My Publications

Code

import bibtexparser
import textwrap

def format_apa(entry):
    # Extract necessary fields
    authors = entry.get('author', '').replace(' and ', ' & ')
    year = entry.get('year', 'n.d.')
    title = entry.get('title', 'No title')
    journal = entry.get('journal', 'No journal')
    volume = entry.get('volume', '')
    issue = entry.get('number', '')
    pages = entry.get('pages', '')
    doi = entry.get('doi', '')

    # Format the APA citation
    citation = f"{authors} ({year}). {title}. "
    if journal:
        citation += f"{journal}, "
    if volume:
        citation += f"{volume}"
    if issue:
        citation += f"({issue})"
    if pages:
        citation += f", {pages}."
    else:
        citation = citation.rstrip(', ') + '.'

    # Append DOI as a complete link if available
    if doi:
        citation += f" https://doi.org/{doi}"

    return citation

# Load the .bib file
with open('./works.bib', 'r', encoding='utf-8') as bibfile:
    bib_database = bibtexparser.load(bibfile)

# List the contents of the .bib file in APA format with DOI link and limited line length
line_length = 80  # Set your desired line length
for entry in bib_database.entries:
    apa_citation = format_apa(entry)
    wrapped_citation = textwrap.fill(apa_citation, width=line_length)
    print(wrapped_citation)
    print()  # Add a blank line between entries

Barry, David J. & Marcotti, Stefania & Gerontogianni, Lina & Kelly, Gavin
(2025). Enhancing Reproducibility Through Bioimage Analysis: The Significance of
Effect Sizes and Controls. No journal. https://doi.org/10.1101/2025.02.10.637409

Marcotti, Stefania & Jones, Martin L. & Slater, Thomas J. A. & Barry, David J.
(2024). Enhancing Research Through Image Analysis Workshops: Experiences and
Best Practices. Microscopy Research and Technique.
https://doi.org/10.1002/jemt.24769

Sivagurunathan, Suganya & Marcotti, Stefania & Nelson, Carl J & Jones, Martin L
& Barry, David J & Slater, Thomas J A & Eliceiri, Kevin W & Cimini, Beth A
(2023). Bridging imaging users to imaging analysis – A community survey. Journal
of Microscopy, 296(3), 199–213. https://doi.org/10.1111/jmi.13229

Jones, Rebecca A. & Cooper, Fay & Kelly, Gavin & Barry, David & Renshaw, Matthew
J. & Sapkota, Gopal & Smith, James C. (2024). Zebrafish reveal new roles for
Fam83f in hatching and the DNA damage-mediated autophagic response. No journal.
https://doi.org/10.1101/2024.02.10.579757

Jones, Rebecca A & Renshaw, Matthew J & Barry, David J (2023). Automated staging
of zebrafish embryos with deep learning. Life Science Alliance, 7(1),
e202302351. https://doi.org/10.26508/lsa.202302351

Nakagawa, Rinako & Llorian, Miriam & Varsani-Brown, Sunita & Chakravarty, Probir
& Camarillo, Jeannie M. & Barry, David & George, Roger & Blackledge, Neil P. &
Duddy, Graham & Kelleher, Neil L. & Klose, Robert J. & Turner, Martin & Calado,
Dinis P. (2023). Epi-microRNA mediated metabolic reprogramming ensures affinity
maturation. No journal. https://doi.org/10.1101/2023.07.31.551250

Sivagurunathan, Suganya & Marcotti, Stefania & Nelson, Carl J & Jones, Martin L
& Barry, David J & Slater, Thomas J A & Eliceiri, Kevin W & Cimini, Beth A
(2023). Bridging Imaging Users to Imaging Analysis - A community survey. No
journal. https://doi.org/10.1101/2023.06.05.543701

Jones, Rebecca A. & Renshaw, Matthew J. & Devenport, Danelle & Barry, David J.
(2023). Automated staging of zebrafish embryos with deep learning. No journal.
https://doi.org/10.1101/2023.01.13.523922

David J. Barry & Claudia Gerri & Donald M. Bell & Rocco
D{\textquotesingle}Antuono & Kathy K. Niakan (2022). {GIANI}: open-source
software for automated analysis of 3D microscopy images. Journal of Cell
Science. https://doi.org/10.1242/jcs.259511

Chan, Eunice H. Y. & Zhou, Yanxiang & Aerne, Birgit L. & Holder, Maxine V. &
Weston, Anne & Barry, David J. & Collinson, Lucy & Tapon, Nicolas (2021).
RASSF8-mediated transport of Echinoid via the exocyst promotesDrosophilawing
elongation and epithelial ordering. Development, 148(20).
https://doi.org/10.1242/dev.199731

Chiara Galloni & Davide Carra & Jasmine V.G. Abella & Svend Kj{\ae}r & Pavithra
Singaravelu & David J. Barry & Naoko Kogata & Christophe Gu{\'{e}}rin & Laurent
Blanchoin & Michael Way (2021). {MICAL}2 enhances branched actin network
disassembly by oxidizing Arp3B-containing Arp2/3 complexes. Journal of Cell
Biology, 220(8). https://doi.org/10.1083/jcb.202102043

Wershof, Esther & Park, Danielle & Barry, David J & Jenkins, Robert P & Rullan,
Antonio & Wilkins, Anna & Schlegelmilch, Karin & Roxanis, Ioannis & Anderson,
Kurt I & Bates, Paul A & Sahai, Erik (2021). A FIJI macro for quantifying
pattern in extracellular matrix. Life Science Alliance, 4(3), e202000880.
https://doi.org/10.26508/lsa.202000880

Barry, David J. & Gerri, Claudia & Bell, Donald M. & D’Antuono, Rocco & Niakan,
Kathy K. (2020). GIANI: open-source software for automated analysis of 3D
microscopy images. No journal. https://doi.org/10.1101/2020.10.15.340810

Galloni, Chiara & Carra, Davide & Abella, Jasmine V. G. & Kjær, Svend &
Singaravelu, Pavithra & Barry, David J & Kogata, Naoko & Guérin, Christophe &
Blanchoin, Laurent & Way, Michael (2020). MICAL2 acts through Arp3B isoform-
specific Arp2/3 complexes to destabilize branched actin networks. No journal.
https://doi.org/10.1101/2020.09.21.306522

Victoria M.-Y. Wang & Rute M. M. Ferreira & Jorge Almagro & Theodore Evan &
Nathalie Legrave & May Zaw Thin & David Frith & Joana Carvalho & David J. Barry
& Ambrosius P. Snijders & Eleanor Herbert & Emma L. Nye & James I. MacRae & Axel
Behrens (2019). {CD}9 identifies pancreatic cancer stem cells and modulates
glutamine metabolism to fuel tumour growth. Nature Cell Biology, 21(11), 1425--
1435. https://doi.org/10.1038/s41556-019-0407-1

Madushi Wanaguru & David J. Barry & Donald J. Benton & Nicola J. O'Reilly & Kate
N. Bishop (2018). Murine leukemia virus p12 tethers the capsid-containing pre-
integration complex to chromatin by binding directly to host nucleosomes in
mitosis. {PLOS} Pathogens, 14(6), e1007117.
https://doi.org/10.1371/journal.ppat.1007117

Sansregret, L. & Patterson, J.O. & Dewhurst, S. & L{\'o}pez-Garc{\'i}a, C. &
Koch, A. & McGranahan, N. & Chao, W.C.H. & Barry, D.J. & Rowan, A. & Instrell,
R. & Horswell, S. & Way, M. & Howell, M. & Singleton, M.R. & Medema, R.H. &
Nurse, P. & Petronczki, M. & Swanton, C. (2017). APC/C dysfunction limits
excessive cancer chromosomal instability. Cancer Discovery, 7(2), 218-233.

Kakui, Y. & Rabinowitz, A. & Barry, D.J. & Uhlmann, F. (2017). Condensin-
mediated remodeling of the mitotic chromatin landscape in fission yeast. Nature
Genetics, 49(10), 1553-1557.

Abella, J.V.G. & Galloni, C. & Pernier, J. & Barry, D.J. & Kj?r, S. & Carlier,
M.-F. & Way, M. (2016). Isoform diversity in the Arp2/3 complex determines actin
filament dynamics. Nature Cell Biology, 18(1), 76-86.

Barry, D.J. & Williams, G.A. & Chan, C. (2015). Automated analysis of
filamentous microbial morphology with AnaMorf. Biotechnology Progress, 31(3),
849-852.

Barry, D.J. & Durkin, C.H. & Abella, J.V. & Way, M. (2015). Open source software
for quantification of cell migration, protrusions, and fluorescence intensities.
Journal of Cell Biology, 209(1), 163-180.

Chen, X. & Squarr, A. & Stephan, R. & Chen, B. & Higgins, T.E. & Barry, D.J. &
Martin, M.C. & Rosen, M.K. & Bogdan, S. & Way, M. (2014). Ena/VASP proteins
cooperate with the WAVE complex to regulate the actin cytoskeleton.
Developmental Cell, 30(5), 569-584.

Young, J.C. & Clements, A. & Lang, A.E. & Garnett, J.A. & Munera, D. & Arbeloa,
A. & Pearson, J. & Hartland, E.L. & Matthews, S.J. & Mousnier, A. & Barry, D.J.
& Way, M. & Schlosser, A. & Aktories, K. & Frankel, G. (2014). The Escherichia
coli effector EspJ blocks Src kinase activity via amidation and ADP
ribosylation. Nature communications, 5.

Barry, D. & Roque, H. & Dumoux, M. & Kriston-Vizi, J. & Bodea, G.O. & Harper, C.
(2013). Meeting report - imaging in cell biology: where next?. Journal of cell
science, 126(Pt 1), 43-44.

Barry, D.J. (2013). Quantifying the branching frequency of virtual filamentous
microbes using fractal analysis. Biotechnology and Bioengineering, 110(2),
437-447.

Humphries, A.C. & Dodding, M.P. & Barry, D.J. & Collinson, L.M. & Durkin, C.H. &
Way, M. (2012). Clathrin potentiates vaccinia-induced actin polymerization to
facilitate viral spread. Cell Host and Microbe, 12(3), 346-359.

Barry, D.J. & Williams, G.A. (2011). Microscopic characterisation of filamentous
microbes: Towards fully automated morphological quantification through image
analysis. Journal of Microscopy, 244(1), 1-20.

Barry, D.J. & Chan, C. & Williams, G.A. (2009). Morphological quantification of
filamentous fungal development using membrane immobilization and automatic image
analysis. Journal of Industrial Microbiology and Biotechnology, 36(6), 787-800.

Barry, D.J. & Chan, C. & Williams, G.A. (2007). Nitrocellulose as a general tool
for fungal slide mounts [2]. Journal of Clinical Microbiology, 45(3), 1074-1075.