Ramit Bharanikumar
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View article: Antigen-driven expansion of public clonal T cell populations in inflammatory bowel diseases
Antigen-driven expansion of public clonal T cell populations in inflammatory bowel diseases Open
Background Inflammatory Bowel Diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are known to involve shifts in the T-cell repertoires of affected individuals. These include a reduction in regulatory T cells in bo…
View article: 43 Tumor mutational burden corrected for human leukocyte antigen somatic defects predicts response to checkpoint blockade in advanced non-small cell lung cancer
43 Tumor mutational burden corrected for human leukocyte antigen somatic defects predicts response to checkpoint blockade in advanced non-small cell lung cancer Open
Background Tumor mutational burden (TMB) has been proposed as a biomarker for predicting response to immune checkpoint blockade (ICB) therapies in patients with non-small cell lung cancer (NSCLC). However, a subset of patients with high TM…
View article: Comparison of the tumor immune microenvironment and checkpoint blockade biomarkers between stage III and IV non-small cell lung cancer
Comparison of the tumor immune microenvironment and checkpoint blockade biomarkers between stage III and IV non-small cell lung cancer Open
Background Adjuvant immune checkpoint blockade (ICB) following chemoradiotherapy and adding ICB to chemotherapy have been key advances for stages III-IV non-small cell lung cancer (NSCLC) treatment. However, known biomarkers like PD-L1 are…
View article: 68 Rapid detection of somatic variants in human leukocyte antigen class 1 genes from solid tumor samples
68 Rapid detection of somatic variants in human leukocyte antigen class 1 genes from solid tumor samples Open
Background Human Leukocyte Antigens (HLA) class 1 proteins are important for recognizing tumor specific mutations (neoantigens) and presenting them to CD8+ T-cells. Somatic mutations in HLA genes can potentially reduce the set of neoantige…
View article: Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy
Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy Open
Riboswitches are cis-regulatory genetic elements that use an aptamer to control gene expression. Specificity to cognate ligand and diversity of such ligands have expanded the functional repertoire of riboswitches to mediate mounting…
View article: Riboflow: using deep learning to classify riboswitches with ~99% accuracy
Riboflow: using deep learning to classify riboswitches with ~99% accuracy Open
Riboswitches are cis-regulatory genetic elements that use an aptamer to control gene expression. Specificity to cognate ligand and diversity of such ligands have expanded the functional repetoire of riboswitches to mediate mounting apt res…
View article: Peer Review #3 of "PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence (v0.2)"
Peer Review #3 of "PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence (v0.2)" Open
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ 70 factor of RNA polymerase.σ 70 promoters are ubiquitously used in recombinant DNA technology, but char…
View article: PromoterPredict: sequence-based modelling of <i>Escherichia coli</i> σ <sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence
PromoterPredict: sequence-based modelling of <i>Escherichia coli</i> σ <sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence Open
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ 70 factor of RNA polymerase. σ 70 promoters are ubiquitously used in recombinant DNA technology, but cha…
View article: Peer Review #3 of "PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence (v0.1)"
Peer Review #3 of "PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence (v0.1)" Open
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ 70 factor of RNA polymerase.σ 70 promoters are ubiquitously used in recombinant DNA technology, but char…
View article: Peer Review #3 of "PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence (v0.3)"
Peer Review #3 of "PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence (v0.3)" Open
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ 70 factor of RNA polymerase.σ 70 promoters are ubiquitously used in recombinant DNA technology, but char…
View article: PromoterPredict: sequence-based modelling of <i>Escherichia coli</i> σ <sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence
PromoterPredict: sequence-based modelling of <i>Escherichia coli</i> σ <sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence Open
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ 70 factor of RNA polymerase. σ 70 promoters are ubiquitously used in recombinant DNA technology, but cha…
View article: PromoterPredict: sequence-based modelling of <i>Escherichia coli </i>σ<sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence
PromoterPredict: sequence-based modelling of <i>Escherichia coli </i>σ<sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence Open
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ 70 factor of RNA polymerase. σ 70 promoters are ubiquitously used in recombinant DNA technology, but cha…
View article: PromoterPredict: sequence-based modelling of <i>Escherichia coli</i> σ <sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence
PromoterPredict: sequence-based modelling of <i>Escherichia coli</i> σ <sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence Open
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ 70 factor of RNA polymerase. σ 70 promoters are ubiquitously used in recombinant DNA technology, but cha…
View article: PromoterPredict: sequence-based modelling of <i>Escherichia coli</i> σ<sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence
PromoterPredict: sequence-based modelling of <i>Escherichia coli</i> σ<sup>70</sup> promoter strength yields logarithmic dependence between promoter strength and sequence Open
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ 70 factor of RNA polymerase. σ 70 promoters are ubiquitously used in recombinant DNA technology, but cha…
View article: PromoterPredict: sequence-based modelling of promoter strength: supplementary information
PromoterPredict: sequence-based modelling of promoter strength: supplementary information Open
1. FIMO results for -35 and -10 regions (2 files)2. Random promoter sequences and results (Folder)
View article: RNA thermometer optimised for Bacillus subtilis and converting the translational regulatory property of the RNA thermometer into transcriptional regulation in Escherichia coli
RNA thermometer optimised for Bacillus subtilis and converting the translational regulatory property of the RNA thermometer into transcriptional regulation in Escherichia coli Open