Publications can be found at: https://www.ncbi.nlm.nih.gov/pubmed/?term=daniela+fera
**Undergraduate researchers are underlined.
2022
23. Finkelstein*, M.T, Parker Miller*, E., Erdman, M.C., and Fera, D. (2022) Analysis of Two Cooperating Antibodies Unveils Immune Pressure Imposed on HIV Env to Elicit a V3-Glycan Supersite Broadly Neutralizing Antibody Lineage. Frontiers in Immunology. 13:962939. doi: https://doi.org/10.3389/fimmu.2022.962939 (*equal contribution)
2021
22. Tao*, K., Tzou*, P.L., Nouhin, J., Gupta, R.K., de Oliveira, T., Kosakovsky-Pond, S.L., Fera, D. and, Shafer, R.W., (2021) The biological and clinical significance of emerging SARS-CoV-2 variants. Nature Reviews Genetics. DOI: https://doi.org/10.1038/s41576-021-00408-x (*equal contribution)
21. Parker Miller*, E., Finkelstein*, M.T, Erdman, M.C., Seth, P.C., and Fera, D. (2021) A Structural Update of Neutralizing Epitopes on the HIV Envelope, a Moving Target. Viruses. 13(9), 1774. DOI: https://doi.org/10.3390/v13091774 (*equal contribution)
20. Williams, W.B, Meyerhoff, R.R., Edwards R.J., Li, H., Manne, K., Nicely, N., Henderson, R., Zhou, Y., Janowska, K., Mansouri, K., Gobeil, S., Evangelous, T., Hora, B., Madison, B., Abuahmad, A.Y., Sprenz, J., Deyton, M., Stalls, V., Kopp, M., Hsu, A., Borgnia, M., Stewart-Jones, G., Lee, M., Bronkema, N., Moody, M.A., Wiehe, K., Bradley, T., Alam, S.M., Parks, R.J., Foulger, A., Oguin, T., Bonsignori, M., LaBranche, C.C., Montefiori, D.C., Seaman, M., Santra, S., Perfect, J., Francica, J., Lynn, G., Aussedet, B., Walkowicz, W.E., Laga, R., Kelsoe, G., Saunders, K.O, Fera, D., Kwong P.D., Seder, R., Bartesaghi, A., Shaw, G.M., Acharya, P., and Haynes, B.F., (2021) Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell. 184 (11) 2955-2972.e25. DOI: https://doi.org/10.1016/j.cell.2021.04.042
19.Finkelstein*, M.T, Mermelstein*, A.G., Parker Miller, E., Seth, P.C., Stancofski, E.D., and Fera, D. (2021) Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies. Viruses. 13(1), 134; DOI: 10.3390/v13010134 (*equal contribution)
2020
18.Nguyen, D., Lin, Y, Zhou, J.O., Kibby, E., Sia, T., Tillis, T., Vapuryan, N., Xu, M.R., Potluri, R., Shin, Y.J., Erler, E., Bronkema, N., Boehlmer, D., Chung, C., Burkhard, C., Zeng, S.H., Grasso, M., Acevedo, L.A., Marmorstein, R., and Fera, D. (2020) Identification and Characterization of a Critical Alpha Helix in B-Raf Kinase Critical for the Activity of MEK Kinase in MAPK Signaling. Biochemistry. 59, 4755-4765
DOI: 10.1021/acs.biochem.0c00598
17. Zhou, J.O., Zaidi, H.A., Ton, T., and Fera, D. (2020). The effects of framework mutations at the variable domain interface on antibody affinity maturation in an HIV-1 broadly neutralizing antibody lineage. Frontiers in Immunology. 11:1529 DOI: 10.3389/fimmu.2020.01529
16.Bajic, G., Maron, M., Caradonna, T., Tian, M., Mermelstein, A., Fera, D., Kelsoe, G., Kuraoka, M, Schmidt, A. (2020) Structure-guided molecular grafting of a complex broadly neutralizing viral epitope. ACS Infect Dis. 6(5):1182-1191. DOI: 10.1021/acsinfecdis.0c00008.
2018
15. Zhou, J.O., Ton, T., Morriss, J.W., Nguyen, D., Fera, D., (2018) Structural Insights from HIV-Antibody Co-Evolution and Related Immunization Studies. AIDS Research and Human Retroviruses. 34(9):760-768. DOI: 10.1089/AID.2018.0097.
14. Fera, D., Lee, M.S., Wiehe, K., Meyerhoff, R.R., Piai, A., Bonsignori, M., Aussedat, B.,Walkowicz, W.E., Ton, T., Zhou, J.O., Danishefsky, S., Haynes, B.F., and Harrison, S.C. (2018) HIV Envelope V3 Region Mimic Embodies Key Features of a Broadly Neutralizing Antibody Lineage Epitope. Nature Communications. 9(1111). DOI: 10.1038/s41467-018-03565-6
2017
13. Williams*, W.B., Han*, Q., Jiang*, C., Zhang*, J., Nicely*, N., Fera*, D., Luo, K., Moody, M.A., Liao, H.X., Alam, S.A., Kepler, T., Wiehe, K., Ramesh, A., Bradley, T., Saunders, K., Parks, R., Foulger, A., Shen, S., Tomaras, G., Xia, S.M., Montefiori, D.C., Louder, M., Santra, S., Scearce, R., Sutherland, L., Newman, A., Bouton-Verville, H., Bowman, C., Marshall, D.J., Whitesides, J.F., Reed, S., Fox, C., Clary, K., Koutsoukos, M., Franco, D., Mascola, J.R., Harrison, S.C., Haynes, B.F. and Verkozy, L. (2017) Initiation of Neutralizing B Cell Lineages with Sequential Envelope Immunizations. Nature Communications. Nov 23;8(1):1732. DOI: 10.1038/s41467-017-01336-3 (*equal contribution)
12. Horwitz*, J.A., Bar-On*, Y., Lu*, C.L., Fera, D., Lockhart, A.A.K., Lorenzi, J., Nogueira, L., Golijanin, J., Scheid, J.F., Seaman, M.S., Gazumyan, A., Zolla-Pazner, S. and Nussenzweig, M.C. (2017) Non-Neutralizing Antibodies Alter the Course of HIV-1 Infection in vivo. Cell. 170(4):637-648. DOI: 10.1016/j.cell.2017.06.048. (*equal contribution)
11. Bonsignori*, M., Kreider*, E.F., Fera*, D., Meyerhoff*, R.R., Bradley*, T., Wiehe, K., Alam, S. A., Aussedat, B., Walkowicz, W.E., Hwang, K.K., Saunders, K.O., Zhang, R., Gladden, M.A., Monroe, A., Kumar, A., Xia, S.M., Cooper, M., Louder, M.K., McKee, K., Bailer, R.T., Pier, B.W., Jette, C.A., Kelsoe, G., Williams, W.B., Morris, L., Kappes, J., Wagh, K., Kamanga, G., Cohen, M.S., Hraber, P.T., Montefiori, D.C., Trama, A., Liao, H.X., Kepler, T.B., Moody, M.A., Gao, F., Danishefsky, S.J., Mascola, J.R., Shaw, G.M., Hahn, B.H., Harrison, S.C., Korber, B.T., Haynes, B.F. (2017) Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies. Science Translational Medicine.9(381). DOI: 10.1126/scitranslmed.aai7514. (*equal contribution)
10. Easterhoff, R., Moody, M. A., Fera, D., Cheng, H., Ackerman, M., Wiehe, K., Saunders, K.O., Vandergrift, N., Parks, R., Kim, J., Michael, N.L., O’Connell, R.J., Excler, J.L., Robb, M.L., Vasan, S., Rerks-Ngarm, S., Kaewkungwal, J., Pitisuttithum, P., Nitayaphan, S., Sinangil, F., Tartaglia, J., Phogat, S., Kepler, T.B., Alam, S.M., Liao, H.X., Ferrari, G., Seaman, M.S., Montefiori, D.C., Tomaras, G.D., Harrison, S.C. and Haynes, B.F. (2017) HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region boosted with a HIV vaccine. PLoS Pathogens. 13(2). DOI: 10.1371/journal.ppat.1006182.
2016
9. Bradley*, T., Fera*, D., Bhiman, J., Eslamizar, L., Lu, X., Anasti, K., Zhang, R., Sutherland, L.L., Scearce, R.M., Stolarchuk, C., Lloyd, K.E., Parks, R., Martelli, A., Foulger, A., Abdool-Karim, S.S., Barnett, S., Kepler, T.B., Alam, S.M., Montefiori, D.C., Moody, M.A., Liao, H.X., Morris, L., Santra, S., Harrison, S.C., and Haynes, B.F. (2016) Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor Binding Site. Cell Reports, 14; 1-12. DOI: 10.1016/j.celrep.2015.12.017. (*equal contribution)
2014
8. Fera, D., Schmidt, A.G, Haynes, B.F., Gao, F., Liao, H.X., Kepler, T.B., and Harrison, S.C. (2014) Affinity Maturation in an HIV Broadly Neutralizing B-cell Lineage Through Reorientation of Variable Domains. PNAS, 111; 10275-10280. DOI: 10.1073/pnas.1409954111.
7. Malecka*, K.A., Fera*, D., Schultz, D.C., Hodawadekar, S., Reichman, M., Donover, P.S., Murphy, M., and Marmorstein, R. (2014) Identification and characterization of small molecule human papillomavirus E6 inhibitors. ACS Chemical Biology, 9; 1603-12. DOI: 10.1021/cb500229d. (*equal contribution)
2012
6. Fera, D. and Marmorstein R. (2012) Different Regions of the HPV E7 and Ad E1A Viral Oncoproteins Bind Competitively but Through Distinct Mechanisms to the CH1 Transactivation Domain of p300. Biochemistry, 51; 9524-9534. DOI: 10.1021/bi3011863.
5. Fera, D., Schultz, D.C., Hodawadekar, S., Reichman, M., Donover, P.S., Melvin, J., Huryn, D.M., and Marmorstein, R. (2012) Identification and Characterization of Small Molecule Antagonists of pRb Inactivation by Viral Oncoproteins. Chemistry and Biology, 19; 518-528. DOI: 10.1016/j.chembiol.2012.03.007.
2011
4. Yi, C., Troutman, S., Fera, D., Stemmer-Rachamimov, A., Avila, J. L., Christian, N., Luna Persson, N., Shimono, A., Speicher, D. W., Marmorstein, R., Holmgren, L., and Kissil, J.(2011) Tight Junction-Associated Merlin-Angiomotin Complex Mediates Merlin's Regulation of Mitogenic Signaling and Tumor Suppressive Functions. Cancer Cell, 19; 527-540. DOI: 10.1016/j.ccr.2011.02.017.
2007
3. Elmatad, Y., Zitolo, M., Fera, D., and Jerschow, A. (2007) Examining Gas Kinetics in MATLAB. Chem. Educator. 12; 89-93
2004
2. Fera, D., Kim, N., Shiffeldrim, N., Zorn, J, Laserson, U., Gan, H.H., and Schlick, T. (2004) RAG: RNA-As-Graphs web resource. BMC Bioinformatics. 5:88. DOI: 10.1186/1471-2105-5-88
1. Gan, H.H, Fera, D., Zorn, J, Shiffeldrim, N., Laserson, U., Kim, N., and Schlick, T. (2004) RAG: RNA-As-Graphs Database - Concepts, Analysis, and Features. Bioinformatics, 20; 1285-1291. DOI: 10.1093/bioinformatics/bth084
**Undergraduate researchers are underlined.
2022
23. Finkelstein*, M.T, Parker Miller*, E., Erdman, M.C., and Fera, D. (2022) Analysis of Two Cooperating Antibodies Unveils Immune Pressure Imposed on HIV Env to Elicit a V3-Glycan Supersite Broadly Neutralizing Antibody Lineage. Frontiers in Immunology. 13:962939. doi: https://doi.org/10.3389/fimmu.2022.962939 (*equal contribution)
2021
22. Tao*, K., Tzou*, P.L., Nouhin, J., Gupta, R.K., de Oliveira, T., Kosakovsky-Pond, S.L., Fera, D. and, Shafer, R.W., (2021) The biological and clinical significance of emerging SARS-CoV-2 variants. Nature Reviews Genetics. DOI: https://doi.org/10.1038/s41576-021-00408-x (*equal contribution)
21. Parker Miller*, E., Finkelstein*, M.T, Erdman, M.C., Seth, P.C., and Fera, D. (2021) A Structural Update of Neutralizing Epitopes on the HIV Envelope, a Moving Target. Viruses. 13(9), 1774. DOI: https://doi.org/10.3390/v13091774 (*equal contribution)
20. Williams, W.B, Meyerhoff, R.R., Edwards R.J., Li, H., Manne, K., Nicely, N., Henderson, R., Zhou, Y., Janowska, K., Mansouri, K., Gobeil, S., Evangelous, T., Hora, B., Madison, B., Abuahmad, A.Y., Sprenz, J., Deyton, M., Stalls, V., Kopp, M., Hsu, A., Borgnia, M., Stewart-Jones, G., Lee, M., Bronkema, N., Moody, M.A., Wiehe, K., Bradley, T., Alam, S.M., Parks, R.J., Foulger, A., Oguin, T., Bonsignori, M., LaBranche, C.C., Montefiori, D.C., Seaman, M., Santra, S., Perfect, J., Francica, J., Lynn, G., Aussedet, B., Walkowicz, W.E., Laga, R., Kelsoe, G., Saunders, K.O, Fera, D., Kwong P.D., Seder, R., Bartesaghi, A., Shaw, G.M., Acharya, P., and Haynes, B.F., (2021) Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell. 184 (11) 2955-2972.e25. DOI: https://doi.org/10.1016/j.cell.2021.04.042
19.Finkelstein*, M.T, Mermelstein*, A.G., Parker Miller, E., Seth, P.C., Stancofski, E.D., and Fera, D. (2021) Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies. Viruses. 13(1), 134; DOI: 10.3390/v13010134 (*equal contribution)
2020
18.Nguyen, D., Lin, Y, Zhou, J.O., Kibby, E., Sia, T., Tillis, T., Vapuryan, N., Xu, M.R., Potluri, R., Shin, Y.J., Erler, E., Bronkema, N., Boehlmer, D., Chung, C., Burkhard, C., Zeng, S.H., Grasso, M., Acevedo, L.A., Marmorstein, R., and Fera, D. (2020) Identification and Characterization of a Critical Alpha Helix in B-Raf Kinase Critical for the Activity of MEK Kinase in MAPK Signaling. Biochemistry. 59, 4755-4765
DOI: 10.1021/acs.biochem.0c00598
17. Zhou, J.O., Zaidi, H.A., Ton, T., and Fera, D. (2020). The effects of framework mutations at the variable domain interface on antibody affinity maturation in an HIV-1 broadly neutralizing antibody lineage. Frontiers in Immunology. 11:1529 DOI: 10.3389/fimmu.2020.01529
16.Bajic, G., Maron, M., Caradonna, T., Tian, M., Mermelstein, A., Fera, D., Kelsoe, G., Kuraoka, M, Schmidt, A. (2020) Structure-guided molecular grafting of a complex broadly neutralizing viral epitope. ACS Infect Dis. 6(5):1182-1191. DOI: 10.1021/acsinfecdis.0c00008.
2018
15. Zhou, J.O., Ton, T., Morriss, J.W., Nguyen, D., Fera, D., (2018) Structural Insights from HIV-Antibody Co-Evolution and Related Immunization Studies. AIDS Research and Human Retroviruses. 34(9):760-768. DOI: 10.1089/AID.2018.0097.
14. Fera, D., Lee, M.S., Wiehe, K., Meyerhoff, R.R., Piai, A., Bonsignori, M., Aussedat, B.,Walkowicz, W.E., Ton, T., Zhou, J.O., Danishefsky, S., Haynes, B.F., and Harrison, S.C. (2018) HIV Envelope V3 Region Mimic Embodies Key Features of a Broadly Neutralizing Antibody Lineage Epitope. Nature Communications. 9(1111). DOI: 10.1038/s41467-018-03565-6
2017
13. Williams*, W.B., Han*, Q., Jiang*, C., Zhang*, J., Nicely*, N., Fera*, D., Luo, K., Moody, M.A., Liao, H.X., Alam, S.A., Kepler, T., Wiehe, K., Ramesh, A., Bradley, T., Saunders, K., Parks, R., Foulger, A., Shen, S., Tomaras, G., Xia, S.M., Montefiori, D.C., Louder, M., Santra, S., Scearce, R., Sutherland, L., Newman, A., Bouton-Verville, H., Bowman, C., Marshall, D.J., Whitesides, J.F., Reed, S., Fox, C., Clary, K., Koutsoukos, M., Franco, D., Mascola, J.R., Harrison, S.C., Haynes, B.F. and Verkozy, L. (2017) Initiation of Neutralizing B Cell Lineages with Sequential Envelope Immunizations. Nature Communications. Nov 23;8(1):1732. DOI: 10.1038/s41467-017-01336-3 (*equal contribution)
12. Horwitz*, J.A., Bar-On*, Y., Lu*, C.L., Fera, D., Lockhart, A.A.K., Lorenzi, J., Nogueira, L., Golijanin, J., Scheid, J.F., Seaman, M.S., Gazumyan, A., Zolla-Pazner, S. and Nussenzweig, M.C. (2017) Non-Neutralizing Antibodies Alter the Course of HIV-1 Infection in vivo. Cell. 170(4):637-648. DOI: 10.1016/j.cell.2017.06.048. (*equal contribution)
11. Bonsignori*, M., Kreider*, E.F., Fera*, D., Meyerhoff*, R.R., Bradley*, T., Wiehe, K., Alam, S. A., Aussedat, B., Walkowicz, W.E., Hwang, K.K., Saunders, K.O., Zhang, R., Gladden, M.A., Monroe, A., Kumar, A., Xia, S.M., Cooper, M., Louder, M.K., McKee, K., Bailer, R.T., Pier, B.W., Jette, C.A., Kelsoe, G., Williams, W.B., Morris, L., Kappes, J., Wagh, K., Kamanga, G., Cohen, M.S., Hraber, P.T., Montefiori, D.C., Trama, A., Liao, H.X., Kepler, T.B., Moody, M.A., Gao, F., Danishefsky, S.J., Mascola, J.R., Shaw, G.M., Hahn, B.H., Harrison, S.C., Korber, B.T., Haynes, B.F. (2017) Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies. Science Translational Medicine.9(381). DOI: 10.1126/scitranslmed.aai7514. (*equal contribution)
10. Easterhoff, R., Moody, M. A., Fera, D., Cheng, H., Ackerman, M., Wiehe, K., Saunders, K.O., Vandergrift, N., Parks, R., Kim, J., Michael, N.L., O’Connell, R.J., Excler, J.L., Robb, M.L., Vasan, S., Rerks-Ngarm, S., Kaewkungwal, J., Pitisuttithum, P., Nitayaphan, S., Sinangil, F., Tartaglia, J., Phogat, S., Kepler, T.B., Alam, S.M., Liao, H.X., Ferrari, G., Seaman, M.S., Montefiori, D.C., Tomaras, G.D., Harrison, S.C. and Haynes, B.F. (2017) HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region boosted with a HIV vaccine. PLoS Pathogens. 13(2). DOI: 10.1371/journal.ppat.1006182.
2016
9. Bradley*, T., Fera*, D., Bhiman, J., Eslamizar, L., Lu, X., Anasti, K., Zhang, R., Sutherland, L.L., Scearce, R.M., Stolarchuk, C., Lloyd, K.E., Parks, R., Martelli, A., Foulger, A., Abdool-Karim, S.S., Barnett, S., Kepler, T.B., Alam, S.M., Montefiori, D.C., Moody, M.A., Liao, H.X., Morris, L., Santra, S., Harrison, S.C., and Haynes, B.F. (2016) Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor Binding Site. Cell Reports, 14; 1-12. DOI: 10.1016/j.celrep.2015.12.017. (*equal contribution)
2014
8. Fera, D., Schmidt, A.G, Haynes, B.F., Gao, F., Liao, H.X., Kepler, T.B., and Harrison, S.C. (2014) Affinity Maturation in an HIV Broadly Neutralizing B-cell Lineage Through Reorientation of Variable Domains. PNAS, 111; 10275-10280. DOI: 10.1073/pnas.1409954111.
7. Malecka*, K.A., Fera*, D., Schultz, D.C., Hodawadekar, S., Reichman, M., Donover, P.S., Murphy, M., and Marmorstein, R. (2014) Identification and characterization of small molecule human papillomavirus E6 inhibitors. ACS Chemical Biology, 9; 1603-12. DOI: 10.1021/cb500229d. (*equal contribution)
2012
6. Fera, D. and Marmorstein R. (2012) Different Regions of the HPV E7 and Ad E1A Viral Oncoproteins Bind Competitively but Through Distinct Mechanisms to the CH1 Transactivation Domain of p300. Biochemistry, 51; 9524-9534. DOI: 10.1021/bi3011863.
5. Fera, D., Schultz, D.C., Hodawadekar, S., Reichman, M., Donover, P.S., Melvin, J., Huryn, D.M., and Marmorstein, R. (2012) Identification and Characterization of Small Molecule Antagonists of pRb Inactivation by Viral Oncoproteins. Chemistry and Biology, 19; 518-528. DOI: 10.1016/j.chembiol.2012.03.007.
2011
4. Yi, C., Troutman, S., Fera, D., Stemmer-Rachamimov, A., Avila, J. L., Christian, N., Luna Persson, N., Shimono, A., Speicher, D. W., Marmorstein, R., Holmgren, L., and Kissil, J.(2011) Tight Junction-Associated Merlin-Angiomotin Complex Mediates Merlin's Regulation of Mitogenic Signaling and Tumor Suppressive Functions. Cancer Cell, 19; 527-540. DOI: 10.1016/j.ccr.2011.02.017.
2007
3. Elmatad, Y., Zitolo, M., Fera, D., and Jerschow, A. (2007) Examining Gas Kinetics in MATLAB. Chem. Educator. 12; 89-93
2004
2. Fera, D., Kim, N., Shiffeldrim, N., Zorn, J, Laserson, U., Gan, H.H., and Schlick, T. (2004) RAG: RNA-As-Graphs web resource. BMC Bioinformatics. 5:88. DOI: 10.1186/1471-2105-5-88
1. Gan, H.H, Fera, D., Zorn, J, Shiffeldrim, N., Laserson, U., Kim, N., and Schlick, T. (2004) RAG: RNA-As-Graphs Database - Concepts, Analysis, and Features. Bioinformatics, 20; 1285-1291. DOI: 10.1093/bioinformatics/bth084