Selected Publications

Predicting sepsis severity at first clinical presentation: The role of endotypes and mechanistic signatures

Arjun Baghela, Olga M. Pena, Amy H. Lee, Beverlie Baquir, Reza Falsafi,
Andy An, Susan W. Farmer, Andrew Hurlburt, Alvaro Mondragon-Cardona, Juan Diego Rivera, Andrew Baker, Uriel Trahtemberg, Maryam Shojaei, Carlos Eduardo Jimenez-Canizales, Claudia C. dos Santos, Benjamin Tang, Hjalmar R. Bouma, Gabriela V. Cohen Freue, and Robert E.W. Hancock (2022) eBiomedicine 75: 103776

Persistence is Key: Unresolved Immune Dysfunction is Lethal in Both COVID-19 and non-COVID-19 Sepsis

Ay An, A Baghela, PGY Zhang, R Falsafi, AH Lee, U Trahtemberg, A Baker, CC Dos Santos, R.E.W. Hancock (2023) Front. Immunol. 14:

Antibiotic failure: Beyond antimicrobial resistance

Fuente-Nunez, Cesar de la; Angela Cesaro; Robert E.W. Hancock (2023) Drug Resist. Updates 71: 10.1016/j.drup.2023.101012

Antibiofilm peptides enhance the corrosion resistance of titanium in the presence of Streptococcus mutans

Wang D, Yue Y, Liu H, Zhang T, Haney EF, Hancock REW, Yu J, Shen Y. (2024) Front Bioeng Biotechnol 11: 10.3389/fbioe.2023.1339912

Gene Expression Profiling: Identification of Novel Pathways and Potential Biomarkers in Severe Acute Pancreatitis

Nesvaderani, Maryam; Dhillon, Bhavjinder K; Chew, Tracy; Tang, Benjamin F; Baghela, Arjun; Hancock, Robert EW; Eslick, Guy F; Cox, Michael (2022) Journal of the American College of Surgeons 10.1097/XCS.0000000000000115

Predictive gene expression signature diagnoses neonatal sepsis before clinical presentation

An, Andy Y; E Acton, OT Idoko, CP Shannon, TM Blimkie, R Falsafi, Q Wariri, A Imam, T Dibbasey, TB Bennike, KK Smolen, J Diray-Arce, R Ben-Othman, S Montante, A Angelidou, OA Odumade, D martino, SJ Tebbut, O Levy, H Steen, TR Kollman, B Kampmann, REW Hancock, AH Lee (2024) eBiomedicine 105411: 10.1016/j.ebiom.2024.105411

Antimicrobial resistance: a concise update

Ho CS, Wong CTH, Aung TT, Lakshminarayanan R, Mehta JS, Rauz S, McNally A, Kintses B, Peacock SJ, de la Fuente-Nunez C, Hancock REW, Ting DSJ. (2024) Lancet Microbe 100947: 10.1016/j.lanmic.2024.07.010 Free article

A machine learning and centrifugal microfluidics platform for bedside prediction of sepsis

Malic L, Zhang PGY, Plant PJ, Clime L, Nassif C, Da Fonte D, Haney EE, Moon BU, Sit VM, Brassard D, Mounier M, Churcher E, Tsoporis JT, Falsafi R, Bains M, Baker A, Trahtemberg U, Lukic L, Marshall JC, Geissler M, Hancock REW, Veres T, Dos Santos CC (2025) Lancet Microbe 16(1): 10.1038/s41467-025-59227-x

A scalable reinforcement learning approach for screening large peptide libraries for bioactive peptide discovery

Pandey, M., J. Foo, S. Massah, M.A. Alford, H. Mslati, G. Subbaraj, M. Saba, F. Gentile, N. Lallous, E.F. Haney, R.E.W. Hancock, M. Ester and A. Cherkasov. (2025) Nat Commun 16: doi.org/10.1038/s41467-025-66748-y

Longitudinal gene expression analysis in COVID-19 sepsis highlights dynamic immune, cellular, and metabolic dysfunction in high severity patients

An, A.Y., Baghela, A., Zhang, P. Blimkie T.M., Gauthier J., Kaufmann D.E., Acton E., Lee A.H.Y., Levesque R.C., Hancock R.E.W. (2025) Sci Rep 10.1038/s41598-025-32557-y

Design of highly potent anti-biofilm, antimicrobial peptides using explainable artificial intelligence.

Pikalyova, K., T. Akhmetshin, A. Orlov, E.F. Haney, N. Akhoundsadegh, J. You, R.E.W. Hancock, D. Horvath, G. Marcou, A. Cherkasov, and A. Varnek. (2026) J Chem Info Model 66: 10.1021/acs.jcim.5c01992

The use of DeepQSAR models for the discovery of peptides with enhanced antimicrobial and antibiofilm potential.

You, J.; Mslati, H.; Haney, EF; Akhoundsadegh, N.; Hancock, R.E.W. Cherkasov, A. (2026) Molecular Informatics 45: doi.org/10.1002/minf.70029

Population-specific heterogeneity in ontogeny of the broadly-conserved blood transcriptional program during the first week of life

Dhillon, BK; Blimkie, TM; Idoko, OT; Ford, R; Angelidou, A; Ben-Othman, R; Montante S; Amenyogbe, N; Dibassey, T; Diray-Arce, J; Falsafi, R; Imam, A; Odumade, OA; Ozonoff, A; Pomat, WS; Richmond, PC; Smolen, KK; Wariri, O; Levy, O; van den Biggelaar, AHJ; Kampmann, Beate; Kollman, TR; Lee, AHY; Hancock, REW (2026) Nat Commun https://doi.org/10.1038/s41467-026-73244-4