Computational Biology

  • United Kingdom

Research Output

2020

3 tera-basepairs as a fundamental limit for robust DNA replication

Al Mamun, M., Albergante, L., Blow, J. & Newman, T., 30 Jun 2020, In : Physical Biology. 17, 4, 046002.

Research output: Contribution to journalArticle

Open Access
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30 Downloads (Pure)

A two-lane mechanism for selective biological ammonium transport

Williamson, G., Tamburrino, G., Bizior, A., Boeckstaens, M., Dias Mirandela, G., Bage, M., Pisliakov, A., Ives, C. M., Terras, E., Hoskisson, P. A., Marini, A-M., Zachariae, U. & Javelle, A., 14 Jul 2020, In : eLife. 9, e57183.

Research output: Contribution to journalArticle

Open Access
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6 Downloads (Pure)
Open Access
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57 Downloads (Pure)

Genomic Differences between Listeria monocytogenes EGDe Isolates Reveal Crucial Roles for SigB and Wall Rhamnosylation in Biofilm Formation

Hsu, C-Y., Cairns, L., Hobley, L., Abbott, J., O'Byrne, C. & Stanley-Wall, N. R., 11 Mar 2020, In : Journal of Bacteriology. 202, 7, p. 1-13 13 p., e00692-19.

Research output: Contribution to journalArticle

Open Access
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1 Citation (Scopus)
37 Downloads (Pure)

GPCRmd uncovers the dynamics of the 3D-GPCRome

Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J. K. S., Aranda-García, D., Ramírez-Anguita, J. M., Stepniewski, T. M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Medel-Lacruz, B., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J., Deupi, X., Filipek, S., Filizola, M., Gómez-Tamayo, J. C., Gonzalez, A., Gutiérrez-de-Terán, H. & 27 others, Jiménez-Rosés, M., Jespers, W., Kapla, J., Khelashvili, G., Kolb, P., Latek, D., Marti-Solano, M., Matricon, P., Matsoukas, M. T., Miszta, P., Olivella, M., Perez-Benito, L., Provasi, D., Ríos, S., Torrecillas, I. R., Sallander, J., Sztyler, A., Vasile, S., Weinstein, H., Zachariae, U., Hildebrand, P. W., De Fabritiis, G., Sanz, F., Gloriam, D. E., Cordomi, A., Guixà-González, R. & Selent, J., 13 Jul 2020, In : Nature Methods.

Research output: Contribution to journalArticle

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Parker, M. T., Knop, K., Sherwood, A. V., Schurch, N. J., Mackinnon, K., Gould, P. D., Hall, A. J. W., Barton, G. J. & Simpson, G. G., 14 Jan 2020, In : eLife. 9, p. 1-35 35 p., e49658.

Research output: Contribution to journalArticle

Open Access
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10 Citations (Scopus)
67 Downloads (Pure)

On the ion coupling mechanism of the MATE transporter ClbM

Krah, A., Huber, R. G., Zachariae, U. & Bond, P. J., 1 Feb 2020, In : Biochimica et Biophysica Acta - Biomembranes. 1862, 2, p. 1-9 9 p., 183137.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Positively selected modifications in the pore of TbAQP2 allow pentamidine to enter Trypanosoma brucei

Alghamdi, A. H., Munday, J. C., Campagnaro, G. D., Gurvic, D., Svensson, F., Okpara, C. E., Kumar, A., Quintana, J. F., Abril, M. E. M., Milić, P., Watson, L., Paape, D., Settimo, L., Dimitriou, A., Wielinska, J., Smart, G., Anderson, L. F., Woodley, C. M., Kelley, S. P. Y., Ibrahim, H. M. S. & 12 others, Hulpia, F., Al-Salabi, M. I., Eze, A. A., Gudin, S., Field, M., Dardonville, C., Tidwell, R. R., Carrington, M., O'Neill, P. M., Boykin, D. W., Zachariae, U. & de Koning, H. P., 7 Aug 2020, In : eLife. p. 1-97 97 p., e56416.

Research output: Contribution to journalArticle

Open Access
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Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome

Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J. K. S., Aranda-García, D., Ramírez-Anguita, J. M., Stepniewski, T. M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Medel-Lacruz, B., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J., Deupi, X., Filipek, S., Filizola, M., Gómez-Tamayo, J. C., Gonzalez, A., Gutiérrez-de-Terán, H. & 27 others, Jiménez-Rosés, M., Jespers, W., Kapla, J., Khelashvili, G., Kolb, P., Latek, D., Marti-Solano, M., Matricon, P., Matsoukas, M. T., Miszta, P., Olivella, M., Perez-Benito, L., Provasi, D., Ríos, S., Torrecillas, I. R., Sallander, J., Sztyler, A., Vasile, S., Weinstein, H., Zachariae, U., Hildebrand, P. W., De Fabritiis, G., Sanz, F., Gloriam, D. E., Cordomi, A., Guixà-González, R. & Selent, J., Aug 2020, In : Nature Methods. 17, p. 861-862 2 p.

Research output: Contribution to journalComment/debate

Wnt regulates amino-acid transporter Slc7a5 and so constrains the integrated stress response in mouse embryos

Poncet, N., Halley, P., Lipina, C., Gierlinski, M., Dady, A., Singer, G., Febrer, M., Shi, Y-B., Yamaguchi, T. P., Taylor, P. & Storey, K., 7 Jan 2020, In : EMBO Reports. 21, 1, p. 1-20 20 p., e48469.

Research output: Contribution to journalArticle

Open Access
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1 Citation (Scopus)
62 Downloads (Pure)
2019

Detection and Mitigation of Spurious Antisense RNA-seq Reads with RoSA

Mourão, K., Schurch, N. J., Lukoszek, R., Froussios, K., Mackinnon, K., Duc, C., Simpson, G. & Barton, G., 7 Jun 2019, In : F1000 Research. 8, p. 1-7 7 p., 819.

Research output: Contribution to journalArticle

Open Access
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100 Downloads (Pure)

Distinct signals and immune cells drive liver pathology and glomerulonephritis in ABIN1[D485N] mice

Nanda, S. K., Petrova, T., Marchesi, F., Gierlinski, M., Razsolkov, M., Lee, K. L., Wright, S. W., Rao, V. R., Cohen, P. & Arthur, J. S. C., 1 Dec 2019, In : Life Science Alliance. 2, 6, 19 p., e201900533.

Research output: Contribution to journalArticle

Open Access
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21 Downloads (Pure)

EMSY expression affects multiple components of the skin barrier with relevance to atopic dermatitis

Elias, M. S., Wright, S. C., Remenyi, J., Abbott, J. C., Bray, S. E., Cole, C., Edwards, S., Gierlinski, M., Glok, M., McGrath, J. A., Nicholson, W. V., Paternoster, L., Prescott, A. R., Have, S. T., Whitfield, P. D., Lamond, A. I. & Brown, S. J., Aug 2019, In : Journal of Allergy and Clinical Immunology. 144, 2, p. 470-481 12 p.

Research output: Contribution to journalArticle

Open Access
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5 Citations (Scopus)
10 Downloads (Pure)

High-resolution experimental and computational electrophysiology reveals weak β-lactam binding events in the porin PorB

Bartsch, A., Llabres, S., Pein, F., Kattner, C., Schön, M., Diehn, M., Tanabe, M., Munk, A., Zachariae, U. & Steinem, C., 4 Feb 2019, In : Scientific Reports. 9, p. 1-11 11 p., 1264.

Research output: Contribution to journalArticle

Open Access
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1 Citation (Scopus)
117 Downloads (Pure)
Open Access
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75 Downloads (Pure)

Hypoxia induces rapid changes to histone methylation and reprograms chromatin

Batie, M., Frost, J., Frost, M., Wilson, J. W., Schofield, P. & Rocha, S., 15 Mar 2019, In : Science. 363, 6432, p. 1222-1226 5 p.

Research output: Contribution to journalArticle

45 Citations (Scopus)

Live imaging of marked chromosome regions reveals their dynamic resolution and compaction in mitosis

Eykelenboom, J., Gierlinski, M., Yue, Z., Hegarat, N., Pollard, H., Fukagawa, T., Hochegger, H. & Tanaka, T., 6 May 2019, In : Journal of Cell Biology. 218, 5, p. 1531-1552 22 p.

Research output: Contribution to journalArticle

Open Access
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6 Citations (Scopus)
117 Downloads (Pure)

Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: Insights from accelerated molecular dynamics simulations

Bueren-Calabuig, J., Bage, M., Cowling, V. & Pisliakov, A., 19 Sep 2019, In : Nucleic Acids Research. 47, 16, p. 8675-8692 18 p., gkz613.

Research output: Contribution to journalArticle

Open Access
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Pulcherrimin formation controls growth arrest of the Bacillus subtilis biofilm

Arnaouteli, S., Matoz Fernandez, D., Porter, M., Kalamara, M., Abbott, J., MacPhee, C. E., Davidson, F. & Stanley-Wall, N., 2 Jul 2019, In : Proceedings of the National Academy of Sciences. 116, 27, p. 13553-13562 10 p.

Research output: Contribution to journalArticle

Open Access
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3 Citations (Scopus)
110 Downloads (Pure)
Open Access
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2 Citations (Scopus)
93 Downloads (Pure)

The Dundee Resource for Sequence Analysis and Structure Prediction

MacGowan, S., Madeira, F., Britto-Borges, T., Warowny, M., Drozdetskiy, A., Procter, J. & Barton, G., 28 Nov 2019, In : Protein Science. 29, 1, p. 277-297 21 p.

Research output: Contribution to journalArticle

Open Access
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2 Citations (Scopus)
64 Downloads (Pure)

The lipid environment determines the activity of the Escherichia coli ammonium transporter AmtB

Mirandela, G. D., Tamburrino, G., Hoskisson, P. A., Zachariae, U. & Javelle, A., Feb 2019, In : FASEB Journal. 33, 2, p. 1989-1999 11 p.

Research output: Contribution to journalArticle

Open Access
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6 Citations (Scopus)
107 Downloads (Pure)

Triggering MSR1 promotes JNK-mediated inflammation in IL-4 activated macrophages

Guo, M., Härtlova, A., Gierlinski, M., Prescott, A., Castellvi, J., Hernandez Losa, J., Petersen, S. K., Wenzel, U. A., Dill, B. D., Emmerich, C. H., Ramon Y Cajal, S., Russell, D. G. & Trost, M., 3 Jun 2019, In : EMBO Journal. 38, 11, p. 1-15 15 p., e100299.

Research output: Contribution to journalArticle

Open Access
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5 Citations (Scopus)
187 Downloads (Pure)
2018

Dynamically generated patterns in dense suspensions of active filaments

Kokkoorakunnel Ramankutty, P., Henkes, S. & Sknepnek, R., 12 Feb 2018, In : Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 97, 2, 022606.

Research output: Contribution to journalArticle

Open Access
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18 Citations (Scopus)
154 Downloads (Pure)

Faster growth with shorter antigens can explain a VSG hierarchy during African trypanosome infections: a feint attack by parasites

Liu, D., Albergante, L., Newman, T. & Horn, D., 2018, In : Scientific Reports. 8, p. 1-10 10 p., 10922.

Research output: Contribution to journalArticle

Open Access
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4 Citations (Scopus)
148 Downloads (Pure)
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77 Downloads (Pure)

JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure

Troshin, P. V., Procter, J. B., Sherstnev, A., Barton, D. L., Madeira, F. & Barton, G. J., 1 Jun 2018, In : Bioinformatics. 34, 11, p. 1939-1940 2 p., byt045.

Research output: Contribution to journalArticle

Open Access
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5 Citations (Scopus)
174 Downloads (Pure)

Live-cell imaging of marked chromosome regions reveals dynamics of mitotic chromosome resolution and compaction

Eykelenboom, J. K., Gierlinski, M., Yue, Z., Hegarat, N., Pollard, H., Fukagawa, T., Hochegger, H. & Tanaka, T. U., 17 May 2018, In : BioRxiv. 53 p.

Research output: Contribution to journalArticle

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78 Downloads (Pure)

mRNA cap methyltransferase, RNMT-RAM, promotes RNA pol II-dependent transcription

Varshney, D., Lombardi, O., Schweikert, G., Dunn, S., Suska, O. & Cowling, V., May 2018, In : Cell Reports. 23, 5, p. 1530-1542 13 p.

Research output: Contribution to journalArticle

Open Access
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9 Citations (Scopus)
137 Downloads (Pure)

Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers

Meier, B., Volkova, N. V., Hong, Y., Schofield, P., Campbell, P. J., Gerstung, M. & Gartner, A., May 2018, In : Genome Research. 28, 5, p. 666-675 10 p.

Research output: Contribution to journalArticle

Open Access
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19 Citations (Scopus)
183 Downloads (Pure)

Mutations involving the SRY-related gene SOX8 are associated with a spectrum of human reproductive anomalies.

Portnoi, M-F., Dumargne, M-C., Rojo, S., Witchel, S. F., Duncan, A. J., Eozenou, C., Bignon-Topalovic, J., Yatsenko, S. A., Rajkovic, A., Reyes-Mugica, M., Almstrup, K., Fusee, L., Srivastava, Y., Chantot-Bastaraud, S., Hyon, C., Louis-Sylvestre, C., Validire, P., de Malleray Pichard, C., Ravel, C., Christin-Maitre, S. & 18 others, Brauner, R., Rossetti, R., Persani, L., Charreau, E. H., Dain, L., Chiauzzi, V. A., Mazen, I., Rouba, H., Schluth-Bolard, C., MacGowan, S., McLean, W. H. I., Patin, E., Rajpert-De Meyts, E., Jauch, R., Achermann, J. C., Siffroi, J-P., McElreavey, K. & Bashamboo, A., 1 Apr 2018, In : Human Molecular Genetics. 27, 7, p. 1228-1240 13 p.

Research output: Contribution to journalArticle

Open Access
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21 Citations (Scopus)
164 Downloads (Pure)

Neural differentiation, selection and transcriptomic profiling of human neuromesodermal progenitor-like cells in vitro

Verrier, L., Davidson, L., Gierlinski, M., Dady, A. & Storey, K., 12 Jul 2018, In : Development. 145, 16, 10 p., dev166215.

Research output: Contribution to journalArticle

Open Access
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9 Citations (Scopus)
106 Downloads (Pure)
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3 Citations (Scopus)
129 Downloads (Pure)

Proteus: an R package for downstream analysis of MaxQuant output

Gierlinski, M., Gastaldello, F., Cole, C. & Barton, G., 20 Sep 2018, In : BioRxiv. 10 p.

Research output: Contribution to journalArticle

Open Access
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405 Downloads (Pure)

Reply to Jiménez-Alonso et al., Schooling and Zhao, and Mortazavi: Further discussion on the immunological model of carcinogenesis

Palmer, S., Albergante, L., Blackburn, C. C. & Newman, T. J., 8 May 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 19, p. E4319-E4321 3 p.

Research output: Contribution to journalLetter

Open Access

The O-GlcNAc Transferase Intellectual Disability Mutation L254F Distorts the TPR Helix

Gundogdu, M., Llabres, S., Gorelik, A., Ferenbach, A., Zachariae, U. & Van Aalten, D., 17 May 2018, In : Cell Chemical Biology. 25, 5, p. 513-518.e4 10 p.

Research output: Contribution to journalArticle

Open Access
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11 Citations (Scopus)
160 Downloads (Pure)

Thermal proteome profiling of breast cancer cells reveals proteasomal activation by CDK4/6 inhibitor palbociclib

Miettinen, T. P., Peltier, J., Härtlova, A., Gierliński, M., Jansen, V. M., Trost, M. & Björklund, M., 15 May 2018, In : EMBO Journal. 37, 10, p. 1-19 19 p., e98359.

Research output: Contribution to journalArticle

Open Access
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26 Citations (Scopus)
222 Downloads (Pure)

Thymic involution and rising disease incidence with age

Palmer, S., Albergante, L., Blackburn, C. C. & Newman, T. J., 20 Feb 2018, In : Proceedings of the National Academy of Sciences. 115, 8, p. 1883-1888 6 p.

Research output: Contribution to journalArticle

Open Access
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51 Citations (Scopus)
208 Downloads (Pure)

Visualization of Biomedical Data

O'Donoghue, S. I., Baldi, B. F., Clark, S. J., Darling, A. E., Hogan, J. M., Kaur, S., Maier-Hein, L., McCarthy, D. J., Moore, W., Stenau, E., Swedlow, J., Vuong, J. & Procter, J., 20 Jul 2018, In : Annual Review of Biomedical Data Science. 1

Research output: Contribution to journalArticle

Open Access
2017
Open Access
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5 Citations (Scopus)
192 Downloads (Pure)

A mechanistic target of rapamycin complex 1/2 (mTORC1)/V-Akt murine thymoma viral oncogene homolog 1 (AKT1)/cathepsin H axis controls filaggrin expression and processing in skin, a novel mechanism for skin barrier disruption in patients with atopic dermatitis

Naeem, A. S., Tommasi, C., Cole, C., Brown, S. J., Zhu, Y., Way, B., Willis Owen, S. A. G., Moffatt, M., Cookson, W. O., Harper, J. I., Di, W. L., Brown, S. J., Reinheckel, T. & O'Shaughnessy, R. F. L., Apr 2017, In : Journal of Allergy and Clinical Immunology. 139, 4, p. 1228-1241 14 p.

Research output: Contribution to journalArticle

Open Access
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7 Citations (Scopus)
196 Downloads (Pure)

A Proteomic Approach to Analyze the Aspirin-mediated Lysine Acetylome

Tatham, M. H., Cole, C., Scullion, P., Wilkie, R., Westwood, N. J., Stark, L. A. & Hay, R. T., 1 Feb 2017, In : Molecular & Cellular Proteomics. 16, 2, p. 310-326 17 p.

Research output: Contribution to journalArticle

Open Access
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21 Citations (Scopus)
184 Downloads (Pure)

Correction: A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase

Britto Borges, T. & Barton, G., 27 Dec 2017, In : PLoS ONE. 12, 12, p. 1 1 p., e0190461.

Research output: Contribution to journalComment/debate

Open Access
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Examining the role of individual movement in promoting coexistence in a spatially explicit prisoner's dilemma

Burgess, A. E. F., Lorenzi, T., Schofield, P. G., Hubbard, S. F. & Chaplain, M. A. J., 21 Apr 2017, In : Journal of Theoretical Biology. 419, p. 323-332 10 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Human Missense Variation is Constrained by Domain Structure and Highlights Functional and Pathogenic Residues

MacGowan, S., Madeira, F., Britto Borges, T., Schmittner, M. S., Cole, C. & Barton, G., 13 Apr 2017, In : BioRxiv. 35 p.

Research output: Contribution to journalArticle

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93 Downloads (Pure)

Improved annotation with de novo transcriptome assembly in four social amoeba species

Singh, R., Lawal, H. M., Schilde, C., Glöckner, G., Barton, G. J., Schaap, P. & Cole, C., 31 Jan 2017, In : BMC Genomics. 18, p. 1-17 17 p., 120.

Research output: Contribution to journalArticle

Open Access
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1 Citation (Scopus)
108 Downloads (Pure)

Insights into proton translocation in cbb3 oxidase from MD simulations

Carvalheda, C. A. & Pisliakov, A. V., May 2017, In : Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1858, 5, p. 396-406 11 p.

Research output: Contribution to journalArticle

Open Access
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4 Citations (Scopus)
139 Downloads (Pure)

Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress

Van Nues, R., Schweikert, G., De Leau, E., Selega, A., Langford, A., Franklin, R., Iosub, I., Wadsworth, P., Sanguinetti, G. & Granneman, S., 11 Apr 2017, In : Nature Communications. 8, 1, 12.

Research output: Contribution to journalArticle

Open Access
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17 Citations (Scopus)
82 Downloads (Pure)

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: A proposed framework

Glusman, G., Rose, P. W., Prlić, A., Dougherty, J., Duarte, J. M., Hoffman, A. S., Barton, G. J., Bendixen, E., Bergquist, T., Bock, C., Brunk, E., Buljan, M., Burley, S. K., Cai, B., Carter, H., Gao, J. J., Godzik, A., Heuer, M., Hicks, M., Hrabe, T. & 17 others, Karchin, R., Leman, J. K., Lane, L., Masica, D. L., Mooney, S. D., Moult, J., Omenn, G. S., Pearl, F., Pejaver, V., Reynolds, S. M., Rokem, A., Schwede, T., Song, S., Tilgner, H., Valasatava, Y., Zhang, Y. & Deutsch, E. W., 18 Dec 2017, In : Genome Medicine. 9, 1, p. 1-10 10 p., 113.

Research output: Contribution to journalArticle

Open Access
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18 Citations (Scopus)
139 Downloads (Pure)

Mechanisms mitigating problems with multiple kinetochores on one microtubule in early mitosis

Yue, Z., Komoto, S., Gierlinski, M., Pasquali, D., Kitamura, E. & Tanaka, T. U., 15 Jul 2017, In : Journal of Cell Science. 130, 14, p. 2266-2276 11 p.

Research output: Contribution to journalArticle

Open Access
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116 Downloads (Pure)