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Nucleic Acids Research, ‎0305-1048

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  1. Identifying ribosome heterogeneity using ribosome profiling

    Alkan, F., Wilkins, O. G., Hernández-Pérez, S., Ramalho, S., Silva, J., Ule, J. & Faller, W. J., 9 Sep 2022, In: Nucleic Acids Research. 50, 16, p. e95

    Research output: Contribution to journalArticlepeer-review

  2. GEOexplorer: a webserver for gene expression analysis and visualisation

    Iacoangeli, A., Dobson, R. & Al-Chalabi, A., 25 Apr 2022, (Accepted/In press) In: Nucleic Acids Research.

    Research output: Contribution to journalArticlepeer-review

  3. Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1

    Conte, M. R., 11 Jan 2022, In: Nucleic Acids Research. 50, 1, p. 522-535 14 p.

    Research output: Contribution to journalArticlepeer-review

  4. PDBe-KB: collaboratively defining the biological context of structural data

    PDBe-KB consortium , 2022, In: Nucleic Acids Research. 50, D1, p. D534-D542

    Research output: Contribution to journalArticlepeer-review

  5. HDAC1 is required for GATA-1 transcription activity, global chromatin occupancy and hematopoiesis

    Yan, B., Yang, J., Kim, M. Y., Luo, H., Cesari, N., Yang, T., Strouboulis, J., Zhang, J., Hardison, R., Huang, S. & Qiu, Y., 27 Sep 2021, In: Nucleic Acids Research. 49, 17, p. 9783-9798 16 p.

    Research output: Contribution to journalArticlepeer-review

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. Che-1/AATF binds to RNA polymerase I machinery and sustains ribosomal RNA gene transcription

    Sorino, C., Catena, V., Bruno, T., De Nicola, F., Scalera, S., Bossi, G., Fabretti, F., Mano, M., De Smaele, E., Fanciulli, M. & Iezzi, S., 2020, In: Nucleic Acids Research. 48, 11, p. 5891-5906 16 p.

    Research output: Contribution to journalArticlepeer-review

  14. FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA

    Carter, J. M., Emmett, W., Mozos, I. R. D. L., Kotter, A., Helm, M., Ule, J. & Hussain, S., 4 Nov 2019, In: Nucleic Acids Research. 47, 19, p. E113

    Research output: Contribution to journalArticlepeer-review

  15. 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

  16. Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock

    Castelo-Szekely, V., De Matos, M., Tusup, M., Pascolo, S., Ule, J. & Gatfield, D., 4 Jun 2019, In: Nucleic Acids Research. 47, 10, p. 5193-5209 17 p.

    Research output: Contribution to journalArticlepeer-review

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. Mechanistic insight into the assembly of the HerA–NurA helicase–nuclease DNA end resection complex

    Politis, A., 22 Sep 2017, (E-pub ahead of print) In: Nucleic Acids Research.

    Research output: Contribution to journalArticlepeer-review

  23. 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

  24. 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

  25. 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

  26. The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

    Llorian, M., Gooding, C., Bellora, N., Hallegger, M., Buckroyd, A., Wang, X., Rajgor, D., Kayikci, M., Feltham, J., Ule, J., Eyras, E. & Smith, C. W. J., 14 Oct 2016, In: Nucleic Acids Research. 44, 18, p. 8933-8950 18 p.

    Research output: Contribution to journalArticlepeer-review

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

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

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

    Research output: Contribution to journalArticlepeer-review

  33. Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends

    Tajnik, M., Vigilante, A., Braun, S., Hänel, H., Luscombe, N. M., Ule, J., Zarnack, K. & König, J., 22 Sep 2015, In: Nucleic Acids Research. 43, 21, p. 10492-10505 14 p.

    Research output: Contribution to journalArticlepeer-review

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis

    Papadopoulos, G. L., Karkoulia, E., Tsamardinos, I., Porcher, C., Ragoussis, J., Bungert, J. & Strouboulis, J., May 2013, In: Nucleic Acids Research. 41, 9, p. 4938-48 11 p.

    Research output: Contribution to journalArticlepeer-review

  41. 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

  42. 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

  43. 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

  44. DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence

    Furini, S., Barbini, P. & Domene, C., 2013, (E-pub ahead of print) In: Nucleic Acids Research.

    Research output: Contribution to journalArticlepeer-review

  45. 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

  46. 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

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