Publications – Krebs Group

Identification of transcription factor co-binding patterns with non-negative matrix factorization.

Rauluseviciute I, Launay T, Barzaghi G, Nikumbh S, Lenhard B, Krebs AR, Castro-Mondragon JA, Mathelier A

Nucleic acids research, 2024

doi:10.1093/nar/gkae743.

Relevance of DNA methylation at enhancers for the acquisition of cell identities.

Kreibich E, Krebs AR

FEBS letters, 2023

doi:10.1002/1873-3468.14686.

Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation.

Kreibich E, Kleinendorst R, Barzaghi G, Kaspar S, Krebs AR

Molecular cell, 2023

doi:10.1016/j.molcel.2023.01.017.

DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions.

Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T

Nature genetics, 2022

doi:10.1038/s41588-022-01210-z.

Cofactors: a new layer of specificity to enhancer regulation.

Kreibich E, Krebs AR

Trends in biochemical sciences, 2022

doi:10.1016/j.tibs.2022.07.008.

Single molecule multi-omics reveals context-dependent regulation of enhancers by DNA methylation.

Kreibich E, Kleinendorst R, Barzaghi G, Kaspar S, Krebs AR

bioRxiv.org, 2022

doi:10.1101/2022.05.19.492653.

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting.

Kleinendorst RWD, Barzaghi G, Smith ML, Zaugg JB, Krebs AR

Nature protocols, 2021

doi:10.1038/s41596-021-00630-1.

BANP opens chromatin and activates CpG-island-regulated genes.

Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D

Nature, 2021

doi:10.1038/s41586-021-03689-8.

Studying transcription factor function in the genome at molecular resolution.

Krebs AR

Trends in genetics : TIG, 2021

doi:10.1016/j.tig.2021.03.008.

Molecular co-occupancy identifies transcription factor binding cooperativity in vivo.

Sönmezer C, Kleinendorst R, Imanci D, Barzaghi G, Villacorta L, Schübeler D, Benes V, Molina N, Krebs AR

Molecular cell, 2020

doi:10.1016/j.molcel.2020.11.015.

A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity.

Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, Zilbermann F, Peters AHFM, Edenhofer F, Smallwood SA, Krebs AR, Schübeler D

Nature communications, 2020

doi:10.1038/s41467-020-16354-x.

McQ – an open-source multiplexed SARS-CoV-2 quantification platform.

Vonesch SC, Bredikhin D, Dobrev N, Villacorta L, Kleinendorst R, Cacace E, Flock J, Frank M, Jung F, Kornienko J, Mitosch K, Osuna-Lopez M, Zimmermann J, Goettig S, Hamprecht A, Kraeusslich H, Knop M, Typas A, Steinmetz LM, Benes V, Remans K, Krebs AR

medRxiv, 2020

doi:10.1101/2020.12.02.20242628.

Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates and humans.

Jüttner J, Szabo A, Gross-Scherf B, Morikawa RK, Rompani SB, Hantz P, Szikra T, Esposti F, Cowan CS, Bharioke A, Patino-Alvarez CP, Keles Ö, Kusnyerik A, Azoulay T, Hartl D, Schübeler D, Krebs AR, Lukats A, Hajdu RI, Nagy ZZ, Nemeth J, Wu RH, Wu KC, Fang XL, Xiang L, Goldblum D, Jin ZB, Scholl HPN, Hasler PW, Roska B, Krol J

Nature neuroscience, 2019

doi:10.1038/s41593-019-0431-2.