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List of works by Dennis Shasha

A collaborative approach to computational reproducibility

A subgraph isomorphism algorithm and its application to biochemical data.

scientific article

A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis

scientific article

An approximate search engine for structural databases

An approximate search engine for structural databases

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

scientific article

Computational reproducibility

Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics

scientific article published on 21 February 2019

Fast structural search in phylogenetic databases.

scientific article published on January 2005

GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures

scientific article (publication date: 2013)

Gene regulatory networks in plants: learning causality from time and perturbation

scientific article published on 27 June 2013

GraphClust: A Method for Clustering Database of Graphs

GraphFind: enhancing graph searching by low support data mining techniques

scientific article

Homology search for genes

scientific article

I/O Model of Computation

Image

Implication of Constraints

In vitro and in silico cloning of Xenopus laevis SOD2 cDNA and its phylogenetic analysis

scientific article

Inexpensive, non-invasive biomarkers predict Alzheimer transition using machine learning analysis of the Alzheimer's Disease Neuroimaging (ADNI) database

scientific article published on 27 July 2020

MetricMap: an embedding technique for processing distance-based queries in metric spaces

scientific article published in October 2005

Negative example selection for protein function prediction: the NoGO database

scientific article

NetMatchStar: an enhanced Cytoscape network querying app

scientific article published on 5 August 2015

Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions

scientific article published on 05 April 2019

Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand.

scientific article published on 24 October 2011

Packing experiments for sharing and publication

Parametric Bayesian priors and better choice of negative examples improve protein function prediction

scientific article published on 19 March 2013

Repeatability and workability evaluation of SIGMOD 2011

ReproZip

scholarly article

ReproZip: The Reproducibility Packer

scientific article published in December 2016

SING: subgraph search in non-homogeneous graphs

scientific article

SafePredict: A Meta-Algorithm for Machine Learning That Uses Refusals to Guarantee Correctness

scientific article published on 01 August 2019

SuperNoder: a tool to discover over-represented modular structures in networks

scholarly article by Danilo Dessì published in September 2018

Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools

scientific article

TACITuS: transcriptomic data collector, integrator, and selector on big data platform

scientific article published on 22 November 2019

Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants.

scientific article

Term Weighting

scientific article

The Proteome Folding Project: proteome-scale prediction of structure and function

scientific article

The dangers of replication and a solution

scientific article (publication date: 1996)

Trait-to-gene: a computational method for predicting the function of uncharacterized genes

scientific article published in January 2003

Tuple-Generating Dependencies

miR-EdiTar: a database of predicted A-to-I edited miRNA target sites

scientific article

miR-Synth: a computational resource for the design of multi-site multi-target synthetic miRNAs

scientific article

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