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Academic Journal

FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.

  • Authors : Shang GD; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China.; University of Chinese Academy of Sciences (UCAS), Shanghai, 200032, P. R. China.

Subjects: Software* ; Transcription Factors*/Transcription Factors*/Transcription Factors*/genetics; Chromatin Immunoprecipitation Sequencing

  • Source: BMC genomics [BMC Genomics] 2022 Apr 07; Vol. 23 (Suppl 1), pp. 272. Date of Electronic Publication: 2022 Apr 07.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Comparative transcriptome analysis of two contrasting wolfberry genotypes during fruit development and ripening and characterization of the LrMYB1 transcription factor that regulates flavonoid biosynthesis.

  • Authors : Wang C; State Key Laboratory of Seedling Bioengineering, Ningxia Forestry Institute, Yinchuan, 750004, China. .; Agricultural Biotechnology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China. .

Subjects: Gene Expression Profiling/Gene Expression Profiling/Gene Expression Profiling/*methods ; Lycium/Lycium/Lycium/*physiology ; Transcription Factors/Transcription Factors/Transcription Factors/*genetics

  • Source: BMC genomics [BMC Genomics] 2020 Apr 10; Vol. 21 (1), pp. 295. Date of Electronic Publication: 2020 Apr 10.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq.

  • Authors : Kodama M; Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. .; Genome Research and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .

Subjects: Gene Expression Regulation, Plant*; Anthocyanins/Anthocyanins/Anthocyanins/*biosynthesis ; Daucus carota/Daucus carota/Daucus carota/*genetics

  • Source: BMC genomics [BMC Genomics] 2018 Nov 08; Vol. 19 (1), pp. 811. Date of Electronic Publication: 2018 Nov 08.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information.

  • Authors : Nettling M; Institute of Computer Science, Martin Luther University, Halle (Saale), Germany. .; Treutler H

Subjects: Binding Sites* ; Chromatin Immunoprecipitation* ; High-Throughput Nucleotide Sequencing*

  • Source: BMC genomics [BMC Genomics] 2016 May 10; Vol. 17, pp. 347. Date of Electronic Publication: 2016 May 10.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors.

  • Authors : Piper J; Warwick Systems Biology Centre, University of Warwick, Coventry, CV4 7AL, UK.; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK.

Subjects: Binding Sites* ; DNA Footprinting*/DNA Footprinting*/DNA Footprinting*/methods ; High-Throughput Nucleotide Sequencing*

  • Source: BMC genomics [BMC Genomics] 2015 Nov 25; Vol. 16, pp. 1000. Date of Electronic Publication: 2015 Nov 25.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.

Subjects: Binding Sites* ; Chromatin Immunoprecipitation* ; High-Throughput Nucleotide Sequencing*

  • Source: BMC genomics [BMC Genomics] 2014 Jun 13; Vol. 15, pp. 472. Date of Electronic Publication: 2014 Jun 13.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC).

  • Authors : Wang Y; Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA.; Guo X

Subjects: Genomics*; Carcinoma, Renal Cell/Carcinoma, Renal Cell/Carcinoma, Renal Cell/*genetics ; Gene Expression Regulation, Neoplastic/Gene Expression Regulation, Neoplastic/Gene Expression Regulation, Neoplastic/*genetics

  • Source: BMC genomics [BMC Genomics] 2016 Aug 22; Vol. 17 Suppl 7, pp. 515. Date of Electronic Publication: 2016 Aug 22.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Changes in Bacillus anthracis CodY regulation under host-specific environmental factor deprived conditions.

  • Authors : Kim SK; Department of Molecular and Life Science, Hanyang University ERICA, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do, 15588, Republic of Korea.; Jung KH

Subjects: Environment* ; Gene Expression Regulation, Bacterial* ; Gene-Environment Interaction*

  • Source: BMC genomics [BMC Genomics] 2016 Aug 17; Vol. 17, pp. 645. Date of Electronic Publication: 2016 Aug 17.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.

  • Authors : Liu H; Department of Bio-Engineering Sciences, Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.; Wang K

Subjects: Binding Sites* ; Genome-Wide Association Study*; DNA-Binding Proteins/DNA-Binding Proteins/DNA-Binding Proteins/*metabolism

  • Source: BMC genomics [BMC Genomics] 2016 Aug 08; Vol. 17, pp. 569. Date of Electronic Publication: 2016 Aug 08.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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Academic Journal

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells.

  • Authors : Gonzales-Cope M; Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .; Sidoli S

Subjects: Epigenesis, Genetic*; Embryonic Stem Cells/Embryonic Stem Cells/Embryonic Stem Cells/*cytology ; Embryonic Stem Cells/Embryonic Stem Cells/Embryonic Stem Cells/*metabolism

  • Source: BMC genomics [BMC Genomics] 2016 Feb 04; Vol. 17, pp. 95. Date of Electronic Publication: 2016 Feb 04.Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium:

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