Search Results - "David, Matei"

Detecting DNA cytosine methylation using nanopore sequencing by Simpson, Jared T, Workman, Rachael E, Zuzarte, P C, David, Matei, Dursi, L J, Timp, Winston

“…A hidden Markov model (HMM)-based tool enables detection of 5-methylcytosine (5-mC) from single-molecule nanopore-sequencing data generated directly from human…”
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SHRiMP2: Sensitive yet Practical Short Read Mapping by DAVID, Matei, DZAMBA, Misko, LISTER, Dan, ILIE, Lucian, BRUDNO, Michael

“…We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to…”
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Nanocall: an open source basecaller for Oxford Nanopore sequencing data by David, Matei, Dursi, L J, Yao, Delia, Boutros, Paul C, Simpson, Jared T

“…The highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently…”
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A community effort to create standards for evaluating tumor subclonal reconstruction by Salcedo, Adriana, Tarabichi, Maxime, Espiritu, Shadrielle Melijah G., Deshwar, Amit G., David, Matei, Wilson, Nathan M., Dentro, Stefan, Wintersinger, Jeff A., Liu, Lydia Y., Ko, Minjeong, Sivanandan, Srinivasan, Zhang, Hongjiu, Zhu, Kaiyi, Ou Yang, Tai-Hsien, Chilton, John M., Buchanan, Alex, Lalansingh, Christopher M., P’ng, Christine, Anghel, Catalina V., Umar, Imaad, Lo, Bryan, Zou, William, Simpson, Jared T., Stuart, Joshua M., Anastassiou, Dimitris, Guan, Yuanfang, Ewing, Adam D., Ellrott, Kyle, Wedge, David C., Morris, Quaid, Van Loo, Peter, Boutros, Paul C.

“…Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of…”
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Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs by Voellenkle, Christine, Rooij, Jeroen van, Guffanti, Alessandro, Brini, Elena, Fasanaro, Pasquale, Isaia, Eleonora, Croft, Larry, David, Matei, Capogrossi, Maurizio C, Moles, Anna, Felsani, Armando, Martelli, Fabio

“…In order to understand the role of microRNAs (miRNAs) in vascular physiopathology, we took advantage of deep-sequencing techniques to accurately and…”
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Detecting Alu insertions from high-throughput sequencing data by David, Matei, Mustafa, Harun, Brudno, Michael

“…High-throughput sequencing technologies have allowed for the cataloguing of variation in personal human genomes. In this manuscript, we present alu-detect, a…”
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Tradeoff lower lounds for stack machines by David, Matei, Papakonstantinou, Periklis A.

“…A space-bounded Stack Machine is a regular Turing Machine with a read-only input tape, several space-bounded read-write work tapes, and an unbounded stack…”
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Assembly and characterization of novel Alu inserts detected from next-generation sequencing data by Mustafa, Harun, David, Matei, Brudno, Michael

“…Repetitive elements generally, and Alu inserts specifically are a large contributor to the recent evolution of the human genome. By assembling the sequences of…”
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How strong is Nisanʼs pseudo-random generator? by David, Matei, Papakonstantinou, Periklis A., Sidiropoulos, Anastasios

“…We study the resilience of the classical pseudo-random generator (PRG) of Nisan (1992) [6] against space-bounded machines that make multiple passes over the…”
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Multiparty Communication Complexity by David, Matei

“…Communication complexity is an area of complexity theory that studies an abstract model of computation called a communication protocol. In a k-player…”
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Trade-Off Lower Bounds for Stack Machines by David, Matei, Papakonstantinou, Periklis A

“…A space bounded Stack Machine is a regular Turing Machine with a read-only input tape, several space bounded read-write work tapes, and an unbounded stack…”
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Multiparty Communication Complexity by David, Matei

“…Communication complexity is an area of complexity theory that studies an abstract model of computation called a communication protocol. In a k-player…”
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Wait-free linearizable queue implementations by David, Matei

“…We study wait-free linearizable Queue implementations in asynchronous shared-memory systems from other consensus number 2 types, such as Fetch&Add and Swap. It…”
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Separating NOF communication complexity classes RP and NP by David, Matei, Pitassi, Toniann

“…We provide a non-explicit separation of the number-on-forehead communication complexity classes RP and NP when the number of players is up to \delta log(n) for…”
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