Bibliographic record
Abstract
The interaction specificities between proteins and DNA has been termed the “second genetic code”. Despite the central importance of DNA‐binding activities to cell biology, physiology, development, and evolution, the complete binding activity of only a small minority of DNA‐binding proteins has been experimentally established. We have used microarrays to examine the binding specificities of over 300 mouse DNA‐binding proteins representing 23 different structural classes. Our results reveal a surprisingly complex landscape of DNA‐binding activities, with most proteins possessing unique and complex binding profiles, such that consensus and position weight matrix representations can have both low specificity and sensitivity. We propose that the evolutionary success of many DNA‐binding protein families, typically attributed to modularity in spatial expression or protein‐protein interactions, is also be due to diversity and malleability in DNA sequence recognition, which in turn could facilitate evolution of regulatory programs. We anticipate that the data resulting from this effort will be invaluable for understanding both gene regulation and genome evolution.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.003 | 0.009 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.001 | 0.008 |
| Scholarly communication | 0.003 | 0.005 |
| Open science | 0.001 | 0.004 |
| Research integrity | 0.002 | 0.005 |
| Insufficient payload (model declined to judge) | 0.007 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".