Biology subjects

Kirby, A.

Publications and source records attributed to Kirby, A..

17 recordsLinked to original sources

bioRxiv2026

Beta-band dynamics during a naturalistic motor task: an OPM-MEG study

Beta oscillations are a fundamental feature of brain activity, linked to long-range connectivity within canonical networks, inhibition of sensorimotor cortices and the maintenance of a stable sensorimotor state in situations where the external world is predictable. The importance of beta oscillations in brain function is underscored by observations of their perturbation in neurological and psychiatric disorders. However, the precise role played by beta activity, particularly in mediating complex or skilful movements, remains incompletely understood. Here, we used a newly developed wearable optically pumped magnetometer-based magnetoencephalography (OPM-MEG) system to measure beta dynamics as participants learned to play a musical instrument. Twenty-two novice players took part in a study in which OPM-MEG data were recorded during two scanning sessions, while participants attempted to play a tune on a violin. Between the two sessions, participants received a violin lesson from an expert teacher. Results showed that robust data could be acquired during this naturalistic task, with beta oscillations decreasing in amplitude during movement and increasing upon movement cessation, as expected. Moreover, beta power whilst playing, in the motor and pre-motor areas, was significantly elevated after the lesson compared to before, and the movement-related modulation of beta amplitude was more pronounced after the lesson. These findings align with predictive coding models which suggest that beta amplitude should increase when individuals have greater certainty over the movements they carry out. Our study adds to an expanding literature on the role of beta oscillations and provides further evidence for the utility of OPM-MEG in naturalistic neuroscience.

neuroscience↗

bioRxiv2026

The biodistribution and effect of post-exposure neutralising monoclonal antibody treatment in a mouse model of SARS-CoV-2 infection with viral spread to the brain

Ronapreve, a combination of two neutralising monoclonal antibodies, casirivimab and imdevimab, was amongst the authorised treatments against SARS-CoV-2 early in the COVID-19 pandemic. Ronapreve has lost some of its efficiency with the rise of new virus variants, however, it remains a valuable tool for experimental studies to gain insights into the mechanisms and effects of anti-viral drugs. In this study we combined morphological, pharmacokinetic and molecular approaches (including multiomics) to investigate the biodistribution of Ronapreve in the K18-hACE2 murine model of SARS-CoV-2 neuroinvasion, as well as possible consequences for the brain. We also investigated the effect of the treatment on the infection status. Our results showed that after intraperitoneal injection, Ronapreve accumulates in the serum and is unable to cross the blood-brain barrier, thus not reaching the brain parenchyma; treatment has only a minimal effect on the brain transcriptome, with no significant changes in the brain lipidome or metabolome. Nonetheless, post-exposure Ronapreve treatment resulted in reduced viral loads in the lung and, in particular, the brain, with markedly reduced tissue response in the brain, as shown by the transcriptomic analysis. The results suggest a peripheral mode of action of Ronapreve to block brain infection, possibly by lowering viral replication in the nasal epithelium, reducing a subsequent spread to the brain.

pathology↗

bioRxiv2026

Nanobodies against the S2 region of the spike protein potently neutralize SARS-CoV-2 viruses and show resistance to virus escape

Entry of coronaviruses into cells is mediated by the viral spike (S) glycoproteins each consisting of S1 receptor binding and S2 membrane fusion subunits. The sequence of the S2 region is very highly conserved amongst variants of SARS-CoV-2 and compared to the S1 unit shares significant sequence identity amongst different beta-coronavirus lineages. By targeting the S2 of SARS-CoV-2 we have identified two selective and potent neutralizing nanobodies (BA.1-C2 and BA.1-D3) that bind to two different quaternary epitopes in the S2 formed by the Heptad Repeat 2 (HR2) trimer at the base of the spike protein. The HR2 sequence is identical in SARS-CoV and SARS-CoV-2 but differs in other beta-coronaviruses explaining the lack of binding to the spike proteins of MERS-CoV or HuCoV-OC43. No viral escape was observed following serial passaging of SARS-CoV-2 (JN.1) with a combination of BA.1-C2 and BA.1-D3 and the most potent of these nanobodies reduced viral load in the hamster model of COVID-19, following intranasal administration. Overall, the results show the value of nanobody technology for identifying novel neutralising epitopes in the S2 region of beta-coronaviruses with potential for the development of new selective anti-viral agents.

molecular biology↗

bioRxiv2025

The pharmacokinetics, bio-distribution and therapeutic efficacy of a trimeric nanobody against SARS-CoV-2 in the Syrian golden hamster COVID-19 model

The rapid emergence of SARS-CoV-2 prompted the development of anti-viral therapies and vaccines to combat the COVID-19 pandemic. The continuous emergence of variants of concern has necessitated the development of platforms that can be rapidly adapted. Nanobodies, offer advantages over conventional monoclonal antibodies, including low molecular weight, high antigen-binding affinity, enhanced tissue penetration, blood-brain barrier permeability, and simplified production. Previous studies have demonstrated the efficacy of nanobodies against respiratory viruses such as SARS-CoV-2, respiratory syncytial virus, and influenza A virus in animal models. We previously reported the protective effects of nanobody trimers against SARS-CoV-2. However, pharmacokinetic and biodistribution data for nanobodies remain limited. To address this, we evaluated the efficacy, biodistribution and longevity of action of a nanobody trimer (A8) administered intranasally (IN) or intraperitoneally (IP) in Syrian golden hamsters. Our findings revealed that the A8 trimer reached peak concentrations shortly after administration and was subsequently cleared from the system via both routes. Importantly, early administration of A8 trimer reduced virus mediated weight loss and viral load compared with untreated controls supporting its potential as a therapeutic candidate for SARS-CoV-2 infection.

microbiology↗

bioRxiv2025

Investigation of anti-SARS CoV-2 multimeric bicyclic peptide inhibitors in a range of pre-clinical therapeutic settings

The spread of respiratory viruses, such as Influenza and SARS-CoV-2 has presented significant challenges over the last 30 years with few effective therapeutic options available to this day. Bi-cyclic peptides represent a unique, modular, modality in the antiviral armamentarium against future pandemics. This study provides a deeper evaluation of multivalent bi-cyclic (Bicycle(R)) molecule efficacy in several preclinical SARS-CoV-2 challenge settings. We explore both pre-exposure prophylaxis and post-exposure therapeutic settings via subcutaneous and intranasal routes of administration. We contextualize this further in bespoke scenarios of immune compromisation, and viral transmission. Promisingly, in all studies we observe efficacy, significantly reducing infectious viral burden at each study endpoint. These data further support candidacy of Bicycle molecules as a differentiated antiviral therapeutic class in the context of pandemic preparedness. ImportanceThe COVID-19 pandemic, triggered a rapid wave of innovation, accelerating the delivery of new vaccine technology and anti-viral treatments. In our first paper, we described the discovery and molecular optimization of Bicycle molecules as a novel drug class for the potential treatment of SARS CoV-2. Here, we have performed deeper characterization of these molecules in established animal models that simulate SARS-CoV-2 transmission, testing more convenient delivery routes, such as intra-nasal. The Bicycle molecules demonstrated positive outcomes in each of these studies and suggest that Bicycle molecules, as convenient and effective anti-viral treatments, could be an important addition to help future preparedness against new viral pandemics.

pharmacology and toxicology↗

bioRxiv2025

Hypoxia inducible factors regulate Pneumovirus replication by enhancing innate immune sensing

The immune mechanisms responsible for protection and pathogenesis in pneumoviral infection are not well defined. We demonstrated that pharmacological activation of the hypoxic inducible factor (HIF) signalling axis using Daprodustat limited viral replication through enhanced immune signalling. Transcriptomic analysis revealed HIF augmented activation of innate immune response genes, including interferon-stimulated gene 15 (Isg15), in the lung and spleen of mice infected with pneumonia virus of mice (PVM). In human respiratory syncytial virus (hRSV) infected airway epithelial cells, Daprodustat inhibited viral replication and enhanced ISG15 expression in a HIF-dependent manner. Importantly, inhibition of type I interferon signalling or the RIG-I sensing pathway abrogated the antiviral activity of HIF. Moreover, Daprodustat increased interferon signalling in response to viral RNA, suggesting that HIF inhibits pneumovirus replication through enhancing viral RNA sensing. Mechanistically, Daprodustat reduced N6-methyladenosine modification of viral RNA through upregulation of RNA demethylases, promoting detection by innate immune sensors. This study highlights the intricate interplay between hypoxia and antiviral immunity and offers valuable insights into pneumovirus-host interactions and potential therapeutic interventions. SIGNIFICANCE STATEMENTThis study explores the role of the hypoxic inducible factor (HIF) signalling pathway in limiting pneumoviral infections, such as respiratory syncytial virus (hRSV) and pneumonia virus of mice (PVM). Using Daprodustat, a clinically approved activator of HIF signalling we demonstrated that stimulation of this pathway enhanced innate immune signalling and limited viral replication. Transcriptomic analysis showed that HIF promoted innate immune response genes in mice infected with PVM and human airway epithelial cells infected with hRSV. Importantly, inhibition of type I interferon signalling or the RIG-I sensing pathway abrogated the antiviral activity of HIF. We uncovered a role for HIF to regulate the levels of N6-methyladenosine modification of viral RNA transcripts, resulting in the increased activation of nucleic acid sensing.

microbiology↗

bioRxiv2025

SARS-CoV-2 infection of the brain: the K18-hACE2 mouse model to illustrate the role and response of the vasculature in neurotropic viral infection

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) primarily affects the respiratory tract and lungs; however, the associated disease, coronavirus disease 2019 (COVID-19), can involve the central nervous system (CNS) in both its acute and long-term (Long COVID) clinical manifestation. The pathomechanisms underlying neurological impairments in COVID-19 are not yet fully understood, hence experimental studies to clarify the direct effect of SARS-CoV-2 in the brain can provide further insight. In the present study we used the K18-hACE2 model, intranasally challenged with SARS-CoV-2 ancestral and Delta isolates at low or medium doses, to address the hypothesis that the inflammatory response raised in the brain of infected mice is secondary to neuronal infection. Our data confirmed that the virus reaches the brain even after low dose (102 PFU/mouse, Delta isolate) infection where it targets the neurons without overt neuropathic effect, sparing the blood vessels. In situ investigation of the resulting inflammatory response showed the recruitment of leukocytes via postcapillary venules, with their accumulation in the perivascular space and occasional migration into the neuroparenchyma, without targeting and/or damage to the vessel wall. These changes were reflected in the brain transcriptome and proteome which showed positive enrichment of pathways and up-regulation of genes involved in the inflammatory response including the recruitment (including adhesion and migration) and activity of leukocytes. Additionally, morphological and transcriptome/proteome changes suggest minimal associated blood-brain barrier dysfunction. The brain metabolome and lipidome showed minimal changes; these were consistent with oxidative stress and inflammatory and immune/antiviral responses. The results obtained from our model indicate that SARS-CoV-2 infection of the neurons can result in limited neuroinflammation. These data can help to understand more fully the reaction of the CNS in COVID-19 patients, and neurotropic virus infections in general.

pathology↗

bioRxiv2025

An ultra-long heavy chain bovine antibody neutralizes SARS-CoV-2 and reacts broadly with sarbecoviruses.

The ongoing threat of new SARS-CoV-2 variants and other sarbecoviruses has driven efforts to develop broadly neutralizing monoclonal antibodies (mAbs). This study used immunized cattle, known for producing antibodies with ultra-long CDRH3 domains, to generate 33 mAbs, ten of which had ultra-long CDRH3s (>50 amino acids). Of these, mAbs P7 and 99, demonstrated broad and potent neutralization. Notably, mAb P7 neutralized all tested variants, including SARS-CoV-1, with IC50 values between 0.05 and 9.2 {micro}g/mL, and showed cross-reactivity with RBDs from various sarbecoviruses. Structural analysis revealed that mAb 99 binds the spike proteins RBD at the ACE2 binding site. Although the exact binding of P7 wasnt resolved, evidence suggests it targets a hidden epitope, promoting spike trimer dissociation via its extended CDRH3. In Syrian hamsters, both mAbs significantly reduced lung viral loads. These results support the potential of bovine-derived mAbs, particularly those with ultra-long CDRH3s, for future antiviral therapies.

immunology↗

bioRxiv2024

The golden Syrian hamster (Mesocricetus auratus) as a model to decipher relevant pathogenic aspects of sheep-associated malignant catarrhal fever

Malignant catarrhal fever (MCF) is an often fatal sporadic gammaherpesvirus-induced disease of ruminants with global relevance. Ovine gammaherpesvirus-2 (OvHV-2), with sheep as reservoir host, is a major cause of MCF in susceptible species. Despite extensive research on the molecular aspects of the disease, its pathogenesis is not yet fully understood. The present study re-established the Syrian golden hamster (Mesocricetus auratus) as amenable animal model of MCF and applied complementary in situ approaches to confirm recent findings in natural disease that could shed new light on pathogenetic aspects of MCF. These showed that systemic OvHV-2 infection is associated with T cell and macrophage dominated mononuclear infiltrates and vasculitis in various organs. Both T cells and monocytes/macrophages harbor the virus, and infected leukocytes are abundant in the infiltrates. The results also indicate that OvHV-2 has a broader target cell spectrum, including vascular endothelial cells and selected squamous epithelia. The former supports the interpretation that the inflammatory processes develop due to circulating activated, infected T cells and monocytes that home to tissues and emigrate from vessels prone to leukocyte emigration, possibly with direct interaction between virus infected leukocytes and endothelial cells. The latter supports the hypothesis of a graft versus host disease scenario, without viral cytopathic effect on epithelial cells but infiltration of the mucosa by infected T cells and macrophages. The disease processes are accompanied by evidence of expansion of the T cell compartments and the monocyte/macrophage pool in lymphatic tissues and bone marrow.

pathology↗

bioRxiv2024

Aldehydic load as an objective imaging biomarker of mild traumatic brain injury

Concussion is a mild traumatic brain injury (mTBI) defined as complex neurological impairment induced by biomechanical forces without structural brain damage. There does not yet exist an objective diagnostic tool for concussion. Downstream injury from mTBI stems from oxidative damage leading to the production of neurotoxic aldehydes. A collagen-based 3D corticomimetic scaffold was developed affording an in vitro model of concussion, which confirmed increased aldehyde production in live neurons following impact. To evaluate total aldehyde levels in vivo following mTBI, a novel CEST-MRI contrast agent, ProxyNA3, has been implemented in a new model of closed-head, awake, single-impact concussion developed in aged and young mice with aldehyde dehydrogenase 2 (ALDH2) deficiency. Behavioural tests confirm deficits immediately after injury. ProxyNA3-MRI was performed before impact, and on days two- and seven- post-impact. MRI signal enhancement significantly increased at two days post-injury and decreased to baseline seven days post-injury in all mice. An increase in astrocyte activation at seven days post-injury confirms the onset of a neuroinflammatory response following aldehyde production in the brain. The data suggest that advanced age and ALDH2 deficiency contribute to increased aldehydic load following mTBI. Overall, ProxyNA3 was capable of mapping concussion-associated aldehydes, supporting its application as an objective diagnostic tool for concussion.

biochemistry↗

bioRxiv2024

The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in infected and immune suppressed mice

SynopsisO_ST_ABSObjectivesC_ST_ABSImmunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context during the first 7 days of infection. MethodsMice were immunosuppressed using cyclophosphamide and infected with a B daughter lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed. ResultsTreatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of G>A and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir. Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs). ConclusionsFurther investigations are warranted to fully understand the role of immunocompromised individuals in VOC development, especially by taking persistence into consideration, and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.

pharmacology and toxicology↗

bioRxiv2023

Hypoxia inducible factors inhibit respiratory syncytial virus infection by modulation of nucleolin expression

Respiratory syncytial virus (RSV) is a global healthcare problem, causing respiratory illness in young children and elderly individuals. However, our knowledge of the host pathways that define susceptibility to RSV infection and disease severity is limited. Hypoxia inducible factors (HIFs) define cellular metabolic processes in response to low oxygen and are recognised to play a key role in regulating inflammatory responses in the lower respiratory tract. We demonstrate a role for hypoxia inducible factors (HIFs) to suppress RSV entry and RNA replication. We show that hypoxia and HIF prolyl-hydroxylase inhibitors significantly reduce expression of the RSV entry receptor nucleolin and inhibit viral driven cell-cell fusion. We identify a HIF regulated microRNA, miR-494, that regulates nucleolin expression. In RSV-infected mice, treatment with the clinically approved HIF prolyl-hydroxylase inhibitor, Daprodustat, reduced the level of infectious virus and infiltrating monocytes and neutrophils in the lung. This study highlights a role for HIF-signalling to limit multiple aspects of RSV infection and associated inflammation and informs future therapeutic approaches for treating this respiratory pathogen.

molecular biology↗

bioRxiv2023

Recombinant SARS-CoV-2 lacking initiating and internal methionine codons within ORF10 is attenuated in vivo

SARS-CoV-2 has been proposed to encode ORF10 as the 3 terminal gene in the viral genome. However, the potential role and even existence of a functional ORF10 product has been the subject of debate. There are significant structural features in the viral genomic RNA that could, by themselves, explain the retention of the ORF10 nucleotide sequences without the need for a functional protein product. To explore this question further we made two recombinant viruses, firstly a control virus (WT) based on the genome sequence of the original Wuhan isolate and with the inclusion of the early D614G mutation in the Spike protein. We also made a second virus, identical to WT except for two additional changes that replaced the initiating ORF10 start codon and an internal methionine codon for stop codons (ORF10KO). Here we show that the two viruses have apparently identical growth kinetics in a VeroE6 cell line that over expresses TMPRSS2 (VTN cells). However, in A549 cells over expressing ACE2 and TMPRSS2 (A549-AT cells) the ORF10KO virus appears to have a small growth rate advantage. Growth competition experiments were used whereby the two viruses were mixed, passaged in either VTN or A549-AT cells and the resulting output virus was sequenced. We found that in VTN cells the WT virus quickly dominated whereas in the A549-AT cells the ORF10KO virus dominated. We then used a hamster model of SARS-CoV-2 infection and determined that the ORF10KO virus has attenuated pathogenicity (as measured by weight loss). We found an almost 10-fold reduction in viral titre in the lower respiratory tract for ORF10KO vs WT. In contrast, the WT and ORF10KO viruses had similar titres in the upper respiratory tract. Sequencing of viral RNA in the lungs of hamsters infected with ORF10KO virus revealed that this virus frequently reverts to WT. Our data suggests that the retention of a functional ORF10 sequence is highly desirable for SARS-CoV-2 infection of hamsters and affects the viruss ability to propagate in the lower respiratory tract.

microbiology↗

bioRxiv2023

Measuring C. elegans Ageing Through Non-Invasive Monitoring of Movement across Large Populations

Finding new interventions that slow ageing and maintain human health is a huge challenge of our time. The nematode Caenorhabditis elegans, offers a rapid in vivo method to determine whether a compound extends its 2-3 week lifespan. However, the standard C. elegans lifespan assay is hard to scale for large screens. Lifespan analysis produces only one data point per animal with no information about health. Here we describe automated monitoring of movement from early to mid-adulthood as a healthspan-based alternative to measure ageing. Using our WormGazer technology, over 100 petri dishes containing C. elegans worms are imaged simultaneously and non-invasively by an array of cameras. This approach demonstrates that most functional decline in C. elegans occurs during the first week of adulthood. We find 7 days of imaging is sufficient to measure the dose-dependent efficacy of sulfamethoxazole to slow ageing, compared to 40 days required for a parallel lifespan experiment. Understanding any negative consequences of interventions that slow ageing is important. We show that the long-lived mutant age-1(hx546) stays active for longer than the wild type but it moves slower in early adulthood. Thus, continuous analysis of movement can rapidly identify interventions that slow ageing while simultaneously revealing any negative effects on health.

physiology↗

bioRxiv2023

Contrasting walking styles map to discrete neural substrates in the mouse brainstem

Walking is a slow gait which is particularly adaptable to meet internal or external needs and is prone to maladaptive alterations that lead to gait disorders. Alterations can affect speed, but also style (the way one walks). While slowed speed may signify the presence of a problem, style represents the hallmark essential for clinical classification of gait disorders. However, it has been challenging to objectively capture key stylistic features while uncovering neural substrates driving these features. Here we revealed brainstem hotspots that drive strikingly different walking styles by employing an unbiased mapping assay that combines quantitative walking signatures with focal, cell type specific activation. We found that activation of inhibitory neurons that mapped to the ventromedial caudal pons induced slow motion-like style. Activation of excitatory neurons that mapped to the ventromedial upper medulla induced shuffle-like style. Contrasting shifts in walking signatures distinguished these styles. Activation of inhibitory and excitatory neurons outside these territories or of serotonergic neurons modulated walking speed, but without walking signature shifts. Consistent with their contrasting modulatory actions, hotspots for slow-motion and shuffle-like gaits preferentially innervated different substrates. These findings lay the basis for new avenues to study mechanisms underlying (mal)adaptive walking styles and gait disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/537568v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1e88ef1org.highwire.dtl.DTLVardef@100a47corg.highwire.dtl.DTLVardef@12ecc7borg.highwire.dtl.DTLVardef@172bd97_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2021

SARS-CoV-2 Omicron-B.1.1.529 Variant leads to less severe disease than Pango B and Delta variants strains in a mouse model of severe COVID-19

COVID-19 is a spectrum of clinical symptoms in humans caused by infection with SARS-CoV-2. The B.1.1.529 Omicron variant is rapidly emerging and has been designated a Variant of Concern (VOC). The variant is highly transmissible and partially or fully evades a spectrum of neutralising antibodies due to a high number of substitutions in the spike glycoprotein. A major question is the relative severity of disease caused by the Omicron variant compared with previous and currently circulating variants of SARS-CoV-2. To address this, a mouse model of infection that recapitulates severe disease in humans, K18-hACE2 mice, were infected with either a Pango B, Delta or Omicron variant of SARS-CoV-2 and their relative pathogenesis compared. In contrast to mice infected with Pango B and Delta variant viruses, those infected with the Omicron variant had less severe clinical signs (weight loss), showed recovery and had a lower virus load in both the lower and upper respiratory tract. This is also reflected by less extensive inflammatory processes in the lungs. Although T cell epitopes may be conserved, the antigenic diversity of Omicron from previous variants would suggest that a change in vaccine may be required to mitigate against the higher transmissibility and global disease burden. However, the lead time to develop such a response may be too late to mitigate the spread and effects of Omicron. These animal model data suggest the clinical consequences of infection with the Omicron variant may be less severe but the higher transmissibility could still place huge burden upon healthcare systems even if a lower proportion of infected patients are hospitalised.

microbiology↗

bioRxiv2019

Target Gene Notebook: Connecting genetics and drug discovery

Target Gene Notebook was developed to enable more efficient linking of genetic associations to functional biological information. This process is essential to translating genetic insights into therapeutic hypotheses and, eventually, drug discovery. Although many public databases provide access to unfiltered genome annotations and genetic results, there was no existing tool to maintain group curation and integration with proprietary experimental data. We provide Target Gene Notebook freely via the MIT open-source license for the purposes of assisting therapeutic target evaluation and the creation of durable institutional and public knowledge bases. Implemented as a Java backend serving mainly Javascript content derived from gene-specific SQLite databases, Target Gene Notebook enables automated access to the most widely used sources of genetic association, expression and protein QTL data, provides intuitive interfaces to credible set and colocalization information, and enables comprehensive literature review and annotation by multiple users simultaneously to create a consistent target knowledgebase within an organization or across a consortium. TargetGeneNotebook is freely available from GitHub https://github.com/targetgenenotebook/tgn.git under the MIT open-source end-user license agreement and a live version of the interface is provided at http://tgn.broadinstitute.org/.

genomics↗