Publications

Jonathan Werner, Sara Ballouz, John Hover, Jesse Gillis (2022). Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events. Developmental Cell.

Benjamin Kaminow, Sara Ballouz, Jesse Gillis, Alexander Dobin (2022). Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses. Genome Research.

Chi Nam Ignatius Pang, Sara Ballouz, Daniel Weissberger, Loïc M Thibaut, Joshua J Hamey, Jesse Gillis, Marc R Wilkins, Gene Hart-Smith (2020). Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes. Molecular & Cellular Proteomics.

John Lee, Manthan Shah, Sara Ballouz, Megan Crow, Jesse Gillis (2020). CoCoCoNet: conserved and comparative co-expression across a diverse set of species. NAR.

Sara Ballouz (2020). Single-cell Transcriptomics. eLS.

Sara Ballouz, Alexander Dobin, Jesse A. Gillis (2019). Is it time to change the reference genome?. Genome Biology.

Megan Crow, Nathaniel Lim, Sara Ballouz, Paul Pavlidis, Jesse Gillis (2019). Predictability of human differential gene expression. Proceedings of the National Academy of Sciences of the United States of America.

Sara Ballouz, Alexander Dobin, Thomas R. Gingeras, Jesse Gillis (2018). The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Research.

Megan Crow, Anirban Paul, Sara Ballouz, Z. Josh Huang, Jesse Gillis (2018). Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nature Communications.

Sara Ballouz, Paul Pavlidis, Jesse Gillis (2017). Using predictive specificity to determine when gene set analysis is biologically meaningful. Nucleic Acids Research.

Sara Ballouz, Jesse Gillis (2017). Strength of functional signature correlates with effect size in autism. Genome Medicine.

Sara Ballouz, Melanie Weber, Paul Pavlidis, Jesse Gillis (2017). EGAD: ultra-fast functional analysis of gene networks. Bioinformatics (Oxford, England).

Megan Crow, Anirban Paul, Sara Ballouz, Z. Josh Huang, Jesse Gillis (2016). Exploiting single-cell expression to characterize co-expression replicability. Genome Biology.

Sara Ballouz, Jesse Gillis (2016). AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PLoS computational biology.

Wim Verleyen, Sara Ballouz, Jesse Gillis (2016). Positive and negative forms of replicability in gene network analysis. Bioinformatics (Oxford, England).

Matthew J. O'Meara, Sara Ballouz, Brian K. Shoichet, Jesse Gillis (2016). Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PloS One.

Sara Ballouz, Wim Verleyen, Jesse Gillis (2015). Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. Bioinformatics (Oxford, England).

Wim Verleyen, Sara Ballouz, Jesse Gillis (2015). Measuring the wisdom of the crowds in network-based gene function inference. Bioinformatics (Oxford, England).

Mani P. Grover, Sara Ballouz, Kaavya A. Mohanasundaram, Richard A. George, Andrzej Goscinski, Tamsyn M. Crowley, Craig D. H. Sherman, Merridee A. Wouters (2015). Novel therapeutics for coronary artery disease from genome-wide association study data. BMC medical genomics.

Jesse Gillis, Sara Ballouz, Paul Pavlidis (2014). Bias tradeoffs in the creation and analysis of protein-protein interaction networks. Journal of Proteomics.

Mani P. Grover, Sara Ballouz, Kaavya A. Mohanasundaram, Richard A. George, Craig D. H. Sherman, Tamsyn M. Crowley, Merridee A. Wouters (2014). Identification of novel therapeutics for complex diseases from genome-wide association data. BMC medical genomics.

Sara Ballouz, Jason Y. Liu, Martin Oti, Bruno Gaeta, Diane Fatkin, Melanie Bahlo, Merridee A. Wouters (2014). Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease. Molecular Genetics & Genomic Medicine.

Sara Ballouz, Jason Y. Liu, Richard A. George, Naresh Bains, Arthur Liu, Martin Oti, Bruno Gaeta, Diane Fatkin, Merridee A. Wouters (2013). Gentrepid V2.0: a web server for candidate disease gene prediction. BMC bioinformatics.

Sara Ballouz, Jason Y. Liu, Martin Oti, Bruno Gaeta, Diane Fatkin, Melanie Bahlo, Merridee A. Wouters (2011). Analysis of genome-wide association study data using the protein knowledge base. BMC genetics.

Martin Oti, Sara Ballouz, Merridee A. Wouters (2011). Web tools for the prioritization of candidate disease genes. Methods in Molecular Biology (Clifton, N.J.).

Sara Ballouz, Andrew R. Francis, Ruiting Lan, Mark M. Tanaka (2010). Conditions for the evolution of gene clusters in bacterial genomes. PLoS computational biology.

Erdahl T. Teber, Jason Y. Liu, Sara Ballouz, Diane Fatkin, Merridee A. Wouters (2009). Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. BMC bioinformatics.

Sara Ballouz, Melissa M Mangala, Matthew D Perry, Stewart Heitmann, Jesse A Gillis, Adam P Hill, Jamie I Vandenberg (0001). Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events. Cardiovascular Research.