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Research Output

2020

CDK13 cooperates with CDK12 to control global RNA polymerase II processivity

Fan, Z., Devlin, J. R., Hogg, S. J., Doyle, M. A., Harrison, P. F., Todorovski, I., Cluse, L. A., Knight, D. A., Sandow, J. J., Gregory, G., Fox, A., Beilharz, T. H., Kwiatkowski, N., Scott, N. E., Vidakovic, A. T., Kelly, G. P., Svejstrup, J. Q., Geyer, M., Gray, N. S., Vervoort, S. J. & 1 others, Johnstone, R. W., 29 Apr 2020, In : Science Advances. 6, 18, 18 p., eaaz5041.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Dissecting the Roles of Mitochondrial Complex I Intermediate Assembly Complex Factors in the Biogenesis of Complex I

Formosa, L. E., Muellner-Wong, L., Reljic, B., Sharpe, A. J., Jackson, T. D., Beilharz, T. H., Stojanovski, D., Lazarou, M., Stroud, D. A. & Ryan, M. T., 21 Apr 2020, In : Cell Reports. 31, 3, 14 p., 107541.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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1 Citation (Scopus)

FGF13 promotes metastasis of triple-negative breast cancer

Johnstone, C. N., Pattison, A. D., Harrison, P. F., Powell, D. R., Lock, P., Ernst, M., Anderson, R. L. & Beilharz, T. H., 1 Jul 2020, In : International Journal of Cancer. 147, 1, p. 230-243 14 p.

Research output: Contribution to journalArticleResearchpeer-review

The YEATS Domain Histone Crotonylation Readers Control Virulence-Related Biology of a Major Human Pathogen

Wang, Q., Verma, J., Vidan, N., Wang, Y., Tucey, T. M., Lo, T. L., Harrison, P. F., See, M., Swaminathan, A., Kuchler, K., Tscherner, M., Song, J., Powell, D. R., Sopta, M., Beilharz, T. H. & Traven, A., 21 Apr 2020, In : Cell Reports. 31, 3, 16 p., 107528.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2019

3′-UTRs and the Control of Protein Expression in Space and Time

Beilharz, T. H., See, M. M. & Boag, P. R., 2019, The Biology of mRNA: Structure and Function. Oeffinger, M. & Zenklusen, D. (eds.). Switzerland: Springer, p. 133-148 16 p. (Advances in Experimental Medicine and Biology; vol. 1203).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

1 Citation (Scopus)

PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A)-Length Distribution in Yeast Transcriptomes

Swaminathan, A., Harrison, P. F., Preiss, T. & Beilharz, T. H., 2019, Yeast Systems Biology: Methods and Protocols. Oliver, S. G. & Castrillo, J. I. (eds.). 2nd ed. New York, NY: Humana Press, p. 141-164 24 p. (Methods in Molecular Biology; vol. 2049).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

1 Citation (Scopus)

Topconfects: A package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list

Harrison, P. F., Pattison, A. D., Powell, D. R. & Beilharz, T. H., 28 Mar 2019, In : Genome Biology. 20, 1, 12 p., 67.

Research output: Contribution to journalArticleOtherpeer-review

Open Access
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1 Citation (Scopus)
2018

Alternative polyadenylation in the regulation and dysregulation of gene expression

Turner, R. E., Pattison, A. D. & Beilharz, T. H., Mar 2018, In : Seminars in Cell and Developmental Biology. 75, p. 61-69 9 p.

Research output: Contribution to journalArticleOtherpeer-review

12 Citations (Scopus)

A Metabolic Checkpoint for the Yeast-to-Hyphae Developmental Switch Regulated by Endogenous Nitric Oxide Signaling

Koch, B., Barugahare, A. A., Lo, T. L., Huang, C., Schittenhelm, R. B., Powell, D. R., Beilharz, T. H. & Traven, A., 20 Nov 2018, In : Cell Reports. 25, 8, p. 2244-2258 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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14 Citations (Scopus)

Functional and genomic characterisation of a xenograft model system for the study of metastasis in triple-negative breast cancer

Johnstone, C. N., Pattison, A. D., Gorringe, K. L., Harrison, P. F., Powell, D. R., Lock, P., Baloyan, D., Ernst, M., Stewart, A. G., Beilharz, T. H. & Anderson, R. L., 29 May 2018, In : Disease Models and Mechanisms. 11, 5, 14 p., 032250.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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5 Citations (Scopus)

Glucose Homeostasis Is Important for Immune Cell Viability during Candida Challenge and Host Survival of Systemic Fungal Infection

Tucey, T. M., Verma, J., Harrison, P. F., Snelgrove, S. L., Lo, T. L., Scherer, A. K., Barugahare, A. A., Powell, D. R., Wheeler, R. T., Hickey, M. J., Beilharz, T. H., Naderer, T. & Traven, A., 1 May 2018, In : Cell Metabolism. 27, 5, p. 988-1006.e7 27 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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37 Citations (Scopus)

miR-222 isoforms are differentially regulated by type-I interferon

Nejad, C., Pillman, K. A., Siddle, K. J., Pépin, G., Anko, M. L., McCoy, C. E., Beilharz, T. H., Quintana-Murci, L., Goodall, G. J., Bracken, C. P. & Gantier, M. P., 1 Mar 2018, In : RNA. 24, 3, p. 332-341 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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12 Citations (Scopus)

SRSF3 promotes pluripotency through nanog mRNA export and coordination of the pluripotency gene expression program

Ratnadiwakara, M., Archer, S. K., Dent, C. I., Ruiz De Los Mozos, I., Beilharz, T. H., Knaupp, A. S., Nefzger, C. M., Polo, J. M. & Anko, M-L., 9 May 2018, In : eLife. 7, 28 p., e37419.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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9 Citations (Scopus)
2017

Coordination of cell cycle progression and mitotic spindle assembly involves histone H3 lysine 4 methylation by set1/COMPASS

Beilharz, T. H., Harrison, P. F., Miles, D. M., See, M. M., Le, U. M. M., Kalanon, M., Curtis, M. J., Hasan, Q., Saksouk, J., Margaritis, T., Holstege, F., Geli, V. & Dichtl, B., 1 Jan 2017, In : Genetics. 205, 1, p. 185-199 15 p.

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

Lin-41 and oma ribonucleoprotein complexes mediate a translational repression-to-activation switch controlling oocyte meiotic maturation and the oocyte-to-embryo transition in caenorhabditis elegans

Tsukamoto, T., Gearhart, M. D., Spike, C. A., Huelgas-Morales, G., Mews, M., Boag, P. R., Beilharz, T. H. & Greenstein, D., 2017, In : Genetics. 206, 4, p. 2007-2039 33 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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16 Citations (Scopus)

PiRNAs and Aubergine cooperate with Wispy poly(A) polymerase to stabilize mRNAs in the germ plasm

Dufourt, J., Bontonou, G., Chartier, A., Jahan, C., Meunier, A. C., Pierson, S., Harrison, P. F., Papin, C., Beilharz, T. H. & Simonelig, M., 1 Dec 2017, In : Nature Communications. 8, 1, 12 p., 1305.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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14 Citations (Scopus)

Translation complex profile sequencing to study the in vivo dynamics of mRNA-ribosome interactions during translation initiation, elongation and termination

Shirokikh, N. E., Archer, S. K., Beilharz, T. H., Powell, D. & Preiss, T., 1 Apr 2017, In : Nature Protocols. 12, 4, p. 697-731 35 p.

Research output: Contribution to journalArticleResearchpeer-review

14 Citations (Scopus)
2016

Accessory subunits are integral for assembly and function of human mitochondrial complex I

Stroud, D. A., Surgenor, E. E., Formosa, L. E., Reljic, B., Frazier, A. E., Dibley, M. G., Osellame, L. D., Stait, T., Beilharz, T. H., Thorburn, D. R., Salim, A. & Ryan, M. T., 6 Oct 2016, In : Nature. 538, 7623, p. 123-126 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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114 Citations (Scopus)

Dynamics of ribosome scanning and recycling revealed by translation complex profiling

Archer, S. K., Shirokikh, N. E., Beilharz, T. H. & Preiss, T., 28 Jul 2016, In : Nature. 535, 7613, p. 570-574 5 p.

Research output: Contribution to journalLetterResearchpeer-review

65 Citations (Scopus)

Epitope-tagged yeast strains reveal promoter driven changes to 3'-end formation and convergent antisense-transcription from common 3' UTRs

Swaminathan, A. & Beilharz, T. H., 8 Jan 2016, In : Nucleic Acids Research. 44, 1, p. 377-386 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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5 Citations (Scopus)

Role of miRNAs and alternative mRNA 3'-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy

Soetanto, R., Hynes, C. J., Patel, H. R., Humphreys, D. T., Evers, M., Duan, G., Parker, B. J., Archer, S. K., Clancy, J. L., Graham, R. M., Beilharz, T. H., Smith, N. J. & Preiss, T., May 2016, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1859, 5, p. 744-756 13 p.

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

Understanding the regulation of coding and noncoding transcription in cell populations

Beilharz, T. H., 2016, In : Current Genetics. 62, 2, p. 317-319 3 p.

Research output: Contribution to journalReview ArticleOtherpeer-review

3 Citations (Scopus)
2015

Integration of posttranscriptional gene networks into metabolic adaptation and biofilm maturation in candida albicans

Verma-Gaur, J., Qu, Y., Harrison, P. F., Lo, T. L., Quenault, T. L., Dagley, M. J., Belousoff, M. J., Powell, D. R., Beilharz, T. H. & Traven, A., 2015, In : PLoS Genetics. 11, 10, 28 p., e1005590.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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22 Citations (Scopus)

PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome

Harrison, P. F., Powell, D. R., Clancy, J. L., Preiss, T., Boag, P. R., Traven, A., Seemann, T. & Beilharz, T. H., 2015, In : Rna-A Publication of the Rna Society. 21, 8, p. 1502 - 1510 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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34 Citations (Scopus)

POS-1 promotes endo-mesoderm development by inhibiting the cytoplasmic polyadenylation of neg-1 mRNA

Elewa, A., Shirayama, M., Kaymak, E., Harrison, P. F., Powell, D. R., Du, Z., Chute, C. D., Woolf, H., Yi, D., Ishidate, T., Srinivasan, J., Bao, Z., Beilharz, T. H., Ryder, S. P. & Mello, C. C., 2015, In : Developmental Cell. 34, 1, p. 108 - 118 11 p.

Research output: Contribution to journalArticleResearchpeer-review

5 Citations (Scopus)

Probing the closed-loop model of mRNA translation in living cells

Archer, S. K., Shirokikh, N. E., Hallwirth, C. V., Beilharz, T. H. & Priess, T., 2015, In : RNA Biology. 12, 3, p. 248 - 254 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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28 Citations (Scopus)
2014

Using Klenow-mediated extension to measure poly(A)-tail length and position in the transcriptome

Lee, M. C., Jaenicke, A. & Beilharz, T. H., 2014, In : Methods in Molecular Biology. 1125, p. 25 - 42 18 p.

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)
2013

ifet-1 is a broad-scale translational repressor required for normal P granule formation in C. elegans

Sengupta, M. S., Low, W. Y. L., Patterson, J. R., Kim, H-M., Traven, A., Beilharz, T. H., Colaiacovo, M. P., Schisa, J. A. & Boag, P. R., 2013, In : Journal of Cell Science. 126, 3, p. 850 - 859 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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18 Citations (Scopus)

Introns regulate gene expression in Cryptococcus neoformans in a Pab2p dependent pathway

Goebels, C., Thonn, A., Gonzalez-Hilarion, S., Rolland, O., Moyrand, F., Beilharz, T. H. & Janbon, G., 2013, In : PLoS Genetics. 9, 8, 15 p., e1003686.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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24 Citations (Scopus)

In vivo mutation of pre-mRNA processing factor 8 (Prpf8) affects transcript splicing, cell survival and myeloid differentiation

Keightley, M-C., Crowhurst, M., Layton, J. E., Beilharz, T. H., Markmiller, S. J., Varma, S., Hogan, B. M., de Jong-Curtain, T. A., Heath, J. K. & Lieschke, G., 2013, In : FEBS Letters. 587, 14, p. 2150 - 2157 8 p.

Research output: Contribution to journalArticleResearchpeer-review

33 Citations (Scopus)

Yeast hEST1A/B (SMG5/6)-like proteins contribute to environment-sensing adaptive gene expression responses

Lai, X., Beilharz, T. H., Au, W-C., Hammet, A., Preiss, T., Basrai, M. A. & Heierhorst, J., 2013, In : G3: Genes, Genomes, Genetics. 3, 10, p. 1649 - 1659 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2 Citations (Scopus)
2012

A model system for mitochondrial biogenesis reveals evolutionary rewiring of protein import and membrane assembly pathways

Hewitt, V. L., Heinz, E., Shingu-Vazquez, M. A., Qu, Y., Jelicic, B., Lo, T. L., Beilharz, T. H., Dumsday, G., Gabriel, K., Traven, A. & Lithgow, T. J., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 49, p. E3358 - E3366 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
17 Citations (Scopus)

ePAT: a simple method to tag adenylated RNA to measure poly(A)-tail length and other 3' RACE applications

Jaenicke, A., Vancuylenberg, J., Boag, P., Traven, A. & Beilharz, T. H., 2012, In : Rna-A Publication of the Rna Society. 18, 6, p. 1289 - 1295 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
50 Citations (Scopus)

Mitochondrial sorting and assembly machinery subunit Sam37 in Candida albicans: insight into the roles of mitochondria in fitness, cell wall integrity, and virulence

Qu, Y., Jelicic, B., Pettolino, F. A., Perry, A. J., Lo, T., Hewitt, V. L., Bantun, F., Beilharz, T. H., Peleg, A. Y., Lithgow, T. J., Djordjevic, J. & Traven, A., 2012, In : Eukaryotic Cell. 11, 4, p. 532 - 544 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
32 Citations (Scopus)

The functions of mediator in Candida albicans support a role in shaping species-specific gene expression

Uwamahoro, N., Qu, Y., Jelicic, B., Lo, T., Beaurepaire, C., Bantun, F., Quenault, T., Boag, P., Ramm, G., Callaghan, J. M., Beilharz, T. H., Nantel, A., Peleg, A. Y. & Traven, A., 2012, In : PLoS Genetics. 8, 4 (Art. ID: e1002613), p. 1 - 18 18 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
31 Citations (Scopus)

The mRNA decay pathway regulates expressionof the Flo11 adhesin and biofilm formation in Saccharomyces cerevisiae

Lo, T. L., Qu, Y., Uwamahoro, N., Quenault, T. L., Beilharz, T. H. & Traven, A., 2012, In : Genetics. 191, 4, p. 1387 - 1391 5 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

Transcriptional profiling of a yeast colony provides new insight into the heterogeneity of multicellular fungal communities

Traven, A., Jaenicke, A., Harrison, P., Swaminathan, A., Seemann, T. & Beilharz, T. H., 2012, In : PLoS ONE. 7, 9, 11 p., e46243.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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24 Citations (Scopus)
2011

Cell wall integrity is linked to mitochondria and phospholipid homeostasis in Candida albicans through the activity of the post-transcriptional regulator Ccr4-Pop2

Dagley, M. J., Gentle, I. E., Beilharz, T. H., Pettolino, F. A., Djordjevic, J., Lo, T., Uwamahoro, N., Rupasinghe, T. W. T., Tull, D., McConville, M. J., Beaurepaire, C., Nantel, A., Lithgow, T. J., Mitchell, A. P. & Traven, A., 2011, In : Molecular Microbiology. 79, 4, p. 968 - 989 22 p.

Research output: Contribution to journalArticleResearchpeer-review

75 Citations (Scopus)

mRNA isoform diversity can obscure detection of miRNA-mediated control of translation

Clancy, J. L., Wei, G. H., Echner, N., Humphreys, D. T., Beilharz, T. H. & Preiss, T., 2011, In : Rna-A Publication of the Rna Society. 17, 6, p. 1025 - 1031 7 p.

Research output: Contribution to journalArticleResearchpeer-review

23 Citations (Scopus)

Polyadenylation state microarray (PASTA) analysis

Beilharz, T. & Preiss, T., 2011, Yeast Systems Biology: Methods and Protocols. Castrillo, J. I. & Oliver, S. G. (eds.). 1st ed. USA: Humana Press, p. 133 - 147 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Other

4 Citations (Scopus)

Probing connectivity between transcriptional and post-transcriptional gene networks

Boyd, S., Keith, J. M., Traven, A. & Beilharz, T. H., 1 Nov 2011, In : Microbiology Australia. 32, 4, p. 166-168 3 p.

Research output: Contribution to journalArticleOtherpeer-review

Open Access
2010

miRNA effects on mRNA closed-loop formation during translation initiation

Beilharz, T. H., Humphreys, D. T. & Preiss, T., 2010, miRNA Regulation of the Translational Machinery. Rhoads, R. E. (ed.). 1st ed. Germany: Springer, p. 99 - 112 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

13 Citations (Scopus)
2009

microRNA-mediated messenger RNA deadenylation contributes to translational repression in mammalian cells

Beilharz, T. H., Humphreys, D. T., Clancy, J. L., Thermann, R., Martin, D. IK., Hentze, M. W. & Preiss, T., 2009, In : PLoS ONE. 4, 8, p. e6783-1 - e6783-12 12 p.

Research output: Contribution to journalArticleResearchpeer-review

68 Citations (Scopus)

The Ccr4-Pop2-NOT mRNA deadenylase contributes to septin organization in Saccharomyces cerevisiae

Traven, A., Beilharz, T. H., Lo, T. L., Lueder, F. B., Preiss, T. & Heierhorst, J., 2009, In : Genetics. 182, 4, p. 955 - 966 12 p.

Research output: Contribution to journalArticleResearchpeer-review

17 Citations (Scopus)

Transcriptome-wide measurement of mRNA polyadenylation state

Beilharz, T. H. & Preiss, T., 2009, In : Methods. 48, 3, p. 294 - 300 7 p.

Research output: Contribution to journalArticleResearchpeer-review

18 Citations (Scopus)
2007

A network of multiple regulatory layers shapes gene expression in fission yeast

Lackner, D. H., Beilharz, T. H., Marguerat, S., Mata, J., Watt, S., Schubert, F., Preiss, T. & Bahler, J., 2007, In : Molecular Cell. 26, 1, p. 145 - 155 11 p.

Research output: Contribution to journalArticleResearchpeer-review

148 Citations (Scopus)

Methods to Analyze MicroRNA-Mediated Control of mRNA Translation

Clancy, J. L., Nousch, M., Humphreys, D. T., Westman, B. J., Beilharz, T. H. & Preiss, T., 2007, Translation Initiation: Cell Biology, High Throughput Methods, and Chemical Based Approaches. Vol. 431. p. 83-111 29 p. (Methods in Enzymology; vol. 431).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

37 Citations (Scopus)

Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome

Beilharz, T. H. & Preiss, T., 2007, In : Rna-A Publication of the Rna Society. 13, 7, p. 982 - 997 16 p.

Research output: Contribution to journalArticleResearchpeer-review

95 Citations (Scopus)
2006

Ccr4 contributes to tolerance of replication stress through control of CRT1 mRNA poly(A) tail length

Woolstencroft, R. N., Beilharz, T. H., Crook, M. A., Preiss, T., Durocher, D. & Tyers, M., 2006, In : Journal of Cell Science. 119, Pt 24, p. 5178 - 5192 15 p.

Research output: Contribution to journalArticleResearchpeer-review

45 Citations (Scopus)

Integral membrane proteins in the mitochondrial outer membrane of Saccharomyces cerevisiae

Burri, L., Vascotto, K., Gentle, I. E., Chan, N. C., Beilharz, T., Stapleton, D. I., Ramage, L. & Lithgow, T. J., 2006, In : FEBS Journal. 273, 7, p. 1507 - 1515 9 p.

Research output: Contribution to journalArticleResearchpeer-review

36 Citations (Scopus)