Mercedeh Javanbakht Movassagh
Associate Research Scientist
Research & Publications
Biography
Extensive Research Description
Detailed expertise and methods development:
Development of computational and statistical methods for infectious disease genomics and sequencing data analysis (mirTarRnaSeq, mbQTL, VDJdive, RNA2DNAlign and PathSeeker).
Machine learning (Random Forest, SVMs, Topic Models, Clustering, Elastic Nets, Regressions, etc).
Next generation sequencing (NGS) analysis (RNA, microRNA (miRNA), whole genome sequencing (WGS), microbiome sequencing (16s rRNA) and T cell receptor (TCR) single cell sequencing.
Population genetics and ancestry analysis for WGS.
Genome wide association studies (GWAS).
Scalable processing of sparse sequencing data such as microbiome data.
Detailed Research interests:
Infectious disease (microbial, viral, parasitic and fungal), neonatal sepsis, hydrocephalus, RNAs and ncRNAs, computational biology, bioinformatics and biostatistics, machine learning, tropical medicine, global public health, and pathogenic cancers such as Burkitt Lymphoma, and interplay of host and human microbiome.
Coauthors
Research Interests
Bacteria; Haiti; Host-Parasite Interactions; Malaria; Parasites; Public Health; Tanzania; Trypanosoma; Uganda; Vietnam; Viruses; Global Health; Democratic Republic of the Congo; Malaria, Falciparum; Malaria, Cerebral; Blood-Borne Pathogens; Computational Biology; Biostatistics; Machine Learning; Host Microbial Interactions
Public Health Interests
Infectious Diseases; Statistical Computing
Selected Publications
- 1328. Paenibacillosis: An Emerging Cause of Neonatal Sepsis and Postinfectious HydrocephalusEricson J, Burgoine K, Hehnly C, Kumbakumba E, Ochora M, Bajunirwe F, Bazira J, Fronterre C, Hagmann C, Kulkarni A, Kumar M, Magombe J, Mbabazi-Kabachelor E, Morton S, Movassagh M, Mugamba J, Mulondo R, Muwanguzi A, Natukwatsa D, Kaaya B, Olupot-Olupot P, Onen J, Sheldon K, Smith J, Ssentongo P, Ssenyonga P, Warf B, Wegoye E, Zhang L, Broach J, Kiwanuka J, Paulson J, Schiff S. 1328. Paenibacillosis: An Emerging Cause of Neonatal Sepsis and Postinfectious Hydrocephalus Open Forum Infectious Diseases 2022, 9: ofac492.1158. PMCID: PMC9752957, DOI: 10.1093/ofid/ofac492.1158.
- B.3 Activated gene pathways in post-infectious hydrocephalus (PIH):: proteogenomics and the PIH expressomeIsaacs A, Morton S, Movassagh M, Zhang Q, Hehnly C, Zhang L, Morales D, Townsend R, Limbrick D, Paulson J, Schiff S. B.3 Activated gene pathways in post-infectious hydrocephalus (PIH):: proteogenomics and the PIH expressome Canadian Journal Of Neurological Sciences / Journal Canadien Des Sciences Neurologiques 2022, 49: s5-s5. DOI: 10.1017/cjn.2022.98.
- Disentangling the genetic basis of rhizosphere microbiome assembly in tomatoOyserman B, Flores S, Griffioen T, Pan X, van der Wijk E, Pronk L, Lokhorst W, Nurfikari A, Paulson J, Movassagh M, Stopnisek N, Kupczok A, Cordovez V, Carrión V, Ligterink W, Snoek B, Medema M, Raaijmakers J. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato Nature Communications 2022, 13: 3228. PMID: 35710629, PMCID: PMC9203511, DOI: 10.1038/s41467-022-30849-9.
- mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction AnalysisMovassagh M, Morton S, Hehnly C, Smith J, Doan T, Irizarry R, Broach J, Schiff S, Bailey J, Paulson J. mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis BMC Genomics 2022, 23: 439. PMID: 35698050, PMCID: PMC9191533, DOI: 10.1186/s12864-022-08558-w.
- C.3 Activated Gene Pathways in Post-Infectious Hydrocephalus (PIH): Proteogenomics and the PIH ExpressomeIsaacs A, Morton S, Movassagh M, Zhang Q, Hehnly C, Zhang L, Morales D, Townsend R, Limbrick D, Paulson J, Schiff S. C.3 Activated Gene Pathways in Post-Infectious Hydrocephalus (PIH): Proteogenomics and the PIH Expressome Canadian Journal Of Neurological Sciences / Journal Canadien Des Sciences Neurologiques 2021, 48: s18-s19. DOI: 10.1017/cjn.2021.279.
- SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq dataPrashant N, Alomran N, Chen Y, Liu H, Bousounis P, Movassagh M, Edwards N, Horvath A. SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data BMC Genomics 2021, 22: 689. PMID: 34551708, PMCID: PMC8459565, DOI: 10.1186/s12864-021-07974-8.
- Vaginal microbiome topic modeling of laboring Ugandan women with and without feverMovassagh M, Bebell L, Burgoine K, Hehnly C, Zhang L, Moran K, Sheldon K, Sinnar S, Mbabazi-Kabachelor E, Kumbakumba E, Bazira J, Ochora M, Mulondo R, Nsubuga B, Weeks A, Gladstone M, Olupot-Olupot P, Ngonzi J, Roberts D, Meier F, Irizarry R, Broach J, Schiff S, Paulson J. Vaginal microbiome topic modeling of laboring Ugandan women with and without fever Npj Biofilms And Microbiomes 2021, 7: 75. PMID: 34508087, PMCID: PMC8433417, DOI: 10.1038/s41522-021-00244-1.
- Immune activation during Paenibacillus brain infection in African infants with frequent cytomegalovirus co-infectionIsaacs A, Morton S, Movassagh M, Zhang Q, Hehnly C, Zhang L, Morales D, Sinnar S, Ericson J, Mbabazi-Kabachelor E, Ssenyonga P, Onen J, Mulondo R, Hornig M, Warf B, Broach J, Townsend R, Limbrick D, Paulson J, Schiff S. Immune activation during Paenibacillus brain infection in African infants with frequent cytomegalovirus co-infection IScience 2021, 24: 102351. PMID: 33912816, PMCID: PMC8065213, DOI: 10.1016/j.isci.2021.102351.
- Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemiaMovassagh M, Oduor C, Forconi C, Moormann A, Bailey J. Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia Scientific Reports 2019, 9: 20321. PMID: 31889055, PMCID: PMC6937232, DOI: 10.1038/s41598-019-56472-1.
- Systematic pan-cancer analysis of somatic allele frequencySpurr L, Li M, Alomran N, Zhang Q, Restrepo P, Movassagh M, Trenkov C, Tunnessen N, Apanasovich T, Crandall K, Edwards N, Horvath A. Systematic pan-cancer analysis of somatic allele frequency Scientific Reports 2018, 8: 7735. PMID: 29769535, PMCID: PMC5956099, DOI: 10.1038/s41598-018-25462-0.
- Overexpressed somatic alleles are enriched in functional elements in Breast CancerRestrepo P, Movassagh M, Alomran N, Miller C, Li M, Trenkov C, Manchev Y, Bahl S, Warnken S, Spurr L, Apanasovich T, Crandall K, Edwards N, Horvath A. Overexpressed somatic alleles are enriched in functional elements in Breast Cancer Scientific Reports 2017, 7: 8287. PMID: 28811643, PMCID: PMC5557904, DOI: 10.1038/s41598-017-08416-w.
- Co-Occurrence of COMT and BRCA1/2 Variants in a PopulationMovassagh M, Mudvari P, Horvath A. Co-Occurrence of COMT and BRCA1/2 Variants in a Population New England Journal Of Medicine 2017, 376: 2090-2091. PMID: 28538113, DOI: 10.1056/nejmc1701592.
- Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt LymphomaOduor C, Movassagh M, Kaymaz Y, Chelimo K, Otieno J, Ong'echa J, Moormann A, Bailey J. Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma Frontiers In Microbiology 2017, 8: 501. PMID: 28400759, PMCID: PMC5368269, DOI: 10.3389/fmicb.2017.00501.
- RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing dataMovassagh M, Alomran N, Mudvari P, Dede M, Dede C, Kowsari K, Restrepo P, Cauley E, Bahl S, Li M, Waterhouse W, Tsaneva-Atanasova K, Edwards N, Horvath A. RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data Nucleic Acids Research 2016, 44: e161-e161. PMID: 27576531, PMCID: PMC5159535, DOI: 10.1093/nar/gkw757.
- SNPlice: variants that modulate Intron retention from RNA-sequencing dataMudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards N, Golestaneh N, Horvath A. SNPlice: variants that modulate Intron retention from RNA-sequencing data Bioinformatics 2014, 31: 1191-1198. PMID: 25481010, PMCID: PMC4393518, DOI: 10.1093/bioinformatics/btu804.
- Analysis for co-occurring sequence features identifies link between common synonymous variant and an early-terminated NPC1 isoformMovassagh M, Mudvari P, Kokkinaki M, Edwards N, Golestaneh N, Horvath A. Analysis for co-occurring sequence features identifies link between common synonymous variant and an early-terminated NPC1 isoform Journal Of Clinical Bioinformatics 2014, 4: 14. DOI: 10.1186/2043-9113-4-14.
- Two Methods for Establishing Primary Human Endometrial Stromal Cells from Hysterectomy SpecimensJividen K, Movassagh M, Jazaeri A, Li H. Two Methods for Establishing Primary Human Endometrial Stromal Cells from Hysterectomy Specimens Journal Of Visualized Experiments 2014 DOI: 10.3791/51513-v.
- Two methods for establishing primary human endometrial stromal cells from hysterectomy specimens.Jividen K, Movassagh M, Jazaeri A, Li H. Two methods for establishing primary human endometrial stromal cells from hysterectomy specimens. Journal Of Visualized Experiments 2014 PMID: 24894444, PMCID: PMC4207099, DOI: 10.3791/51513.
- A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis ProcessYuan H, Qin F, Movassagh M, Park H, Golden W, Xie Z, Zhang P, Sklar J, Li H. A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis Process Cancer Discovery 2013, 3: 1394-1403. PMID: 24089019, DOI: 10.1158/2159-8290.cd-13-0186.