Gene Regulation and Expression

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2017

Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans

Harvald, E. B., Sprenger, R. R., Dall, K. B., Ejsing, C. S., Nielsen, R., Mandrup, S., Brenes Murillo, A., Larance, M., Gartner, A., Lamond, A. & Færgeman, N. J., 26 Jul 2017, In : Cell Systems. 5, 1, p. 38-52.e4 13 p.

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6 Citations (Scopus)
185 Downloads (Pure)

New Apex in Proteome Analysis

Ly, T. & Lamond, A. I., 28 Jun 2017, In : Cell Systems. 4, 6, p. 581-582 2 p.

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Parkin–phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity

Kumar, A., Chaugule, V. K., Condos, T. E. C., Barber, K. R., Johnson, C., Toth, R., Sundaramoorthy, R., Knebel, A., Shaw, G. S. & Walden, H., May 2017, In : Nature Structural & Molecular Biology. 24, 5, p. 475-483 9 p.

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36 Citations (Scopus)
231 Downloads (Pure)

Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells

Ishikawa, H., Yoshikawa, H., Izumikawa, K., Miura, Y., Taoka, M., Nobe, Y., Yamauchi, Y., Nakayama, H., Simpson, R. J., Isobe, T. & Takahashi, N., 7 Apr 2017, In : Nucleic Acids Research. 45, 6, p. 3437-3447 11 p.

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16 Citations (Scopus)
204 Downloads (Pure)

Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations

Nielsen, S. V., Stein, A., Dinitzen, A. B., Papaleo, E., Tatham, M. H., Poulsen, E. G., Kassem, M. M., Rasmussen, L. J., Lindorff-Larsen, K. & Hartmann-Petersen, R., 19 Apr 2017, In : PLoS Genetics. 13, 4, 26 p., e1006739.

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25 Citations (Scopus)
173 Downloads (Pure)

Prediction of protein complexes in Trypanosoma brucei by protein correlation profiling mass spectrometry and machine learning

Crozier, T. W. M., Tinti, M., Larance, M., Lamond, A. I. & Ferguson, M. A. J., 1 Dec 2017, In : Molecular & Cellular Proteomics. 16, 12, p. 2254-2267 14 p.

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6 Citations (Scopus)
153 Downloads (Pure)

Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS

Ly, T., Whigham, A., Clarke, R., Brenes-Murillo, A. J., Estes, B., Madhessian, D., Lundberg, E., Wadsworth, P. & Lamond, A. I., 20 Oct 2017, In : eLife. 6, p. 1-35 35 p., e27574.

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15 Citations (Scopus)
191 Downloads (Pure)

Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity

Howden, A. J. M., Stam, R., Martinez Heredia, V., Motion, G. B., Hodge, K., ten Have, S., Marques Monteiro Amaro, T. M. & Huitema, E., Jul 2017, In : New Phytologist. 215, 1, p. 309-322 14 p.

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7 Citations (Scopus)
217 Downloads (Pure)

Recognition of a glycosylation substrate by the O-GlcNAc transferase TPR repeats

Rafie, K., Raimi, O., Ferenbach, A. T., Borodkin, V. S., Kapuria, V. & van Aalten, D. M. F., 28 Jun 2017, In : Open Biology. 7, p. 1-9 9 p., 70078.

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17 Citations (Scopus)
129 Downloads (Pure)

Reversal of DDK-mediated MCM phosphorylation by Rif1-PP1 regulates replication initiation and replisome stability independently of ATR/Chk1

Alver, R. C., Chadha, G. S., Gillespie, P. J. & Blow, J. J., 7 Mar 2017, In : Cell Reports. 18, 10, p. 2508-2520 13 p.

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32 Citations (Scopus)
144 Downloads (Pure)
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9 Citations (Scopus)
151 Downloads (Pure)

Structural and Functional analysis of the GABARAP interaction motif (GIM)

Rogov, V. V., Stolz, A., Ravicahandran, A. C., Rios Szwed, D. O., Suzuki, H., Kniss, A., Lohr, F., Wakatsuki, S., Dotsch, V., Dikic, I., Dobson, R. C. J. & McEwan, D. G., 27 Jun 2017, In : EMBO Reports. 18, 8, p. 1382-1396 15 p., e201643587.

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51 Citations (Scopus)
190 Downloads (Pure)

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

Sundaramoorthy, R., Hughes, A. L., Singh, V., Wiechens, N., Ryan, D. P., El-Mkami, H., Petoukhov, M., Svergun, D. I., Treutlein, B., Quack, S., Fischer, M., Michaelis, J., Bottcher, B., Norman, D. G. & Owen-Hughes, T., 13 Apr 2017, In : eLife. 6, 28 p., e22510.

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27 Citations (Scopus)
141 Downloads (Pure)

Structure of PINK1 and mechanisms of Parkinson's disease associated mutations

Kumar, A., Tamjar, J., Waddell, A. D., Woodroof, H. I., Raimi, O. G., Shaw, A. M., Peggie, M., Muqit, M. M. K. & van Aalten, D. M. F., 9 Nov 2017, In : eLife. 6, p. 1-16 16 p., e29985.

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27 Citations (Scopus)
175 Downloads (Pure)

TDP-43 stabilises the processing intermediates of mitochondrial transcripts

Izumikawa, K., Nobe, Y., Yoshikawa, H., Ishikawa, H., Miura, Y., Nakayama, H., Nonaka, T., Hasegawa, M., Egawa, N., Inoue, H., Nishikawa, K., Yamano, K., Simpson, R. J., Taoka, M., Yamauchi, Y., Isobe, T. & Takahashi, N., 9 Aug 2017, In : Scientific Reports. 7, p. 1-14 14 p., 7709.

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15 Citations (Scopus)
135 Downloads (Pure)

The chromatin assembly factor complex 1 (CAF1) and 5-Azacytidine (5-AzaC) affect cell motility in Src-transformed human epithelial cells

Endo, A., Ly, T., Pippa, R., Bensaddek, D., Nicolas, A. & Lamond, A. I., 6 Jan 2017, In : Journal of Biological Chemistry. 292, 1, p. 172-184 13 p.

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7 Citations (Scopus)
180 Downloads (Pure)

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription

Akay, A., Di Domenico, T., Suen, K. M., Nabih, A., Parada, G. E., Larance, M., Medhi, R., Berkyurek, A. C., Zhang, X., Wedeles, C. J., Rudolph, K. L. M., Engelhardt, J., Hemberg, M., Ma, P., Lamond, A. I., Claycomb, J. M. & Miska, E. A., 7 Aug 2017, In : Developmental Cell. 42, 3, p. 241-255.e6 21 p.

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15 Citations (Scopus)
150 Downloads (Pure)

The High-Affinity Interaction between ORC and DNA that Is Required for Replication Licensing Is Inhibited by 2-Arylquinolin-4-Amines

Gardner, N. J., Gillespie, P. J., Carrington, J. T., Shanks, E. J., McElroy, S. P., Haagensen, E. J., Frearson, J. A., Woodland, A. & Blow, J. J., 17 Aug 2017, In : Cell Chemical Biology. 24, 8, p. 981-992.e4 16 p.

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5 Citations (Scopus)
127 Downloads (Pure)

The Image Data Resource: a bioimage data integration and publication platform

Williams, E., Moore, J., Li, S. W., Rustici, G., Tarkowska, A., Chessel, A., Leo, S., Antal, B., Ferguson, R. K., Sarkans, U., Brazma, A., Carzo Salas, R. E. & Swedlow, J. R., Aug 2017, In : Nature Methods. 14, 8, p. 775-781 7 p.

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46 Citations (Scopus)
302 Downloads (Pure)

The Ndc80 complex targets Bod1 to human mitotic kinetochores

Schleicher, K., Porter, M., ten Have, S., Sundaramoorthy, R., Porter, I. M. & Swedlow, J. R., 15 Nov 2017, In : Open Biology. 7, p. 1-14 14 p., 170099.

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3 Citations (Scopus)
134 Downloads (Pure)

Ufd1-Npl4 recruit Cdc48 for disassembly of ubiquitylated CMG helicase at the end of chromosome replication

Maric, M., Mukherjee, P., Tatham, M. H., Hay, R. & Labib, K., 28 Mar 2017, In : Cell Reports. 18, 13, p. 3033-3042 10 p.

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9 Citations (Scopus)
196 Downloads (Pure)

Unlocking the nucleosome

Flaus, A. & Owen-Hughes, T., 20 Jan 2017, In : Science. 355, 6322, p. 245-246 2 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Use of a Yeast tRNase Killer Toxin to Diagnose Kti12 Motifs Required for tRNA Modification by Elongator

Mehlgarten, C., Prochaska, H., Hammermeister, A., Abdel-Fattah, W., Wagner, M., Krutyhołowa, R., Jun, S. E., Kim, G-T., Glatt, S., Breunig, K. D., Stark, M. J. R. & Schaffrath, R., 5 Sep 2017, In : Toxins. 9, 9, p. 1-13 13 p.

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6 Citations (Scopus)
162 Downloads (Pure)
2016

A Generic Platform for Cellular Screening Against Ubiquitin Ligases

Maculins, T., Carter, N., Dorval, T., Hudson, K., Nissink, J. W. M., Hay, R. T. & Alwan, H., 8 Jan 2016, In : Scientific Reports. 6, 18940.

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11 Citations (Scopus)
119 Downloads (Pure)

BOD1 Is Required for Cognitive Function in Humans and Drosophila

Esmaeeli-Nieh, S., Fenckova, M., Porter, I. M., Motazacker, M. M., Nijhof, B., Castells-Nobau, A., Asztalos, Z., Weißmann, R., Behjati, F., Tzschach, A., Felbor, U., Scherthan, H., Sayfati, S. M., Ropers, H. H., Kahrizi, K., Najmabadi, H., Swedlow, J. R., Schenck, A. & Kuss, A. W., 11 May 2016, In : PLoS Genetics. 12, 5, p. 1-22 22 p., e1006022.

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7 Citations (Scopus)
112 Downloads (Pure)

BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation

Feng, Y., Vlassis, A., Roques, C., Lalonde, M. E., González-Aguilera, C., Lambert, J. P., Lee, S. B., Zhao, X., Alabert, C., Johansen, J. V., Paquet, E., Yang, X. J., Gingras, A. C., Côté, J. & Groth, A., 18 Jan 2016, In : EMBO Journal. 35, 2, p. 176-192 17 p.

Research output: Contribution to journalArticle

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40 Citations (Scopus)

CDK1-Cyclin B1 Activates RNMT, Coordinating mRNA Cap Methylation with G1 Phase Transcription

Aregger, M., Kaskar, A., Varshney, D., Fernandez-Sanchez, M. E., Inesta-Vaquera, F. A., Weidlich, S. & Cowling, V. H., 3 Mar 2016, In : Molecular Cell. 61, 5, p. 734-746 13 p.

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19 Citations (Scopus)
129 Downloads (Pure)

CDK-dependent phosphorylation of PHD1 on serine 130 alters its substrate preference in cells

Ortmann, B., Bensaddek, D., Carvalhal, S., Moser, S. C., Mudie, S., Griffis, E. R., Swedlow, J. R., Lamond, A. I. & Rocha, S., Jan 2016, In : Journal of Cell Science. 129, 1, p. 191-205 15 p.

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10 Citations (Scopus)
184 Downloads (Pure)

Chronic p53-independent p21 expression causes genomic instability by deregulating replication licensing

Galanos, P., Vougas, K., Walter, D., Polyzos, A., Maya-Mendoza, A., Haagensen, E. J., Kokkalis, A., Roumelioti, F-M., Gagos, S., Tzetis, M., Canovas, B., Igea, A., Ahuja, A. K., Zellweger, R., Havaki, S., Kanavakis, E., Kletsas, D., Roninson, I. B., Garbis, S. D., Lopes, M. & 7 others, Nebreda, A., Thanos, D., Blow, J. J., Townsend, P., Sørensen, C. S., Bartek, J. & Gorgoulis, V. G., Jul 2016, In : Nature Cell Biology. 18, 7, p. 777-789 13 p.

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101 Citations (Scopus)
510 Downloads (Pure)

Chtop (Chromatin target of Prmt1) auto-regulates its expression level via intron retention and nonsense-mediated decay of its own mRNA

Izumikawa, K., Yoshikawa, H., Ishikawa, H., Nobe, Y., Yamauchi, Y., Philipsen, S., Simpson, R. J., Isobe, T. & Takahashi, N., Nov 2016, In : Nucleic Acids Research. 44, 20, p. 9847-9859 13 p.

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8 Citations (Scopus)
294 Downloads (Pure)

c-Myc deregulation induces mRNA capping enzyme dependency

Lombardi, O., Varshney, D., Phillips, N. M. & Cowling, V. H., 16 Oct 2016, In : Oncotarget. 7, 50, p. 82273-82288 16 p.

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6 Citations (Scopus)
138 Downloads (Pure)

Deep Proteome Analysis Identifies Age-Related Processes in C. elegans

Narayan, V., Ly, T., Pourkarimi, E., Brenes Murillo, A., Gartner, A., Lamond, A. & Kenyon, C., 24 Aug 2016, In : Cell Systems. 3, 2, p. 144-159 15 p.

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32 Citations (Scopus)
268 Downloads (Pure)

Direct non transcriptional role of NF-Y in DNA replication

Benatti, P., Belluti, S., Miotto, B., Neusiedler, J., Dolfini, D., Drac, M., Basile, V., Schwob, E., Mantovani, R., Blow, J. J. & Imbriano, C., 1 Apr 2016, In : Biochimica et Biophysica Acta. Molecular Cell Research. 1863, 4, p. 673-685 13 p.

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8 Citations (Scopus)
121 Downloads (Pure)

E4 ligase-specific ubiquitination hubs coordinate DNA double-strand-break repair and apoptosis

Ackermann, L., Schell, M., Pokrzywa, W., Kevei, É., Gartner, A., Schumacher, B. & Hoppe, T., Nov 2016, In : Nature Structural & Molecular Biology. 23, 11, p. 995-1002 8 p.

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11 Citations (Scopus)
665 Downloads (Pure)

Enhanced snoMEN Vectors Facilitate Establishment of GFP–HIF-1α Protein Replacement Human Cell Lines

Ono, M., Ono, K., Bensaddek, D., Afzal, V., Biddlestone, J., Ortmann, B., Mudie, S., Boivin, V., S. Scott, M., Rocha, S. & Lamond, A. I., 29 Apr 2016, In : PLoS ONE. 11, 4, 28 p., e0154759.

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1 Citation (Scopus)
161 Downloads (Pure)

Establishment of a High-throughput Setup for Screening Small Molecules That Modulate c-di-GMP Signaling in Pseudomonas aeruginosa

Rugjee, K. N., An, S. & Ryan, R. P., 30 Jun 2016, In : JoVE: Journal of Visualized Experiments. 112, 7 p., e54115.

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2 Citations (Scopus)
149 Downloads (Pure)

Establishment of a promoter based chromatin architecture on recently replicated DNA can accommodate variable internucleosome spacing

Fennessy, R. T. & Owen-Hughes, T., 6 Sep 2016, In : Nucleic Acids Research. 44, 15, p. 7189-7203 15 p.

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27 Citations (Scopus)
157 Downloads (Pure)

Global membrane protein interactome analysis using in vivo crosslinking and MS-based protein correlation profiling

Larance, M., Kirkwood, K. J., Tinti, M., Brenes Murillo, A., Ferguson, M. & Lamond, A., 1 Jul 2016, In : Molecular & Cellular Proteomics. 15, 7, p. 2476-2490 15 p.

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27 Citations (Scopus)
107 Downloads (Pure)

H4K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex

Saredi, G., Huang, H., Hammond, C. M., Alabert, C., Bekker-Jensen, S., Forne, I., Reverón-Gómez, N., Foster, B. M., Mlejnkova, L., Bartke, T., Cejka, P., Mailand, N., Imhof, A., Patel, D. J. & Groth, A., 22 Jun 2016, In : Nature. 534, 7609, p. 714-718 5 p.

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56 Citations (Scopus)
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6 Citations (Scopus)
161 Downloads (Pure)

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G., Owen-Hughes, T., Blaxter, M. & Barton, G. J., Jun 2016, In : RNA: a Publication of the RNA Society. 22, 6, p. 839-851 13 p.

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185 Citations (Scopus)
175 Downloads (Pure)

Human IFIT1 inhibits mRNA translation of rubulaviruses but not other members of the Paramyxoviridae family

Young, D. F., Andrejeva, J., Li, X., Inesta-Vaquera, F., Dong, C., Cowling, V. H., Goodbourn, S. & Randall, R. E., 15 Oct 2016, In : Journal of Virology. 90, 20, p. 9446-9456 11 p.

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15 Citations (Scopus)
132 Downloads (Pure)

Hypoxia Induced NF-κB

D'Ignazio, L. & Rocha, S., 8 Mar 2016, In : Cells. 5, 1, 8 p., 10.

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Identification of RNF168 as a PML nuclear body regulator

Shire, K., Wong, A. I., Tatham, M. H., Anderson, O. F., Ripsman, D., Gulstene, S., Moffat, J., Hay, R. T. & Frappier, L., 1 Feb 2016, In : Journal of Cell Science. 129, 3, p. 580-591 12 p.

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9 Citations (Scopus)
142 Downloads (Pure)

Inevitability and containment of replication errors for eukaryotic genome lengths spanning Megabase to Gigabase

Al Mamun, M., Albergante, L., Moreno, A., Carrington, J. T., Blow, J. & Newman, T. J., 27 Sep 2016, In : Proceedings of the National Academy of Sciences. 113, 39, p. E5765-E5774 10 p.

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12 Citations (Scopus)
381 Downloads (Pure)

Intricate macrophage-colorectal cancer cell communication in response to radiation

Pinto, A. T., Pinto, M. L., Velho, S., Pinto, M. T., Cardoso, A. P., Figueira, R., Monteiro, A., Marques, M., Seruca, R., Barbosa, M. A., Mareel, M., Oliveira, M. J. & Rocha, S., 11 Aug 2016, In : PLoS ONE. 11, 8, p. 1-20 20 p., e0160891.

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10 Citations (Scopus)
149 Downloads (Pure)

Ionizing radiation modulates human macrophages towards a pro-inflammatory phenotype preserving their pro-invasive and pro-angiogenic capacities

Teresa Pinto, A., Laranjeiro Pinto, M., Patrícia Cardoso, A., Monteiro, C., Teixeira Pinto, M., Filipe Maia, A., Castro, P., Figueira, R., Monteiro, A., Marques, M., Mareel, M., Dos Santos, S. G., Seruca, R., Adolfo Barbosa, M., Rocha, S. & JoséOliveira, M., 6 Jan 2016, In : Scientific Reports. 6, 18765.

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42 Citations (Scopus)
126 Downloads (Pure)

Loss of ubiquitin E2 Ube2w rescues hypersensitivity of Rnf4 mutant cells to DNA damage

Maure, J. F., Moser, S. C., Jaffray, E. G., Alpi, A. F. & Hay, R. T., 17 May 2016, In : Scientific Reports. 6, 10 p., 26178.

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3 Citations (Scopus)
128 Downloads (Pure)

Mechanoaccumulative elements of the mammalian actin cytoskeleton

Schiffhauer, E. S., Luo, T., Mohan, K., Srivastava, V., Qian, X., Griffis, E. R., Iglesias, P. A. & Robinson, D. N., 6 Jun 2016, In : Current Biology. 26, 11, p. 1473-1479 7 p.

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28 Citations (Scopus)
326 Downloads (Pure)

Metadata management for high content screening in OMERO

Li, S., Besson, S., Blackburn, C., Carroll, M., Ferguson, R. K., Flynn, H., Gillen, K., Leigh, R., Lindner, D., Linkert, M., Moore, W. J., Ramalingam, B., Rozbicki, E., Rustici, G., Tarkowska, A., Walczysko, P., Williams, E., Allan, C., Burel, J. M., Moore, J. & 1 others, Swedlow, J. R., 1 Mar 2016, In : Methods. 96, p. 27-32 6 p.

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14 Citations (Scopus)
112 Downloads (Pure)