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Nucleic Acids Research, 0305-1048

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  1. The phase separation-dependent FUS interactome reveals nuclear and cytoplasmic function of liquid-liquid phase separation

    Reber, S., Jutzi, D., Lindsay, H., Devoy, A., Mechtersheimer, J., Levone, B. R., Domanski, M., Bentmann, E., Dormann, D., Mühlemann, O., Barabino, S. M. L. & Ruepp, M-D., 21 Jul 2021, In: Nucleic Acids Research. 49, 13, p. 7713-7731 19 p.

    Research output: Contribution to journalArticlepeer-review

  2. INetModels 2.0: An interactive visualization and database of multi-omics data

    Arif, M., Zhang, C., Li, X., Güngör, C., Çakmak, B., Arslantürk, M., Tebani, A., Özcan, B., Subaş, O., Zhou, W., Piening, B., Turkez, H., Fagerberg, L., Price, N., Hood, L., Snyder, M., Nielsen, J., Uhlen, M. & Mardinoglu, A., 2 Jul 2021, In: Nucleic Acids Research. 49, W1, p. W271-W276

    Research output: Contribution to journalArticlepeer-review

  3. DGLinker: flexible knowledge-graph prediction of disease-gene associations

    Iacoangeli, A., 7 May 2021, (Accepted/In press) In: Nucleic Acids Research.

    Research output: Contribution to journalArticlepeer-review

  4. GENCODE 2021

    Frankish, A., Diekhans, M., Jungreis, I., Lagarde, J., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Armstrong, J., Barnes, I., Berry, A., Bignell, A., Boix, C., Sala, S. C., Cunningham, F., Domenico, T. D., Donaldson, S., Fiddes, I. T., Girón, C. G., Gonzalez, J. M. & 36 others, Grego, T., Hardy, M., Hourlier, T., Howe, K. L., Hunt, T., Izuogu, O. G., Johnson, R., Martin, F. J., Martínez, L., Mohanan, S., Muir, P., Navarro, F. C. P., Parker, A., Pei, B., Pozo, F., Riera, F. C., Ruffier, M., Schmitt, B. M., Stapleton, E., Suner, M. M., Sycheva, I., Uszczynska-Ratajczak, B., Wolf, M. Y., Xu, J., Yang, Y. T., Yates, A., Zerbino, D., Zhang, Y., Choudhary, J. S., Gerstein, M., Guigó, R., Hubbard, T. J. P., Kellis, M., Paten, B., Tress, M. L. & Flicek, P., 8 Jan 2021, In: Nucleic Acids Research. 49, D1, p. D916-D923

    Research output: Contribution to journalArticlepeer-review

  5. Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing

    Amante, S., Montibus, B., Cowley, M., Barkas, N., Setiadi, J., Saadeh, H., Giemza, J., Contreras Castillo, S., Fleischanderl, K., Schulz, R. & Oakey, R., 4 Sep 2020, In: Nucleic Acids Research. 48, 15, p. 8349-8359 11 p.

    Research output: Contribution to journalArticlepeer-review

  6. FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention

    Humphrey, J., Birsa, N., Milioto, C., McLaughlin, M., Ule, A. M., Robaldo, D., Eberle, A. B., Kräuchi, R., Bentham, M., Brown, A-L., Jarvis, S., Bodo, C., Garone, M. G., Devoy, A., Soraru, G., Rosa, A., Bozzoni, I., Fisher, E. M. C., Mühlemann, O., Schiavo, G. & 4 others, Ruepp, M-D., Isaacs, A. M., Plagnol, V. & Fratta, P., 9 Jul 2020, In: Nucleic Acids Research. 48, 12, p. 6889-6905 17 p.

    Research output: Contribution to journalArticlepeer-review

  7. PDBE-KB: A community-driven resource for structural and functional annotations

    PDBe-KB consortium , 1 Jan 2020, In: Nucleic Acids Research. 48, p. D344-D353

    Research output: Contribution to journalArticlepeer-review

  8. Chromatin condensation fluctuations rather than steady-state predict chromatin accessibility

    Auduge, N., Padilla-Parra, S., Tramier, M., Borghi, N. & Coppey-Moisan, M., 9 Jul 2019, In: Nucleic Acids Research. 47, 12, p. 6184-6194

    Research output: Contribution to journalArticlepeer-review

  9. GENCODE reference annotation for the human and mouse genomes

    Frankish, A., Diekhans, M., Ferreira, A. M., Johnson, R., Jungreis, I., Loveland, J., Mudge, J. M., 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, I. T., García Girón, C. & 35 others, Gonzalez, J. M., Grego, T., Hardy, M., Hourlier, T., Hunt, T., Izuogu, O. G., Lagarde, J., Martin, F. J., Martínez, L., Mohanan, S., Muir, P., Navarro, F. C. P., Parker, A., Pei, B., Pozo, F., Ruffier, M., Schmitt, B. M., Stapleton, E., Suner, M. M., Sycheva, I., Uszczynska-Ratajczak, B., Xu, J., Yates, A., Zerbino, D., Zhang, Y., Aken, B., Choudhary, J. S., Gerstein, M., Guigó, R., Hubbard, T. J. P., Kellis, M., Paten, B., Reymond, A., Tress, M. L. & Flicek, P., 8 Jan 2019, In: Nucleic Acids Research. 47, D1, p. D766-D773

    Research output: Contribution to journalArticlepeer-review

  10. TCSBN: a database of tissue and cancer specific biological networks

    Lee, S., Zhang, C., Arif, M., Liu, Z., Benfeitas, R., Bidkhori, G., Deshmukh, S., Al Shobky, M., Lovric, A., Boren, J., Nielsen, J., Uhlen, M. & Mardinoglu, A., 4 Jan 2018, In: Nucleic Acids Research. 46, D1, p. D595-D600

    Research output: Contribution to journalArticlepeer-review

  11. BRepertoire: a user-friendly web server for analysing antibody repertoire data.

    Margreitter, C., Lu, H-C., Townsend, C. L., Stewart, A., Dunn-Walters, D. K. & Fraternali, F., 2018, In: Nucleic Acids Research. doi: 10.1093/nar/gky276.

    Research output: Contribution to journalArticlepeer-review

  12. A mechanism underlying position-specific regulation of alternative splicing

    Hamid, F. M. & Makeyev, E. V., 1 Dec 2017, In: Nucleic Acids Research. 45, 21, p. 12455-12468 14 p.

    Research output: Contribution to journalArticlepeer-review

  13. Mechanistic insight into the assembly of the HerA-NurA helicase-nuclease DNA end resection complex

    Ahdash, Z., Lau, A. M., Byrne, R. T., Lammens, K., Stüetzer, A., Urlaub, H., Booth, P. J., Reading, E., Hopfner, K. P. & Politis, A., 16 Nov 2017, In: Nucleic Acids Research. 45, 20, p. 12025-12038 14 p.

    Research output: Contribution to journalArticlepeer-review

  14. An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion

    Collins, K. M., Kainov, Y. A., Christodolou, E., Ray, D., Morris, Q., Hughes, T., Taylor, I. A., Makeyev, E. V. & Ramos, A., 20 Jun 2017, In: Nucleic Acids Research. 45, 11, p. 6761-6774 14 p.

    Research output: Contribution to journalArticlepeer-review

  15. Modulation of nonsense mediated decay by rapamycin

    Martinez Nunez, R. T., Wallace, A., Coyne, D., Bailey, J., Jansson, L., Ennajdaoui, H., Rush, M., Deinhardt, K., Sanchez-Elsner, T. & Sanford, J., 7 Apr 2017, In: Nucleic Acids Research. 45, 6, p. 3448–3459

    Research output: Contribution to journalArticlepeer-review

  16. Nuclear poly(A)-binding protein aggregates misplace a pre-mRNA outside of SC35 speckle causing its abnormal splicing

    Klein, P., Oloko, M., Roth, F., Montel, V., Malerba, A., Jarmin, S., Gidaro, T., Popplewell, L., Perie, S., St Guily, J. L., De La Grange, P., Antoniou, M. N., Dickson, G., Butler-Browne, G., Bastide, B., Mouly, V. & Trollet, C., 1 Dec 2016, In: Nucleic Acids Research. 44, 22, p. 10929-10945 17 p.

    Research output: Contribution to journalArticlepeer-review

  17. Deciphering the mechanisms of developmental disorders: Phenotype analysis of embryos from mutant mouse lines

    Wilson, R., McGuire, C., Mohun, T., Adams, D., Baldock, R., Bhattacharya, S., Collins, J., Fineberg, E., Firminger, L., Galli, A., Geyer, S., Grifiths, M., Hassan, A., Hemberger, M., Houart, C., Melvin, D., Prin, F., Ramirez-Solis, R., Reissig, L., Robertson, E. & 8 others, Rose, J., Schneider, J., Smith, J., Szumska, D., Tudor, C., Vernet, A., Weninger, W. & White, J., 11 Aug 2016, In: Nucleic Acids Research. 44, D1, p. D855-D861

    Research output: Contribution to journalArticlepeer-review

  18. Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis

    Lee, S., Mardinoglu, A., Zhang, C., Lee, D. & Nielsen, J., 8 Jul 2016, In: Nucleic Acids Research. 44, 12, p. 5529-5539

    Research output: Contribution to journalArticlepeer-review

  19. iGEMS: An integrated model for identification of alternative exon usage events

    Sood, S., Szkop, K. J., Nakhuda, A., Gallagher, I. J., Murie, C., Brogan, R. J., Kaprio, J., Kainulainen, H., Atherton, P. J., Kujala, U. M., Gustafsson, T., Larsson, O. & Timmons, J. A., 20 Jun 2016, In: Nucleic Acids Research. 44, 11, e109.

    Research output: Contribution to journalArticlepeer-review

  20. RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth.

    Gunnell, A., Webb, H. M., Wood, C. D., McClellan, M. J., Wichaidit, B., Kempkes, B., Jenner, R. G., Osborne, C., Farrell, P. J. & West, M. J., 2 Jun 2016, In: Nucleic Acids Research. 44, 10, p. 4636-4650 15 p.

    Research output: Contribution to journalArticlepeer-review

  21. NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings

    An, O., Dall'Olio, G. M., Mourikis, T. P. & Ciccarelli, F., 4 Jan 2016, In: Nucleic Acids Research. 44, D1, p. D992–D999

    Research output: Contribution to journalArticlepeer-review

  22. PepComposer: computational design of peptides binding to a given protein surface

    Iacoangeli, A., 2016, In: Nucleic Acids Research.

    Research output: Contribution to journalArticlepeer-review

  23. U1 snRNP is mislocalized in ALS patient fibroblasts bearing NLS mutations in FUS and is required for motor neuron outgrowth in zebrafish

    Yu, Y., Chi, B., Xia, W., Gangopadhyay, J., Yamazaki, T., Winkelbauer-Hurt, M. E., Yin, S., Eliasse, Y., Adams, E., Shaw, C. E. & Reed, R., 3 Mar 2015, In: Nucleic Acids Research. 43, 6, p. 3208-3218 11 p.

    Research output: Contribution to journalArticlepeer-review

  24. Genomic and proteomic analysis of transcription factor TFII-I reveals insight into the response to cellular stress

    Fan, A. X., Papadopoulos, G. L., Hossain, M. A., Lin, I-J., Hu, J., Tang, T. M., Kilberg, M. S., Renne, R., Strouboulis, J. & Bungert, J., 8 Jul 2014, In: Nucleic Acids Research. 42, 12, p. 7625-7641 17 p.

    Research output: Contribution to journalArticlepeer-review

  25. Current status and new features of the Consensus Coding Sequence database

    Farrell, C. M., O'Leary, N. A., Harte, R. A., Loveland, J. E., Wilming, L. G., Wallin, C., Diekhans, M., Barrell, D., Searle, S. M. J., Aken, B., Hiatt, S. M., Frankish, A., Suner, M-M., Rajput, B., Steward, C. A., Brown, G. R., Bennett, R., Murphy, M., Wu, W., Kay, M. P. & 23 others, Hart, J., Rajan, J., Weber, J., Snow, C., Riddick, L. D., Hunt, T., Webb, D., Thomas, M., Tamez, P., Rangwala, S. H., McGarvey, K. M., Pujar, S., Shkeda, A., Mudge, J. M., Gonzalez, J. M., Gilbert, J. G. R., Trevanion, S. J., Baertsch, R., Harrow, J. L., Hubbard, T., Ostell, J. M., Haussler, D. & Pruitt, K. D., 1 Jan 2014, In: Nucleic Acids Research. 42, D1, p. D865-D872 8 p., N/A.

    Research output: Contribution to journalArticlepeer-review

  26. Ensembl 2014

    Flicek, P., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., Gil, L., Girón, C. G., Gordon, L., Hourlier, T., Hunt, S., Johnson, N., Juettemann, T., Kähäri, A. K., Keenan, S., Kulesha, E. & 32 others, Martin, F. J., Maurel, T., McLaren, W. M., Murphy, D. N., Nag, R., Overduin, B., Pignatelli, M., Pritchard, B., Pritchard, E., Riat, H. S., Ruffier, M., Sheppard, D., Taylor, K., Thormann, A., Trevanion, S. J., Vullo, A., Wilder, S. P., Wilson, M., Zadissa, A., Aken, B. L., Birney, E., Cunningham, F., Harrow, J., Herrero, J., Hubbard, T. J. P., Kinsella, R., Muffato, M., Parker, A., Spudich, G., Yates, A., Zerbino, D. R. & Searle, S. M. J., 1 Jan 2014, In: Nucleic Acids Research. 42, D1, p. D749-D755 7 p., N/A.

    Research output: Contribution to journalArticlepeer-review

  27. Estimating telomere length from whole genome sequence data

    Ding, Z., Mangino, M., Aviv, A., Spector, T., Durbin, R. & UK10K Consortium, 2014, In: Nucleic Acids Research. 42, 9, 4 p., e75.

    Research output: Contribution to journalArticlepeer-review

  28. Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport

    Laponogov, I., Veselkov, D. A., Crevel, I. M-T., Pan, X-S., Fisher, L. M. & Sanderson, M. R., Nov 2013, In: Nucleic Acids Research. 41, 21, p. 9911-9923 13 p.

    Research output: Contribution to journalArticlepeer-review

  29. Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies

    Ramasamy, A., Trabzuni, D., Gibbs, J. R., Dillman, A., Hernandez, D. G., Arepalli, S., Walker, R., Smith, C., Ilori, G. P., Shabalin, A. A., Li, Y., Singleton, A. B., Cookson, M. R., Hardy, J., Ryten, M., Weale, M. E., NABEC & UKBEC, Apr 2013, In: Nucleic Acids Research. 41, 7, 12 p., e88.

    Research output: Contribution to journalArticlepeer-review

  30. Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

    Tanaka, K., Henry, C. S., Zinner, J. F., Jolivet, E., Cohoon, M. P., Xia, F., Bidnenko, V., Ehrlich, S. D., Stevens, R. L. & Noirot, P., 7 Jan 2013, In: Nucleic Acids Research. 41, 1, p. 687-699 13 p.

    Research output: Contribution to journalArticlepeer-review

  31. Ensembl 2013

    Flicek, P., Ahmed, I., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gil, L., García-Girón, C., Gordon, L., Hourlier, T., Hunt, S., Juettemann, T., Kähäri, A. K., Keenan, S., Komorowska, M. & 35 others, Kulesha, E., Longden, I., Maurel, T., McLaren, W. M., Muffato, M., Nag, R., Overduin, B., Pignatelli, M., Pritchard, B., Pritchard, E., Riat, H. S., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sheppard, D., Sobral, D., Taylor, K., Thormann, A., Trevanion, S., White, S., Wilder, S. P., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Harrow, J., Herrero, J., Hubbard, T. J. P., Johnson, N., Kinsella, R., Parker, A., Spudich, G., Yates, A., Zadissa, A. & Searle, S. M. J., Jan 2013, In: Nucleic Acids Research. 41, D1, p. D48-D55 8 p., N/A.

    Research output: Contribution to journalArticlepeer-review

  32. Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus

    Cowley, M., Wood, A. J., Böhm, S., Schulz, R. & Oakey, R. J., Oct 2012, In: Nucleic Acids Research. 40, 18, p. 8917-8926 10 p.

    Research output: Contribution to journalArticlepeer-review

  33. Argonaute identity defines the length of mature mammalian microRNAs

    Juvvuna, P. K., Khandelia, P., Lee, L. M. & Makeyev, E., Aug 2012, In: Nucleic Acids Research. 40, 14, p. 6808-6820 13 p., N/A.

    Research output: Contribution to journalArticlepeer-review

  34. Analysis of the interaction with the hepatitis C virus mRNA reveals an alternative mode of RNA recognition by the human La protein

    Martino, L., Pennell, S., Kelly, G., Bui, T. T. T., Kotik-Kogan, O., Smerdon, S. J., Drake, A. F., Curry, S. & Conte, M. R., Feb 2012, In: Nucleic Acids Research. 40, 3, p. 1381 - 1394 14 p.

    Research output: Contribution to journalArticlepeer-review

  35. Ensembl 2012

    Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gil, L., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kähäri, A. K., Keefe, D., Keenan, S., Kinsella, R., Komorowska, M. & 37 others, Koscielny, G., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Muffato, M., Overduin, B., Pignatelli, M., Pritchard, B., Riat, H. S., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sobral, D., Tang, Y. A., Taylor, K., Trevanion, S., Vandrovcova, J., White, S., Wilson, M., Wilder, S. P., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández-Suarez, X. M., Harrow, J., Herrero, J., Hubbard, T. J. P., Parker, A., Proctor, G., Spudich, G., Vogel, J., Yates, A., Zadissa, A. & Searle, S. M. J., Jan 2012, In: Nucleic Acids Research. 40, D1 (Database Issue), p. D84-D90 7 p., N/A.

    Research output: Contribution to journalArticlepeer-review

  36. Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes

    D'Antonio, M., Pendino, V., Sihna, S. & Ciccarelli, F., Jan 2012, In: Nucleic Acids Research. 40, D1, p. D978-D983 6 p., N/A.

    Research output: Contribution to journalArticlepeer-review

  37. RNA-binding protein HuR autoregulates its expression by promoting alternative polyadenylation site usage

    Dai, W., Zhang, G. & Makeyev, E. V., Jan 2012, In: Nucleic Acids Research. 40, 2, p. 787-800 14 p.

    Research output: Contribution to journalArticlepeer-review

  38. Identification of potentially cytotoxic lesions induced by UVA photoactivation of DNA 4-thiothymidine in human cells

    Reelfs, O., Macpherson, P., Ren, X., Xu, Y-Z., Karran, P. & Young, A. R., Dec 2011, In: Nucleic Acids Research. 39, 22, p. 9620 - 9632 13 p.

    Research output: Contribution to journalArticlepeer-review

  39. Effect of base sequence on the DNA cross-linking properties of pyrrolobenzodiazepine (PBD) dimers

    Rahman, K., James, CH. & Thurston, DE., Jul 2011, In: Nucleic Acids Research. 39, 13, p. 5800-5812 13 p.

    Research output: Contribution to journalArticlepeer-review

  40. Human imprinted retrogenes exhibit non-canonical imprint chromatin signatures and reside in non-imprinted host genes

    Monk, D., Arnaud, P., Frost, J. M., Wood, A. J., Cowley, M., Martin-Trujillo, A., Guillaumet-Adkins, A., Platas, I. I., Camprubi, C., Bourc'his, D., Feil, R., Moore, G. E. & Oakey, R. J., Jun 2011, In: Nucleic Acids Research. 39, 11, p. 4577 - 4586 10 p.

    Research output: Contribution to journalArticlepeer-review

  41. Ensembl 2011

    Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kähäri, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E. & 32 others, Larsson, P., Longden, I., McLaren, W., Overduin, B., Pritchard, B., Riat, H. S., Rios, D., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, Y. A., Trevanion, S., Vandrovcova, J., Vilella, A. J., White, S., Wilder, S. P., Zadissa, A., Zamora, J., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández-Suarez, X. M., Herrero, J., Hubbard, T. J. P., Parker, A., Proctor, G., Vogel, J. & Searle, S. M. J., Jan 2011, In: Nucleic Acids Research. 39, Suppl 1 (Database issue), p. D800-D806 7 p., N/A.

    Research output: Contribution to journalArticlepeer-review

  42. The 68 kDa subunit of mammalian cleavage factor I interacts with the U7 small nuclear ribonucleoprotein and participates in 3'-end processing of animal histone mRNAs

    Ruepp, M. D., Vivarelli, S., Pillai, R. S., Kleinschmidt, N., Azzouz, T. N., Barabino, S. M. & Schumperli, D., 1 Nov 2010, In: Nucleic Acids Research. 38, 21, p. 7637-7650 14 p.

    Research output: Contribution to journalArticlepeer-review

  43. Counter-selection recombineering of the baculovirus genome: a strategy for seamless modification of repeat-containing BACs

    Westenberg, M., Soedling, H. M., Mann, D. A., Nicholson, L. J. & Dolphin, C. T., 9 Jul 2010, In: Nucleic Acids Research. 38, 16, e166.

    Research output: Contribution to journalArticlepeer-review

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