Nuno Alberto Paulino da Fonseca


AuthID: R-000-DK8

Confirmed Publications: 119



21
TITLE: Combined burden and functional impact tests for cancer driver discovery using DriverPower
AUTHORS: Shuai, S; Abascal, F; Amin, SB; Bader, GD; Bandopadhayay, P; Barenboim, J; Beroukhim, R; Bertl, J; Boroevich, KA; Brunak, S; Campbell, PJ; Carlevaro Fita, J; Chakravarty, D; Chan, CWY; Chen, K; Choi, JK; Deu Pons, J; Dhingra, P; Diamanti, K; Feuerbach, L; Fink, JL; Fonseca, NA ; Frigola, J; Gambacorti Passerini, C; Garsed, DW; Gerstein, M; Getz, G; Guo, Q; Gut, IG; Haan, D; Hamilton, MP; Haradhvala, NJ; Harmanci, AO; Helmy, M; Herrmann, C; Hess, JM; Hobolth, A; Hodzic, E; Hong, C; Hornshøj, H; Isaev, K; Izarzugaza, JMG; Johnson, R; Johnson, TA; Juul, M; Juul, RI; Kahles, A; Kahraman, A; Kellis, M; Khurana, E; Kim, J; Kim, JK; Kim, Y; Komorowski, J; Korbel, JO; Kumar, S; Lanzós, A; Larsson, E; Lawrence, MS; Lee, D; Lehmann, KV; Li, S; Li, X; Lin, Z; Liu, EM; Lochovsky, L; Lou, S; Madsen, T; Marchal, K; Martincorena, I; Martinez Fundichely, A; Maruvka, YE; McGillivray, PD; Meyerson, W; Muiños, F; Mularoni, L; Nakagawa, H; Nielsen, MM; Paczkowska, M; Park, K; Park, K; Pedersen, JS; Pons, T; Pulido Tamayo, S; Raphael, BJ; Reimand, J; Reyes Salazar, I; Reyna, MA; Rheinbay, E; Rubin, MA; Rubio Perez, C; Sahinalp, SC; Saksena, G; Salichos, L; Sander, C; Schumacher, SE; Shackleton, M; Shapira, O; Shen, C; Shrestha, R; Shuai, S; Sidiropoulos, N; Sieverling, L; Sinnott Armstrong, N; Stein, LD; Stuart, JM; Tamborero, D; Tiao, G; Tsunoda, T; Umer, HM; Uusküla Reimand, L; Valencia, A; Vazquez, M; Verbeke, LPC; Wadelius, C; Wadi, L; Wang, J; Warrell, J; Waszak, SM; Weischenfeldt, J; Wheeler, DA; Wu, G; Yu, J; Zhang, J; Zhang, X; Zhang, Y; Zhao, Z; Zou, L; von Mering, C; Gallinger, S; Stein, L; ...More
PUBLISHED: 2020, SOURCE: Nature Communications, VOLUME: 11, ISSUE: 1
INDEXED IN: Scopus CrossRef: 35
IN MY: ORCID
22
TITLE: Complete Genome Sequences of Walnut-Associated Xanthomonas euroxanthea Strains CPBF 367 and CPBF 426 Obtained by Illumina/Nanopore Hybrid Assembly
AUTHORS: Teixeira, M; Martins, L; Fernandes, C; Chaves, C; Pinto, J; Tavares, F ; Fonseca, NA ;
PUBLISHED: 2020, SOURCE: MICROBIOLOGY RESOURCE ANNOUNCEMENTS, VOLUME: 9, ISSUE: 45
INDEXED IN: Scopus WOS CrossRef: 5
IN MY: ORCID
23
TITLE: Expression Atlas update: from tissues to single cells  Full Text
AUTHORS: Papatheodorou, I; Moreno, P; Manning, J; Fuentes, AMP; George, N; Fexova, S; Fonseca, NA ; Fullgrabe, A; Green, M; Huang, N; Huerta, L; Lqbal, H; Jianu, M; Mohammed, S; Zhao, LY; Jarnuczak, AF; Jupp, S; Marioni, J; Meyer, K; Petryszak, R; Medina, CAP; Talavera Lopez, C; Teichmann, S; Vizcaino, JA; Brazma, A; ...More
PUBLISHED: 2020, SOURCE: NUCLEIC ACIDS RESEARCH, VOLUME: 48, ISSUE: D1
INDEXED IN: Scopus WOS DBLP CrossRef: 187
IN MY: ORCID | DBLP
24
25
TITLE: Genomic basis for RNA alterations in cancer  Full Text
AUTHORS: Claudia Calabrese; PCAWG Transcriptome Core Group, ; Natalie R Davidson; Deniz Demircioğlu; Nuno A Fonseca ; Yao He; André Kahles; Kjong-Van Lehmann; Fenglin Liu; Yuichi Shiraishi; Cameron M Soulette; Lara Urban; Liliana Greger; Siliang Li; Dongbing Liu; Marc D Perry; Qian Xiang; Fan Zhang; Junjun Zhang; Peter Bailey; Serap Erkek; Katherine A Hoadley; Yong Hou; Matthew R Huska; Helena Kilpinen; Jan O Korbel; Maximillian G Marin; Julia Markowski; Tannistha Nandi; Qiang Pan-Hammarström; Chandra Sekhar Pedamallu; Reiner Siebert; Stefan G Stark; Hong Su; Patrick Tan; Sebastian M Waszak; Christina Yung; Shida Zhu; Philip Awadalla; Chad J Creighton; Matthew Meyerson; Francis F F Ouellette; Kui Wu; Huanming Yang; Alvis Brazma; Angela N Brooks; Jonathan Göke; Gunnar Rätsch; Roland F Schwarz; Oliver Stegle; Zemin Zhang; PCAWG Transcriptome Working Group, ; PCAWG Consortium, ; ...More
PUBLISHED: 2020, SOURCE: Nat., VOLUME: 578, ISSUE: 7793
INDEXED IN: Scopus DBLP CrossRef: 267
IN MY: ORCID | DBLP
26
TITLE: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
AUTHORS: Yiqun Zhang; Fengju Chen; Nuno A Fonseca ; Yao He; Masashi Fujita; Hidewaki Nakagawa; Zemin Zhang; Alvis Brazma; Chad J Creighton;
PUBLISHED: 2020, SOURCE: Nature Communications, VOLUME: 11, ISSUE: 1
INDEXED IN: Scopus CrossRef: 40
IN MY: ORCID
27
TITLE: Integrative pathway enrichment analysis of multivariate omics data
AUTHORS: Paczkowska, M; Barenboim, J; Sintupisut, N; Fox, NS; Zhu, H; Abd Rabbo, D; Mee, MW; Boutros, PC; Abascal, F; Amin, SB; Bader, GD; Beroukhim, R; Bertl, J; Boroevich, KA; Brunak, S; Campbell, PJ; Carlevaro Fita, J; Chakravarty, D; Chan, CWY; Chen, K; Choi, JK; Deu Pons, J; Dhingra, P; Diamanti, K; Feuerbach, L; Fink, JL; Fonseca, NA ; Frigola, J; Gambacorti Passerini, C; Garsed, DW; Gerstein, M; Getz, G; Gonzalez Perez, A; Guo, Q; Gut, IG; Haan, D; Hamilton, MP; Haradhvala, NJ; Harmanci, AO; Helmy, M; Herrmann, C; Hess, JM; Hobolth, A; Hodzic, E; Hong, C; Hornshøj, H; Isaev, K; Izarzugaza, JMG; Johnson, R; Johnson, TA; Juul, M; Juul, RI; Kahles, A; Kahraman, A; Kellis, M; Khurana, E; Kim, J; Kim, JK; Kim, Y; Komorowski, J; Korbel, JO; Kumar, S; Lanzós, A; Lawrence, MS; Lee, D; Lehmann, KV; Li, S; Li, X; Lin, Z; Liu, EM; Lochovsky, L; Lou, S; Madsen, T; Marchal, K; Martincorena, I; Martinez Fundichely, A; Maruvka, YE; McGillivray, PD; Meyerson, W; Muiños, F; Mularoni, L; Nakagawa, H; Nielsen, MM; Park, K; Park, K; Pedersen, JS; Pich, O; Pons, T; Pulido Tamayo, S; Raphael, BJ; Reyes Salazar, I; Reyna, MA; Rheinbay, E; Rubin, MA; Rubio Perez, C; Sabarinathan, R; Sahinalp, SC; Saksena, G; Salichos, L; Sander, C; Schumacher, SE; Shackleton, M; Shapira, O; Shen, C; Shrestha, R; Shuai, S; Sidiropoulos, N; Sieverling, L; Sinnott Armstrong, N; Stein, LD; Stuart, JM; Tamborero, D; Tiao, G; Tsunoda, T; Umer, HM; Uusküla Reimand, L; Valencia, A; Vazquez, M; Verbeke, LPC; Wadelius, C; Wadi, L; Wang, J; Warrell, J; Waszak, SM; Weischenfeldt, J; Wheeler, DA; Wu, G; Yu, J; Zhang, J; Zhang, X; Zhang, Y; Zhao, Z; Zou, L; von Mering, C; Reimand, J; ...More
PUBLISHED: 2020, SOURCE: Nature Communications, VOLUME: 11, ISSUE: 1
INDEXED IN: Scopus CrossRef: 115
IN MY: ORCID
28
TITLE: Pan-cancer analysis of whole genomes
AUTHORS: The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, ;
PUBLISHED: 2020, SOURCE: NATURE, VOLUME: 578, ISSUE: 7793
INDEXED IN: Scopus WOS CrossRef: 1831
IN MY: ORCID
29
TITLE: Pathway and network analysis of more than 2500 whole cancer genomes
AUTHORS: Reyna, MA; Haan, D; Paczkowska, M; Verbeke, LPC; Vazquez, M; Kahraman, A; Pulido Tamayo, S; Barenboim, J; Wadi, L; Dhingra, P; Shrestha, R; Getz, G; Lawrence, MS; Pedersen, JS; Rubin, MA; Wheeler, DA; Brunak, S; Izarzugaza, JMG; Khurana, E; Marchal, K; von Mering, C; Sahinalp, SC; Valencia, A; Abascal, F; Amin, SB; Bader, GD; Bandopadhayay, P; Beroukhim, R; Bertl, J; Boroevich, KA; Busanovich, J; Campbell, PJ; Carlevaro Fita, J; Chakravarty, D; Chan, CWY; Chen, K; Choi, JK; Deu Pons, J; Diamanti, K; Feuerbach, L; Fink, JL; Fonseca, NA ; Frigola, J; Gambacorti Passerini, C; Garsed, DW; Gerstein, M; Guo, Q; Gut, IG; Hamilton, MP; Haradhvala, NJ; Harmanci, AO; Helmy, M; Herrmann, C; Hess, JM; Hobolth, A; Hodzic, E; Hong, C; Hornshøj, H; Isaev, K; Johnson, R; Johnson, TA; Juul, M; Juul, RI; Kahles, A; Kellis, M; Kim, J; Kim, JK; Kim, Y; Komorowski, J; Korbel, JO; Kumar, S; Lanzós, A; Larsson, E; Lee, D; Lehmann, KV; Li, S; Li, X; Lin, Z; Liu, EM; Lochovsky, L; Lou, S; Madsen, T; Martincorena, I; Martinez Fundichely, A; Maruvka, YE; McGillivray, PD; Meyerson, W; Muiños, F; Mularoni, L; Nakagawa, H; Nielsen, MM; Park, K; Park, K; Pons, T; Reyes Salazar, I; Rheinbay, E; Rubio Perez, C; Saksena, G; Salichos, L; Sander, C; Schumacher, SE; Shackleton, M; Shapira, O; Shen, C; Shuai, S; Sidiropoulos, N; Sieverling, L; Sinnott Armstrong, N; Stein, LD; Tamborero, D; Tiao, G; Tsunoda, T; Umer, HM; Uusküla Reimand, L; Wadelius, C; Wang, J; Warrell, J; Waszak, SM; Weischenfeldt, J; Wu, G; Yu, J; Zhang, J; Zhang, X; Zhang, Y; Zhao, Z; Zou, L; Reimand, J; Stuart, JM; Raphael, BJ; ...More
PUBLISHED: 2020, SOURCE: Nature Communications, VOLUME: 11, ISSUE: 1
INDEXED IN: Scopus CrossRef: 66
IN MY: ORCID
30
TITLE: Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes (Nature Biotechnology, (2020), 10.1038/s41587-019-0360-3)  Full Text
AUTHORS: Yakneen, S; Waszak, SM; Yakneen, S; Aminou, B; Bartolome, J; Boroevich, KA; Boyce, R; Brooks, AN; Buchanan, A; Buchhalter, I; Butler, AP; Byrne, NJ; Cafferkey, A; Campbell, PJ; Chen, Z; Cho, S; Choi, W; Clapham, P; Davis Dusenbery, BN; De La Vega, FM; Demeulemeester, J; Dow, MT; Dursi, LJ; Eils, J; Eils, R; Ellrott, K; Farcas, C; Favero, F; Fayzullaev, N; Ferretti, V; Flicek, P; Fonseca, NA ; Gelpi, JL; Getz, G; Gibson, B; Grossman, RL; Harismendy, O; Heath, AP; Heinold, MC; Hess, JM; Hofmann, O; Hong, JH; Hudson, TJ; Hutter, B; Hutter, CM; Hübschmann, D; Imoto, S; Ivkovic, S; Jeon, SH; Jiao, W; Jung, J; Kabbe, R; Kahles, A; Kerssemakers, JNA; Kim, HL; Kim, H; Kim, J; Kim, Y; Kleinheinz, K; Koscher, M; Koures, A; Kovacevic, M; Lawerenz, C; Leshchiner, I; Liu, J; Livitz, D; Mihaiescu, GL; Mijalkovic, S; Mijalkovic Lazic, A; Miyano, S; Miyoshi, N; Nahal Bose, HK; Nakagawa, H; Nastic, M; Newhouse, SJ; Nicholson, J; O’Connor, BD; Ocana, D; Ohi, K; Ohno Machado, L; Omberg, L; Ouellette, BFF; Paramasivam, N; Perry, MD; Pihl, TD; Prinz, M; Puiggròs, M; Radovic, P; Raine, KM; Rheinbay, E; Rosenberg, M; Royo, R; Rätsch, G; Saksena, G; Schlesner, M; Shorser, SI; Short, C; Sofia, HJ; Spring, J; Stein, LD; Struck, AJ; Tiao, G; Tijanic, N; Torrents, D; Van Loo, P; Vazquez, M; Vicente, D; Wala, JA; Wang, Z; Waszak, SM; Weischenfeldt, J; Werner, J; Williams, A; Woo, Y; Wright, AJ; Xiang, Q; Yang, L; Yuen, D; Yung, CK; Zhang, J; Korbel, JO; Gertz, M; Korbel, JO; ...More
PUBLISHED: 2020, SOURCE: Nature Biotechnology
INDEXED IN: Scopus CrossRef
IN MY: ORCID
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