Computational Biology

  • United Kingdom

Research Output 1987 2019

2019
20 Downloads (Pure)

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

Mourao, K., Schurch, N., Lukoszek, R., Froussios, K., Mackinnon, K., Duc, C., Simpson, G. & Barton, G., 10 Jun 2019, In : F1000 Research. 8, 7 p., 819.

Research output: Contribution to journalArticle

Open Access
File
Antisense RNA
RNA
Gene Expression
Genes
Arabidopsis

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
Atopic Dermatitis
Skin
Genome-Wide Association Study
Keratinocytes
Skin Diseases
49 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
File
Lactams
Porins
Electrophysiology
Anti-Bacterial Agents
Gram-Negative Bacteria
27 Downloads (Pure)
Open Access
File
Differential Expression
Eukaryota
RNA
Gene expression
Gene Expression
8 Citations (Scopus)

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

Histone Demethylases
Histones
Methylation
Chromatin
Dioxygenases
1 Citation (Scopus)
49 Downloads (Pure)

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
File
Mitosis
Chromatids
Chromosomes
Prophase
G2 Phase
6 Downloads (Pure)
Open Access
File
Guanine
Methyltransferases
Molecular Dynamics Simulation
RNA
S-Adenosylmethionine
24 Downloads (Pure)
Open Access
File
Biofilms
Bacillus subtilis
Growth
Iron
pulcherriminic acid
26 Downloads (Pure)
Open Access
File
RNA Isoforms
Protein Isoforms
RNA
Transcriptome
Drosophila
2 Citations (Scopus)
40 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
File
Phosphatidylglycerols
Ammonium Compounds
Escherichia coli
Lipids
Protein Unfolding
56 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., 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
File
Scavenger Receptors
Macrophages
Interleukin-4
Inflammation
Chemical activation
2018
12 Citations (Scopus)
76 Downloads (Pure)

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
File
Filament
filaments
Active Particles
Langevin Dynamics
bundles
1 Citation (Scopus)
74 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., 19 Jul 2018, In : Scientific Reports. 8, 1, p. 1-10 10 p., 10922.

Research output: Contribution to journalArticle

Open Access
File
Trypanosomiasis
Membrane Glycoproteins
Parasites
Antigens
Growth
31 Downloads (Pure)
File
Kinetochores
Microtubules
Chromosome Segregation
Aurora Kinase B
Spindle Poles
2 Citations (Scopus)
80 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
File
RNA Secondary Structure
Sequence Alignment
Bioinformatics
Computational Biology
RNA
25 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

File
Chromatids
Chromosomes
Prophase
Genomic Instability
G2 Phase
5 Citations (Scopus)
46 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
File
RNA Polymerase II
Methyltransferases
Random access storage
Transcription
Messenger RNA
9 Citations (Scopus)
88 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
File
DNA Repair-Deficiency Disorders
DNA Mismatch Repair
Neoplasms
Genome
Cytosine
11 Citations (Scopus)
76 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
File
Sexual Development
Mutation
Genes
Primary Ovarian Insufficiency
Male Infertility
4 Citations (Scopus)
38 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
File
Stem Cells
Spinal Cord
Embryonic Structures
Clustered Regularly Interspaced Short Palindromic Repeats
Population
1 Citation (Scopus)
50 Downloads (Pure)
File
Proteome
Breast
Epithelial Cells
Proteins
Oncogenes
157 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
File
Proteus
Peptides
Mass Spectrometry
Proteins

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
2 Citations (Scopus)
82 Downloads (Pure)

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
File
Intellectual Disability
Mutation
Acetylglucosamine
Post Translational Protein Processing
Brain
12 Citations (Scopus)
66 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
File
Proteome
Hot Temperature
Proteasome Endopeptidase Complex
Chemical activation
Cells
22 Citations (Scopus)
130 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
File
Incidence
Neoplasms
Communicable Diseases
T-Lymphocytes
Allergy and Immunology

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
Learning
Metagenomics
Foster Home Care
Genomics
Research
2017
3 Citations (Scopus)
101 Downloads (Pure)
Open Access
File
Dictyostelium
Adenylyl Cyclases
Genes
Cell Movement
bis(3',5')-cyclic diguanylic acid
5 Citations (Scopus)
128 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
File
Cathepsin H
Thymoma
Atopic Dermatitis
Oncogenes
Skin
14 Citations (Scopus)
105 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
File
Acetylation
Proteomics
Aspirin
Lysine
acetylsalicylic acid lysinate
36 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
File
4 Citations (Scopus)

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

Prisoners' Dilemma
semiochemicals
Pheromones
Coexistence
Individual-based Model
12 Downloads (Pure)

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

File
RNA Splice Sites
Ligands
Proteins
Sequence Alignment
DNA-Binding Proteins
1 Citation (Scopus)
33 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
File
Amoeba
Transcriptome
Genome
RNA Sequence Analysis
Molecular Sequence Annotation
4 Citations (Scopus)
66 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
File
Protons
Proton transfer
Oxygen
Water
Protonation
10 Citations (Scopus)
8 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
File
gene expression
Transcriptome
Gene expression
Complementary DNA
RNA
13 Citations (Scopus)
65 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
File
Proteins
Education
Protein Databases
Precision Medicine
Mutation
68 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
File
Kinetochores
Mitosis
Microtubules
Spindle Poles
Chromosome Segregation
20 Citations (Scopus)
6 Downloads (Pure)

MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain

Lagger, S., Connelly, J. C., Schweikert, G., Webb, S., Selfridge, J., Ramsahoye, B. H., Yu, M., He, C., Sanguinetti, G., Sowers, L. C., Walkinshaw, M. D. & Bird, A., 12 May 2017, In : PLoS Genetics. 13, 5, e1006793.

Research output: Contribution to journalArticle

Open Access
File
cytosine
Cytosine
brain
Nucleotides
transcription (genetics)
121 Downloads (Pure)

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
File
Neisseria gonorrhoeae
Membrane Fusion Proteins
Electrophysiology
Lipid Bilayers
Microbial Drug Resistance
6 Citations (Scopus)
63 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
File
Kinetochores
Microtubules
Saccharomycetales
Mitosis
10 Citations (Scopus)
74 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
Desmoglein 1
Palmoplantar Keratoderma
Genetic Testing
Phenotype
Mutation
6 Citations (Scopus)
53 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
File
Glucosyltransferases
Genetic Databases
Mutation
Proteins
Keratin-5
85 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
File
Heme
Protons
Oxidoreductases
Aquaporins
Pathogens
39 Citations (Scopus)
108 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
File
Lepidium
Adenosine Triphosphate
Periplasmic Proteins
Cryoelectron Microscopy
Periplasm
1 Citation (Scopus)
119 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
File
Gene Regulatory Networks
Regulator Genes
Gene Expression
Escherichia coli K12
Tuberculosis
2016
7 Citations (Scopus)
98 Downloads (Pure)
Open Access
File
phylogeny
genome
protein
proteins
Dictyostelium
13 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
DNA Sequence Analysis
Quality Control
Documentation
Technology
2 Citations (Scopus)
27 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
File
Quality Control
DNA Sequence Analysis
Sequencing
High Throughput
Quality control
4 Citations (Scopus)

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

Evolutionary Game
Continuum
Motion
Game
Individual-based Model