Benner C - Search Results

1

MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates.

Delos Santos NP, Texari L, Benner C. Delos Santos NP, et al. Among authors: benner c. BMC Bioinformatics. 2020 Sep 16;21(1):410. doi: 10.1186/s12859-020-03739-4. BMC Bioinformatics. 2020. PMID: 32938397 Free PMC article.

2

Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.

Barrera L, Benner C, Tao YC, Winzeler E, Zhou Y. Barrera L, et al. Among authors: benner c. BMC Bioinformatics. 2004 Apr 20;5:42. doi: 10.1186/1471-2105-5-42. BMC Bioinformatics. 2004. PMID: 15099405 Free PMC article.

3

Transcription Elongation Can Affect Genome 3D Structure.

Heinz S, Texari L, Hayes MGB, Urbanowski M, Chang MW, Givarkes N, Rialdi A, White KM, Albrecht RA, Pache L, Marazzi I, García-Sastre A, Shaw ML, Benner C. Heinz S, et al. Among authors: benner c. Cell. 2018 Sep 6;174(6):1522-1536.e22. doi: 10.1016/j.cell.2018.07.047. Epub 2018 Aug 23. Cell. 2018. PMID: 30146161 Free PMC article.

4

Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers.

Brigidi GS, Hayes MGB, Delos Santos NP, Hartzell AL, Texari L, Lin PA, Bartlett A, Ecker JR, Benner C, Heinz S, Bloodgood BL. Brigidi GS, et al. Among authors: benner c. Cell. 2019 Oct 3;179(2):373-391.e27. doi: 10.1016/j.cell.2019.09.004. Cell. 2019. PMID: 31585079 Free PMC article.

5

ARTDeco: automatic readthrough transcription detection.

Roth SJ, Heinz S, Benner C. Roth SJ, et al. Among authors: benner c. BMC Bioinformatics. 2020 May 26;21(1):214. doi: 10.1186/s12859-020-03551-0. BMC Bioinformatics. 2020. PMID: 32456667 Free PMC article.

6

MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function.

Shen Z, Hoeksema MA, Ouyang Z, Benner C, Glass CK. Shen Z, et al. Among authors: benner c. Bioinformatics. 2020 Jul 1;36(Suppl_1):i84-i92. doi: 10.1093/bioinformatics/btaa476. Bioinformatics. 2020. PMID: 32657363 Free PMC article.

7

MEPP: more transparent motif enrichment by profiling positional correlations.

Delos Santos NP, Duttke S, Heinz S, Benner C. Delos Santos NP, et al. Among authors: benner c. NAR Genom Bioinform. 2022 Oct 17;4(4):lqac075. doi: 10.1093/nargab/lqac075. eCollection 2022 Dec. NAR Genom Bioinform. 2022. PMID: 36267125 Free PMC article.

8

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA. Young JA, et al. Among authors: benner c. BMC Genomics. 2008 Feb 7;9:70. doi: 10.1186/1471-2164-9-70. BMC Genomics. 2008. PMID: 18257930 Free PMC article.

9

Nascent RNA sequencing reveals distinct features in plant transcription.

Hetzel J, Duttke SH, Benner C, Chory J. Hetzel J, et al. Among authors: benner c. Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12316-12321. doi: 10.1073/pnas.1603217113. Epub 2016 Oct 11. Proc Natl Acad Sci U S A. 2016. PMID: 27729530 Free PMC article.

10

Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages.

Fonseca GJ, Tao J, Westin EM, Duttke SH, Spann NJ, Strid T, Shen Z, Stender JD, Sakai M, Link VM, Benner C, Glass CK. Fonseca GJ, et al. Among authors: benner c. Nat Commun. 2019 Jan 24;10(1):414. doi: 10.1038/s41467-018-08236-0. Nat Commun. 2019. PMID: 30679424 Free PMC article.

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