Christopher Maher, Ph.D.,  McDonnell Genome Institute

Dr. Christopher Maher is an Assistant Professor of Medicine in the Medical Oncology section of Washington University's Department of Medicine. He is also an Assistant Director at the McDonnell Genome Institute. His interests include computational biology and bioinformatics as they apply to cancer genomics. He is working to integrate the analysis of high-throughput genomic technologies into the development of novel diagnostic, prognostic, and therapeutic strategies in cancer.

Dr. Maher's main research focus is on the development of novel computational tools and approaches to help analyze and interpret data from high-throughput genomic technologies. He led the development of the ChimeraScan tool that can detect gene fusions within next-generation transcriptome sequencing data. By applying this tool to prostate cancer transcriptome data, Dr. Maher and his colleagues discovered a clinically relevant class of gene fusions that respond to currently available FDA approved drugs.

Dr. Maher has also been on the forefront of understanding the emerging roles of long intergenic non-coding RNAs (lncRNAs) in multiple solid tumors. Building upon these successes, his lab focuses on the discovery and characterization of novel lncRNAs, elucidating lncRNA functionality, and assessing their clinical applicability. This is accomplished through an integrated team of experimental and computational biologists that combine large-scale genomic analyses with molecular biology, cellular biology, and biochemistry.

Dr. Maher completed his B.S. degree at Cornell University and his M.S./Ph.D. degrees at Cold Spring Harbor Laboratory and Stony Brook University in New York. Most recently he was a Research Investigator at the University of Michigan.

Further information about Dr. Maher can be found through the Washington University Divisions of Hematology & Oncology.

Publication listings available here.


title citation publication date
Genomic and transcriptomic heterogeneity in metaplastic carcinomas of the breast. NPJ Breast Cancer. 2017 Dec 1;3:48. doi: 10.1038/s41523-017-0048-0. eCollection 2017 1970-08-22
INTEGRATE-Vis: a tool for comprehensive gene fusion visualization. Sci Rep. 2017 Dec 19;7(1):17808. doi: 10.1038/s41598-017-18257-2. 1970-08-22
ClonEvol: clonal ordering and visualization in cancer sequencing. Ann Oncol. 2017 Sep 11. doi: 10.1093/annonc/mdx517. [Epub ahead of print] 1970-08-22
Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. Exp Hematol. 2017 Jul 28. pii: S0301-472X(17)30701-4. doi: 10.1016/j.exphem.2017.07.008. [Epub ahead of print] 1970-08-22
Breast Cancer Neoantigens Can Induce CD8+ T-Cell Responses and Antitumor Immunity. Cancer Immunol Res. 2017 Jul;5(7):516-523. doi: 10.1158/2326-6066.CIR-16-0264. Epub 2017 Jun 15. 1970-08-22
Increased breast tissue receptor activator of nuclear factor- ?B ligand (RANKL) gene expression is associated with higher mammographic density in premenopausal women. Oncotarget. 2017 May 17. doi: 10.18632/oncotarget.17909. [Epub ahead of print] 1970-08-22
INTEGRATE-Neo: A pipeline for Personalized Gene Fusion Neoantigen Discovery. Bioinformatics. 2016 Oct 24. pii: btw674. [Epub ahead of print] 2016-10-24
Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia Exp Hematol. 2016 Jul;44(7):603-13. doi: 10.1016/j.exphem.2016.04.011. Epub 2016 May 13 2016-07-01
A genomic case study of mixed fibrolamellar hepatocellular carcinoma. Ann Oncol. 2016 Mar 30. pii: mdw135. [Epub ahead of print] 2016-03-30
Optimizing cancer genome sequencing and analysis. Cell Syst. 2015 Sep 23;1(3):210-223. 2015-09-23
INTEGRATE: gene fusion discovery using whole genome and transcriptome data. Genome Res. 2015 Nov 10. [Epub ahead of print] 2015-11-10
An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer. Mol Cell Proteomics. 2015 Dec 2. pii: mcp.M115.056226. [Epub ahead of print] 2015-12-02
Clonotyping for precision oncology. Drug Discov Today. 2015 Oct 19. pii: S1359-6446(15)00387-6. doi: 10.1016/j.drudis.2015.10.010. [Epub ahead of print] 2015-10-19
NFATc1 promotes prostate tumorigenesis and overcomes PTEN loss-induced senescence. Oncogene. 2015 Oct 19. doi: 10.1038/onc.2015.389. [Epub ahead of print] 2015-10-19
Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. doi: 10.1371/journal.pcbi.1004274. eCollection 2015. 2015-07-09
Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function. RNA Biol. 2015 Apr 11:0. [Epub ahead of print] 2015-04-11
Loss of Trop2 causes ErbB3 activation through a neuregulin-1-dependent mechanism in the mesenchymal subtype of HNSCC. Oncotarget. 2014 Sep 2. [Epub ahead of print] 2014-09-02
Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer. Genome Biol. 2014 Aug 13;15(8):429. [Epub ahead of print] 2014-08-13
SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples. Nucleic Acids Res. 2014 Jul 16. pii: gku521. [Epub ahead of print] 2014-07-16
Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31;511(7511):543-50. doi: 10.1038/nature13385. Epub 2014 Jul 9. 2014-07-09
cDNA Hybrid Capture Improves Transcriptome Analysis on Low-Input and Archived Samples. J Mol Diagn. 2014 May 8. pii: S1525-1578(14)00072-5. doi: 10.1016/j.jmoldx.2014.03.004. [Epub ahead of print] 2014-05-08
Characterization of the genomic features and expressed fusion genes in micropapillary carcinomas of the breast. J Pathol. 2014 Jan 6. doi: 10.1002/path.4325. [Epub ahead of print] 2014-01-06
A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells. Front Genet. 2013 Oct 29;4:209. doi: 10.3389/fgene.2013.00209. 2013-10-29
Transcription Factors OVOL1 and OVOL2 Induce the Mesenchymal to Epithelial Transition in Human Cancer. PLoS One. 2013 Oct 4;8(10):e76773. doi: 10.1371/journal.pone.0076773. 2013-10-04
Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts. Cell Rep. 2013 Sep 18. pii: S2211-1247(13)00463-4. doi: 10.1016/j.celrep.2013.08.022. [Epub ahead of print] 2013-09-18
Characterization of the EZH2-MMSET histone methyltransferase regulatory axis in cancer. Mol Cell. 2013 Jan 10;49(1):80-93. doi: 10.1016/j.molcel.2012.10.008. Epub 2012 Nov 15. 2013-01-10
Recurrent reciprocal RNA chimera involving YPEL5 and PPP1CB in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):3035-40. doi: 10.1073/pnas.1214326110. Epub 2013 Feb 4. 2013-02-19
Recurrent rearrangements in prostate cancer: causes and therapeutic potential. Curr Drug Targets. 2013 Apr;14(4):450-9. 2013-04-01
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol. 2011 Jul 31;29(8):742-9. doi: 10.1038/nbt.1914. 2011-07-31
ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011 Oct 15;27(20):2903-4. doi: 10.1093/bioinformatics/btr467. Epub 2011 Aug 11. 2011-10-15
Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers Cell. 2012 Sep 14;150(6):1121-34. doi: 10.1016/j.cell.2012.08.024. 2012-09-14
Comprehensive genomic characterization of squamous cell lung cancers Nature. 2012 Sep 9. doi: 10.1038/nature11404. [Epub ahead of print] 2012-09-09
Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012 Jun 10;486(7403):353-60. doi: 10.1038/nature11143. 2012-06-10
Chromothripsis and human disease: piecing together the shattering process. Cell. 2012 Jan 20;148(1-2):29-32. 2012-01-20