Arthur L. Delcher

MUMmer4: A fast and versatile genome alignment system

Guillaume Marçais, Arthur L. Delcher, Adam M. Phillippy, Rachel Coston et autres

The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major release of MUMmer version 3 in 2004, it has been applied to many types of problems …

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Unexpected Properties of Short Genomic Tandem Repeats

Irina Glotova, Michael Molla, Arthur L. Delcher, Simon Kasif

Abstract Length polymorphisms in genomic short tandem repeats have been implicated in a variety of diseases, most notably human neurodegenerative disorders. Expansions of tandem repeats are also associated with genomic instability in cancer. Our previous study of length-3 tandem repeats uncovered a …

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New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Antoine Dara, Elliott F. Drábek, Mark A. Travassos, Kara A. Moser et autres

BACKGROUND: Encoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion and severe malaria disease. Sequencing and assembling the 40-60 var gene complement for individual infections has …

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Additional file 3: of New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Antoine Dara, Elliott DrĂĄbek, Mark Travassos, Kara A. Moser et autres

A file containing Supplementary Figures S1â S5. Figure S1: Domain organization of PfEMP1 in each of 12 Malian isolates. Figure S2: Maximum likelihood phylogeny of DBLÎą domain sequences. Figure S3: Maximum likelihood phylogeny of CIDRÎą domain sequences. Figure S4: Detection and visualization …

Additional file 2: of New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Antoine Dara, Elliott DrĂĄbek, Mark Travassos, Kara A. Moser et autres

Contig pile-ups of the genome of 12 P. falciparum isolates from Mali aligned against the reference 3D7 genome. The genome assembly of each of the 12 isolates, represented by its constituent contigs (blue lines in between blue circles) is aligned against each …

Additional file 3: of New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Antoine Dara, Elliott DrĂĄbek, Mark Travassos, Kara A. Moser et autres

A file containing Supplementary Figures S1â S5. Figure S1: Domain organization of PfEMP1 in each of 12 Malian isolates. Figure S2: Maximum likelihood phylogeny of DBLÎą domain sequences. Figure S3: Maximum likelihood phylogeny of CIDRÎą domain sequences. Figure S4: Detection and visualization …

Additional file 1: of New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Antoine Dara, Elliott DrĂĄbek, Mark Travassos, Kara A. Moser et autres

A file containing Supplementary Tables S1â S7. Table S1: Samples and respective metadata. Table S2: Genomic DNA: Illumina and PacBio Sequencing Statistics. Table S3: Assembly characteristics for 12 Malian samples generated by Sprai and Celera assemblers. Table S4: Exon 1 var sequences …

Additional file 1: of New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Antoine Dara, Elliott DrĂĄbek, Mark Travassos, Kara A. Moser et autres

A file containing Supplementary Tables S1â S7. Table S1: Samples and respective metadata. Table S2: Genomic DNA: Illumina and PacBio Sequencing Statistics. Table S3: Assembly characteristics for 12 Malian samples generated by Sprai and Celera assemblers. Table S4: Exon 1 var sequences …

Additional file 2: of New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Antoine Dara, Elliott DrĂĄbek, Mark Travassos, Kara A. Moser et autres

Contig pile-ups of the genome of 12 P. falciparum isolates from Mali aligned against the reference 3D7 genome. The genome assembly of each of the 12 isolates, represented by its constituent contigs (blue lines in between blue circles) is aligned against each …

Logarithmic-Time Updates and Queries in Probabilistic Networks

Arthur L. Delcher, Adam J. Grove, Simon Kasif, Judea Pearl

In this paper we propose a dynamic data structure that supports efficient algorithms for updating and querying singly connected Bayesian networks (causal trees and polytrees). In the conventional algorithms, new evidence in absorbed in time O(1) and queries are processed in time …

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GAGE: A critical evaluation of genome assemblies and assembly algorithms (Genome Research (2012) 22 (557-567))

Steven L. Salzberg, Adam M. Phillippy, Aleksey V. Zimin, Daniela Puiu et autres

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

Michael C. Schatz, Adam M. Phillippy, Doron D. Sommer, Arthur L. Delcher et autres

Since its launch in 2004, the open-source AMOS project has released several innovative DNA sequence analysis applications including: Hawkeye, a visual analytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pipelines for systematically evaluating the quality of …

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