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TF-COMB - Discovering grammar of transcription factor binding sites.

Bentsen M, Heger V, Schultheis H, Kuenne C, Looso M. · Computational and structural biotechnology journal · 2022 · Journal publication

Original publication · Original publication · Original publication

Recorded summary

Reference associated with Fractal TFBS Analysis / Fractal Chromatin 3D Organisation.

Recorded limitations

Bibliographic metadata matched; scientific claims await appraisal.

Evidence and provenance

Chapter Trust Factor uses a minimum of three distinct qualifying studies. Publication records retain their own evidence and assessment.

Study design and assessment
design
Journal publication
assessment
Not recorded
trust Factor
scope
Paper
status
unassessed
score
Not recorded
basis
Bibliographic identity checks do not establish study design, blinding or evidential strength.
jadad
status
unassessed
score
Not recorded
evidence
Not recorded
Topics and recorded topic scores
  1. key
    general:imaging-transcriptomics
    title
    Imaging, Transcriptomics and Gene Regulation
    collection
    general
    trust Score
    Not recorded
Citation snapshot and identifiers
id
hsi-22a43f552b2b2f
doi
10.1016/j.csbj.2022.07.025
pmid
35983231
citation Snapshot
Not recorded
citations By Collection
general
Not recorded
Complete approved library record
id
hsi-22a43f552b2b2f
aliases
None recorded
source References
  1. ref
    NPL-218
    record Id
    hsi-22a43f552b2b2f
    source Type
    Journal publication
    title
    TF-COMB - Discovering grammar of transcription factor binding sites.
    authors
    Bentsen M, Heger V, Schultheis H, Kuenne C, Looso M.
    year
    2022
    journal
    Computational and structural biotechnology journal
    doi
    10.1016/j.csbj.2022.07.025
    pmid
    35983231
    pmcid
    PMC9358416
    patent Number
    Not recorded
    original Assignee
    Not recorded
    original Citation
    Bentsen M, Heger V, Schütte H, Lim CH, Kchouk C, Braun T, Looso M (2022). "TF-COMB — Discovering grammar of transcription factor binding sites." Computational and Structural Biotechnology Journal 20:4040–4051. DOI: 10.1016/j.csbj.2022.07.025 — Market basket analysis framework for global TF co-occurrence inference across eight ENCODE cell lines; reveals preferred binding distances, orientations, and network relationships; TF pairs exhibit grammar-level features (distance periodicity, directional preferences) encoding biological function
    original Section
    Fractal TFBS Analysis / Fractal Chromatin 3D Organisation
    metadata Status
    metadata-matched
    claim Review
    Not independently appraised
    source URL
    https://www.notion.so/3807b9c99c5680599be7d8337c817b15
    publication URL
    https://pubmed.ncbi.nlm.nih.gov/35983231/
    metadata URL
    https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.1016%2Fj.csbj.2022.07.025%22&format=json&resultType=core&pageSize=4
    corrections
    None recorded
    topic Id
    imaging-transcriptomics
    role
    Focused chapter source
source Type
Journal publication
source Verification
Bibliographic metadata matched; scientific claims await appraisal.
source Collection
Hyperspectral Imaging · patent section 2.4
title
TF-COMB - Discovering grammar of transcription factor binding sites.
journal
Computational and structural biotechnology journal
neurotransmitters
None recorded
year
2022
authors
Bentsen M, Heger V, Schultheis H, Kuenne C, Looso M.
design
Journal publication
kind
Journal publication
identity Conflict
Not recorded
doi
10.1016/j.csbj.2022.07.025
pmid
35983231
urls

https://pubmed.ncbi.nlm.nih.gov/35983231/ · https://doi.org/10.1016/j.csbj.2022.07.025 · https://pmc.ncbi.nlm.nih.gov/articles/PMC9358416/

collections

general

categories

Hyperspectral Imaging

targets
None recorded
priority
1
quotes
None recorded
summary
Reference associated with Fractal TFBS Analysis / Fractal Chromatin 3D Organisation.
limitation
Bibliographic metadata matched; scientific claims await appraisal.
citation Count
Not recorded
paper Trust Assessment
scope
Paper
status
unassessed
score
Not recorded
basis
Bibliographic identity checks do not establish study design, blinding or evidential strength.
citations By Collection
general
Not recorded
topics
  1. key
    general:imaging-transcriptomics
    title
    Imaging, Transcriptomics and Gene Regulation
    collection
    general
    trust Score
    Not recorded
journal Key
computationalandstructuralbiotechnologyjournal
journal Label
Computational and structural biotechnology journal
chapter Entries
  1. id
    general-imaging-transcriptomics-hsi-22a43f552b2b2f
    record Id
    hsi-22a43f552b2b2f
    title
    TF-COMB - Discovering grammar of transcription factor binding sites.
    journal
    Computational and structural biotechnology journal
    year
    2022
    authors
    Bentsen M, Heger V, Schultheis H, Kuenne C, Looso M.
    design
    Journal publication
    urls

    https://pubmed.ncbi.nlm.nih.gov/35983231/ · https://doi.org/10.1016/j.csbj.2022.07.025 · https://pmc.ncbi.nlm.nih.gov/articles/PMC9358416/

    quotes
    None recorded
    summary
    Reference associated with Fractal TFBS Analysis / Fractal Chromatin 3D Organisation.
    related Versions
    None recorded
    limitation
    Bibliographic metadata matched; scientific claims await appraisal.
    citation Count
    Not recorded
    source Pages
    None recorded
    doi
    10.1016/j.csbj.2022.07.025
    pmid
    35983231
    targets
    None recorded
    categories

    Hyperspectral Imaging

    source References
    1. ref
      NPL-218
      record Id
      hsi-22a43f552b2b2f
      source Type
      Journal publication
      title
      TF-COMB - Discovering grammar of transcription factor binding sites.
      authors
      Bentsen M, Heger V, Schultheis H, Kuenne C, Looso M.
      year
      2022
      journal
      Computational and structural biotechnology journal
      doi
      10.1016/j.csbj.2022.07.025
      pmid
      35983231
      pmcid
      PMC9358416
      patent Number
      Not recorded
      original Assignee
      Not recorded
      original Citation
      Bentsen M, Heger V, Schütte H, Lim CH, Kchouk C, Braun T, Looso M (2022). "TF-COMB — Discovering grammar of transcription factor binding sites." Computational and Structural Biotechnology Journal 20:4040–4051. DOI: 10.1016/j.csbj.2022.07.025 — Market basket analysis framework for global TF co-occurrence inference across eight ENCODE cell lines; reveals preferred binding distances, orientations, and network relationships; TF pairs exhibit grammar-level features (distance periodicity, directional preferences) encoding biological function
      original Section
      Fractal TFBS Analysis / Fractal Chromatin 3D Organisation
      metadata Status
      metadata-matched
      claim Review
      Not independently appraised
      source URL
      https://www.notion.so/3807b9c99c5680599be7d8337c817b15
      publication URL
      https://pubmed.ncbi.nlm.nih.gov/35983231/
      metadata URL
      https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A%2210.1016%2Fj.csbj.2022.07.025%22&format=json&resultType=core&pageSize=4
      corrections
      None recorded
      topic Id
      imaging-transcriptomics
      role
      Focused chapter source
    source Type
    Journal publication
    source Verification
    Bibliographic metadata matched; scientific claims await appraisal.
    collection
    general
    chapter Number
    11
    topic Id
    imaging-transcriptomics
    topic Title
    Imaging, Transcriptomics and Gene Regulation
    trust Score
    Not recorded
    paper Trust Assessment
    scope
    Paper
    status
    unassessed
    score
    Not recorded
    basis
    Bibliographic identity checks do not establish study design, blinding or evidential strength.
jadad
status
unassessed
score
Not recorded
condition Evidence
None recorded
conditions
None recorded
topic Trust Scores
None recorded
full Text
status
not-indexed
retrieval Available
false

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