Genomics support at the RTB is located at 3 primary locations: 1) The Pathogen Surveillance Sequencing (PSS) at the Rocky Mountain Laboratories (RML) in Hamilton, Montana; 2) The Genomics Technologies Unit (GTU) on the NIH main campus in Bethesda, Maryland; and the Integrated Research Facility (IRF) Genomics Core at Ft. Detrick in Frederick, Maryland. Across these 3 locations, Genomics staff support collaborators in experimental design, sample preparation for any sequencing-based –omics application, high throughput sequencing through in-house platforms as well as partnering with both internal and external providers for platforms not available in-house, initial data quality control and processing, and facilitating downstream computational analysis. This approach ensures intramural NIAID investigators have access to state-of-the-art applications in next generation sequencing and by integrating experimental design, sample prep, data generation and downstream analysis it ensures data is optimally generated for the collaborator’s scientific question.
Computer generated model depicting RNA polymerase
Major Areas of Support
- General sample library prep for NGS applications
- Short- and Long-read Next-generation DNA and RNA sequencing
- Multi-omic single cell processing and analysis
- Bulk and single-cell immune repertoire profiling
- 16S and shotgun metagenomic sample prep and sequencing
- Shotgun and capture-based viral sequencing
- Custom amplicon design and sequencing
- TaqMan (RT-qPCR) analysis
- Droplet Digital PCR
Instrumentation
Rocky Mountain Laboratories
- Illumina MiSeq
- Illumina NextSeq 2000
- Oxford Nanopore MinION
- 10x Genomics Chromium X
- Applied Biosystems QuantStudio
- Bio-Rad Droplet Digital PCR
Bethesda
- Illumina NextSeq 2000
- 10X Genomics Chromium X
- PerkinElmer SciClone G3 NGSx
IRF-Frederick
- Illumina NextSeq 2000
- Illumina iSeq 100
- 10X Genomics Chromium X
- 10x Genomics Visium CytAssist
- PerkinElmer SciClone G3 NGSx
- Oxford Nanopore Technologies MinION Mk1C
Selected Publications
Migration arrest and transendothelial trafficking of human pathogenic-like Th17 cells are mediated by differentially positioned chemokines.
Parween F, Singh SP, Kathuria N, Zhang HH, Ashida S, Otaizo-Carrasquero FA, Shamsaddini A, Gardina PJ, Ganesan S, Kabat J, Lorenzi HA, Riley DJ, Myers TG, Pittaluga S, Bielekova B, Farber JM. Nat Commun. 2025. Feb 26;16(1):1978. doi: 10.1038/s41467-025-57002-6. PMID: 40000641; PMCID: PMC11861662.
Monkeypox Virus Clade IIa Infections, Liberia, 2023-2024.
Nyan DC, Berry IM, Shobayo BI, Mehta M, Worwa G, Hirsch S, Klim SE, Taweh F, Donzo KS, Freeman BM, Corvah AB, Jaryan F, Gilayeneh JSM, Crozier I, Renken C, McNay L, Moses JS, Kuhn JH, Hensley LE, Zufan SE. Emerg Infect Dis. 2025 Sep;31(9):1848-1851. doi: 10.3201/eid3109.250271. Epub 2025 Aug 5. PMID: 40763194; PMCID: PMC12407201.
The fetal trophoblast cell marker HLA-G activates a type I interferon response in primary NK cells through the receptor KIR2DL4.
Rajagopalan S, Majumder S, Wang C, Hibler W, Shamsaddini A, Gardina P, Long EO. Sci Signal. 2026 Feb 3;19(923):eadv2400. doi: 10.1126/scisignal.adv2400. Epub 2026 Feb 3. PMID: 41632833.
Eos plays a critical role in Treg homeostasis and modulates the function of recirculating thymic Tregs in the control of Treg development.
Xie X, Thornton AM, Tanwar S, Korty P, Wells AC, Segrist E, Teijeiro A, Rivera CA, Wei D, Chen X, Zhu J, Khleborodova A, Hill T, Markowitz TE, Smelkinson M, Kabat J, Veres T, Schwartz OM, Otaizo-Carrasquero F, Gardina P, Shamsaddini A, Martens C, Cho K, Lin CC, Khillan JS, Levin Y, Wu Y, Shevach EM. Cell Rep. 2026 Jan 27;45(1):116838. doi: 10.1016/j.celrep.2025.116838. Epub 2025 Dec 29. PMID: 41474621; PMCID: PMC12869356.
Pathway-instructed therapeutic selection of ruxolitinib reduces neuroinflammation in fungal postinfectious inflammatory syndrome.
Hargarten JC, Ssebambulidde K, Anjum SH, Vaughan MJ, Xu J, Ganguly A, Dulek B, Otaizo-Carrasquero F, Song B, Tao S, Park YD, Scott TL, Höltermann TA, Schinazi RF, Chittiboina P, Billioux BJ, Hammoud DA, Olszewski MA, Williamson PR. Sci Adv. 2025 Mar 21;11(12):eadi9885. doi: 10.1126/sciadv.adi9885. Epub 2025 Mar 21. PMID: 40117367; PMCID: PMC11927619.
Intranasal immunization with avian paramyxovirus type 3 expressing SARS-CoV-2 spike protein protects hamsters against SARS-CoV-2.
Park HS, Matsuoka Y, Luongo C, Yang L, Santos C, Liu X, Ahlers LRH, Moore IN, Afroz S, Johnson RF, Lafont BAP, Dorward DW, Fischer ER, Martens C, Samal SK, Munir S, Buchholz UJ, Le Nouën C. NPJ Vaccines. 2022 Jun 28;7(1):72. doi: 10.1038/s41541-022-00493-x.PMID: 35764659
A single intranasal dose of a live-attenuated parainfluenza virus-vectored SARS-CoV-2 vaccine is protective in hamsters.
Liu X, Luongo C, Matsuoka Y, Park HS, Santos C, Yang L, Moore IN, Afroz S, Johnson RF, Lafont BAP, Martens C, Best SM, Munster VJ, Hollý J, Yewdell JW, Le Nouën C, Munir S, Buchholz UJ. Proc Natl Acad Sci U S A. 2021 Dec 14;118(50):e2109744118. doi: 10.1073/pnas.2109744118.PMID: 34876520
Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer.
Avanzato VA, Matson MJ, Seifert SN, Pryce R, Williamson BN, Anzick SL, Barbian K, Judson SD, Fischer ER, Martens C, Bowden TA, de Wit E, Riedo FX, Munster VJ. Cell. 2020 Dec 23;183(7):1901-1912.e9. doi: 10.1016/j.cell.2020.10.049. Epub 2020 Nov 4.PMID: 33248470
Therapeutic responses to Roseomonas mucosa in atopic dermatitis may involve lipid-mediated TNF-related epithelial repair.
Myles IA, Castillo CR, Barbian KD, Kanakabandi K, Virtaneva K, Fitzmeyer E, Paneru M, Otaizo-Carrasquero F, Myers TG, Markowitz TE, Moore IN, Liu X, Ferrer M, Sakamachi Y, Garantziotis S, Swamydas M, Lionakis MS, Anderson ED, Earland NJ, Ganesan S, Sun AA, Bergerson JRE, Silverman RA, Petersen M, Martens CA, Datta SK. Sci Transl Med. 2020 Sep 9;12(560):eaaz8631. doi: 10.1126/scitranslmed.aaz8631.PMID: 32908007
Chromoanasynthesis as a cause of Jacobsen syndrome.
Anzick S, Thurm A, Burkett S, Velez D, Cho E, Chlebowski C, Virtaneva K, Bruno D, Martin CB, Lang DM, Brooks B, Martens C, McDermott DH, Murphy PM. Am J Med Genet A. 2020 Nov;182(11):2533-2539. doi: 10.1002/ajmg.a.61824. Epub 2020 Aug 25.PMID: 32841469
SARS-CoV-2 infection dynamics in lungs of African green monkeys.
Speranza E, Williamson BN, Feldmann F, Sturdevant GL, Pérez-Pérez L, Mead-White K, Smith BJ, Lovaglio J, Martens C, Munster VJ, Okumura A, Shaia C, Feldmann H, Best SM, de Wit E. bioRxiv. 2020 Aug 20:2020.08.20.258087. doi: 10.1101/2020.08.20.258087. Preprint.PMID: 32839775
Access
To initiate a new project with NIAID Genomics, please submit a request through the Technology Accessioning System (TAS) or email Craig Martens from the PSS, Francisco Otaizo-Carrasquero from the GTU, Monika Mehta from IRF-Genomics, or Justin Lack.
Leadership
Craig Martens, Ph.D.
Chief, Pathogen Surveillance Sequencing
Craig Martens, Ph.D.
Francisco Otaizo-Carrasquero
Genomics Technologies Unit Manager
Monika Mehta, Ph.D.
IRF-Genomics Manager
Justin Lack, Ph.D.
