K
Katharina E. Hayer
Researcher at Children's Hospital of Philadelphia
Publications - 55
Citations - 1723
Katharina E. Hayer is an academic researcher from Children's Hospital of Philadelphia. The author has contributed to research in topics: Biology & RNA splicing. The author has an hindex of 15, co-authored 40 publications receiving 1118 citations. Previous affiliations of Katharina E. Hayer include University of Pennsylvania.
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Journal ArticleDOI
CircaDB: a database of mammalian circadian gene expression profiles
TL;DR: A new database of circadian transcriptional profiles from time course expression experiments from mice and humans, where each transcript’s expression was evaluated by three separate algorithms, JTK_Cycle, Lomb Scargle and DeLichtenberg.
Journal ArticleDOI
Simulation-based comprehensive benchmarking of RNA-seq aligners.
Giacomo Baruzzo,Katharina E. Hayer,Eun Ji Kim,Barbara Di Camillo,Garret A. FitzGerald,Gregory R. Grant +5 more
TL;DR: The most widely cited tool underperforms for most metrics, particularly when using default settings, and performance varied by genome complexity, and accuracy and popularity were poorly correlated.
Journal ArticleDOI
Impaired Death Receptor Signaling in Leukemia Causes Antigen-Independent Resistance by Inducing CAR T-cell Dysfunction
Nathan Singh,Yong Gu Lee,Olga Shestova,Pranali Ravikumar,Katharina E. Hayer,Seok Jae Hong,Xueqing Maggie Lu,Raymone Pajarillo,Sangya Agarwal,Shunichiro Kuramitsu,Elena Orlando,Karen Thudium Mueller,Charly R. Good,Shelley L. Berger,Ophir Shalem,Ophir Shalem,Matthew D. Weitzman,Matthew D. Weitzman,Noelle V. Frey,Shannon L. Maude,Stephan A. Grupp,Carl H. June,Saar Gill,Marco Ruella +23 more
TL;DR: It is suggested that inherent dysregulation of death receptor signaling in ALL directly leads to CAR T cell failure by impairing T cell cytotoxicity and promoting progressiveCAR T cell dysfunction.
Journal ArticleDOI
IVT-seq reveals extreme bias in RNA sequencing
Nicholas F. Lahens,Ibrahim Halil Kavakli,Ray Zhang,Katharina E. Hayer,Michael B Black,Hannah Dueck,Angel Pizarro,Junhyong Kim,Rafael A. Irizarry,Russell S. Thomas,Gregory R. Grant,John B. Hogenesch +11 more
TL;DR: It is found rRNA depletion is responsible for substantial, unappreciated biases in coverage introduced during library preparation, which suggest exon-level expression analysis may be inadvisable, and the utility of IVT-seq for promoting better understanding of bias introduced by RNA-seq is shown.
Journal ArticleDOI
Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data
TL;DR: Most methods are inaccurate even using idealized data, and that no method is highly accurate once multiple splice forms, polymorphisms, intron signal, sequencing errors, alignment errors, annotation errors and other complicating factors are present, which point to the pressing need for further algorithm development.