Our algorithms process large data sets within a minute. by Manu Aggarwal (15990691)

Algorithmic assessment reveals functional implications of GABRD gene variants linked to idiopathic generalized epilepsy by Ayla Arslan (17943365)

“…</p> <p>The study employs a combination of in silico algorithms to analyze 82 variants of unknown clinical significance of GABRD gene sourced from the ClinVar database. …”

An expectation-maximization algorithm for finding noninvadable stationary states. by Robert Marsland (8616483)

“…<i>(c)</i> Pseudocode for self-consistently computing <b>R</b>* and , which is identical to standard expectation-maximization algorithms employed for problems with latent variables in machine learning.…”

Frequency of frameshift mutations in tumor suppressor genes within TCGA and DFCI cohorts. by Alexis M. Thornton (11068403)

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<b>Opti2Phase</b>: Python scripts for two-stage focal reducer by Morgan Najera (21540776)

“…</li></ul><p dir="ltr">The scripts rely on the following Python packages. Where available, repository links are provided:</p><ol><li><b>NumPy</b>, version 1.22.1</li><li><b>SciPy</b>, version 1.7.3</li><li><b>PyGAD</b>, version 3.0.1 — https://pygad.readthedocs.io/en/latest/#</li><li><b>bees-algorithm</b>, version 1.0.2 — https://pypi.org/project/bees-algorithm</li><li><b>KrakenOS</b>, version 1.0.0.19 — https://github.com/Garchupiter/Kraken-Optical-Simulator</li><li><b>matplotlib</b>, version 3.5.2</li></ol><p dir="ltr">All scripts are modular and organized to reflect the design stages described in the manuscript.…”

Identification and functional analysis of hub genes. by Wei Ya Lan (22403712)

“…(B) PPI network visualized using Cytoscape software. (C, D) Top 10 hub genes identified using the Maximal Clique Centrality (MCC) algorithm; darker colors indicate higher centrality within the PPI network. …”

Listed python codes of our algorithm with explanations (Python 3.9 recommended). by Takayuki Niizato (162226)

Highly interrelated genes and their biological functions among 21 cancers. by Qunlun Shen (11668968)

Identification of hub genes from the PPI network by bottleneck algorithm using the cytoHubba Cytoscape plugin. by Cihat Erdogan (12529243)

Core genes were selected through PPI analysis based on three algorithms. by Dong-Hee Han (140305)

“…<b>(B)</b> The priority of the top 10 genes was evaluated through MNC, which identifies clusters of protein nodes that are more functionally connected to each other and selects the central proteins within the cluster. …”

Test functions. by Kejia Liu (5699651)

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Biological functions and network analysis of highly interrelated genes selected by ADC across modalities. by Qunlun Shen (11668968)

Multimodal reference functions. by Ruiyu Zhan (21602031)

“…We performed comparative analyses against other methodologies across various functions and public datasets to assess their effectiveness. …”

Python-based Monte Carlo Simulation Tool by Yangfan Jiang (9372782)

Summary of gene-gene cosine similarities within pathways in TRANSPATH®. by Halima Alachram (11570633)

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Summary of gene-gene cosine similarities within pathways in Reactome. by Halima Alachram (11570633)

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Gene-gene cosine similarities within TRANSPATH® pathways of given number of genes. by Halima Alachram (11570633)

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Gene-gene cosine similarities within Reactome pathways of given number of genes. by Halima Alachram (11570633)

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The convergence curves of the test functions. by Ruiyu Zhan (21602031)

“…We performed comparative analyses against other methodologies across various functions and public datasets to assess their effectiveness. …”

Single-peaked reference functions. by Ruiyu Zhan (21602031)

“…We performed comparative analyses against other methodologies across various functions and public datasets to assess their effectiveness. …”