The Experts below are selected from a list of 291 Experts worldwide ranked by ideXlab platform
Jean-françois Lutz - One of the best experts on this subject based on the ideXlab platform.
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Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation
Nature Communications, 2017Co-Authors: Abdelaziz Al Ouahabi, Jean-arthur Amalian, Laurence Charles, Jean-françois LutzAbstract:In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found.Digital information can be stored in monomer sequences of non-natural macromolecules, but only short chains can be read. Here the authors show long multi-byte digital polymers sequenced in a moderate resolution mass spectrometer. Full sequence coverage can be attained without pre-analysis digestion or the help from sequence databases.
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Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation
Nature Communications, 2017Co-Authors: Abdelaziz Al Ouahabi, Jean-arthur Amalian, Laurence Charles, Jean-françois LutzAbstract:In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found.Digital information can be stored in monomer sequences of non-natural macromolecules, but only short chains can be read. Here the authors show long multi-byte digital polymers sequenced in a moderate resolution mass spectrometer. Full sequence coverage can be attained without pre-analysis digestion or the help from sequence databases.
Sreeram Kannan - One of the best experts on this subject based on the ideXlab platform.
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models and information theoretic bounds for nanopore sequencing
IEEE Transactions on Information Theory, 2018Co-Authors: Suhas Diggavi, Sreeram KannanAbstract:Nanopore sequencing is an emerging new technology for sequencing Deoxyribonucleic acid (DNA), which can read long fragments of DNA (~50 000 bases), in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore Sequencers can acquire long reads, the high error rates (20%–30%) pose a technical challenge. In a nanopore Sequencer, a DNA is migrated through a nanopore, and current variations are measured. The DNA sequence is inferred from this observed current pattern using an algorithm called a base-caller . In this paper, we propose a mathematical model for the “channel” from the input DNA sequence to the observed current, and calculate bounds on the information extraction capacity of the nanopore Sequencer. This model incorporates impairments, such as (non-linear) inter-symbol interference, deletions, and random response. These information bounds have two-fold application: 1) The decoding rate with a uniform input distribution can be used to calculate the average size of the plausible list of DNA sequences given an observed current trace. This bound can be used to benchmark existing base-calling algorithms, as well as serving a performance objective to design better nanopores. 2) When the nanopore Sequencer is used as a reader in a DNA storage system, the storage capacity is quantified by our bounds.
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models and information theoretic bounds for nanopore sequencing
International Symposium on Information Theory, 2017Co-Authors: Suhas Diggavi, Sreeram KannanAbstract:Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (∼50,000 bases) unlike most current Sequencers which can only read hundreds of bases. While nanopore Sequencers can acquire long reads, the high error rates (≈ 30%) pose a technical challenge. In a nanopore Sequencer, a DNA is migrated through a nanopore and current variations are measured. The DNA sequence is inferred from this observed current pattern using an algorithm called a base-caller. In this paper, we propose a mathematical model for the “channel” from the input DNA sequence to the observed current, and calculate bounds on the information extraction capacity of the nanopore Sequencer. This model incorporates impairments like inter-symbol interference, deletions, as well as random response. The practical application of such information bounds is two-fold: (1) benchmarking present base-calling algorithms, and (2) offering an optimization objective for designing better nanopore Sequencers.
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ISIT - Models and information-theoretic bounds for nanopore sequencing
2017 IEEE International Symposium on Information Theory (ISIT), 2017Co-Authors: Suhas Diggavi, Sreeram KannanAbstract:Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (∼50,000 bases) unlike most current Sequencers which can only read hundreds of bases. While nanopore Sequencers can acquire long reads, the high error rates (≈ 30%) pose a technical challenge. In a nanopore Sequencer, a DNA is migrated through a nanopore and current variations are measured. The DNA sequence is inferred from this observed current pattern using an algorithm called a base-caller. In this paper, we propose a mathematical model for the “channel” from the input DNA sequence to the observed current, and calculate bounds on the information extraction capacity of the nanopore Sequencer. This model incorporates impairments like inter-symbol interference, deletions, as well as random response. The practical application of such information bounds is two-fold: (1) benchmarking present base-calling algorithms, and (2) offering an optimization objective for designing better nanopore Sequencers.
Abdelaziz Al Ouahabi - One of the best experts on this subject based on the ideXlab platform.
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Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation
Nature Communications, 2017Co-Authors: Abdelaziz Al Ouahabi, Jean-arthur Amalian, Laurence Charles, Jean-françois LutzAbstract:In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found.Digital information can be stored in monomer sequences of non-natural macromolecules, but only short chains can be read. Here the authors show long multi-byte digital polymers sequenced in a moderate resolution mass spectrometer. Full sequence coverage can be attained without pre-analysis digestion or the help from sequence databases.
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Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation
Nature Communications, 2017Co-Authors: Abdelaziz Al Ouahabi, Jean-arthur Amalian, Laurence Charles, Jean-françois LutzAbstract:In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found.Digital information can be stored in monomer sequences of non-natural macromolecules, but only short chains can be read. Here the authors show long multi-byte digital polymers sequenced in a moderate resolution mass spectrometer. Full sequence coverage can be attained without pre-analysis digestion or the help from sequence databases.
Tetsuo Hashimoto - One of the best experts on this subject based on the ideXlab platform.
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mitochondrial type hsp70 genes of the amitochondriate protists giardia intestinalis entamoeba histolytica and two microsporidians
Parasitology International, 2002Co-Authors: Nobuko Arisue, Lidya B. Sánchez, Tetsuo Hashimoto, Louis M. Weiss, Miklós MüllerAbstract:Genes encoding putative mitochondrial-type heat shock protein 70 (mit-hsp70) were isolated and sequenced from amitochondriate protists, Giardia intestinalis, Entamoeba histolytica, and two microsporidians, Encephalitozoon hellem and Glugea plecoglossi. The deduced mit-hsp70 sequences were analyzed by sequence alignments and phylogenetic reconstructions. The mit-hsp70 sequence of these four amitochondriate protists were divergent from other mit-hsp70 sequences of mitochondriate eukaryotes. However, all of these sequences were clearly located within a eukaryotic mitochondrial clade in the tree including various type hsp70 sequences, supporting the emerging notion that none of these amitochondriate lineages are primitively amitochodrial, but lost their mitochondria secondarily in their evolutionary past.
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mitochondrial type hsp70 genes of the amitochondriate protists giardia intestinalis entamoeba histolytica and two microsporidians
Parasitology International, 2002Co-Authors: Nobuko Arisue, Lidya B. Sánchez, Tetsuo Hashimoto, Louis M. Weiss, Miklós MüllerAbstract:Genes encoding putative mitochondrial-type heat shock protein 70 (mit-hsp70) were isolated and sequenced from amitochondriate protists, Giardia intestinalis, Entamoeba histolytica, and two microsporidians, Encephalitozoon hellem and Glugea plecoglossi. The deduced mit-hsp70 sequences were analyzed by sequence alignments and phylogenetic reconstructions. The mit-hsp70 sequence of these four amitochondriate protists were divergent from other mit-hsp70 sequences of mitochondriate eukaryotes. However, all of these sequences were clearly located within a eukaryotic mitochondrial clade in the tree including various type hsp70 sequences, supporting the emerging notion that none of these amitochondriate lineages are primitively amitochodrial, but lost their mitochondria secondarily in their evolutionary past.
Jean-arthur Amalian - One of the best experts on this subject based on the ideXlab platform.
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Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation
Nature Communications, 2017Co-Authors: Abdelaziz Al Ouahabi, Jean-arthur Amalian, Laurence Charles, Jean-françois LutzAbstract:In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found.Digital information can be stored in monomer sequences of non-natural macromolecules, but only short chains can be read. Here the authors show long multi-byte digital polymers sequenced in a moderate resolution mass spectrometer. Full sequence coverage can be attained without pre-analysis digestion or the help from sequence databases.
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Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation
Nature Communications, 2017Co-Authors: Abdelaziz Al Ouahabi, Jean-arthur Amalian, Laurence Charles, Jean-françois LutzAbstract:In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found.Digital information can be stored in monomer sequences of non-natural macromolecules, but only short chains can be read. Here the authors show long multi-byte digital polymers sequenced in a moderate resolution mass spectrometer. Full sequence coverage can be attained without pre-analysis digestion or the help from sequence databases.
