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Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters.
Epigenetics Chromatin. 2018 Nov 10;11(1):66. doi: 10.1186/s13072-018-0236-7.
Epigenetics Chromatin. 2018.
PMID: 30414612
Free PMC article.
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.
Schmidt F, Gasparoni N, Gasparoni G, Gianmoena K, Cadenas C, Polansky JK, Ebert P, Nordström K, Barann M, Sinha A, Fröhler S, Xiong J, Dehghani Amirabad A, Behjati Ardakani F, Hutter B, Zipprich G, Felder B, Eils J, Brors B, Chen W, Hengstler JG, Hamann A, Lengauer T, Rosenstiel P, Walter J, Schulz MH.
Schmidt F, et al. Among authors: behjati ardakani f.
Nucleic Acids Res. 2017 Jan 9;45(1):54-66. doi: 10.1093/nar/gkw1061. Epub 2016 Nov 29.
Nucleic Acids Res. 2017.
PMID: 27899623
Free PMC article.
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Predicting transcription factor binding using ensemble random forest models.
Behjati Ardakani F, Schmidt F, Schulz MH.
Behjati Ardakani F, et al.
F1000Res. 2018 Oct 4;7:1603. doi: 10.12688/f1000research.16200.2. eCollection 2018.
F1000Res. 2018.
PMID: 31723409
Free PMC article.
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Prediction of single-cell gene expression for transcription factor analysis.
Behjati Ardakani F, Kattler K, Heinen T, Schmidt F, Feuerborn D, Gasparoni G, Lepikhov K, Nell P, Hengstler J, Walter J, Schulz MH.
Behjati Ardakani F, et al.
Gigascience. 2020 Oct 30;9(11):giaa113. doi: 10.1093/gigascience/giaa113.
Gigascience. 2020.
PMID: 33124660
Free PMC article.
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The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data.
Hecker D, Behjati Ardakani F, Karollus A, Gagneur J, Schulz MH.
Hecker D, et al. Among authors: behjati ardakani f.
Bioinformatics. 2023 Feb 3;39(2):btad062. doi: 10.1093/bioinformatics/btad062.
Bioinformatics. 2023.
PMID: 36708003
Free PMC article.
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Computational tools for inferring transcription factor activity.
Hecker D, Lauber M, Behjati Ardakani F, Ashrafiyan S, Manz Q, Kersting J, Hoffmann M, Schulz MH, List M.
Hecker D, et al. Among authors: behjati ardakani f.
Proteomics. 2023 Dec;23(23-24):e2200462. doi: 10.1002/pmic.202200462. Epub 2023 Sep 14.
Proteomics. 2023.
PMID: 37706624
Review.
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