Ballouz, Sara Publications

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Ballouz, Sara

Number of items at this level: 16.

Paper

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)

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

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