Cancer Crusaders Next Generation Sequence Analysis Core


The Tulane Cancer Crusaders Next Generation Sequence Analysis Core provides a robust infrastructure of hardware, software and expertise to support a highly interactive approach for the next generation sequence analysis needs of investigators in the Tulane community as well as other investigators throughout the world. Through encouraging active investigator participation with guided one-on-one training and/or a service model, we are able to facilitate maximal data value with minimal overhead. There are currently no charges for services but we ask that you at least acknowledge support from the Tulane Cancer Center Cancer Crusaders Next Generation Sequence Analysis Core.


1 - 32GB, 2 x 2.26 GHz Quad-Core Intel Xeon Mac Pro

6 - 64GB, 2 x 2.66 GHz 12-Core Intel Xeon Mac Pro

2 - 96GB, 2 x 2.93 GHz 12-Core Intel Xeon Mac Pro

2 - 96GB, 2 x 3.06 GHz 12-Core Intel Xeon Mac Pro

10 terminals for data visualization and interpretation


Tulane Sphynx cluster



- Genome alignment

--------STAR, Novoalign, BWA, Bowtie/Tophat, GMAP (Pacbio)

- Transcript quantification (RSEM/EB-seq)

- Fusion gene discovery

- Circular RNA discovery

- Differential splicing assessment

- miRNA quantification

- Viral integration analysis

- Deconvolution of cell subtypes within mixed cell populations

- Microbiome analysis

- Virome analysis

- Nucleotide variation analysis (SNV/indels)

- CNV (copy number variation)

- de novo assembly

- Chip-seq analysis

- Data visualization

- Etc


Erik Flemington, Ph.D.

Core Director

Zimmerman Professor, Tulane Cancer Center

Cancer Crusaders Next Generation Sequence Analysis

Telephone: 504-988-1167

erik at

Melody Baddoo, M.S.

Core Manager

Senior Research Scientist

Cancer Crusaders Next Generation Sequence Analysis

Telephone: 504-988-1345

mbaddoo at

Core-associated publications:


Liu YZ, Maney P, Puri J, Zhou Y, Baddoo M, Strong M, Wang YP, Flemington E, Deng HW. RNA-sequencing study of peripheral blood monocytes in chronic periodontitis. Gene. 2016 May 1;581(2):152-60. doi: 10.1016/j.gene.2016.01.036. PMCID: PMC4767619

Kines KJ, Sokolowski M, deHaro DL, Christian CM, Baddoo M, Smither ME, Belancio VP. The endonuclease domain of the LINE-1 ORF2 protein can tolerate multiple mutations. Mob DNA. 2016 Apr 19;7:8. doi: 10.1186/s13100-016-0064-x. PMCID: PMC4837594

Zhang J, Baddoo M, Han C, Strong MJ, Cvitanovic J, Moroz K, Dash S, Flemington EK, Wu T. Gene network analysis reveals a novel 22-gene signature of carbon metabolism in hepatocellular carcinoma. Oncotarget. 2016 Jun 23. doi: 10.18632/oncotarget.10249. PMID: 27.63021

Kim JH, Baddoo MC, Park EY, Stone JK, Park H, Butler TW, Huang G, Yan X, Pauli-Behn F, Myers RM, Tan M, Flemington EK, Lim ST, Ahn EY. SON and Its Alternatively Spliced Isoforms Control MLL Complex-Mediated H3K4me3 and Transcription of Leukemia-Associated Genes. Mol Cell. 2016 mar 17;611(6):859-73. doi: 10.1016/j.molcel.2016.02.024. PMCID: PMC4799497

Grive JK, Gustafson EA, Seymour KA, Baddoo M, Schorl C, Golnoski K, Rajkovic A, Brodsky AS, Freiman RN. TAF4b Regulates Oocyte-Specific Genes Essential for Meiosis. PLoS Genet. 2016 Jun 24;12(6):e1006182. doi: 10.1371/journal.pgen.1006128. PMCID: PMC4920394

Strong, MJ, Blanchard, E 4th, Lin, Z, Morris, CA, Baddoo, M, Taylor, CM, Ware, ML, Flemington, EK. A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus – tumor association. Acta Neuropathol Commun. 2016 Jul 11;4(1):71. Doi: 10.1186/s40478-016-0338-z. PMCID: PMC4940872

Zhou X, Hao Q, Liao P, Luo S, Zhang M, Hu G, Liu H, Zhang Y, Cao B, Baddoo M, Flemington EK, Zeng SX, Lu H. Nerve growth factor receptor negates the tumor suppressor p53 as a feedback regulator. Elife. 2016 Jun 10;5. pii: e15099. doi: 10.7554/eLife. 15099. PMCID: PMC4943851

Liu YZ, Roy-Engel AM, Baddoo MC, Flemington EK, Wang G, Wang H. The impact of oil spill to lung health--Insights from an RNA-seq study of human airway epithelial cells. Gene. 2016 Mar 1;578(1):38-51. doi: 10.1016/j.gene.2015.12.016. PMID: 26692141

Harrison L, Abshire C, Prasai K, Soto I, Shi R, Concha M, Baddoo M, Flemington E, Ennis D, Scott R. Exposure of Mycobacterium marinum to Low Shear Modeled Microgravity: Effect on Growth, the Transcriptome, and Survival under Stress. Npj Microgravity. Accepted for Publication.

O'Grady, T, Wang, X, Höner Zu Bentrup, K, Baddoo, M, Concha, M, Flemington, EK. Global transcript structure resolution of high gene density genomes through multi-platform data integration. Nucleic Acids Res. 2016 Jul 12. Pii: gkw629.



Rhodes LV, Martin EC, Segar HC, Miller DF, Buechlein A, Rusch DB, Nephew KP, Burow Me, Collins-Burow BM. Dual regulation by microRNA-200b-3p and microRNA-200b-5p in the inhibition of epithelial-to-mesenchymal transition in triple-negative breast cancer. Oncotarget. 2015 Jun 30;6(18):16638-52. PMCID: PMC4599295

Cao, S, Moss, W, O'Grady, C, Concha, M, Strong, MJ, Wang, X, Yu, Y, Baddoo, M, Zhang, K, Fewell, C, Lin, Z, Dong, Y, and Flemington, EK. New noncoding lytic transcripts derived from the Epstein Barr virus latency origin of replication oriP are hyperedited, bind the paraspeckle protein, NONO/p54nrb, and support lytic viral transcription. J Virol. 2015 Jul;89(14):7120-32. PMCID: PMC4473578

Streva VA, Jordan VE, Linker S, Hedges DH, Batzer MA, Deininger PL. Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals. BMC Genomics. 2015 Mar 21; 16:220. doi: 10.1186/s12864-015-1374-y. PMCID: PMC4381410

Strong MJ, Laskow T, Nakhoul H, Blanchard E, Liu Y, Wang X, Baddoo M, Lin Z, Yin Q, Flemington, EK. Latent Expression of the Epstein-Barr Virus (EBV)-Encoded Major Histocompatibility Complex Class I TAP Inhibitor, BNLF2a, in EBV-Positive Gastric Carcinomas. J Virol. 2015 Oct;89(19):10110-4. doi: 10.1128/JVI.01110-15. Epub 2015 Jul 15. PMCID: PMC4577887

Li Y, Liu J, Li W, Brown A, Baddoo M, Li M, Carroll T, Oxburgh L, Feng Y, Saifudeen Z. p53 Enables metabolic fitness and self-renewal of nephron progenitor cells. Development. 2015 Apr 1;142(7):1228-41. doi: 10.1242/dev.111617. PMCID: PMC4378244

Cao, S, Strong, MJ, Wang, X, Moss, W, Concha, M, Lin, Z, O’Grady, T, Baddoo, M, Fewell, C, Renne, R, and Flemington, EK. High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia project. J Virol. 2015; 89:713-729 PMCID: PMC4301145.



Martin EC, Krebs AE, Burks HE, Elliot S, Baddoo M, Collins-Burow BM, Flemington EK, Burow ME. miR-155 induced transcriptome changes in the MCF-7 breast cancer cell line leads to enhanced mitogen activation protein kinase signaling. Genes Cancer. 2014 Sept;5(9-10):353-64. doi: 10.18632/genesand cancer.33. PMCID: PMC4209600

O’Grady, T, Cao, S, Strong, MJ, Concha, M, Wang, X, Splinter BonDurant, S, Adams, M, Baddoo, M, Srivastav, SK, Lin, Z, Fewell, C, Yin, Q, and Flemington, EK. Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. J Virol. 2014 88: 1604-1616. PMCID: PMC3911580

Xu, G, Strong, MJ, Lacey, MR, Baribault, C, Flemington, EK, Taylor, CM. RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets. PloS One 2014 Feb 25;9(2):e89445. PMCID: PMC3934900

Martin, EC, Rhodes, LV, Elliot, S, Krebs, EA, Nephew, KP, Flemington, EK, Collins-Burow, BM, Burow, ME. microRNA regulation of mammalian target of rapamycin expression and activity controls estrogen receptor function and RAD001 sensitivity. Mol Cancer 2014 Oct 6;13(1):229. PMCID: PMC4203920

Strong, MJ, Lin, Z, Flemington, EK. Expanding the conversation on high-throughput virome sequencing standards to include consideration of microbial contamination sources. MBio. 2014 Oct 28;5(6):e01989. doi: 10.1128/mBio.01989-14. PMCID: PMC4217176

Kines KJ, Sokolowski M, deHaro DL, Christian CM, Belancio VP. Potential for genomic instability associated with retrotranspositionally-incompetent L1 loci. Nucleic Acids Res. 2014;42(16):10488-502. doi: 10.1093/nar/gku687. PMCID: PMC4176336

Strong, MJ, Xu, G, Morici, L, Splinter Bon-Durant, S, Baddoo, M, Lin, Z, Fewell, C, Taylor, CM, and Flemington, EK. Microbial contamination in next generation sequencing: Implications for sequence-based analysis of clinical samples. Plos Pathogens 2014 Nov 20;10(11):e1004437. Doi: 10.1371 PMCID: PMC4239086

Terragni J, Zhang G, Sun Z, Pradhan S, Song L, Crawford GE, Lacey M, Ehrlich M. Notch signaling genes: myogenic DNA hypomethylation and 5-hydroxymethylcytosine. Epigenetics. 2014 June;9(6):842-50. doi: 10.4161/epi.28597. PMCID: PMC4065182



Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Baddoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, Ehrlich M. Early de novo DNA methylation and proglonged demethylation in the muscle lineage. Epigenetics. 2013 Mar; 8(3):317-32. doi: 10.4161/epi.23989. PMCID: PMC3669123

Strong, MJ, O’Grady, T, Lin, Z, Xu, G, Baddoo, M, Parsons, C, Zhang, K, Taylor, CM, and Flemington, EK. Epstein-Barr Virus and Human Herpesvirus 6 Detection in a non-Hodgkin’s Diffuse Large B-Cell Lymphoma Cohort using RNA-Seq. J Virol. 2013; 87:13059-13062. PMID: 24049168

Gopalakrishnan AM, Kumar N. Opposing roles for two molecular forms of replication protein A in Rad51-Rad54-mediated DNA recombination in Plasmodium falciparum. MBio. 2013 Apr 30;4(3):e00252-13. doi: 10.1128/mBio.00252-13. PMCID: PMC3648904

Lin, Z, Wang, X, Strong, MJ, Concha, M, Baddoo, M, Xu, G, Baribault, C, Fewell, C, Hulme, W, Hedges, D, Taylor, CM, Flemington, EK. Whole genome sequencing of the Akata and Mutu Epstein-Barr virus strains. J Virol. 2013; 87:1172-1182 PMID: 23152513.

Li Y, Liu J, McLaughlin N, Bachvarov D, Saifudeen Z, El-Dahr SS. Genome-wide analysis of the p53 gene regulatory network in the developing mouse kidney. Physiol Genomics. 2013 Oct 16;45(20):948-64. doi: 10.1152/physiolgenomics.00113.2013

Strong, MJ, Xu, G, Coco, J, Baribault, C, Vinay, DS, Lacey, MR, Strong, AL, Lehman, TA, Seddon, MB, Lin, Z, Concha, M, Baddoo, M, Ferris, MB, Swan, KF, Sullivan, DE, Burow, ME, Taylor, CM and Flemington, EK. Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity; implications for possible immune adjuvant therapy. PLOS Pathogens 2013; 9: e1003341. PMID: 23671415

Tsumagari K, Baribault C, Terragni J, Chandra S, Renshaw C, Sun Z, Song L, Crawford GE, Pradhan S, Lacey M, Ehrlich M. DNA methylation and differentiation: HOX genes in muscle cells. Epigenetics Chromatin. 2013 Aug 2;6(1);25. doi: 10.1186/1756-8935-6-25. PMCID: PMC3750649