Turano P, Akbulut E, Dewald H, Vasilopoulos T, Fitzgerald-Bocarsly P, Herbig U
bioRxiv. 2025; .
PMID: 39896543
PMC: 11785101.
DOI: 10.1101/2025.01.17.633634.
Monteiro C, Duarte M, Machado M, Mascarenhas R, Palma P, Garcia H
Front Immunol. 2024; 15:1376655.
PMID: 39328409
PMC: 11425717.
DOI: 10.3389/fimmu.2024.1376655.
Liao M, Zhu X, Lu Y, Yi X, Hu Y, Zhao Y
Nat Commun. 2024; 15(1):7324.
PMID: 39183203
PMC: 11345415.
DOI: 10.1038/s41467-024-51624-y.
Mehlferber M, Kuyumcu-Martinez M, Miller C, Sheynkman G
Curr Stem Cell Rep. 2024; 9(2):31-41.
PMID: 38939410
PMC: 11210451.
DOI: 10.1007/s40778-023-00227-2.
Unger Avila P, Padvitski T, Leote A, Chen H, Saez-Rodriguez J, Kann M
Nat Rev Nephrol. 2024; 20(9):616-633.
PMID: 38867109
DOI: 10.1038/s41581-024-00849-7.
Predicting Transcription Factor Binding Sites with Deep Learning.
Ghosh N, Santoni D, Saha I, Felici G
Int J Mol Sci. 2024; 25(9).
PMID: 38732207
PMC: 11084193.
DOI: 10.3390/ijms25094990.
Individual transcription factors modulate both the micromovement of chromatin and its long-range structure.
Shaban H, Friman E, Deluz C, Tollenaere A, Katanayeva N, Suter D
Proc Natl Acad Sci U S A. 2024; 121(18):e2311374121.
PMID: 38648478
PMC: 11067044.
DOI: 10.1073/pnas.2311374121.
Integrated transcriptomic analysis of human induced pluripotent stem cell-derived osteogenic differentiation reveals a regulatory role of KLF16.
Ru Y, Ma M, Zhou X, Kriti D, Cohen N, DSouza S
bioRxiv. 2024; .
PMID: 38405902
PMC: 10888757.
DOI: 10.1101/2024.02.11.579844.
A Bayesian noisy logic model for inference of transcription factor activity from single cell and bulk transcriptomic data.
Arriojas A, Patalano S, Macoska J, Zarringhalam K
NAR Genom Bioinform. 2023; 5(4):lqad106.
PMID: 38094309
PMC: 10716740.
DOI: 10.1093/nargab/lqad106.
Transcriptional regulation of the HIV-1 inhibitory factor human mannose receptor 1 by the myeloid-specific transcription factor PU.1.
Mallorson R, Miyagi E, Kao S, Sukegawa S, Saito H, Fabryova H
J Virol. 2023; 98(1):e0170223.
PMID: 38078733
PMC: 10804955.
DOI: 10.1128/jvi.01702-23.
Understanding blood development and leukemia using sequencing-based technologies and human cell systems.
Heuts B, Martens J
Front Mol Biosci. 2023; 10:1266697.
PMID: 37886034
PMC: 10598665.
DOI: 10.3389/fmolb.2023.1266697.
Identification and characterization of Hand2 upstream genomic enhancers active in developing stomach and limbs.
Ferguson C, Firulli B, Zoia M, Osterwalder M, Firulli A
Dev Dyn. 2023; 253(2):215-232.
PMID: 37551791
PMC: 11365009.
DOI: 10.1002/dvdy.646.
An extended transcription factor regulatory network controls hepatocyte identity.
Dubois-Chevalier J, Gheeraert C, Berthier A, Boulet C, Dubois V, Guille L
EMBO Rep. 2023; 24(9):e57020.
PMID: 37424431
PMC: 10481658.
DOI: 10.15252/embr.202357020.
Escape from oncogene-induced senescence is controlled by POU2F2 and memorized by chromatin scars.
Martinez-Zamudio R, Stefa A, Nabuco Leva Ferreira Freitas J, Vasilopoulos T, Simpson M, Dore G
Cell Genom. 2023; 3(4):100293.
PMID: 37082139
PMC: 10112333.
DOI: 10.1016/j.xgen.2023.100293.
Microfat exerts an anti-fibrotic effect on human hypertrophic scar via fetuin-A/ETV4 axis.
Yu Q, Dai Q, Huang Z, Li C, Yan L, Fu X
J Transl Med. 2023; 21(1):231.
PMID: 37004048
PMC: 10064544.
DOI: 10.1186/s12967-023-04065-y.
A synthetic transcription platform for programmable gene expression in mammalian cells.
Chen W, Gaidukov L, Lai Y, Wu M, Cao J, Gutbrod M
Nat Commun. 2022; 13(1):6167.
PMID: 36257931
PMC: 9579178.
DOI: 10.1038/s41467-022-33287-9.
Common genetic aspects between COVID-19 and sarcoidosis: A network-based approach using gene expression data.
Mogal M, Sompa S, Junayed A, Mahmod M, Abedin M, Sikder M
Biochem Biophys Rep. 2022; 29:101219.
PMID: 35128085
PMC: 8803645.
DOI: 10.1016/j.bbrep.2022.101219.
Molecular and cellular mechanisms that regulate human erythropoiesis.
Caulier A, Sankaran V
Blood. 2021; 139(16):2450-2459.
PMID: 34936695
PMC: 9029096.
DOI: 10.1182/blood.2021011044.
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network.
Han K, Shen L, Zhu Y, Xu J, Song J, Yu D
Brief Bioinform. 2021; 23(1).
PMID: 34664074
PMC: 8769703.
DOI: 10.1093/bib/bbab445.
ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination.
Xu Q, Georgiou G, Frolich S, van der Sande M, Veenstra G, Zhou H
Nucleic Acids Res. 2021; 49(14):7966-7985.
PMID: 34244796
PMC: 8373078.
DOI: 10.1093/nar/gkab598.