Search Results - "Schlesinger, Felix"

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications by Chen, Xiaoyu, Schulz-Trieglaff, Ole, Shaw, Richard, Barnes, Bret, Schlesinger, Felix, Källberg, Morten, Cox, Anthony J, Kruglyak, Semyon, Saunders, Christopher T

“…: We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and…”
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STAR: ultrafast universal RNA-seq aligner by Dobin, Alexander, Davis, Carrie A, Schlesinger, Felix, Drenkow, Jorg, Zaleski, Chris, Jha, Sonali, Batut, Philippe, Chaisson, Mark, Gingeras, Thomas R

“…Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively…”
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The reality of pervasive transcription by Clark, Michael B, Amaral, Paulo P, Schlesinger, Felix J, Dinger, Marcel E, Taft, Ryan J, Rinn, John L, Ponting, Chris P, Stadler, Peter F, Morris, Kevin V, Morillon, Antonin, Rozowsky, Joel S, Gerstein, Mark B, Wahlestedt, Claes, Hayashizaki, Yoshihide, Carninci, Piero, Gingeras, Thomas R, Mattick, John S

“…In parallel, whole chromosome tiling array interrogation of the RNA content of a variety of human tissues and cell lines revealed that, collectively, at least…”
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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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Synthetic spike-in standards for RNA-seq experiments by Jiang, Lichun, Schlesinger, Felix, Davis, Carrie A, Zhang, Yu, Li, Renhua, Salit, Marc, Gingeras, Thomas R, Oliver, Brian

“…High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of…”
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ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions by Dolzhenko, Egor, Deshpande, Viraj, Schlesinger, Felix, Krusche, Peter, Petrovski, Roman, Chen, Sai, Emig-Agius, Dorothea, Gross, Andrew, Narzisi, Giuseppe, Bowman, Brett, Scheffler, Konrad, van Vugt, Joke J F A, French, Courtney, Sanchis-Juan, Alba, Ibáñez, Kristina, Tucci, Arianna, Lajoie, Bryan R, Veldink, Jan H, Raymond, F Lucy, Taft, Ryan J, Bentley, David R, Eberle, Michael A

“…Abstract Summary We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to…”
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Developmental Validation of the MiSeq FGx Forensic Genomics System for Targeted Next Generation Sequencing in Forensic DNA Casework and Database Laboratories by Jäger, Anne C, Alvarez, Michelle L, Davis, Carey P, Guzmán, Ernesto, Han, Yonmee, Way, Lisa, Walichiewicz, Paulina, Silva, David, Pham, Nguyen, Caves, Glorianna, Bruand, Jocelyne, Schlesinger, Felix, Pond, Stephanie J.K, Varlaro, Joe, Stephens, Kathryn M, Holt, Cydne L

“…Graphical abstract…”
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Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster by Oliver, Brian, Lieb, Jason D, Disteche, Christine M, Deng, Xinxian, Hiatt, Joseph B, Nguyen, Di Kim, Ercan, Sevinc, Sturgill, David, Hillier, LaDeana W, Schlesinger, Felix, Davis, Carrie A, Reinke, Valerie J, Gingeras, Thomas R, Shendure, Jay, Waterston, Robert H

“…Brian Oliver, Jason Lieb, Christine Disteche and colleagues present an analysis of expression data in mammals, C. elegans and Drosophila . They conclude that…”
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De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements by Schlesinger, Felix, Smith, Andrew D, Gingeras, Thomas R, Hannon, Gregory J, Hodges, Emily

“…Deep sequencing of mammalian DNA methylomes has uncovered a previously unpredicted number of discrete hypomethylated regions in intergenic space (iHMRs). Here,…”
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Abstract LB-329: Enhancing the resolution and accelerating the pace of translational fusion characterization in oncology by RNA sequencing by Watson, Lisa C., Gross, Stephen M., Schlesinger, Felix, Mai, Anthony, Kellogg, Mariko, Lee, Steve, Attwooll, Claire, Brenca, Monica, Swanson, David, Wong, Andrew, Dei Tos, Angelo P., Haferlach, Claudia, Haferlach, Torsten, Kern, Wolfgang, Maestro, Roberta, Meggendorfer, Manja, Nadarajah, Niroshan, Polano, Maurizio, Rossi, Sabrina, Sbaraglia, Marta, Charames, George S., Schroth, Gary P., DeSantis, Grace

“…Abstract Chromosomal rearrangements are common markers of cancer progression across a wide range of cancer types, and therefore, identification of fusion…”
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Results of the “Evaluation of NGS in AML-Diagnostics (ELAN)” Study – an Inter-Laboratory Comparison Performed in 10 European Laboratories by Thiede, Christian, Bullinger, Lars, Hernández-Rivas, Jesús M, Heuser, Michael, Preudhomme, Claude, Best, Steven, Colomer, Dolors, Lo Coco, Francesco, Martinelli, Giovanni, Schuh, Anna, Benito, Rocí­o, Dolnik, Anna, Enjuanes, Anna, Geffroy, Sandrine, Lavorgna, Serena, Lea, Nicholas, Mason, Joanne, Ottaviani, Emanuela, Otto, Anne, Thol, Felicitas, Bhuju, Sabin, Döhner, Konstanze, Eberlein, Christian, Hamblin, Angela, Nibourel, Olivier, Ottone, Tiziana, Laginestra, Maria Antonella, Pratcorona, Marta, del Rey, Mónica, Schlesinger, Felix

“…Background: The invention of Next Generation Sequencing (NGS) has spurred research into human diseases, especially in the field of malignancy. In acute myeloid…”
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Detection of Novel Fusion Transcript VTI1A-CFAP46 in Hepatocellular Carcinoma by Tsuge, Shunichi, Saberi, Behnam, Cheng, Yulan, Wang, Zhixiong, Kim, Amy, Luu, Harry, Abraham, John M., Ybanez, Maria D., Hamilton, James P., Selaru, Florin M., Villacorta-Martin, Carlos, Schlesinger, Felix, Philosophe, Benjamin, Cameron, Andrew M., Zhu, Qingfeng, Anders, Robert, Gurakar, Ahmet, Meltzer, Stephen J.

“…Background: Hepatocellular carcinoma (HCC) is now the second-highest cause of cancer death worldwide. Recent studies have discovered a wide range of somatic…”
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