URochester Medicine / Labs / Topham Lab / Publications

Publications from the Topham Lab

1. Geber A
2. Groff B
3. McMurry J
4. Laniewski N
5. Tyrlik A
6. Kean C
7. Wang R
8. Castro-Melendez D
9. Narvaez-Miranda J
10. Vance N
11. Pryhuber G
12. Mosmann T
13. Rudd BD
14. Thakar J
15. Topham DJ
16. Grimson A
17. Scheible K
Single cell analysis of neonatal naïve CD8α + T cells reveals novel subsets bridging the innate-adaptive spectrum.; bioRxiv : the preprint server for biology. 2026 Mar 09.
1. Bender W
2. Zhang Y
3. Corbett A
4. Chu C
5. Grier A
6. Wang L
7. Qiu X
8. McCall MN
9. Topham DJ
10. Walsh EE
11. Mariani TJ
12. Scheuermann R
13. Caserta MT
14. Anderson CS
Association of disease severity and genetic variation during primary Respiratory Syncytial Virus infections.; BMC medical genomics; Vol 17(1), pp. 165. 2024 Jun 19.
1. Sportiello M
2. Topham DJ
MousebreedeR: A novel software to assist in the design of breeding schema for complex genotypes of experimental organisms.; Journal of open source software; Vol 9(98). 2024 Jun 04.
1. Piepenbrink M
2. Oladunni F
3. Nogales A
4. Khalil AM
5. Fitzgerald T
6. Hilimire TA
7. Basu M
8. Fucile C
9. Topham DJ
10. Rosenberg AF
11. Martinez-Sobrido L
12. Kobie JJ
Correction for Piepenbrink et al., "Highly Cross-Reactive and Protective Influenza A Virus H3N2 Hemagglutinin- and Neuraminidase-Specific Human Monoclonal Antibodies".; Microbiology spectrum. 2024 Jan 30.
1. Sportiello M
2. Poindexter A
3. Reilly EC
4. Geber A
5. Lambert Emo K
6. Jones TN
7. Topham DJ
Mouse Memory CD8 T Cell Subsets Defined by Tissue-Resident Memory Integrin Expression Exhibit Distinct Metabolic Profiles.; ImmunoHorizons; Vol 7(10), pp. 652-669. 2023 Oct 01.
1. Brady MT
2. Laniewski N
3. Strawderman M
4. Chu CC
5. Kanagaiah P
6. Sangster MY
7. Topham DJ
8. Friedberg JW
9. Zent CS
Long-term results of vaccination with adjuvanted recombinant varicella zoster glycoprotein E during initial Bruton tyrosine kinase inhibitors therapy for chronic lymphocytic leukemia or lymphoplasmacytic lymphoma.; American journal of hematology. 2023 Jul 23.
1. Piepenbrink M
2. Oladunni F
3. Nogales A
4. Khalil AM
5. Fitzgerald T
6. Basu M
7. Fucile C
8. Topham DJ
9. Rosenberg AF
10. Martinez-Sobrido L
11. Kobie JJ
Highly Cross-Reactive and Protective Influenza A Virus H3N2 Hemagglutinin- and Neuraminidase-Specific Human Monoclonal Antibodies.; Microbiology spectrum. 2023 Jun 15.
1. Villamayor L
2. Rivero V
3. López-García D
4. Topham DJ
5. Martínez-Sobrido L
6. Nogales A
7. DeDiego ML
Interferon alpha inducible protein 6 is a negative regulator of innate immune responses by modulating RIG-I activation.; Frontiers in immunology; Vol 14, pp. 1105309. 2023 Jan 30.
1. Yu J
2. Tycksen E
3. Yang W
4. Mariani TJ
5. Bhattacharya S
6. Falsey AR
7. Topham DJ
8. Storch GA
Use of Host Response to Refine the Diagnosis of Group A Streptococcal Pharyngitis.; Journal of the Pediatric Infectious Diseases Society. 2022 Sep 25.
1. McDavid A
2. Laniewski N
3. Grier A
4. Gill AL
5. Kessler HA
6. Huyck H
7. Carbonell E
8. Holden-Wiltse J
9. Bandyopadhyay S
10. Carnahan J
11. Dylag AM
12. Topham DJ
13. Falsey AR
14. Caserta MT
15. Pryhuber GS
16. Gill SR
17. Scheible KM
Aberrant newborn T cell and microbiota developmental trajectories predict respiratory compromise during infancy.; iScience; Vol 25(4). 2022 Apr 15.
1. Moritzky SA
2. Richards KA
3. Glover MA
4. Krammer F
5. Chaves FA
6. Topham DJ
7. Branche A
8. Nayak JL
9. Sant AJ
The negative effect of pre-existing immunity on influenza vaccine responses transcends the impact of vaccine formulation type and vaccination history.; The Journal of infectious diseases. 2022 Feb 24.
1. Embong AK
2. Nguyen-Contant P
3. Wang J
4. Kanagaiah P
5. Chaves FA
6. Fitzgerald TF
7. Zhou Q
8. Kosoy G
9. Branche AR
10. Miller BL
11. Zand MS
12. Sangster MY
13. Topham DJ
Formation and Expansion of Memory B Cells against Coronavirus in Acutely Infected COVID-19 Individuals.; Pathogens (Basel, Switzerland); Vol 11(2). 2022 Jan 29.
1. McCall MN
2. Chu CY
3. Wang L
4. Benoodt L
5. Thakar J
6. Corbett A
7. Holden-Wiltse J
8. Slaunwhite C
9. Grier A
10. Gill SR
11. Falsey AR
12. Topham DJ
13. Caserta MT
14. Walsh EE
15. Qiu X
16. Mariani TJ
A systems genomics approach uncovers molecular associates of RSV severity.; PLoS computational biology; Vol 17(12). 2021 Dec 28.
1. Young BE
2. Seppo AE
3. Diaz N
4. Rosen-Carole C
5. Nowak-Wegrzyn A
6. Cruz Vasquez JM
7. Ferri-Huerta R
8. Nguyen-Contant P
9. Fitzgerald T
10. Sangster MY
11. Topham DJ
12. Järvinen KM
Association of Human Milk Antibody Induction, Persistence, and Neutralizing Capacity With SARS-CoV-2 Infection vs mRNA Vaccination.; JAMA pediatrics. 2021 Nov 10.
1. Yee Mon KJ
2. Zhu H
3. Daly CWP
4. Vu LT
5. Smith NL
6. Patel R
7. Topham DJ
8. Scheible K
9. Jambo K
10. Le MTN
11. Rudd BD
12. Grimson A
MicroRNA-29 specifies age-related differences in the CD8+ T cell immune response.; Cell reports; Vol 37(6). 2021 Nov 09.
1. Nguyen-Contant P
2. Sangster MY
3. Topham DJ
Squalene-Based Influenza Vaccine Adjuvants and Their Impact on the Hemagglutinin-Specific B Cell Response.; Pathogens (Basel, Switzerland); Vol 10(3). 2021 Mar 17.
1. Wang L
2. Chu CY
3. McCall MN
4. Slaunwhite C
5. Holden-Wiltse J
6. Corbett A
7. Falsey AR
8. Topham DJ
9. Caserta MT
10. Mariani TJ
11. Walsh EE
12. Qiu X
Airway gene-expression classifiers for respiratory syncytial virus (RSV) disease severity in infants.; BMC medical genomics; Vol 14(1). 2021 Feb 25.
1. Pace RM
2. Williams JE
3. Järvinen KM
4. Belfort MB
5. Pace CDW
6. Lackey KA
7. Gogel AC
8. Nguyen-Contant P
9. Kanagaiah P
10. Fitzgerald T
11. Ferri R
12. Young B
13. Rosen-Carole C
14. Diaz N
15. Meehan CL
16. Caffé B
17. Sangster MY
18. Topham D
19. McGuire MA
20. Seppo A
21. McGuire MK
Characterization of SARS-CoV-2 RNA, Antibodies, and Neutralizing Capacity in Milk Produced by Women with COVID-19.; mBio; Vol 12(1). 2021 Feb 09.
1. Lorbach JN
2. Fitzgerald T
3. Nolan C
4. Nolting JM
5. Treanor JJ
6. Topham DJ
7. Bowman AS
Gaps in Serologic Immunity against Contemporary Swine-Origin Influenza A Viruses among Healthy Individuals in the United States.; Viruses; Vol 13(1). 2021 Jan 18.
1. Reilly EC
2. Sportiello M
3. Emo KL
4. Amitrano AM
5. Jha R
6. Kumar ABR
7. Laniewski NG
8. Yang H
9. Kim M
10. Topham DJ
CD49a Identifies Polyfunctional Memory CD8 T Cell Subsets that Persist in the Lungs After Influenza Infection.; Frontiers in immunology; Vol 12. 2021.
1. Nguyen-Contant P
2. Embong AK
3. Topham DJ
4. Sangster MY
Analysis of Antigen-Specific Human Memory B Cell Populations Based on In Vitro Polyclonal Stimulation.; Current protocols in immunology; Vol 131(1). 2020 Dec.
1. Alon R
2. Sportiello M
3. Kozlovski S
4. Kumar A
5. Reilly EC
6. Zarbock A
7. Garbi N
8. Topham DJ
Leukocyte trafficking to the lungs and beyond: lessons from influenza for COVID-19.; Nature reviews. Immunology. 2020 Nov 19.
1. Zent CS
2. Brady MT
3. Delage C
4. Strawderman M
5. Laniewski N
6. Contant PN
7. Kanagaiah P
8. Sangster MY
9. Barr PM
10. Chu CC
11. Topham DJ
12. Friedberg JW
Short term results of vaccination with adjuvanted recombinant varicella zoster glycoprotein E during initial BTK inhibitor therapy for CLL or lymphoplasmacytic lymphoma.; Leukemia. 2020 Oct 30.
1. Nguyen-Contant P
2. Embong AK
3. Kanagaiah P
4. Chaves FA
5. Yang H
6. Branche AR
7. Topham DJ
8. Sangster MY
S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit.; mBio; Vol 11(5). 2020 Sep 25.
1. Steiner DJ
2. Cognetti JS
3. Luta EP
4. Klose AM
5. Bucukovski J
6. Bryan MR
7. Schmuke JJ
8. Nguyen-Contant P
9. Sangster MY
10. Topham DJ
11. Miller BL
Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients.; Biosensors & bioelectronics; Vol 169. 2020 Sep 21.
1. Pace RM
2. Williams JE
3. Järvinen KM
4. Belfort MB
5. Pace CD
6. Lackey KA
7. Gogel AC
8. Nguyen-Contant P
9. Kanagaiah P
10. Fitzgerald T
11. Ferri R
12. Young B
13. Rosen-Carole C
14. Diaz N
15. Meehan C
16. Caffe B
17. Sangster MY
18. Topham DJ
19. McGuire MA
20. Seppo A
21. McGuire MK
COVID-19 and human milk: SARS-CoV-2, antibodies, and neutralizing capacity.; medRxiv : the preprint server for health sciences. 2020 Sep 18.
1. Grier A
2. Gill AL
3. Kessler HA
4. Corbett A
5. Bandyopadhyay S
6. Java J
7. Holden-Wiltse J
8. Falsey AR
9. Topham DJ
10. Mariani TJ
11. Caserta MT
12. Walsh EE
13. Gill SR
Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection.; The Journal of infectious diseases. 2020 Sep 14.
1. Chu CY
2. Qiu X
3. McCall MN
4. Wang L
5. Corbett A
6. Holden-Wiltse J
7. Slaunwhite C
8. Grier A
9. Gill SR
10. Pryhuber GS
11. Falsey AR
12. Topham DJ
13. Caserta MT
14. Walsh EE
15. Mariani TJ
Airway gene expression correlates of RSV disease severity and microbiome composition in infants.; The Journal of infectious diseases. 2020 Sep 14.
1. Gouma S
2. Kim K
3. Weirick ME
4. Gumina ME
5. Branche A
6. Topham DJ
7. Martin ET
8. Monto AS
9. Cobey S
10. Hensley SE
Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility.; Nature communications; Vol 11(1). 2020 Sep 11.
1. Richards KA
2. Moritzky S
3. Shannon I
4. Fitzgerald T
5. Yang H
6. Branche A
7. Topham DJ
8. Treanor JJ
9. Nayak J
10. Sant AJ
Recombinant HA-based vaccine outperforms split and subunit vaccines in elicitation of influenza-specific CD4 T cells and CD4 T cell-dependent antibody responses in humans.; NPJ vaccines; Vol 5(1). 2020 Aug 26.
1. Thakar J
2. Qian Y
3. Benoodt L
4. Roumanes D
5. Qiu X
6. Laniewski N
7. Chu C
8. Slaunwhite C
9. Wang L
10. Mandava A
11. Chang I
12. Falsey AR
13. Caserta MT
14. Mariani TJ
15. Scheuermann RH
16. Walsh EE
17. Topham DJ
Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein.; Vaccine: X; Vol 5. 2020 Aug 07.
1. Lim K
2. Kim TH
3. Trzeciak A
4. Amitrano AM
5. Reilly EC
6. Prizant H
7. Fowell DJ
8. Topham DJ
9. Kim M
In situ neutrophil efferocytosis shapes T cell immunity to influenza infection.; Nature immunology. 2020 Aug 03.
1. Vom Steeg LG
2. Dhakal S
3. Woletsadik YA
4. Park HS
5. Mulka KR
6. Reilly EC
7. Topham DJ
8. Klein SL
Androgen receptor signaling in the lungs mitigates inflammation and improves the outcome of influenza in mice.; PLoS pathogens; Vol 16(7). 2020 Jul 09.
1. McDavid A
2. Corbett AM
3. Dutra JL
4. Straw AG
5. Topham DJ
6. Pryhuber GS
7. Caserta MT
8. Gill SR
9. Scheible KM
10. Holden-Wiltse J
Eight practices for data management to enable team data science.; Journal of clinical and translational science; Vol 5(1). 2020 Jun 23.
1. Anderson CS
2. Sangster MY
3. Yang H
4. Mariani TJ
5. Chaudhury S
6. Topham DJ
Implementing sequence-based antigenic distance calculation into immunological shape space model.; BMC bioinformatics; Vol 21(1). 2020 Jun 19.
1. Reilly EC
2. Lambert Emo K
3. Buckley PM
4. Reilly NS
5. Smith I
6. Chaves FA
7. Yang H
8. Oakes PW
9. Topham DJ
TRM integrins CD103 and CD49a differentially support adherence and motility after resolution of influenza virus infection.; Proceedings of the National Academy of Sciences of the United States of America; Vol 117(22). 2020 Jun 02.
1. Meilleur CE
2. Memarnejadian A
3. Shivji AN
4. Benoit JM
5. Tuffs SW
6. Mele TS
7. Singh B
8. Dikeakos JD
9. Topham DJ
10. Mu HH
11. Bennink JR
12. McCormick JK
13. Haeryfar SMM
Discordant rearrangement of primary and anamnestic CD8+ T cell responses to influenza A viral epitopes upon exposure to bacterial superantigens: Implications for prophylactic vaccination, heterosubtypic immunity and superinfections.; PLoS pathogens; Vol 16(5). 2020 May.
1. Moore KA
2. Ostrowsky JT
3. Mehr AJ
4. Osterholm MT
Influenza response planning for the centers of excellence for influenza research and surveillance: Science preparedness for enhancing global health security.; Influenza and other respiratory viruses. 2020 Apr 19.
1. Topham DJ
Serendipity: Reflections on Being Mentored by Dr. Peter Doherty.; Viral immunology; Vol 33(3). 2020 Apr.
1. Martinez-Sobrido L
2. Blanco-Lobo P
3. Rodriguez L
4. Fitzgerald T
5. Zhang H
6. Nguyen P
7. Anderson CS
8. Holden-Wiltse J
9. Bandyopadhyay S
10. Nogales A
11. DeDiego ML
12. Wasik BR
13. Miller BL
14. Henry C
15. Wilson PC
16. Sangster MY
17. Treanor JJ
18. Topham DJ
19. Byrd-Leotis L
20. Steinhauer DA
21. Cummings RD
22. Luczo JM
23. Tompkins SM
24. Sakamoto K
25. Jones CA
26. Steel J
27. Lowen AC
28. Danzy S
29. Tao H
30. Fink AL
31. Klein SL
32. Wohlgemuth N
33. Fenstermacher KJ
34. El Najjar F
35. Pekosz A
36. Sauer L
37. Lewis MK
38. Shaw-Saliba K
39. Rothman RE
40. Liu ZY
41. Chen KF
42. Parrish CR
43. Voorhees IEH
44. Kawaoka Y
45. Neumann G
46. Chiba S
47. Fan S
48. Hatta M
49. Kong H
50. Zhong G
51. Wang G
52. Uccellini MB
53. García-Sastre A
54. Perez DR
55. Ferreri LM
56. Herfst S
57. Richard M
58. Fouchier R
59. Burke D
60. Pattinson D
61. Smith DJ
62. Meliopoulos V
63. Freiden P
64. Livingston B
65. Sharp B
66. Cherry S
67. Dib JC
68. Yang G
69. Russell CJ
70. Barman S
71. Webby RJ
72. Krauss S
73. Danner A
74. Woodard K
75. Peiris M
76. Perera RAPM
77. Chan MCW
78. Govorkova EA
79. Marathe BM
80. Pascua PNQ
81. Smith G
82. Li YT
83. Thomas PG
84. Schultz-Cherry S
Characterizing Emerging Canine H3 Influenza Viruses.; PLoS pathogens; Vol 16(4). 2020 Apr.
1. Veazey JM
2. Eliseeva SI
3. Hillman SE
4. Stiles K
5. Smyth TR
6. Morrissey CE
7. Tillotson EJ
8. Topham DJ
9. Chapman TJ
10. Georas SN
Inhibiting Protein Kinase D Promotes Airway Epithelial Barrier Integrity in Mouse Models of Influenza A Virus Infection.; Frontiers in immunology; Vol 11. 2020.
1. Emo K
2. Reilly EC
3. Sportiello M
4. Yang H
5. Topham DJ
T cell and chemokine receptors differentially control CD8 T cell motility behavior in the infected airways immediately before and after virus clearance in a primary infection.; PloS one; Vol 15(8). 2020.
1. Richards KA
2. Moritzky S
3. Shannon I
4. Fitzgerald T
5. Yang H
6. Branche A
7. Topham DJ
8. Treanor JJ
9. Nayak J
10. Sant AJ
Recombinant HA-based vaccine outperforms split and subunit vaccines in elicitation of influenza-specific CD4 T cells and CD4 T cell-dependent antibody responses in humans.; NPJ vaccines; Vol 5. 2020.
1. Topham DJ
2. DeDiego ML
3. Nogales A
4. Sangster MY
5. Sant A
Immunity to Influenza Infection in Humans.; Cold Spring Harbor perspectives in medicine. 2019 Dec 30.
1. Smith A
2. Rodriguez L
3. Ghouayel ME
4. Nogales A
5. Chamberlain JM
6. Sortino K
7. Reilly E
8. Feng C
9. Topham DJ
10. Martínez-Sobrido L
11. Dewhurst S
A live-attenuated influenza vaccine (LAIV) elicits enhanced heterologous protection when the internal genes of the vaccine are matched to the challenge virus.; Journal of virology. 2019 Nov 20.
1. DeDiego ML
2. Martinez-Sobrido L
3. Topham DJ
Novel Functions of IFI44L as a Feedback Regulator of Host Antiviral Responses.; Journal of virology; Vol 93(21). 2019 Nov 01.
1. Henry C
2. Palm AE
3. Utset HA
4. Huang M
5. Ho IY
6. Zheng NY
7. Fitzgerald T
8. Neu KE
9. Chen YQ
10. Krammer F
11. Treanor JJ
12. Sant AJ
13. Topham DJ
14. Wilson PC
Monoclonal Antibody Responses after Recombinant Hemagglutinin Vaccine versus Subunit Inactivated Influenza Virus Vaccine: a Comparative Study.; Journal of virology; Vol 93(21). 2019 Nov 01.
1. Topham DJ
2. Reilly EC
3. Emo KL
4. Sportiello M
Formation and Maintenance of Tissue Resident Memory CD8+ T Cells after Viral Infection.; Pathogens (Basel, Switzerland); Vol 8(4). 2019 Oct 18.
1. Rodriguez L
2. Blanco-Lobo P
3. Reilly EC
4. Maehigashi T
5. Nogales A
6. Smith A
7. Topham DJ
8. Dewhurst S
9. Kim B
10. Martínez-Sobrido L
Comparative Study of the Temperature Sensitive, Cold Adapted and Attenuated Mutations Present in the Master Donor Viruses of the Two Commercial Human Live Attenuated Influenza Vaccines.; Viruses; Vol 11(10). 2019 Oct 10.
1. Gouma S
2. Zost SJ
3. Parkhouse K
4. Branche A
5. Topham DJ
6. Cobey S
7. Hensley SE
Comparison of human H3N2 antibody responses elicited by egg-based, cell-based, and recombinant protein-based influenza vaccines during the 2017-2018 season.; Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2019 Oct 09.