BIC Codes: Bit Insertion-based Constrained Codes with Error Correction for DNA Storage

In this paper, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained code called bit insertion-based constrained (BIC) code. BIC codes convert a binary data sequence to multiple oligo sequences satisfying the maxi...

Celý popis

Uloženo v:

Podrobná bibliografie
Vydáno v:	IEEE transactions on emerging topics in computing Ročník 11; číslo 3; s. 1 - 15
Hlavní autoři:	Park, Seong-Joon, Park, Hosung, Kwak, Hee-Youl, No, Jong-Seon
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	New York IEEE 01.07.2023 The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Témata:	Algorithms Binary data Bit insertion technique Codes constrained coding Constraints Decoding DNA DNA storage Encoding Error analysis Error correcting codes Error correction Error correction codes GC-content Insertion low-density parity-check (LDPC) code maxmimum homopolymer run Parity check codes rate-compatible code
ISSN:	2168-6750, 2168-6750
On-line přístup:	Získat plný text
Tagy:	Přidat tag Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!

Abstract	In this paper, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained code called bit insertion-based constrained (BIC) code. BIC codes convert a binary data sequence to multiple oligo sequences satisfying the maximum homopolymer run (i.e., run-length (RL)) constraint by inserting dummy bits. We show that the BIC codes nearly achieves the capacity in terms of information density while the simple structure of the BIC codes allows linear-time encoding and fast parallel decoding. Also, by combining a balancing technique with the BIC codes, we obtain the constrained coding algorithm to satisfy the GC-content constraint as well as the RL constraint. Next, for DNA storage channel with errors, we integrate the proposed constrained coding algorithm with a rate-compatible low-density parity-check (LDPC) code to correct errors and erasures. Specifically, we incorporate LDPC codes adopted in the 5G new radio standard because they have powerful error-correction capability and appealing features for the integration. Simulation results show that the proposed integrated coding algorithm outperforms existing coding algorithms in terms of information density and error correctability.
AbstractList	In this paper, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained code called bit insertion-based constrained (BIC) code. BIC codes convert a binary data sequence to multiple oligo sequences satisfying the maximum homopolymer run (i.e., run-length (RL)) constraint by inserting dummy bits. We show that the BIC codes nearly achieves the capacity in terms of information density while the simple structure of the BIC codes allows linear-time encoding and fast parallel decoding. Also, by combining a balancing technique with the BIC codes, we obtain the constrained coding algorithm to satisfy the GC-content constraint as well as the RL constraint. Next, for DNA storage channel with errors, we integrate the proposed constrained coding algorithm with a rate-compatible low-density parity-check (LDPC) code to correct errors and erasures. Specifically, we incorporate LDPC codes adopted in the 5G new radio standard because they have powerful error-correction capability and appealing features for the integration. Simulation results show that the proposed integrated coding algorithm outperforms existing coding algorithms in terms of information density and error correctability. In this article, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained code called bit insertion-based constrained (BIC) code. BIC codes convert a binary data sequence to multiple oligo sequences satisfying the maximum homopolymer run (i.e., run-length (RL)) constraint by inserting dummy bits. We show that the BIC codes nearly achieves the capacity in terms of information density while the simple structure of the BIC codes allows linear-time encoding and fast parallel decoding. Also, by combining a balancing technique with the BIC codes, we obtain the constrained coding algorithm to satisfy the GC-content constraint as well as the RL constraint. Next, for DNA storage channel with errors, we integrate the proposed constrained coding algorithm with a rate-compatible low-density parity-check (LDPC) code to correct errors and erasures. Specifically, we incorporate LDPC codes adopted in the 5 G new radio standard because they have powerful error-correction capability and appealing features for the integration. Simulation results show that the proposed integrated coding algorithm outperforms existing coding algorithms in terms of information density and error correctability.
Author	Kwak, Hee-Youl Park, Hosung Park, Seong-Joon No, Jong-Seon
Author_xml	– sequence: 1 givenname: Seong-Joon orcidid: 0000-0002-4524-0302 surname: Park fullname: Park, Seong-Joon organization: Department of Electrical and Computer Engineering, INMC, Seoul National University, Seoul, Korea – sequence: 2 givenname: Hosung orcidid: 0000-0001-7854-7792 surname: Park fullname: Park, Hosung organization: Department of Computer Engineering, Chonnam National University, Gwangju, South Korea – sequence: 3 givenname: Hee-Youl orcidid: 0000-0002-4381-1968 surname: Kwak fullname: Kwak, Hee-Youl organization: Department of Electrical and Computer Engineering, INMC, Seoul National University, Seoul, Korea – sequence: 4 givenname: Jong-Seon orcidid: 0000-0002-3946-0958 surname: No fullname: No, Jong-Seon organization: Department of Electrical and Computer Engineering, INMC, Seoul National University, Seoul, Korea
BookMark	eNp9kE1PAyEQhompibX2B5h42MTzVmD5Wm_tWrVJowerV8ICq9vUpQKN8d_LWg-NB7nMMDzvMPOegkHnOgvAOYIThGB5tZqvqgmGuJgUmAnMyREYYsREzjiFg4P8BIxDWMN0BGIl40PwMltUWeWMDdfZrI3ZogvWx9Z1ea2CNempC9GrtvvJE5Z9tvEtm3vvfCp4b3VPZ0263jxMs6fovHq1Z-C4UZtgx79xBJ5v05D3-fLxblFNl7nGJYm5MRoiURSEUo4YJ8xQhhjlNdZaN7Ss6wYKKKiyWlGrjWGMYGUY1Q0hRWGKEbjc991697GzIcq12_kufSmxYIjQkgqYKL6ntHcheNtI3UbVz92vtpEIyt5H2fsoex_lr49Jif4ot759V_7rX83FXtNaaw94BDlPy34Dodh-qQ
CODEN	ITETBT
CitedBy_id	crossref_primary_10_1093_bib_bbae463 crossref_primary_10_1109_LCOMM_2024_3481265 crossref_primary_10_1016_j_csbj_2023_09_004 crossref_primary_10_1007_s13222_023_00460_3 crossref_primary_10_1109_TMBMC_2024_3403488 crossref_primary_10_1038_s41598_025_05717_3
Cites_doi	10.1038/s41598-017-05188-1 10.1109/LCOMM.2019.2912572 10.1109/ACCESS.2020.3021700 10.1109/TIT.1986.1057136 10.1109/LCOMM.2017.2775608 10.23919/JCN.2022.000008 10.1109/LCOMM.2018.2866566 10.1002/adma.202001249 10.1109/ACCESS.2021.3116245 10.1038/nbt.4079 10.1109/TIT.2021.3066430 10.1109/ISIT.2019.8849814 10.1038/nature11875 10.1186/s12859-016-0976-y 10.1093/bib/bbac484 10.1109/LCOMM.2019.2930970 10.1109/ALLERTON.2019.8919890 10.1038/nmeth.2137 10.1109/TETC.2019.2932685 10.3389/fbioe.2014.00049 10.1126/science.aaj2038 10.1109/MCOM.2018.1700839 10.1017/CBO9780511791338 10.1073/pnas.2004821117 10.1093/bioinformatics/btab246 10.1038/s41540-022-00233-w 10.1186/gb-2013-14-5-r51 10.1126/science.1226355 10.1021/acs.nanolett.0c00755 10.1038/s41598-019-45832-6 10.1109/ACCESS.2020.2980036 10.1186/s13036-019-0211-2
ContentType	Journal Article
Copyright	Copyright The Institute of Electrical and Electronics Engineers, Inc. (IEEE) 2023
Copyright_xml	– notice: Copyright The Institute of Electrical and Electronics Engineers, Inc. (IEEE) 2023
DBID	97E RIA RIE AAYXX CITATION 7SC 8FD JQ2 L7M L~C L~D
DOI	10.1109/TETC.2023.3268274
DatabaseName	IEEE All-Society Periodicals Package (ASPP) 2005–Present IEEE All-Society Periodicals Package (ASPP) 1998–Present IEEE Electronic Library (IEL) CrossRef Computer and Information Systems Abstracts Technology Research Database ProQuest Computer Science Collection Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional
DatabaseTitle	CrossRef Computer and Information Systems Abstracts Technology Research Database Computer and Information Systems Abstracts – Academic Advanced Technologies Database with Aerospace ProQuest Computer Science Collection Computer and Information Systems Abstracts Professional
DatabaseTitleList	Computer and Information Systems Abstracts
Database_xml	– sequence: 1 dbid: RIE name: IEEE Electronic Library (IEL) url: https://ieeexplore.ieee.org/ sourceTypes: Publisher
DeliveryMethod	fulltext_linktorsrc
Discipline	Engineering
EISSN	2168-6750
EndPage	15
ExternalDocumentID	10_1109_TETC_2023_3268274 10107718
Genre	orig-research
GroupedDBID	0R~ 6IK 97E AAJGR AARMG AASAJ AAWTH ABAZT ABJNI ABQJQ ABVLG ACGFS AGQYO AHBIQ AKJIK AKQYR ALMA_UNASSIGNED_HOLDINGS ATWAV BEFXN BFFAM BGNUA BKEBE BPEOZ EBS EJD IEDLZ IFIPE IPLJI JAVBF KQ8 M43 O9- OCL RIA RIE AAYXX CITATION 7SC 8FD JQ2 L7M L~C L~D
ID	FETCH-LOGICAL-c294t-ddc01833455716746d561657b2cccf59bbf08085aeca5ecdd6642ad65cf4433d3
IEDL.DBID	RIE
ISICitedReferencesCount	5
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=001063339400015&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	2168-6750
IngestDate	Mon Jun 30 04:20:06 EDT 2025 Tue Nov 18 21:32:25 EST 2025 Sat Nov 29 04:00:27 EST 2025 Wed Aug 27 02:14:16 EDT 2025
IsPeerReviewed	true
IsScholarly	true
Issue	3
Language	English
License	https://ieeexplore.ieee.org/Xplorehelp/downloads/license-information/IEEE.html https://doi.org/10.15223/policy-029 https://doi.org/10.15223/policy-037
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c294t-ddc01833455716746d561657b2cccf59bbf08085aeca5ecdd6642ad65cf4433d3
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14
ORCID	0000-0002-4524-0302 0000-0001-7854-7792 0000-0002-4381-1968 0000-0002-3946-0958
PQID	2861459580
PQPubID	4437215
PageCount	15
ParticipantIDs	proquest_journals_2861459580 ieee_primary_10107718 crossref_primary_10_1109_TETC_2023_3268274 crossref_citationtrail_10_1109_TETC_2023_3268274
PublicationCentury	2000
PublicationDate	2023-07-01
PublicationDateYYYYMMDD	2023-07-01
PublicationDate_xml	– month: 07 year: 2023 text: 2023-07-01 day: 01
PublicationDecade	2020
PublicationPlace	New York
PublicationPlace_xml	– name: New York
PublicationTitle	IEEE transactions on emerging topics in computing
PublicationTitleAbbrev	TETC
PublicationYear	2023
Publisher	IEEE The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher_xml	– name: IEEE – name: The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
References	ref15 ref14 ref31 ref30 ref11 ref33 ref10 ref32 ref2 ref1 ref17 ref16 ref19 ref18 immink (ref12) 2004 goldman (ref13) 2013; 494 ref24 ref23 ref26 ref25 ref20 ref22 ref21 (ref34) 0 ref28 ref27 ref29 ref8 ref7 ref9 ref4 ref3 ref6 ref5
References_xml	– ident: ref29 doi: 10.1038/s41598-017-05188-1 – year: 2004 ident: ref12 publication-title: Codes for Mass Data Storage Systems – ident: ref17 doi: 10.1109/LCOMM.2019.2912572 – ident: ref10 doi: 10.1109/ACCESS.2020.3021700 – ident: ref30 doi: 10.1109/TIT.1986.1057136 – ident: ref15 doi: 10.1109/LCOMM.2017.2775608 – year: 0 ident: ref34 – ident: ref19 doi: 10.23919/JCN.2022.000008 – ident: ref26 doi: 10.1109/LCOMM.2018.2866566 – ident: ref4 doi: 10.1002/adma.202001249 – ident: ref21 doi: 10.1109/ACCESS.2021.3116245 – ident: ref33 doi: 10.1038/nbt.4079 – ident: ref20 doi: 10.1109/TIT.2021.3066430 – ident: ref8 doi: 10.1109/ISIT.2019.8849814 – volume: 494 start-page: 77 year: 2013 ident: ref13 article-title: Towards practical, high-capacity, low-maintenance information storage in synthesized DNA publication-title: Nature doi: 10.1038/nature11875 – ident: ref32 doi: 10.1186/s12859-016-0976-y – ident: ref23 doi: 10.1093/bib/bbac484 – ident: ref14 doi: 10.1109/LCOMM.2019.2930970 – ident: ref9 doi: 10.1109/ALLERTON.2019.8919890 – ident: ref27 doi: 10.1038/nmeth.2137 – ident: ref3 doi: 10.1109/TETC.2019.2932685 – ident: ref11 doi: 10.3389/fbioe.2014.00049 – ident: ref2 doi: 10.1126/science.aaj2038 – ident: ref24 doi: 10.1109/MCOM.2018.1700839 – ident: ref25 doi: 10.1017/CBO9780511791338 – ident: ref22 doi: 10.1073/pnas.2004821117 – ident: ref7 doi: 10.1093/bioinformatics/btab246 – ident: ref6 doi: 10.1038/s41540-022-00233-w – ident: ref28 doi: 10.1186/gb-2013-14-5-r51 – ident: ref1 doi: 10.1126/science.1226355 – ident: ref5 doi: 10.1021/acs.nanolett.0c00755 – ident: ref31 doi: 10.1038/s41598-019-45832-6 – ident: ref16 doi: 10.1109/ACCESS.2020.2980036 – ident: ref18 doi: 10.1186/s13036-019-0211-2
SSID	ssj0000816967
Score	2.302632
Snippet	In this paper, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained... In this article, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained...
SourceID	proquest crossref ieee
SourceType	Aggregation Database Enrichment Source Index Database Publisher
StartPage	1
SubjectTerms	Algorithms Binary data Bit insertion technique Codes constrained coding Constraints Decoding DNA DNA storage Encoding Error analysis Error correcting codes Error correction Error correction codes GC-content Insertion low-density parity-check (LDPC) code maxmimum homopolymer run Parity check codes rate-compatible code
Title	BIC Codes: Bit Insertion-based Constrained Codes with Error Correction for DNA Storage
URI	https://ieeexplore.ieee.org/document/10107718 https://www.proquest.com/docview/2861459580
Volume	11
WOSCitedRecordID	wos001063339400015&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: PRVIEE databaseName: IEEE Electronic Library (IEL) customDbUrl: eissn: 2168-6750 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000816967 issn: 2168-6750 databaseCode: RIE dateStart: 20130101 isFulltext: true titleUrlDefault: https://ieeexplore.ieee.org/ providerName: IEEE
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3dS8MwEA9u-KAPfk6cTsmDT0Jn1-aj8W2bG-5lCE7ZW2lzKQyklW7z7_eSdjIRBd9CSUpz17v8Lsndj5Ab0RNJasLAU5qlHkuk8SLhMy8K0ojzhGcCKrIJOZ1G87l6qpPVXS6MMcZdPjNd23Rn-VDotd0qQwvHYAWdaYM0pBRVstbXhoplkFBC1ieXPV_dzUazYdfSg3cRo0SBZN_WHkem8sMDu2VlfPjPDzoiBzV-pP1K4cdkx-QnZH-rquApeR1MhnRYgFne08FiRSe5PXFH-Xt2yQJqOTodM4RrYzdqN2PpqCyLEh-UzgcWOUU4Sx-mffqMYTl6nRZ5GeNUH72aPsHTgWIrD0D7aLAh41zaXAMBiJUEl2mgtc64StMM4WLEE6MTbjSAwFgkAcF1xlgYQnhGmnmRm3NCQYIJecalnwHr-aBCEAoA0Z5RKuCmTfyNYGNd1xa3E3mLXYzhq9jqIra6iGtdtMnt15D3qrDGX51bVvhbHSu5t0lno764tr1lHEQIObjikX_xy7BLsmffXt267ZDmqlybK7KrP1aLZXntfqtP-1jJ_g
linkProvider	IEEE
linkToHtml	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3NS-wwEB_8AvWgT11x_czB04Ou2TZJG2-6Ki76FuGt4q20mRQEaaW7-vc7SasoouAtlIQ2mc7MbzKZ_AAOVV9luY3CQBuRByKLbZAoLoIkzBMpM1kobMgm4tEoub_XN22xuq-Fsdb6w2e255o-l4-VeXZbZaThFKyQMZ2FeSlEyJtyrfctFcchoVXc5i77XB-Nz8eDniMI7xFKScJYfPI-nk7liw32juVi9Zef9AdWWgTJThqRr8GMLddh-cO9ghtwdzocsEGFdnLMTh-mbFi6nDtJIHBOC5lj6fTcEL5N3ZjbjmXndV3V9KD2VrAqGQFadjY6Yf8pMCe704HbC5rqZdASKAQm1GIaIBpOKhsJKWNXbaCQ0JKScR4aYwqp87wgwJjIzJpMWoOoKBrJUElTCBFFGG3CXFmVdgsYxmgjWciYFyj6HHWESiMS3rNah9J2gb8tbGra28XdRB5TH2VwnTpZpE4WaSuLLvx9H_LUXK3xU-eOW_wPHZt178Lum_jSVvsmaZgQ6JBaJnz7m2EHsHg5_nedXg9HVzuw5N7UnMHdhblp_Wz3YMG8TB8m9b7_xV4Bp6LNRQ
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=BIC+Codes%3A+Bit+Insertion-based+Constrained+Codes+with+Error+Correction+for+DNA+Storage&rft.jtitle=IEEE+transactions+on+emerging+topics+in+computing&rft.au=Park%2C+Seong-Joon&rft.au=Park%2C+Hosung&rft.au=Kwak%2C+Hee-Youl&rft.au=No%2C+Jong-Seon&rft.date=2023-07-01&rft.pub=IEEE&rft.eissn=2168-6750&rft.spage=1&rft.epage=15&rft_id=info:doi/10.1109%2FTETC.2023.3268274&rft.externalDocID=10107718
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2168-6750&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2168-6750&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2168-6750&client=summon