Search Results - "Sedlazeck, 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…”
Get full text

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,…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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,…”
Get full text

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…”
Get full text

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…”
Get full text

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions by Butler, Daniel, Mozsary, Christopher, Meydan, Cem, Foox, Jonathan, Rosiene, Joel, Shaiber, Alon, Danko, David, Afshinnekoo, Ebrahim, MacKay, Matthew, Sedlazeck, Fritz J., Ivanov, Nikolay A., Sierra, Maria, Pohle, Diana, Zietz, Michael, Gisladottir, Undina, Ramlall, Vijendra, Sholle, Evan T., Schenck, Edward J., Westover, Craig D., Hassan, Ciaran, Ryon, Krista, Young, Benjamin, Bhattacharya, Chandrima, Ng, Dianna L., Granados, Andrea C., Santos, Yale A., Servellita, Venice, Federman, Scot, Ruggiero, Phyllis, Fungtammasan, Arkarachai, Chin, Chen-Shan, Pearson, Nathaniel M., Langhorst, Bradley W., Tanner, Nathan A., Kim, Youngmi, Reeves, Jason W., Hether, Tyler D., Warren, Sarah E., Bailey, Michael, Gawrys, Justyna, Meleshko, Dmitry, Xu, Dong, Couto-Rodriguez, Mara, Nagy-Szakal, Dorottya, Barrows, Joseph, Wells, Heather, O’Hara, Niamh B., Rosenfeld, Jeffrey A., Chen, Ying, Steel, Peter A. D., Shemesh, Amos J., Xiang, Jenny, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Iftner, Angelika, Bezdan, Daniela, Sanchez, Elizabeth, Campion, Thomas R., Sipley, John, Cong, Lin, Craney, Arryn, Velu, Priya, Melnick, Ari M., Shapira, Sagi, Hajirasouliha, Iman, Borczuk, Alain, Iftner, Thomas, Salvatore, Mirella, Loda, Massimo, Westblade, Lars F., Cushing, Melissa, Wu, Shixiu, Levy, Shawn, Chiu, Charles, Schwartz, Robert E., Tatonetti, Nicholas, Rennert, Hanna, Imielinski, Marcin, Mason, Christopher E.

“…In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City…”
Get full text

Chromosome-scale, haplotype-resolved assembly of human genomes by Garg, Shilpa, Fungtammasan, Arkarachai, Carroll, Andrew, Chou, Mike, Schmitt, Anthony, Zhou, Xiang, Mac, Stephen, Peluso, Paul, Hatas, Emily, Ghurye, Jay, Maguire, Jared, Mahmoud, Medhat, Cheng, Haoyu, Heller, David, Zook, Justin M., Moemke, Tobias, Marschall, Tobias, Sedlazeck, Fritz J., Aach, John, Chin, Chen-Shan, Church, George M., Li, Heng

“…Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for…”
Get full text

Discovery and population genomics of structural variation in a songbird genus by Weissensteiner, Matthias H., Bunikis, Ignas, Catalán, Ana, Francoijs, Kees-Jan, Knief, Ulrich, Heim, Wieland, Peona, Valentina, Pophaly, Saurabh D., Sedlazeck, Fritz J., Suh, Alexander, Warmuth, Vera M., Wolf, Jochen B. W.

“…Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide…”
Get full text

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line by Nattestad, Maria, Goodwin, Sara, Ng, Karen, Baslan, Timour, Sedlazeck, Fritz J, Rescheneder, Philipp, Garvin, Tyler, Fang, Han, Gurtowski, James, Hutton, Elizabeth, Tseng, Elizabeth, Chin, Chen-Shan, Beck, Timothy, Sundaravadanam, Yogi, Kramer, Melissa, Antoniou, Eric, McPherson, John D, Hicks, James, McCombie, W Richard, Schatz, Michael C

“…The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be…”
Get full text

Genomic variant benchmark: if you cannot measure it, you cannot improve it by Majidian, Sina, Agustinho, Daniel Paiva, Chin, Chen-Shan, Sedlazeck, Fritz J, Mahmoud, Medhat

“…Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing…”
Get full text

Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data by Liu, Yunxi, Kearney, Joshua, Mahmoud, Medhat, Kille, Bryce, Sedlazeck, Fritz J., Treangen, Todd J.

“…Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost. Tracking low frequency intra-host…”
Get full text