Publications

 

Updated: May 2020

You can find a full list of our publications here

 


Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H,
Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni
L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P,
Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY,
Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP,
Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, 
Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L,
Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling 
L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM,
Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE,
Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael
BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R,
Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and
Functional Interpretation Working Group; PCAWG Structural Variation Working
Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG
Consortium.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Nature. 2020 Feb;578(7793):102-111. 


ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.

Pan-cancer analysisof whole genomes.

Nature. 2020 Feb;578(7793):82-93. 


Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS;
PCAWG Drivers and Functional Interpretation Group, Johnson R; PCAWG Consortium.
Cancer LncRNA Census reveals evidence for deep functional conservation of long
noncoding RNAs in tumorigenesis.

Commun Biol. 2020 Feb 5;3(1):56. 


Bergadà-Pijuan J, Pulido-Quetglas C, Vancura A, Johnson R.

CASPR, an analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target
selection for long non-coding RNAs.

Bioinformatics. 2020 Mar 1;36(6):1673-1680.


Carlevaro-Fita J, Liu L, Zhou Y, Zhang S, Chouvardas P, Johnson R, Li J.
LnCompare: gene set feature analysis for human long non-coding RNAs.

Nucleic Acids Res. 2019 Jul 2;47(W1):W523-W529

 

- Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization

J Carlevaro-Fita, R Johnson

Molecular cell (2019)

PMID: 30587508; DOI: 10.1016/j.molcel.2019.02.008

- Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening

R Esposito, N Bosch, A Lanzós, T Polidori, C Pulido-Quetglas, R Johnson

Cancer cell (2019)

PMID: 30827888; DOI: 10.1016/j.ccell.2019.01.019

- Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs

J Carlevaro-Fita, T Polidori, M Das, C Navarro, TI Zoller, R Johnson

Genome research (2018)

PMID: 30587508; DOI: 10.1101/gr.229922.117

 

- GENCODE reference annotation for the human and mouse genomes

A Frankish, M Diekhans, AM Ferreira, R Johnson, ...

NAR (2018)

PMID: 30357393; DOI: 10.1093/nar/gky955

 

- Capturing a Long Look at Our Genetic Library

J Lagarde, R Johnson

Cell systems (2018)

PMID: 29494803; DOI: 10.1016/j.cels.2018.02.003

 

- Nearly all new protein-coding predictions in the CHESS database are not protein-coding

I Jungreis, ML Tress, J Mudge, C Sisu, T Hunt, R Johnson, ...

bioRxiv, 360602 (2018)

 

- Towards a complete map of the human long non-coding RNA transcriptome

B Uszczynska-Ratajczak, J Lagarde, A Frankish, R Guigó, R Johnson

Nature Reviews Genetics (2018)

PMID: 29795125; DOI: 10.1038/s41576-018-0017-y

- High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R.

Nature Genetics (2017)

PMID: 29106417; DOI: 10.1038/ng.3988

- LncATLAS database for subcellular localization of long noncoding RNAs

Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido T, Guigo R, Johnson R.

RNA (2017)

PMID: 28386015; DOI: 10.1261/rna.060814.117

- Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion

Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso T, Palumbo E, Ponomarenko J, Guigo R, Johnson R.

PLoS Computational Biology (2017)

PMID: 28253259; DOI: 10.1371/journal.pcbi.1005341

 

- Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features

Lanzós A, Carlevaro-Fita J, Mularoni L, Reverter F, Palumbo E, Guigó R, Johnson R.

Scientific Reports (2017)

PMID: 28128360; DOI: 10.1038/srep41544

 

- Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Carlevaro-Fita J, Rahim A, Guigó R, Vardy LA, Johnson R.

RNA (2016)

PMID: 27090285; DOI: 10.1261/rna.053561.115

 

- DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs

Aparicio-Prat E, Arnan C, Sala I, Bosch N, Guigó R, Johnson R.

BMC Genomics (2015)

PMID: 26493208; DOI: 10.1186/s12864-015-2086-z

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