Steve Baker, PhD
Assistant Professor
Microbiology & Immunology
Research Interests:
- We focus on how host alternative RNA splicing contributes to the control of viral infection and immune regulation
Education
PhD: University of Rochester School of Medicine & Dentistry
BS: University at Buffalo (State University of New York)
Publications/Research Listings
PUBLICATIONS (C, CO-/CORRESPONDING; *, CO-FIRST AUTHOR; R, IN REVISION; S, SUBMITTED; #, IN PREPARATION)
# Boudreault S, Hernansaiz-Ballesteros R, Gabor A, Singh Gc, Baker SFc. (2026). Conserved and unique
RNA splicing programs initiated by type-I interferon or influenza A virus infection. Front. Immunol. Invited
long- and short-read transcriptomics analysis paper, in preparation.
# Ohman M, Riley BA, Gonzalez EM, Pontelli MC, Meganck RM, Whelan SPJ, Hancks DC, Baker SFc.
(2026). Lysosome protein TMEM106B snares and degrades nuclear-trafficking influenza polymerase. In
preparation.
S Aniseia Y, Waltari E, Frank M, Lima L, Rahman G, Zhou A, Kim Y-J, Huang H, Baker SF, Senbabaoglu Y,
Peng D, Balla K. (2026). RNAquarium: an archive-scale atlas of zebrafish gene expression coupled with
pan-taxonomic profiling reveals diverse viral drivers of transcriptomic state. bioRxiv.
Doi.org/10.64898/2026.06.17.732950. (submitted).
R Hancks DC, Baker SFc. (2026). From the factory to the fray: mitochondrial proteins with moonlighting
immune functions. J. Virol. Invited minireview for New Voices in Virology, in revision at J. Virol.
R Nath H, Guo Y, Baker SFc. (2026). A novel ISG15 transcript restricts influenza A virus infection. bioRxiv.
Doi: 10.64898/2026.01.15.699784. In revision at Nucleic Acids Res.
Jiang L, Hurwitz I, Wylezinski LS, Racke MK, Yan F, Ye F, Sheng Q, Leng S, Chung C, Stein CM, Li C-I,
Kumar N, Ceccarelli M, Baker SF, Perkins DJ, Spurlock CF, Han L, Guo Y. (2026). ImmuSeeker: deep
mining of immune-related gene family signatures through lineage reconstruction. Genome Biol. PMID:
41888873
Nath H, Arndt A, Mann JM, Baker SFc. (2025). Tandem split-GFP influenza A viruses for sensitive and
accurate replication analyses. Microbiol Spectr. PMID: 41247244
Jiang L, Baker SF, Ceccarelil M, Guo Y. (2025). Comprehensive Profiling of Computational Techniques for
Sequencing-Based HLA Immune Signatures Extraction. HLA. PMID: 39957309
Mann JT, Riley BA, Baker SFc. (2023). All differential on the splicing front: Host alternative splicing alters the
landscape of virus-host conflict. Semin. Cell Dev. Biol. PMID: 36737258
Mrass P, Kinjyo I, Byrum JR, Torres D, Baker SF, Cannon JL. (2022). CXCR4 controls movement and
degranulation of CD8+ T cells in the influenza-infected lung via differential effects on interaction and
tissue scanning. bioRxiv. Doi: 10.1101/2022.09.13.507813. Note: this article is a pre-print.
Baker SFc, Meistermann H, Tzouros M, Baker A, Golling S, Siebourg Polster J, Ledwith MP, Gitter A,
Augustin A, Javanbakht H, Mehle A. (2022). Alternative splicing liberates a cryptic cytoplasmic isoform of
mitochondrial MECR that antagonizes influenza virus. PLoS Biol. PMID: 36542656. c, co-corresponding.
Larson GP, Tran V, Yú S, Caí Y, Higgins CA, Smith DM, Baker SF, Radoshitzky SR, Kuhn JH, Mehle A.
EPS8 facilitates uncoating of influenza A virus. (2019). Cell Rep. PMID: 31747592
Baker SF, Mehle A. (2019). ANP32B, or not to be, that is the question for influenza virus. eLife.
PMID: 31179971
Baker SF, Ledwith MP, Mehle A. (2018). Differential Splicing of ANP32A in Birds Alters Its Ability to
Stimulate RNA Synthesis by Restricted Influenza Polymerase. Cell Rep. PMID: 30184493
In Faculty Opinions (formerly F1000 Prime), 12 Aug 2019; 10.3410/f.733951272.793563552
Mondal A, Dawson AR, Potts GK, Freiberger EC, Baker SF, Moser LA, Bernard KA, Coon JJ, Mehle A.
(2017). Influenza virus recruits host protein kinase C to control assembly and activity of its replication
machinery. eLife. PMID: 28758638
Romero-Beltran L, Baker SF, Puerto-Solís M, González-Losa R, Conde-Ferraez L, Alvarez-Sánchez LC,
Martínez-Sobrido L, Ayora-Talavera G. (2016). Mutations at highly conserved residues in influenza
A(H1N1)pdm09 virus affect neuraminidase activity. Virus Res. PMID: 27596738
Breen M, Nogales A, Baker SF, Martínez-Sobrido L. (2016). Replication-Competent Influenza A Viruses
Expressing Reporter Genes. Viruses. PMID: 27347991
Jiang T, Nogales A, Baker SF, Martinez-Sobrido L, Turner DH. (2016). Mutations Designed by Ensemble
Defect to Misfold Conserved RNA Structures of Influenza A Segments 7 and 8 Affect Splicing and
Attenuate Viral Replication in Cell Culture. PLOS One. PMID: 27272307
Breen M, Nogales A, Baker SF, Perez DR, Martínez-Sobrido L. (2016). Replication-Competent Influenza A
and B Viruses Expressing a Fluorescent Dynamic Timer Protein for In Vitro and In Vivo Studies. PLoS
One. PMID: 26809059
Nogales A*, Baker SF*, Domm W, Martínez-Sobrido L. Development and applications of single-cycle
infectious influenza A virus (sciIAV). (2016). Virus Res. PMID: 26220478.
Halliley JL, Khurana S, Krammer F, Fitzgerald T, Baker SF, Yang H, Martínez-Sobrido L, Treanor JJ,
Subbarao K, Golding H, Topham DJ, Sangster MY. (2015). High affinity H7 head and stalk domainspecific
antibody responses to an inactivated influenza H7N7 vaccine after priming with live attenuated
influenza vaccine. J. Infect. Dis. PMID: 25838266
Baker SF, Nogales A, Santiago FW, Topham DJ, Martínez-Sobrido L. (2015). Competitive detection of
influenza neutralizing antibodies using a novel bivalent fluorescence-based microneutralization assay
(BiFMA). Vaccine. PMID: 26044496
Baker SF*, Nogales A*, Martínez-Sobrido L. (2015). Downregulating viral gene expression: codon usage
bias manipulation for the generation of novel influenza A virus vaccines. Future Virol. PMID: 26213563
Yang H, Baker SF, Martínez-Sobrido L, González ME, Zand M, Holden-Wiltse J, Wu H. (2015). An improved
method for estimating antibody titers in microneutralization assays using green fluorescent protein. J.
Biopharm. Stat. PMID: 26010892
Cox A*, Baker SF*, Nogales A, Martínez-Sobrido L, Dewhurst S. (2015). Development of a mouse-adapted,
live-attenuated influenza virus that permits in vivo analysis of enhancements to the safety of live
attenuated influenza virus vaccine. J. Virol. Spotlight article of significant interest, PMID: 25552727
Nogales A*, Baker SF*, Martínez-Sobrido L. (2015). Replication-competent influenza A viruses expressing a
red fluorescent protein. Virology. Selected as cover image, PMID: 25553516
Laguio-Vila MR, Thompson MG, Reynolds S, Spencer SM, Gaglani M, Naleway A, Ball S, Bozeman S,
Baker S, Martínez-Sobrido L, Levine M, Katz J, Fry AM, Treanor JJ. (2015). Comparison of serum
hemagglutinin and neuraminidase inhibition antibodies after 2010-2011 trivalent inactivated influenza
vaccination in healthcare personnel. Open Forum Infect. Dis. PMID: 25884004
Ramon S, Baker SF, Sahler JM, Kim N, Feldsott EA, Serhan CN, Martínez-Sobrido L, Topham DJ, Phipps
RP. (2014). The specialized proresolving mediator 17-HDHA enhances the antibody-mediated immune
response against influenza virus: a new class of adjuvant? J. Immunol. PMID: 25392529
Guo H*, Baker SF*, Martínez-Sobrido L, Topham DJ. (2014). Induction of CD8 T Cell heterologous
protection by a single dose of single-cycle infectious influenza virus. J. Virol. PMID: 25100831
Baker SF, Nogales A, Finch C, Tuffy K, Domm W, Perez DR, Topham DJ, Martínez-Sobrido L. (2014).
Influenza A and B intertypic reassortment through compatible viral packaging signals. J. Virol. PMID:
25008914
Nogales A, Baker SF, Ortiz-Riaño E, Dewhurst S, Topham DJ, Martínez-Sobrido L. (2014). Influenza A virus
attenuation by codon deoptimization of the NS gene for vaccine development. J. Virol. PMID: 24965472
Domm W, Brewer M, Baker SF, Feng C, Martínez-Sobrido L, Treanor J, Dewhurst S. (2013). Use of
bacteriophage particles displaying influenza virus hemagglutinin for the detection of hemagglutinationinhibition
antibodies. J. Virol. Methods. PMID: 24316333
Bauman JD, Patel D, Baker SF, Vijayan RSK, Xiang A, Parhi AK, Martínez-Sobrido L, LaVoie EJ, Das K,
Arnold E. (2013). Crystallographic fragment screening and structure-based optimization yields a new
class of influenza endonuclease inhibitors. ACS Chem. Biol. PMID: 23978130
Baker SF*, Guo H*, Albrecht RA, García-Sastre A, Topham DJ, Martínez-Sobrido L. (2013). Protection
against lethal influenza with a viral mimic. J. Virol. PMID: 23720727