Sort by
Items per page

Send to

Choose Destination

Search results

Items: 25


Is it time to change the reference genome?

Ballouz S, Dobin A, Gillis JA.

Genome Biol. 2019 Aug 9;20(1):159. doi: 10.1186/s13059-019-1774-4.


Predictability of human differential gene expression.

Crow M, Lim N, Ballouz S, Pavlidis P, Gillis J.

Proc Natl Acad Sci U S A. 2019 Mar 26;116(13):6491-6500. doi: 10.1073/pnas.1802973116. Epub 2019 Mar 7.


The fractured landscape of RNA-seq alignment: the default in our STARs.

Ballouz S, Dobin A, Gingeras TR, Gillis J.

Nucleic Acids Res. 2018 Jun 1;46(10):5125-5138. doi: 10.1093/nar/gky325.


Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor.

Crow M, Paul A, Ballouz S, Huang ZJ, Gillis J.

Nat Commun. 2018 Feb 28;9(1):884. doi: 10.1038/s41467-018-03282-0.


Strength of functional signature correlates with effect size in autism.

Ballouz S, Gillis J.

Genome Med. 2017 Jul 7;9(1):64. doi: 10.1186/s13073-017-0455-8.


Using predictive specificity to determine when gene set analysis is biologically meaningful.

Ballouz S, Pavlidis P, Gillis J.

Nucleic Acids Res. 2017 Feb 28;45(4):e20. doi: 10.1093/nar/gkw957.


EGAD: ultra-fast functional analysis of gene networks.

Ballouz S, Weber M, Pavlidis P, Gillis J.

Bioinformatics. 2017 Feb 15;33(4):612-614. doi: 10.1093/bioinformatics/btw695.


Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction.

O'Meara MJ, Ballouz S, Shoichet BK, Gillis J.

PLoS One. 2016 Jul 28;11(7):e0160098. doi: 10.1371/journal.pone.0160098. eCollection 2016.


Exploiting single-cell expression to characterize co-expression replicability.

Crow M, Paul A, Ballouz S, Huang ZJ, Gillis J.

Genome Biol. 2016 May 6;17:101. doi: 10.1186/s13059-016-0964-6.


AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

Ballouz S, Gillis J.

PLoS Comput Biol. 2016 Apr 15;12(4):e1004868. doi: 10.1371/journal.pcbi.1004868. eCollection 2016 Apr.


Positive and negative forms of replicability in gene network analysis.

Verleyen W, Ballouz S, Gillis J.

Bioinformatics. 2016 Apr 1;32(7):1065-73. doi: 10.1093/bioinformatics/btv734. Epub 2015 Dec 14.


Novel therapeutics for coronary artery disease from genome-wide association study data.

Grover MP, Ballouz S, Mohanasundaram KA, George RA, Goscinski A, Crowley TM, Sherman CD, Wouters MA.

BMC Med Genomics. 2015;8 Suppl 2:S1. doi: 10.1186/1755-8794-8-S2-S1. Epub 2015 May 29.


Guidance for RNA-seq co-expression network construction and analysis: safety in numbers.

Ballouz S, Verleyen W, Gillis J.

Bioinformatics. 2015 Jul 1;31(13):2123-30. doi: 10.1093/bioinformatics/btv118. Epub 2015 Feb 24.


Measuring the wisdom of the crowds in network-based gene function inference.

Verleyen W, Ballouz S, Gillis J.

Bioinformatics. 2015 Mar 1;31(5):745-52. doi: 10.1093/bioinformatics/btu715. Epub 2014 Oct 29.


Identification of novel therapeutics for complex diseases from genome-wide association data.

Grover MP, Ballouz S, Mohanasundaram KA, George RA, Sherman CD, Crowley TM, Wouters MA.

BMC Med Genomics. 2014;7 Suppl 1:S8. doi: 10.1186/1755-8794-7-S1-S8. Epub 2014 May 8.


Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease.

Ballouz S, Liu JY, Oti M, Gaeta B, Fatkin D, Bahlo M, Wouters MA.

Mol Genet Genomic Med. 2014 Jan;2(1):44-57. doi: 10.1002/mgg3.40. Epub 2013 Nov 13.


Bias tradeoffs in the creation and analysis of protein-protein interaction networks.

Gillis J, Ballouz S, Pavlidis P.

J Proteomics. 2014 Apr 4;100:44-54. doi: 10.1016/j.jprot.2014.01.020. Epub 2014 Jan 27.


Gentrepid V2.0: a web server for candidate disease gene prediction.

Ballouz S, Liu JY, George RA, Bains N, Liu A, Oti M, Gaeta B, Fatkin D, Wouters MA.

BMC Bioinformatics. 2013 Aug 16;14:249. doi: 10.1186/1471-2105-14-249.


Analysis of genome-wide association study data using the protein knowledge base.

Ballouz S, Liu JY, Oti M, Gaeta B, Fatkin D, Bahlo M, Wouters MA.

BMC Genet. 2011 Nov 13;12:98. doi: 10.1186/1471-2156-12-98.


Web tools for the prioritization of candidate disease genes.

Oti M, Ballouz S, Wouters MA.

Methods Mol Biol. 2011;760:189-206. doi: 10.1007/978-1-61779-176-5_12.


Strategies for reducing cancer incidence and mortality in African American and Arab American and Chaldean communities in the Detroit metropolitan area.

Vicini FA, Shah C, Wallace M, Jones P, Dykes V, Tull J, Akhtar A, Ballouz S, Boxwala I, Douglas-Nikitin V, Rivers A, Clark R, Jaiyesimi I, Fakhouri M.

Am J Clin Oncol. 2012 Aug;35(4):316-21. doi: 10.1097/COC.0b013e318210f9b5.


Phase I study of conformal radiotherapy and concurrent full-dose gemcitabine with erlotinib for unresected pancreatic cancer.

Robertson JM, Margolis J, Jury RP, Balaraman S, Cotant MB, Ballouz S, Boxwala IG, Jaiyesimi IA, Nadeau L, Hardy-Carlson M, Marvin KS, Wallace M, Ye H.

Int J Radiat Oncol Biol Phys. 2012 Feb 1;82(2):e187-92. doi: 10.1016/j.ijrobp.2010.08.050. Epub 2011 May 5.


Conditions for the evolution of gene clusters in bacterial genomes.

Ballouz S, Francis AR, Lan R, Tanaka MM.

PLoS Comput Biol. 2010 Feb 12;6(2):e1000672. doi: 10.1371/journal.pcbi.1000672.


Composite biclonal marginal zone lymphoma of lung and chronic lymphocytic leukemia: pathologic, phenotypic, cytogenetic, and molecular study.

Bhagavathi S, Micale MA, Douglas-Nikitin V, Ballouz S, Neumann K, Blenc AM.

Int J Surg Pathol. 2011 Jun;19(3):377-81. doi: 10.1177/1066896909332454. Epub 2009 Apr 15.


Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies.

Teber ET, Liu JY, Ballouz S, Fatkin D, Wouters MA.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S69. doi: 10.1186/1471-2105-10-S1-S69.

Supplemental Content

Loading ...
Support Center