Featured Publications

Technology & Benchmarks

  • Jensen TL, Frasketi M, Conway K, Villarroel L, Hill H, Krampis K, Goll JB. RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting. F1000Research. 2018 Apr 13;6.
  • Jensen TL, Hooper WF, Cherikh SR, Goll JB. RP-REP Ribosomal Profiling Reports: an open-source cloud-enabled framework for reproducible ribosomal profiling data processing, analysis, and result reporting. F1000Research. 2021 Feb 24;10(143):143.
  • Goll, Johannes B., et al. “The Vacc-SeqQC project: Benchmarking RNA-Seq for clinical vaccine studies.” Frontiers in immunology 13 (2023): 1093242.

Machine Learning for Biomarker Discovery

  • DeZern, Amy E., et al. “Utility of targeted gene sequencing to differentiate myeloid malignancies from other cytopenic conditions.” Blood Advances 7.14 (2023): 3749-3759.
  • Natrajan, Muktha S., et al. “Systems vaccinology for a live attenuated tularemia vaccine reveals unique transcriptional signatures that predict humoral and cellular immune responses.” Vaccines 8.1 (2019): 4.

Genomics & Epigenomics

  • Miller, Christopher A., et al. “Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence.” The Journal of Molecular Diagnostics 24.3 (2022): 219-223.
  • Krushkal, Julia, et al. “Increased copy number of imprinted genes in the chromosomal region 20q11-q13. 32 is associated with resistance to antitumor agents in cancer cell lines.” Clinical Epigenetics 14.1 (2022): 161.
  • Minaya MA, Jensen TL, Goll JB, Korom M, Datla SH, Belshe RB, Morrison LA. Molecular Evolution of Herpes Simplex Virus 2 Complete Genomes: Comparison between Primary and Recurrent Infections. Journal of Virology. 2017 Dec 1. 19(23): e00942-17
  • Ross, Shannon, et al. “Cytomegalovirus genetic diversity following primary infection.” The Journal of infectious diseases (2019).

 Transcriptomics

  • Silver, Richard F., et al. “Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination.” Nature Communications 14.1 (2023): 8507.
  • Hamzabegovic, Fahreta, et al. “Flagellin adjuvanted F1/V subunit plague vaccine induces T cell and functional antibody responses with unique gene signatures.” NPJ vaccines 5.1 (2020): 6.
  • Howard, Leigh M., et al. “AS03-Adjuvanted H5N1 Avian Influenza Vaccine Modulates Early Innate Immune Signatures in Human Peripheral Blood Mononuclear Cells.” The Journal of infectious diseases 219.11 (2018): 1786-1798.
  • Howard, Leigh M., et al. “Cell-based systems biology analysis of human AS03-adjuvanted H5N1 avian influenza vaccine responses: a phase I randomized controlled trial.” PloS one 12.1 (2017): e0167488.

Proteomics

  • Goll, Johannes B., et al. “The antibody landscapes following AS03 and MF59 adjuvanted H5N1 vaccination.” npj Vaccines 7.1 (2022): 103.
  • Frey, Sharon E., et al. “Human antibody responses following vaccinia immunization using protein microarrays and correlation with cell-mediated immunity and antibody-dependent cellular cytotoxicity responses.” The Journal of Infectious Diseases 224.8 (2021): 1372-1382.
  • Chang YH, Duong DM, Goll JB, Wood DC, Jensen TL, Yin L, Gelber CE, Seyfried NT, Anderson E, Natrajan MS, Rouphael N. Proteomic Analysis of Human Immune Responses to Live-Attenuated Tularemia Vaccine. Vaccines. 2020 Sep;8(3):413.
  • Galassie, Allison C., et al. “Proteomics show antigen presentation processes in human immune cells after AS03‐H5N1 vaccination.” Proteomics 17.12 (2017): 1600453.

Metabolomics & Lipidomics

  • Howard, Leigh M., et al. “Metabolomic Signatures Differentiate Immune Responses in Avian Influenza Vaccine Recipients.” The Journal of Infectious Diseases (2024): jiad611.
  • Goll JB, Li S, Edwards JL, Bosinger SE, Jensen TL, Wang Y, Hooper WF, Gelber CE, Sanders KL, Anderson EJ, Rouphael N. Transcriptomic and metabolic responses to a live-attenuated Francisella tularensis vaccine. Vaccines. 2020 Sep;8(3):412.
  • Chang, Yie-Hwa, et al. “Proteomic Analysis of Human Immune Responses to Live-Attenuated Tularemia Vaccine.” Vaccines 8.3 (2020): 413.
  • Maner-Smith K, Ford DA, Goll JB, Khadka M, Jensen TL, Colucci JK, Gelber CE, Albert CJ, Bosinger SE, Franke JD, Natrajan M. Alterations in the human plasma lipidome in response to Tularemia vaccination. Vaccines. 2020 Sep;8(3):415.