The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

A Rizzi, T Jensen, DR Slochower, M Aldeghi… - Journal of computer …, 2020 - Springer
Approaches for computing small molecule binding free energies based on molecular
simulations are now regularly being employed by academic and industry practitioners to study …

[HTML][HTML] Genetic tools for advancement of Synechococcus sp. PCC 7002 as a cyanobacterial chassis

AM Ruffing, TJ Jensen, LM Strickland - Microbial Cell Factories, 2016 - Springer
Background Successful implementation of modified cyanobacteria as hosts for industrial
applications requires the development of a cyanobacterial chassis. The cyanobacterium …

[HTML][HTML] Cell-based systems biology analysis of human AS03-adjuvanted H5N1 avian influenza vaccine responses: a phase I randomized controlled trial

…, X Niu, LE Gordy, CB Creech, N Prasad, TL Jensen… - PLoS …, 2017 - journals.plos.org
Background Vaccine development for influenza A/H5N1 is an important public health priority,
but H5N1 vaccines are less immunogenic than seasonal influenza vaccines. Adjuvant …

[HTML][HTML] Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

CA Miller, JR Walker, TL Jensen, WF Hooper… - The Journal of Molecular …, 2022 - Elsevier
The U2AF1 gene is a core part of mRNA splicing machinery and frequently contains somatic
mutations that contribute to oncogenesis in myelodysplastic syndrome, acute myeloid …

[HTML][HTML] The antibody landscapes following AS03 and MF59 adjuvanted H5N1 vaccination

JB Goll, A Jain, TL Jensen, R Assis, R Nakajima… - npj Vaccines, 2022 - nature.com
Current seasonal and pre-pandemic influenza vaccines induce short-lived predominantly
strain-specific and limited heterosubtypic responses. To better understand how vaccine …

Adaptive ensemble biomolecular applications at scale

V Balasubramanian, T Jensen, M Turilli, P Kasson… - SN Computer …, 2020 - Springer
Recent advances in both theory and methods have created opportunities to simulate
biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based …

[HTML][HTML] Systems vaccinology for a live attenuated tularemia vaccine reveals unique transcriptional signatures that predict humoral and cellular immune responses

MS Natrajan, N Rouphael, L Lai, D Kazmin, TL Jensen… - Vaccines, 2019 - mdpi.com
Background: Tularemia is a potential biological weapon due to its high infectivity and ease
of dissemination. This study aimed to characterize the innate and adaptive responses …

Molecular evolution of herpes simplex virus 2 complete genomes: comparison between primary and recurrent infections

MA Minaya, TL Jensen, JB Goll, M Korom… - Journal of …, 2017 - Am Soc Microbiol
Herpes simplex virus 1 (HSV-1) and HSV-2 are large, double-stranded DNA viruses that
cause lifelong persistent infections characterized by periods of quiescence and recurrent …

Human antibody responses following vaccinia immunization using protein microarrays and correlation with cell-mediated immunity and antibody-dependent cellular …

…, TM Kaufman, TP Blevins, TL Jensen… - The Journal of …, 2021 - academic.oup.com
Background There are limited data regarding immunological correlates of protection for the
modified vaccinia Ankara (MVA) smallpox vaccine. Methods A total of 523 vaccinia-naive …

[HTML][HTML] Transcriptomic and Metabolic Responses to a Live-Attenuated Francisella tularensis Vaccine

JB Goll, S Li, JL Edwards, SE Bosinger, TL Jensen… - Vaccines, 2020 - mdpi.com
The immune response to live-attenuated Francisella tularensis vaccine and its host evasion
mechanisms are incompletely understood. Using RNA-Seq and LC–MS on samples …