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Details

Details

  • Name

    Nuno Fonseca
  • Cluster

    Computer Science
  • Role

    External Research Collaborator
  • Since

    01st June 2009
Publications

2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Authors
Rheinbay, E; PCAWG Drivers and Functional Interpretation Working Group,; 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, K; 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, C; 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; Weischenfeldt, J; Beroukhim, R; Martincorena, I; Pedersen, JS; Getz, G; PCAWG Structural Variation Working Group,; PCAWG Consortium,;

Publication
Nature

Abstract

2020

Genomic basis for RNA alterations in cancer

Authors
Calabrese, C; PCAWG Transcriptome Core Group,; Davidson, NR; Demircioglu, D; Fonseca, NA; He, Y; Kahles, A; Lehmann, K; Liu, F; Shiraishi, Y; Soulette, CM; Urban, L; Greger, L; Li, S; Liu, D; Perry, MD; Xiang, Q; Zhang, F; Zhang, J; Bailey, P; Erkek, S; Hoadley, KA; Hou, Y; Huska, MR; Kilpinen, H; Korbel, JO; Marin, MG; Markowski, J; Nandi, T; Pan-Hammarström, Q; Pedamallu, CS; Siebert, R; Stark, SG; Su, H; Tan, P; Waszak, SM; Yung, C; Zhu, S; Awadalla, P; Creighton, CJ; Meyerson, M; Ouellette, BFF; Wu, K; Yang, H; Brazma, A; Brooks, AN; Göke, J; Rätsch, G; Schwarz, RF; Stegle, O; Zhang, Z; PCAWG Transcriptome Working Group,; PCAWG Consortium,;

Publication
Nature

Abstract

2020

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

Authors
Zhang, Y; PCAWG Transcriptome Working Group,; Chen, F; Fonseca, NA; He, Y; Fujita, M; Nakagawa, H; Zhang, Z; Brazma, A; Creighton, CJ; PCAWG Structural Variation Working Group,; PCAWG Consortium,;

Publication
Nature Communications

Abstract

2020

Pan-cancer analysis of whole genomes

Authors
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium,;

Publication
Nature

Abstract

2019

ArrayExpress update – from bulk to single-cell expression data

Authors
Athar, A; Fullgrabe, A; George, N; Iqbal, H; Huerta, L; Ali, A; Snow, C; Fonseca, NA; Petryszak, R; Papatheodorou, I; Sarkans, U; Brazma, A;

Publication
Nucleic Acids Research

Abstract