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Hire Dr. Daniel H.

United Kingdom

Bioinformatics Scientist

Profile Summary

First and foremost, I consider myself to be a lifelong learner. This is the main reason why I decided to pursue a career in multidisciplinary science. Here, I have had the opportunity to develop skills and competencies in a wide range of bleeding-edge research techniques in the fields of Bioinformatics, Structural Biology, Molecular Simulation, and Machine Learning. With this diverse, multidisciplinary "toolkit" of skills, I feel that I am able to provide answers to challenging questions using unique strategies. My many years of performing scientific research have helped me to become comfortable in the analysis of large, complex data sets. Indeed, as a matter of routine, I use statistical packages (R Statistics) and scripting languages (Python, Perl, C shell) to analyse and process image and simulation data. While I can work independently or as part of a team, my best achievements have resulted from taking a leading role within the multidisciplinary team of researchers. As the project lead, I like to identify and use the key competencies of the individual team members. This strategy has led to a number of successful publications.

Subject Matter Expertise

• ☆ Molecular Modeling
• ☆ Zika Virus
• ☆ Bioinformatics

Services

• Writing
• Data & AI

Writing Technical Writing

Data & AI Statistical Analysis, Data Visualization

Work Experience

Founder and CEO

Codigana

February 2020 - Present

Bioinformatics Scientist

YouSeq

May 2019 - Present

Education

Doctor of Philosophy

University of Southampton

September 2009 - September 2013

Master's Degree in Bionformatics

University of Oxford

September 2009 - June 2010

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Huber, R.G., Berglund, N.A., Kargas, V., Marzinek, J.K., Holdbrook, D.A., Khalid, S., Piggot, T.J., Schmidtchen, A., Bond, P.J.(2018). A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway . Structure.

Daniel Holdbrook, Jan K. Marzinek, Roland G. Huber, Chandra Verma, Peter J. Bond(2017). Simulations Help Unravel Flavivirus Envelope Structure and Function . Biophysical Journal. 112. (3). p. 309a. Elsevier {BV}

Huber, R.G., Marzinek, J.K., Holdbrook, D.A., Bond, P.J.(2017). Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses . Progress in Biophysics and Molecular Biology. 128. p. 121-132.

Holdbrook, D.A., Burmann, B.M., Huber, R.G., Petoukhov, M.V., Svergun, D.I., Hiller, S., Bond, P.J.(2017). A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone . Structure. 25. (7). p. 1079-1088.e3.

Kargas, V., Marzinek, J.K., Holdbrook, D.A., Yin, H., Ford, R.C., Bond, P.J.(2017). A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4 . Biochimica et Biophysica Acta - Biomembranes. 1859. (10). p. 2086-2095.

Marzinek, J.K., Holdbrook, D.A., Huber, R.G., Verma, C., Bond, P.J.(2016). Pushing the Envelope: Dengue Viral Membrane Coaxed into Shape by Molecular Simulations . Structure. 24. (8). p. 1410-1420.

Holdbrook, D.A., Huber, R.G., Piggot, T.J., Bond, P.J., Khalid, S.(2016). Dynamics of crowded vesicles: Local and global responses to membrane composition . PLoS ONE. 11. (6).

Maurer-Stroh, S., Mak, T., Ng, Y., Phuah, S., Huber, R.G., Marzinek, J.K., Holdbrook, D.A., Lee, R.T., Cui, L., Lin, R.T., et al.(2016). South-east Asian Zika virus strain linked to cluster of cases in Singapore, August 2016 . Eurosurveillance. 21. (38).

Björn M. Burmann, Daniel A. Holdbrook, Morgane Callon, Peter J. Bond, Sebastian Hiller(2015). Revisiting the Interaction between the Chaperone Skp and Lipopolysaccharide . Biophysical Journal. 108. (6). p. 1516--1526. Elsevier {BV}

Nils A. Berglund, Daniel A. Holdbrook, Syma Khalid, Peter J. Bond(2015). The Structural Basis for Lipid a Recognition in the {CD}14 Innate Immune Co-Receptor . Biophysical Journal. 108. (2). p. 350a--351a. Elsevier {BV}

Khalid, S., Berglund, N.A., Holdbrook, D.A., Leung, Y.M., Parkin, J.(2015). The membranes of Gram-negative bacteria: Progress in molecular modelling and simulation . Biochemical Society Transactions. 43. p. 162-167.

Leung, Y.M., Holdbrook, D.A., Piggot, T.J., Khalid, S.(2014). The NorM MATE transporter from N. gonorrhoeae: Insights into drug and ion binding from atomistic molecular dynamics simulations . Biophysical Journal. 107. (2). p. 460-468.

Syma Khalid, Thomas J. Piggot, Daniel A. Holdbrook, Jamie Parkin(2013). The Complexities of the E.Coli Cell Envelope: Details Revealed by {MD} Simulations . Biophysical Journal. 104. (2). p. 548a. Elsevier {BV}

Holdbrook, D.A., Piggot, T.J., Sansom, M.S.P., Khalid, S.(2013). Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment . Biochimica et Biophysica Acta - Biomembranes. 1828. (2). p. 715-723.

Piggot, T.J., Holdbrook, D.A., Khalid, S.(2013). Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study . Biochimica et Biophysica Acta - Biomembranes. 1828. (2). p. 284-293.

Joseph Goose, Daniel A. Holdbrook, Syma Khalid, Mark Sansom(2012). The Role of Instantaneous Lipid {\textquotedblleft}Flows{\textquotedblright} Within the E. coli Outer Membrane . Biophysical Journal. 102. (3). p. 299a. Elsevier {BV}

Daniel A. Holdbrook, Thomas J. Piggot, Syma Khalid(2012). The Autotransporter $\upbeta$ Domain: Insights into Structure and Function through Molecular Dynamics Simulations . Biophysical Journal. 102. (3). p. 624a. Elsevier {BV}

Thomas J. Piggot, Daniel A. Holdbrook, Syma Khalid(2011). Environmental Influences on the Conformational Dynamics of Tonb-Dependent Transporters: Molecular Dynamics Simulations of Complex Membrane Models . Biophysical Journal. 100. (3). p. 359a. Elsevier {BV}

Phedra Marius, Daniel A. Holdbrook, Syma Khalid, Philip T.F. Williamson(2011). A Putative Role for Lipid-Protein Interactions in the Localisation of Glycosyltransferases within the Cell? . Biophysical Journal. 100. (3). p. 636a--637a. Elsevier {BV}

Piggot, T.J., Holdbrook, D.A., Khalid, S.(2011). Electroporation of the E. coli and S. aureus membranes: Molecular dynamics simulations of complex bacterial membranes . Journal of Physical Chemistry B. 115. (45). p. 13381-13388.

Holdbrook, D.A., Leung, Y.M., Piggot, T.J., Marius, P., Williamson, P.T.F., Khalid, S.(2010). Stability and membrane orientation of the fukutin transmembrane domain: A combined multiscale molecular dynamics and circular dichroism study . Biochemistry. 49. (51). p. 10796-10802.

Vohra, S., Hall, B.A., Holdbrook, D.A., Khalid, S., Biggin, P.C.(2010). Bookshelf: a simple curation system for the storage of biomolecular simulation data . Database : the journal of biological databases and curation. 2010.

OTHER

Jiang Yeow, Kang Wei Tan, Daniel A Holdbrook, Zhi-Soon Chong, Jan K Marzinek, Peter J Bond, Shu Sin Chng(2017). Molecular basis for the maintenance of lipid asymmetry in the outer membrane of Escherichia coli . Cold Spring Harbor Laboratory

Rathi Saravanan, Daniel A Holdbrook, Jitka Petrlova, Shalini Singh, Nils A Berglund, Yeu Khai Choong, Peter J Bond, Martin Malmsten, Artur Schmidtchen(2017). Structural basis for endotoxin neutralization and anti-inflammatory activity of thrombin-derived C-terminal peptides . Cold Spring Harbor Laboratory

Teresa Paramo, Diana Garzón, Daniel A. Holdbrook, Syma Khalid, Peter J. Bond(2012). The Simulation Approach to Lipid{\textendash}Protein Interactions . 435--455Humana Press

CONFERENCE PAPER

Khalid, S., Goose, J., Holdbrook, D.A., Piggot, T.J., Sansom, M.S.P.(2013). Diffusion, aggregation and penetration: Modelling the complex cell envelope of E.coli . IFMBE Proceedings. 40 IFMBE. p. 376-379.