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Thompson, J. S.

Publications and source records attributed to Thompson, J. S..

13 recordsLinked to original sources

Gene model for the ortholog of DENR in Drosophila pseudoobscura

Gene model for the ortholog of Density regulated protein (DENR) in the Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3) Genome Assembly (GenBank Accession: GCA_000001765.2) of Drosophila pseudoobscura. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of raptor in Drosophila eugracilis

Gene model for the ortholog of raptor in the D. eugracilis Apr. 2013 (BCM-HGSC/Deug_2.0) (DeugGB2) Genome Assembly (GenBank Accession: GCA_000236325.2) of Drosophila eugracilis. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of DENR in Drosophila grimshawi

Gene model for the ortholog of Density regulated protein (DENR) in the May 2011 (Agencourt dgri_caf1/DgriCAF1) Genome Assembly (GenBank Accession: GCA_000005155.1) of D. grimshawi. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of raptor in Drosophila erecta

Gene model for the ortholog of raptor in the May 2011 (Agencourt Dere_CAF1/DereCAF1) Genome Assembly (GenBank Accession: GCA_000005135.1) of Drosophila erecta. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of raptor in Drosophila grimshawi

Gene model for the ortholog of raptor in the D. grimshawi May 2011 (Agencourt dgri_caf1/DgriCAF1) Genome Assembly (GenBank Accession: GCA_000005155.1) of Drosophila grimshawi. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of DENR in Drosophila eugracilis

Gene model for the ortholog of Density regulated protein (DENR) in the Apr. 2013 (BCM-HGSC/Deug_2.0) (DeugGB2) Genome Assembly (GenBank Accession: GCA_000236325.2) of D. eugracilis. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of Ilp4 in Drosophila eugracilis

Gene Model for Insulin-like peptide 4 (Ilp4) in the D. eugracilis (DeugGB2) assembly (GCA_000236325.2). The characterization of this ortholog was carried out as part of a larger, ongoing dataset designed to explore the evolution of the insulin/insulin-like growth factor signaling (IIS) pathway across the genus Drosophila, utilizing the Genomics Education Partnership gene annotation protocol within Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of Ilp4 in Drosophila grimshawi

Gene Model for the Insulin-like peptide 4 (Ilp4) ortholog in the D. grimshawi (dgriCAF1) assembly (GeneBank Accession: GCA_000005155.1) of Drosophila grimshawi. The characterization of this ortholog was conducted as part of a broader, developing dataset aimed at investigating the evolution of the Insulin/insulin-like growth factor signaling (IIS) pathway across the genus Drosophila, using the Genomics Education Partnership gene annotation protocol within Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of cnk in Drosophila erecta

Gene model for the ortholog of connector enhancer of ksr (cnk) in the Dere_CAF1 Genome Assembly (GenBank Accession: GCA_000005135.1) of Drosophila erecta. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of Pi3K21B in Drosophila eugracilis

Gene model for the ortholog of Phosphatidylinositol 3-kinase 21B (Pi3K21B) in the D. eugracilis May 2021 (Stanford ASM1815383v1/DeugRefSeq2) Genome Assembly (GenBank Accession: GCF_018153835.1) of Drosophila eugracilis. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

Gene model for the ortholog of Glyp in Drosophila pseudoobscura

Gene model for the ortholog of Glycogen phosphorylase (Glyp) in the Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3) Genome Assembly of D. pseudoobscura (GCA_000001765.2). This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

Forecasting oncogene amplification and tumour suppressor deletion

Oncogene amplification and tumour suppressor deletion can drive tumour initiation, progression and treatment resistance. Detection at diagnosis often signals poor prognosis, but it can also enable opportunities for treatment with highly effective targeted therapies. Predicting the likelihood that a patient will acquire these driver alterations in the future using a genomic test represents an opportunity to realise the benefits of interventions earlier, potentially with preventative intent. Here, we present a forecasting framework that takes as input a DNA copy number profile and predicts whether the tumour will acquire an oncogene amplification or tumour suppressor deletion in the future. This framework leverages mutation rate estimates from the input tumour, alongside gene-specific selection coefficients derived from a large cohort of 7,880 tumours. We demonstrate feasibility using 7,042 single-time-point samples and longitudinally collected tumour pairs from 44 prostate and 100 lung cancers, identifying tumours that went on to acquire amplifications at a later time point with an average AUC of 0.87. We show potential clinical utility by forecasting poor prognosis in low-grade gliomas via CDK4/PDGFRA amplification or CDKN2A deletion, and osimertinib resistance in lung cancers via MET amplification. This study serves as a proof-of-concept for a new class of biomarker, wherein selective pressures and mutation-generating processes can be harnessed to anticipate future genomic alterations.

genomics↗

The effect of pre-resection obesity on post-resection body composition after 75% small bowel resection in rats

BackgroundIn patients with short bowel syndrome, an elevated pre-resection Body Mass Index may be protective of post-resection body composition. We hypothesized that rats with diet-induced obesity would lose less lean body mass after undergoing massive small bowel resection compared to non-obese rats. MethodsRats (CD(R)IGS; age = 2 mo; N = 80) were randomly assigned to either a high-fat (obese rats) or a low-fat diet (non-obese rats), and fed ad lib for six months. Each diet group then was randomized to either underwent a 75% distal small bowel resection (massive resection) or small bowel transection with re-anastomosis (sham resection). All rats then were fed ad lib with an intermediate-fat diet (25% of total calories) for two months. Body weight and quantitative magnetic resonance-determined body composition were monitored. ResultsPreoperative body weight was 884 {+/-} 95 vs. 741 {+/-} 75 g, and preoperative percent body fat was 35.8 {+/-} 3.9 vs. 24.9 {+/-} 4.6%; high-fat vs. low fat diet, respectively (p < 0.0001); preoperative diet type had no effect on lean mass. Regarding total body weight, massive resection produced an 18% vs. 5% decrease in high-fat vs. low-fat rats respectively, while sham resection produced a 2% decrease vs. a 7% increase, respectively (p < 0.0001, preoperative vs. necropsy data). Sham resection had no effect on lean mass; after massive resection, both high-fat and low-fat rats lost lean mass, but these changes were not different between the latter two rat groups. ConclusionThe high-fat diet and low-fat diet induced obesity and marginal obesity, respectively. The massive resection produced greater weight loss in high-fat rats compared to low-fat rats. The type of dietary preconditioning had no effect on lean mass loss after massive resection. A protective effect of pre-existing obesity on lean mass after massive intestinal resection was not demonstrated.

physiology↗