Prof Aedin Culhane
PI
Group Leader
LDCRC
Professor, University of Limerick
Our Team
Meet Our Team
We bring together experts in computational biology, bioinformatics, and cancer genomics to tackle the most pressing challenges in oncology research.
Principal Investigator
Core Team Members
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Extended Team & Collaborators
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Alumni
Our former team members continue to make significant contributions to science and medicine at leading institutions worldwide.
Lauren Hsu
PhD Candidate in Biostatistics at Harvard
Publications: (Hsu and Culhane 2020; Lê Cao et al. 2021; Hsu and Culhane 2023)
Azfar Basunia
Diagnostic Radiology Resident at Penn Medicine. Department of Radiology
Publications: (Ramos et al. 2017; Meng et al. 2019; Schwede et al. 2020)
Chen Meng
Center Leader Bioinformatics at the Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS)
Publications: (Meng et al. 2016, 2019, 2014; Lê Cao et al. 2021; Meng and Culhane 2016; Thorsson et al. 2019)
Daniel Gusenleitner
Head of Computational Biology at Mercy BioAnalytics, Inc.
Publications: (Gusenleitner et al. 2012; Schröder et al. 2013; Culhane et al. 2011)
Matthew Schwede
Hematology Oncology Fellow at Stanford University School of Medicine
Publications: (Wang et al. 2012; Schwede et al. 2013, 2020; Santagata et al. 2014; Chittenden et al. 2010)
Oana Zeleznik
Instructor in Medicine, Harvard Medical School and Associate Epidemiologist, Brigham and Women’s Hospital
Publications: (Meng et al. 2016)
References
Chittenden, Thomas W., Jane Pak, Renee Rubio, Hailing Cheng, Kristina Holton, Niall Prendergast, Vladimir Glinskii, et al. 2010. “Therapeutic Implications of GIPC1 Silencing in Cancer.” Edited by Pawel Michalak. PLoS ONE 5 (12): e15581. https://doi.org/10.1371/journal.pone.0015581.
Culhane, A. C., M. S. Schroder, R. Sultana, S. C. Picard, E. N. Martinelli, C. Kelly, B. Haibe-Kains, et al. 2011. “GeneSigDB: A Manually Curated Database and Resource for Analysis of Gene Expression Signatures.” Nucleic Acids Research 40 (D1): D1060–66. https://doi.org/10.1093/nar/gkr901.
Gusenleitner, Daniel, Eleanor A Howe, Stefan Bentink, John Quackenbush, and Aedín C Culhane. 2012. “iBBiG: Iterative Binary Bi-Clustering of Gene Sets.” Bioinformatics (Oxford, England) 28 (19): 2484–92. https://doi.org/10.1093/bioinformatics/bts438.
Hsu, Lauren L., and Aedin C. Culhane. 2020. “Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data.” Frontiers in Oncology 10: 973. https://doi.org/10.3389/fonc.2020.00973.
Hsu, Lauren L., and Aedín C. Culhane. 2023. “Correspondence Analysis for Dimension Reduction, Batch Integration, and Visualization of Single-Cell RNA-Seq Data.” Scientific Reports 13 (1). https://doi.org/10.1038/s41598-022-26434-1.
Lê Cao, Kim-Anh, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, et al. 2021. “Community-Wide Hackathons to Identify Central Themes in Single-Cell Multi-Omics.” Genome Biology 22 (1). https://doi.org/10.1186/s13059-021-02433-9.
Meng, Chen, Azfar Basunia, Bjoern Peters, Amin Moghaddas Gholami, Bernhard Kuster, and Aedín C. Culhane. 2019. “MOGSA: Integrative Single Sample Gene-Set Analysis of Multiple Omics Data.” Molecular & Cellular Proteomics 18 (8): S153–68. https://doi.org/10.1074/mcp.tir118.001251.
Meng, Chen, and Aedin Culhane. 2016. “Integrative Exploratory Analysis of Two or More Genomic Datasets.” In, 19–38. Springer New York. https://doi.org/10.1007/978-1-4939-3578-9_2.
Meng, Chen, Bernhard Kuster, Aedín C Culhane, and Amin Moghaddas Gholami. 2014. “A Multivariate Approach to the Integration of Multi-Omics Datasets.” BMC Bioinformatics 15 (1). https://doi.org/10.1186/1471-2105-15-162.
Meng, Chen, Oana A. Zeleznik, Gerhard G. Thallinger, Bernhard Kuster, Amin M. Gholami, and Aedín C. Culhane. 2016. “Dimension Reduction Techniques for the Integrative Analysis of Multi-Omics Data.” Briefings in Bioinformatics 17 (4): 628–41. https://doi.org/10.1093/bib/bbv108.
Ramos, Marcel, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, et al. 2017. “Software for the Integration of Multiomics Experiments in Bioconductor.” Cancer Research 77 (21): e39–42. https://doi.org/10.1158/0008-5472.can-17-0344.
Santagata, Sandro, Ankita Thakkar, Ayse Ergonul, Bin Wang, Terri Woo, Rong Hu, J. Chuck Harrell, et al. 2014. “Taxonomy of Breast Cancer Based on Normal Cell Phenotype Predicts Outcome.” Journal of Clinical Investigation 124 (2): 859–70. https://doi.org/10.1172/jci70941.
Schröder, Markus S., Daniel Gusenleitner, John Quackenbush, Aedín C. Culhane, and Benjamin Haibe-Kains. 2013. “RamiGO: An R/Bioconductor Package Providing an AmiGO Visualize Interface.” Bioinformatics 29 (5): 666–68. https://doi.org/10.1093/bioinformatics/bts708.
Schwede, Matthew, Dimitrios Spentzos, Stefan Bentink, Oliver Hofmann, Benjamin Haibe-Kains, David Harrington, John Quackenbush, and Aedín C. Culhane. 2013. “Stem Cell-Like Gene Expression in Ovarian Cancer Predicts Type II Subtype and Prognosis.” Edited by Vincenzo Coppola. PLoS ONE 8 (3): e57799. https://doi.org/10.1371/journal.pone.0057799.
Schwede, Matthew, Levi Waldron, Samuel C. Mok, Wei Wei, Azfar Basunia, Melissa A. Merritt, Constantine S. Mitsiades, et al. 2020. “The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer.” Cancer Epidemiology, Biomarkers & Prevention 29 (2): 509–19. https://doi.org/10.1158/1055-9965.epi-18-1359.
Thorsson, Vésteinn, David L. Gibbs, Scott D. Brown, Denise Wolf, Dante S. Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, et al. 2019. “The Immune Landscape of Cancer.” Immunity 51 (2): 411–12. https://doi.org/10.1016/j.immuni.2019.08.004.
Wang, Zhigang C., Nicolai Juul Birkbak, Aedín C. Culhane, Ronny Drapkin, Aquila Fatima, Ruiyang Tian, Matthew Schwede, et al. 2012. “Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome.” Clinical Cancer Research 18 (20): 5806–15. https://doi.org/10.1158/1078-0432.ccr-12-0857.