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profileChristoph Bock, Ph.D.

TitlePost-Doctoral Fellow in Stem Cell & Regenerative Biology (EXT)
InstitutionFaculty of Arts & Sciences
DepartmentStem Cell and Regenerative Biology
AddressMeissner Lab
Bauer Laboratory, Room 208
7 Divinity Ave
Cambridge MA 02138
Phone617/496-5172
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Collapse Bibliographic 
Collapse selected publications
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. Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R, Schuster M, Bock C, Ideker T, Jackson SP, Menche J, Loizou JI. Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia. Nat Commun. 2017 Nov 01; 8(1):1238. PMID: 29089570.
    View in: PubMed
  2. Göschl L, Preglej T, Hamminger P, Bonelli M, Andersen L, Boucheron N, Gülich AF, Müller L, Saferding V, Mufazalov IA, Hirahara K, Seiser C, Matthias P, Penz T, Schuster M, Bock C, Waisman A, Steiner G, Ellmeier W. A T cell-specific deletion of HDAC1 protects against experimental autoimmune encephalomyelitis. J Autoimmun. 2017 Sep 27. PMID: 28964722.
    View in: PubMed
  3. Andergassen D, Dotter CP, Wenzel D, Sigl V, Bammer PC, Muckenhuber M, Mayer D, Kulinski TM, Theussl HC, Penninger JM, Bock C, Barlow DP, Pauler FM, Hudson QJ. Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression. Elife. 2017 Aug 14; 6. PMID: 28806168.
    View in: PubMed
  4. Albrecht F, List M, Bock C, Lengauer T. DeepBlueR: large-scale epigenomic analysis in R. Bioinformatics. 2017 Jul 01; 33(13):2063-2064. PMID: 28334349.
    View in: PubMed
  5. Licciardello MP, Ringler A, Markt P, Klepsch F, Lardeau CH, Sdelci S, Schirghuber E, Müller AC, Caldera M, Wagner A, Herzog R, Penz T, Schuster M, Boidol B, Dürnberger G, Folkvaljon Y, Stattin P, Ivanov V, Colinge J, Bock C, Kratochwill K, Menche J, Bennett KL, Kubicek S. A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor. Nat Chem Biol. 2017 Jul; 13(7):771-778. PMID: 28530711.
    View in: PubMed
  6. Müller H, Jimenez-Heredia R, Krolo A, Hirschmugl T, Dmytrus J, Boztug K, Bock C. VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data. Nucleic Acids Res. 2017 May 17. PMID: 28520890.
    View in: PubMed
  7. Sheffield NC, Pierron G, Klughammer J, Datlinger P, Schönegger A, Schuster M, Hadler J, Surdez D, Guillemot D, Lapouble E, Freneaux P, Champigneulle J, Bouvier R, Walder D, Ambros IM, Hutter C, Sorz E, Amaral AT, de Álava E, Schallmoser K, Strunk D, Rinner B, Liegl-Atzwanger B, Huppertz B, Leithner A, de Pinieux G, Terrier P, Laurence V, Michon J, Ladenstein R, Holter W, Windhager R, Dirksen U, Ambros PF, Delattre O, Kovar H, Bock C, Tomazou EM. DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma. Nat Med. 2017 Mar; 23(3):386-395. PMID: 28134926.
    View in: PubMed
  8. Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, Schuster LC, Kuchler A, Alpar D, Bock C. Pooled CRISPR screening with single-cell transcriptome readout. Nat Methods. 2017 Mar; 14(3):297-301. PMID: 28099430.
    View in: PubMed
  9. Romanov RA, Zeisel A, Bakker J, Girach F, Hellysaz A, Tomer R, Alpár A, Mulder J, Clotman F, Keimpema E, Hsueh B, Crow AK, Martens H, Schwindling C, Calvigioni D, Bains JS, Máté Z, Szabó G, Yanagawa Y, Zhang MD, Rendeiro A, Farlik M, Uhlén M, Wulff P, Bock C, Broberger C, Deisseroth K, Hökfelt T, Linnarsson S, Horvath TL, Harkany T. Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. Nat Neurosci. 2017 Feb; 20(2):176-188. PMID: 27991900.
    View in: PubMed
  10. Li J, Casteels T, Frogne T, Ingvorsen C, Honoré C, Courtney M, Huber KV, Schmitner N, Kimmel RA, Romanov RA, Sturtzel C, Lardeau CH, Klughammer J, Farlik M, Sdelci S, Vieira A, Avolio F, Briand F, Baburin I, Májek P, Pauler FM, Penz T, Stukalov A, Gridling M, Parapatics K, Barbieux C, Berishvili E, Spittler A, Colinge J, Bennett KL, Hering S, Sulpice T, Bock C, Distel M, Harkany T, Meyer D, Superti-Furga G, Collombat P, Hecksher-Sørensen J, Kubicek S. Artemisinins Target GABAA Receptor Signaling and Impair a Cell Identity. Cell. 2017 Jan 12; 168(1-2):86-100.e15. PMID: 27916275.
    View in: PubMed
  11. Farlik M, Halbritter F, Müller F, Choudry FA, Ebert P, Klughammer J, Farrow S, Santoro A, Ciaurro V, Mathur A, Uppal R, Stunnenberg HG, Ouwehand WH, Laurenti E, Lengauer T, Frontini M, Bock C. DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation. Cell Stem Cell. 2016 Dec 01; 19(6):808-822. PMID: 27867036.
    View in: PubMed
  12. Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G. Erratum to: Making sense of big data in health research: towards an EU action plan. Genome Med. 2016 11 07; 8(1):118. PMID: 27821178.
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  13. Bock C. Preserve personal freedom in networked societies. Nature. 2016 09 01; 537(7618):9. PMID: 27582189.
    View in: PubMed
  14. Martínez-Cardús A, Moran S, Musulen E, Moutinho C, Manzano JL, Martinez-Balibrea E, Tierno M, Élez E, Landolfi S, Lorden P, Arribas C, Müller F, Bock C, Tabernero J, Esteller M. Epigenetic Homogeneity Within Colorectal Tumors Predicts Shorter Relapse-Free and Overall Survival Times for Patients With Locoregional Cancer. Gastroenterology. 2016 Nov; 151(5):961-972. PMID: 27521480.
    View in: PubMed
  15. Mass E, Ballesteros I, Farlik M, Halbritter F, Günther P, Crozet L, Jacome-Galarza CE, Händler K, Klughammer J, Kobayashi Y, Gomez-Perdiguero E, Schultze JL, Beyer M, Bock C, Geissmann F. Specification of tissue-resident macrophages during organogenesis. Science. 2016 09 09; 353(6304). PMID: 27492475.
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  16. Rendeiro AF, Schmidl C, Strefford JC, Walewska R, Davis Z, Farlik M, Oscier D, Bock C. Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks. Nat Commun. 2016 Jun 27; 7:11938. PMID: 27346425.
    View in: PubMed
  17. Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G. Making sense of big data in health research: Towards an EU action plan. Genome Med. 2016 06 23; 8(1):71. PMID: 27338147; PMCID: PMC4919856.
  18. Bock C, Farlik M, Sheffield NC. Multi-Omics of Single Cells: Strategies and Applications. Trends Biotechnol. 2016 Aug; 34(8):605-608. PMID: 27212022; PMCID: PMC4959511.
  19. Sdelci S, Lardeau CH, Tallant C, Klepsch F, Klaiber B, Bennett J, Rathert P, Schuster M, Penz T, Fedorov O, Superti-Furga G, Bock C, Zuber J, Huber KV, Knapp S, Müller S, Kubicek S. Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. Nat Chem Biol. 2016 Jul; 12(7):504-10. PMID: 27159579.
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  20. Feichtinger J, Hernández I, Fischer C, Hanscho M, Auer N, Hackl M, Jadhav V, Baumann M, Krempl PM, Schmidl C, Farlik M, Schuster M, Merkel A, Sommer A, Heath S, Rico D, Bock C, Thallinger GG, Borth N. Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time. Biotechnol Bioeng. 2016 Oct; 113(10):2241-53. PMID: 27072894; PMCID: PMC5006888.
  21. Albrecht F, List M, Bock C, Lengauer T. DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. Nucleic Acids Res. 2016 Jul 08; 44(W1):W581-6. PMID: 27084938; PMCID: PMC4987868.
  22. Mazouzi A, Stukalov A, Müller AC, Chen D, Wiedner M, Prochazkova J, Chiang SC, Schuster M, Breitwieser FP, Pichlmair A, El-Khamisy SF, Bock C, Kralovics R, Colinge J, Bennett KL, Loizou JI. A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN. Cell Rep. 2016 Apr 14. PMID: 27149854.
    View in: PubMed
  23. Alexander J, Kalev O, Mehrabian S, Traykov L, Raycheva M, Kanakis D, Drineas P, Lutz MI, Ströbel T, Penz T, Schuster M, Bock C, Ferrer I, Paschou P, Kovacs GG. Familial early-onset dementia with complex neuropathologic phenotype and genomic background. Neurobiol Aging. 2016 Jun; 42:199-204. PMID: 27143436.
    View in: PubMed
  24. Li J, Klughammer J, Farlik M, Penz T, Spittler A, Barbieux C, Berishvili E, Bock C, Kubicek S. Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types. EMBO Rep. 2016 Feb; 17(2):178-87. PMID: 26691212; PMCID: PMC4784001.
  25. Klughammer J, Datlinger P, Printz D, Sheffield NC, Farlik M, Hadler J, Fritsch G, Bock C. Differential DNA Methylation Analysis without a Reference Genome. Cell Rep. 2015 Dec 22; 13(11):2621-2633. PMID: 26673328; PMCID: PMC4695333.
  26. Sheffield NC, Bock C. LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. Bioinformatics. 2016 Feb 15; 32(4):587-9. PMID: 26508757; PMCID: PMC4743627.
  27. Grebien F, Vedadi M, Getlik M, Giambruno R, Grover A, Avellino R, Skucha A, Vittori S, Kuznetsova E, Smil D, Barsyte-Lovejoy D, Li F, Poda G, Schapira M, Wu H, Dong A, Senisterra G, Stukalov A, Huber KV, Schönegger A, Marcellus R, Bilban M, Bock C, Brown PJ, Zuber J, Bennett KL, Al-Awar R, Delwel R, Nerlov C, Arrowsmith CH, Superti-Furga G. Erratum: Pharmacological targeting of the Wdr5-MLL interaction in C/EBPa N-terminal leukemia. Nat Chem Biol. 2015 Oct; 11(10):815. PMID: 26379026.
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  28. Milosevic Feenstra JD, Nivarthi H, Gisslinger H, Leroy E, Rumi E, Chachoua I, Bagienski K, Kubesova B, Pietra D, Gisslinger B, Milanesi C, Jäger R, Chen D, Berg T, Schalling M, Schuster M, Bock C, Constantinescu SN, Cazzola M, Kralovics R. Whole-exome sequencing identifies novel MPL and JAK2 mutations in triple-negative myeloproliferative neoplasms. Blood. 2016 Jan 21; 127(3):325-32. PMID: 26423830; PMCID: PMC4752213.
  29. Schmidl C, Rendeiro AF, Sheffield NC, Bock C. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015 Oct; 12(10):963-965. PMID: 26280331; PMCID: PMC4589892.
  30. Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel JO, Lichter P, Mason CE, Navin N, Pe'er D, Polyak K, Roberts CW, Siu L, Snyder A, Stower H, Swanton C, Verhaak RG, Zenklusen JC, Zuber J, Zucman-Rossi J. Toward understanding and exploiting tumor heterogeneity. Nat Med. 2015 Aug; 21(8):846-53. PMID: 26248267; PMCID: PMC4785013.
  31. Grebien F, Vedadi M, Getlik M, Giambruno R, Grover A, Avellino R, Skucha A, Vittori S, Kuznetsova E, Smil D, Barsyte-Lovejoy D, Li F, Poda G, Schapira M, Wu H, Dong A, Senisterra G, Stukalov A, Huber KVM, Schönegger A, Marcellus R, Bilban M, Bock C, Brown PJ, Zuber J, Bennett KL, Al-Awar R, Delwel R, Nerlov C, Arrowsmith CH, Superti-Furga G. Pharmacological targeting of the Wdr5-MLL interaction in C/EBPa N-terminal leukemia. Nat Chem Biol. 2015 Aug; 11(8):571-578. PMID: 26167872; PMCID: PMC4511833.
  32. Tobi EW, Goeman JJ, Monajemi R, Gu H, Putter H, Zhang Y, Slieker RC, Stok AP, Thijssen PE, Müller F, van Zwet EW, Bock C, Meissner A, Lumey LH, Eline Slagboom P, Heijmans BT. Corrigendum: DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun. 2015 Jul 07; 6:7740. PMID: 26151124.
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  33. Dobbs K, Domínguez Conde C, Zhang SY, Parolini S, Audry M, Chou J, Haapaniemi E, Keles S, Bilic I, Okada S, Massaad MJ, Rounioja S, Alwahadneh AM, Serwas NK, Capuder K, Çiftçi E, Felgentreff K, Ohsumi TK, Pedergnana V, Boisson B, Haskologlu S, Ensari A, Schuster M, Moretta A, Itan Y, Patrizi O, Rozenberg F, Lebon P, Saarela J, Knip M, Petrovski S, Goldstein DB, Parrott RE, Savas B, Schambach A, Tabellini G, Bock C, Chatila TA, Comeau AM, Geha RS, Abel L, Buckley RH, Ikinciogullari A, Al-Herz W, Helminen M, Dogu F, Casanova JL, Boztug K, Notarangelo LD. Inherited DOCK2 Deficiency in Patients with Early-Onset Invasive Infections. N Engl J Med. 2015 Jun 18; 372(25):2409-22. PMID: 26083206.
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  34. Amabile G, Di Ruscio A, Müller F, Welner RS, Yang H, Ebralidze AK, Zhang H, Levantini E, Qi L, Martinelli G, Brummelkamp T, Le Beau MM, Figueroa ME, Bock C, Tenen DG. Dissecting the role of aberrant DNA methylation in human leukaemia. Nat Commun. 2015 May 22; 6:7091. PMID: 25997600; PMCID: PMC4443494.
  35. Kulinski TM, Casari MR, Guenzl PM, Wenzel D, Andergassen D, Hladik A, Datlinger P, Farlik M, Theussl HC, Penninger JM, Knapp S, Bock C, Barlow DP, Hudson QJ. Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern. Dev Biol. 2015 Jun 15; 402(2):291-305. PMID: 25912690; PMCID: PMC4454777.
  36. Ebert P, Bock C. Improving reference epigenome catalogs by computational prediction. Nat Biotechnol. 2015 Apr; 33(4):354-5. PMID: 25850057.
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  37. Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, Bock C. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep. 2015 Mar 03; 10(8):1386-97. PMID: 25732828; PMCID: PMC4542311.
  38. Tomazou EM, Sheffield NC, Schmidl C, Schuster M, Schönegger A, Datlinger P, Kubicek S, Bock C, Kovar H. Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1. Cell Rep. 2015 Feb 24; 10(7):1082-95. PMID: 25704812; PMCID: PMC4542316.
  39. Tobi EW, Goeman JJ, Monajemi R, Gu H, Putter H, Zhang Y, Slieker RC, Stok AP, Thijssen PE, Müller F, van Zwet EW, Bock C, Meissner A, Lumey LH, Eline Slagboom P, Heijmans BT. DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun. 2014 Nov 26; 5:5592. PMID: 25424739; PMCID: PMC4246417.
  40. Ichida JK, W JT, 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. Erratum: Notch inhibition allows oncogene-independent generation of iPS cells. Nat Chem Biol. 2014 Nov 13; 10(12):1074. PMID: 25393494.
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  41. Ichida JK, W JT, 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. Erratum: Notch inhibition allows oncogene-independent generation of iPS cells. Nat Chem Biol. 2014 Nov 13; 10(12):1074. PMID: 25393496.
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  42. Assenov Y, Müller F, Lutsik P, Walter J, Lengauer T, Bock C. Comprehensive analysis of DNA methylation data with RnBeads. Nat Methods. 2014 Nov; 11(11):1138-1140. PMID: 25262207; PMCID: PMC4216143.
  43. Deplus R, Blanchon L, Rajavelu A, Boukaba A, Defrance M, Luciani J, Rothé F, Dedeurwaerder S, Denis H, Brinkman AB, Simmer F, Müller F, Bertin B, Berdasco M, Putmans P, Calonne E, Litchfield DW, de Launoit Y, Jurkowski TP, Stunnenberg HG, Bock C, Sotiriou C, Fraga MF, Esteller M, Jeltsch A, Fuks F. Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a. Cell Rep. 2014 Aug 07; 8(3):743-53. PMID: 25066127.
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  44. 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.
  45. Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurevic N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilaš J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdic G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potocnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidakovic M, Widschwendter M. Relationship between genome and epigenome--challenges and requirements for future research. BMC Genomics. 2014 Jun 18; 15:487. PMID: 24942464; PMCID: PMC4073504.
  46. Bock C. Synergy and competition between cancer genome sequencing and epigenome mapping projects. Genome Med. 2014; 6(5):41. PMID: 25031623; PMCID: PMC4062064.
  47. Becker D, Lutsik P, Ebert P, Bock C, Lengauer T, Walter J. BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W501-7. PMID: 24875479; PMCID: PMC4086109.
  48. Sun D, Luo M, Jeong M, Rodriguez B, Xia Z, Hannah R, Wang H, Le T, Faull KF, Chen R, Gu H, Bock C, Meissner A, Göttgens B, Darlington GJ, Li W, Goodell MA. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell. 2014 May 01; 14(5):673-88. PMID: 24792119; PMCID: PMC4070311.
  49. Planello AC, Ji J, Sharma V, Singhania R, Mbabaali F, Müller F, Alfaro JA, Bock C, De Carvalho DD, Batada NN. Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors. Cell Regen (Lond). 2014; 3(1):4. PMID: 25408883; PMCID: PMC4230737.
  50. Klampfl T, Milosevic JD, Puda A, Schönegger A, Bagienski K, Berg T, Harutyunyan AS, Gisslinger B, Rumi E, Malcovati L, Pietra D, Elena C, Della Porta MG, Pieri L, Guglielmelli P, Bock C, Doubek M, Dvorakova D, Suvajdzic N, Tomin D, Tosic N, Racil Z, Steurer M, Pavlovic S, Vannucchi AM, Cazzola M, Gisslinger H, Kralovics R. Complex patterns of chromosome 11 aberrations in myeloid malignancies target CBL, MLL, DDB1 and LMO2. PLoS One. 2013; 8(10):e77819. PMID: 24147083; PMCID: PMC3797696.
  51. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct; 10(10):949-55. PMID: 24076989.
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  52. Sandoval J, Mendez-Gonzalez J, Nadal E, Chen G, Carmona FJ, Sayols S, Moran S, Heyn H, Vizoso M, Gomez A, Sanchez-Cespedes M, Assenov Y, Müller F, Bock C, Taron M, Mora J, Muscarella LA, Liloglou T, Davies M, Pollan M, Pajares MJ, Torre W, Montuenga LM, Brambilla E, Field JK, Roz L, Lo Iacono M, Scagliotti GV, Rosell R, Beer DG, Esteller M. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. J Clin Oncol. 2013 Nov 10; 31(32):4140-7. PMID: 24081945.
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  53. Bürckstümmer T, Banning C, Hainzl P, Schobesberger R, Kerzendorfer C, Pauler FM, Chen D, Them N, Schischlik F, Rebsamen M, Smida M, Fece de la Cruz F, Lapao A, Liszt M, Eizinger B, Guenzl PM, Blomen VA, Konopka T, Gapp B, Parapatics K, Maier B, Stöckl J, Fischl W, Salic S, Taba Casari MR, Knapp S, Bennett KL, Bock C, Colinge J, Kralovics R, Ammerer G, Casari G, Brummelkamp TR, Superti-Furga G, Nijman SM. A reversible gene trap collection empowers haploid genetics in human cells. Nat Methods. 2013 Oct; 10(10):965-71. PMID: 24161985.
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  54. Stelzer Y, Ronen D, Bock C, Boyle P, Meissner A, Benvenisty N. Identification of novel imprinted differentially methylated regions by global analysis of human-parthenogenetic-induced pluripotent stem cells. Stem Cell Reports. 2013; 1(1):79-89. PMID: 24052944; PMCID: PMC3757747.
  55. Cao K, Lailler N, Zhang Y, Kumar A, Uppal K, Liu Z, Lee EK, Wu H, Medrzycki M, Pan C, Ho PY, Cooper GP, Dong X, Bock C, Bouhassira EE, Fan Y. High-resolution mapping of h1 linker histone variants in embryonic stem cells. PLoS Genet. 2013; 9(4):e1003417. PMID: 23633960; PMCID: PMC3636266.
  56. Bock C, Wutz A. DNA methylation: a matter of culture. Nat Struct Mol Biol. 2013 Mar; 20(3):249-51. PMID: 23463307.
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  57. Beerman I, Bock C, Garrison BS, Smith ZD, Gu H, Meissner A, Rossi DJ. Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging. Cell Stem Cell. 2013 Apr 04; 12(4):413-25. PMID: 23415915.
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  58. Simmer F, Brinkman AB, Assenov Y, Matarese F, Kaan A, Sabatino L, Villanueva A, Huertas D, Esteller M, Lengauer T, Bock C, Colantuoni V, Altucci L, Stunnenberg HG. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics. 2012 Dec 01; 7(12):1355-67. PMID: 23079744; PMCID: PMC3528691.
  59. Halachev K, Bast H, Albrecht F, Lengauer T, Bock C. EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol. 2012 Oct 03; 13(10):R96. PMID: 23034089; PMCID: PMC3491424.
  60. Bock C. Analysing and interpreting DNA methylation data. Nat Rev Genet. 2012 Oct; 13(10):705-19. PMID: 22986265.
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  61. Bock C, Beerman I, Lien WH, Smith ZD, Gu H, Boyle P, Gnirke A, Fuchs E, Rossi DJ, Meissner A. DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol Cell. 2012 Aug 24; 47(4):633-47. PMID: 22841485; PMCID: PMC3428428.
  62. Bock C, Lengauer T. Managing drug resistance in cancer: lessons from HIV therapy. Nat Rev Cancer. 2012 06 07; 12(7):494-501. PMID: 22673150.
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  63. Mekhoubad S, Bock C, de Boer AS, Kiskinis E, Meissner A, Eggan K. Erosion of dosage compensation impacts human iPSC disease modeling. Cell Stem Cell. 2012 May 04; 10(5):595-609. PMID: 22560080; PMCID: PMC3603710.
  64. Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 2012 Jun; 22(6):1128-38. PMID: 22466170; PMCID: PMC3371717.
  65. Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, Lernmark Å, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S. BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol. 2012 Mar 07; 30(3):224-6. PMID: 22398613.
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  66. Feuerbach L, Halachev K, Assenov Y, Müller F, Bock C, Lengauer T. Analyzing epigenome data in context of genome evolution and human diseases. Methods Mol Biol. 2012; 856:431-67. PMID: 22399470.
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  67. 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.
  68. Xi Y, Bock C, Müller F, Sun D, Meissner A, Li W. RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics. 2012 Feb 01; 28(3):430-2. PMID: 22155871; PMCID: PMC3268241.
  69. Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JP, Godley LA, Li W, Goodell MA. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet. 2011 Dec 04; 44(1):23-31. PMID: 22138693; PMCID: PMC3637952.
  70. Shearstone JR, Pop R, Bock C, Boyle P, Meissner A, Socolovsky M. Global DNA demethylation during mouse erythropoiesis in vivo. Science. 2011 Nov 11; 334(6057):799-802. PMID: 22076376; PMCID: PMC3230325.
  71. Xu H, Yi BA, Wu H, Bock C, Gu H, Lui KO, Park JH, Shao Y, Riley AK, Domian IJ, Hu E, Willette R, Lepore J, Meissner A, Wang Z, Chien KR. Highly efficient derivation of ventricular cardiomyocytes from induced pluripotent stem cells with a distinct epigenetic signature. Cell Res. 2012 Jan; 22(1):142-54. PMID: 22064699; PMCID: PMC3351933.
  72. Calvanese V, Fernández AF, Urdinguio RG, Suárez-Alvarez B, Mangas C, Pérez-García V, Bueno C, Montes R, Ramos-Mejía V, Martínez-Camblor P, Ferrero C, Assenov Y, Bock C, Menendez P, Carrera AC, Lopez-Larrea C, Fraga MF. A promoter DNA demethylation landscape of human hematopoietic differentiation. Nucleic Acids Res. 2012 Jan; 40(1):116-31. PMID: 21911366; PMCID: PMC3245917.
  73. Zacharek SJ, Fillmore CM, Lau AN, Gludish DW, Chou A, Ho JW, Zamponi R, Gazit R, Bock C, Jäger N, Smith ZD, Kim TM, Saunders AH, Wong J, Lee JH, Roach RR, Rossi DJ, Meissner A, Gimelbrant AA, Park PJ, Kim CF. Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell. 2011 Sep 02; 9(3):272-81. PMID: 21885022; PMCID: PMC3167236.
  74. Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, Yamamoto H, Hidalgo M, Tan AC, Galm O, Ferrer I, Sanchez-Cespedes M, Villanueva A, Carmona J, Sanchez-Mut JV, Berdasco M, Moreno V, Capella G, Monk D, Ballestar E, Ropero S, Martinez R, Sanchez-Carbayo M, Prosper F, Agirre X, Fraga MF, Graña O, Perez-Jurado L, Mora J, Puig S, Prat J, Badimon L, Puca AA, Meltzer SJ, Lengauer T, Bridgewater J, Bock C, Esteller M. A DNA methylation fingerprint of 1628 human samples. Genome Res. 2012 Feb; 22(2):407-19. PMID: 21613409; PMCID: PMC3266047.
  75. Lutsik P, Feuerbach L, Arand J, Lengauer T, Walter J, Bock C. BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W551-6. PMID: 21565797; PMCID: PMC3125748.
  76. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc. 2011 Apr; 6(4):468-81. PMID: 21412275.
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  77. 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.
  78. Carone BR, Fauquier L, Habib N, Shea JM, Hart CE, Li R, Bock C, Li C, Gu H, Zamore PD, Meissner A, Weng Z, Hofmann HA, Friedman N, Rando OJ. Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell. 2010 Dec 23; 143(7):1084-96. PMID: 21183072; PMCID: PMC3039484.
  79. Bock C, Tomazou EM, Brinkman AB, Müller F, Simmer F, Gu H, Jäger N, Gnirke A, Stunnenberg HG, Meissner A. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol. 2010 Oct; 28(10):1106-14. PMID: 20852634; PMCID: PMC3066564.
  80. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. PMID: 20852635; PMCID: PMC2955169.
  81. Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods. 2010 Feb; 7(2):133-6. PMID: 20062050; PMCID: PMC2860480.
  82. Bock C, Von Kuster G, Halachev K, Taylor J, Nekrutenko A, Lengauer T. Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy. Methods Mol Biol. 2010; 628:275-96. PMID: 20238087.
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  83. Schüffler P, Mikeska T, Waha A, Lengauer T, Bock C. MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays. Genome Biol. 2009; 10(10):R105. PMID: 19804638; PMCID: PMC2784320.
  84. Bock C. Epigenetic biomarker development. Epigenomics. 2009 Oct; 1(1):99-110. PMID: 22122639.
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  85. Smith ZD, Gu H, Bock C, Gnirke A, Meissner A. High-throughput bisulfite sequencing in mammalian genomes. Methods. 2009 Jul; 48(3):226-32. PMID: 19442738; PMCID: PMC2864123.
  86. Zhang Y, Rohde C, Tierling S, Jurkowski TP, Bock C, Santacruz D, Ragozin S, Reinhardt R, Groth M, Walter J, Jeltsch A. DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLoS Genet. 2009 Mar; 5(3):e1000438. PMID: 19325872; PMCID: PMC2653639.
  87. Bock C, Halachev K, Büch J, Lengauer T. EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol. 2009 Feb 10; 10(2):R14. PMID: 19208250.
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  88. Kircher M, Bock C, Paulsen M. Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region. BMC Genomics. 2008 Jul 23; 9:346. PMID: 18651963; PMCID: PMC2500034.
  89. Moser D, Ekawardhani S, Kumsta R, Palmason H, Bock C, Athanassiadou Z, Lesch KP, Meyer J. Functional analysis of a potassium-chloride co-transporter 3 (SLC12A6) promoter polymorphism leading to an additional DNA methylation site. Neuropsychopharmacology. 2009 Jan; 34(2):458-67. PMID: 18536702.
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  90. Bock C, Walter J, Paulsen M, Lengauer T. Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res. 2008 Jun; 36(10):e55. PMID: 18413340; PMCID: PMC2425484.
  91. Bock C, Lengauer T. Computational epigenetics. Bioinformatics. 2008 Jan 01; 24(1):1-10. PMID: 18024971.
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  92. Mikeska T, Bock C, El-Maarri O, Hübner A, Ehrentraut D, Schramm J, Felsberg J, Kahl P, Büttner R, Pietsch T, Waha A. Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis. J Mol Diagn. 2007 Jul; 9(3):368-81. PMID: 17591937; PMCID: PMC1899414.
  93. Bock C, Walter J, Paulsen M, Lengauer T. CpG island mapping by epigenome prediction. PLoS Comput Biol. 2007 Jun; 3(6):e110. PMID: 17559301; PMCID: PMC1892605.
  94. Bock C, Paulsen M, Tierling S, Mikeska T, Lengauer T, Walter J. CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet. 2006 Mar; 2(3):e26. PMID: 16520826; PMCID: PMC1386721.
  95. Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics. 2005 Nov 01; 21(21):4067-8. PMID: 16141249.
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