Browse by CSHL Author

Paper

Werner, Jonathan M, Ballouz, Sara, Hover, John, Gillis, Jesse (July 2022) Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events. Developmental Cell, 57 (16). S1534-5807(22)00496. ISSN 1534-5807

Kaminow, Benjamin, Ballouz, Sara, Gillis, Jesse, Dobin, Alexander (March 2022) Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses. Genome Research. gr.275613.121-gr.275613.121. ISSN 1088-9051

Werner, Jonathan, Ballouz, Sara, Hover, John, Gillis, Jesse (September 2021) Cross-tissue analysis of allelic X-chromosome inactivation ratios resolves features of human development. BioRxiv. (Unpublished)

Kaminow, Benjamin, Ballouz, Sara, Gillis, Jesse, Dobin, Alexander (December 2020) Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses. BioRxiv. (Unpublished)

Ballouz, Sara, Mangala, Melissa M, Perry, Matthew D, Heitmann, Stewart, Gillis, Jesse A, Hill, Adam P, Vandenberg, Jamie I (October 2020) Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events. Cardiovascular Research. ISSN 0008-6363

Lee, J., Shah, M., Ballouz, S., Crow, M., Gillis, J. (May 2020) CoCoCoNet: conserved and comparative co-expression across a diverse set of species. Nucleic Acids Research. ISSN 0305-1048

Lee, John, Shah, Manthan, Ballouz, Sara, Crow, Megan, Gillis, Jesse (April 2020) CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species. BioRxiv. (Unpublished)

Ballouz, S., Dobin, A., Gillis, J. A. (August 2019) Is it time to change the reference genome? Genome Biol, 20 (1). ISSN 1474-7596

Ballouz, Sara, Dobin, Alexander, Gillis, Jesse (January 2019) Is it time to change the reference genome? BioRxiv. (Unpublished)

Ballouz, S., Dobin, A., Gingeras, T. R., Gillis, J. (May 2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res. ISSN 0305-1048

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (February 2018) Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat Commun, 9 (1). p. 884. ISSN 2041-1723

Ballouz, S., Gillis, J. (October 2017) DISTINGUISHING BIOLOGICAL FROM TECHNOLOGICAL SIGNALS IN THE FUNCTIONAL INTERPRETATION OF NEUROPSYCHIATRIC DISEASE GENES. European Neuropsychopharmacology, 27 (Supple). Abstract 31; S223-S224. ISSN 0924-977X

Ballouz, S., Gillis, J. (July 2017) Strength of functional signature correlates with effect size in autism. Genome Med, 9 (1). p. 64. ISSN 1756-994x

Ballouz, S., Weber, M., Pavlidis, P., Gillis, J. (February 2017) EGAD: ultra-fast functional analysis of gene networks. Bioinformatics, 33 (4). pp. 612-614. ISSN 1367-4803

Ballouz, S., Pavlidis, P., Gillis, J. (October 2016) Using predictive specificity to determine when gene set analysis is biologically meaningful. Nucleic Acids Res. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Ballouz, Sara, Weber, Melanie, Pavlidis, Paul, Gillis, Jesse (May 2016) EGAD: Ultra-fast functional analysis of gene networks. BioRxiv. (Unpublished)

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (May 2016) Exploiting single-cell expression to characterize co-expression replicability. Genome Biol, 17 (1). p. 101. ISSN 1474-760X (Electronic)1474-7596 (Linking) (Public Dataset)

Ballouz, S., Gillis, J. (April 2016) AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PLoS Comput Biol, 12 (4). e1004868. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Verleyen, W., Ballouz, S., Gillis, J. (April 2016) Positive and negative forms of replicability in gene network analysis. Bioinformatics, 32 (7). pp. 1065-73. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

O'Meara, M. J., Ballouz, S., Shoichet, B. K., Gillis, J. (2016) Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PLoS One, 11 (7). e0160098. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Grover, M. P., Ballouz, S., Mohanasundaram, K. A., George, R. A., Goscinski, A., Crowley, T. M., Sherman, C. D., Wouters, M. A. (May 2015) Novel therapeutics for coronary artery disease from genome-wide association study data. BMC Med Genomics, 8 (Suppl ). S1. ISSN 1755-8794 (Electronic)1755-8794 (Linking)

Verleyen, W., Ballouz, S., Gillis, J. (March 2015) Measuring the wisdom of the crowds in network-based gene function inference. Bioinformatics, 31 (5). pp. 745-752. ISSN 1367-4803

Ballouz, S., Verleyen, W., Gillis, J. (February 2015) Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. Bioinformatics. ISSN 1367-4803

Gillis, J., Ballouz, S., Pavlidis, P. (January 2014) Bias tradeoffs in the creation and analysis of protein-protein interaction networks. Journal of Proteomics, 100. pp. 44-54.

Grover, M. P., Ballouz, S., Mohanasundaram, K. A., George, R. A., H Sherman, C. D., Crowley, T. M., Wouters, M. A. (2014) Identification of novel therapeutics for complex diseases from genome-wide association data. BMC Medical Genomics, 7 (SUPPL.). ISSN 17558794 (ISSN)

Ballouz, S., Liu, J. Y., George, R. A., Bains, N., Liu, A., Oti, M., Gaeta, B., Fatkin, D., Wouters, M. A. (August 2013) Gentrepid V2.0: a web server for candidate disease gene prediction. BMC Bioinformatics, 14. ISSN 1471-2105