PUBLICATIONS — BROOKE LAB

SELECTED PREPRINTS:

Ranoa DRE, Holland RL, Alnaji FG, Green KJ, Wang L, Brooke CB, Burke MD, Fan TM, and Hergenrother PJ. 2020.

Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction.

bioRxiv. doi: 10.1101/2020.06.18.159434

SELECTED PUBLICATIONS:

Farjo M, Koelle K, Martin MA, Gibson LL, Walden KKO, Rendon G, Fields CJ, Alnaji FG, Gallagher N, Luo CH, Mostafa HH, Manade YC, Pekosz A, Smith RL, McManus DD, and Brooke CB. 2024.

Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

J. Virology. doi: 10.1128/jvi.01618-23

Rivera-Cardona J and Brooke CB

How influenza shuts down host transcription

Nature Microbiology. doi: 10.1038/s41564-023-01416-9

Farjo M and Brooke CB. 2023.

When influenza viruses don’t play well with others

Nature. doi: 10.1038/d41586-023-00983-5

Farjo M and Brooke CB. 2023.

Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2

mSphere. doi: 10.1128/mSphere.00400-22.

Liu T, Wang Y, Tan TJC, Wu NC, and Brooke CB. 2022.

The evolutionary potential of the influenza A virus hemagglutinin is highly constrained by epistatic interactions with neuraminidase.

Cell Host & Microbe. doi: https://doi.org/10.1016/j.chom.2022.09.003.

Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, and Brooke CB. 2022.

Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

Nature Microbiology. doi: 10.1038/s41564-022-01105-z

Diefenbacher M, Tan TJC, Bauer DLV, Stadtmueller B, Wu NC, Brooke CB. 2022.

Interactions between influenza A virus nucleoprotein and gene segment UTRs facilitate selective modulation of viral gene expression

J. Virology. doi: 10.1128/jvi.00205-22

Ke R, Martinez PP, Smith RL, Gibson LL, Achenbach CJ, McFall S, Qi C, Jacob J, Dembele E, Bundy C, Simons LM, Ozer EA, Hultquist JF, Lorenzo-Redondo R, Opdycke AK, Hawkins C, Murphy RL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Farjo M, Rendon G, Fields CJ, Wang L, Fredrickson R, Baughman ME, Chiu KK, Choi H, Scardina KR, Owens AN, Broach J, Barton B, Lazar P, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, and Brooke CB. 2022.

Longitudinal analysis of SARS-CoV-2 vaccine breakthrough infections reveal limited infectious virus shedding and restricted tissue distribution.

Open Forum Infect. Dis.. doi: 10.1093/ofid/ofac192

Alnaji FG, Reiser WK, Rivera Cardona J, te Velthuis A, and Brooke CB. 2021.

Influenza A virus defective viral genomes are inefficiently packaged into virions relative to wild-type genomic RNAs.

mBio. doi: 10.1128/mBio.02959-21

Smith RL, Gibson LL, Martinez PP, Ke R, Mirza A, Conte M, Gallagher N, Conte A, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Jensen TW, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Owens AN, Broach J, Barton B, Lazar P, Henness D, Young T, Dunnett A, Robinson ML, Mostafa HH, Pekosz A, Manabe YC, Heetderks WJ, McManus DD, and Brooke CB. 2021.

Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection.

J. Infect. Dis.. doi: 10.1093/infdis/jiab337/6311835

Martin BE, Harris JD, Sun J, Koelle K, and Brooke CB. 2020

Cellular co-infection can modulate efficiency of influenza A virus production and shape the interferon response

PLOS Pathogens. doi: 10.1371/journal.ppat.1008974

Sun J, Vera JC, Drnevich J, Lin YT, Ke R, and Brooke CB. 2020.

Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection

PLOS Pathogens. doi: 10.1371/journal.ppat.1008671

Alnaji FG and Brooke CB. 2020.

Influenza virus DI particles: Defective interfering or delightfully interesting?

PLOS Pathogens. doi: 10.1371/journal.ppat.1008436

Koelle K, Farrell A, Brooke CB, and Ke R. 2019.