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Publications

Citation data online: http://scholar.google.com/citations?user=9qSsTcIAAAAJ 

Main Publications (*corresponding author; #shared first / shared last author)

1.                    

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* (2016). DNA methylation dynamics of human hematopoietic stem cell differentiation. Cell Stem Cell, DOI: 10.1016/j.stem.2016.10.019. [part of the IHEC/BLUEPRINT collection of epigenome mapping studies, press releases by CeMM and the BLUEPRINT consortium, PaperClip in Cell]

2.                    

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* (2016). Specification of tissue-resident macrophages during organogenesis. Science 353, 6304. [published in the long format of a Research Article, press release by collaborator, Preview article published in the Immunity journal]

3.                    

Rendeiro AF, Schmidl C#, Strefford JC#, Walewska R, Davis Z, Farlik M, Oscier D, Bock C* (2016). Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks. Nature Communications 7, 11938. [coordinated press release by CeMM, University College London, and the BLUEPRINT consortium, highlighted on GenomeWeb etc.]

4.                    

Bock C*, Halbritter F, Carmona FJ, Tierling S, Datlinger P, Assenov Y, Berdasco M, Bergmann AK, Booher K, Busato F, Campan M, Dahl C, Dahmcke CM, Diep D, Fernández AF, Gerhauser C, Haake A, Heilmann K, Holcomb T, Hussmann D, Ito M, Kreutz M, Kulis M, Lopez V, Nair SS, Paul DS, Plongthongkum N, Qu W, Queirós AC, Sauter G, Schlomm T, Stirzaker C, Statham A, Strogantsev R, Urdinguio RG, Walter K, Weichenhan D, Weisenberger DJ, Beck S, Clark SJ, Esteller M, Ferguson-Smith AC, Fraga MF, Guldberg P, Hansen LL, Laird PW, Martin-Subero JI, Nygren AOH, Peist R, Plass C, Shames DS, Siebert R, Sun X, Tost J, Walter J, Zhang K, for the BLUEPRINT consortium (2016). Quantitative comparison of DNA methylation assays for large-scale validation and epigenetic biomarker development. Nature Biotechnology 34, 726-737. [press release by CeMM, University College London, and the BLUEPRINT consortium, highlighted on cover & on GenomeWeb etc., Altmetric score of 182, corresponding to online Twitter/blogging attention in the 98th percentile]

5.                    

Bock C*, Farlik M, Sheffield NC (2016). Multi-omics of single cells: Strategies and applications. Trends in Biotechnology 34, 605-608. [invited review article, journal’s 2nd most accessed paper within 90 days of publication]

6.                    

Li J, Klughammer J#, Farlik M#, Penz T#, Spittler A, Barbieux C, Berishvili E, Bock C*, Kubicek S* (2016). Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types. EMBO Reports 17, 178-187.[first single-cell RNA-seq paper from Austria; press release by CeMM]

7.                    

Sheffield NC*, Bock C* (2016). LOLA: Enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. Bioinformatics 32, 587-589. [tool usage statistics: 760 users since 2015]

8.                    

Klughammer J, Datlinger P, Printz D, Sheffield NC, Farlik M, Hadler J, Fritsch G, Bock C* (2015). Differential DNA methylation analysis without a reference genome. Cell Reports 13, 2621-2633. [featured on GenomeWeb]

9.                    

Schmidl C, Rendeiro AF#, Sheffield NC, Bock C* (2015). ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nature Methods 12, 963-965. [featured on GenomeWeb and on EpiGenie; Altmetric score of 50, corresponding to online Twitter/blogging attention in the 96th percentile]

10.                

Farlik M, Sheffield NC#, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, Bock C* (2015). Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Reports 10, 1386-1397. [journal cover image, highlighted in Nature Methods and F1000Prime, interviews in the Cell Reporter Blog and on EpiGenie; Altmetric score of 40, corresponding to online Twitter/blogging attention in the 95th percentile]

11.                

Tomazou EM, Sheffield NC#, Schmidl C, Schuster M, Schönegger A, Datlinger P, Kubicek S, Bock C*, Kovar H* (2015). Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1. Cell Reports 10, 1082-1095. [press release by the collaboration partner: St. Anna Children’s Cancer Research Institute]

12.                

Assenov Y, Müller F#*, Lutsik P#, Walter J, Lengauer T, Bock C* (2014). Comprehensive analysis of DNA methylation data with RnBeads. Nature Methods 11, 1138-1140. [highlighted on cover; tool usage statistics: 4,000 users since 2014]

13.                

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 (2013). Recommendations for the design and analysis of epigenome-wide association studies. Nature Methods 10, 949-955. [invited review/whitepaper]

14.                

Halachev K*, Bast H, Albrecht F, Lengauer T, Bock C* (2012). EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biology 13, R96. [tool usage: 4,600 analysis sessions since 2012]

15.                

Bock C* (2012). Analysing and interpreting DNA methylation data. Nature Reviews Genetics 13, 705-719. [invited review article, most accessed paper in the NRG journal in the month of publication]

16.                

Bock C, Beerman I, Lien WH, Smith Z, Gu H, Boyle P, Gnirke A, Fuchs E, Rossi DJ, Meissner A* (2012). DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Molecular Cell 47, 633-47.

17.                

Bock C*, Lengauer T (2012). Managing drug resistance in cancer: Lessons from HIV therapy. Nature Reviews Cancer, 12, 494-501. [invited perspectives article; press releases by CeMM and Max Planck Society]

18.                

Xi Y, Bock C#, Müller F, Sun D, Meissner A, Li W* (2011). RRBSMAP: A fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics 28, 430-432.

19.                

Lutsik P, Feuerbach L, Arand J, Lengauer T, Walter J*, Bock C* (2011). BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing, Nucleic Acids Research 39 Suppl 2, W551-556. [highlighted by the editor as a featured top-5% article]

20.                

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* (2011). Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 144, 439-452. [press releases by the Broad Institute and Harvard University; highlight articles in Nature Reviews Genetics, Nature Biotechnology, Nature Methods, etc.]

21.                

Bock C*, Tomazou EM#, Brinkman AB, Müller F, Simmer F, Gu H, Jäger N, Gnirke A, Stunnenberg HG, Meissner A* (2010). Quantitative comparison of genome-wide DNA methylation mapping technologies, Nature Biotechnology 28, 1106-1114. [highlighted in a News & Views article in the same issue]

22.                

Gu H, Bock C#, Mikkelsen TS, Jäger N, Smith ZD, Tomazou EM, Gnirke A, Lander ES, Meissner A* (2010). Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nature Methods, 7, 133-136. [highlighted on cover; summary/comment article in F1000]

23.              

Bock C* (2009) Epigenetic biomarker development. Epigenomics 1: 99-110. [invited review]

24.                

Schüffler P, Mikeska T, Waha A, Lengauer T, Bock C* (2009). MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays. Genome Biology 10: R105. [marked as “highly accessed” on the journal’s website; tool usage statistics: 400 users, 2,100 analyses since 2008]

25.                

Bock C*, Halachev K, Büch J, Lengauer T (2009). EpiGRAPH: User-friendly software for statistical analysis and prediction of epigenomic data. Genome Biology 10: R14. [tool usage statistics: 2,900 users since 2007]

26.                

Bock C*, Walter J, Paulsen M, Lengauer T (2008). Inter-individual variation of DNA methylation and its implica­tions for large-scale epigenome mapping. Nucleic Acids Research 36: e55. [journal cover image]

27.                

Bock C*, Lengauer T (2008). Computational epigenetics. Bioinformatics, 24, 1-10. [invited review article; most frequently accessed paper in the Bioinformatics journal in 2008]

28.                

Bock C*, Walter J, Paulsen M, Lengauer T (2007) CpG island mapping by epigenome prediction. PLoS Computational Biology 3: e110. [press release by the Max Planck Society]

29.                

Bock C*, Paulsen M, Tierling S, Mikeska T, Lengauer T, Walter J (2006). CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genetics 2: e26. [journal cover image; press release by the Max Planck Society]

30.                

Bock C*, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T (2005). BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 21: 4067-4068. [tool usage statistics: 7,500 users, 82,000 analyses since 2005]

 

Additional Publications from Collaborative Research

31.                

Gapp BV, Konopka T, Penz T, Dalal V, Bürckstümmer T, Bock C, Nijman SM (2016). Parallel reverse genetic screening in mutant human cells using transcriptomics. Molecular Systems Biology 12, 879.

32.                

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 (2016). Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. Nature Chemical Biology 12, 504-510.

33.                

Mazouzi A, Stukalov A, Muller 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 (2016). A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN. Cell Reports, doi:10.1016/j.celrep.2016.03.077.

34.                

Alexander J, Kalev O, Mehrabian S, Traykov L, Raycheva M, Kanakis D, Drineas P, Lutz MI, Strobel T, Penz T, Schuster M, Bock C, Ferrer I, Paschou P, Kovacs GG (2016). Familial early-onset dementia with complex neuropathologic phenotype and genomic background. Neurobiology of Aging 42, 199-204.

35.                

Albrecht F, List M, Bock C, Lengauer T (2016). DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. Nucleic Acids Research, 44, W581-586.

36.                

Feichtinger J, Hernandez 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 (2016). Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time. Biotechnology and Bioengineering. doi:10.1002/bit.25990

37.                

Milosevic Feenstra JD, Nivarthi H, Gisslinger H, Leroy E, Rumi E, Chachoua I, Bagienski K, Kubesova B, Pietra D, Gisslinger B, Milanesi C, Jager R, Chen D, Berg T, Schalling M, Schuster M, Bock C, Constantinescu SN, Cazzola M, Kralovics R (2016). Whole-exome sequencing identifies novel MPL and JAK2 mutations in triple-negative myeloproliferative neoplasms. Blood 127, 325-332.

38.                

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, Schonegger 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 (2015). Pharmacological targeting of the Wdr5-MLL interaction in C/EBPalpha N-terminal leukemia. Nature Chemical Biology 11, 571-578.

39.                

Dobbs K, Dominguez 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, Ciftci 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 (2015). Inherited DOCK2 deficiency in patients with early-onset invasive infections. New England Journal of Medicine 372, 2409-2422.

40.                

Amabile G, Ruscio AD, Müller F, Welner RS, Yang H, Ebralidze AK, Zhang H, Levantini E, Qi L, Martinelli G, Brummelkamp T, Beau MML, Figueroa ME, Bock C, Tenen DG (2015). Dissecting the role of aberrant DNA methylation in human leukaemia. Nature Communications 6, 7091.

41.                

Malinowska-Ozdowy K, Frech C, Schönegger A, Eckert C, Cazzaniga G, Stanulla M, Zur Stadt U, Mecklenbrauker A, Schuster M, Kneidinger D, von Stackelberg A, Locatelli F, Schrappe M, Horstmann MA, Attarbaschi A, Bock C, Mann G, Haas OA, Panzer-Grümayer R (2015). KRAS and CREBBP mutations: a relapse-linked malicious liaison in childhood high hyperdiploid acute lymphoblastic leukemia. Leukemia 29, 1656-1667. [shared senior author]

42.                

Dahlberg A, Woo S, Delaney C, Boyle P, Gnirke A, Bock C, Bernstein BE, Meissner A, Gottardo R, Bernstein ID (2015). Notch-mediated expansion of cord blood progenitors: maintenance of transcriptional and epigenetic fidelity. Leukemia 29, 1948-1951.

43.                

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 (2015). Imprinted Expression in Cystic Embryoid Bodies Shows an Embryonic And Not An Extra-Embryonic Pattern. Developmental Biology 402, 291-305.

44.                

Roadmap Epigenomics Consortium et al. (2015). Integrative analysis of 111 reference human epigenomes.
Nature 518, 317-330. [listed in the consortium longlist as “Analysis and production contributor”]

45.                

Licciardello MP, Müllner MK, Durnberger G, Kerzendorfer C, Boidol B, Trefzer C, Sdelci S, Berg T, Penz T, Schuster M, Bock C, Kralovics R, Superti-Furga G, Colinge J, Nijman SM, Kubicek S (2014). NOTCH1 activation in breast cancer confers sensitivity to inhibition of SUMOylation. Oncogene 34, 3780-3790.

46.                

Tobi EW, Goeman JJ, Monajemi R, Gu H, Putter H, Zhang Y, Slieker RC, Stok AP, Thijssen PE, Muller F, van Zwet EW, Bock C, Meissner A, Lumey LH, Eline Slagboom P, Heijmans BT (2014). DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nature Communications 5, 5592.

47.                

Planello AC, Ji J, Sharma V, Singhania R, Mbabaali F, Muller F, Alfaro JA, Bock C, De Carvalho DD, Batada NN (2014). Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors. Cell Regeneration 3, 4.

48.                

Deplus R, Blanchon L, Rajavelu A, Boukaba A, Defrance M, Luciani J, Rothe F, Dedeurwaerder S, Denis H, Brinkman AB, Simmer F, Muller 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 (2014). Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a. Cell Reports 8, 743-753.

49.                

Ichida JK, T CWJ, 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 (2014). Notch inhibition allows oncogene-independent generation of iPS cells. Nature Chemical Biology 10, 632-639.

50.                

Becker D, Lutsik P, Ebert P, Bock C, Lengauer T, Walter J (2014). BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives. Nucleic Acids Research 42, W501-507.

51.                

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 (2014). Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell 14, 673-688.

52.                

Sanchez-Mut JV, Aso E, Heyn H, Matsuda T, Bock C, Ferrer I, Esteller M (2014). Promoter hypermethylation of the phosphatase DUSP22 mediates PKA-dependent TAU phosphorylation and CREB activation in Alzheimer's disease. Hippocampus 24, 363-368.

53.                

Klampfl T, Gisslinger H, Harutyunyan AS, Nivarthi H, Rumi E, Milosevic JD, Them NC, Berg T, Gisslinger B, Pietra D, Chen D, Vladimer GI, Bagienski K, Milanesi C, Casetti IC, Sant'Antonio E, Ferretti V, Elena C, Schischlik F, Cleary C, Six M, Schalling M, Schönegger A, Bock C, Malcovati L, Pascutto C, Superti-Furga G, Cazzola M, Kralovics R (2013). Somatic mutations of calreticulin in myeloproliferative neoplasms. New England Journal of Medicine 369, 2379-2390.

54.                

Bürckstümmer T, Banning C, Hainzl P, Schobesberger R, Kerzendorfer C, Pauler FM, Chen D, Them N, Schischlik F, Rebsamen M, Smida M, de la Cruz FF, 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 (2013). A reversible gene trap collection empowers haploid genetics in human cells. Nature Methods 10, 965-971.

55.                

Klampfl T, Milosevic JD, Puda A, Schonegger 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 (2013). Complex patterns of chromosome 11 aberrations in myeloid malignancies target CBL, MLL, DDB1 and LMO2. PLoS One 8, e77819.

56.                

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 (2013). A prognostic DNA methylation signature for stage I non-small-cell lung cancer. Journal of Clinical Oncology 31, 4140-4147.

57.                

Stelzer Y, Ronen D, Bock C, Boyle P, Meissner A, Benvenisty N (2013). Identification of novel imprinted differentially methylated regions by global analysis of human parthenogenetic induced pluripotent stem cells. Stem Cell Reports, 1, 79-89.

58.                

Kollmann K, Heller G, Schneckenleithner C, Warsch W, Scheicher R, Ott RG, Schafer M, Fajmann S, Schlederer M, Schiefer AI, Reichart U, Mayerhofer M, Hoeller C, Zöchbauer-Müller S, Kerjaschki D, Bock C, Kenner L, Hoefler G, Freissmuth M, Green AR, Moriggl R, Busslinger M, Malumbres M, Sexl V (2013). A kinase-independent function of CDK6 links the cell cycle to tumor angiogenesis. Cancer Cell 24, 167-181.

59.                

Cao K, Lailler N, Zhang Y, Kumar A, Uppal K, Liu Z, Lee EK, Wu H, Medrzycki M, Pan C, Ho PY, Cooper GP, Jr., Dong X, Bock C, Bouhassira EE, Fan Y (2013). High-resolution mapping of H1 linker histone variants in embryonic stem cells. PLOS Genetics 9, e1003417.

60.                

Beerman I, Bock C, Garrison BS, Smith ZD, Gu H, Meissner A, Rossi DJ (2013). Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging. Cell Stem Cell 12, 413-425.

61.                

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 (2012). Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics 7, 1355-1367.

62.                

Mikeska T, Bock C, Do H, Dobrovic A (2012). DNA methylation biomarkers in cancer: progress towards clinical implementation. Expert Reviews in Molecular Diagnostics 12, 473-487. [invited review]

63.                

Mekhoubad S, Bock C, de Boer AS, Kiskinis E, Meissner A, Eggan K (2012). Erosion of dosage compensation impacts human iPSC disease modeling. Cell Stem Cell 10, 595-609.

64.                

Brinkman AB, Bartels SJ, Gu H, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG (2012). Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Research 22, 1128-1138.

65.                

Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A (2011). Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLOS Genetics 7, e1002389.

66.                

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 (2011). Dnmt3a is essential for hematopoietic stem cell differentiation. Nature Genetics 44, 23-31.

67.                

Shearstone JR, Pop R, Bock C, Boyle P, Meissner A, Socolovsky M (2011). Global DNA demethylation during mouse erythropoiesis in vivo. Science 334, 799-802.

68.                

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 (2012). Highly efficient derivation of ventricular cardiomyocytes from induced pluripotent stem cells with a distinct epigenetic signature. Cell Research 22, 142-154.

69.                

Calvanese V, Fernandez AF, Urdinguio RG, Suarez-Alvarez B, Mangas C, Perez-Garcia V, Bueno C, Montes R, Ramos-Mejia V, Martinez-Camblor P, Ferrero C, Assenov Y, Bock C, Menendez P, Carrera AC, Lopez-Larrea C, Fraga MF (2012). A promoter DNA demethylation landscape of human hematopoietic differentiation. Nucleic Acids Research 40, 116-131.

70.                

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 (2011). Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell 9, 272-281.

71.                

Fernandez AF, Assenov Y, Martin-Subero J, 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 M, Grana O, Perez-Jurado L, Mora J, Puig S, Prat J, Badimon L, Puca A, Meltzer S, Lengauer T, Bridgewater J, Bock C, Esteller M (2012) A DNA methylation fingerprint of 1628 human samples. Genome Research 22, 407-419.

72.                

Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A (2011). Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nature Protocols 6, 468-481.

73.                

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 (2010). Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell 143, 1084-1096.

74.                

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 (2010). Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology 28, 1097-1105.

75.                

Smith ZD, Gu H, Bock C, Gnirke A, Meissner A (2009) High-throughput bisulfite sequencing in mammalian genomes. Methods 48: 226-232.

76.                

Zhang Y, Rohde C, Tierling S, Jurkowski TP, Bock C, Santacruz D, Ragozin S, Reinhardt R, Groth M, Walter J, Jeltsch A (2009) DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLOS Genetics 5: e1000438.

77.                

Kircher M, Bock C, Paulsen M (2008) Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region. BMC Genomics 9: 346.

78.                

Moser D, Ekawardhani S, Kumsta R, Palmason H, Bock C, Athanassiadou Z, Lesch KP, Meyer J (2008) Functional analysis of a potassium-chloride co-transporter 3 (SLC12A6) promoter polymorphism leading to an additional DNA methylation site. Neuropsychopharmacology 34: 458-467.

79.                

Mikeska T, Bock C, El-Maarri O, Hübner A, Ehrentraut D, Schramm J, Felsberg J, Kahl P, Büttner R, Pietsch T, Waha A (2007) Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis. Journal of Molecular Diagnostics 9: 368-381.

80.                

Liu F, Tostesen E, Sundet JK, Jenssen TK, Bock C, Jerstad GI, Thilly WG, Hovig E (2007) The human genomic melting map. PLOS Computational Biology 3: e93.

 

Other Publications (comments, book chapters, conference papers, correspondences, theses, etc.)

81.                

Bock C (2016). Preserve personal freedom in networked societies. Nature 537, 9. [comment article in Nature’s World View column. Tweeted 208 times to ~1.5 million followers, resulting in an Altmetrics score of 125]

82.                

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 A, 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, JR IM, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaino JA, Wubbe JP, Zanetti G (2016). Making sense of big data in health research: Towards an EU action plan. Genome Medicine 8, 71. [EU workshop report on research strategies in the field of big data and health]

83.                

Veillard AC, Datlinger P, Laczik M, Squazzo S, Bock C (2016). Diagenode premium RRBS technology: cost-effective DNA methylation mapping with superior coverage. Nature Methods (Application Note) 13. [description and evaluation of a commercial RRBS kit licensed to Diagenode]

84.                

Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer K, Nentwich M, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E (2015). Recommendations for the transition to open access in Austria. Working Group “National Strategy” of the Open Access Network Austria. doi:10.5281/zenodo.34079. [draft of the Austrian national open access strategy being adopted by Universities Austria & the Austrian Science Fund]

85.                

Bock C, Bortolussi L, Krüger T, Mikeev L, Wolf V (2015). Model-Based Whole-Genome Analysis of DNA Methylation Fidelity. Hybrid Systems Biology: Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015 Revised Selected Papers, A. Abate, and D. Šafránek, eds. (Cham, Springer International), pp. 141-155. [conference paper describing a biomathematical model of mitotic DNA methylation inheritance and fidelity]

86.                

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 (2015). Toward understanding and exploiting tumor heterogeneity. Nature Medicine 21, 846-853. [perspective article on the importance of studying the biological basis and medical implications of tumor heterogeneity]

87.                

Marx V (2015). Visualizing epigenomic data. Nature Methods 12, 499-502. [editorial news piece (“Technology Feature”) that discusses several bioinformatics contributions of the group]

88.                

Ebert P, Bock C (2015). Improving reference epigenome catalogs by computational prediction. Nature Biotechnology 33, 354-355. [News & Views article for Ernst & Kellis 2015, doi:10.1038/nbt.3157]

89.                

Bock C (2014). Synergy and competition between cancer genome sequencing and epigenome mapping projects. Genome Medicine 6, 41. [Comment article outlining the interplay between cancer genome & epigenome projects]

90.                

Bock C (2014). Towards a predictive genealogy of the PX sculpture series - a quantitative analysis of artist-directed evolution using bioinformatic methods. In: Bedrooms and other experimental arrangements, B. Ermacora, and D. Golz, eds. (Nürnberg, Verlag für moderne Kunst). [computational analysis of an artist’s oeuvre]

91.                

Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, de Paillerets BB, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurevi NA, Gut I, Heijmans BT, Hermouet S, Houwing Duistermaat J, Iacobucci I, Ila J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdi 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, Poto Nik 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, Vidakovi M, Widschwendter M (2014). Relationship between genome and epigenome - challenges and requirements for future research. BMC Genomics 15, 487. [EU workshop report on strategy in genome and epigenome research]

92.                

Bock C, Wutz A (2013). DNA methylation: a matter of culture. Nature Structural & Molecular Biology 20, 249-251. [News & Views article for Leitch et al. 2013, doi:10.1038/nsmb.2510]

93.                

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, Kuppers R, Lehrach H, Lengauer T, Lernmark A, 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 (2012). BLUEPRINT to decode the epigenetic signature written in blood. Nature Biotechnology 30, 224-226. [marker paper outlining the vision and strategy of the EU-FP7 “High Impact Project” BLUEPRINT]

94.                

Bock C (2013). Personalisierte Kombinationstherapien: Was die Krebsforschung von den Erfolgen in der HIV-Behandlung lernen kann. Universum Innere Medizin 02|2013, 16-18. [German-language overview article on precision medicine written for medical doctors in Austria]

95.                

Feuerbach L, Halachev K, Assenov Y, Müller F, Bock C, Lengauer T (2012). Analyzing epigenome data in context of genome evolution and human diseases. Methods in Molecular Biology 856, 431-467.

96.                

Bock C, Lengauer T (2012). Epigenom-Karten erstellen und nutzen. BIOspektrum 18, 138-141. [German-language overview article on epigenome mapping written for biologists in Germany, Austria, and Switzerland]

97.                

Bock C, Von Kuster G, Halachev K, Taylor J, Nekrutenko A, Lengauer T (2010) Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy. Methods Molecular Biology 628, 275-296. [hands-on tutorial describing key steps of epigenome data analysis using web-based software tools]

98.              

Bock C (2008) IVF: stars may have to consider the risk of stolen parenthood. Nature 454, 938.

99.                

Bock C (2008) Computational Epigenetics – Bioinformatic methods for epigenome prediction, DNA methylation mapping and cancer epigenetics, Saarland University. PhD Thesis. Saarbrücken, Oct 2008. Grade: summa cum laude (best out of four possible grades, typically awarded for the 5-10 percent best theses at this department)

100.             

Bock C, Lengauer T (2007) Computational Epigenetics: Bioinformatik für neue Wege in der Krebsforschung, Jahrbuch 2007. Max-Planck-Gesellschaft. [German-language overview article about computational epigenetics research published in an annual summary report of selected ongoing research in the Max Planck Society]

101.             

Bock C (2006) Bioinformatik: Neue Strategien gegen Krebs, Deutsches Ärzteblatt, 103, PRAXiS 10. [German-language overview article on cancer bioinformatics written for medical doctors in Germany]

102.             

Bock C, Hesser J (2006). Analysis and prediction of helix shift errors in homology modeling. In Silico Biology 6, 131-145. [paper on protein structure prediction summarizing the main result of the Master thesis]

103.             

Bock C (2004) Prediction of helix shift errors in homology modelling at an above 75% accuracy, University of Mannheim. Master Thesis. Mannheim, July 2004. Grade: 1.0 (out of a 1-to-6 range, 1.0 being best)

104.             

Xu, YY, Hsieh R, Lu YL, Shen YC, Chuang SC, Fu HC, Bock C, Pao HT (2004). Forecasting electricity market prices: a neural network based approach, In: IEEE International Joint Conference on Neural Networks 2004. Proceedings, pp. 2789-2794. [conference paper using machine learning technology for an economics application]

 

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