Nabeel Ahmed

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Publications (12)

• mRNAfold: Co-optimization of Global Stability, Local Structure, and Codon Choice via Suboptimal Folding
  2026 DOI: 10.64898/2026.01.23.701221
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• RiboA: a web application to identify ribosome A-site locations in ribosome profiling data
  BMC Bioinformatics 2021 DOI: 10.1186/s12859-021-04068-w
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• Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates
  Journal of Molecular Biology 2020 DOI: 10.1016/j.jmb.2020.10.030
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• Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates
  2020 DOI: 10.1101/2020.04.20.051839
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• Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling
  Journal of the American Chemical Society 2020 DOI: 10.1021/jacs.9b12264
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• A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data
  PLoS Computational Biology 2019 DOI: 10.1371/journal.pcbi.1007070
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• Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming
  Scientific Reports 2019 DOI: 10.1038/s41598-019-42348-x
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• A Chemical Kinetic Basis for Measuring Translation Initiation and Elongation Rates from Ribosome Profiling data
  bioRxiv 2018 DOI: 10.1101/490730
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• Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times
  Physical Review E 2018 DOI: 10.1103/PhysRevE.97.022409
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• Identifying A- And P-site locations on ribosome-protected mRNA fragments using Integer Programming
  bioRxiv 2018 DOI: 10.1101/490755
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