Software Code for paper on codonGPT and codonGPT-RL by Anuj Guruacharya (22332988)

Subjects:

Software Code for paper on codonGPT and codonGPT-RL by Anuj Guruacharya (22332988)

Subjects:

Table 1_Impact of codon optimization on vip3Aa11 gene expression and insecticidal efficacy in maize.docx by Shengyan Li (4028975)

“…The vip3Aa11 gene from Bacillus thuringiensis is a promising candidate for controlling Spodoptera frugiperda.</p>Methods and results<p>To develop insect-resistant maize, we designed two codon-optimized vip3Aa11 variants (vip3Aa11-m1 and vip3Aa11-m2) based on maize codon usage bias. …”

RiboDecode by Yupeng Li (21103070)

Summarized results of predicted HTL epitopes, the method utilized, IFN status and antigenicity and allergenicity profiling. by Habiba Naz (20685373)

Data Sheet 1_Characterization of the complete chloroplast genome and comparative analysis of the phylogeny and codon usage bias of three Yunnan wild rice species.zip by Rongxin Li (3552779)

“…Fourteen optimal codons were identified, with 13 ending in A/U and one ending in C. …”

Construction of stimulus cluster maps for selected drug regimes. by Emily R. Bozich (12116745)

Cluster Dendrogram. by Zahra Zinati (12068304)

Gene dendrogram and module colors. by Zahra Zinati (12068304)

Primers. by Jan-Ole Krischek (21213122)

“…Using mDNase1 expression as a guideline, we were able to increase the yield of hDNASE1 fourfold by optimizing parameters like nutrients, cultivation temperature, methanol supply, and codon usage. …”

Table 1_Discovery and development of a safe and efficient COVID-19 mRNA vaccine, STP2104, using a novel capping library screening method.docx by Kanghyun Choi (21507536)

“…We developed a COVID-19 mRNA vaccine encoding a codon-optimized full-length ancestral spike (S) protein with a signal peptide, which employs our novel patented co-transcriptional 5′-capping reagent, SmartCap^®. …”

Supplemental data by Xueyin Mei (20537855)

BFmonitor overview. by Nayim González-Rodríguez (22662799)

Changing and stable fitness landscapes. by Thibault Latrille (4514248)

Table 15_Rational design of an epitope-centric vaccine against Pseudomonas aeruginosa using pangenomic insights and immunoinformatics approach.docx by Santhosh Mudipalli Elavarasu (22152916)

“…Studies using molecular docking and dynamic simulation have shown stable interactions between the vaccine and TLRs, with the POA_V_RS09 construct exhibiting the highest stability. Codon optimization indicated high expression efficiency in E. coli. …”

Table 1_Rational design of an epitope-centric vaccine against Pseudomonas aeruginosa using pangenomic insights and immunoinformatics approach.docx by Santhosh Mudipalli Elavarasu (22152916)

“…Studies using molecular docking and dynamic simulation have shown stable interactions between the vaccine and TLRs, with the POA_V_RS09 construct exhibiting the highest stability. Codon optimization indicated high expression efficiency in E. coli. …”

Table 10_Rational design of an epitope-centric vaccine against Pseudomonas aeruginosa using pangenomic insights and immunoinformatics approach.docx by Santhosh Mudipalli Elavarasu (22152916)

“…Studies using molecular docking and dynamic simulation have shown stable interactions between the vaccine and TLRs, with the POA_V_RS09 construct exhibiting the highest stability. Codon optimization indicated high expression efficiency in E. coli. …”

Table 4_Rational design of an epitope-centric vaccine against Pseudomonas aeruginosa using pangenomic insights and immunoinformatics approach.docx by Santhosh Mudipalli Elavarasu (22152916)

“…Studies using molecular docking and dynamic simulation have shown stable interactions between the vaccine and TLRs, with the POA_V_RS09 construct exhibiting the highest stability. Codon optimization indicated high expression efficiency in E. coli. …”

Table 7_Rational design of an epitope-centric vaccine against Pseudomonas aeruginosa using pangenomic insights and immunoinformatics approach.docx by Santhosh Mudipalli Elavarasu (22152916)

“…Studies using molecular docking and dynamic simulation have shown stable interactions between the vaccine and TLRs, with the POA_V_RS09 construct exhibiting the highest stability. Codon optimization indicated high expression efficiency in E. coli. …”

Table 12_Rational design of an epitope-centric vaccine against Pseudomonas aeruginosa using pangenomic insights and immunoinformatics approach.docx by Santhosh Mudipalli Elavarasu (22152916)

“…Studies using molecular docking and dynamic simulation have shown stable interactions between the vaccine and TLRs, with the POA_V_RS09 construct exhibiting the highest stability. Codon optimization indicated high expression efficiency in E. coli. …”