Publications

*: Co-first author, #: Co-corresponding author
2025
Antibody evasion and receptor binding of SARS-CoV-2 LP. 8.1. 1, NB. 1.8. 1, XFG, and related subvariants
Mellis, I.A.*, Wu, M.*, Wang, Q.*, Bowen, A.*, Gherasim, C., Pierce, V.M., Shah, J.G., Purpura, L.J., Yin, M.T., Gordon, A., Guo, Y., Ho., D.D.
bioRxiv (2025):2025.07.18.662329 (Accepted, Cell Reports)
2025
Optimizing a human monoclonal antibody for better neutralization of SARS-CoV-2
Wang, Q., Guo, Y., Casner, R.G., Yu, J., Nair, M.S., Ho, J., Reddem, E.R., Mellis, I.A., Wu, M., Tzang, C.C. Hong, H., Huang, Y., Shapiro, L., Ho, D.D.
Nature Communications 16, no. 1 (2025): 6195
2025
Do Existing COVID-19 Vaccines Need to Be Updated in 2025?
Mellis, I.A.*, Wu, M.*, Wang, Q.*, Bowen, A.*, Gherasim, C., Pierce, V.M., Shah, J.G., Purpura, L.J., Yin, M.T., Gordon, A., Guo, Y., Ho., D.D.
bioRxiv (2025):2025.05.02.651777
2025
Antibody evasiveness of SARS-CoV-2 subvariants KP.3.1.1 and XEC
Wang, Q.*, Guo, Y.*, Mellis, I.A.*, Wu, M.*, Mohri, H., Gherasim, C., Valdez, R., Purpura, L.J., Yin, M.T., Gordon, A., Ho., D.D.
Cell Reports 44, no. 4 (2025):115543.
2025
Variant-specific antibody correlates of protection against SARS-CoV-2 Omicron symptomatic and overall infections
Zambrana, J.V.*, Mellis, I.A.*, Shotwell, A., Maier, H.E., Saborio, Y., Barillas, C., Lopez, R., Vasquez, G., Plazaola, M., Sanchez, N., Ojeda, S., Gilbertson, I., Kuan, G., Wang, Q., Liu, L., Balmaseda, A., Ho, D.D., Gordon, A.
medRxiv (2025): 2025.02.11.25322066 (Accepted, Nature Communications)
2025
KP. 2-based monovalent mRNA vaccines robustly boost antibody responses to SARS-CoV-2
Wang, Q.*, Mellis, I.A.*, Wu, M.*, Bowen, A.*, Gherasim, C., Valdez, R., Shah, J., Purpura, L.J., Yin, M.T., Gordon, A.#, Guo, Y#, Ho., D.D.#
The Lancet Infectious Diseases (2025)
2024
Robust SARS-CoV-2-neutralizing antibodies sustained through 6 months post XBB. 1.5 mRNA vaccine booster
Wang, Q.*, Mellis, I.A.*, Guo, Y.*, Gherasim, C., Valdez, R., Gordon, A.#, Liu, L.#, Ho., D.D.#
Cell Reports Medicine 5, no. 9 (2024): 101701
2024
Recurrent SARS-CoV-2 spike mutations confer growth advantages to select JN.1 sublineages
Wang, Q.*, Mellis, I.A.*, Ho, J.*, Bowen, A., Kowalski-Dobson, T., Valdez, R., Katsamba, P.S., Wu, M., Lee, C., Shapiro, L., Gordon, A.#, Guo, Y.#, Ho., D.D.#, Liu, L.#
Emerging Microbes & Infections 13, no. 1 (2024): 2402880.
2024
Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells
Mellis, I.A.#, Melzer, M., Bodkin, N., Goyal, Y.#
Genome Biology 25, no. 1 (2024): 217.
2024
SARS-CoV-2 Omicron BA. 2.87.1 Exhibits Higher Susceptibility to Serum Neutralization Than EG.5.1 and JN.1
Wang, Q.*, Guo, Y.*, Schwanz, L.T.*, Mellis, I.A.*, Sun, Y., Qu, Y., Urtecho, G., Valdez, R., Stoneman, E., Gordon, A., Wang, H.H., Liu, L.#, Ho., D.D.#
Emerging Microbes & Infections, 13(1).
2024
XBB.1.5 monovalent mRNA vaccine booster elicits robust neutralizing antibodies against XBB subvariants and JN.1
Wang, Q.*, Guo, Y.*, Bowen, A.*, Mellis, I.A.*, Valdez, R., Gherasim, C., Gordon, A.#, Liu, L.#, Ho., D.D.#
Cell Host & Microbe 32, 315–321.e3 (2024)
2024
Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells
Jain, N., Goyal, Y., Dunagin, M.C., Cote, C.J., Mellis, I.A., Emert, B., Jiang, C.L., Dardani, I.P., Reffsin, S., Arnett, M., Yang, W., and Raj, A.
Cell Systems 15, 109–133.e10 (2024)
2023
Evolving antibody evasion and receptor affinity of the Omicron BA.2.75 sublineage of SARS-CoV-2
Wang, Q.*, Li, Z.*, Guo, Y.*, Mellis, I.A.*, Iketani, S., Liu, M., Yu, J., Valdez, R., Lauring, A.S., Sheng, Z., Gordon, A., Liu, L.#, Ho, D.D.#
iScience 26, no. 11 (2023)
2023
Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells
Goyal, Y.#, Busch, G.T., Pillai, M., Li, J., Boe, R.H., Grody, E.I., Chelvanambi, M., Dardani, I.P., Emert, B., Bodkin, N., Braun, J., Fingerman, D., Kaur, A., Jain, N., Ravindran, P.T., Mellis, I.A., Kiani, K., Alicea, G.M., Fane, M.E., Ahmed, S.S., Li, H., Chen, Y., Chai, C., Kaster, J., Witt, R.G., Lazcano, R., Ingram, D.R., Johnson, S.B., Wani, K., Dunagin, M.C., Lazar, A.J., Weeraratna, A.T., Wargo, J.A., Herlyn, M., Raj, A.#
Nature 620, no. 7974 (2023): 651-659.
2023
SARS-CoV-2 Neutralizing Antibodies After Bivalent vs. Monovalent Booster
Wang, Q.*, Bowen, A.D.*, Tam, A.R., Valdez, R., Stoneman, E., Mellis, I.A., Gordon, A.#, Liu, L.#, Ho, D.D.#
The Lancet Infectious Diseases 23, no. 5 (2023): 527-528.
2022
Cell type determination for cardiac differentiation occurs soon after seeding of human induced pluripotent stem cells
Jiang, C.L., Goyal, Y., Jain, N., Wang, Q., Truitt, R.E., Cote, A.J., Emert, B., Mellis, I.A., Kiani, K., Yang, W., Jain, R.#, Raj, A.#
Genome Biology 23, no. 1 (2022): 1-29.
2021
Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro
Mellis, I.A., Edelstein, H.I., Truitt, R., Beck, L.E., Symmons, O., Goyal, Y., Linares Saldana, R.A., Shah, P.P., Pérez-Bermejo, J.A., Padmanabhan, A., Yang, W., Jain, R.#, Raj, A.#
Cell Systems 12, no. 9 (2021): 885-899.
2021
Association of Neighborhood-Level Factors and COVID-19 Infection Patterns in Philadelphia Using Spatial Regression
Boland, M.R., Liu, J., Balocchi, C., Meeker, J., Bai, R., Mellis, I.A., Mowery, D.L., Herman, D.
AMIA Summits on Translational Science Proc. 2021 (2021): 545.
2021
Genetic screening for single-cell variability modulators driving therapy resistance
Torre, E.A., Arai, E., Bayatpour, S., Jiang, C.L., Beck, L.E., Emert, B.L., Shaffer, S.M., Mellis, I.A., Fane, M.E., Alicea, G.M., Budinich, K.A., Weeraratna, A., Shi, J.#, Raj, A.#
Nature Genetics 53, no. 1 (2021): 76-85.
2019
Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting
Symmons, O., Chang, M., Mellis, I.A., Kalish, J.M., Park, J., Susztak, K., Bartolomei, M.S., Raj, A.
PLoS Genetics 15, no. 1 (2019): e1007874
2018
ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification
Rouhanifard, S.H., Mellis, I.A., Dunagin, M., Bayatpour, S., Jiang, C.L., Dardani, I., Symmons, O., Emert, B., Torre, E., Cote, A., Sullivan, A., Stamatoyannopoulos. J.A., Raj, A.
Nature Biotechnology 37, no. 1 (2019): 84-89.
2018
Remodeling of the collagen matrix in aging skin promotes melanoma metastasis and affects immune cell motility
Kaur A., Ecker B.L., Douglass S.M., Kugel C.H., Webster M.R., Almeida F.V., Somasundaram R., Hayden J., Ban E., Ahmadzadeh H., Franco-Barraza J., Shah N., Mellis, I.A., Keeney F., Kossenkov A., Tang H.Y., Yin X., Liu Q., Xu X., Fane M., Brafford P., Herlyn M., Speicher D.W., Wargo J.A., Tetzlaff M.T., Haydu L.E., Raj A., Shenoy V., Cukierman E., Weeraratna A.T.
Cancer Discovery 9, no. 1 (2019): 64-81
2017
Visualizing adenosine to inosine RNA editing in single mammalian cells
Mellis, I.A., Gupte, R.K., Raj, A., Rouhanifard, S.H.
Nature Methods 14, no. 8 (2017): 801-804.
2016
An Alzheimer’s disease-derived biomarker signature identifies Parkinson’s disease patients with dementia
Berlyand, Y., Weintraub, D., Xie, S.X., Mellis, I.A., Doshi, J., Rick, J., McBride, J., Davatzikos, C., Shaw, L.M., Hurtig, H., Trojanowski, J.Q., Chen-Plotkin, A.S.
PLoS one 11, no. 1 (2016): e0147319.
2015
Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?
Mellis, I.A., Raj, A.
Genome Research 25, no. 10 (2015): 1466-1472.
2013
Conditionals by inversion provide a universal method for the generation of conditional alleles
Economides, A.N., Frendewey, D., Yang, P., Dominguez, M.G., Dore, A.T., Lobov, I.B., Persaud, T., Rojas, J., McClain, J., Lengyel, P., Groguett, G., Chernomorsky, R., Stevens, S., Auerbach, W., DeChiara, T.M., Pouyemirou, W., Cruz, J.M., Feeley, K., Mellis, I.A., Yasenchack, J., Hatsell, S.J, Xie, L., Latres, E., Huang, L., Zhang, Y., Pefanis, E., Skokos, D., Deckelbaum, R.A., Croll, S.D., Davis, S., Valenzuela, D.M., Gale, N.W., Murphy, A.J., Yancopoulos G.D.
PNAS 110, no. 34 (2013): E3179-E3188.