2018 10 02; 9(1):4047. PMID: 30279449.
    Citations:    Fields:    Translation:HumansCells
  5. Ahmad R, Sportelli V, Ziller M, Spengler D, Hoffmann A. Tracing Early Neurodevelopment in Schizophrenia with Induced Pluripotent Stem Cells. Cells. 2018 Sep 17; 7(9). PMID: 30227641.
    Citations:    
  6. Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C. Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. Cell Syst. 2018 Sep 26; 7(3):258-268.e3. PMID: 30195438.
    Citations:    Fields:    
  7. Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A. Author Correction: Global delay in nascent strand DNA methylation. Nat Struct Mol Biol. 2018 Apr; 25(4):355. PMID: 29581568.
    Citations:    Fields:    
  8. Ziller MJ, Ortega JA, Quinlan KA, Santos DP, Gu H, Martin EJ, Galonska C, Pop R, Maidl S, Di Pardo A, Huang M, Meltzer HY, Gnirke A, Heckman CJ, Meissner A, Kiskinis E. Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology. Cell Stem Cell. 2018 04 05; 22(4):559-574.e9. PMID: 29551301.
    Citations:    Fields:    
  9. Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A. Global delay in nascent strand DNA methylation. Nat Struct Mol Biol. 2018 Apr; 25(4):327-332. PMID: 29531288.
    Citations: 2     Fields:    
  10. Hoffmann A, Sportelli V, Ziller M, Spengler D. From the Psychiatrist's Couch to Induced Pluripotent Stem Cells: Bipolar Disease in a Dish. Int J Mol Sci. 2018 Mar 08; 19(3). PMID: 29517996.
    Citations: 1     Fields:    Translation:HumansCells
  11. Galonska C, Charlton J, Mattei AL, Donaghey J, Clement K, Gu H, Mohammad AW, Stamenova EK, Cacchiarelli D, Klages S, Timmermann B, Cantz T, Schöler HR, Gnirke A, Ziller MJ, Meissner A. Genome-wide tracking of dCas9-methyltransferase footprints. Nat Commun. 2018 02 09; 9(1):597. PMID: 29426832.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  12. Donaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke A, Ziller MJ, Meissner A. Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nat Genet. 2018 02; 50(2):250-258. PMID: 29358654.
    Citations: 5     Fields:    
  13. 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.
    Citations: 1     Fields:    Translation:Humans
  14. Yu VWC, 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 02 23; 168(5):944-945. PMID: 28235203.
    Citations: 5     Fields:    
  15. 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.
    Citations: 4     Fields:    Translation:HumansCells
  16. Hoffmann A, Ziller M, Spengler D. The Future is The Past: Methylation QTLs in Schizophrenia. Genes (Basel). 2016 Nov 24; 7(12). PMID: 27886132.
    Citations: 2     
  17. Yu VWC, 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.
    Citations: 24     Fields:    Translation:AnimalsCells
  18. 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 06 27; 7:11306. PMID: 27346250.
    Citations: 6     Fields:    Translation:HumansCells
  19. 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 07; 34(7):691-693. PMID: 27347755.
    Citations: 3     Fields:    
  20. 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.
    Citations: 21     Fields:    Translation:AnimalsCells
  21. 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.
    Citations: 25     Fields:    Translation:AnimalsCells
  22. 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.
    Citations: 39     Fields:    Translation:HumansCells
  23. 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.
    Citations: 86     Fields:    Translation:HumansAnimalsCells
  24. 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.
    Citations: 13     Fields:    Translation:HumansCells
  25. 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.
    Citations: 61     Fields:    Translation:HumansCells
  26. 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.
    Citations: 964     Fields:    Translation:HumansCells
  27. 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.
    Citations: 48     Fields:    Translation:HumansCells
  28. 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):813-825. PMID: 25490447.
    Citations: 59     Fields:    Translation:HumansCells
  29. 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.
    Citations: 42     Fields:    Translation:HumansCells
  30. 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.
    Citations: 15     Fields:    Translation:HumansAnimalsCells
  31. 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.
    Citations: 105     Fields:    Translation:HumansCells
  32. 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.
    Citations: 389     Fields:    Translation:HumansCells
  33. 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.
    Citations: 7     Fields:    
  34. 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.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  35. 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.
    Citations: 148     Fields:    Translation:HumansCells
  36. 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.
    Citations: 64     Fields:    Translation:HumansAnimalsCells
  37. 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.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  38. 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.
    Citations: 135     Fields:    Translation:HumansAnimalsCells
  39. 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.
    Citations: 345     Fields:    Translation:HumansCells
  40. 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.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  41. 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.
    Citations: 14     Fields:    Translation:Cells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.