Search Results - "MARTH, Gabor T"

ART: a next-generation sequencing read simulator by Huang, Weichun, Li, Leping, Myers, Jason R., Marth, Gabor T.

“…ART is a set of simulation tools that generate synthetic next-generation sequencing reads. This functionality is essential for testing and benchmarking tools…”
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MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping by Lee, Wan-Ping, Stromberg, Michael P, Ward, Alistair, Stewart, Chip, Garrison, Erik P, Marth, Gabor T

“…MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current…”
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SpeedSeq: ultra-fast personal genome analysis and interpretation by Chiang, Colby, Layer, Ryan M, Faust, Gregory G, Lindberg, Michael R, Rose, David B, Garrison, Erik P, Marth, Gabor T, Quinlan, Aaron R, Hall, Ira M

“…SpeedSeq is an open-source software suite offering very fast, accurate and comprehensive analysis of single-nucleotide and structural variants from whole…”
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The variant call format and VCFtools by Danecek, Petr, Auton, Adam, Abecasis, Goncalo, Albers, Cornelis A., Banks, Eric, DePristo, Mark A., Handsaker, Robert E., Lunter, Gerton, Marth, Gabor T., Sherry, Stephen T., McVean, Gilean, Durbin, Richard

“…The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with…”
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SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications by Zhao, Mengyao, Lee, Wan-Ping, Garrison, Erik P, Marth, Gabor T

“…The Smith-Waterman algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read…”
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GIGGLE: a search engine for large-scale integrated genome analysis by Layer, Ryan M, Pedersen, Brent S, DiSera, Tonya, Marth, Gabor T, Gertz, Jason, Quinlan, Aaron R

“…GIGGLE is a genome interval search engine that enables extremely fast queries of genome features from thousands of genome annotation sets. GIGGLE is a genomics…”
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BamTools: a C++ API and toolkit for analyzing and managing BAM files by BARNETT, Derek W, GARRISON, Erik K, QUINLAN, Aaron R, STRÖMBERG, Michael P, MARTH, Gabor T

“…Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging,…”
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Pyrobayes: an improved base caller for SNP discovery in pyrosequences by Marth, Gábor T, Quinlan, Aaron R, Stewart, Donald A, Strömberg, Michael P

“…Previously reported applications of the 454 Life Sciences pyrosequencing technology have relied on deep sequence coverage for accurate polymorphism discovery…”
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Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing by Hellwig, Sabine, Nix, David A, Gligorich, Keith M, O'Shea, John M, Thomas, Alun, Fuertes, Carrie L, Bhetariya, Preetida J, Marth, Gabor T, Bronner, Mary P, Underhill, Hunter R

“…Circulating tumor-derived cell-free DNA (ctDNA) enables non-invasive diagnosis, monitoring, and treatment susceptibility testing in human cancers. However,…”
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A comprehensive map of mobile element insertion polymorphisms in humans by Stewart, Chip, Kural, Deniz, Strömberg, Michael P, Walker, Jerilyn A, Konkel, Miriam K, Stütz, Adrian M, Urban, Alexander E, Grubert, Fabian, Lam, Hugo Y K, Lee, Wan-Ping, Busby, Michele, Indap, Amit R, Garrison, Erik, Huff, Chad, Xing, Jinchuan, Snyder, Michael P, Jorde, Lynn B, Batzer, Mark A, Korbel, Jan O, Marth, Gabor T

“…As a consequence of the accumulation of insertion events over evolutionary time, mobile elements now comprise nearly half of the human genome. The Alu, L1, and…”
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A DOC2 Protein Identified by Mutational Profiling Is Essential for Apicomplexan Parasite Exocytosis by Farrell, Andrew, Thirugnanam, Sivasakthivel, Lorestani, Alexander, Dvorin, Jeffrey D., Eidell, Keith P., Ferguson, David J.P., Anderson-White, Brooke R., Duraisingh, Manoj T., Marth, Gabor T., Gubbels, Marc-Jan

“…Exocytosis is essential to the lytic cycle of apicomplexan parasites and required for the pathogenesis of toxoplasmosis and malaria. DOC2 proteins recruit the…”
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The functional spectrum of low-frequency coding variation by Marth, Gabor T, Yu, Fuli, Indap, Amit R, Garimella, Kiran, Gravel, Simon, Leong, Wen Fung, Tyler-Smith, Chris, Bainbridge, Matthew, Blackwell, Tom, Zheng-Bradley, Xiangqun, Chen, Yuan, Challis, Danny, Clarke, Laura, Ball, Edward V, Cibulskis, Kristian, Cooper, David N, Fulton, Bob, Hartl, Chris, Koboldt, Dan, Muzny, Donna, Smith, Richard, Sougnez, Carrie, Stewart, Chip, Ward, Alistair, Yu, Jin, Xue, Yali, Altshuler, David, Bustamante, Carlos D, Clark, Andrew G, Daly, Mark, DePristo, Mark, Flicek, Paul, Gabriel, Stacey, Mardis, Elaine, Palotie, Aarno, Gibbs, Richard

“…Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population…”
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bam.iobio: a web-based, real-time, sequence alignment file inspector by Miller, Chase A, Qiao, Yi, DiSera, Tonya, D'Astous, Brian, Marth, Gabor T

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The stochastic nature of errors in next-generation sequencing of circulating cell-free DNA by Nix, David A, Hellwig, Sabine, Conley, Christopher, Thomas, Alun, Fuertes, Carrie L, Hamil, Cindy L, Bhetariya, Preetida J, Garrido-Laguna, Ignacio, Marth, Gabor T, Bronner, Mary P, Underhill, Hunter R

“…Challenges with distinguishing circulating tumor DNA (ctDNA) from next-generation sequencing (NGS) artifacts limits variant searches to established solid tumor…”
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Tangram: a comprehensive toolbox for mobile element insertion detection by Wu, Jiantao, Lee, Wan-Ping, Ward, Alistair, Walker, Jerilyn A, Konkel, Miriam K, Batzer, Mark A, Marth, Gabor T

“…Mobile elements (MEs) constitute greater than 50% of the human genome as a result of repeated insertion events during human genome evolution. Although most of…”
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The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations by Marth, Gabor T, Czabarka, Eva, Murvai, Janos, Sherry, Stephen T

“…We have studied a genome-wide set of single-nucleotide polymorphism (SNP) allele frequency measures for African-American, East Asian, and European-American…”
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Clonal dynamics of aggressive systemic mastocytosis on avapritinib therapy by Huang, Xiaomeng, Pomicter, Anthony D., Ahmann, Jonathan, Qiao, Yi, Chen, Opal S., George, Tracy I., Cruz-Rodriguez, Nataly, Guru, Sameer Ahmad, Marth, Gabor T., Deininger, Michael W.

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Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy by Ostrander, Betsy E. P., Butterfield, Russell J., Pedersen, Brent S., Farrell, Andrew J., Layer, Ryan M., Ward, Alistair, Miller, Chase, DiSera, Tonya, Filloux, Francis M., Candee, Meghan S., Newcomb, Tara, Bonkowsky, Joshua L., Marth, Gabor T., Quinlan, Aaron R.

“…Early infantile epileptic encephalopathy (EIEE) is a devastating epilepsy syndrome with onset in the first months of life. Although mutations in more than 50…”
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The Extracellular Milieu of Toxoplasma's Lytic Cycle Drives Lab Adaptation, Primarily by Transcriptional Reprogramming by Primo, Vincent A, Rezvani, Yasaman, Farrell, Andrew, Murphy, Connor Q, Lou, Jingjing, Vajdi, Amir, Marth, Gabor T, Zarringhalam, Kourosh, Gubbels, Marc-Jan

“…Evolve and resequencing (E&R) was applied to lab adaptation of Toxoplasma gondii for over 1,500 generations with the goal of mapping host-independent in vitro…”
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Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains by Yang, Ninghan, Farrell, Andrew, Niedelman, Wendy, Melo, Mariane, Lu, Diana, Julien, Lindsay, Marth, Gabor T, Gubbels, Marc-Jan, Saeij, Jeroen P J

“…Toxoplasma gondii has a largely clonal population in North America and Europe, with types I, II and III clonal lineages accounting for the majority of strains…”
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