Organizing genome engineering for the gigabase scale | Paper Citation Record

Observation a6f6d0dc-a967-41f5-a031-d97262fd3a41 · outbound

This paper cites The Genome Project-Write.

Organizing genome engineering for the gigabase scale The Genome Project-Write

Reference 1

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Observation 6f295e4e-3121-4d84-8a80-5522544dfc39 · outbound

This paper cites Biology Is Technology : The Promise, Peril, and New Business of Engineering Life (Harvard University Press, 2011).

Organizing genome engineering for the gigabase scale Biology Is Technology : The Promise, Peril, and New Business of Engineering Life (Harvard University Press, 2011)

Reference 2

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Observation 972c1a84-0d99-4e2a-a9c5-657e256c6308 · outbound

This paper cites Synthetic DNA synthesis and assembly: putting the synthetic in syn- thetic biology.

Organizing genome engineering for the gigabase scale Synthetic DNA synthesis and assembly: putting the synthetic in syn- thetic biology

Reference 3

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Observation 8fb5237d-c61d-496f-9a03-4dc20944b2b5 · outbound

This paper cites Beyond editing to writing large genomes.

Organizing genome engineering for the gigabase scale Beyond editing to writing large genomes

Reference 4

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Observation ee753b16-9254-4851-a485-08e1dd239a5e · outbound

This paper cites Total synthesis of a gene.

Organizing genome engineering for the gigabase scale Total synthesis of a gene

Reference 5

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Observation 0e0c27ba-7ecf-4e27-818b-79b47a4ef792 · outbound

This paper cites A totally synthetic plasmid for general cloning, gene expression and mutagenesis in Escherichia coli.

Organizing genome engineering for the gigabase scale A totally synthetic plasmid for general cloning, gene expression and mutagenesis in Escherichia coli

Reference 6

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Observation 95054ef0-257c-4e92-ad38-3d83a06eda58 · outbound

This paper cites Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.

Organizing genome engineering for the gigabase scale Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides

Reference 7

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Observation e0e57826-c92d-4f08-a1e6-9294a63f6a8a · outbound

This paper cites Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template.

Organizing genome engineering for the gigabase scale Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template

Reference 8

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Observation 5f214ddd-449f-407a-9e2a-9fb19e47fdb7 · outbound

This paper cites Accurate multiplex gene synthesis from programmable DNA microchips.

Organizing genome engineering for the gigabase scale Accurate multiplex gene synthesis from programmable DNA microchips

Reference 9

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Observation aa202616-e999-4edb-a4f7-b5166d0c9cca · outbound

This paper cites Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster.

Organizing genome engineering for the gigabase scale Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster

Reference 10

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Observation 6f222066-9add-45ba-8175-842491c38590 · outbound

This paper cites Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.

Organizing genome engineering for the gigabase scale Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome

Reference 11

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Observation ece113f1-a514-47b2-b045-bea57c320da2 · outbound

This paper cites Creation of a bacterial cell controlled by a chemically synthesized genome.

Organizing genome engineering for the gigabase scale Creation of a bacterial cell controlled by a chemically synthesized genome

Reference 12

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Observation 572f7a4e-d554-453f-8b2a-6a4a60bd8d71 · outbound

This paper cites Design, synthesis, and testing toward a 57-codon genome.

Organizing genome engineering for the gigabase scale Design, synthesis, and testing toward a 57-codon genome

Reference 13

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Observation 9a5b1644-d545-4bd8-bc51-dbd80517ffee · outbound

This paper cites Total synthesis of Escherichia coli with a recoded genome.

Organizing genome engineering for the gigabase scale Total synthesis of Escherichia coli with a recoded genome

Reference 14

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Observation 9a27f488-e707-49bb-9100-56b0b1537eb4 · outbound

This paper cites Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA.

Organizing genome engineering for the gigabase scale Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA

Reference 15

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Observation 64bdb7cd-8df5-444e-a6c3-e98e2854fe2e · outbound

This paper cites Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.

Organizing genome engineering for the gigabase scale Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

Reference 16

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Observation 2e32d8a4-6d74-4666-b9ae-3858c381c343 · outbound

This paper cites Total synthesis of a functional designer eukaryotic chromosome.

Organizing genome engineering for the gigabase scale Total synthesis of a functional designer eukaryotic chromosome

Reference 17

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Observation 79428246-da20-4e2f-874f-ec88f844f924 · outbound

This paper cites Design of a synthetic yeast genome.

Organizing genome engineering for the gigabase scale Design of a synthetic yeast genome

Reference 18

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Observation 62b49632-843a-437f-aafb-70f98b2373dd · outbound

This paper cites Ultra-safe Cells Resistant to Natural Viruses Announced as First GP- write Grand-scale Project 2018.

Organizing genome engineering for the gigabase scale Ultra-safe Cells Resistant to Natural Viruses Announced as First GP- write Grand-scale Project 2018

Reference 19

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Observation 6138e892-72c6-4f5c-beed-af7f5977cbf3 · outbound

This paper cites Neal Stewart, J & Tekotte, H.

Organizing genome engineering for the gigabase scale Neal Stewart, J & Tekotte, H

Reference 20

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Observation 9cca7fce-d2c3-4d7f-b955-6d6325c7aebb · outbound

This paper cites Needs and opportunities in bio-design automa- tion: four areas for focus.

Organizing genome engineering for the gigabase scale Needs and opportunities in bio-design automa- tion: four areas for focus

Reference 21

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Observation 840ca4de-cb95-43cb-8ce6-b7a75a3f3077 · outbound

This paper cites An automated design-build-test-learn pipeline for enhanced micro- bial production of ﬁne chemicals.

Organizing genome engineering for the gigabase scale An automated design-build-test-learn pipeline for enhanced micro- bial production of ﬁne chemicals

Reference 22

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Observation 2bcf519b-27c9-40f9-8c1a-6723f54ccf17 · outbound

This paper cites Synthesis aided design: The biological design- build-test engineering paradigm? Biotechnology and Bioengineering 113, 7–10 (2016).

Organizing genome engineering for the gigabase scale Synthesis aided design: The biological design- build-test engineering paradigm? Biotechnology and Bioengineering 113, 7–10 (2016)

Reference 23

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Observation 825b1c3e-f636-49a1-a276-2c5c9fcdf234 · outbound

This paper cites Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform.

Organizing genome engineering for the gigabase scale Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform

Reference 24

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Observation 597b4b23-0e65-403a-92da-027ecf201a63 · outbound

This paper cites From plant metabolic engineering to plant synthetic biology: The evolution of the design/build/test/learn cycle.

Organizing genome engineering for the gigabase scale From plant metabolic engineering to plant synthetic biology: The evolution of the design/build/test/learn cycle

Reference 25

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Observation 1169fd3e-dd05-4d1f-a5f2-e7ed7d1216dd · outbound

This paper cites Design and synthesis of a minimal bacterial genome.

Organizing genome engineering for the gigabase scale Design and synthesis of a minimal bacterial genome

Reference 26

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Observation 396148ff-27fa-465f-a33f-c76c9ce67445 · outbound

This paper cites The second wave of synthetic biology: from modules to systems.

Organizing genome engineering for the gigabase scale The second wave of synthetic biology: from modules to systems

Reference 27

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Observation 1c508c12-6798-4238-9b8d-de5e77d9bd69 · outbound

This paper cites The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Organizing genome engineering for the gigabase scale The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

Reference 28

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Observation e475ae10-e920-4658-8b7b-ea9ee6e4fad4 · outbound

This paper cites Sharing structure and function in biological design with SBOL 2.0.ACS Synthetic Biology 5, 498–506 (2016).

Organizing genome engineering for the gigabase scale Sharing structure and function in biological design with SBOL 2.0.ACS Synthetic Biology 5, 498–506 (2016)

Reference 29

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Observation 42ab6cfe-65fd-4052-8904-dc4c83417ac0 · outbound

This paper cites Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol.

Organizing genome engineering for the gigabase scale Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol

Reference 30

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Observation 373a6c1d-0eab-41a9-8b74-6c90e72cef5f · outbound

This paper cites Bio-CAD modeling and its applications in computer-aided tissue engineering.

Organizing genome engineering for the gigabase scale Bio-CAD modeling and its applications in computer-aided tissue engineering

Reference 31

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Observation 6f4fc14f-794f-4191-9b03-5001ccbde1fd · outbound

This paper cites The International Nucleotide Sequence Database collaboration.

Organizing genome engineering for the gigabase scale The International Nucleotide Sequence Database collaboration

Reference 32

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Observation ea6581a8-a98f-4cb6-8c0d-1a329af0c176 · outbound

This paper cites Ensembl 2019.

Organizing genome engineering for the gigabase scale Ensembl 2019

Reference 33

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Observation 072ae43c-574b-46bb-a31d-9851a1d5d9fb · outbound

This paper cites Ensembl Genomes 2016: more genomes, more complexity.

Organizing genome engineering for the gigabase scale Ensembl Genomes 2016: more genomes, more complexity

Reference 34

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Observation 4f20ef72-6173-4495-8bfa-73e586f5b218 · outbound

This paper cites Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

Organizing genome engineering for the gigabase scale Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Reference 35

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Observation 542e2315-bb39-47a3-8ba3-1c6d9be743b0 · outbound

This paper cites RefSeq: an update on prokaryotic genome annotation and curation.

Organizing genome engineering for the gigabase scale RefSeq: an update on prokaryotic genome annotation and curation

Reference 36

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Observation 76c871a1-e048-400d-adaf-a2dad61677ea · outbound

This paper cites DNA Data Bank of Japan (DDBJ) progress report.

Organizing genome engineering for the gigabase scale DNA Data Bank of Japan (DDBJ) progress report

Reference 37

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.449578Z

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Observation cd3d4b64-82f1-411d-a1db-0ee507eed9ad · outbound

This paper cites Genome Data Viewer <https://www.ncbi.nlm.

Organizing genome engineering for the gigabase scale Genome Data Viewer <https://www.ncbi.nlm

Reference 38

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.432299Z

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Observation 5c9f16bd-ff97-470e-9fd1-5cc75411f320 · outbound

This paper cites WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs.

Organizing genome engineering for the gigabase scale WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

Reference 39

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.416540Z

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Observation 32b84eb4-543d-453e-b640-25441f4d479f · outbound

This paper cites Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

Organizing genome engineering for the gigabase scale Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Reference 40

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.401611Z

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Observation d765e6b7-9024-4879-91e0-941b601ddfb8 · outbound

This paper cites Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant eﬀect prediction.

Organizing genome engineering for the gigabase scale Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant eﬀect prediction

Reference 41

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.386065Z

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Observation 36e55ec6-c2f5-40ed-b04b-e22b621c52a4 · outbound

This paper cites Choice of transcripts and software has a large eﬀect on variant annotation.

Organizing genome engineering for the gigabase scale Choice of transcripts and software has a large eﬀect on variant annotation

Reference 42

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.369662Z

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Observation 5833ff57-427d-4d94-bed1-4ec49b7e1be3 · outbound

This paper cites in The Gene Ontology Handbook 245–259 (Humana Press, New York, NY, 2017).

Organizing genome engineering for the gigabase scale in The Gene Ontology Handbook 245–259 (Humana Press, New York, NY, 2017)

Reference 43

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.353754Z

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Observation 70b7e1ae-d14c-4553-b420-5b3352c894c0 · outbound

This paper cites The Sequence Ontology: a tool for the uniﬁcation of genome annotations.

Organizing genome engineering for the gigabase scale The Sequence Ontology: a tool for the uniﬁcation of genome annotations

Reference 44

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.337762Z

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Observation 2c864f59-9359-41cf-99e9-67ea0b761f31 · outbound

This paper cites Synthetic Biology Open Language (SBOL) version 2.2.

Organizing genome engineering for the gigabase scale Synthetic Biology Open Language (SBOL) version 2.2

Reference 45

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.320890Z

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Observation a8010281-63de-4557-ab88-354dc0d16e03 · outbound

This paper cites Recon 2.2: from reconstruction to model of human metabolism.

Organizing genome engineering for the gigabase scale Recon 2.2: from reconstruction to model of human metabolism

Reference 46

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.304674Z

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Observation 3bac793b-8fa7-4004-be82-eeffcf4cbc86 · outbound

This paper cites iML1515, a knowledgebase that computes Escherichia coli traits.

Organizing genome engineering for the gigabase scale iML1515, a knowledgebase that computes Escherichia coli traits

Reference 47

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.288934Z

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Observation 5333721c-6812-415b-a017-0644f54283f4 · outbound

This paper cites A whole-cell computational model predicts phenotype from genotype.

Organizing genome engineering for the gigabase scale A whole-cell computational model predicts phenotype from genotype

Reference 48

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.274214Z

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Observation 10c4de67-b592-4895-8816-4412aee7b821 · outbound

This paper cites IMG: the integrated microbial genomes database and comparative analysis system.

Organizing genome engineering for the gigabase scale IMG: the integrated microbial genomes database and comparative analysis system

Reference 49

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.258710Z

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Observation da8b4dc0-3fd7-4421-a95e-49a7e063dc2d · outbound

This paper cites The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

Organizing genome engineering for the gigabase scale The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Reference 50

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.242433Z

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Observation c4704502-00b7-46e5-8ed6-b5592d244f9c · outbound

This paper cites A knowledge-based approach to design for manu- facturability.

Organizing genome engineering for the gigabase scale A knowledge-based approach to design for manu- facturability

Reference 51

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.225851Z

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Observation 8835f4fe-6f1f-4f1d-9ff1-e5acff9b44d4 · outbound

This paper cites an unresolved cited work.

Organizing genome engineering for the gigabase scale Unresolved cited work

Reference 52

Resolution: unresolved; raw_fallback, observed 2026-08-14T05:20:11.208990Z

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Observation d22b63e4-0f50-4126-b6ed-ac7bca6fdeab · outbound

This paper cites Streamlining the design-to-build transition with build-optimization software tools.

Organizing genome engineering for the gigabase scale Streamlining the design-to-build transition with build-optimization software tools

Reference 53

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.191470Z

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Observation 243179c9-d383-42cf-ad6c-4110398f8763 · outbound

This paper cites Golden gate shuﬄing: a one-pot DNA shuﬄing method based on type IIs restriction enzymes.

Organizing genome engineering for the gigabase scale Golden gate shuﬄing: a one-pot DNA shuﬄing method based on type IIs restriction enzymes

Reference 54

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.173250Z

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Observation 1c2b498a-af45-4ca3-9775-94f8738616d3 · outbound

This paper cites A modular cloning system for stan- dardized assembly of multigene constructs.

Organizing genome engineering for the gigabase scale A modular cloning system for stan- dardized assembly of multigene constructs

Reference 55

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.156104Z

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Observation f1cd08fa-e15e-4c72-9f53-791e66bdf29d · outbound

This paper cites Enzymatic assembly of DNA molecules up to several hundred kilobases.

Organizing genome engineering for the gigabase scale Enzymatic assembly of DNA molecules up to several hundred kilobases

Reference 56

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.140301Z

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Observation 54aa8029-37b5-4363-95c6-13b1628bea59 · outbound

This paper cites One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome.

Organizing genome engineering for the gigabase scale One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome

Reference 57

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.125808Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation c35d4732-f40b-4d36-b203-564d937efeea · outbound

This paper cites BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks.

Organizing genome engineering for the gigabase scale BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks

Reference 58

Resolution: unresolved; no resolver link, observed 2026-08-14T05:20:09.823699Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 5d81e5e9-e6b1-4b6d-9f30-29e0a18ecdde · outbound

This paper cites Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

Organizing genome engineering for the gigabase scale Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools

Reference 59

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.106402Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation c53b36c0-2045-49bc-9d9c-a4405da35fa6 · outbound

This paper cites SynBioHub: a standards-enabled design repository for synthetic biology.

Organizing genome engineering for the gigabase scale SynBioHub: a standards-enabled design repository for synthetic biology

Reference 60

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.089807Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 162f8ec9-37cd-407b-925b-dc90ae9faaec · outbound

This paper cites A standard variation ﬁle format for human genome sequences.

Organizing genome engineering for the gigabase scale A standard variation ﬁle format for human genome sequences

Reference 61

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.072902Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 427e1136-794e-4932-8fde-608fbbf8e2ad · outbound

This paper cites Standardization, calibration, and control in ﬂow cytometry.

Organizing genome engineering for the gigabase scale Standardization, calibration, and control in ﬂow cytometry

Reference 62

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.057336Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 1fc13bbc-b7b1-4bea-93fc-2eeafb242248 · outbound

This paper cites Quantiﬁcation of bacterial ﬂuorescence using independent calibrants.

Organizing genome engineering for the gigabase scale Quantiﬁcation of bacterial ﬂuorescence using independent calibrants

Reference 63

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.041456Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 7b686a0e-53d7-4d91-a184-d5961bef9540 · outbound

This paper cites General calibration of microbial growth in microplate readers.

Organizing genome engineering for the gigabase scale General calibration of microbial growth in microplate readers

Reference 64

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.024311Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 011389e2-384b-43fa-b776-5ada6331d310 · outbound

This paper cites External RNA controls consortium beta version update.

Organizing genome engineering for the gigabase scale External RNA controls consortium beta version update

Reference 65

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:11.009908Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation b0f1bac9-5879-413a-8066-c94c96b4f71c · outbound

This paper cites RightField: embedding ontology annotation in spreadsheets.

Organizing genome engineering for the gigabase scale RightField: embedding ontology annotation in spreadsheets

Reference 66

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.993932Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation a9c847ed-5a0a-4afb-bf6f-2df1e746c50b · outbound

This paper cites OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans.

Organizing genome engineering for the gigabase scale OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans

Reference 67

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.977548Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation e7eaa414-a84c-40e6-b893-0f8003883c9f · outbound

This paper cites The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Organizing genome engineering for the gigabase scale The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

Reference 68

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.961743Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation bf3e8541-3894-4401-b288-0fb225660a7d · outbound

This paper cites Modeling sample variables with an Experimental Factor Ontology.

Organizing genome engineering for the gigabase scale Modeling sample variables with an Experimental Factor Ontology

Reference 69

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.946144Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 7caae1a2-39b6-4bf2-a218-77e7ac5aae22 · outbound

This paper cites Emerging whole-cell modeling principles and methods.

Organizing genome engineering for the gigabase scale Emerging whole-cell modeling principles and methods

Reference 70

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.929808Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 9a832894-1467-496f-b0c1-377e5b382a1e · outbound

This paper cites A blueprint for human whole-cell modeling.

Organizing genome engineering for the gigabase scale A blueprint for human whole-cell modeling

Reference 71

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.912948Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 1ced3fe6-57b3-4dd5-8e75-bd9801a95d97 · outbound

This paper cites Standard virtual biological parts: a repository of modular modeling components for synthetic biology.

Organizing genome engineering for the gigabase scale Standard virtual biological parts: a repository of modular modeling components for synthetic biology

Reference 72

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.896630Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 93d568d0-13f2-4d0d-aee5-a92276911803 · outbound

This paper cites Model selection in systems and synthetic biology.

Organizing genome engineering for the gigabase scale Model selection in systems and synthetic biology

Reference 73

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.879522Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation e3b4ebd4-d0af-46a2-959f-2f752dbbf99a · outbound

This paper cites BioModels: expanding horizons to include more modelling ap- proaches and formats.

Organizing genome engineering for the gigabase scale BioModels: expanding horizons to include more modelling ap- proaches and formats

Reference 74

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.864001Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 01ff9235-4e5b-4121-9179-a98ac03b0155 · outbound

This paper cites Model exchange with the NeuroML model database.

Organizing genome engineering for the gigabase scale Model exchange with the NeuroML model database

Reference 75

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.848742Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation f9e06889-becd-49fb-bf50-2032c937b1eb · outbound

This paper cites Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits.

Organizing genome engineering for the gigabase scale Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits

Reference 76

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.834111Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation ea8ec1db-0208-46c6-bf56-89cdc99e25ee · outbound

This paper cites The Physiome Model Repository 2.

Organizing genome engineering for the gigabase scale The Physiome Model Repository 2

Reference 77

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.817846Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 31c3798a-87d7-4e9c-9b93-a30b5d3a35ed · outbound

This paper cites Metabolic ﬂux analysis and metabolic engineering of microorganisms.

Organizing genome engineering for the gigabase scale Metabolic ﬂux analysis and metabolic engineering of microorganisms

Reference 78

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.799774Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation c7fbc669-093a-482e-8805-4bd5d9b8390f · outbound

This paper cites Several design heuristics are also already commonly used.

Organizing genome engineering for the gigabase scale Several design heuristics are also already commonly used

Reference 79

Resolution: unresolved; no resolver link, observed 2026-08-14T05:20:09.534854Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 9f03066f-257b-4824-ba98-52c39f4b8e02 · outbound

This paper cites PSORTb 3.0: improved protein subcellular localization prediction with reﬁned localization subcategories and predictive capabilities for all prokaryotes.

Organizing genome engineering for the gigabase scale PSORTb 3.0: improved protein subcellular localization prediction with reﬁned localization subcategories and predictive capabilities for all prokaryotes

Reference 80

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.784266Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation e9107472-cb71-4dc1-b3bc-c6b16a2bafae · outbound

This paper cites Gene Designer: a synthetic biology tool for constructing artiﬁcial DNA segments.

Organizing genome engineering for the gigabase scale Gene Designer: a synthetic biology tool for constructing artiﬁcial DNA segments

Reference 81

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.767545Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation f0b809a0-127b-4137-9edc-e128e12d1967 · outbound

This paper cites The CellML 1.1 speciﬁcation.

Organizing genome engineering for the gigabase scale The CellML 1.1 speciﬁcation

Reference 82

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.751454Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation e975627d-9ebe-4437-acee-ad68aa8df2be · outbound

This paper cites Development of NeuroML version 2.0: greater exten- sibility, support for abstract neuronal models and interaction with systems biology languages.

Organizing genome engineering for the gigabase scale Development of NeuroML version 2.0: greater exten- sibility, support for abstract neuronal models and interaction with systems biology languages

Reference 83

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.736904Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation c088a3e5-8a50-467d-9c5a-7d54d1ca3b6f · outbound

This paper cites The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models.

Organizing genome engineering for the gigabase scale The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models

Reference 84

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.720235Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 68b00aa3-2b14-4764-93a4-0b78da150435 · outbound

This paper cites DockerHub <https://hub.docker.com> (2019).

Organizing genome engineering for the gigabase scale DockerHub <https://hub.docker.com> (2019)

Reference 85

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.703534Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 9349c41d-731d-4245-8c39-e9fa5911041b · outbound

This paper cites A standard-enabled workﬂow for synthetic biology.

Organizing genome engineering for the gigabase scale A standard-enabled workﬂow for synthetic biology

Reference 86

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.687569Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 895aed21-cbae-4df6-a932-80dd1a4c994b · outbound

This paper cites An implemen- tation-focused bio/algorithmic workﬂow for synthetic biology.

Organizing genome engineering for the gigabase scale An implemen- tation-focused bio/algorithmic workﬂow for synthetic biology

Reference 87

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.671531Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 5ca0fa45-f98b-4b07-9487-ea975f8c9102 · outbound

This paper cites Harnessing QbD, programming languages, and automation for reproducible biology.

Organizing genome engineering for the gigabase scale Harnessing QbD, programming languages, and automation for reproducible biology

Reference 88

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.655253Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation d7883a60-9393-4820-990a-25fe7f32690e · outbound

This paper cites Trends in laboratory information management system.

Organizing genome engineering for the gigabase scale Trends in laboratory information management system

Reference 89

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.639209Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation f8c3c293-2ab0-49ca-86c4-835ec6134801 · outbound

This paper cites Achieving reproducibility and closed-loop automation in biological experimenta- tion with an IoT-enabled Lab of the future.

Organizing genome engineering for the gigabase scale Achieving reproducibility and closed-loop automation in biological experimenta- tion with an IoT-enabled Lab of the future

Reference 90

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.621579Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 0f4c6bb9-cdb1-41b4-9420-9a1c09fd95de · outbound

This paper cites Aquarium: The laboratory operating system version 2.6.0.

Organizing genome engineering for the gigabase scale Aquarium: The laboratory operating system version 2.6.0

Reference 91

Resolution: verified exact; doi, observed 2026-08-14T05:20:10.126107Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation d880e125-d0c6-4a97-99a5-1cab13020a4e · outbound

This paper cites Antha <http://www.antha-lang.org> (2019).

Organizing genome engineering for the gigabase scale Antha <http://www.antha-lang.org> (2019)

Reference 92

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.486533Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 98521e69-9c20-4884-bb00-165bff30e0b6 · outbound

This paper cites Synthetic bistability and diﬀerentiation in yeast.

Organizing genome engineering for the gigabase scale Synthetic bistability and diﬀerentiation in yeast

Reference 93

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.470190Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation f650587e-1b5a-4e7a-98f7-77d9d6d6c4e9 · outbound

This paper cites The Workﬂow Description Language and Cromwell <https://software.broadin- stitute.org/wdl> (2019).

Organizing genome engineering for the gigabase scale The Workﬂow Description Language and Cromwell <https://software.broadin- stitute.org/wdl> (2019)

Reference 94

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.453994Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 580f3570-27d6-4ce0-98a0-e40d25c6b28e · outbound

This paper cites Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Organizing genome engineering for the gigabase scale Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

Reference 95

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.436331Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 9154c0a9-fd42-4f88-95d2-50be56464ac7 · outbound

This paper cites Nextﬂow enables reproducible computational workﬂows.

Organizing genome engineering for the gigabase scale Nextﬂow enables reproducible computational workﬂows

Reference 96

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.420587Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 6ce7c581-a3da-40b1-8908-b956ea1f4b64 · outbound

This paper cites Toil enables reproducible, open source, big biomedical data analyses.

Organizing genome engineering for the gigabase scale Toil enables reproducible, open source, big biomedical data analyses

Reference 97

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.402490Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 2ef7ac3f-1471-4a72-99f4-4eb351fe44da · outbound

This paper cites Common Workﬂow Language, v1.0 2016.

Organizing genome engineering for the gigabase scale Common Workﬂow Language, v1.0 2016

Reference 98

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.383072Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation dfdd72ba-069b-43b3-899c-b24be57ba64f · outbound

This paper cites The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workﬂows.

Organizing genome engineering for the gigabase scale The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workﬂows

Reference 99

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.367511Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 1491ef4e-c9eb-4235-805b-1ec031ae0152 · outbound

This paper cites myExperiment: a repository and social network for the sharing of bioinformatics workﬂows.

Organizing genome engineering for the gigabase scale myExperiment: a repository and social network for the sharing of bioinformatics workﬂows

Reference 100

Resolution: verified fuzzy; raw_fallback, observed 2026-08-14T05:20:10.350858Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

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Reference resolution

Outbound references

Pith citing papers