B
Barbara Uszczynska-Ratajczak
Researcher at University of Warsaw
Publications - 25
Citations - 3407
Barbara Uszczynska-Ratajczak is an academic researcher from University of Warsaw. The author has contributed to research in topics: GENCODE & Mitochondrion. The author has an hindex of 9, co-authored 20 publications receiving 1857 citations. Previous affiliations of Barbara Uszczynska-Ratajczak include International Institute of Minnesota & Pompeu Fabra University.
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Journal ArticleDOI
GENCODE reference annotation for the human and mouse genomes.
Adam Frankish,Mark Diekhans,Anne-Maud Ferreira,Rory Johnson,Irwin Jungreis,Irwin Jungreis,Jane E. Loveland,Jonathan M. Mudge,Cristina Sisu,Cristina Sisu,James C. Wright,Joel Armstrong,If Barnes,Andrew Berry,Alexandra Bignell,Silvia Carbonell Sala,Jacqueline Chrast,Fiona Cunningham,Tomás Di Domenico,Sarah Donaldson,Ian T. Fiddes,Carlos García Girón,Jose Manuel Gonzalez,Tiago Grego,Matthew P. Hardy,Thibaut Hourlier,Toby Hunt,Osagie G. Izuogu,Julien Lagarde,Fergal J. Martin,Laura Martinez,Shamika Mohanan,Paul R. Muir,Fabio C. P. Navarro,Anne Parker,Baikang Pei,Fernando Pozo,Magali Ruffier,Bianca M. Schmitt,Eloise Stapleton,Marie-Marthe Suner,Irina Sycheva,Barbara Uszczynska-Ratajczak,Jinuri Xu,Andrew D. Yates,Daniel R. Zerbino,Yan Zhang,Yan Zhang,Bronwen Aken,Jyoti S. Choudhary,Mark Gerstein,Roderic Guigó,Tim Hubbard,Manolis Kellis,Manolis Kellis,Benedict Paten,Alexandre Reymond,Michael L. Tress,Paul Flicek +58 more
TL;DR: This work generates primary data, creates bioinformatics tools and provides analysis to support the work of expert manual gene annotators and automated gene annotation pipelines to identify and characterise gene loci to the highest standard.
Journal ArticleDOI
Towards a complete map of the human long non-coding RNA transcriptome
TL;DR: The state of currently available long non-coding RNA annotations and the impact of emerging technologies such as long-read sequencing are discussed.
Journal ArticleDOI
Gencode 2021
Adam Frankish,Mark Diekhans,Irwin Jungreis,Julien Lagarde,Jane E. Loveland,Jonathan M. Mudge,Cristina Sisu,James C. Wright,Joel Armstrong,If Barnes,Andrew Berry,Alexandra Bignell,Carles Boix,S. Carbonell Sala,Fiona Cunningham,T. Di Domenico,Sarah Donaldson,Ian T. Fiddes,C. Garcia Giron,José M. González,Tiago Grego,Matthew Hardy,Thibaut Hourlier,Kerstin Howe,Toby Hunt,Osagie G. Izuogu,Rory Johnson,Fergal J. Martin,Laura Martinez,S. Mohanan,Paul R. Muir,Fabio C. P. Navarro,Anne Parker,Baikang Pei,Fernando Pozo,F. C. Riera,Magali Ruffier,Bianca M. Schmitt,E. Stapleton,Marie Marthe Suner,I. Sycheva,Barbara Uszczynska-Ratajczak,Maxim Y Wolf,Jinrui Xu,Y. T. Yang,Andrew D. Yates,Daniel R. Zerbino,Yan Zhang,Jyoti S. Choudhary,Mark Gerstein,Roderic Guigó,Tim Hubbard,Manolis Kellis,Benedict Paten,Michael L. Tress,Paul Flicek +55 more
TL;DR: The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics as mentioned in this paper. But the annotation process does not support the creation of transcript structures and the determination of their function.
Journal ArticleDOI
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Julien Lagarde,Barbara Uszczynska-Ratajczak,Silvia Carbonell,Sílvia Pérez-Lluch,Amaya Abad,Carrie A. Davis,Thomas R. Gingeras,Adam Frankish,Jennifer Harrow,Roderic Guigó,Rory Johnson,Rory Johnson +11 more
TL;DR: An experimental reannotation of the GENCODE intergenic lncRNA populations in matched human and mouse tissues resulted in novel transcript models for 3,574 and 561 gene loci, respectively, which enabled us to definitively characterize the genomic features of lncRNAs, including promoter and gene structure, and protein-coding potential.
Journal ArticleDOI
Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).
Julien Lagarde,Barbara Uszczynska-Ratajczak,Javier Santoyo-Lopez,José M. González,Electra Tapanari,Electra Tapanari,Jonathan M. Mudge,Charles A. Steward,Laurens G. Wilming,Andrea Tanzer,Andrea Tanzer,Cédric Howald,Jacqueline Chrast,Alicia Vela-Boza,Antonio Rueda,Francisco J. López-Domingo,Joaquín Dopazo,Alexandre Reymond,Roderic Guigó,Jennifer Harrow +19 more
TL;DR: This work applies RACE-Seq to 398 human lncRNA genes in seven tissues, leading to the discovery of 2,556 on-target, novel transcripts and suggests that lncRNAs are as long, have as many exons and undergo as much alternative splicing as protein-coding genes, contrary to current assumptions.