A multi-scale expression and regulation knowledge base forEscherichia coli Article Swipe
Cameron Lamoureux
,
Katherine Decker
,
Anand V. Sastry
,
Kevin Rychel
,
Ye Gao
,
John Luke McConn
,
Daniel C. Zielinski
,
Bernhard Ø. Palsson
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkad750
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkad750
Transcriptomic data is accumulating rapidly; thus, scalable methods for extracting knowledge from this data are critical. Here, we assembled a top-down expression and regulation knowledge base for Escherichia coli. The expression component is a 1035-sample, high-quality RNA-seq compendium consisting of data generated in our lab using a single experimental protocol. The compendium contains diverse growth conditions, including: 9 media; 39 supplements, including antibiotics; 42 heterologous proteins; and 76 gene knockouts. Using this resource, we elucidated global expression patterns. We used machine learning to extract 201 modules that account for 86% of known regulatory interactions, creating the regulatory component. With these modules, we identified two novel regulons and quantified systems-level regulatory responses. We also integrated 1675 curated, publicly-available transcriptomes into the resource. We demonstrated workflows for analyzing new data against this knowledge base via deconstruction of regulation during aerobic transition. This resource illuminates the E. coli transcriptome at scale and provides a blueprint for top-down transcriptomic analysis of non-model organisms.
Related Topics
Concepts
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkad750
- https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad750/51607870/gkad750.pdf
- OA Status
- gold
- Cited By
- 54
- References
- 91
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4386764170
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4386764170Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/nar/gkad750Digital Object Identifier
- Title
-
A multi-scale expression and regulation knowledge base forEscherichia coliWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-09-15Full publication date if available
- Authors
-
Cameron Lamoureux, Katherine Decker, Anand V. Sastry, Kevin Rychel, Ye Gao, John Luke McConn, Daniel C. Zielinski, Bernhard Ø. PalssonList of authors in order
- Landing page
-
https://doi.org/10.1093/nar/gkad750Publisher landing page
- PDF URL
-
https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad750/51607870/gkad750.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad750/51607870/gkad750.pdfDirect OA link when available
- Concepts
-
Biology, Escherichia coli, Scale (ratio), Base (topology), Knowledge base, Expression (computer science), Computational biology, Genetics, Gene, World Wide Web, Computer science, Programming language, Quantum mechanics, Mathematical analysis, Physics, MathematicsTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
54Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 21, 2024: 25, 2023: 8Per-year citation counts (last 5 years)
- References (count)
-
91Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
Full payload
| id | https://openalex.org/W4386764170 |
|---|---|
| doi | https://doi.org/10.1093/nar/gkad750 |
| ids.doi | https://doi.org/10.1093/nar/gkad750 |
| ids.pmid | https://pubmed.ncbi.nlm.nih.gov/37713610 |
| ids.openalex | https://openalex.org/W4386764170 |
| fwci | 10.02620201 |
| mesh[0].qualifier_ui | Q000235 |
| mesh[0].descriptor_ui | D004926 |
| mesh[0].is_major_topic | True |
| mesh[0].qualifier_name | genetics |
| mesh[0].descriptor_name | Escherichia coli |
| mesh[1].qualifier_ui | Q000378 |
| mesh[1].descriptor_ui | D004926 |
| mesh[1].is_major_topic | True |
| mesh[1].qualifier_name | metabolism |
| mesh[1].descriptor_name | Escherichia coli |
| mesh[2].qualifier_ui | Q000235 |
| mesh[2].descriptor_ui | D029968 |
| mesh[2].is_major_topic | False |
| mesh[2].qualifier_name | genetics |
| mesh[2].descriptor_name | Escherichia coli Proteins |
| mesh[3].qualifier_ui | Q000378 |
| mesh[3].descriptor_ui | D029968 |
| mesh[3].is_major_topic | False |
| mesh[3].qualifier_name | metabolism |
| mesh[3].descriptor_name | Escherichia coli Proteins |
| mesh[4].qualifier_ui | |
| mesh[4].descriptor_ui | D020869 |
| mesh[4].is_major_topic | False |
| mesh[4].qualifier_name | |
| mesh[4].descriptor_name | Gene Expression Profiling |
| mesh[5].qualifier_ui | |
| mesh[5].descriptor_ui | D015964 |
| mesh[5].is_major_topic | False |
| mesh[5].qualifier_name | |
| mesh[5].descriptor_name | Gene Expression Regulation, Bacterial |
| mesh[6].qualifier_ui | |
| mesh[6].descriptor_ui | D051188 |
| mesh[6].is_major_topic | True |
| mesh[6].qualifier_name | |
| mesh[6].descriptor_name | Knowledge Bases |
| mesh[7].qualifier_ui | |
| mesh[7].descriptor_ui | D059467 |
| mesh[7].is_major_topic | False |
| mesh[7].qualifier_name | |
| mesh[7].descriptor_name | Transcriptome |
| mesh[8].qualifier_ui | Q000235 |
| mesh[8].descriptor_ui | D004926 |
| mesh[8].is_major_topic | True |
| mesh[8].qualifier_name | genetics |
| mesh[8].descriptor_name | Escherichia coli |
| mesh[9].qualifier_ui | Q000378 |
| mesh[9].descriptor_ui | D004926 |
| mesh[9].is_major_topic | True |
| mesh[9].qualifier_name | metabolism |
| mesh[9].descriptor_name | Escherichia coli |
| mesh[10].qualifier_ui | Q000235 |
| mesh[10].descriptor_ui | D029968 |
| mesh[10].is_major_topic | False |
| mesh[10].qualifier_name | genetics |
| mesh[10].descriptor_name | Escherichia coli Proteins |
| mesh[11].qualifier_ui | Q000378 |
| mesh[11].descriptor_ui | D029968 |
| mesh[11].is_major_topic | False |
| mesh[11].qualifier_name | metabolism |
| mesh[11].descriptor_name | Escherichia coli Proteins |
| mesh[12].qualifier_ui | |
| mesh[12].descriptor_ui | D020869 |
| mesh[12].is_major_topic | False |
| mesh[12].qualifier_name | |
| mesh[12].descriptor_name | Gene Expression Profiling |
| mesh[13].qualifier_ui | |
| mesh[13].descriptor_ui | D015964 |
| mesh[13].is_major_topic | False |
| mesh[13].qualifier_name | |
| mesh[13].descriptor_name | Gene Expression Regulation, Bacterial |
| mesh[14].qualifier_ui | |
| mesh[14].descriptor_ui | D051188 |
| mesh[14].is_major_topic | True |
| mesh[14].qualifier_name | |
| mesh[14].descriptor_name | Knowledge Bases |
| mesh[15].qualifier_ui | |
| mesh[15].descriptor_ui | D059467 |
| mesh[15].is_major_topic | False |
| mesh[15].qualifier_name | |
| mesh[15].descriptor_name | Transcriptome |
| type | article |
| title | A multi-scale expression and regulation knowledge base forEscherichia coli |
| awards[0].id | https://openalex.org/G7042228497 |
| awards[0].funder_id | https://openalex.org/F4320325957 |
| awards[0].display_name | |
| awards[0].funder_award_id | NNF20CC0035580 |
| awards[0].funder_display_name | Novo Nordisk Fonden |
| biblio.issue | 19 |
| biblio.volume | 51 |
| biblio.last_page | 10193 |
| biblio.first_page | 10176 |
| topics[0].id | https://openalex.org/T10521 |
| topics[0].field.id | https://openalex.org/fields/13 |
| topics[0].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[0].score | 0.9983999729156494 |
| topics[0].domain.id | https://openalex.org/domains/1 |
| topics[0].domain.display_name | Life Sciences |
| topics[0].subfield.id | https://openalex.org/subfields/1312 |
| topics[0].subfield.display_name | Molecular Biology |
| topics[0].display_name | RNA and protein synthesis mechanisms |
| topics[1].id | https://openalex.org/T10120 |
| topics[1].field.id | https://openalex.org/fields/13 |
| topics[1].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[1].score | 0.9962000250816345 |
| topics[1].domain.id | https://openalex.org/domains/1 |
| topics[1].domain.display_name | Life Sciences |
| topics[1].subfield.id | https://openalex.org/subfields/1311 |
| topics[1].subfield.display_name | Genetics |
| topics[1].display_name | Bacterial Genetics and Biotechnology |
| topics[2].id | https://openalex.org/T10044 |
| topics[2].field.id | https://openalex.org/fields/13 |
| topics[2].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[2].score | 0.9955000281333923 |
| topics[2].domain.id | https://openalex.org/domains/1 |
| topics[2].domain.display_name | Life Sciences |
| topics[2].subfield.id | https://openalex.org/subfields/1312 |
| topics[2].subfield.display_name | Molecular Biology |
| topics[2].display_name | Protein Structure and Dynamics |
| funders[0].id | https://openalex.org/F4320325957 |
| funders[0].ror | https://ror.org/04txyc737 |
| funders[0].display_name | Novo Nordisk Fonden |
| is_xpac | False |
| apc_list.value | 3630 |
| apc_list.currency | USD |
| apc_list.value_usd | 3630 |
| apc_paid.value | 3630 |
| apc_paid.currency | USD |
| apc_paid.value_usd | 3630 |
| concepts[0].id | https://openalex.org/C86803240 |
| concepts[0].level | 0 |
| concepts[0].score | 0.9262617230415344 |
| concepts[0].wikidata | https://www.wikidata.org/wiki/Q420 |
| concepts[0].display_name | Biology |
| concepts[1].id | https://openalex.org/C547475151 |
| concepts[1].level | 3 |
| concepts[1].score | 0.7489572167396545 |
| concepts[1].wikidata | https://www.wikidata.org/wiki/Q25419 |
| concepts[1].display_name | Escherichia coli |
| concepts[2].id | https://openalex.org/C2778755073 |
| concepts[2].level | 2 |
| concepts[2].score | 0.5523343086242676 |
| concepts[2].wikidata | https://www.wikidata.org/wiki/Q10858537 |
| concepts[2].display_name | Scale (ratio) |
| concepts[3].id | https://openalex.org/C42058472 |
| concepts[3].level | 2 |
| concepts[3].score | 0.5025911331176758 |
| concepts[3].wikidata | https://www.wikidata.org/wiki/Q810214 |
| concepts[3].display_name | Base (topology) |
| concepts[4].id | https://openalex.org/C4554734 |
| concepts[4].level | 2 |
| concepts[4].score | 0.43604832887649536 |
| concepts[4].wikidata | https://www.wikidata.org/wiki/Q593744 |
| concepts[4].display_name | Knowledge base |
| concepts[5].id | https://openalex.org/C90559484 |
| concepts[5].level | 2 |
| concepts[5].score | 0.42932188510894775 |
| concepts[5].wikidata | https://www.wikidata.org/wiki/Q778379 |
| concepts[5].display_name | Expression (computer science) |
| concepts[6].id | https://openalex.org/C70721500 |
| concepts[6].level | 1 |
| concepts[6].score | 0.4212121069431305 |
| concepts[6].wikidata | https://www.wikidata.org/wiki/Q177005 |
| concepts[6].display_name | Computational biology |
| concepts[7].id | https://openalex.org/C54355233 |
| concepts[7].level | 1 |
| concepts[7].score | 0.3823418617248535 |
| concepts[7].wikidata | https://www.wikidata.org/wiki/Q7162 |
| concepts[7].display_name | Genetics |
| concepts[8].id | https://openalex.org/C104317684 |
| concepts[8].level | 2 |
| concepts[8].score | 0.20497402548789978 |
| concepts[8].wikidata | https://www.wikidata.org/wiki/Q7187 |
| concepts[8].display_name | Gene |
| concepts[9].id | https://openalex.org/C136764020 |
| concepts[9].level | 1 |
| concepts[9].score | 0.11046251654624939 |
| concepts[9].wikidata | https://www.wikidata.org/wiki/Q466 |
| concepts[9].display_name | World Wide Web |
| concepts[10].id | https://openalex.org/C41008148 |
| concepts[10].level | 0 |
| concepts[10].score | 0.06929385662078857 |
| concepts[10].wikidata | https://www.wikidata.org/wiki/Q21198 |
| concepts[10].display_name | Computer science |
| concepts[11].id | https://openalex.org/C199360897 |
| concepts[11].level | 1 |
| concepts[11].score | 0.06749284267425537 |
| concepts[11].wikidata | https://www.wikidata.org/wiki/Q9143 |
| concepts[11].display_name | Programming language |
| concepts[12].id | https://openalex.org/C62520636 |
| concepts[12].level | 1 |
| concepts[12].score | 0.0 |
| concepts[12].wikidata | https://www.wikidata.org/wiki/Q944 |
| concepts[12].display_name | Quantum mechanics |
| concepts[13].id | https://openalex.org/C134306372 |
| concepts[13].level | 1 |
| concepts[13].score | 0.0 |
| concepts[13].wikidata | https://www.wikidata.org/wiki/Q7754 |
| concepts[13].display_name | Mathematical analysis |
| concepts[14].id | https://openalex.org/C121332964 |
| concepts[14].level | 0 |
| concepts[14].score | 0.0 |
| concepts[14].wikidata | https://www.wikidata.org/wiki/Q413 |
| concepts[14].display_name | Physics |
| concepts[15].id | https://openalex.org/C33923547 |
| concepts[15].level | 0 |
| concepts[15].score | 0.0 |
| concepts[15].wikidata | https://www.wikidata.org/wiki/Q395 |
| concepts[15].display_name | Mathematics |
| keywords[0].id | https://openalex.org/keywords/biology |
| keywords[0].score | 0.9262617230415344 |
| keywords[0].display_name | Biology |
| keywords[1].id | https://openalex.org/keywords/escherichia-coli |
| keywords[1].score | 0.7489572167396545 |
| keywords[1].display_name | Escherichia coli |
| keywords[2].id | https://openalex.org/keywords/scale |
| keywords[2].score | 0.5523343086242676 |
| keywords[2].display_name | Scale (ratio) |
| keywords[3].id | https://openalex.org/keywords/base |
| keywords[3].score | 0.5025911331176758 |
| keywords[3].display_name | Base (topology) |
| keywords[4].id | https://openalex.org/keywords/knowledge-base |
| keywords[4].score | 0.43604832887649536 |
| keywords[4].display_name | Knowledge base |
| keywords[5].id | https://openalex.org/keywords/expression |
| keywords[5].score | 0.42932188510894775 |
| keywords[5].display_name | Expression (computer science) |
| keywords[6].id | https://openalex.org/keywords/computational-biology |
| keywords[6].score | 0.4212121069431305 |
| keywords[6].display_name | Computational biology |
| keywords[7].id | https://openalex.org/keywords/genetics |
| keywords[7].score | 0.3823418617248535 |
| keywords[7].display_name | Genetics |
| keywords[8].id | https://openalex.org/keywords/gene |
| keywords[8].score | 0.20497402548789978 |
| keywords[8].display_name | Gene |
| keywords[9].id | https://openalex.org/keywords/world-wide-web |
| keywords[9].score | 0.11046251654624939 |
| keywords[9].display_name | World Wide Web |
| keywords[10].id | https://openalex.org/keywords/computer-science |
| keywords[10].score | 0.06929385662078857 |
| keywords[10].display_name | Computer science |
| keywords[11].id | https://openalex.org/keywords/programming-language |
| keywords[11].score | 0.06749284267425537 |
| keywords[11].display_name | Programming language |
| language | en |
| locations[0].id | doi:10.1093/nar/gkad750 |
| locations[0].is_oa | True |
| locations[0].source.id | https://openalex.org/S134668137 |
| locations[0].source.issn | 0305-1048, 1362-4954, 1362-4962 |
| locations[0].source.type | journal |
| locations[0].source.is_oa | True |
| locations[0].source.issn_l | 0305-1048 |
| locations[0].source.is_core | True |
| locations[0].source.is_in_doaj | True |
| locations[0].source.display_name | Nucleic Acids Research |
| locations[0].source.host_organization | https://openalex.org/P4310311648 |
| locations[0].source.host_organization_name | Oxford University Press |
| locations[0].source.host_organization_lineage | https://openalex.org/P4310311648, https://openalex.org/P4310311647 |
| locations[0].source.host_organization_lineage_names | Oxford University Press, University of Oxford |
| locations[0].license | cc-by-nc |
| locations[0].pdf_url | https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad750/51607870/gkad750.pdf |
| locations[0].version | publishedVersion |
| locations[0].raw_type | journal-article |
| locations[0].license_id | https://openalex.org/licenses/cc-by-nc |
| locations[0].is_accepted | True |
| locations[0].is_published | True |
| locations[0].raw_source_name | Nucleic Acids Research |
| locations[0].landing_page_url | https://doi.org/10.1093/nar/gkad750 |
| locations[1].id | pmid:37713610 |
| locations[1].is_oa | False |
| locations[1].source.id | https://openalex.org/S4306525036 |
| locations[1].source.issn | |
| locations[1].source.type | repository |
| locations[1].source.is_oa | False |
| locations[1].source.issn_l | |
| locations[1].source.is_core | False |
| locations[1].source.is_in_doaj | False |
| locations[1].source.display_name | PubMed |
| locations[1].source.host_organization | https://openalex.org/I1299303238 |
| locations[1].source.host_organization_name | National Institutes of Health |
| locations[1].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[1].license | |
| locations[1].pdf_url | |
| locations[1].version | publishedVersion |
| locations[1].raw_type | |
| locations[1].license_id | |
| locations[1].is_accepted | True |
| locations[1].is_published | True |
| locations[1].raw_source_name | Nucleic acids research |
| locations[1].landing_page_url | https://pubmed.ncbi.nlm.nih.gov/37713610 |
| locations[2].id | pmh:oai:pubmedcentral.nih.gov:10602906 |
| locations[2].is_oa | True |
| locations[2].source.id | https://openalex.org/S2764455111 |
| locations[2].source.issn | |
| locations[2].source.type | repository |
| locations[2].source.is_oa | False |
| locations[2].source.issn_l | |
| locations[2].source.is_core | False |
| locations[2].source.is_in_doaj | False |
| locations[2].source.display_name | PubMed Central |
| locations[2].source.host_organization | https://openalex.org/I1299303238 |
| locations[2].source.host_organization_name | National Institutes of Health |
| locations[2].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[2].license | cc-by-nc |
| locations[2].pdf_url | https://pmc.ncbi.nlm.nih.gov/articles/PMC10602906/pdf/gkad750.pdf |
| locations[2].version | submittedVersion |
| locations[2].raw_type | Text |
| locations[2].license_id | https://openalex.org/licenses/cc-by-nc |
| locations[2].is_accepted | False |
| locations[2].is_published | False |
| locations[2].raw_source_name | Nucleic Acids Res |
| locations[2].landing_page_url | https://www.ncbi.nlm.nih.gov/pmc/articles/10602906 |
| locations[3].id | pmh:oai:escholarship.org:ark:/13030/qt8bv7f35r |
| locations[3].is_oa | True |
| locations[3].source | |
| locations[3].license | cc-by-nc |
| locations[3].pdf_url | |
| locations[3].version | submittedVersion |
| locations[3].raw_type | article |
| locations[3].license_id | https://openalex.org/licenses/cc-by-nc |
| locations[3].is_accepted | False |
| locations[3].is_published | False |
| locations[3].raw_source_name | |
| locations[3].landing_page_url | https://escholarship.org/uc/item/8bv7f35r |
| locations[4].id | pmh:oai:pure.atira.dk:publications/352ff50b-749e-457e-9789-6e6bb69038c0 |
| locations[4].is_oa | True |
| locations[4].source.id | https://openalex.org/S4306400216 |
| locations[4].source.issn | |
| locations[4].source.type | repository |
| locations[4].source.is_oa | False |
| locations[4].source.issn_l | |
| locations[4].source.is_core | False |
| locations[4].source.is_in_doaj | False |
| locations[4].source.display_name | Research Portal (King's College London) |
| locations[4].source.host_organization | https://openalex.org/I183935753 |
| locations[4].source.host_organization_name | King's College London |
| locations[4].source.host_organization_lineage | https://openalex.org/I183935753 |
| locations[4].license | cc-by-nc |
| locations[4].pdf_url | |
| locations[4].version | submittedVersion |
| locations[4].raw_type | article |
| locations[4].license_id | https://openalex.org/licenses/cc-by-nc |
| locations[4].is_accepted | False |
| locations[4].is_published | False |
| locations[4].raw_source_name | Lamoureux , C R , Decker , K T , Sastry , A V , Rychel , K , Gao , Y , McConn , J L , Zielinski , D C & Palsson , B O 2023 , ' A multi-scale expression and regulation knowledge base for Escherichia coli ' , Nucleic Acids Research , vol. 51 , no. 19 , gkad750 , pp. 10176-10193 . https://doi.org/10.1093/nar/gkad750 |
| locations[4].landing_page_url | https://orbit.dtu.dk/en/publications/352ff50b-749e-457e-9789-6e6bb69038c0 |
| indexed_in | crossref, doaj, pubmed |
| authorships[0].author.id | https://openalex.org/A5012946533 |
| authorships[0].author.orcid | |
| authorships[0].author.display_name | Cameron Lamoureux |
| authorships[0].countries | US |
| authorships[0].affiliations[0].institution_ids | https://openalex.org/I36258959 |
| authorships[0].affiliations[0].raw_affiliation_string | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[0].institutions[0].id | https://openalex.org/I36258959 |
| authorships[0].institutions[0].ror | https://ror.org/0168r3w48 |
| authorships[0].institutions[0].type | education |
| authorships[0].institutions[0].lineage | https://openalex.org/I36258959 |
| authorships[0].institutions[0].country_code | US |
| authorships[0].institutions[0].display_name | University of California, San Diego |
| authorships[0].author_position | first |
| authorships[0].raw_author_name | Cameron R Lamoureux |
| authorships[0].is_corresponding | False |
| authorships[0].raw_affiliation_strings | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[1].author.id | https://openalex.org/A5003021162 |
| authorships[1].author.orcid | https://orcid.org/0000-0001-8320-8736 |
| authorships[1].author.display_name | Katherine Decker |
| authorships[1].countries | US |
| authorships[1].affiliations[0].institution_ids | https://openalex.org/I36258959 |
| authorships[1].affiliations[0].raw_affiliation_string | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[1].institutions[0].id | https://openalex.org/I36258959 |
| authorships[1].institutions[0].ror | https://ror.org/0168r3w48 |
| authorships[1].institutions[0].type | education |
| authorships[1].institutions[0].lineage | https://openalex.org/I36258959 |
| authorships[1].institutions[0].country_code | US |
| authorships[1].institutions[0].display_name | University of California, San Diego |
| authorships[1].author_position | middle |
| authorships[1].raw_author_name | Katherine T Decker |
| authorships[1].is_corresponding | False |
| authorships[1].raw_affiliation_strings | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[2].author.id | https://openalex.org/A5047222181 |
| authorships[2].author.orcid | https://orcid.org/0000-0002-8293-3909 |
| authorships[2].author.display_name | Anand V. Sastry |
| authorships[2].countries | US |
| authorships[2].affiliations[0].institution_ids | https://openalex.org/I36258959 |
| authorships[2].affiliations[0].raw_affiliation_string | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[2].institutions[0].id | https://openalex.org/I36258959 |
| authorships[2].institutions[0].ror | https://ror.org/0168r3w48 |
| authorships[2].institutions[0].type | education |
| authorships[2].institutions[0].lineage | https://openalex.org/I36258959 |
| authorships[2].institutions[0].country_code | US |
| authorships[2].institutions[0].display_name | University of California, San Diego |
| authorships[2].author_position | middle |
| authorships[2].raw_author_name | Anand V Sastry |
| authorships[2].is_corresponding | False |
| authorships[2].raw_affiliation_strings | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[3].author.id | https://openalex.org/A5091471112 |
| authorships[3].author.orcid | https://orcid.org/0000-0002-4769-2804 |
| authorships[3].author.display_name | Kevin Rychel |
| authorships[3].countries | US |
| authorships[3].affiliations[0].institution_ids | https://openalex.org/I36258959 |
| authorships[3].affiliations[0].raw_affiliation_string | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[3].institutions[0].id | https://openalex.org/I36258959 |
| authorships[3].institutions[0].ror | https://ror.org/0168r3w48 |
| authorships[3].institutions[0].type | education |
| authorships[3].institutions[0].lineage | https://openalex.org/I36258959 |
| authorships[3].institutions[0].country_code | US |
| authorships[3].institutions[0].display_name | University of California, San Diego |
| authorships[3].author_position | middle |
| authorships[3].raw_author_name | Kevin Rychel |
| authorships[3].is_corresponding | False |
| authorships[3].raw_affiliation_strings | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[4].author.id | https://openalex.org/A5015472372 |
| authorships[4].author.orcid | https://orcid.org/0000-0001-8519-1392 |
| authorships[4].author.display_name | Ye Gao |
| authorships[4].countries | US |
| authorships[4].affiliations[0].institution_ids | https://openalex.org/I36258959 |
| authorships[4].affiliations[0].raw_affiliation_string | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[4].institutions[0].id | https://openalex.org/I36258959 |
| authorships[4].institutions[0].ror | https://ror.org/0168r3w48 |
| authorships[4].institutions[0].type | education |
| authorships[4].institutions[0].lineage | https://openalex.org/I36258959 |
| authorships[4].institutions[0].country_code | US |
| authorships[4].institutions[0].display_name | University of California, San Diego |
| authorships[4].author_position | middle |
| authorships[4].raw_author_name | Ye Gao |
| authorships[4].is_corresponding | False |
| authorships[4].raw_affiliation_strings | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[5].author.id | https://openalex.org/A5028054799 |
| authorships[5].author.orcid | |
| authorships[5].author.display_name | John Luke McConn |
| authorships[5].countries | US |
| authorships[5].affiliations[0].institution_ids | https://openalex.org/I36258959 |
| authorships[5].affiliations[0].raw_affiliation_string | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[5].institutions[0].id | https://openalex.org/I36258959 |
| authorships[5].institutions[0].ror | https://ror.org/0168r3w48 |
| authorships[5].institutions[0].type | education |
| authorships[5].institutions[0].lineage | https://openalex.org/I36258959 |
| authorships[5].institutions[0].country_code | US |
| authorships[5].institutions[0].display_name | University of California, San Diego |
| authorships[5].author_position | middle |
| authorships[5].raw_author_name | John Luke McConn |
| authorships[5].is_corresponding | False |
| authorships[5].raw_affiliation_strings | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[6].author.id | https://openalex.org/A5070567302 |
| authorships[6].author.orcid | https://orcid.org/0000-0001-6452-483X |
| authorships[6].author.display_name | Daniel C. Zielinski |
| authorships[6].countries | US |
| authorships[6].affiliations[0].institution_ids | https://openalex.org/I36258959 |
| authorships[6].affiliations[0].raw_affiliation_string | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[6].institutions[0].id | https://openalex.org/I36258959 |
| authorships[6].institutions[0].ror | https://ror.org/0168r3w48 |
| authorships[6].institutions[0].type | education |
| authorships[6].institutions[0].lineage | https://openalex.org/I36258959 |
| authorships[6].institutions[0].country_code | US |
| authorships[6].institutions[0].display_name | University of California, San Diego |
| authorships[6].author_position | middle |
| authorships[6].raw_author_name | Daniel C Zielinski |
| authorships[6].is_corresponding | False |
| authorships[6].raw_affiliation_strings | Department of Bioengineering, University of California , San Diego, La Jolla , CA 92093 , USA |
| authorships[7].author.id | https://openalex.org/A5051097609 |
| authorships[7].author.orcid | https://orcid.org/0000-0003-2357-6785 |
| authorships[7].author.display_name | Bernhard Ø. Palsson |
| authorships[7].countries | DK |
| authorships[7].affiliations[0].institution_ids | https://openalex.org/I2801134892, https://openalex.org/I96673099 |
| authorships[7].affiliations[0].raw_affiliation_string | Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Kemitorvet, Building 220, 2800 Kgs. Lyngby , Denmark |
| authorships[7].affiliations[1].institution_ids | https://openalex.org/I2801134892, https://openalex.org/I96673099 |
| authorships[7].affiliations[1].raw_affiliation_string | Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark |
| authorships[7].institutions[0].id | https://openalex.org/I2801134892 |
| authorships[7].institutions[0].ror | https://ror.org/04txyc737 |
| authorships[7].institutions[0].type | facility |
| authorships[7].institutions[0].lineage | https://openalex.org/I2801134892 |
| authorships[7].institutions[0].country_code | DK |
| authorships[7].institutions[0].display_name | Novo Nordisk Foundation |
| authorships[7].institutions[1].id | https://openalex.org/I96673099 |
| authorships[7].institutions[1].ror | https://ror.org/04qtj9h94 |
| authorships[7].institutions[1].type | education |
| authorships[7].institutions[1].lineage | https://openalex.org/I96673099 |
| authorships[7].institutions[1].country_code | DK |
| authorships[7].institutions[1].display_name | Technical University of Denmark |
| authorships[7].author_position | last |
| authorships[7].raw_author_name | Bernhard O Palsson |
| authorships[7].is_corresponding | False |
| authorships[7].raw_affiliation_strings | Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Kemitorvet, Building 220, 2800 Kgs. Lyngby , Denmark, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark |
| has_content.pdf | True |
| has_content.grobid_xml | True |
| is_paratext | False |
| open_access.is_oa | True |
| open_access.oa_url | https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad750/51607870/gkad750.pdf |
| open_access.oa_status | gold |
| open_access.any_repository_has_fulltext | False |
| created_date | 2023-09-16T00:00:00 |
| display_name | A multi-scale expression and regulation knowledge base forEscherichia coli |
| has_fulltext | True |
| is_retracted | False |
| updated_date | 2025-11-06T03:46:38.306776 |
| primary_topic.id | https://openalex.org/T10521 |
| primary_topic.field.id | https://openalex.org/fields/13 |
| primary_topic.field.display_name | Biochemistry, Genetics and Molecular Biology |
| primary_topic.score | 0.9983999729156494 |
| primary_topic.domain.id | https://openalex.org/domains/1 |
| primary_topic.domain.display_name | Life Sciences |
| primary_topic.subfield.id | https://openalex.org/subfields/1312 |
| primary_topic.subfield.display_name | Molecular Biology |
| primary_topic.display_name | RNA and protein synthesis mechanisms |
| related_works | https://openalex.org/W2360987025, https://openalex.org/W2387178301, https://openalex.org/W3144733943, https://openalex.org/W2785993273, https://openalex.org/W2382269147, https://openalex.org/W3184323118, https://openalex.org/W2799462113, https://openalex.org/W36834100, https://openalex.org/W2385713529, https://openalex.org/W2599749361 |
| cited_by_count | 54 |
| counts_by_year[0].year | 2025 |
| counts_by_year[0].cited_by_count | 21 |
| counts_by_year[1].year | 2024 |
| counts_by_year[1].cited_by_count | 25 |
| counts_by_year[2].year | 2023 |
| counts_by_year[2].cited_by_count | 8 |
| locations_count | 5 |
| best_oa_location.id | doi:10.1093/nar/gkad750 |
| best_oa_location.is_oa | True |
| best_oa_location.source.id | https://openalex.org/S134668137 |
| best_oa_location.source.issn | 0305-1048, 1362-4954, 1362-4962 |
| best_oa_location.source.type | journal |
| best_oa_location.source.is_oa | True |
| best_oa_location.source.issn_l | 0305-1048 |
| best_oa_location.source.is_core | True |
| best_oa_location.source.is_in_doaj | True |
| best_oa_location.source.display_name | Nucleic Acids Research |
| best_oa_location.source.host_organization | https://openalex.org/P4310311648 |
| best_oa_location.source.host_organization_name | Oxford University Press |
| best_oa_location.source.host_organization_lineage | https://openalex.org/P4310311648, https://openalex.org/P4310311647 |
| best_oa_location.source.host_organization_lineage_names | Oxford University Press, University of Oxford |
| best_oa_location.license | cc-by-nc |
| best_oa_location.pdf_url | https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad750/51607870/gkad750.pdf |
| best_oa_location.version | publishedVersion |
| best_oa_location.raw_type | journal-article |
| best_oa_location.license_id | https://openalex.org/licenses/cc-by-nc |
| best_oa_location.is_accepted | True |
| best_oa_location.is_published | True |
| best_oa_location.raw_source_name | Nucleic Acids Research |
| best_oa_location.landing_page_url | https://doi.org/10.1093/nar/gkad750 |
| primary_location.id | doi:10.1093/nar/gkad750 |
| primary_location.is_oa | True |
| primary_location.source.id | https://openalex.org/S134668137 |
| primary_location.source.issn | 0305-1048, 1362-4954, 1362-4962 |
| primary_location.source.type | journal |
| primary_location.source.is_oa | True |
| primary_location.source.issn_l | 0305-1048 |
| primary_location.source.is_core | True |
| primary_location.source.is_in_doaj | True |
| primary_location.source.display_name | Nucleic Acids Research |
| primary_location.source.host_organization | https://openalex.org/P4310311648 |
| primary_location.source.host_organization_name | Oxford University Press |
| primary_location.source.host_organization_lineage | https://openalex.org/P4310311648, https://openalex.org/P4310311647 |
| primary_location.source.host_organization_lineage_names | Oxford University Press, University of Oxford |
| primary_location.license | cc-by-nc |
| primary_location.pdf_url | https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad750/51607870/gkad750.pdf |
| primary_location.version | publishedVersion |
| primary_location.raw_type | journal-article |
| primary_location.license_id | https://openalex.org/licenses/cc-by-nc |
| primary_location.is_accepted | True |
| primary_location.is_published | True |
| primary_location.raw_source_name | Nucleic Acids Research |
| primary_location.landing_page_url | https://doi.org/10.1093/nar/gkad750 |
| publication_date | 2023-09-15 |
| publication_year | 2023 |
| referenced_works | https://openalex.org/W2993166334, https://openalex.org/W2931264270, https://openalex.org/W2765268771, https://openalex.org/W2259938310, https://openalex.org/W1533942137, https://openalex.org/W3108101741, https://openalex.org/W2924070408, https://openalex.org/W3016489277, https://openalex.org/W2952239877, https://openalex.org/W3203588026, https://openalex.org/W3088521497, https://openalex.org/W6716701172, https://openalex.org/W2099741732, https://openalex.org/W2791975541, https://openalex.org/W3113079090, https://openalex.org/W3039562686, https://openalex.org/W4226297814, https://openalex.org/W3208712063, https://openalex.org/W4220802959, https://openalex.org/W3091901779, https://openalex.org/W2605897695, https://openalex.org/W3174663170, https://openalex.org/W2124985265, https://openalex.org/W2137586531, https://openalex.org/W2138207763, https://openalex.org/W2432815617, https://openalex.org/W2179438025, https://openalex.org/W6675354045, https://openalex.org/W2141224535, https://openalex.org/W4225610651, https://openalex.org/W2900007277, https://openalex.org/W2981155415, https://openalex.org/W3125165012, https://openalex.org/W2990783874, https://openalex.org/W2981438196, https://openalex.org/W2890423752, https://openalex.org/W3044812170, https://openalex.org/W3048092778, https://openalex.org/W2010698369, https://openalex.org/W3105956856, https://openalex.org/W3023407376, https://openalex.org/W1931984331, https://openalex.org/W2061659241, https://openalex.org/W2065625648, https://openalex.org/W2043341032, https://openalex.org/W2191824721, https://openalex.org/W3082397379, https://openalex.org/W2914166505, https://openalex.org/W3193971631, https://openalex.org/W2342682081, https://openalex.org/W4212929907, https://openalex.org/W2806609811, https://openalex.org/W3193916265, https://openalex.org/W3116625060, https://openalex.org/W3021320798, https://openalex.org/W3023422908, https://openalex.org/W3128033315, https://openalex.org/W2162386520, https://openalex.org/W2099245280, https://openalex.org/W1560847820, https://openalex.org/W2097970036, https://openalex.org/W1989075680, https://openalex.org/W2080688660, https://openalex.org/W2951764736, https://openalex.org/W2116041602, https://openalex.org/W2768848446, https://openalex.org/W3014477971, https://openalex.org/W2010907389, https://openalex.org/W2022863863, https://openalex.org/W2124896722, https://openalex.org/W2023949620, https://openalex.org/W4244151339, https://openalex.org/W2105534300, https://openalex.org/W2510001437, https://openalex.org/W1969206674, https://openalex.org/W2008604062, https://openalex.org/W2066177000, https://openalex.org/W2041807493, https://openalex.org/W2202740953, https://openalex.org/W2110904027, https://openalex.org/W2134701031, https://openalex.org/W2407233100, https://openalex.org/W4225272203, https://openalex.org/W4372291602, https://openalex.org/W4225388180, https://openalex.org/W4283587730, https://openalex.org/W4304957333, https://openalex.org/W2903357856, https://openalex.org/W2416083568, https://openalex.org/W1987005877, https://openalex.org/W2997591727 |
| referenced_works_count | 91 |
| abstract_inverted_index.9 | 58 |
| abstract_inverted_index.a | 20, 34, 47, 151 |
| abstract_inverted_index.39 | 60 |
| abstract_inverted_index.42 | 64 |
| abstract_inverted_index.76 | 68 |
| abstract_inverted_index.E. | 144 |
| abstract_inverted_index.We | 79, 112, 122 |
| abstract_inverted_index.at | 147 |
| abstract_inverted_index.in | 43 |
| abstract_inverted_index.is | 3, 33 |
| abstract_inverted_index.of | 40, 91, 135, 157 |
| abstract_inverted_index.to | 83 |
| abstract_inverted_index.we | 18, 74, 102 |
| abstract_inverted_index.201 | 85 |
| abstract_inverted_index.86% | 90 |
| abstract_inverted_index.The | 30, 51 |
| abstract_inverted_index.and | 23, 67, 107, 149 |
| abstract_inverted_index.are | 15 |
| abstract_inverted_index.for | 9, 27, 89, 125, 153 |
| abstract_inverted_index.lab | 45 |
| abstract_inverted_index.new | 127 |
| abstract_inverted_index.our | 44 |
| abstract_inverted_index.the | 96, 120, 143 |
| abstract_inverted_index.two | 104 |
| abstract_inverted_index.via | 133 |
| abstract_inverted_index.1675 | 115 |
| abstract_inverted_index.This | 140 |
| abstract_inverted_index.With | 99 |
| abstract_inverted_index.also | 113 |
| abstract_inverted_index.base | 26, 132 |
| abstract_inverted_index.coli | 145 |
| abstract_inverted_index.data | 2, 14, 41, 128 |
| abstract_inverted_index.from | 12 |
| abstract_inverted_index.gene | 69 |
| abstract_inverted_index.into | 119 |
| abstract_inverted_index.that | 87 |
| abstract_inverted_index.this | 13, 72, 130 |
| abstract_inverted_index.used | 80 |
| abstract_inverted_index.Here, | 17 |
| abstract_inverted_index.Using | 71 |
| abstract_inverted_index.coli. | 29 |
| abstract_inverted_index.known | 92 |
| abstract_inverted_index.novel | 105 |
| abstract_inverted_index.scale | 148 |
| abstract_inverted_index.these | 100 |
| abstract_inverted_index.thus, | 6 |
| abstract_inverted_index.using | 46 |
| abstract_inverted_index.during | 137 |
| abstract_inverted_index.global | 76 |
| abstract_inverted_index.growth | 55 |
| abstract_inverted_index.media; | 59 |
| abstract_inverted_index.single | 48 |
| abstract_inverted_index.RNA-seq | 37 |
| abstract_inverted_index.account | 88 |
| abstract_inverted_index.aerobic | 138 |
| abstract_inverted_index.against | 129 |
| abstract_inverted_index.diverse | 54 |
| abstract_inverted_index.extract | 84 |
| abstract_inverted_index.machine | 81 |
| abstract_inverted_index.methods | 8 |
| abstract_inverted_index.modules | 86 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.analysis | 156 |
| abstract_inverted_index.contains | 53 |
| abstract_inverted_index.creating | 95 |
| abstract_inverted_index.curated, | 116 |
| abstract_inverted_index.learning | 82 |
| abstract_inverted_index.modules, | 101 |
| abstract_inverted_index.provides | 150 |
| abstract_inverted_index.rapidly; | 5 |
| abstract_inverted_index.regulons | 106 |
| abstract_inverted_index.resource | 141 |
| abstract_inverted_index.scalable | 7 |
| abstract_inverted_index.top-down | 21, 154 |
| abstract_inverted_index.analyzing | 126 |
| abstract_inverted_index.assembled | 19 |
| abstract_inverted_index.blueprint | 152 |
| abstract_inverted_index.component | 32 |
| abstract_inverted_index.critical. | 16 |
| abstract_inverted_index.generated | 42 |
| abstract_inverted_index.including | 62 |
| abstract_inverted_index.knowledge | 11, 25, 131 |
| abstract_inverted_index.non-model | 158 |
| abstract_inverted_index.patterns. | 78 |
| abstract_inverted_index.proteins; | 66 |
| abstract_inverted_index.protocol. | 50 |
| abstract_inverted_index.resource, | 73 |
| abstract_inverted_index.resource. | 121 |
| abstract_inverted_index.workflows | 124 |
| abstract_inverted_index.compendium | 38, 52 |
| abstract_inverted_index.component. | 98 |
| abstract_inverted_index.consisting | 39 |
| abstract_inverted_index.elucidated | 75 |
| abstract_inverted_index.expression | 22, 31, 77 |
| abstract_inverted_index.extracting | 10 |
| abstract_inverted_index.identified | 103 |
| abstract_inverted_index.including: | 57 |
| abstract_inverted_index.integrated | 114 |
| abstract_inverted_index.knockouts. | 70 |
| abstract_inverted_index.organisms. | 159 |
| abstract_inverted_index.quantified | 108 |
| abstract_inverted_index.regulation | 24, 136 |
| abstract_inverted_index.regulatory | 93, 97, 110 |
| abstract_inverted_index.responses. | 111 |
| abstract_inverted_index.Escherichia | 28 |
| abstract_inverted_index.conditions, | 56 |
| abstract_inverted_index.illuminates | 142 |
| abstract_inverted_index.transition. | 139 |
| abstract_inverted_index.1035-sample, | 35 |
| abstract_inverted_index.accumulating | 4 |
| abstract_inverted_index.antibiotics; | 63 |
| abstract_inverted_index.demonstrated | 123 |
| abstract_inverted_index.experimental | 49 |
| abstract_inverted_index.heterologous | 65 |
| abstract_inverted_index.high-quality | 36 |
| abstract_inverted_index.supplements, | 61 |
| abstract_inverted_index.interactions, | 94 |
| abstract_inverted_index.systems-level | 109 |
| abstract_inverted_index.transcriptome | 146 |
| abstract_inverted_index.Transcriptomic | 1 |
| abstract_inverted_index.deconstruction | 134 |
| abstract_inverted_index.transcriptomes | 118 |
| abstract_inverted_index.transcriptomic | 155 |
| abstract_inverted_index.publicly-available | 117 |
| cited_by_percentile_year.max | 100 |
| cited_by_percentile_year.min | 99 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 8 |
| citation_normalized_percentile.value | 0.98673215 |
| citation_normalized_percentile.is_in_top_1_percent | True |
| citation_normalized_percentile.is_in_top_10_percent | True |