@article{brochu_song_zhang_zeng_shafi_robinson_humphrey_croy_peavy_perera_et al._2024, title={A program for real-time surveillance of SARS-CoV-2 genetics}, url={https://doi.org/10.1101/2024.04.18.24306026}, DOI={10.1101/2024.04.18.24306026}, abstractNote={The COVID-19 pandemic brought forth an urgent need for widespread genomic surveillance for rapid detection and monitoring of emerging SARS-CoV-2 variants. It necessitated design, development, and deployment of a nationwide infrastructure designed for sequestration, consolidation, and characterization of patient samples that disseminates de-identified information to public authorities in tight turnaround times. Here, we describe our development of such an infrastructure, which sequenced 594,832 high coverage SARS-CoV-2 genomes from isolates we collected in the U.S. from March 13th 2020 to July 3rd 2023. Our sequencing protocol ('Virseq') generates mutation-resistant sequencing of the entire SARS-CoV-2 genome, capturing all major lineages. We also characterize 379 clinically relevant SARS-CoV-2 multi-strain co-infections and ensure robust detection of emerging lineages via simulation. The modular infrastructure, sequencing, and analysis capabilities we describe support the U.S. Centers for Disease Control national surveillance program and serve as a model for rapid response to emerging pandemics at a national scale.}, author={Brochu, Hayden N and Song, Kuncheng and Zhang, Qimin and Zeng, Qiandong and Shafi, Adib and Robinson, Matthew and Humphrey, Jake and Croy, Bobbi and Peavy, Lydia and Perera, Minoli and et al.}, year={2024}, month={Apr} }
 @article{brochu_smith_jeong_carlson_hansen_tisoncik-go_law_picker_gale_peng_2024, title={Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques}, url={https://doi.org/10.1101/2024.02.27.582186}, DOI={10.1101/2024.02.27.582186}, abstractNote={ABSTRACT}, author={Brochu, Hayden N. and Smith, Elise and Jeong, Sangmi and Carlson, Michelle and Hansen, Scott G. and Tisoncik-Go, Jennifer and Law, Lynn and Picker, Louis J. and Gale, Michael, Jr. and Peng, Xinxia}, year={2024}, month={Feb} }
 @article{brochu_wang_tollison_pyo_thomas_tseng_law_picker_gale_geraghty_et al._2022, title={Alternative splicing and genetic variation of MHC-E: Implications for rhesus cytomegalovirus-based vaccines}, url={https://doi.org/10.21203/rs.3.rs-1633558/v1}, DOI={10.21203/rs.3.rs-1633558/v1}, abstractNote={Abstract}, author={Brochu, Hayden and Wang, Ruihan and Tollison, Tammy and Pyo, Chu-Woo and Thomas, Alexander and Tseng, Elizabeth and Law, Lynn and Picker, Louis and Gale, Michael and Geraghty, Daniel and et al.}, year={2022}, month={Jun} }
 @article{brochu_wang_tollison_pyo_thomas_tseng_law_picker_gale_geraghty_et al._2022, title={Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines}, volume={5}, ISSN={["2399-3642"]}, url={https://doi.org/10.1038/s42003-022-04344-2}, DOI={10.1038/s42003-022-04344-2}, abstractNote={Abstract}, number={1}, journal={COMMUNICATIONS BIOLOGY}, author={Brochu, Hayden and Wang, Ruihan and Tollison, Tammy and Pyo, Chul-Woo and Thomas, Alexander and Tseng, Elizabeth and Law, Lynn and Picker, Louis J. and Gale, Michael and Geraghty, Daniel E. and et al.}, year={2022}, month={Dec} }
 @article{huang_callahan_wu_holloway_brochu_lu_peng_tzeng_2022, title={Phylogeny-guided microbiome OTU-specific association test (POST)}, volume={10}, ISSN={["2049-2618"]}, DOI={10.1186/s40168-022-01266-3}, abstractNote={Abstract}, number={1}, journal={MICROBIOME}, author={Huang, Caizhi and Callahan, Benjamin John and Wu, Michael C. and Holloway, Shannon T. and Brochu, Hayden and Lu, Wenbin and Peng, Xinxia and Tzeng, Jung-Ying}, year={2022}, month={Jun} }
 @article{walsh_tollison_brochu_shaw_diveley_chou_law_kirk_gale_peng_2022, title={Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques}, volume={208}, ISSN={["1550-6606"]}, url={https://doi.org/10.4049/jimmunol.2100824}, DOI={10.4049/jimmunol.2100824}, abstractNote={Abstract}, number={3}, journal={JOURNAL OF IMMUNOLOGY}, author={Walsh, Evan S. and Tollison, Tammy S. and Brochu, Hayden N. and Shaw, Brian I and Diveley, Kayleigh R. and Chou, Hsuan and Law, Lynn and Kirk, Allan D. and Gale, Michael, Jr. and Peng, Xinxia}, year={2022}, month={Feb}, pages={762–771} }
 @article{nagarajan_cho_gyorke_nagarajan_ezzell_brochu_huntress_harrell_peng_2021, title={Tumor Necrosis Factor Alpha-Induced Interleukin-1 Alpha Synthesis and Cell Death Is Increased in Mouse Epithelial Cells Infected With Chlamydia muridarum}, volume={224}, ISSN={["1537-6613"]}, DOI={10.1093/infdis/jiab168}, abstractNote={Abstract}, journal={JOURNAL OF INFECTIOUS DISEASES}, author={Nagarajan, Uma M. and Cho, Crescentia and Gyorke, Clare E. and Nagarajan, Shanmugam and Ezzell, J. Ashley and Brochu, Hayden and Huntress, Ian and Harrell, Erin and Peng, Xinxia}, year={2021}, month={Aug}, pages={S47–S55} }
 @article{dinh_paudel_brochu_popowski_gracieux_cores_huang_hensley_harrell_vandergriff_et al._2020, title={Inhalation of lung spheroid cell secretome and exosomes promotes lung repair in pulmonary fibrosis}, volume={11}, ISSN={["2041-1723"]}, url={http://dx.doi.org/10.1038/s41467-020-14344-7}, DOI={10.1038/s41467-020-14344-7}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, publisher={Springer Science and Business Media LLC}, author={Dinh, Phuong-Uyen C. and Paudel, Dipti and Brochu, Hayden and Popowski, Kristen D. and Gracieux, M. Cyndell and Cores, Jhon and Huang, Ke and Hensley, M. Taylor and Harrell, Erin and Vandergriff, Adam C. and et al.}, year={2020}, month={Feb} }
 @article{brochu_tseng_smith_thomas_jones_diveley_law_hansen_picker_gale_et al._2020, title={Systematic Profiling of Full-Length Ig and TCR Repertoire Diversity in Rhesus Macaque through Long Read Transcriptome Sequencing}, volume={204}, ISSN={["1550-6606"]}, DOI={10.4049/jimmunol.1901256}, abstractNote={Abstract}, number={12}, journal={JOURNAL OF IMMUNOLOGY}, author={Brochu, Hayden N. and Tseng, Elizabeth and Smith, Elise and Thomas, Matthew J. and Jones, Aiden M. and Diveley, Kayleigh R. and Law, Lynn and Hansen, Scott G. and Picker, Louis J. and Gale, Michael, Jr. and et al.}, year={2020}, month={Jun}, pages={3434–3444} }
 @article{catherine m. o'connell_brochu_girardi_harrell_jones_darville_sena_peng_2019, title={Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis}, volume={6}, ISSN={["2311-2638"]}, DOI={10.15698/mic2019.03.672}, abstractNote={Pelvic inflammatory disease (PID) is a female upper genital tract inflammatory disorder that arises after sexually transmitted bacterial infections (STI). Factors modulating risk for reproductive sequelae include co-infection, microbiota, host genetics and physiology. In a pilot study of cervical samples obtained from women at high risk for STIs, we examined the potential for unbiased characterization of host, pathogen and microbiome interactions using whole transcriptome sequencing analysis of ribosomal RNA-depleted total RNAs (Total RNA-Seq). Only samples from women with STI infection contained pathogen-specific sequences (3 to 38% transcriptome coverage). Simultaneously, we identified and quantified their active microbial communities. After integration with host-derived reads from the same data, we detected clustering of host transcriptional profiles that reflected microbiome differences and STI infection. Together, our study suggests that total RNA profiling will advance understanding of the interplay of pathogen, host and microbiota during natural infection and may reveal novel, outcome-relevant biomarkers.}, number={3}, journal={MICROBIAL CELL}, author={Catherine M. O'Connell and Brochu, Hayden and Girardi, Jenna and Harrell, Erin and Jones, Aiden and Darville, Toni and Sena, Arlene C. and Peng, Xinxia}, year={2019}, month={Mar}, pages={177–183} }
 @misc{lemler_brochu_yang_harrell_peng_2017, title={Elucidating the role of host long non-coding RNA during viral infection: Challenges and paths forward}, volume={5}, number={4}, journal={Vaccines}, author={Lemler, D. J. and Brochu, H. N. and Yang, F. and Harrell, E. A. and Peng, X. X.}, year={2017} }