Computational Biology

  • United Kingdom

Research Output

2017

Modulation of the Neisseria gonorrhoeae drug efflux conduit MtrE

Tamburrino, G., Llabrés, S., Vickery, O. N., Pitt, S. J. & Zachariae, U., 6 Dec 2017, In : Scientific Reports. 7, 10 p., 17091.

Research output: Contribution to journalArticle

Open Access
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203 Downloads (Pure)

Molecular mechanisms facilitating the initial kinetochore encounter with spindle microtubules

Vasileva, V., Gierlinski, M., Yue, Z., O'Reilly, N., Kitamura, E. & Tanaka, T. U., 26 Apr 2017, In : Journal of Cell Biology. 216, 6, p. 1809-1822 14 p.

Research output: Contribution to journalArticle

Open Access
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8 Citations (Scopus)
143 Downloads (Pure)

Mutations in desmoglein-1 cause diverse inherited palmoplantar keratoderma phenotypes: implications for genetic screening

Lovgren, M-L., McAleer, M. A., Irvine, A. D., Wilson, N. J., Tavadia, S., Schwartz, M. E., Cole, C., Sandilands, A., Smith, F. J. D. & Zamiri, M., 2 Apr 2017, In : British Journal of Dermatology.

Research output: Contribution to journalArticle

Open Access
File
12 Citations (Scopus)
159 Downloads (Pure)

Mutations in POGLUT1 in Galli-Galli/Dowling Degos-disease

Wilson, N. J., Cole, C., Kroboth, K., Hunter, W. N., Mann, J. A., Irwin McLean, W. H., Kernland Lang, K., Beltraminelli, H., Sabroe, R. A., Tiffin, N., Sobey, G. J., Borradori, L., Simpson, E. & Smith, F. J. D., Jan 2017, In : British Journal of Dermatology. 176, 1, p. 270-274 5 p.

Research output: Contribution to journalLetter

Open Access
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8 Citations (Scopus)
101 Downloads (Pure)

On the role of subunit M in cytochrome cbb3 oxidase

Carvalheda, C. A. & Pisliakov, A. V., 9 Sep 2017, In : Biochemical and Biophysical Research Communications. 491, 1, p. 47-52 6 p.

Research output: Contribution to journalArticle

Open Access
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171 Downloads (Pure)

Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump

Fitzpatrick, A. W. P., Llabres, S., Neuberger, A., Blaza, J. N., Bai, X-C., Okada, U., Murakami, S., van Veen, H. W., Zachariae, U., Scheres, S. H. W., Luisi, B. F. & Du, D., 15 May 2017, In : Nature Microbiology. 2, p. 1-8 8 p., 17070.

Research output: Contribution to journalArticle

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

Universal attenuators and their interactions with feedback loops in gene regulatory networks

Liu, D., Albergante, L. & Newman, T. J., 7 Jul 2017, In : Nucleic Acids Research. 45, 12, p. 7078-7093 16 p.

Research output: Contribution to journalArticle

Open Access
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1 Citation (Scopus)
196 Downloads (Pure)
2016
Open Access
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9 Citations (Scopus)
177 Downloads (Pure)

AlmostSignificant: Simplifying quality control of high-throughput sequencing data

Ward, J., Cole, C., Febrer, M. & Barton, G., 16 May 2016, 2 p. BioRxiv.

Research output: Other contribution

File
76 Downloads (Pure)

AlmostSignificant: simplifying quality control of high-throughput sequencing data

Ward, J., Cole, C., Febrer, M. & Barton, G. J., 15 Dec 2016, In : Bioinformatics. 32, 24, p. 3850-3851 2 p.

Research output: Contribution to journalArticle

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

Dynamical Patterns of Coexisting Strategies in a Hybrid Discrete-continuum Spatial Evolutionary Game Model

Burgess, A. E. F., Schofield, P. G., Hubbard, S. F., Chaplain, M. A. J. & Lorenzi, T., 7 Dec 2016, In : Mathematical Modelling of Natural Phenomena. 11, 5, p. 49-64 16 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)
Open Access
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7 Citations (Scopus)
173 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.

Research output: Contribution to journalArticle

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

Impact of Ser17 phosphorylation on the conformational dynamics of the oncoprotein MDM2

Bueren-Calabuig, J. A. & Michel, J., 3 May 2016, In : Biochemistry. 55, 17, p. 2500-2509 10 p.

Research output: Contribution to journalArticle

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

Improved Annotation with de novo Transcriptome Assembly in Four Social Amoeba Species

Singh, R., Lawal, H. M., Schilde, C., Gloeckner, G., Barton, G., Schaap, P. & Cole, C., 24 May 2016, 34 p. BioRxiv.

Research output: Other contribution

File
85 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.

Research output: Contribution to journalArticle

Open Access
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13 Citations (Scopus)
449 Downloads (Pure)

Insights into biological complexity from simple foundations

Albergante, L., Liu, D., Palmer, S. & Newman, T. J., 19 May 2016, Biophysics of infection. Leake, M. C. (ed.). Switzerland: Springer International Publishing, p. 295-305 11 p. (Advances in experimental medicine and biology; vol. 915).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

3 Citations (Scopus)

Isolated recessive nail dysplasia caused by FZD6 mutations: report of three families and review of the literature

Kasparis, C., Reid, D., Wilson, N. J., Okur, V., Cole, C., Hansen, C. D., Bosse, K., Betz, R. C., Khan, M. & Smith, F. J. D., Dec 2016, In : Clinical and Experimental Dermatology. 41, 8, p. 884-889 6 p.

Research output: Contribution to journalArticle

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

Keratin 12 missense mutation induces the unfolded protein response and apoptosis in meesmann epithelial corneal dystrophy

Allen, E. H. A., Courtney, D. G., Atkinson, S. D., Moore, J. E., Mairs, L., Poulsen, E. T., Schiroli, D., Maurizi, E., Cole, C., Hickerson, R. P., James, J., Murgatroyd, H., Smith, F. J. D., MacEwen, C., Enghild, J. J., Nesbit, M. A., Leslie Pedrioli, D. M., McLean, W. H. I. & Moore, C. B. T., 15 Mar 2016, In : Human Molecular Genetics. 25, 6, p. 1176-1191 16 p., ddw001.

Research output: Contribution to journalArticle

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

Membrane Potentials Regulating GPCRs: Insights From Experiments and Molecular Dynamics Simulation

Vickery, O., Machtens, J-P. & Zachariae, U., Oct 2016, In : Current Opinion in Pharmacology. 30, p. 44-50 7 p.

Research output: Contribution to journalArticle

Open Access
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14 Citations (Scopus)
159 Downloads (Pure)

Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM

Varshney, D., Petit, A-P., Bueren-Calabuig, J. A., Jansen, C., Fletcher, D. A., Peggie, M., Weidlich, S., Scullion, P., Pisliakov, A. V. & Cowling, V. H., 1 Dec 2016, In : Nucleic Acids Research. 44, 21, p. 10423-10436 14 p.

Research output: Contribution to journalArticle

Open Access
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15 Citations (Scopus)
365 Downloads (Pure)

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

Yachdav, G., Wilzbach, S., Rauscher, B., Sheridan, R., Sillitoe, I., Procter, J., Lewis, S. E., Rost, B. & Goldberg, T., 15 Nov 2016, In : Bioinformatics. 32, 22, p. 3501-3503 3 p.

Research output: Contribution to journalArticle

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

Stepwise Simulation of 3,5-Dihydro-5-methylidene-4H-imidazol-4-one (MIO) Biogenesis in Histidine Ammonia-lyase

Sánchez-Murcia, P. A., Bueren-Calabuig, J. A., Camacho-Artacho, M., Cortés-Cabrera, Á. & Gago, F., 18 Oct 2016, In : Biochemistry. 55, 41, p. 5854-5864 11 p.

Research output: Contribution to journalArticle

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

The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription

Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S. & Owen-Hughes, T., 28 Mar 2016, In : PLoS Genetics. 12, 3, e1005940.

Research output: Contribution to journalArticle

Open Access
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30 Citations (Scopus)
149 Downloads (Pure)

Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells

Moreno, A., Carrington, J. T., Albergante, L., Al Mamun, M., Haagensen, E. J., Komseli, E-S., Gorgoulis, V. G., Newman, T. J. & Blow, J., 27 Sep 2016, In : Proceedings of the National Academy of Sciences. 113, 39, p. E5757-E5764 8 p.

Research output: Contribution to journalArticle

Open Access
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48 Citations (Scopus)
366 Downloads (Pure)

What's in a name? Word inflation, punctuation, abbreviation and cloud formation

Schofield, S. J. & Schofield, P. G., Dec 2016, In : Medical Education. 50, 12, p. 1264-1268 5 p.

Research output: Contribution to journalArticle

Open Access
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4 Citations (Scopus)
178 Downloads (Pure)
2015

14-3-3-Pred: Improved methods to predict 14-3-3-binding phosphopeptides

Madeira, F., Tinti, M., Murugesan, G., Berrett, E., Stafford, M., Toth, R., Cole, C., MacKintosh, C. & Barton, G. J., 2015, In : Bioinformatics.

Research output: Contribution to journalArticle

Open Access
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58 Citations (Scopus)
315 Downloads (Pure)

Cohort comparison study of cardiac disease and atherosclerotic burden in type 2 diabetic adults using whole body cardiovascular magnetic resonance imaging

Duce, S. L., Weir-McCall, J. R., Gandy, S. J., Matthew, S. Z., Cassidy, D. B., McCormick, L., Rauchhaus, P., Looker, H., Colhoun, H. M. & Houston, J. G., 18 Sep 2015, In : Cardiovascular Diabetology. 14, 11 p., 122.

Research output: Contribution to journalArticle

Open Access
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13 Citations (Scopus)
134 Downloads (Pure)

Correlation between the photon index and X-ray luminosity of black hole X-ray binaries and active galactic nuclei: Observations and interpretation

Yang, Q. X., Xie, F. G., Yuan, F., Zdziarski, A. A., Gierliński, M., Ho, L. C. & Yu, Z., 21 Feb 2015, In : Monthly Notices of the Royal Astronomical Society. 447, 2, p. 1692-1704 13 p.

Research output: Contribution to journalArticle

52 Citations (Scopus)

Expanding the clinical spectrum of hereditary fibrosing poikiloderma with tendon contractures, myopathy and pulmonary fibrosis due to FAM111B mutations

Mercier, S., Küry, S., Salort-Campana, E., Magot, A., Agbim, U., Besnard, T., Bodak, N., Bou-Hanna, C., Bréhéret, F., Brunelle, P., Caillon, F., Chabrol, B., Cormier-Daire, V., David, A., Eymard, B., Faivre, L., Figarella-Branger, D., Fleurence, E., Ganapathi, M., Gherardi, R. & 34 others, Goldenberg, A., Hamel, A., Igual, J., Irvine, A. D., Israël-Biet, D., Kannengiesser, C., Laboisse, C., Le Caignec, C., Mahé, J. Y., Mallet, S., MacGowan, S., McAleer, M. A., McLean, I., Méni, C., Munnich, A., Mussini, J. M., Nagy, P. L., Odel, J., O'Regan, G. M., Péréon, Y., Perrier, J., Piard, J., Puzenat, E., Sampson, J. B., Smith, F., Soufir, N., Tanji, K., Thauvin, C., Ulane, C., Watson, R. M., Khumalo, N. P., Mayosi, B. M., Barbarot, S. & Bézieau, S., 15 Oct 2015, In : Orphanet Journal of Rare Diseases. 10, 16 p., 135.

Research output: Contribution to journalArticle

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

Expanding the phenotypic spectrum of Olmsted syndrome

Wilson, N. J., Cole, C., Milstone, L. M., Kiszewski, A. E., Hansen, C. D., O'Toole, E. A., Schwartz, M. E., McLean, W. H. I. & Smith, F. J. D., Nov 2015, In : Journal of Investigative Dermatology. 135, 11, p. 2879-2883 5 p.

Research output: Contribution to journalLetter

13 Citations (Scopus)

Haemophilus influenzae responds to glucocorticoids used in asthma therapy by modulation of biofilm formation and antibiotic resistance

Earl, C. S., Keong, T. W., An, S-Q., Murdoch, S., McCarthy, Y., Garmendia, J., Ward, J., Dow, J. M., Yang, L., O'Toole, G. A. & Ryan, R. P., 1 Aug 2015, In : Embo Molecular Medicine. 7, 8, p. 1018-1033 16 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

High-resolution quantitative proteome analysis reveals substantial differences between phagosomes of RAW 264.7 and bone marrow-derived macrophages

Guo, M., Härtlova, A., Dill, B. D., Prescott, A. R., Gierliński, M. & Trost, M., Sep 2015, In : Proteomics. 15, 18, p. 3169-3174 6 p.

Research output: Contribution to journalArticle

Open Access
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31 Citations (Scopus)
127 Downloads (Pure)

JPred4: a protein secondary structure prediction server

Drozdetskiy, A., Cole, C., Procter, J. & Barton, G. J., 1 Jul 2015, In : Nucleic Acids Research. 43, W1, p. W389-W394 6 p.

Research output: Contribution to journalArticle

Open Access
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671 Citations (Scopus)
293 Downloads (Pure)

Loss-of-function mutations in CAST cause peeling skin, leukonychia, acral punctate keratoses, cheilitis, and knuckle pads

Lin, Z., Zhao, J., Nitoiu, D., Scott, C. A., Plagnol, V., Smith, F. J. D., Wilson, N. J., Cole, C., Schwartz, M. E., McLean, W. H. I., Wang, H., Feng, C., Duo, L., Zhou, E. Y., Ren, Y., Dai, L., Chen, Y., Zhang, J., Xu, X., O'Toole, E. A. & 2 others, Kelsell, D. P. & Yang, Y., 5 Mar 2015, In : American Journal of Human Genetics. 96, 3, p. 440-447 8 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

M 3 D: A kernel-based test for spatially correlated changes in methylation profiles

Mayo, T. R., Schweikert, G. & Sanguinetti, G., 15 Mar 2015, In : Bioinformatics. 31, 6, p. 809-816 8 p.

Research output: Contribution to journalArticle

Open Access
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12 Citations (Scopus)
91 Downloads (Pure)

Novel autosomal dominant mutation in loricrin presenting as prominent ichthyosis

Pohler, E., Cunningham, F., Sandilands, A., Cole, C., Digby, S., McMillan, J. R., Aristodemou, S., McGrath, J. A., Smith, F. J. D., Mclean, W. H. I., Munro, C. S. & Zamiri, M., 26 Nov 2015, In : British Journal of Dermatology. 173, 5, p. 1292-1294 4 p.

Research output: Contribution to journalLetter

Open Access
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3 Citations (Scopus)
140 Downloads (Pure)

Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1

Lai, Y-C., Kondapalli, C., Lehneck, R., Procter, J. B., Dill, B. D., Woodroof, H. I., Gourlay, R., Peggie, M., Macartney, T. J., Corti, O., Corvol, J-C., Campbell, D. G., Itzen, A., Trost, M. & Muqit, M. MK., 12 Nov 2015, In : EMBO Journal. 34, 22, p. 2840-2861 22 p.

Research output: Contribution to journalArticle

Open Access
96 Citations (Scopus)

Proteotoxic stress reprograms the chromatin landscape of SUMO modification

Seifert, A., Schofield, P., Barton, G. & Hay, R., 7 Jul 2015, In : Science Signaling. 8, 384, p. rs7 14 p.

Research output: Contribution to journalArticle

Open Access
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36 Citations (Scopus)
212 Downloads (Pure)

Quantitative proteome analysis of temporally-resolved phagosomes following uptake via key phagocytic receptors

Dill, B., Gierliński, M., Härtlova, A., González Arandilla, A., Guo, M., Clarke, R. G. & Trost, M., 1 May 2015, In : Molecular & Cellular Proteomics. 14, 5, p. 1334 1349 p., 16.

Research output: Contribution to journalArticle

Open Access
29 Citations (Scopus)

Role of structural dynamics at the receptor G protein interface for signal transduction

Rose, A. S., Zachariae, U., Grubmüller, H., Hofmann, K. P., Scheerer, P. & Hildebrand, P. W., 25 Nov 2015, In : PLoS ONE. 10, 11, 13 p., e0143399.

Research output: Contribution to journalArticle

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

Severe dermatitis, multiple allergies, and metabolic wasting syndrome caused by a novel mutation in the N-terminal plakin domain of desmoplakin

McAleer, M. A., Pohler, E., Smith, F. J. D., Wilson, N. J., Cole, C., MacGowan, S., Koetsier, J. L., Godsel, L. M., Harmon, R. M., Gruber, R., Crumrine, D., Elias, P. M., McDermott, M., Butler, K., Broderick, A., Sarig, O., Sprecher, E., Green, K. J., McLean, W. H. I. & Irvine, A. D., Nov 2015, In : Journal of Allergy and Clinical Immunology. 136, 5, p. 1268-1276 9 p.

Research output: Contribution to journalArticle

62 Citations (Scopus)

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment

Gierlinski, M., Cole, C., Schofield, P., Schurch, N. J., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G., Owen-Hughes, T., Blaxter, M. & Barton, G. J., 15 Nov 2015, In : Bioinformatics. 31, 22, p. 3625-3630 6 p.

Research output: Contribution to journalArticle

Open Access
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33 Citations (Scopus)
165 Downloads (Pure)
2014

Evaluation of the diagnostic accuracy of prototype rapid tests for human African trypanosomiasis

Sternberg, J. M., Gierlinski, M., Biéler, S., Ferguson, M. A. J. & Ndung'u, J. M., Dec 2014, In : PLoS Neglected Tropical Diseases. 8, 12, p. e3373 8 p.

Research output: Contribution to journalArticle

Open Access
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24 Citations (Scopus)
156 Downloads (Pure)

Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo

Olivera-Martinez, I., Schurch, N., Li, R., Song, J., Halley, P. A., Das, R. M., Burt, D. W., Barton, G. J. & Storey, K. G., Aug 2014, In : Development. 141, 16, p. 3266-3276 11 p.

Research output: Contribution to journalArticle

Open Access
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23 Citations (Scopus)
143 Downloads (Pure)

Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence

An, S., Caly, D. L., McCarthy, Y., Murdoch, S. L., Ward, J., Febrer, M., Dow, J. M. & Ryan, R. P., 16 Oct 2014, In : PLoS Pathogens. 10, 10, 12 p., e1004429.

Research output: Contribution to journalArticle

Open Access
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28 Citations (Scopus)
168 Downloads (Pure)

Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling

Atrih, A., Mudaliar, M. A. V., Zakikhani, P., Lamont, D. J., Huang, J. T-J., Bray, S. E., Barton, G., Fleming, S. & Nabi, G., 2014, In : British Journal of Cancer. 110, 6, p. 1622-1633 12 p.

Research output: Contribution to journalArticle

Open Access
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39 Citations (Scopus)
165 Downloads (Pure)
2013

3D MRI Analysis of the Lower Legs of Treated Idiopathic Congenital Talipes Equinovarus (Clubfoot)

Duce, S. L., D'Alessandro, M., Du, Y., Jagpal, B., Gilbert, F. J., Crichton, L., Barker, S., Collinson, J. M. & Miedzybrodzka, Z., 30 Jan 2013, In : PLoS ONE. 8, 1, 10 p., e54100.

Research output: Contribution to journalArticle

Open Access
13 Citations (Scopus)

Crystal structure and functional mechanism of a human antimicrobial membrane channel

Song, C., Weichbrodt, C., Salnikov, E. S., Dynowski, M., Forsberg, B. O., Bechinger, B., Steinem, C., De Groot, B. L., Zachariae, U. & Zeth, K., 19 Mar 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 12, p. 4586-4591 6 p.

Research output: Contribution to journalArticle

Open Access
73 Citations (Scopus)