Nuno A Fonseca
Nuno A Fonseca
Unknown affiliation
Verified email at fc.up.pt - Homepage
Title
Cited by
Cited by
Year
Two independent modes of chromosome organization are revealed by cohesin removal
FS Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pekowska ...
Nature, 2017
711*2017
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
KR Bradnam, JN Fass, A Alexandrov, P Baranay, M Bechner, I Birol, ...
GigaScience 2 (1), 2047-217X-2-10, 2013
6922013
Pan-cancer analysis of whole genomes
PJ Campbell, G Getz, JO Korbel, P Consortium
Nature 578 (7793), 82-93, 2020
667*2020
Assemblathon 1: a competitive assessment of de novo short read assembly methods
D Earl, K Bradnam, JS John, A Darling, D Lin, J Fass, HOK Yu, V Buffalo, ...
Genome research 21 (12), 2224-2241, 2011
5662011
Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants
R Petryszak, M Keays, YA Tang, NA Fonseca, E Barrera, T Burdett, ...
Nucleic acids research 44 (D1), D746-D752, 2016
5502016
Tools for mapping high-throughput sequencing data
NA Fonseca, J Rung, A Brazma, JC Marioni
Bioinformatics 28 (24), 3169-3177, 2012
3562012
Expression Atlas update—a database of gene and transcript expression from microarray-and sequencing-based functional genomics experiments
R Petryszak, T Burdett, B Fiorelli, NA Fonseca, M Gonzalez-Porta, ...
Nucleic acids research 42 (D1), D926-D932, 2014
3422014
ArrayExpress update–from bulk to single-cell expression data
A Athar, A Füllgrabe, N George, H Iqbal, L Huerta, A Ali, C Snow, ...
Nucleic acids research 47 (D1), D711-D715, 2019
2802019
Expression Atlas: gene and protein expression across multiple studies and organisms
I Papatheodorou, NA Fonseca, M Keays, YA Tang, E Barrera, W Bazant, ...
Nucleic acids research 46 (D1), D246-D251, 2018
2672018
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
E Rheinbay, MM Nielsen, F Abascal, JA Wala, O Shapira, G Tiao, ...
Nature 578 (7793), 102-111, 2020
2612020
Expression Atlas update: from tissues to single cells
I Papatheodorou, P Moreno, J Manning, AMP Fuentes, N George, ...
Nucleic acids research 48 (D1), D77-D83, 2020
2052020
Genomic basis for RNA alterations in cancer
C Calabrese, NR Davidson, D Demircioğlu, NA Fonseca, Y He, A Kahles, ...
Nature 578 (7793), 129-136, 2020
149*2020
Long-range enhancers regulating Myc expression are required for normal facial morphogenesis
VV Uslu, M Petretich, S Ruf, K Langenfeld, NA Fonseca, JC Marioni, ...
Nature genetics 46 (7), 753-758, 2014
1272014
Gramene 2016: comparative plant genomics and pathway resources
MK Tello-Ruiz, J Stein, S Wei, J Preece, A Olson, S Naithani, ...
Nucleic acids research 44 (D1), D1133-D1140, 2016
1262016
Gramene 2018: unifying comparative genomics and pathway resources for plant research
MK Tello-Ruiz, S Naithani, JC Stein, P Gupta, M Campbell, A Olson, ...
Nucleic acids research 46 (D1), D1181-D1189, 2018
1162018
RNA-seq gene profiling-a systematic empirical comparison
NA Fonseca, J Marioni, A Brazma
Plos one 9 (9), e107026, 2014
1012014
Transcription factor activities enhance markers of drug sensitivity in cancer
LM Garcia-Alonso, F Iorio, A Matchan, NA Fonseca, P Jaaks, G Peat, ...
Cancer Research, canres. 1679.2017, 2017
992017
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
A Frankish, B Uszczynska, GRS Ritchie, JM Gonzalez, D Pervouchine, ...
BMC genomics 16 (8), 1-11, 2015
822015
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface
BM Schmitt, KLM Rudolph, P Karagianni, NA Fonseca, RJ White, ...
Genome research 24 (11), 1797-1807, 2014
762014
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
J Carlevaro-Fita, A Lanzós, L Feuerbach, C Hong, D Mas-Ponte, ...
Communications biology 3 (1), 1-16, 2020
732020
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