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Bioinformatics and data structure lead You will drive the lab’s computational strategy and data ecosystem. You will establish lab-wide data standards, ensure reproducibility, and develop integrative analytic frameworks that support high-impact research, grant submissions, and translational discovery...

PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs.

Publication: Journal Article

Yeganeh, Pourya Naderi, Yue Y Teo, Dimitra Karagkouni, Yered Pita-Juárez, Sarah L Morgan, Frank J Slack, Ioannis S Vlachos, and Winston A Hide. 2023. “PanomiR: a Systems Biology Framework for Analysis of Multi-Pathway Targeting by MiRNAs.”. Briefings in Bioinformatics 24 (6).

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients.

Publication: Journal Article

Pita-Juárez, Yered, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C Melms, Sebastian Niezen, Toni M Delorey, Adam L Essene, et al. 2022. “A Single-Nucleus and Spatial Transcriptomic Atlas of the COVID-19 Liver Reveals Topological, Functional, and Regenerative Organ Disruption in Patients.”. BioRxiv : The Preprint Server for Biology.

Reply to Neupane et al.: Replication study of AD-associated rare variants.

Publication: Journal Article

Prokopenko, Dmitry, Sarah L Morgan, Christoph Lange, Winston Hide, Lars Bertram, and Rudolph E Tanzi. 2022. “Reply to Neupane Et al.: Replication Study of AD-Associated Rare Variants.”. Alzheimer’s & Dementia : The Journal of the Alzheimer’s Association 18 (4): 863-64.

Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models.

Publication: Journal Article

Wan, Ying-Wooi, Rami Al-Ouran, Carl G Mangleburg, Thanneer M Perumal, Tom Lee V, Katherine Allison, Vivek Swarup, et al. 2020. “Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models.”. Cell Reports 32 (2): 107908.

The relative resistance of children to sepsis mortality: from pathways to drug candidates.

Publication: Journal Article

Joachim, Rose B, Gabriel M Altschuler, John N Hutchinson, Hector R Wong, Winston A Hide, and Lester Kobzik. 2018. “The Relative Resistance of Children to Sepsis Mortality: From Pathways to Drug Candidates.”. Molecular Systems Biology 14 (5): e7998.

Relatively frequent switching of transcription start sites during cerebellar development.

Publication: Journal Article

Zhang, Peter, Emmanuel Dimont, Thomas Ha, Douglas J Swanson, FANTOM Consortium, Winston Hide, and Dan Goldowitz. 2017. “Relatively Frequent Switching of Transcription Start Sites During Cerebellar Development.”. BMC Genomics 18 (1): 461.

A data-driven approach links microglia to pathology and prognosis in amyotrophic lateral sclerosis.

Publication: Journal Article

Cooper-Knock, Johnathan, Claire Green, Gabriel Altschuler, Wenbin Wei, Joanna J Bury, Paul R Heath, Matthew Wyles, et al. 2017. “A Data-Driven Approach Links Microglia to Pathology and Prognosis in Amyotrophic Lateral Sclerosis.”. Acta Neuropathologica Communications 5 (1): 23.

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.

Publication: Journal Article

Karp, Peter D, Bonnie Berger, Diane Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, and Burkhard Rost. 2015. “Message from the ISCB: ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.”. Bioinformatics (Oxford, England) 31 (4): 616-7.

CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.

Publication: Journal Article

Dimont, Emmanuel, Oliver Hofmann, Shannan J Ho Sui, Alistair R R Forrest, Hideya Kawaji, FANTOM Consortium, and Winston Hide. 2014. “CAGExploreR: an R Package for the Analysis and Visualization of Promoter Dynamics across Multiple Experiments.”. Bioinformatics (Oxford, England) 30 (8): 1183-84.