Search Results - "Fritz, J"

Towards population-scale long-read sequencing by De Coster, Wouter, Weissensteiner, Matthias H., Sedlazeck, Fritz J.

“…Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to…”
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Structural variant calling: the long and the short of it by Mahmoud, Medhat, Gobet, Nastassia, Cruz-Dávalos, Diana Ivette, Mounier, Ninon, Dessimoz, Christophe, Sedlazeck, Fritz J

“…Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases,…”
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NextGenMap: fast and accurate read mapping in highly polymorphic genomes by Sedlazeck, Fritz J, Rescheneder, Philipp, von Haeseler, Arndt

“…When choosing a read mapper, one faces the trade off between speed and the ability to map reads in highly polymorphic regions. Here, we report NextGenMap, a…”
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Piercing the dark matter: bioinformatics of long-range sequencing and mapping by Sedlazeck, Fritz J., Lee, Hayan, Darby, Charlotte A., Schatz, Michael C.

“…Several new genomics technologies have become available that offer long-read sequencing or long-range mapping with higher throughput and higher resolution…”
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Accurate detection of complex structural variations using single-molecule sequencing by Sedlazeck, Fritz J., Rescheneder, Philipp, Smolka, Moritz, Fang, Han, Nattestad, Maria, von Haeseler, Arndt, Schatz, Michael C.

“…Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule…”
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RaGOO: fast and accurate reference-guided scaffolding of draft genomes by Alonge, Michael, Soyk, Sebastian, Ramakrishnan, Srividya, Wang, Xingang, Goodwin, Sara, Sedlazeck, Fritz J, Lippman, Zachary B, Schatz, Michael C

“…We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve…”
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GenomeScope: fast reference-free genome profiling from short reads by Vurture, Gregory W, Sedlazeck, Fritz J, Nattestad, Maria, Underwood, Charles J, Fang, Han, Gurtowski, James, Schatz, Michael C

“…GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat…”
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Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast by Jeffares, Daniel C., Jolly, Clemency, Hoti, Mimoza, Speed, Doug, Shaw, Liam, Rallis, Charalampos, Balloux, Francois, Dessimoz, Christophe, Bähler, Jürg, Sedlazeck, Fritz J.

“…Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic…”
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A multi-task convolutional deep neural network for variant calling in single molecule sequencing by Luo, Ruibang, Sedlazeck, Fritz J., Lam, Tak-Wah, Schatz, Michael C.

“…The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule…”
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Smooth and clumpy dust distributions in AGN: a direct comparison of two commonly explored infrared emission models by Feltre, A., Hatziminaoglou, E., Fritz, J., Franceschini, A.

“…Abstract The geometry of dust distribution within the inner regions of active galactic nuclei (AGN) is still a debated issue and relates directly to the AGN…”
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Targeted nanopore sequencing with Cas9-guided adapter ligation by Gilpatrick, Timothy, Lee, Isac, Graham, James E., Raimondeau, Etienne, Bowen, Rebecca, Heron, Andrew, Downs, Bradley, Sukumar, Saraswati, Sedlazeck, Fritz J, Timp, Winston

“…Despite recent improvements in sequencing methods, there remains a need for assays that provide high sequencing depth and comprehensive variant detection…”
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Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree by Dylus, David, Altenhoff, Adrian, Majidian, Sina, Sedlazeck, Fritz J., Dessimoz, Christophe

“…Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints…”
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Truvari: refined structural variant comparison preserves allelic diversity by English, Adam C, Menon, Vipin K, Gibbs, Richard A, Metcalf, Ginger A, Sedlazeck, Fritz J

“…The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common…”
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Towards accurate and reliable resolution of structural variants for clinical diagnosis by Liu, Zhichao, Roberts, Ruth, Mercer, Timothy R, Xu, Joshua, Sedlazeck, Fritz J, Tong, Weida

“…Structural variants (SVs) are a major source of human genetic diversity and have been associated with different diseases and phenotypes. The detection of SVs…”
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PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation by Mahmoud, Medhat, Doddapaneni, Harshavardhan, Timp, Winston, Sedlazeck, Fritz J

“…Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV,…”
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The corticotopic organization of the human basal forebrain as revealed by regionally selective functional connectivity profiles by Fritz, Hans‐Christian J., Ray, Nicola, Dyrba, Martin, Sorg, Christian, Teipel, Stefan, Grothe, Michel J.

“…The cholinergic basal forebrain (CBF), comprising different groups of cortically projecting cholinergic neurons, plays a crucial role in higher cognitive…”
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Phased diploid genome assembly with single-molecule real-time sequencing by Chin, Chen-Shan, Peluso, Paul, Sedlazeck, Fritz J, Nattestad, Maria, Concepcion, Gregory T, Clum, Alicia, Dunn, Christopher, O'Malley, Ronan, Figueroa-Balderas, Rosa, Morales-Cruz, Abraham, Cramer, Grant R, Delledonne, Massimo, Luo, Chongyuan, Ecker, Joseph R, Cantu, Dario, Rank, David R, Schatz, Michael C

“…The open-source FALCON and FALCON-Unzip software utilize long-read sequencing data to generate contiguous, accurate and phased diploid assemblies, even from…”
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Paragraph: a graph-based structural variant genotyper for short-read sequence data by Chen, Sai, Krusche, Peter, Dolzhenko, Egor, Sherman, Rachel M, Petrovski, Roman, Schlesinger, Felix, Kirsche, Melanie, Bentley, David R, Schatz, Michael C, Sedlazeck, Fritz J, Eberle, Michael A

“…Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical…”
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Chromosome territories and the global regulation of the genome by Fritz, Andrew J., Sehgal, Nitasha, Pliss, Artem, Xu, Jinhui, Berezney, Ronald

“…Spatial positioning is a fundamental principle governing nuclear processes. Chromatin is organized as a hierarchy from nucleosomes to Mbp chromatin domains…”
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Multiple genome alignment in the telomere-to-telomere assembly era by Kille, Bryce, Balaji, Advait, Sedlazeck, Fritz J., Nute, Michael, Treangen, Todd J.

“…Abstract With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately…”
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