8 citations · 17 across the 14 of their papers we have counts for
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BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model
Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, Hamidreza Chitsaz
RNA-RNA interaction (RRI) is ubiquitous and has complex roles in the cellular functions. In human health studies, miRNA-target and lncRNAs are among an elite class of RRIs that hav…
Exact Learning of RNA Energy Parameters From Structure
Hamidreza Chitsaz, Mohammad Aminisharifabad
We consider the problem of exact learning of parameters of a linear RNA energy model from secondary structure data. A necessary and sufficient condition for learnability of paramet…
The RNA Newton Polytope and Learnability of Energy Parameters
Elmirasadat Forouzmand, Hamidreza Chitsaz
Despite nearly two scores of research on RNA secondary structure and RNA-RNA interaction prediction, the accuracy of the state-of-the-art algorithms are still far from satisfactory…
An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids
Hamidreza Chitsaz, Elmirasadat Forouzmand, Gholamreza Haffari
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of th…
Prediction of RNA-RNA interaction structure by centroids in the Boltzmann ensemble
Hamidreza Chitsaz
New high-throughput sequencing technologies have made it possible to pursue the advent of genome-wide transcriptomics. That progress combined with the recent discovery of regulator…