DOI: 10.1038/msb4100054. Deciphering principles of transcription regulation in eukaryotic genomes

Deciphering principles of transcription regulation in eukaryotic genomes

10.1038/msb4100054

Crossref journal-article

Springer Science and Business Media LLC

Molecular Systems Biology (297)

Bibliography

Nguyen, D. H., & Dâhaeseleer, P. (2006). Deciphering principles of transcription regulation in eukaryotic genomes. Molecular Systems Biology, 2(1). Portico.

Authors 2

Dat H Nguyen (first)
Patrik D'haeseleer (additional)

References 51 Referenced 51

{'journal-title': 'Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables', 'year': '1972', 'author': 'Abramowitz M', 'key': 'e_1_2_5_2_1'} / Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables by Abramowitz M (1972)
{'journal-title': 'An Introduction to Multivariate Statistical Analysis', 'year': '1984', 'author': 'Anderson TW', 'key': 'e_1_2_5_3_1'} / An Introduction to Multivariate Statistical Analysis by Anderson TW (1984)
10.1016/S0092-8674(04)00304-6
{'key': 'e_1_2_5_5_1', 'first-page': '67', 'article-title': 'Regulatory element detection using a probabilistic segmentation model', 'volume': '8', 'author': 'Bussemaker HJ', 'year': '2000', 'journal-title': 'Proc Int Conf Intell Syst Mol Biol'} / Proc Int Conf Intell Syst Mol Biol / Regulatory element detection using a probabilistic segmentation model by Bussemaker HJ (2000)
10.1038/84792
10.1073/pnas.0630591100
10.1073/pnas.0407365101
{'journal-title': 'Genomic Regulatory Systems: Development and Evolution', 'year': '2001', 'author': 'Davidson EH', 'key': 'e_1_2_5_9_1'} / Genomic Regulatory Systems: Development and Evolution by Davidson EH (2001)
10.1007/978-3-0348-9317-6_10
10.1186/1471-2105-5-31
10.1091/mbc.11.12.4241
10.1038/nature00935
{'journal-title': 'Nonlinear Multivariate Analysis', 'year': '1990', 'author': 'Gifi A', 'key': 'e_1_2_5_14_1'} / Nonlinear Multivariate Analysis by Gifi A (1990)
10.1038/349099a0
10.1007/BF01199309
10.1101/gr.228902
{'key': 'e_1_2_5_18_1', 'first-page': '425', 'article-title': 'Identifying muscle regulatory elements and genes in the nematode Caenorhabditis\n elegans', 'author': 'Guhathakurta D', 'year': '2002', 'journal-title': 'Pac Symp Biocomput'} / Pac Symp Biocomput / Identifying muscle regulatory elements and genes in the nematode Caenorhabditis elegans by Guhathakurta D (2002)
10.1038/nature02800
10.1006/jmbi.2000.3519
10.1186/gb-2003-5-1-r2
10.1016/S0022-2836(61)80072-7
10.1038/nature01644
10.1126/science.8372350
10.1093/bioinformatics/15.4.267
{'journal-title': 'Nonparametric Statistical Methods Based on Ranks', 'year': '1975', 'author': 'Lehmann EL', 'key': 'e_1_2_5_26_1'} / Nonparametric Statistical Methods Based on Ranks by Lehmann EL (1975)
10.1038/nature01763
10.1073/pnas.2136632100
Matlab
10.1017/CBO9781139167864
10.1093/nar/28.22.4523
10.1101/gr.10.6.744 / Genome Res / Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes by McGuire AM (2000)
10.1016/S0169-7439(01)00200-3
10.1038/ng724
10.1101/gr.1739204
10.1038/nbt1098-939
10.1038/ng1165
10.1007/BF01195873
10.1016/j.gde.2005.02.004
10.1091/mbc.9.12.3273
10.1093/bioinformatics/16.1.16
10.1101/gr.301202
10.1073/pnas.0502521102
10.1038/10343
10.1038/nature03151
{'journal-title': 'Solutions of Ill‐Posed Problems', 'year': '1977', 'author': 'Tikhonov AN', 'key': 'e_1_2_5_46_1'} / Solutions of Ill‐Posed Problems by Tikhonov AN (1977)
10.1038/nbt1053
10.1137/1.9781611970128
10.1073/pnas.252638199
10.2307/3001968
10.1126/science.285.5429.901
10.1038/nature03441

Dates

Type	When
Created	19 years, 4 months ago (April 12, 2006, 1:03 p.m.)
Deposited	1 year, 8 months ago (Dec. 18, 2023, 3:52 p.m.)
Indexed	1 month ago (July 30, 2025, 6:36 a.m.)
Issued	19 years, 8 months ago (Jan. 1, 2006)
Published	19 years, 8 months ago (Jan. 1, 2006)
Published Online	19 years, 4 months ago (April 18, 2006)
Published Print	19 years, 8 months ago (Jan. 1, 2006)

Funders 0

None

BibTeX

@article{Nguyen_2006, title={Deciphering principles of transcription regulation in eukaryotic genomes}, volume={2}, ISSN={1744-4292}, url={http://dx.doi.org/10.1038/msb4100054}, DOI={10.1038/msb4100054}, number={1}, journal={Molecular Systems Biology}, publisher={Springer Science and Business Media LLC}, author={Nguyen, Dat H and D’haeseleer, Patrik}, year={2006}, month=jan }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        7,
        30
      ]
    ],
    "date-time": "2025-07-30T10:36:07Z",
    "timestamp": 1753871767264,
    "version": "3.41.2"
  },
  "reference-count": 51,
  "publisher": "Springer Science and Business Media LLC",
  "issue": "1",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2006,
            4,
            18
          ]
        ],
        "date-time": "2006-04-18T00:00:00Z",
        "timestamp": 1145318400000
      },
      "content-version": "vor",
      "delay-in-days": 107,
      "URL": "http://onlinelibrary.wiley.com/termsAndConditions#vor"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2006,
        1
      ]
    ]
  },
  "DOI": "10.1038/msb4100054",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2006,
        4,
        12
      ]
    ],
    "date-time": "2006-04-12T17:03:01Z",
    "timestamp": 1144861381000
  },
  "source": "Crossref",
  "is-referenced-by-count": 51,
  "title": "Deciphering principles of transcription regulation in eukaryotic genomes",
  "prefix": "10.1038",
  "volume": "2",
  "author": [
    {
      "given": "Dat H",
      "family": "Nguyen",
      "sequence": "first",
      "affiliation": [
        {
          "name": "Department of Genetics, Harvard Medical School  Boston MA USA"
        }
      ]
    },
    {
      "given": "Patrik",
      "family": "D'haeseleer",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Department of Genetics, Harvard Medical School  Boston MA USA"
        },
        {
          "name": "Biosciences Directorate, Lawrence Livermore National Laboratory  Livermore CA USA"
        }
      ]
    }
  ],
  "member": "297",
  "published-online": {
    "date-parts": [
      [
        2006,
        4,
        18
      ]
    ]
  },
  "reference": [
    {
      "journal-title": "Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables",
      "year": "1972",
      "author": "Abramowitz M",
      "key": "e_1_2_5_2_1"
    },
    {
      "journal-title": "An Introduction to Multivariate Statistical Analysis",
      "year": "1984",
      "author": "Anderson TW",
      "key": "e_1_2_5_3_1"
    },
    {
      "key": "e_1_2_5_4_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(04)00304-6"
    },
    {
      "key": "e_1_2_5_5_1",
      "first-page": "67",
      "article-title": "Regulatory element detection using a probabilistic segmentation model",
      "volume": "8",
      "author": "Bussemaker HJ",
      "year": "2000",
      "journal-title": "Proc Int Conf Intell Syst Mol Biol"
    },
    {
      "key": "e_1_2_5_6_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/84792"
    },
    {
      "key": "e_1_2_5_7_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.0630591100"
    },
    {
      "key": "e_1_2_5_8_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.0407365101"
    },
    {
      "journal-title": "Genomic Regulatory Systems: Development and Evolution",
      "year": "2001",
      "author": "Davidson EH",
      "key": "e_1_2_5_9_1"
    },
    {
      "key": "e_1_2_5_10_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/978-3-0348-9317-6_10"
    },
    {
      "key": "e_1_2_5_11_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1186/1471-2105-5-31"
    },
    {
      "key": "e_1_2_5_12_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1091/mbc.11.12.4241"
    },
    {
      "key": "e_1_2_5_13_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature00935"
    },
    {
      "journal-title": "Nonlinear Multivariate Analysis",
      "year": "1990",
      "author": "Gifi A",
      "key": "e_1_2_5_14_1"
    },
    {
      "key": "e_1_2_5_15_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/349099a0"
    },
    {
      "key": "e_1_2_5_16_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/BF01199309"
    },
    {
      "key": "e_1_2_5_17_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.228902"
    },
    {
      "key": "e_1_2_5_18_1",
      "first-page": "425",
      "article-title": "Identifying muscle regulatory elements and genes in the nematode Caenorhabditis\n                  elegans",
      "author": "Guhathakurta D",
      "year": "2002",
      "journal-title": "Pac Symp Biocomput"
    },
    {
      "key": "e_1_2_5_19_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature02800"
    },
    {
      "key": "e_1_2_5_20_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.2000.3519"
    },
    {
      "key": "e_1_2_5_21_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1186/gb-2003-5-1-r2"
    },
    {
      "key": "e_1_2_5_22_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(61)80072-7"
    },
    {
      "key": "e_1_2_5_23_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature01644"
    },
    {
      "key": "e_1_2_5_24_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.8372350"
    },
    {
      "key": "e_1_2_5_25_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/bioinformatics/15.4.267"
    },
    {
      "journal-title": "Nonparametric Statistical Methods Based on Ranks",
      "year": "1975",
      "author": "Lehmann EL",
      "key": "e_1_2_5_26_1"
    },
    {
      "key": "e_1_2_5_27_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature01763"
    },
    {
      "key": "e_1_2_5_28_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.2136632100"
    },
    {
      "key": "e_1_2_5_29_1",
      "unstructured": "Matlab"
    },
    {
      "key": "e_1_2_5_30_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1017/CBO9781139167864"
    },
    {
      "key": "e_1_2_5_31_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/nar/28.22.4523"
    },
    {
      "key": "e_1_2_5_32_1",
      "doi-asserted-by": "crossref",
      "first-page": "744",
      "DOI": "10.1101/gr.10.6.744",
      "article-title": "Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes",
      "volume": "10",
      "author": "McGuire AM",
      "year": "2000",
      "journal-title": "Genome Res"
    },
    {
      "key": "e_1_2_5_33_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0169-7439(01)00200-3"
    },
    {
      "key": "e_1_2_5_34_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/ng724"
    },
    {
      "key": "e_1_2_5_35_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.1739204"
    },
    {
      "key": "e_1_2_5_36_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nbt1098-939"
    },
    {
      "key": "e_1_2_5_37_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/ng1165"
    },
    {
      "key": "e_1_2_5_38_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/BF01195873"
    },
    {
      "key": "e_1_2_5_39_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.gde.2005.02.004"
    },
    {
      "key": "e_1_2_5_40_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1091/mbc.9.12.3273"
    },
    {
      "key": "e_1_2_5_41_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/bioinformatics/16.1.16"
    },
    {
      "key": "e_1_2_5_42_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.301202"
    },
    {
      "key": "e_1_2_5_43_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.0502521102"
    },
    {
      "key": "e_1_2_5_44_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/10343"
    },
    {
      "key": "e_1_2_5_45_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature03151"
    },
    {
      "journal-title": "Solutions of Ill\u2010Posed Problems",
      "year": "1977",
      "author": "Tikhonov AN",
      "key": "e_1_2_5_46_1"
    },
    {
      "key": "e_1_2_5_47_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nbt1053"
    },
    {
      "key": "e_1_2_5_48_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1137/1.9781611970128"
    },
    {
      "key": "e_1_2_5_49_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.252638199"
    },
    {
      "key": "e_1_2_5_50_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.2307/3001968"
    },
    {
      "key": "e_1_2_5_51_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.285.5429.901"
    },
    {
      "key": "e_1_2_5_52_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature03441"
    }
  ],
  "container-title": "Molecular Systems Biology",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "http://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1038%2Fmsb4100054",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://onlinelibrary.wiley.com/doi/pdf/10.1038/msb4100054",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://onlinelibrary.wiley.com/doi/full-xml/10.1038/msb4100054",
      "content-type": "application/xml",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://www.embopress.org/doi/pdf/10.1038/msb4100054",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        12,
        18
      ]
    ],
    "date-time": "2023-12-18T20:52:58Z",
    "timestamp": 1702932778000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://www.embopress.org/doi/10.1038/msb4100054"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2006,
        1
      ]
    ]
  },
  "references-count": 51,
  "journal-issue": {
    "issue": "1",
    "published-print": {
      "date-parts": [
        [
          2006,
          1
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1038/msb4100054"
  ],
  "URL": "http://dx.doi.org/10.1038/msb4100054",
  "relation": {},
  "ISSN": [
    "1744-4292",
    "1744-4292"
  ],
  "subject": [],
  "container-title-short": "Molecular Systems Biology",
  "published": {
    "date-parts": [
      [
        2006,
        1
      ]
    ]
  },
  "article-number": "2006.0012"
}