Portrait of Ben

Hi, I’m Ben!

I am an Associate Research Scholar and former EMBO Postdoctoral Research Fellow in the Department of Chemistry at Princeton University where I work with Prof. Tom Muir on how cancer seizes control of gene regulation.

In 2021, I received my PhD in Chemical Biology, advised by Prof. Daniel Summerer, for developing proteins that recognize rare DNA modifications in the human genome.

ORCID · Google Scholar · GitHub · LinkedIn

Research interests

My work focuses on:

  • How do small chemical changes in chromatin control cell-type-specific gene regulation?
  • How do diseases exploit or disrupt epigenetic mechanisms?

I study these questions using chemical biology approaches, pooled genetic screens, and integrated analysis of multi-omics data, connecting molecular features to regulatory outcomes and potential therapeutic vulnerabilities.

Publications

Preprints

  • L. Engelhard*; D. Schiller*; M. S. Zambrano-Mila; K. Keliuotyte; B. Buchmuller; S. Tiwari; J. Imig; A. Simeone; C. Schröter; S. Becker; D. Summerer.
    HM-DyadCap – Capture and Mapping of 5-Hydroxymethylcytosine/5-Methylcytosine CpG Dyads in Mammalian DNA.
    bioRxiv 2025. doi:10.1101/2025.10.29.685270 DOI

Original Research

  • B. Kosel; K. Bigler; B. C. Buchmuller; S. R. Acharyya; R. Linser; D. Summerer.
    Evolved Readers of 5‐Carboxylcytosine CpG Dyads Reveal a High Versatility of the Methyl‐CpG‐Binding Domain for Recognition of Noncanonical Epigenetic Marks.
    Angew. Chem. Int. Ed. 2024, 63(17), e202318837. doi:10.1002/anie.202318837 DOI PMID:38284298 PMID
  • H. Singh; C. K. Das; B. C. Buchmuller; L. V. Schäfer; D. Summerer; R. Linser.
    Epigenetic CpG duplex marks probed by an evolved DNA reader via a well-tempered conformational plasticity.
    Nucleic Acids Res. 2023, 51(12), 6495–6506. doi:10.1093/nar/gkad134 DOI PMID:36919612 PMID PMC10325892 PMC
  • J. Nowacki; M. Malenica; S. Schmeing; D. Schiller; B. Buchmuller; G. Amrahova; P. ‘t Hart.
    A translational repression reporter assay for the analysis of RNA-binding protein consensus sites.
    RNA Biol. 2023, 20(1), 85–94. doi:10.1080/15476286.2023.2192553 DOI PMID:36946649 PMID PMC10038052 PMC
  • A. Jung; A. Munõz-López; B. C. Buchmuller; S. Banerjee; D. Summerer.
    Imaging-Based In Situ Analysis of 5‑Methylcytosine at Low Repetitive Single Gene Loci with Transcription-Activator-Like Effector Probes.
    ACS Chem. Biol. 2023, 18(2), 230–236. doi:10.1021/acschembio.2c00857 DOI PMID:36693632 PMID PMC9942090 PMC
  • S. Palei; J. Weisner; M. Vogt; R. Gontla; B. Buchmuller; C. Ehrt; T. Grabe; S. Kleinbölting; M. Müller; G. H. Clever; D. Rauh; D. Summerer.
    A high-throughput effector screen identifies a novel small molecule scaffold for inhibition of ten-eleven translocation dioxygenase 2.
    RSC Med. Chem. 2022, 13(12), 1540–1548. doi:10.1039/d2md00186a DOI PMID:36545435 PMID PMC9749932 PMC
  • B. C. Buchmuller; J. Dröden; H. Singh; S. Palei; M. Drescher; R. Linser; D. Summerer.
    Evolved DNA Duplex Readers for Strand-Asymmetrically Modified 5‑Hydroxymethylcytosine/5-Methylcytosine CpG Dyads.
    JACS 2022, 144(7), 2987–2993. doi:10.1021/jacs.1c10678 DOI PMID:35157801 PMID PMC8874921 PMC
    Impact: First affinity probes enabling selective enrichment of strand-asymmetric epigenetic DNA marks from genomic DNA
  • Á. Muñoz‐López; A. Jung; B. Buchmuller; J. Wolffgramm; S. Maurer; A. Witte; D. Summerer.
    Engineered TALE Repeats for Enhanced Imaging‐Based Analysis of Cellular 5‐Methylcytosine.
    ChemBioChem 2021, 22(4), 645–651. doi:10.1002/cbic.202000563 DOI PMID:32991020 PMID PMC7894354 PMC
  • J. Wolffgramm; B. Buchmuller; S. Palei; Á. Muñoz‐López; J. Kanne; P. Janning; M. R. Schweiger; D. Summerer.
    Light‐Activation of DNA‐Methyltransferases.
    Angew. Chem. Int. Ed. 2021, 60(24), 13507–13512. doi:10.1002/anie.202103945 DOI PMID:33826797 PMID PMC8251764 PMC
  • S. Palei; B. Buchmuller; J. Wolffgramm; A. Muñoz-Lopez; S. Jung; P. Czodrowski; D. Summerer.
    Light-Activatable TET-Dioxygenases Reveal Dynamics of 5‑Methylcytosine Oxidation and Transcriptome Reorganization.
    JACS 2020, 142(16), 7289–7294. doi:10.1021/jacs.0c01193 DOI PMID:32286069 PMID
    Impact: First temporal control of TET dioxygenase activity in mammalian cells enabling time-resolved monitoring of methylation dynamics and transcriptome reorganization
  • J. Fueller; K. Herbst; M. Meurer; K. Gubicza; B. Kurtulmus; J. D. Knopf; D. Kirrmaier; B. C. Buchmuller; G. Pereira; M. K. Lemberg; M. Knop.
    CRISPR-Cas12a–assisted PCR tagging of mammalian genes.
    J. Cell Biol. 2020, 219(6), e201910210. doi:10.1083/jcb.201910210 DOI PMID:32406907 PMID PMC7265327 PMC
    Impact: Extended our CASTLING approach for gene editing to mammalian cells with up to 60% in-frame tagging efficiency; now widely adopted for endogenous protein tagging studies
  • Á. Muñoz‐López; B. Buchmuller; J. Wolffgramm; A. Jung; M. Hussong; J. Kanne; M. R. Schweiger; D. Summerer.
    Designer Receptors for Nucleotide‐Resolution Analysis of Genomic 5‐Methylcytosine by Cellular Imaging.
    Angew. Chem. Int. Ed. 2020, 59(23), 8927–8931. doi:10.1002/anie.202001935 DOI PMID:32167219 PMID PMC7318601 PMC
    Impact: First nucleotide-resolution imaging of 5mC in single cells; enabled direct correlation between epigenetic marks and transcription factor recruitment
  • B. C. Buchmuller; B. Kosel; D. Summerer.
    Complete Profiling of Methyl-CpG-Binding Domains for Combinations of Cytosine Modifications at CpG Dinucleotides Reveals Differential Read-out in Normal and Rett-Associated States.
    Sci. Rep. 2020, 10(1), 4053. doi:10.1038/s41598-020-61030-1 DOI PMID:32132616 PMID PMC7055227 PMC
    Impact: First comprehensive profiling of the human MBD protein family revealing differential recognition of oxidized CpG marks by Rett syndrome-associated MeCP2 mutations
  • B. C. Buchmuller*; K. Herbst*; M. Meurer; D. Kirrmaier; E. Sass; E. D. Levy; M. Knop.
    Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast.
    Nat. Commun. 2019, 10(1), 2960. doi:10.1038/s41467-019-10816-7 DOI PMID:31273196 PMID PMC6609715 PMC
    Impact: CASTLING enables rapid construction of yeast clone libraries with >90% tagging efficiency; method adapted for mammalian gene tagging (Fueller et al. 2020, J Cell Biol) and cited in advanced Cas12a engineering studies
  • M. Gieß; A. Muñoz-López; B. Buchmuller; G. Kubik; D. Summerer.
    Programmable Protein–DNA Cross-Linking for the Direct Capture and Quantification of 5‑Formylcytosine.
    JACS 2019, 141(24), 9453–9457. doi:10.1021/jacs.9b01432 DOI PMID:31180648 PMID
  • S. Maurer; B. Buchmuller; C. Ehrt; J. Jasper; O. Koch; D. Summerer.
    Overcoming conservation in TALE–DNA interactions: a minimal repeat scaffold enables selective recognition of an oxidized 5-methylcytosine.
    Chem. Sci. 2018, 9(36), 7247–7252. doi:10.1039/c8sc01958d DOI PMID:30288245 PMID PMC6148557 PMC
  • M. Meurer; Y. Duan; E. Sass; I. Kats; K. Herbst; B. C. Buchmuller; V. Dederer; F. Huber; D. Kirrmaier; M. Štefl; K. V. Laer; T. P. Dick; M. K. Lemberg; A. Khmelinskii; E. D. Levy; M. Knop.
    Genome-wide C-SWAT library for high-throughput yeast genome tagging.
    Nat. Methods 2018, 15(8), 598–600. doi:10.1038/s41592-018-0045-8 DOI PMID:29988096 PMID
  • C. Liolios; B. Buchmuller; U. Bauder-Wüst; M. Schäfer; K. Leotta; U. Haberkorn; M. Eder; K. Kopka.
    Monomeric and Dimeric 68Ga-Labeled Bombesin Analogues for Positron Emission Tomography (PET) Imaging of Tumors Expressing Gastrin-Releasing Peptide Receptors (GRPrs).
    J. Med. Chem. 2018, 61(5), 2062–2074. doi:10.1021/acs.jmedchem.7b01856 DOI PMID:29432691 PMID

Reviews, Book Chapters, Monographs

* denotes equal contribution ORCID: 0000-0002-4915-5949

Protocols

Good protocols evolve over time, but printed copies often don’t. Here, I share version-controlled write-ups to help track changes. You can check whether your printed copy is current, or just browse for the latest method:

Identifier Title Domain Status Last commit
SOP0001.1 Isolation of nuclei from tissue culture cells Cell biology Public 2025-11-03
SOP0002.1 Whole cell lysates from tissue culture cells Cell biology Internal
SOP0003.1 Native polyacrylamide gel electrophoresis Biochemistry Internal
SOP0004.3 Core histone expression and purification Biochemistry Internal
SOP0005.2 Histone octamer, tetramer, or dimer formation Biochemistry Internal
SOP0006.2 Reconstitution of mononucleosomes and nucleosome arrays Biochemistry Internal
SOP0007.1 Denaturating SDS polyacrylamide gel electrophoresis Biochemistry Internal
SOP0008.1 Western blotting Biochemistry Internal
SOP0009.1 Immunoblotting Biochemistry Internal
SOP0010.1 In-gel protein staining with Coomassie Brilliant Blue Biochemistry Internal
SOP0011.1 In-gel protein staining with silver nitrate Biochemistry Internal
SOP0012.2 Non-viral transfection of animal tissue culture cells Tissue culture Internal
SOP0013.1 Electroporation of animal tissue culture cells Tissue culture Internal
SOP0014.1 Counting cells Tissue culture Internal
SOP0015.1 Cultivating HeLa cells Tissue culture Internal
SOP0016.1 Cultivating MCF 10A cells Tissue culture Internal 2025-10-25
SOP0017.3 Lentiviral generation of stable animal cell lines Tissue culture Internal
SOP0018.1 Generation of stable cell lines using DNA transposases Tissue culture Internal
SOP0019.1 Selection and screening of stable mammalian cell lines Tissue culture Internal
SOP0020.1 Plasmid preparation by alkaline lysis Molecular biology Internal
SOP0021.1 Purification of nucleic acids Molecular biology Internal
SOP0022.1 Purification of nucleic acids from agarose gels Molecular biology Internal
SOP0023.1 Separation of RNA from DNA with guanidinium thiocyanate Molecular biology Internal
SOP0024.1 Extraction of genomic DNA from tissue culture cells Molecular biology Internal
SOP0025.1 Nuclear extraction and fractionation of chromatin-associated proteins Cell biology Internal
SOP0026.1 Acidic extraction of histone proteins Cell biology Internal
SOP0027.1 Immunoprecipitation of nuclear and cytosolic proteins Biochemistry Internal
SOP0028.2 Cell cycle synchronization of mammalian cell lines Tissue culture Internal
SOP0029.1 Cell cycle analysis by fluorescence staining Tissue culture Internal
SOP0030.1 Making reagents and buffers Core skills Public 2025-11-03
SOP0031.1 Designing and performing dilutions Core skills Internal 2025-11-03
SOP0032.1 Making and running agarose gels Molecular biology Internal
SOP0033.1 Restriction digest, end modification, and ligation of DNA Molecular biology Internal
SOP0034.1 Transformation of plasmids into a bacterial host Molecular biology Internal
SOP0035.1 Writing a good protocol Core skills Internal 2025-11-03
SOP0036.1 Banking, tracking, and sharing of materials Core skills Internal 2025-11-03
SOP0037.1 Quantitative amplicon sequencing with unique molecular identifiers Molecular biology Draft
SOP0038.1 Design and cloning of CRISPR guide RNAs Tissue culture Internal
SOP0039.1 Qualitative polymerase chain reactions Molecular biology Internal
SOP0101.1 Version control using Git and GitHub Data management Public 2025-11-03
🚧 This table is still being updated Buy me a coffee · GitHub: (not yet public)