Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: EGAD

https://packages.ecosyste.ms/registries/bioconductor.org/packages/EGAD

Extending guilt by association by degree
1 version
Latest release: 10 months ago
11,942 downloads total

Papers Mentioning EGAD 19

Benchmarking network propagation methods for disease gene identification
Cited by: 29
Author(s): Sergio Picart‐Armada, Steven J. Barrett, David Willé, Alexandre Perera-Lluna, Alex Gutteridge, Benoît H. Dessailly
Software Mentions: 9
Published: almost 5 years ago

10.1186/1472-6807-9-27

PTools: an opensource molecular docking library
Cited by: 34
Author(s): Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, Martin Zacharias
Software Mentions: 9
Published: about 15 years ago

10.1038/s41598-017-09094-4

Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study
Cited by: 33
Author(s): Stephen P. Ficklin, Leland J. Dunwoodie, William L. Poehlman, Christopher Watson, Kimberly Roche, F. Alex Feltus
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41598-019-50885-8

Improved gene co-expression network quality through expression dataset down-sampling and network aggregation
Cited by: 25
Author(s): Franziska Liesecke, Johan-Owen De Craene, Sébastien Besseau, Vincent Courdavault, Marc Clastre, Valentin Vergès, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12870-017-1077-4

Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response
Cited by: 23
Author(s): Shisong Ma, Zehong Ding, Pinghua Li
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0138022

Structure Based Thermostability Prediction Models for Protein Single Point Mutations with Machine Learning Tools
Cited by: 66
Author(s): Lei Jia, Ramya Yarlagadda, Charles C. Reed
Software Mentions: 4
Published: almost 9 years ago

10.3390/ijms15069670

Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics
Cited by: 29
Author(s): Tugba G. Kucukkal, Ye Yang, Steve Chapman, Weiguo Cao, Emil Alexov
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0017459

The Contribution of Coevolving Residues to the Stability of KDO8P Synthase
Cited by: 15
Author(s): Sharon H. Ackerman, Domenico L. Gatti
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0046084

Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency
Cited by: 87
Author(s): Grant Thiltgen, Richard A. Goldstein
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-10-54

TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis
Cited by: 10
Author(s): André Fischer, Nils Enkler, Gerd Neudert, Marco Bocola, Reinhard Sterner, Rainer Merkl
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0092513

Computational Design of Binding Proteins to EGFR Domain II
Cited by: 9
Author(s): Yoon Sup Choi, Soo-Han Yoon, Kyung Lock Kim, Je Hyun Yoo, Parkyong Song, Min‐Soo Kim, Young Eun Shin, Won Jun Yang, Jung Eun Noh, Hyun Soo Cho, Sanguk Kim, Junho Chung, Sung Ho Ryu
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-13-S4-S2

How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis
Cited by: 220
Author(s): Mauno Vihinen
Software Mentions: 1
Published: over 12 years ago

10.1186/1752-0509-5-S1-S5

DBAC: A simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts
Cited by: 12
Author(s): Zhenhua Li, Limsoon Wong, Jinyan Li
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1003129

Engineering a More Thermostable Blue Light Photo Receptor Bacillus subtilis YtvA LOV Domain by a Computer Aided Rational Design Method
Cited by: 25
Author(s): Xiangfei Song, Yefei Wang, Zhiyu Shu, Jingbo Hong, Tong Li, Lishan Yao
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2105-13-S4-S18

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii
Cited by: 51
Author(s): Federico Fogolari, Alessandra Corazza, Vijaylakshmi Yarra, Anusha Jalaru, Paolo Viglino, Gennaro Esposito
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0047247

PROTS-RF: A Robust Model for Predicting Mutation-Induced Protein Stability Changes
Cited by: 43
Author(s): Yunqi Li, Jianwen Fang
Software Mentions: 1
Published: almost 12 years ago

10.3389/fnagi.2017.00162

Age-Related Gene Expression in the Frontal Cortex Suggests Synaptic Function Changes in Specific Inhibitory Neuron Subtypes
Cited by: 33
Author(s): Leon French, Tianzhou Ma, Heung Bum Oh, George C. Tseng, Etienne Sibille
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-04950-9

Computing disease-linked SOD1 mutations: deciphering protein stability and patient-phenotype relations
Cited by: 29
Author(s): Vijay Kumar, Safikur Rahman, Hani Choudhry, Mazin A. Zamzami, Mohammad Sarwar Jamal, Asimul Islam, Faizan Ahmad, Md. Imtaiyaz Hassan
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-019-55661-2

Atomic insights into the effects of pathological mutants through the disruption of hydrophobic core in the prion protein
Cited by: 6
Author(s): Juhwan Lee, Iksoo Chang, Wookyung Yu
Software Mentions: 1
Published: over 4 years ago