Publications

“Either write something worth reading or do something worth reading” – Benjamin Franklin

Table of Contents

2021

  • Silva AP, Almeida ARM, Cachucho A, Neto JL, Demeyer S, Ramos de Matos M, Hogan T, Li Y, Meijerink JP, Cools J, Grosso AR, Seddon B, Barata JT. (2021) Overexpression of wild type IL-7Rα promotes T-cell acute lymphoblastic leukemia/lymphoma, Blood, URL
  • Andrade J, Shi C, Costa ASH, Choi J, Kim J, Doddaballapur A, Sugino T, Ong YT, Castro M, Zimmermann B, Kaulich M, Guenther S, Wilhelm K, Kubota Y, Braun T, Koh GY, Grosso AR, Frezza C, Potente M. (2021) Control of endothelial quiescence by FOXO-regulated metabolites, Nature Cell Biology, 23(4):413-423. URL 
  • Povoa V, Almeida CR, Maia-Gil M, Sobral D, Domingues M, Martinez-Lopez M, Fuzeta MA, Silva C, Grosso AR, Fior R (2021) Innate immune evasion revealed in a colorectal zebrafish xenograft model, Nature Communications, 12(1156).  URL
  • Singh S, Thompson JA, Yilmaz B, Li H, Weis S, Sobral D, Truglio M, et al. (2021) Loss of a-gal during primate evolution enhanced antibody-effector function and resistance to bacterial sepsis. Cell Host & Microbe. URL 
  • Rodrigo AP, Grosso AR, Baptista PV, Fernandes AR, Costa PM (2021) A Transcriptomic Approach to the Recruitment of Venom Proteins in a Marine Annelid, Toxins, 13(2):97.  URL
  • Rodrigo AP, Mendes VM, Manadas B, Grosso AR, Matos APA, Baptista PV, Costa PM, Fernandes AR (2021) Specific Antiproliferative Properties of Proteinaceous Toxin Secretions from the Marine Annelid Eulalia sp. onto Ovarian Cancer Cells, Marine Drugs, 19(1):31.  URL

2020

  • Francisco R, Pascoa C, Marques-da-Silva D, Brasil S, Pimentel-Santos FM, Altassan R, Jaeken J, Grosso AR, Ferreira VR, Videira PA (2020) New Insights into Immunological Involvement in Congenital Disorders of Glycosylation (CDG) from a People-Centric Approach, Journal of Clinical Medicine, 9(7).  URL
  • Prudêncio P, Rebelo K, Grosso AR, Martinho RG, Carmo-Fonseca M (2020) Analysis of Mammalian Native Elongating Transcript sequencing (mNET-seq) high-throughput data, Methods, S1046-2023(18)30484-5. URL
  • Dias A, Lozovska A, Wymeersch FJ, Nóvoa A, Binagui-Casas A, Sobral D, Martins GG, Wilson V, Mallo M (2020) A Tgfbr1/Snai1-dependent developmental module at the core of vertebrate axial elongation. eLife. URL
  • Pjeta R, Lindner H, Kremser L, Salvenmoser W, Sobral D, Ladurner P, Santos R. (2020) Integrative Transcriptome and Proteome Analysis of the Tube Foot and Adhesive Secretions of the Sea Urchin Paracentrotus lividus. International Journal of Molecular Sciences. URL

2019

  • Cunha M, Martins C, Grosso AR, Costa PM. (2019) Mytilus galloprovincialis CYP1A-like mRNAs reveal closer proximity of mytilid CYP1A to the eumetazoan CYP2 familyAquat Toxicol., 214:105260. URL
  • Matos MR, Posa I, Carvalho FS, Morais VA, Grosso AR, de Almeida SF. (2019) A Systematic Pan-Cancer Analysis of Genetic Heterogeneity Reveals Associations with Epigenetic Modifiers. Cancers, 11 (3). URL
  • Vítor AC, Sridhara SC, Sabino JC, Afonso AI, Grosso AR, Martin RM and de Almeida SF (2019) Single-molecule imaging of transcription at damaged chromatinScience Advances; Vol. 5, no. 1, eaau1249. URL

2018

  • Nojima T, Rebelo K, Gomes T, Grosso AR, Proudfoot NJ, Carmo-Fonseca M. (2018) RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing. Molecular Cell; 72(2):369-79. URL

2017

  • Bonnet A, Grosso AR, Elkaoutari A, Coleno E, Presle A, Sridhara SC, Janbon G, Geli V, de Almeida SF, Palancade B. (2017) Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability. Molecular Cell. 67(4):1-14. URL
  • Mancio-Silva L, Slavic K, Ruivo MG, Grosso AR, Modrzynska KK, Vera IM, Sales-dias J, Gomes AR, Macpherson CR, Crozet P, Adamo M, Baena-gonzalez E, Tewari R, Llinás M, Billker O, Mota MM. (2017) Nutrient sensing modulates malaria parasite virulence. Nature. 547(7662):213-216 URL
  • Sridhara SC, Carvalho S, Grosso AR, Marcela L, Carmo-fonseca M, de Almeida SF. (2017) Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phohsphorylation. Cell Reports. 18(2):334-43. URL

2016

  • Posa I, Carvalho S, Tavares J, Grosso AR. (2016) A pan-cancer analysis of MYC-PVT1 reveals CNV-unmediated deregulation and poor prognosis in renal carcinoma.Oncotarget. 7(30):47033-47041. URL
  • Muñoz-ruiz M, Ribot JC, Grosso AR, Gonçalves-sousa N, Pamplona A, Pennington DJ, Regueiro JR, Fernández-malavé E, Silva-santos B. (2016) TCR signal strength controls thymic differentiation of discrete proinflammatory γδT cell subsets. Nature immunology. 17(6):721-727. URL
  • Zerbino, DR; Johnson, N; Juetteman, T; Sheppard, D; Wilder, SP; Lavidas, I; Nuhn, M; Perry, E; Raffaillac-Desfosses, Q; Sobral, D; Keefe, D; Gräf, S; Ahmed, I; Kinsella, R; Pritchard, B; Brent, S; Amode, R; Parker, A; Trevanion, S; Birney, E; Dunham, I; Flicek, P. (2016). Ensembl regulation resources. JOURNAL OF DATABASE MANAGEMENT. URL
  • Passagem-Santos, D; Bonnet, M; Sobral, D; Trancoso, I; Silva, JG; Barreto, VM; Athanasiadis, A; Demengeot, J; Pereira-Leal, JB. 2016. RAG Recombinase as a Selective Pressure for Genome Evolution. Genome Biology and Evolution, 8(11). URL
  • Jesus T , Grosso AR, Almeida-Val VM, Coelho MM. (2016) Transcriptome profiling of two Iberian freshwater fish exposed to thermal stress. Journal of Thermal Biology. 2016;55:54-61. URL

2015

  • Nojima T, Gomes T, Grosso AR, Kimura H, Dye M , Dhir S, Carmo-fonseca M, Proudfoot N . (2015) Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing. Cell. 2015;161:526-40. URL
  • Veigas B, Pedrosa P, Carlos FF, Mancio-Silva L, Grosso AR, Fortunato E, Mota MM, Baptista PV. (2015) One nanoprobe, two pathogens: gold nanoprobes multiplexing for point-of-care. Journal of Nanobiotechnology. 2015;13:48. URL
  • Grosso AR, Leite AP, Carvalho S, Matos MR, Martins FB, Vítor AC, Desterro JM, Carmo-fonseca M, de Almeida SF. (2015) Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma. eLife. 2015;4:e09214. URL


Older Publications

2014

  • Dourado CG, Duarte MA, Grosso AR, Bastos-Silveira C, Marrero P, Oliveira P, Paulo OS, Dias D. (2014) Phylogenetic origin of the endemic pigeons from Madeira (Columba trocaz) and Azores Islands (Columba palumbus azorica). Journal of Ornithology. 2014;155:71-82.
  • Barroso-Batista, J; Sousa, A; Lourenço, M; Bergman, M-L; Sobral, D; Demengeot, J; Xavier, KB; Gordo, I. (2014). The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps. PLoS Genetics, 10(3). URL
  • Guilgur, LG; Prudêncio, P; Sobral, D; Liszekova, D; Rosa, A; Martinho, RG. (2014). Requirement for highly efficient pre-mRNA splicing during Drosophila early embryonic development. eLife, 2014(3), URL

2013

  • Schmolka N, Serre K, Grosso AR, Rei M, Pennington DJ, Gomes AQ, Silva-santos B. (2013) Epigenetic and transcriptional signatures of stable versus plastic differentiation of proinflammatory γδT cell subsets. Nature immunology. 14:1093-100. URL
  • Rodrigues R, Grosso AR, Moita L. (2013) Genome-wide analysis of alternative splicing during dendritic cell response to a bacterial challenge. PloS one. 8:e61975. URL
  • Carvalho S, Raposo AC, Martins FB, Grosso AR, Sridhara SC, Rino J, Carmo-fonseca M, de Almeida SF. (2013) Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription. Nucleic acids research. 41:2881-93. URL
  • Lanca T, Costa MF, Goncalves-Sousa N, Rei M, Grosso AR, Penido C, Silva-Santos B. (2013) Protective role of the inflammatory CCR2/CCL2 chemokine pathway through recruitment of type 1 cytotoxic γδ T lymphocytes to tumor beds. J Immunol. 190:6673-80. URL
  • Flicek, P. and Ahmed, I. and Amode, M. R. and Barrell, D. and Beal, K. and Brent, S. and Carvalho-Silva, D. and Clapham, P. and Coates, G. and Fairley, S. and Fitzgerald, S. and Gil, L. and Garcia-Giron, C. and Gordon, L. and Hourlier, T. and Hunt, S. and Juettemann, T. and Kahari, A. K. and Keenan, S. and Komorowska, M. and Kulesha, E. and Longden, I. and Maurel, T. and McLaren, W. M. and Muffato, M. and Nag, R. and Overduin, B. and Pignatelli, M. and Pritchard, B. and Pritchard, E. and Riat, H. S. and Ritchie, G. R. and Ruffier, M. and Schuster, M. and Sheppard, D. and Sobral, D. and Taylor, K. and Thormann, A. and Trevanion, S. and White, S. and Wilder, S. P. and Aken, B. L. and Birney, E. and Cunningham, F. and Dunham, I. and Harrow, J. and Herrero, J. and Hubbard, T. J. and Johnson, N. and Kinsella, R. and Parker, A. and Spudich, G. and Yates, A. and Zadissa, A. and Searle, S. M.. (2013). Ensembl 2013. NUCLEIC ACIDS RESEARCH, 41(Database issue)

2012

  • Grosso AR, de Almeida SF, Braga J, Carmo-fonseca M (2012) Dynamic transitions in RNA polymerase II density profiles during transcription termination. Genome research. 22:1447-56. URL
  • Dunham, I; Kundaje, A; Aldred, SF; Collins, PJ; Davis, CA; Doyle, F; Epstein, CB; Frietze, S; Harrow, J; Kaul, R; Khatun, J; Lajoie, BR; Landt, SG; Lee, B-K; Pauli, F; Rosenbloom, KR; Sabo, P; Safi, A; Sanyal, A; Shoresh, N; Simon, JM; Song, L; Trinklein, ND; Altshuler, RC; Birney, E; Brown, JB; Cheng, C; Djebali, S; Dong, X; Ernst, J; Furey, TS; Gerstein, M; Giardine, B; Greven, M; Hardison, RC; Harris, RS; Herrero, J; Hoffman, MM; Iyer, S; Kellis, M; Kheradpour, P; Lassmann, T; Li, Q; Lin, X; Marinov, GK; Merkel, A; Mortazavi, A; Parker, SCJ; Reddy, TE; Rozowsky, J; Schlesinger, F; Thurman, RE; Wang, J; Ward, LD; Whitfield, TW; Wilder, SP; Wu, W; Xi, HS; Yip, KY; Zhuang, J; Bernstein, BE; Green, ED; Gunter, C; Snyder, M; Pazin, MJ; Lowdon, RF; Dillon, LAL; Adams, LB; Kelly, CJ; Zhang, J; Wexler, JR; Good, PJ; Feingold, EA; Crawford, GE; Dekker, J; Elnitski, L; Farnham, PJ; Giddings, MC; Gingeras, TR; Guigó, R; Hubbard, TJ; Kent, WJ; Lieb, JD; Margulies, EH; Myers, RM; Stamatoyannopoulos, JA; Tenenbaum, SA; Weng, Z; White, KP; Wold, B; Yu, Y; Wrobel, J; Risk, BA; Gunawardena, HP; Kuiper, HC; Maier, CW; Xie, L; Chen, X; Mikkelsen, TS; Gillespie, S; Goren, A; Ram, O; Zhang, X; Wang, L; Issner, R; Coyne, MJ; Durham, T; Ku, M; Truong, T; Eaton, ML; Dobin, A; Tanzer, A; Lagarde, J; Lin, W; Xue, C; Williams, BA; Zaleski, C; Röder, M; Kokocinski, F; Abdelhamid, RF; Alioto, T; Antoshechkin, I; Baer, MT; Batut, P; Bell, I; Bell, K; Chakrabortty, S; Chrast, J; Curado, J; Derrien, T; Drenkow, J; Dumais, E; Dumais, J; Duttagupta, R; Fastuca, M; Fejes-Toth, K; Ferreira, P; Foissac, S; Fullwood, MJ; Gao, H; Gonzalez, D; Gordon, A; Howald, C; Jha, S; Johnson, R; Kapranov, P; King, B; Kingswood, C; Li, G; Luo, OJ; Park, E; Preall, JB; Presaud, K; Ribeca, P; Robyr, D; Ruan, X; Sammeth, M; Sandhu, KS; Schaeffer, L; See, L-H; Shahab, A; Skancke, J; Suzuki, AM; Takahashi, H; Tilgner, H; Trout, D; Walters, N; Wang, H; Hayashizaki, Y; Reymond, A; Antonarakis, SE; Hannon, GJ; Ruan, Y; Carninci, P; Sloan, CA; Learned, K; Malladi, VS; Wong, MC; Barber, GP; Cline, MS; Dreszer, TR; Heitner, SG; Karolchik, D; Kirkup, VM; Meyer, LR; Long, JC; Maddren, M; Raney, BJ; Grasfeder, LL; Giresi, PG; Battenhouse, A; Sheffield, NC; Showers, KA; London, D; Bhinge, AA; Shestak, C; Schaner, MR; Kim, SK; Zhang, ZZ; Mieczkowski, PA; Mieczkowska, JO; Liu, Z; McDaniell, RM; Ni, Y; Rashid, NU; Kim, MJ; Adar, S; Zhang, Z; Wang, T; Winter, D; Keefe, D; Iyer, VR; Zheng, M; Wang, P; Gertz, J; Vielmetter, J; Partridge, EC; Varley, KE; Gasper, C; Bansal, A; Pepke, S; Jain, P; Amrhein, H; Bowling, KM; Anaya, M; Cross, MK; Muratet, MA; Newberry, KM; McCue, K; Nesmith, AS; Fisher-Aylor, KI; Pusey, B; DeSalvo, G; Parker, SL; Balasubramanian, S; Davis, NS; Meadows, SK; Eggleston, T; Newberry, JS; Levy, SE; Absher, DM; Wong, WH; Blow, MJ; Visel, A; Pennachio, LA; Petrykowska, HM; Abyzov, A; Aken, B; Barrell, D; Barson, G; Berry, A; Bignell, A; Boychenko, V; Bussotti, G; Davidson, C; Despacio-Reyes, G; Diekhans, M; Ezkurdia, I; Frankish, A; Gilbert, J; Gonzalez, JM; Griffiths, E; Harte, R; Hendrix, DA; Hunt, T; Jungreis, I; Kay, M; Khurana, E; Leng, J; Lin, MF; Loveland, J; Lu, Z; Manthravadi, D; Mariotti, M; Mudge, J; Mukherjee, G; Notredame, C; Pei, B; Rodriguez, JM; Saunders, G; Sboner, A; Searle, S; Sisu, C; Snow, C; Steward, C; Tapanari, E; Tress, ML; Van Baren, MJ; Washietl, S; Wilming, L; Zadissa, A; Zhang, Z; Brent, M; Haussler, D; Valencia, A; Addleman, N; Alexander, RP; Auerbach, RK; Balasubramanian, S; Bettinger, K; Bhardwaj, N; Boyle, AP; Cao, AR; Cayting, P; Charos, A; Cheng, Y; Eastman, C; Euskirchen, G; Fleming, JD; Grubert, F; Habegger, L; Hariharan, M; Harmanci, A; Iyengar, S; Jin, VX; Karczewski, KJ; Kasowski, M; Lacroute, P; Lam, H; Lamarre-Vincent, N; Lian, J; Lindahl-Allen, M; Min, R; Miotto, B; Monahan, H; Moqtaderi, Z; Mu, XJ; O'Geen, H; Ouyang, Z; Patacsil, D; Raha, D; Ramirez, L; Reed, B; Shi, M; Slifer, T; Witt, H; Wu, L; Xu, X; Yan, K-K; Yang, X; Struhl, K; Weissman, SM; Penalva, LO; Karmakar, S; Bhanvadia, RR; Choudhury, A; Domanus, M; Ma, L; Moran, J; Victorsen, A; Auer, T; Centanin, L; Eichenlaub, M; Gruhl, F; Heermann, S; Hoeckendorf, B; Inoue, D; Kellner, T; Kirchmaier, S; Mueller, C; Reinhardt, R; Schertel, L; Schneider, S; Sinn, R; Wittbrodt, B; Wittbrodt, J; Jain, G; Balasundaram, G; Bates, DL; Byron, R; Canfield, TK; Diegel, MJ; Dunn, D; Ebersol, AK; Frum, T; Garg, K; Gist, E; Hansen, RS; Boatman, L; Haugen, E; Humbert, R; Johnson, AK; Johnson, EM; Kutyavin, TV; Lee, K; Lotakis, D; Maurano, MT; Neph, SJ; Neri, FV; Nguyen, ED; Qu, H; Reynolds, AP; Roach, V; Rynes, E; Sanchez, ME; Sandstrom, RS; Shafer, AO; Stergachis, AB; Thomas, S; Vernot, B; Vierstra, J; Vong, S; Wang, H; Weaver, MA; Yan, Y; Zhang, M; Akey, JM; Bender, M; Dorschner, MO; Groudine, M; MacCoss, MJ; Navas, P; Stamatoyannopoulos, G; Beal, K; Brazma, A; Flicek, P; Johnson, N; Lukk, M; Luscombe, NM; Sobral, D; Vaquerizas, JM; Batzoglou, S; Sidow, A; Hussami, N; Kyriazopoulou-Panagiotopoulou, S; Libbrecht, MW; Schaub, MA; Miller, W; Bickel, PJ; Banfai, B; Boley, NP; Huang, H; Li, JJ; Noble, WS; Bilmes, JA; Buske, OJ; Sahu, AD; Kharchenko, PV; Park, PJ; Baker, D; Taylor, J; Lochovsky, L. (2012). An integrated encyclopedia of DNA elements in the human genome. NATURE, 489(7414). URL

2011

  • de Almeida SF, Grosso AR, Koch F, Fenouil R, Carvalho S, Andrade J, Levezinho H, Gut M, Eick D, Gut I, Andrau J-, Ferrier P, Carmo-fonseca M. (2011) Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nature structural & molecular biology. 2011;18:977-83. URL

2010

  • Tassy, O; Dauga, D; Daian, F; Sobral, D; Robin, F; Khoueiry, P; Salgado, D; Fox, V; Caillol, D; Schiappa, R; Laporte, B; Rios, A; Luxardi, G; Kusakabe, T; Joly, J-S; Darras, S; Christiaen, L; Contensin, M; Auger, H; Lamy, C; Hudson, C; Rothbächer, U; Gilchrist, MJ; Makabe, KW; Hotta, K; Fujiwara, S; Satoh, N; Satou, Y; Lemaire, P. (2010). The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program. GENOME RESEARCH, 20(10). URL
  • Gomes AQ, Correia DV, Grosso AR, Lança T, Ferreira C, Lacerda JF, Barata JT, da Silva MG, Silva-santos B. (2010) Identification of a panel of ten cell surface protein antigens associated with immunotargeting of leukemias and lymphomas by peripheral blood γδT cells. Haematologica. 95:1397-404. URL
  • Mollet IG, Ben-Dov C, Felício-Silva D, Grosso AR, Eleutério P, Alves R, Staller R, Silva TS, Carmo-fonseca M. (2010) Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome. Nucleic Acids Research. 38:4740-54. URL

2009

  • Sobral, D; Tassy, O; Lemaire, P. (2009). Highly Divergent Gene Expression Programs Can Lead to Similar Chordate Larval Body Plans. CURRENT BIOLOGY, 19(23), URL
  • Correia DV, D'Orey F, Cardoso BA, Lança T, Grosso AR, DeBarros A, Martins LR, Barata JT, Silva-santos B. (2009) Highly active microbial phosphoantigen induces rapid yet sustained MEK/Erk- and PI-3K/Akt-mediated signal transduction in anti-tumor human gammadelta T-cells. PloS one. 4:e5657.  URL
  • Albuquerque SS, Carret C, Grosso AR, Tarun AS, Peng X, Kappe SH, Prudêncio M, Mota MM. (2009) Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events. BMC Genomics. 10:270. URL

2008

  • Abrantes P, Dimopoulos G, Grosso AR, do Rosário VE, Silveira H. (2008) Chloroquine mediated modulation of Anopheles gambiae gene expression. PloS one. 3:e2587. URL
  • Grosso AR, Martins S, Carmo-fonseca M. (2008) The emerging role of splicing factors in cancer. EMBO Rep. 9:1087-93. URL
  • Grosso AR, Gomes AQ, Barbosa-Morais NL, Caldeira S, Thorne NP, Grech G, von Lindern M, Carmo-fonseca M. (2008) Tissue-specific splicing factor gene expression signatures. Nucl. Acids Res. 36:4823-32. URL