Author

Shane Lofgren

Stanford Medicine

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Bioinformatics· 4

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:statistical model· 4 Assay:bulk RNA-seq· 3 Organism:human· 3 Research Focus:differential expression· 2 Research Focus:benchmarking· 1 Research Focus:clustering· 1 Research Focus:database / resource· 1 Research Focus:deconvolution· 1

Frequent Co-Authors

Francesco VallaniaiD· 3 shared Purvesh KhatriiD· 3 shared Andrew Tam· 2 shared Charles Yu LiuiD· 2 shared Erika BongeniD· 2 shared Nigam Haresh ShahiD· 2 shared Winston A. HaynesiD· 2 shared Aurelie TomczakiD· 1 shared

Activity by Year

2016-2018 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

Francesco VallaniaORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Interpretation of biological experiments changes with evolution of Gene Ontology and its annotations

Aurelie Tomczak, Jonathan Mortensen, Rainer Winnenburg, Charles Yu Liu, Dominique T. Alessi, Varsha Swamy, Francesco Vallania, Shane Lofgren, Winston A. Haynes, Nigam Haresh Shah, Mark A. Musen, Purvesh Khatri

The paper evaluates how changes in Gene Ontology (GO) and its annotations over time affect the results of GO enrichment analyses in disease studies.

Scientific Reports · Mar 23, 2018Peer-reviewedBioinformatics

Integrated molecular, clinical, and ontological analysis identifies overlooked disease relationships

Winston A. Haynes, Rohit Vashisht, Francesco Vallania, Charles Liu, Gregory L. Gaskin, Erika Bongen, Shane Lofgren, Timothy E. Sweeney, Paul J. Utz, Nigam Haresh Shah, Purvesh Khatri

The paper integrates transcriptome and clinical data to identify overlooked disease relationships, such as between myositis and interstitial cystitis.

bioRxiv · Feb 16, 2018 · PreprintBioinformatics

Leveraging heterogeneity across multiple data sets increases accuracy of cell-mixture deconvolution and reduces biological and technical biases

Francesco Vallania, Andrew Tam, Shane Lofgren, Steven A. Schaffert, Tej Deepak Azad, Erika Bongen, Meia Alsup, Michael N. Alonso, Mark M. Davis, Edgar G. Engleman, Purvesh Khatri

This paper introduces immunoStates, a basis matrix that reduces biological and technical biases in cell-mixture deconvolution by incorporating diverse disease states and microarray platforms.

bioRxiv · Oct 20, 2017 · PreprintBioinformatics

Empowering Multi-Cohort Gene Expression Analysis to Increase Reproducibility

Winston A. Haynes, Francesco Vallania, Charles Liu, Erika Bongen, Aurelie Tomczak, Marta Andres-Terrè, Shane Lofgren, Andrew Tam, Cole A. Deisseroth, Matthew D. Li, Timothy E. Sweeney, Purvesh Khatri

The paper presents a pipeline and web application for multi-cohort gene expression analysis to improve reproducibility across diverse populations.

bioRxiv · Aug 25, 2016 · PreprintBioinformatics