{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T04:33:56Z","timestamp":1791261236401,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1010346","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,3,22]],"date-time":"2022-03-22T00:00:00Z","timestamp":1647907200000}}],"reference-count":68,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T00:00:00Z","timestamp":1646611200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/R016437\/1"],"award-info":[{"award-number":["BB\/R016437\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/R010188\/1"],"award-info":[{"award-number":["BB\/R010188\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["206194\/Z\/17\/Z"],"award-info":[{"award-number":["206194\/Z\/17\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["Sir Henry Dale Fellowship (Grant 220185\/Z\/20\/Z)"],"award-info":[{"award-number":["Sir Henry Dale Fellowship (Grant 220185\/Z\/20\/Z)"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"crossref","award":["Sir Henry Dale Fellowship (Grant 220185\/Z\/20\/Z)"],"award-info":[{"award-number":["Sir Henry Dale Fellowship (Grant 220185\/Z\/20\/Z)"]}],"id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Early diverging lineages such as trypanosomes can provide clues to the evolution of sexual reproduction in eukaryotes. In\n                    <jats:italic>Trypanosoma brucei<\/jats:italic>\n                    , the pathogen that causes Human African Trypanosomiasis, sexual reproduction occurs in the salivary glands of the insect host, but analysis of the molecular signatures that define these sexual forms is complicated because they mingle with more numerous, mitotically-dividing developmental stages. We used single-cell RNA-sequencing (scRNAseq) to profile 388 individual trypanosomes from midgut, proventriculus, and salivary glands of infected tsetse flies allowing us to identify tissue-specific cell types. Further investigation of salivary gland parasite transcriptomes revealed fine-scale changes in gene expression over a developmental progression from putative sexual forms through metacyclics expressing variant surface glycoprotein genes. The cluster of cells potentially containing sexual forms was characterized by high level transcription of the gamete fusion protein HAP2, together with an array of surface proteins and several genes of unknown function. We linked these expression patterns to distinct morphological forms using immunofluorescence assays and reporter gene expression to demonstrate that the kinetoplastid-conserved gene Tb927.10.12080 is exclusively expressed at high levels by meiotic intermediates and gametes. Further experiments are required to establish whether this protein, currently of unknown function, plays a role in gamete formation and\/or fusion.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1010346","type":"journal-article","created":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T13:35:41Z","timestamp":1646660141000},"page":"e1010346","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["Single-cell transcriptomics reveals expression profiles of Trypanosoma brucei sexual stages"],"prefix":"10.1371","volume":"18","author":[{"given":"Virginia M.","family":"Howick","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lori","family":"Peacock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris","family":"Kay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clare","family":"Collett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wendy","family":"Gibson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mara K. N.","family":"Lawniczak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,3,7]]},"reference":[{"key":"ppat.1010346.ref001","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1242\/jcs.01649","article-title":"The developmental cell biology of Trypanosoma brucei","volume":"118","author":"KR Matthews","year":"2005","journal-title":"J Cell Sci"},{"key":"ppat.1010346.ref002","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1006\/jmbi.2001.5004","article-title":"Multiple procyclin isoforms are expressed differentially during the development of insect forms of Trypanosoma brucei","volume":"312","author":"E Vassella","year":"2001","journal-title":"J Mol Biol"},{"key":"ppat.1010346.ref003","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/S0166-6851(01)00398-X","article-title":"Characterisation and cellular localisation of a GPEET procyclin precursor in Trypanosoma brucei insect forms","volume":"119","author":"P B\u00fctikofer","year":"2002","journal-title":"Mol Biochem Parasitol"},{"key":"ppat.1010346.ref004","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.molbiopara.2006.03.017","article-title":"Energy metabolism of trypanosomatids: adaptation to available carbon sources","volume":"149","author":"F Bringaud","year":"2006","journal-title":"Mol Biochem Parasitol"},{"issue":"Pt 5","key":"ppat.1010346.ref005","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1017\/S0031182099004217","article-title":"Trypanosoma brucei spp. development in the tsetse fly: characterization of the post-mesocyclic stages in the foregut and proboscis","volume":"118","author":"J Van Den Abbeele","year":"1999","journal-title":"Parasitology"},{"key":"ppat.1010346.ref006","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.protis.2007.07.004","article-title":"Asymmetric cell division as a route to reduction in cell length and change in cell morphology in trypanosomes","volume":"159","author":"R Sharma","year":"2008","journal-title":"Protist"},{"key":"ppat.1010346.ref007","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1111\/j.1365-2958.2006.05492.x","article-title":"A family of stage-specific alanine-rich proteins on the surface of epimastigote forms of Trypanosoma brucei","volume":"63","author":"S Urwyler","year":"2007","journal-title":"Mol Microbiol"},{"key":"ppat.1010346.ref008","doi-asserted-by":"crossref","first-page":"3671","DOI":"10.1073\/pnas.1019423108","article-title":"Identification of the meiotic life cycle stage of Trypanosoma brucei in the tsetse fly","volume":"108","author":"L Peacock","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1010346.ref009","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.cub.2013.11.044","article-title":"Meiosis and haploid gametes in the pathogen Trypanosoma brucei","volume":"24","author":"L Peacock","year":"2014","journal-title":"Curr Biol"},{"key":"ppat.1010346.ref010","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/s42003-021-02058-5","article-title":"Sequential production of gametes during meiosis in trypanosomes","volume":"4","author":"L Peacock","year":"2021","journal-title":"Commun Biol"},{"key":"ppat.1010346.ref011","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/nature24280","article-title":"Single-cell RNA sequencing reveals a signature of sexual commitment in malaria parasites","volume":"551","author":"A Poran","year":"2017","journal-title":"Nature"},{"key":"ppat.1010346.ref012","doi-asserted-by":"crossref","first-page":"e33105","DOI":"10.7554\/eLife.33105","article-title":"Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites.","volume":"7","author":"AJ Reid","year":"2018","journal-title":"Elife"},{"key":"ppat.1010346.ref013","first-page":"365","article-title":"The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle","author":"VM Howick","year":"2019","journal-title":"Science"},{"key":"ppat.1010346.ref014","doi-asserted-by":"crossref","first-page":"3196","DOI":"10.1038\/s41467-021-23434-z","article-title":"A single-cell atlas of Plasmodium falciparum transmission through the mosquito","volume":"12","author":"E Real","year":"2021","journal-title":"Nat Commun"},{"key":"ppat.1010346.ref015","doi-asserted-by":"crossref","first-page":"68","DOI":"10.3389\/fcimb.2021.604129","article-title":"Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage","volume":"11","author":"K Witmer","year":"2021","journal-title":"Front Cell Infect Microbiol"},{"key":"ppat.1010346.ref016","doi-asserted-by":"crossref","first-page":"e3000711","DOI":"10.1371\/journal.pbio.3000711","article-title":"Single-cell transcription analysis of Plasmodium vivax blood-stage parasites identifies stage- and species-specific profiles of expression","volume":"18","author":"JM S\u00e0","year":"2020","journal-title":"PLoS Biol"},{"key":"ppat.1010346.ref017","article-title":"There and back again: malaria parasite single-cell transcriptomics comes full circle","author":"C N\u00f6tzel","year":"2021","journal-title":"Trends Parasitol"},{"key":"ppat.1010346.ref018","doi-asserted-by":"crossref","first-page":"5268","DOI":"10.1038\/s41467-021-25607-2","article-title":"Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing","volume":"12","author":"EM Briggs","year":"2021","journal-title":"Nat Commun"},{"key":"ppat.1010346.ref019","article-title":"Single-cell RNA sequencing of Trypanosoma brucei from tsetse salivary glands unveils metacyclogenesis and identifies potential transmission blocking antigens","author":"A Vigneron","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"9","key":"ppat.1010346.ref020","doi-asserted-by":"crossref","first-page":"e1009904","DOI":"10.1371\/journal.ppat.1009904","article-title":"The establishment of variant surface glycoprotein monoallelic expression revealed by single-cell RNA-seq of Trypanosoma brucei in the tsetse fly salivary glands","volume":"17","author":"S Hutchinson","journal-title":"PLoS Pathog"},{"key":"ppat.1010346.ref021","doi-asserted-by":"crossref","first-page":"e1708","DOI":"10.1371\/journal.pntd.0001708","article-title":"Transcript expression analysis of putative Trypanosoma brucei GPI-anchored surface proteins during development in the tsetse and mammalian hosts","volume":"6","author":"AF Savage","year":"2012","journal-title":"PLoS Negl Trop Dis"},{"key":"ppat.1010346.ref022","doi-asserted-by":"crossref","first-page":"e2649","DOI":"10.1371\/journal.pntd.0002649","article-title":"Insights into the trypanosome-host interactions revealed through transcriptomic analysis of parasitized tsetse fly salivary glands","volume":"8","author":"EL Telleria","year":"2014","journal-title":"PLoS Negl Trop Dis"},{"key":"ppat.1010346.ref023","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1126\/science.1229641","article-title":"Developmental progression to infectivity in Trypanosoma brucei triggered by an RNA-binding protein","volume":"338","author":"NG Kolev","year":"2012","journal-title":"Science"},{"key":"ppat.1010346.ref024","doi-asserted-by":"crossref","first-page":"e0168877","DOI":"10.1371\/journal.pone.0168877","article-title":"Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans","volume":"11","author":"AF Savage","year":"2016","journal-title":"PLoS One"},{"key":"ppat.1010346.ref025","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1186\/s12864-018-4600-6","article-title":"RNA-Seq analysis validates the use of culture-derived Trypanosoma brucei and provides new markers for mammalian and insect life-cycle stages","volume":"19","author":"A Naguleswaran","year":"2018","journal-title":"BMC Genomics"},{"key":"ppat.1010346.ref026","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.molbiopara.2015.04.001","article-title":"Synchronous expression of individual metacyclic variant surface glycoprotein genes in Trypanosoma brucei","volume":"200","author":"K Ramey-Butler","year":"2015","journal-title":"Mol Biochem Parasitol"},{"key":"ppat.1010346.ref027","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1111\/mmi.13754","article-title":"The proteome and transcriptome of the infectious metacyclic form of Trypanosoma brucei define quiescent cells primed for mammalian invasion","volume":"106","author":"R Christiano","year":"2017","journal-title":"Mol Microbiol"},{"key":"ppat.1010346.ref028","doi-asserted-by":"crossref","first-page":"e3000741","DOI":"10.1371\/journal.pbio.3000741","article-title":"Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei","volume":"18","author":"E Dole\u017eelov\u00e1","year":"2020","journal-title":"PLoS Biol"},{"key":"ppat.1010346.ref029","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nprot.2014.006","article-title":"Full-length RNA-seq from single cells using Smart-seq2.","volume":"9","author":"S Picelli","year":"2014","journal-title":"Nat Protoc"},{"key":"ppat.1010346.ref030","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.1017\/S003118202100041X","article-title":"Application of single-cell transcriptomics to kinetoplastid research","volume":"148","author":"EM Briggs","year":"2021","journal-title":"Parasitology"},{"issue":"Pt 2","key":"ppat.1010346.ref031","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1042\/bj3260415","article-title":"\u201cGPEET\u201d procyclin is the major surface protein of procyclic culture forms of Trypanosoma brucei brucei strain 427","volume":"326","author":"P B\u00fctikofer","year":"1997","journal-title":"Biochem J"},{"key":"ppat.1010346.ref032","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nmeth.4236","article-title":"SC3: consensus clustering of single-cell RNA-seq data","volume":"14","author":"VY Kiselev","year":"2017","journal-title":"Nat Methods"},{"key":"ppat.1010346.ref033","doi-asserted-by":"crossref","first-page":"e0009504","DOI":"10.1371\/journal.pntd.0009504","article-title":"Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host","volume":"15","author":"A Naguleswaran","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"key":"ppat.1010346.ref034","doi-asserted-by":"crossref","first-page":"26832","DOI":"10.1074\/jbc.M601377200","article-title":"Fumarate is an essential intermediary metabolite produced by the procyclic Trypanosoma brucei","volume":"281","author":"V Coustou","year":"2006","journal-title":"J Biol Chem"},{"key":"ppat.1010346.ref035","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nature07997","article-title":"A surface transporter family conveys the trypanosome differentiation signal","volume":"459","author":"S Dean","year":"2009","journal-title":"Nature"},{"key":"ppat.1010346.ref036","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1093\/oxfordjournals.bmb.a072036","article-title":"Developmental cycles and biology of pathogenic trypanosomes","volume":"41","author":"K. Vickerman","year":"1985","journal-title":"Br Med Bull"},{"key":"ppat.1010346.ref037","doi-asserted-by":"crossref","first-page":"2811","DOI":"10.1093\/gbe\/evu222","article-title":"Comparative genomics reveals multiple genetic backgrounds of human pathogenicity in the Trypanosoma brucei complex","volume":"6","author":"M Sistrom","year":"2014","journal-title":"Genome Biol Evol"},{"key":"ppat.1010346.ref038","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1128\/EC.1.6.1000-1009.2002","article-title":"Ex vivo and in vitro identification of a consensus promoter for VSG genes expressed by metacyclic-stage trypanosomes in the tsetse fly","volume":"1","author":"ML Ginger","year":"2002","journal-title":"Eukaryot Cell"},{"key":"ppat.1010346.ref039","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.molbiopara.2014.06.004","article-title":"Capturing the variant surface glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427","volume":"195","author":"GAM Cross","year":"2014","journal-title":"Mol Biochem Parasitol"},{"key":"ppat.1010346.ref040","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1186\/s12864-018-4772-0","article-title":"Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics","volume":"19","author":"K Street","year":"2018","journal-title":"BMC Genomics"},{"key":"ppat.1010346.ref041","doi-asserted-by":"crossref","DOI":"10.1038\/s41592-020-0820-1","article-title":"Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes.","author":"H Heaton","year":"2020","journal-title":"Nat Methods"},{"key":"ppat.1010346.ref042","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1756-3305-1-4","article-title":"The use of yellow fluorescent hybrids to indicate mating in Trypanosoma brucei","volume":"1","author":"W Gibson","year":"2008","journal-title":"Parasit Vectors"},{"key":"ppat.1010346.ref043","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"A Butler","year":"2018","journal-title":"Nat Biotechnol"},{"key":"ppat.1010346.ref044","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1101\/gad.14.5.615","article-title":"A major surface glycoprotein of trypanosoma brucei is expressed transiently during development and can be regulated post-transcriptionally by glycerol or hypoxia","volume":"14","author":"E Vassella","year":"2000","journal-title":"Genes Dev"},{"key":"ppat.1010346.ref045","doi-asserted-by":"crossref","first-page":"e22","DOI":"10.1371\/journal.ppat.0010022","article-title":"Expression of procyclin mRNAs during cyclical transmission of Trypanosoma brucei","volume":"1","author":"S Urwyler","year":"2005","journal-title":"PLoS Pathog"},{"key":"ppat.1010346.ref046","article-title":"A long non-coding RNA controls parasite differentiation in 2 African trypanosomes","author":"F Guegan","year":"2020","journal-title":"Biorxiv"},{"key":"ppat.1010346.ref047","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1038\/nature12864","article-title":"Genome-wide dissection of the quorum sensing signalling pathway in Trypanosoma brucei","volume":"505","author":"BM Mony","year":"2014","journal-title":"Nature"},{"key":"ppat.1010346.ref048","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.pt.2016.10.009","article-title":"TrypTag.org: A Trypanosome Genome-wide Protein Localisation Resource","volume":"33","author":"S Dean","year":"2017","journal-title":"Trends Parasitol"},{"key":"ppat.1010346.ref049","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.molbiopara.2018.12.003","article-title":"Cellular landmarks of Trypanosoma brucei and Leishmania mexicana","volume":"230","author":"C Halliday","year":"2019","journal-title":"Mol Biochem Parasitol"},{"key":"ppat.1010346.ref050","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1111\/j.1550-7408.1977.tb00987.x","article-title":"New culture medium for maintenance of tsetse tissues and growth of trypanosomatids","volume":"24","author":"I. Cunningham","year":"1977","journal-title":"J Protozool"},{"key":"ppat.1010346.ref051","doi-asserted-by":"crossref","first-page":"2151","DOI":"10.1038\/s41598-018-20372-7","article-title":"A practical solution for preserving single cells for RNA sequencing","volume":"8","author":"M Attar","year":"2018","journal-title":"Sci Rep"},{"key":"ppat.1010346.ref052","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/s12864-018-4512-5","article-title":"High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis","volume":"19","author":"W Wang","year":"2018","journal-title":"BMC Genomics"},{"key":"ppat.1010346.ref053","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/S0166-6851(96)02815-0","article-title":"Vectors for inducible expression of toxic gene products in bloodstream and procyclic Trypanosoma brucei","volume":"85","author":"S Biebinger","year":"1997","journal-title":"Mol Biochem Parasitol"},{"key":"ppat.1010346.ref054","doi-asserted-by":"crossref","first-page":"3231","DOI":"10.1099\/00221287-147-12-3231","article-title":"A novel GFP approach for the analysis of genetic exchange in trypanosomes allowing the in situ detection of mating events","volume":"147","author":"LE Bingle","year":"2001","journal-title":"Microbiology"},{"key":"ppat.1010346.ref055","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"M. Martin","year":"2011","journal-title":"EMBnet.journal"},{"key":"ppat.1010346.ref056","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"D Kim","year":"2015","journal-title":"Nat Methods"},{"key":"ppat.1010346.ref057","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1093\/bib\/bbs038","article-title":"The UCSC genome browser and associated tools","volume":"14","author":"RM Kuhn","year":"2013","journal-title":"Brief Bioinform"},{"key":"ppat.1010346.ref058","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a Python framework to work with high-throughput sequencing data","volume":"31","author":"S Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"ppat.1010346.ref059","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"ppat.1010346.ref060","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"MG Grabherr","year":"2011","journal-title":"Nat Biotechnol"},{"key":"ppat.1010346.ref061","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1038\/nprot.2013.084","article-title":"De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis","volume":"8","author":"BJ Haas","year":"2013","journal-title":"Nat Protoc."},{"issue":"2","key":"ppat.1010346.ref062","doi-asserted-by":"crossref","first-page":"e1010300","DOI":"10.1371\/journal.ppat.1010300","article-title":"Signatures of hybridization in Trypanosoma brucei.","volume":"18","author":"C Kay","journal-title":"PLoS Pathog"},{"key":"ppat.1010346.ref063","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"ppat.1010346.ref064","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/bioinformatics\/btw777","article-title":"Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R","volume":"33","author":"DJ McCarthy","year":"2017","journal-title":"Bioinformatics"},{"key":"ppat.1010346.ref065","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13059-016-0947-7","article-title":"Pooling across cells to normalize single-cell RNA sequencing data with many zero counts","volume":"17","author":"L. Lun AT","year":"2016","journal-title":"Genome Biol"},{"key":"ppat.1010346.ref066","unstructured":"Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv [q-bio.GN]. 2012. Available: http:\/\/arxiv.org\/abs\/1207.3907"},{"key":"ppat.1010346.ref067","doi-asserted-by":"crossref","first-page":"3660","DOI":"10.1038\/s41467-019-11591-1","article-title":"A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing","volume":"10","author":"AA Petti","year":"2019","journal-title":"Nat Commun"},{"key":"ppat.1010346.ref068","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1038\/s41467-020-14766-3","article-title":"Trajectory-based differential expression analysis for single-cell sequencing data","volume":"11","author":"K Van den Berge","year":"2020","journal-title":"Nat Commun"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1010346","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,3,22]],"date-time":"2022-03-22T00:00:00Z","timestamp":1647907200000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1010346","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,18]],"date-time":"2023-11-18T09:18:39Z","timestamp":1700299119000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1010346"}},"subtitle":[],"editor":[{"given":"Lucy","family":"Glover","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,3,7]]},"references-count":68,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2022,3,7]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1010346","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.10.13.463681","asserted-by":"object"}],"has-review":[{"id-type":"doi","id":"10.3410\/f.741774393.793597677","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,3,7]]}}}