Multiplexed Sequence Encoding: A Framework for DNA Communication
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{"title"=>"Multiplexed sequence encoding: A framework for DNA communication", "type"=>"journal", "authors"=>[{"first_name"=>"Bijan", "last_name"=>"Zakeri", "scopus_author_id"=>"55361046200"}, {"first_name"=>"Peter A.", "last_name"=>"Carr", "scopus_author_id"=>"35321781000"}, {"first_name"=>"Timothy K.", "last_name"=>"Lu", "scopus_author_id"=>"7402684461"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84962834131", "sgr"=>"84962834131", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0152774", "pmid"=>"27050646", "pui"=>"609632655"}, "id"=>"868444e4-a0a6-3243-b9a9-01d07194e986", "abstract"=>"Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication-data encoding, data transfer & data extraction-and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system-Multiplexed Sequence Encoding (MuSE)-that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA.", "link"=>"http://www.mendeley.com/research/multiplexed-sequence-encoding-framework-dna-communication", "reader_count"=>31, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>4, "Researcher"=>2, "Student > Ph. D. Student"=>10, "Student > Master"=>5, "Student > Bachelor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>4, "Researcher"=>2, "Student > Ph. D. Student"=>10, "Student > Master"=>5, "Student > Bachelor"=>7}, "reader_count_by_subject_area"=>{"Engineering"=>7, "Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>4, "Chemical Engineering"=>3, "Social Sciences"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>1, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>7}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>3}}, "reader_count_by_country"=>{"France"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4924993"], "description"=>"<p>Identified sequences from NGS analysis.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162307, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identified_sequences_from_NGS_analysis_/3162307", "title"=>"Identified sequences from NGS analysis.", "pos_in_sequence"=>20, "defined_type"=>3, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924582"], "description"=>"<p>By varying the ratios of DNA-1 (orange) and DNA-2 (purple), the degree of chromatogram patterning can be tuned (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g007\" target=\"_blank\">Fig 7</a>). When one partner is present at a lower concentration, chromatogram patterning is still achieved; however, the resulting chromatogram aligns perfectly with the more concentrated partner. Therefore, messages may be discreetly encoded between two DNA strands and revealed in chromatograms, but not identified by sequence alignments. Left: alignment of chromatograms from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g007\" target=\"_blank\">Fig 7</a> with DNA-1. Right: alignment of chromatograms from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g007\" target=\"_blank\">Fig 7</a> with DNA-2. Red lines surround embedded messages.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161926, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g009", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Discreetly_embedded_messages_cannot_be_identified_by_sequence_alignments_/3161926", "title"=>"Discreetly embedded messages cannot be identified by sequence alignments.", "pos_in_sequence"=>9, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924918"], "description"=>"<p>The frequency of letters used in English based on the Concise Oxford Dictionary and adapted from [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.ref017\" target=\"_blank\">17</a>].</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162247, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_frequency_of_letters_used_in_English_based_on_the_Concise_Oxford_Dictionary_and_adapted_from_17_/3162247", "title"=>"The frequency of letters used in English based on the Concise Oxford Dictionary and adapted from [17].", "pos_in_sequence"=>18, "defined_type"=>3, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924792"], "description"=>"<p>WWII communication readouts of tuned and co-sequenced DNA strands.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162130, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g014", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/WWII_communication_readouts_of_tuned_and_co_sequenced_DNA_strands_/3162130", "title"=>"WWII communication readouts of tuned and co-sequenced DNA strands.", "pos_in_sequence"=>14, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924867"], "description"=>"<p>(a) Plasmids containing n1, n2, n3, n4, n5, and n6 sequences (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g010\" target=\"_blank\">Fig 10</a>) were grown and purified in dH<sub>2</sub>O, mixed at equal concentrations of 30 ng/μL, and submitted to an outside party (MIT BioMicro Center) for NGS sequencing and assembly under blind experimental conditions. (b) 300 ng of plasmids containing n1, n2, n3, n4, n5, and n6 sequences were run on a 1% agarose gel to demonstrate purity. (c) The outside party (MIT BioMicro Center) was provided with the number of plasmids, vector sequences, and the size of messages inserted into the vectors and asked to assemble the messages encoded in the plasmids. They assembled 6 sequences (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.t004\" target=\"_blank\">Table 4</a>) that represent the messages n1, n2, n3, n4, n5, and n6. Here the alignment of the 6 assembled sequences with n1, n2, n3, n4, n5, and n6 templates are shown. Shown below is a legend for the color-coding of the templates. Boxes highlight assembled sequences with near perfect alignment to corresponding templates.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162196, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g016", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Next_generation_sequencing_of_the_WWII_communication_/3162196", "title"=>"Next-generation sequencing of the WWII communication.", "pos_in_sequence"=>16, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924348"], "description"=>"<p>(a) Schematic for chromatogram patterning. When two DNA strands are co-sequenced with a common primer via Sanger sequencing, different overlapping nucleotides produce small heterogeneous peaks while matching nucleotides produce large homogeneous peaks. Peaks are kept in alignment via iKey-64. (b) Schematic of chromatogram patterning for the message ‘Massachusetts Institute Technology’ via MuSE. (c) Sequences for ‘Massachusetts Institute Technology’ used in (b) and encoded with iKey-64. (d) Chromatograms observed from Sanger sequencing of the DNA-encoded message described in (b) and (c). When DNA-1 and DNA-2 are co-sequenced at equal concentrations with a common primer (green arrows), chromatogram patterning is achieved during reverse (Primer<sub>ExternalRv</sub>) but not forward (Primer<sub>ExternalFw</sub>) sequencing due to the flanking variable DNA regions. Red lines surround embedded messages.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161749, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Chromatogram_patterning_with_MuSE_/3161749", "title"=>"Chromatogram patterning with MuSE.", "pos_in_sequence"=>4, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924456"], "description"=>"<p>(a) Close-up of the chromatogram for forward co-sequencing of DNA-1+2 encoding the MIT message (red box) from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g004\" target=\"_blank\">Fig 4d</a>. (b) Sequence of the upstream variable DNA regions (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g004\" target=\"_blank\">Fig 4b</a>), corresponding to the upstream flanking region of the MIT message. (c) Close-up of the chromatogram for reverse co-sequencing of DNA-1+2 encoding the MIT message (red box) from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g004\" target=\"_blank\">Fig 4d</a>. (d) Sequence of the downstream variable DNA regions (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g004\" target=\"_blank\">Fig 4b</a>), corresponding to the downstream flanking region of the MIT message. Samples were co-sequenced at equal concentrations and the green arrows depict the sequencing primers (Primer<sub>ExternalFw</sub> and Primer<sub>ExternalRv</sub>).</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161818, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Chromatogram_patterning_requires_the_alignment_of_base_calls_to_be_maintained_during_co_sequencing_of_DNA_strands_/3161818", "title"=>"Chromatogram patterning requires the alignment of base calls to be maintained during co-sequencing of DNA strands.", "pos_in_sequence"=>6, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924486"], "description"=>"<p>Chromatogram patterning can be tuned to discreetly embed information in sequencing data by varying the ratios of DNA-1 (orange) and DNA-2 (purple). Red lines surround embedded messages.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161839, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/MuSE_can_be_tuned_to_hide_information_in_DNA_communications_/3161839", "title"=>"MuSE can be tuned to hide information in DNA communications.", "pos_in_sequence"=>7, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924243"], "description"=>"<p>(a) For Alice to send a message (<i>m</i>) to Bob, she must first write the data into DNA and then physically send the DNA to Bob, who can read the DNA and extract the data. Eve, who is eavesdropping, can physically intercept and read <i>m</i>. Here we have identified three areas to explore within the communication channel between Alice and Bob: data encoding, data transfer, and data extraction. (b) Fragmented DNA communication. Data encoding: <i>m</i> can be mixed with decoy (<i>d</i>) data and fragmented, then written into DNA, where the key (<i>k</i>) is used to encode the data and can itself be written in DNA. Data transfer: DNA encoded <i>k</i> and fragmented <i>m</i>+<i>d</i> components can be transmitted between Alice and Bob using multiple different channels based on a secret-sharing system. Data extraction: chromatogram patterning can be used by Bob to extract data via multiplexed sequencing reactions.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161692, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/DNA_communication_/3161692", "title"=>"DNA communication.", "pos_in_sequence"=>1, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924666"], "description"=>"<p>(a) Workflow for extracting the desired message from the WWII communication. Workflow steps 1, 2, and 3 are highlighted in pink and can be viewed in detail in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g010\" target=\"_blank\">Fig 10</a>. Data containing strands are pooled and sequenced with Primer<sub>Key</sub> to reveal the combination key. Decoding and solving the combination key will reveal the correct strand pairs to analyze with Primer<sub>Message</sub> to reveal the desired message. Analysis of incorrect strand pairs will reveal a decoy message. (b) Chromatograms of an n1 x n6 matrix of DNA strands from the WWII communication (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g010\" target=\"_blank\">Fig 10</a>) tuned and co-sequenced with Primer<sub>Message</sub>. Boxes highlight patterns that communicate either the desired message (green) or the decoy message (red).</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162010, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g011", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_WWII_communication_recreated_in_DNA_/3162010", "title"=>"A WWII communication recreated in DNA.", "pos_in_sequence"=>11, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924537"], "description"=>"<p>A close-up of chromatogram patterns formed with MuSE tuning from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152774#pone.0152774.g007\" target=\"_blank\">Fig 7</a>. Message encoding regions (red box) contain single peaks while variable DNA regions (white box) contain two overlapping peaks whose heights can be adjusted by varying the ratios of DNA-1:DNA-2. The chromatogram close-ups correspond to the boxed region in the MIT message schematic shown above.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161887, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Discreet_embedding_of_information_in_chromatograms_/3161887", "title"=>"Discreet embedding of information in chromatograms.", "pos_in_sequence"=>8, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924954"], "description"=>"<p>Next-generation sequencing statistics of assembled reads under blind experimental conditions.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162274, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Next_generation_sequencing_statistics_of_assembled_reads_under_blind_experimental_conditions_/3162274", "title"=>"Next-generation sequencing statistics of assembled reads under blind experimental conditions.", "pos_in_sequence"=>19, "defined_type"=>3, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924750"], "description"=>"<p>Data extraction from the WWII communication using Primer<sub>ExternalFw</sub> and Primer<sub>ExternalRv</sub> produces poor quality sequencing reads (message encoding regions are between the red lines).</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162091, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g013", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Data_extraction_from_the_WWII_communication_using_Primer_sub_ExternalFw_sub_and_Primer_sub_ExternalRv_sub_produces_poor_quality_sequencing_reads_message_encoding_regions_are_between_the_red_lines_/3162091", "title"=>"Data extraction from the WWII communication using Primer<sub>ExternalFw</sub> and Primer<sub>ExternalRv</sub> produces poor quality sequencing reads (message encoding regions are between the red lines).", "pos_in_sequence"=>13, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924897"], "description"=>"<p>Sequences of the constructs used in this study.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162223, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Sequences_of_the_constructs_used_in_this_study_/3162223", "title"=>"Sequences of the constructs used in this study.", "pos_in_sequence"=>17, "defined_type"=>3, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924825"], "description"=>"<p>Details of the encoded information, strand combinations tuned and co-sequenced, DNA sequence of embedded messages, and close-ups of the chromatogram patterns produced are shown for the WWII communication including: (a) the combination key, (b), (c), (d), the desired message, and (e), (f), (g), the decoy message. Space1 was used for all odd numbered strands (n1, n3, n5) and space2 was used for all even numbered strands (n2, n4, n6) to demarcate words. Space1/2 codons are shown in red.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162160, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g015", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Examination_of_the_peaks_produced_during_co_sequencing_of_the_WWII_communication_/3162160", "title"=>"Examination of the peaks produced during co-sequencing of the WWII communication.", "pos_in_sequence"=>15, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924288"], "description"=>"<p>(a) iKey-64, used to convert plaintext to codons for writing information in DNA molecules. Messages begin with ‘start’, finish with ‘end’, ‘forward’ and ‘reverse’ provide information on the strand containing the desired message, and ‘space1’ and ‘space2’ may be used to produce troughs in chromatograms. The ‘shift’ codon precedes capitalized letters or upper characters. Codons can be randomized to produce up to 24!12!28! = 9.1x10<sup>61</sup> iKey-64 variants. (b) The iKey-64 variant from (a) written in synthetic DNA and read by Sanger sequencing. Shown is the first row and part of the second row of the iKey keyboard (flanked by 10 T nucleotides). (c) Top: iKey-64 buttons and codons were numbered to write the keyboard onto a strand of DNA. Bottom: iKey-64 written in DNA. Codons were flanked by 10 Ts to separate the start and end of the keyboard from surrounding DNA for identification, marked by red lines.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161713, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/64_button_iKey_for_chromatogram_patterning_/3161713", "title"=>"64 button iKey for chromatogram patterning.", "pos_in_sequence"=>2, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924630"], "description"=>"<p>1. Secret-Sharing System: a recreated WWII communication was encoded across six DNA molecules and included watermarks, a combination key, a desired message, and a decoy message. 2. Encoding Key: iKey-64 was used to encode the information included in the WWII communication. 3. Combination Key: identifies which strands contain the desired message, here if strands are sequenced according to the Combination Key—obtained from Pascal’s triangle—with the appropriate primers, then the desired message is revealed.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161971, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g010", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_fragmented_WWII_communication_/3161971", "title"=>"A fragmented WWII communication.", "pos_in_sequence"=>10, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924390"], "description"=>"<p>(a) Red (DNA-1), blue (n1), and orange (iKey-64) strands have different sequences but they all share a common upstream region and sequencing primer (Primer<sub>ExternalFw</sub>). Individual sequencing of each strand produces high quality reads, but the resulting reads are of poor quality when two (red and blue) or three (red, blue, and orange) strands are co-sequenced. (b) Close-up of the chromatogram of red and blue co-sequencing. (c) Close-up of the chromatogram of red, blue, and orange co-sequencing.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161782, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Na_ve_co_sequencing_of_multiple_DNA_strands_/3161782", "title"=>"Naïve co-sequencing of multiple DNA strands.", "pos_in_sequence"=>5, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924318"], "description"=>"<p>The buttons of iKey-64 were separated into 3 categories based on the frequency of use as judged by qualitative measures. Category 1 is for the most frequently used buttons and is encoded by codons that contain three different nucleotides. Category 2 is for less frequently used buttons and is encoded by codons that contain the same nucleotide in the first and third position. Category 3 is for the least frequently used buttons and is encoded by codons that contain two or more homopolymers.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3161725, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Rational_design_of_iKey_64_for_encoding_information_into_DNA_while_reducing_the_incidence_of_homopolymers_and_achieving_chromatogram_patterning_/3161725", "title"=>"Rational design of iKey-64 for encoding information into DNA, while reducing the incidence of homopolymers and achieving chromatogram patterning.", "pos_in_sequence"=>3, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/4924705"], "description"=>"<p>The 525 bp information-encoding regions of the WWII communication were flipped between the forward and reverse strands to provide a camouflage effect against sequencing with random primers (Primer<sub>ExternalFw</sub> and Primer<sub>ExternalRv</sub>). While the external DNA regions surrounding the information containing regions were identical, strands n1/n3/n5 were placed in the forward direction and strands n2/n4/n6 in the reverse direction, with watermarks used to determine the orientation.</p>", "links"=>[], "tags"=>["communication", "DNA molecules", "Multiplexed Sequence Encoding", "address data transfer", "address data extraction", "address data encoding"], "article_id"=>3162046, "categories"=>["Space Science", "Genetics", "Molecular Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified", "Plant Biology"], "users"=>["Bijan Zakeri", "Peter A. Carr", "Timothy K. Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0152774.g012", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/DNA_camouflage_/3162046", "title"=>"DNA camouflage.", "pos_in_sequence"=>12, "defined_type"=>1, "published_date"=>"2016-04-06 04:52:38"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"9", "full-text"=>"11", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"16", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}

Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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