Extracting, filtering and simulating cellular barcodes using CellBarcode tools

Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode ex...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Nature Computational Science Jg. 4; H. 2; S. 128 - 143
Hauptverfasser: Sun, Wenjie, Perkins, Meghan, Huyghe, Mathilde, Faraldo, Marisa M., Fre, Silvia, Perié, Leïla, Lyne, Anne-Marie
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States Nature Publishing Group 01.02.2024
Nature
Nature Publishing Group US
Schlagworte:
Bar codes
Datasets
Decision trees
Deoxyribonucleic acid
DNA
DNA - genetics
DNA Barcoding, Taxonomic - methods
Experiments
Filtration
Gene sequencing
Life Sciences
Polymerase Chain Reaction
Quality control
Reproducibility of Results
Resource
Sequence Analysis, DNA - methods
Simulation
ISSN:2662-8457, 2662-8457
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Abstract Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.
AbstractList Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.The authors introduce two cellular barcoding tools: CellBarcode, for extracting and filtering diverse DNA barcodes from bulk and single-cell sequencing data; and CellBarcodeSim, for simulating barcoding experiments, thus enabling the investigation of the impact of biological and technical factors on barcode detection.
Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.
Abstract Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.
Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.
Author Faraldo, Marisa M.
Lyne, Anne-Marie
Fre, Silvia
Sun, Wenjie
Huyghe, Mathilde
Perié, Leïla
Perkins, Meghan
Author_xml – sequence: 1
  givenname: Wenjie
  orcidid: 0000-0002-3100-2346
  surname: Sun
  fullname: Sun, Wenjie
– sequence: 2
  givenname: Meghan
  surname: Perkins
  fullname: Perkins, Meghan
– sequence: 3
  givenname: Mathilde
  orcidid: 0000-0002-8473-2924
  surname: Huyghe
  fullname: Huyghe, Mathilde
– sequence: 4
  givenname: Marisa M.
  surname: Faraldo
  fullname: Faraldo, Marisa M.
– sequence: 5
  givenname: Silvia
  surname: Fre
  fullname: Fre, Silvia
– sequence: 6
  givenname: Leïla
  orcidid: 0000-0003-0798-4498
  surname: Perié
  fullname: Perié, Leïla
– sequence: 7
  givenname: Anne-Marie
  orcidid: 0000-0002-1779-8392
  surname: Lyne
  fullname: Lyne, Anne-Marie
BackLink https://www.ncbi.nlm.nih.gov/pubmed/38374363$$D View this record in MEDLINE/PubMed
https://hal.science/hal-04467733$$DView record in HAL
BookMark eNpdUctOwzAQtBAISuEHOKBIXEAi4Gdin1CpeEkVXOBsObbTBqVxsZMK_h6HQAVcvKvZ8exj9sF24xoLwBGCFwgSfhkoYZynENMUQiZYmm-BEc4ynHLK8u1f-R44DOEVQogZIjAju2CPcJJTkpEReLx5b73SbdXMz5OyqlvrY5qoxiShWna16iuJtnUdc58UymtnbEi60OPTiF8PUNI6V4cDsFOqOtjD7zgGL7c3z9P7dPZ09zCdzFJNUdbGl0NKBVMlxsjw0ljLrIgRC2ULzKkw2uSlpgpbLUzZB4hKViCqjMkYGYOrQXfVFUtrtG3iFrVc-Wqp_Id0qpJ_K021kHO3lghyIRAiUeFsUFj8-3c_mckeiwNmeU7IGkXu6Xc37946G1q5rEJ_E9VY1wWJBeac0Rz2g538o766zjfxFpJgnEUXEKSRdfx7_E3_H18iAQ8E7V0I3pYbCoKy918O_svov_zyX-bkE-n3owo
Cites_doi 10.1016/j.exphem.2014.05.003
10.1038/nature25969
10.1371/journal.pone.0025785
10.1038/srep43249
10.1093/bioinformatics/btv053
10.1016/j.celrep.2022.110461
10.1093/bioinformatics/btz872
10.5281/zenodo.5645045
10.1038/s41596-019-0247-2
10.1038/nature20777
10.1016/j.celrep.2018.02.046
10.1038/s41596-018-0058-x
10.1038/s41467-019-08595-2
10.18129/B9.bioc.CellBarcode
10.1038/s43588-021-00057-4
10.1038/s41467-018-07406-4
10.1016/j.ccell.2020.12.002
10.1126/science.abm5874
10.1155/2014/287430
10.1093/bioinformatics/bti623
10.1126/science.aaf7907
10.1038/s41598-018-37301-3
10.1101/2023.01.24.525166
10.1038/s41587-023-01931-4
10.1093/bioinformatics/btr708
10.7554/eLife.76541
10.1007/s00239-022-10083-z
10.1073/pnas.91.19.8969
10.5281/zenodo.10492831
10.1016/j.stem.2023.04.001
10.1038/s41577-021-00590-3
10.1038/s41591-020-01182-9
10.1182/blood-2023-178732
10.1038/s41467-023-37167-8
10.1126/scitranslmed.aav0936
10.7554/eLife.66922
10.1371/journal.pone.0036852
10.1002/j.1538-7305.1950.tb00463.x
10.1186/s12859-016-0999-4
10.5281/zenodo.10492761
10.32614/RJ-2011-015
10.1073/pnas.1512977112
10.1038/s41588-022-01047-6
10.3389/fmed.2022.919345
10.1038/s41586-018-0744-4
10.1038/nature23653
10.1093/bioinformatics/btx655
10.1016/j.ygeno.2014.09.005
10.1038/s41586-021-04237-0
10.1038/nbt.4124
10.1016/j.exphem.2018.11.005
10.1038/s41556-018-0108-1
10.1038/nature12013
10.5281/zenodo.8124948
10.5281/zenodo.10027001
10.1093/bioinformatics/btw759
10.1002/1873-3468.12299
10.1038/s41467-018-02832-w
10.1016/j.omtm.2020.03.021
10.1093/nar/25.15.3082
10.1038/nbt.1977
ContentType Journal Article
Copyright 2024. The Author(s).
Copyright Nature Publishing Group Feb 2024
Distributed under a Creative Commons Attribution 4.0 International License
The Author(s) 2024
Copyright_xml – notice: 2024. The Author(s).
– notice: Copyright Nature Publishing Group Feb 2024
– notice: Distributed under a Creative Commons Attribution 4.0 International License
– notice: The Author(s) 2024
DBID AAYXX
CITATION
CGR
CUY
CVF
ECM
EIF
NPM
8FE
8FG
AFKRA
ARAPS
AZQEC
BENPR
BGLVJ
CCPQU
DWQXO
GNUQQ
HCIFZ
JQ2
K7-
P5Z
P62
PHGZM
PHGZT
PKEHL
PQEST
PQGLB
PQQKQ
PQUKI
PRINS
7X8
1XC
VOOES
5PM
DOI 10.1038/s43588-024-00595-7
DatabaseName CrossRef
Medline
MEDLINE
MEDLINE (Ovid)
MEDLINE
MEDLINE
PubMed
ProQuest SciTech Collection
ProQuest Technology Collection
ProQuest Central UK/Ireland
Advanced Technologies & Aerospace Collection (ProQuest)
ProQuest Central Essentials
ProQuest Central
Technology Collection
ProQuest One Community College
ProQuest Central
ProQuest Central Student
SciTech Premium Collection
ProQuest Computer Science Collection
Computer Science Database
Advanced Technologies & Aerospace Database
ProQuest Advanced Technologies & Aerospace Collection
ProQuest Central Premium
ProQuest One Academic
ProQuest One Academic Middle East (New)
ProQuest One Academic Eastern Edition (DO NOT USE)
ProQuest One Applied & Life Sciences
ProQuest One Academic (retired)
ProQuest One Academic UKI Edition
ProQuest Central China
MEDLINE - Academic
Hyper Article en Ligne (HAL)
Hyper Article en Ligne (HAL) (Open Access)
PubMed Central (Full Participant titles)
DatabaseTitle CrossRef
MEDLINE
Medline Complete
MEDLINE with Full Text
PubMed
MEDLINE (Ovid)
Advanced Technologies & Aerospace Collection
Computer Science Database
ProQuest Central Student
Technology Collection
ProQuest One Academic Middle East (New)
ProQuest Advanced Technologies & Aerospace Collection
ProQuest Central Essentials
ProQuest Computer Science Collection
ProQuest One Academic Eastern Edition
SciTech Premium Collection
ProQuest One Community College
ProQuest Technology Collection
ProQuest SciTech Collection
ProQuest Central China
ProQuest Central
Advanced Technologies & Aerospace Database
ProQuest One Applied & Life Sciences
ProQuest One Academic UKI Edition
ProQuest Central Korea
ProQuest Central (New)
ProQuest One Academic
ProQuest One Academic (New)
MEDLINE - Academic
DatabaseTitleList Advanced Technologies & Aerospace Collection

CrossRef

MEDLINE - Academic
MEDLINE
Database_xml – sequence: 1
  dbid: NPM
  name: PubMed
  url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 2
  dbid: P5Z
  name: Advanced Technologies & Aerospace Database
  url: https://search.proquest.com/hightechjournals
  sourceTypes: Aggregation Database
DeliveryMethod fulltext_linktorsrc
Discipline Sciences (General)
EISSN 2662-8457
EndPage 143
ExternalDocumentID PMC10899113
oai:HAL:hal-04467733v1
38374363
10_1038_s43588_024_00595_7
Genre Journal Article
GrantInformation_xml – fundername: Schlumberger Foundation
  grantid: FSER20200211117
– fundername: EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
  grantid: ERC StG 758170-Microbar
– fundername: Centre National de la Recherche Scientifique (National Center for Scientific Research)
  grantid: ATIPAvenir
– fundername: Fondation ARC pour la Recherche sur le Cancer (ARC Foundation for Cancer Research)
  grantid: ARCPGA2021120004232_4874
GroupedDBID 0R~
AARCD
AAYXX
ABJNI
ACBWK
AFANA
AFFHD
AFKRA
AFSHS
AFWHJ
AGHDO
AIBTJ
ALMA_UNASSIGNED_HOLDINGS
ARAPS
ATHPR
BENPR
BGLVJ
CCPQU
CITATION
HCIFZ
K7-
NFIDA
ODYON
PHGZM
PHGZT
PQGLB
RNT
SNYQT
SOJ
AAEEF
AAYZH
CGR
CUY
CVF
ECM
EIF
NPM
8FE
8FG
AZQEC
DWQXO
GNUQQ
JQ2
P62
PKEHL
PQEST
PQQKQ
PQUKI
PRINS
7X8
1XC
VOOES
5PM
ID FETCH-LOGICAL-c416t-c4804495af221d8fdee5e98fd29aeb2849dcd7fc4a2ec9dfa2ec01f5b14add653
IEDL.DBID K7-
ISICitedReferencesCount 1
ISICitedReferencesURI http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=001165788900001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN 2662-8457
IngestDate Tue Nov 04 02:05:52 EST 2025
Tue Oct 14 20:03:20 EDT 2025
Thu Sep 04 15:42:10 EDT 2025
Sat Aug 23 12:48:50 EDT 2025
Wed Feb 19 02:11:52 EST 2025
Sat Nov 29 06:45:21 EST 2025
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 2
Language English
License 2024. The Author(s).
Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-c416t-c4804495af221d8fdee5e98fd29aeb2849dcd7fc4a2ec9dfa2ec01f5b14add653
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ORCID 0000-0002-3100-2346
0000-0002-8473-2924
0000-0003-0798-4498
0000-0002-1779-8392
OpenAccessLink https://pubmed.ncbi.nlm.nih.gov/PMC10899113
PMID 38374363
PQID 3226000104
PQPubID 7343593
PageCount 16
ParticipantIDs pubmedcentral_primary_oai_pubmedcentral_nih_gov_10899113
hal_primary_oai_HAL_hal_04467733v1
proquest_miscellaneous_2928854705
proquest_journals_3226000104
pubmed_primary_38374363
crossref_primary_10_1038_s43588_024_00595_7
PublicationCentury 2000
PublicationDate 2024-02-01
PublicationDateYYYYMMDD 2024-02-01
PublicationDate_xml – month: 02
  year: 2024
  text: 2024-02-01
  day: 01
PublicationDecade 2020
PublicationPlace United States
PublicationPlace_xml – name: United States
– name: New York
PublicationTitle Nature Computational Science
PublicationTitleAlternate Nat Comput Sci
PublicationYear 2024
Publisher Nature Publishing Group
Nature
Nature Publishing Group US
Publisher_xml – name: Nature Publishing Group
– name: Nature
– name: Nature Publishing Group US
References RW Hamming (595_CR38) 1950; 29
W Huang (595_CR39) 2012; 28
J Marsolier (595_CR17) 2022; 54
L Kok (595_CR4) 2022; 22
D Merino (595_CR7) 2019; 10
R Lu (595_CR3) 2011; 29
GV Echeverria (595_CR9) 2018; 9
T Buschmann (595_CR40) 2017; 33
H Wang (595_CR48) 2011; 3
SH Naik (595_CR5) 2013; 496
595_CR57
T Sing (595_CR47) 2005; 21
595_CR51
A McKenna (595_CR12) 2016; 353
A-M Lyne (595_CR22) 2018; 68
E Zorita (595_CR56) 2015; 31
B Lloyd-Lewis (595_CR55) 2022; 38
B Spanjaard (595_CR16) 2018; 36
S Beneyto-Calabuig (595_CR33) 2023; 30
JE Adair (595_CR43) 2020; 17
AM Lilja (595_CR54) 2018; 20
595_CR44
L Thielecke (595_CR26) 2020; 36
RC Bandler (595_CR29) 2022; 601
J Urbanus (595_CR20) 2023; 14
W Pei (595_CR19) 2017; 548
DS Lin (595_CR25) 2018; 22
E Dhimolea (595_CR6) 2021; 39
A Alemany (595_CR14) 2018; 556
Q Marcou (595_CR41) 2018; 9
L Zhao (595_CR27) 2018; 34
S Fre (595_CR53) 2011; 6
JR Blundell (595_CR10) 2014; 104
R Fodde (595_CR50) 1994; 91
MS Johnson (595_CR49) 2023; 91
R Sender (595_CR31) 2021; 27
VG Sankaran (595_CR1) 2022; 378
L Perié (595_CR2) 2016; 590
595_CR34
595_CR35
L Hadj Abed (595_CR23) 2022; 9
LV Bystrykh (595_CR32) 2012; 7
G Weiss (595_CR45) 1997; 25
P McInerney (595_CR46) 2014; 2014
L Mourao (595_CR52) 2019; 9
DA Espinoza (595_CR24) 2021; 1
B Raj (595_CR15) 2018; 13
GV Echeverria (595_CR8) 2019; 11
S Radtke (595_CR37) 2023; 142
J Desponds (595_CR42) 2016; 113
W Kong (595_CR28) 2020; 15
595_CR58
595_CR59
AS Eisele (595_CR30) 2022; 11
BA Biddy (595_CR36) 2018; 564
JB Beltman (595_CR21) 2016; 17
595_CR61
SH Naik (595_CR11) 2014; 42
595_CR62
KL Frieda (595_CR13) 2017; 541
595_CR60
L Thielecke (595_CR18) 2017; 7
References_xml – volume: 42
  start-page: 598
  year: 2014
  ident: 595_CR11
  publication-title: Exp. Hematol.
  doi: 10.1016/j.exphem.2014.05.003
– volume: 556
  start-page: 108
  year: 2018
  ident: 595_CR14
  publication-title: Nature
  doi: 10.1038/nature25969
– volume: 6
  start-page: e25785
  year: 2011
  ident: 595_CR53
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0025785
– volume: 7
  start-page: 43249
  year: 2017
  ident: 595_CR18
  publication-title: Sci. Rep.
  doi: 10.1038/srep43249
– volume: 31
  start-page: 1913
  year: 2015
  ident: 595_CR56
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btv053
– volume: 38
  start-page: 110461
  year: 2022
  ident: 595_CR55
  publication-title: Cell Rep.
  doi: 10.1016/j.celrep.2022.110461
– volume: 36
  start-page: 2189
  year: 2020
  ident: 595_CR26
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btz872
– ident: 595_CR57
  doi: 10.5281/zenodo.5645045
– volume: 15
  start-page: 750
  year: 2020
  ident: 595_CR28
  publication-title: Nat. Protoc.
  doi: 10.1038/s41596-019-0247-2
– volume: 541
  start-page: 107
  year: 2017
  ident: 595_CR13
  publication-title: Nature
  doi: 10.1038/nature20777
– volume: 22
  start-page: 2557
  year: 2018
  ident: 595_CR25
  publication-title: Cell Rep.
  doi: 10.1016/j.celrep.2018.02.046
– volume: 13
  start-page: 2685
  year: 2018
  ident: 595_CR15
  publication-title: Nat. Protoc.
  doi: 10.1038/s41596-018-0058-x
– volume: 10
  year: 2019
  ident: 595_CR7
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-019-08595-2
– ident: 595_CR61
  doi: 10.18129/B9.bioc.CellBarcode
– volume: 1
  start-page: 280
  year: 2021
  ident: 595_CR24
  publication-title: Nat. Comput. Sci.
  doi: 10.1038/s43588-021-00057-4
– volume: 9
  year: 2018
  ident: 595_CR9
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-018-07406-4
– volume: 39
  start-page: 240
  year: 2021
  ident: 595_CR6
  publication-title: Cancer Cell
  doi: 10.1016/j.ccell.2020.12.002
– volume: 378
  start-page: eabm5874
  year: 2022
  ident: 595_CR1
  publication-title: Science
  doi: 10.1126/science.abm5874
– ident: 595_CR44
– volume: 2014
  start-page: 287430
  year: 2014
  ident: 595_CR46
  publication-title: Mol. Biol. Int.
  doi: 10.1155/2014/287430
– volume: 21
  start-page: 3940
  year: 2005
  ident: 595_CR47
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bti623
– volume: 353
  start-page: aaf7907
  year: 2016
  ident: 595_CR12
  publication-title: Science
  doi: 10.1126/science.aaf7907
– volume: 9
  year: 2019
  ident: 595_CR52
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-018-37301-3
– ident: 595_CR35
  doi: 10.1101/2023.01.24.525166
– ident: 595_CR34
  doi: 10.1038/s41587-023-01931-4
– volume: 28
  start-page: 593
  year: 2012
  ident: 595_CR39
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btr708
– ident: 595_CR51
  doi: 10.7554/eLife.76541
– volume: 91
  start-page: 263
  year: 2023
  ident: 595_CR49
  publication-title: J. Mol. Evol.
  doi: 10.1007/s00239-022-10083-z
– volume: 91
  start-page: 8969
  year: 1994
  ident: 595_CR50
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.91.19.8969
– ident: 595_CR62
  doi: 10.5281/zenodo.10492831
– volume: 30
  start-page: 706
  year: 2023
  ident: 595_CR33
  publication-title: Cell Stem Cell
  doi: 10.1016/j.stem.2023.04.001
– volume: 22
  start-page: 283
  year: 2022
  ident: 595_CR4
  publication-title: Nat. Rev. Immunol.
  doi: 10.1038/s41577-021-00590-3
– volume: 27
  start-page: 45
  year: 2021
  ident: 595_CR31
  publication-title: Nat. Med.
  doi: 10.1038/s41591-020-01182-9
– volume: 142
  start-page: 33
  year: 2023
  ident: 595_CR37
  publication-title: Blood
  doi: 10.1182/blood-2023-178732
– volume: 14
  year: 2023
  ident: 595_CR20
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-023-37167-8
– volume: 11
  start-page: eaav0936
  year: 2019
  ident: 595_CR8
  publication-title: Sci. Transl. Med.
  doi: 10.1126/scitranslmed.aav0936
– volume: 11
  start-page: e66922
  year: 2022
  ident: 595_CR30
  publication-title: eLife
  doi: 10.7554/eLife.66922
– volume: 7
  start-page: e36852
  year: 2012
  ident: 595_CR32
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0036852
– volume: 29
  start-page: 147
  year: 1950
  ident: 595_CR38
  publication-title: Bell Syst. Tech. J.
  doi: 10.1002/j.1538-7305.1950.tb00463.x
– volume: 17
  start-page: 151
  year: 2016
  ident: 595_CR21
  publication-title: BMC Bioinformatics
  doi: 10.1186/s12859-016-0999-4
– ident: 595_CR60
  doi: 10.5281/zenodo.10492761
– volume: 3
  start-page: 29
  year: 2011
  ident: 595_CR48
  publication-title: R J.
  doi: 10.32614/RJ-2011-015
– volume: 113
  start-page: 274
  year: 2016
  ident: 595_CR42
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1512977112
– volume: 54
  start-page: 459
  year: 2022
  ident: 595_CR17
  publication-title: Nat. Genet.
  doi: 10.1038/s41588-022-01047-6
– volume: 9
  start-page: 919345
  year: 2022
  ident: 595_CR23
  publication-title: Front. Med.
  doi: 10.3389/fmed.2022.919345
– volume: 564
  start-page: 219
  year: 2018
  ident: 595_CR36
  publication-title: Nature
  doi: 10.1038/s41586-018-0744-4
– volume: 548
  start-page: 456
  year: 2017
  ident: 595_CR19
  publication-title: Nature
  doi: 10.1038/nature23653
– volume: 34
  start-page: 739
  year: 2018
  ident: 595_CR27
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btx655
– volume: 104
  start-page: 417
  year: 2014
  ident: 595_CR10
  publication-title: Genomics
  doi: 10.1016/j.ygeno.2014.09.005
– volume: 601
  start-page: 404
  year: 2022
  ident: 595_CR29
  publication-title: Nature
  doi: 10.1038/s41586-021-04237-0
– volume: 36
  start-page: 469
  year: 2018
  ident: 595_CR16
  publication-title: Nat. Biotechnol.
  doi: 10.1038/nbt.4124
– volume: 68
  start-page: 15
  year: 2018
  ident: 595_CR22
  publication-title: Exp. Hematol.
  doi: 10.1016/j.exphem.2018.11.005
– volume: 20
  start-page: 677
  year: 2018
  ident: 595_CR54
  publication-title: Nat. Cell Biol.
  doi: 10.1038/s41556-018-0108-1
– volume: 496
  start-page: 229
  year: 2013
  ident: 595_CR5
  publication-title: Nature
  doi: 10.1038/nature12013
– ident: 595_CR58
  doi: 10.5281/zenodo.8124948
– ident: 595_CR59
  doi: 10.5281/zenodo.10027001
– volume: 33
  start-page: 920
  year: 2017
  ident: 595_CR40
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btw759
– volume: 590
  start-page: 4068
  year: 2016
  ident: 595_CR2
  publication-title: FEBS Lett.
  doi: 10.1002/1873-3468.12299
– volume: 9
  start-page: 561
  year: 2018
  ident: 595_CR41
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-018-02832-w
– volume: 17
  start-page: 796
  year: 2020
  ident: 595_CR43
  publication-title: Mol. Ther. Methods Clin. Dev.
  doi: 10.1016/j.omtm.2020.03.021
– volume: 25
  start-page: 3082
  year: 1997
  ident: 595_CR45
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/25.15.3082
– volume: 29
  start-page: 928
  year: 2011
  ident: 595_CR3
  publication-title: Nat. Biotechnol.
  doi: 10.1038/nbt.1977
SSID ssj0002513063
Score 2.260003
Snippet Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of...
Abstract Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the...
SourceID pubmedcentral
hal
proquest
pubmed
crossref
SourceType Open Access Repository
Aggregation Database
Index Database
StartPage 128
SubjectTerms Bar codes
Datasets
Decision trees
Deoxyribonucleic acid
DNA
DNA - genetics
DNA Barcoding, Taxonomic - methods
Experiments
Filtration
Gene sequencing
Life Sciences
Polymerase Chain Reaction
Quality control
Reproducibility of Results
Resource
Sequence Analysis, DNA - methods
Simulation
Title Extracting, filtering and simulating cellular barcodes using CellBarcode tools
URI https://www.ncbi.nlm.nih.gov/pubmed/38374363
https://www.proquest.com/docview/3226000104
https://www.proquest.com/docview/2928854705
https://hal.science/hal-04467733
https://pubmed.ncbi.nlm.nih.gov/PMC10899113
Volume 4
WOSCitedRecordID wos001165788900001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
journalDatabaseRights – providerCode: PRVPQU
  databaseName: Advanced Technologies & Aerospace Database
  customDbUrl:
  eissn: 2662-8457
  dateEnd: 20241214
  omitProxy: false
  ssIdentifier: ssj0002513063
  issn: 2662-8457
  databaseCode: P5Z
  dateStart: 20210101
  isFulltext: true
  titleUrlDefault: https://search.proquest.com/hightechjournals
  providerName: ProQuest
– providerCode: PRVPQU
  databaseName: Computer Science Database
  customDbUrl:
  eissn: 2662-8457
  dateEnd: 20241214
  omitProxy: false
  ssIdentifier: ssj0002513063
  issn: 2662-8457
  databaseCode: K7-
  dateStart: 20210101
  isFulltext: true
  titleUrlDefault: http://search.proquest.com/compscijour
  providerName: ProQuest
– providerCode: PRVPQU
  databaseName: ProQuest Central
  customDbUrl:
  eissn: 2662-8457
  dateEnd: 20241214
  omitProxy: false
  ssIdentifier: ssj0002513063
  issn: 2662-8457
  databaseCode: BENPR
  dateStart: 20210101
  isFulltext: true
  titleUrlDefault: https://www.proquest.com/central
  providerName: ProQuest
link http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpR3LbtQwcMS2HLgA5VFSysogDiCwmtjJ2jmhttqqh2q1QoBWXKwkttuVIGmbtOLzmXGyCwsSFy5xYkeJ5RnP2zMAr4schXZVpNx7KchapXjuy5THlMw8p_ztIVn1lzM1m-nFIp8PBrd2CKtc0cRAqG1TkY38ABFvEodsMh8urzhVjSLv6lBCYwTbiUAiTE5Zxdc2FuTdKBHL4axMLPVBi9IBogYyJk7HLjOuNvjR6IKiIf8WNf-MmPyNBZ08-N_JP4T7g_DJDnts2YE7rn4EO8P2btmbIQf128cwm_7owvmp-vw980tyqeMtK2rL2uX3UPILH8nqT2GsrMTt0lj8BIXRn7Nj7D_qu1jXNN_aJ_D5ZPrp-JQPpRd4hRJah1cdp6g7FR6X1Wpvnctcjq3IC9TFdZrbyipfpYVwVW49NXHiszJJkWBOMvkUtuqmds-AWeF1IUTpEA_S0iOBsImqZOwVaj-IQhG8WwHAXPYZNkzwjEttenAZBJcJ4DIqglcIo_WLlBz79PDMUB-5ppWS8jaJYH8FBjNsydb8gkEEL9fDuJlorYraNTetEbnQOktVnEWw20N8_StS5VM5kRHoDVzYmMvmSL28CAm7E_KtJonc-_e8nsM9ETCTgmX2Yau7vnEv4G512y3b6zGM1EKPYftoOpt_HAdEx-s8-_oTKzMFdw
linkProvider ProQuest
linkToHtml http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V1Lb9QwEB6VLRJcgPIogQIBgQSiURPbWTsHhNqy1VZdVhUqqDeTxHa7EiSlSQv8KX4jM3ksLEjceuASJ3aU-PF5PPa8AJ6mCTLtMhWBc5zRaZUMEpeJICRn5gn5b2-cVX-YyOlUHR4m-0vwo7eFIbXKniY2hNqUOZ2RbyDwhmHjTeb1yZeAokaRdLUPodHCYs9-_4pbturV7hsc32eM7YwOtsdBF1UgyJH5qPGqQoHbgtQxFhnljLWxTTBlSYrbTCUSkxvpcpEymyfGURJGLs4igbRgSFEikOQvCy6G8QCWt0bT_XfzUx3kFpAH5511TsjVRoX8CIIRl8KADD3jQC6sgJeOSf_yb-b2Tx3N3xa9nev_W3fdgGsde-1vtvNhBZZscRNWOgJW-c87L9svbsF09K1uLMSKo3XfzUhpAG_9tDB-NfvcBDXDR5JrkKKun2FTSoOfIEOBI38b87faLL8uy0_VbXh_Ie26A4OiLOxd8A1zKmUss4h0kTkkgSaSOQ-dxP0dThIPXvYDrk9aHyK6kf1zpVt4aISHbuChpQdPEBPzF8n993hzoimPhO9Scn4eebDWD7vuiE6lf425B4_nxUguqK_SwpZnlWYJUyoWMow9WG0RNv8VHVYIPuQeqAXsLdRlsaSYHTcuySOSHkcRv_fvej2CK-ODtxM92Z3u3YerrJkVpBq0BoP69Mw-gMv5eT2rTh92E8uHjxcNzp-ZXWTL
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Extracting%2C+filtering+and+simulating+cellular+barcodes+using+CellBarcode+tools&rft.jtitle=Nature+Computational+Science&rft.au=Sun%2C+Wenjie&rft.au=Perkins%2C+Meghan&rft.au=Huyghe%2C+Mathilde&rft.au=Faraldo%2C+Marisa+M&rft.date=2024-02-01&rft.pub=Nature+Publishing+Group&rft.eissn=2662-8457&rft.volume=4&rft.issue=2&rft.spage=128&rft.epage=143&rft_id=info:doi/10.1038%2Fs43588-024-00595-7
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2662-8457&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2662-8457&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2662-8457&client=summon