{"doi":"10.1242/dev.170506","title":"Concepts and limitations for learning developmental trajectories from single cell genomics","abstract":"Single cell genomics has become a popular approach to uncover the cellular heterogeneity of progenitor and terminally differentiated cell types with great precision. This approach can also delineate lineage hierarchies and identify molecular programmes of cell-fate acquisition and segregation. Nowadays, tens of thousands of cells are routinely sequenced in single cell-based methods and even more are expected to be analysed in the future. However, interpretation of the resulting data is challenging and requires computational models at multiple levels of abstraction. In contrast to other applications of single cell sequencing, where clustering approaches dominate, developmental systems are generally modelled using continuous structures, trajectories and trees. These trajectory models carry the promise of elucidating mechanisms of development, disease and stimulation response at very high molecular resolution. However, their reliable analysis and biological interpretation requires an understanding of their underlying assumptions and limitations. Here, we review the basic concepts of such computational approaches and discuss the characteristics of developmental processes that can be learnt from trajectory models.","journal":"Development","year":2019,"id":3361,"datarank":0.839206706940276,"base_score":5.594711379601839,"endowment":5.594711379601839,"self_citation_contribution":0.839206706940276,"citation_network_contribution":0.0,"self_endowment_contribution":0.839206706940276,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":268,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0716,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2019-06-15","fair_score":12.5,"fair_percentile":0.15391380826737028,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":3572,"name":"Maren Büttner","orcid":"0000-0002-6189-3792","position":1,"is_corresponding":false},{"id":3574,"name":"David S. Fischer","orcid":"0000-0002-1293-7656","position":2,"is_corresponding":false},{"id":2914,"name":"Marius Lange","orcid":"0000-0002-4846-1266","position":3,"is_corresponding":false},{"id":2915,"name":"Volker Bergen","orcid":"0000-0003-2486-1473","position":4,"is_corresponding":false},{"id":2920,"name":"Heiko Lickert","orcid":"0000-0002-4597-8825","position":5,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":6,"is_corresponding":false},{"id":34876,"name":"Sophie Tritschler","orcid":"0000-0003-0977-9957","position":0,"is_corresponding":true}],"reference_count":93,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":20.0,"fair_a":30.0,"fair_i":0.0,"fair_r":0.0,"fair_zscore":-2.9589,"fair_rationale":{"fair_score":12.5,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":20.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"datacite=0, pmcid=False, pmid=False","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"The paper does not mention any metadata, machine-readable or otherwise, for the data or code."}]},"A":{"name":"Accessible","score":30.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"No protocol for accessing data or code is provided in the text."}]},"I":{"name":"Interoperable","score":0.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"The text does not reference any standard formats, vocabularies, or identifiers used."}]},"R":{"name":"Reusable","score":0.0,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"not a dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.0,"signal":null,"rationale":"There is no data-availability statement, license, or reproducibility information in the text."}]}},"suggestions":["Include a data-availability statement specifying where data and code can be accessed, with a persistent identifier like a DOI.","Provide metadata in a machine-readable format (e.g., JSON-LD) describing the datasets and methods used.","Use standard file formats (e.g., HDF5 for single-cell data) and reference controlled vocabularies (e.g., Cell Ontology) for cell types.","Add a license (e.g., CC-BY 4.0) to the paper and any associated data/code to clarify reuse terms.","Describe the computational environment and dependencies (e.g., via a Dockerfile or requirements.txt) to enable reproducibility."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v1","fulltext_source":"abstract_only"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v1","fair_fulltext_source":"abstract_only","fair_has_llm":true,"fair_computed_at":"2026-06-14T20:29:17.791168Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}