* - equal contribution
# - correspondence

• Carbonell Sala S*, Uszczyńska-Ratajczak B*, Lagarde J, Johnson R#, Guigó R#. Annotation of Full-length Long Noncoding RNAs with Capture Long-Read Sequencing, Methods Mol Biol., 2021, 2254, 133-159.
  
  
• Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P#. GENCODE 2021, Nucleic Acids Res, 2021, 49(D1), D916-D923.
  
  
• De Palma FDE*, Del Monaco V*, Pol JG*, Kremer M, D'Argenio V, Stoll G, Montanaro D, Uszczyńska-Ratajczak B, Klein CC, Vlasova A, Botti G, D'Aiuto M, Baldi A, Guigó R, Kroemer G, Maiuri MC#, Salvatore F#, Deregulation of LINC01087 decodes the heterogeneity of breast cancer segregating luminal from triple-negative patients and predicting their clinical outcome, Pharmacol Res, 2020, 161, 105249.
  
  
• ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM#, Myers RM#, Ren B#, Graveley BR#, Gerstein MB#, Pennacchio LA#, Snyder MP#, Bernstein BE#, Wold B#, Hardison RC#, Gingeras TR#, Stamatoyannopoulos JA#, Weng Z#, Expanded Encyclopedias of DNA Elements in the Human and Mouse Genome, Nature, 2020, 699-710.
  
  
• ENCODE Project Consortium, Snyder MP#, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM, Perspectives on ENCODE, Nature, 2020, 583(7818), 693-698.
  
  
• Steward CA*#, Roovers J*, Suner MM, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D, Fitzgerald S, Viola M, Stamberger H, Hamdan FF, Ceulemans B, Leroy P, Nava C, Lepine A, Tapanari E, Keiller D, Abbs S, Sanchis-Juan A, Grozeva D, Rogers AS, Diekhans M, Guigó R, Petryszak R, Minassian BA, Cavalleri G, Vitsios D, Petrovski S, Harrow J, Flicek P, Lucy Raymond F, Lench NJ, Jonghe P, Mudge JM, Weckhuysen S, Sisodiya SM, Frankish A#, Re-annotation of 191 developmental and epileptic encephalopathy associated genes unmasks de novo variants in SCN1A, NPJ Genomic Medicine, 2019, 4(31).
  
  
• Topf U*#, Uszczynska-Ratajczak B*, Chacinska A#, Mitochondrial stress-dependent regulation of cellular protein synthesis, Journal of Cell Science, 2019, 132(8).
  
  
• Sokol AM#*, Uszczynska-Ratajczak B*, Collins MM, Bazala M, Topf U, Lundegaard PR, Sugunan S, Guenther S, Kuenne C, Graumann J, Chan SSL, Stainier DYR, Chacinska A#, Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish, PLoS Genetics, 2019, 14(11), e1007743.
  
  
• Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P#, GENCODE reference annotation for the human and mouse genomes, Nucleic Acids Research, 2019, 47(D1):D766-D773.
  
  
• Barbara Uszczynska-Ratajczak, Julien Lagarde, Adam Frankish, Roderic Guigó and Rory Johnson#, Towards a complete map of the human long non-coding RNA transcriptome, Nature Reviews Genetics, 2018, 19(9), 535-548.
  
  
• Luiza Handschuh#, Maciej Kazmierczak, Marek C. Milewski, Michal Góralski, Magdalena Luczak, Marzena Wojtaszewska, Barbara Uszczynska-Ratajczak, Krzysztof Lewandowski, Mieczyslaw Komarnicki, Marek Figlerowicz, Gene expression profiling of acute myeloid leukemia samples from adult patients with AML-M1 and -M2 through boutique microarrays, real-time PCR and droplet digital PCR, International Journal of Oncology, 2018, 52(3), 656-678.
  
  
• Julien Lagarde*, Barbara Uszczynska-Ratajczak*, Silvia Carbonell, Silvia Perez-Lluch, Amaya Abad, Carrie Davis, Thomas Gingeras, Adam Frankish, Jennifer Harrow, Roderic Guigó#, Rory Johnson# High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing, Nature Genetics, 2017, 49(12), 1731-1740.
  
  
• Francisco Altimiras*, Barbara Uszczynska-Ratajczak*, Rolf Biekofsky, Anna Vlasova, Emilio Palumbo, Francisco Camara, Robert Deacon, Roderic Guigó and Patricia Cogram#, Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease, Frontiers in Aging Neuroscience, 2017 9, 64.
  
  
• Julien Lagarde*, Barbara Uszczynska-Ratajczak*, Javier Santoyo-Lopez, Jose Manuel Gonzalez, Electra Tapanari, Jonathan M. Mudge, Charlie Steward, Laurens Wilming, Andrea Tanzer, Cédric Howald, Jacqueline Chrast, Alicia Vela-Boza, Antonio Rueda, Francisco J. Lopez-Domingo, Joaquin Dopazo, Alexandre Reymond, Roderic Guigó# & Jennifer Harrow#, Extension of human lncRNA transcripts by RACE coupled with long read high-throughput sequencing (RACE-Seq) Nature Communications, 2016, 17(7), 12339.
  
  
• Adam Frankish#, Barbara Uszczynska, Graham R.S. Ritchie, Jose Manuel Gonzalez, Dmitri Pervouchine, Robert Petryszak, Jonathan M. Mudge, Nuno Fonseca, Alvis Brazma, Roderic Guigo, Jennifer Harrow#, Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction, BMC Genomics, 2015, Suppl 8:S2.