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Citations

Actinomycetota bioprospecting from ore-forming environments César Aguilar, Amir Alwali, Madeline Mair, Lorena Rodriguez-Orduña, Haydeé Contreras-Peruyero, Ramya Modi, Carson Roberts, Nelly Sélem-Mojica, Cuauhtemoc Licona-Cassani, Elizabeth Ivy Parkinson. Microbiology Society (2024).

A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis). Rachel Young, Lucas Lefevre1, Stephen J. Bush, Akshay Joshi1, Salam Herojeet Singh, Santosh Kumar Jadhav, Velu Dhanikachalam, Zofia M. Lisowski, Daniela Iamartino, Kim M. Summers, John L. Williams, Alan L. Archibald, Suresh Gokhale, Satish Kumar, and David A. Hume. Frontiers in Genetics (2019)

A graph-based approach for the visualisation and analysis of bacterial pangenomes. Joshua D Harling-Lee, Jamie Gorzynski, Gonzalo Yebra, Tim Angus, J Ross Fitzgerald, Tom C Freeman. BMC Bioinformatics (2022).

A novel strain of lumpy skin disease virus causes clinical disease in cattle in Hong Kong. John Flannery, Barbara Shih, Ismar R. Haga, Martin Ashby, Amanda Corla, Simon King, Graham Freimanis, Noemi Polo, Anne Ching‐nga Tse, Christopher J. Brackman, Jason Chan, Patrick Pun, Andrew D. Ferguson, Andy Law, Samantha Lycett, Carrie Batten, Philippa M. Beard. Transboundary and Emerging Diseases (2021).

Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration Maria Kokoli, Evangelos Karatzas, Fotis A Baltoumas, Reinhard Schneider, Evangelos Pafilis, Savvas Paragkamian, Nadezhda T Doncheva, Lars Juhl Jensen, Georgios A Pavlopoulos. NAR Genomics and Bioinformatics (2023).

A Systems-Level Analysis of Total-Body PET Data Reveals Complex Skeletal Metabolism Networks in vivo. Karla J. Suchacki, Carlos J. Alcaide-Corral, Samah Nimale, Mark G. Macaskill, Roland H. Stimson, Colin Farquharson, Tom C. Freeman, Adriana A. S. Tavares. Frontiers in Medicine (2021).

A Systems-Level Analysis of Total-Body PET Data Reveals Complex Skeletal Metabolism Networks in vivo Karla J Suchacki, Carlos J Alcaide-Corral, Samah Nimale, Mark G Macaskill, Roland H Stimson, Colin Farquharson, Tom C Freeman, Adriana A S Tavares. Frontiers in Medicine (2021).

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Mikaela Koutrouli, Foteini Thanati, Kleanthi Voutsadaki, Maria Gkonta, Joana Hotova, Ioannis Kasionis, Pantelis Hatzis, Georgios A. Pavlopoulos. Biomolecules (2021).

Blockchain Analysis of the Bitcoin Market. Igor Makarov, Antoinette Schoar. SSRN Electronic Journal – Preprint (2021).

Bovine host genome acts on rumen microbiome function linked to methane emissions. Marina Martínez-Álvaro, Marc D. Auffret, Carol-Anne Duthie, Richard J. Dewhurst, Matthew A. Cleveland, Mick Watson & Rainer Roehe. Nature Communications (2022).

Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis Anirudh Patir, Anna Raper, Robert Fleming, Beth E P Henderson, Lee Murphy, Neil C Henderson, Emily L Clark, Tom C Freeman, Mark W Barnett. G3 Genes|Genomes|Genetics (2023).

CGG toolkit: Software components for computational genomics Dimitrios Vasileiou, Christos Karapiperis, Ismini Baltsavia, Anastasia Chasapi, Dag Ahrén, Paul J Janssen, Ioannis Iliopoulos, Vasilis J Promponas, Anton J Enright, Christos A Ouzounis. Plos Computational Biology (2023).

Chicken CSF2 and IL-4-, and CSF2-dependent bone marrow cultures differentiate into macrophages over time Dominika Borowska, Samantha Sives, Lonneke Vervelde, Kate M. Sutton. Frontiers in Immunology (2022).

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. Stephen J. Bush, Lucy Freem, Amanda J. MacCallum, Jenny O’Dell, Chunlei Wu, Cyrus Afrasiabi, Androniki Psifidi, Mark P. Stevens, Jacqueline Smith, Kim M. Summers & David A. Hume. BMC Genomics (2018).

Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Nicholas J Dimonaco, Mazdak Salavati, Barbara B Shih. Viruses (2020).

Consolidation of a Molecular Signature of Healing in Cutaneous Leishmaniasis Is Achieved during the First 10 Days of Treatment Lina Giraldo-Parra, David E. Rebellón-Sánchez, Adriana Navas, Ashton Trey Belew, Najib M. El-Sayed, María Adelaida Gómez. The Journal of Immunology (2024).

Development and function of chicken XCR1+ conventional dendritic cells Zhiguang Wu, Barbara Shih, Joni Macdonald, Dominique Meunier, Kris Hogan, Cosmin Chintoan-Uta, Hazel Gilhooley, Tuanjun Hu, Mariana Beltran, Neil C. Henderson, Helen M. Sang, Mark P. Stevens, Michael J. McGrew, Adam Balic. Frontiers in Immunology (2024).

Heterogeneity in Staphylococcus aureus Bacteraemia Clinical Trials Complicates Interpretation of Findings Heather W Dolby, Sarah A Clifford, Ian F Laurenson, Vance G Fowler, Clark D Russell. The Journal of Infectious Diseases (2022).

Infected deep vein thrombophlebitis in people who inject drugs: missed opportunities and potential for alternative antimicrobial approaches. Hugh McCaughan, Clark D. Russell, Dáire T. O’Shea. Infection (2021).

Inflammatory profiles across the spectrum of disease reveal a distinct role for GM-CSF in severe COVID-19. Ryan S Thwaites, et al., Science Immunology (2021).

Integrative high-throughput enhancer surveying and functional verification divulges a YY2-condensed regulatory axis conferring risk for osteoporosis Xiao-Feng Chen, Yuan-Yuan Duan, Ying-Ying Jia, Qian-Hua Dong, Wei Shi, Yan Zhang, Shan-Shan Dong, Meng Li, Zhongbo Liu, Fei Chen, Xiao-Ting Huang, Ruo-Han Hao, Dong-Li Zhu, Rui-Hua Jing, Yan Guo, Tie-Lin Yang. Cell Genomics (2024).

Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species Odion O Ikhimiukor, Stephanie S R Souza, Michael M Marcovici, Griffin J Nye, Robert Gibson, Cheryl P Andam. Communications Biology (2023).

Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock Gonzalo Yebra, Joshua D Harling-Lee, Samantha Lycett, Frank M Aarestrup, Gunhild Larsen, Lina M Cavaco, Keun Seok Seo, Sam Abraham, Jacqueline M Norris, Tracy Schmidt, Marthie M Ehlers, Daniel O Sordelli, Fernanda R Buzzola, Wondwossen A Gebreyes, Juliano L Gonçalves, Marcos V Dos Santos, Zunita Zakaria, Vera L M Rall, Orla M Keane, Dagmara A Niedziela, Gavin K Paterson, Mark A Holmes, Tom C Freeman, J Ross Fitzgerald. PNAS Microbiology (2022).

Prophages in the infant gut are largely induced, and may be functionally relevant to their hosts. Tamsin A. Redgwell, Jonathan Thorsen, Marie-Agnes Petit, Ling Deng, Gisle A. Vestergaard, Jakob Russel, Hans Bisgaard, Dennis S. Nielsen, Søren Sørensen, Jakob Stokholm, Shiraz A. Shah. bioRxiv – Preprint (2021).

Realistic agent-based simulation of infection dynamics and percolation. Kai Nagel, Christian Rakow, Sebastian A. Müller. Physica A Statistical Mechanics and its Applications (2021).

Recent advances in the genomic resources for sheep Shernae A. Woolley, Mazdak Salavati, Emily L. Clark. Mammalian Genome (2023).

SARS‐CoV‐2 neutralizing antibodies decline over one year and patients with severe COVID‐19 pneumonia display a unique cytokine profile. Vimvara Vacharathit, Sirawat Srichatrapimuk, Suwimon Manopwisedjaroen, Suppachok Kirdlarp, Chanya Srisaowakarn, Chavachol Setthaudom, Nanthicha Inrueangsri, Prapaporn Pisitkun, Mongkol Kunakorn, Suradej Hongeng, Somnuek Sungkanuparph, Arunee Thitithanyanont. International Journal of Infectious Diseases (2021).

Streptococcus canis genomic epidemiology reveals the potential for zoonotic transfer Davide Pagnossin, William Weir, Andrew Smith, Manuel Fuentes, Juliana Coelho, Katarina Oravcova. Microbial Genomics (2023).

Temporal dynamics of genetically heterogeneous extended-spectrum cephalosporin-resistant Escherichia coli bloodstream infections William C. Shropshire, Benjamin Strope, Selvalakshmi Selvaraj Anand, Jordan Bremer, Patrick McDaneld, Micah M. Bhatti, Anthony R. Flores, Awdhesh Kalia, Samuel A. Shelburne. mSphere (2023).

Ten simple rules for developing visualization tools in genomics Eloi Durant, Mathieu Rouard, Eric W Ganko, Cedric Muller, Alan M Cleary, Andrew D Farmer, Matthieu Conte, Francois Sabot. Plos Computational Biology (2022).

The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease Claire L. O’Brien, Kim M. Summers, Natalia M. Martin, Dylan Carter-Cusack, Yuanhao Yang, Rasel Barua, Ojas V. A. Dixit, David A. Hume & Paul Pavli. Human Genetics (2024).

The VRNetzer platform enables interactive network analysis in Virtual Reality. Sebastian Pirch, Felix Müller, Eugenia Iofinova, Julia Pazmandi, Christiane V. R. Hütter, Martin Chiettini, Celine Sin, Kaan Boztug, Iana Podkosova, Hannes Kaufmann, Jörg Menche. Nature Communications (2021).

Three Dimensions of Science: A Web Tool for 3D Visualization of Scientific Literature. Jakub Swacha. 2021 ACM/IEEE Joint Conference on Digital Libraries (JCDL) – Proceeding (2021).

Tissue Proteomic Analysis Identifies Mechanisms and Stages of Immunopathology in Fatal COVID-19. Clark D. Russell, Asta Valanciute, Naomi N. Gachanja, Jillian Stephen, Rebekah Penrice-Randal, Stuart D. Armstrong, Sara Clohisey, Bo Wang, Wael Al Qsous, William A. Wallace, Gabriel C. Oniscu, Jo Stevens, David J. Harrison, Kevin Dhaliwal, Julian A. Hiscox, J. Kenneth Baillie, Ahsan R. Akram, David A. Dorward, Christopher D. Lucas. American Journal of Respiratory Cell and Molecular Biology (2022).

Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage. Daniel E. Goszczynski, Michelle M. Halstead, Alma D. Islas-Trejo, Huaijun Zhou, Pablo J. Ross. Genome Research (2021).

Transcriptomic Analysis of Rat Macrophages. Clare Pridans, Katharine M. Irvine, Gemma M. Davis, Lucas Lefevre, Stephen J. Bush, David A. Hume. Frontiers in Immunology (2021).

Transcriptomic analysis of the poultry red mite, Dermanyssus gallinae, across all stages of the lifecycle. Kathryn Bartley, Wan Chen, Richard I. Lloyd Mills, Francesca Nunn, Daniel R. G. Price, Stephane Rombauts, Yves Van de Peer, Lise Roy, Alasdair J. Nisbet, Stewart T. G. Burgess. BMC Genomics (2021).

Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks Kozo Nishida, Junichi Maruyama, Kazunari Kaizu, Koichi Takahashi & Katsuyuki Yugi. npj Systems Biology and Applications volume (2024).