Efficient algorithms to discover alterations with complementary functional association in cancer حسب Rebecca Sarto Basso (6728921)

"…Among such patterns, <i>mutual exclusivity</i> has been employed by several recent methods that have shown its effectiveness in characterizing gene sets associated to cancer. Mutual exclusivity arises because of the complementarity, at the functional level, of alterations in genes which are part of a group (e.g., a <i>pathway</i>) performing a given function. …"

Python-Based Algorithm for Estimating NRTL Model Parameters with UNIFAC Model Simulation Results حسب Se-Hee Jo (20554623)

"…This algorithm conducts a series of procedures: (1) fragmentation of the molecules into functional groups from SMILES, (2) calculation of activity coefficients under predetermined temperature and mole fraction conditions by employing universal quasi-chemical functional group activity coefficient (UNIFAC) model, and (3) regression of NRTL model parameters by employing UNIFAC model simulation results in the differential evolution algorithm (DEA) and Nelder–Mead method (NMM). …"

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

"…</p><p dir="ltr">The package includes:</p><ul><li>Scripts for first-order analysis, third-order modeling, optimization using a Physically Grounded Merit Function (PGMF), and RMS-based refinement.</li><li>A subfolder named <b>Images</b>, which stores the figures generated by six of the seven provided scripts.…"

Average quality scores of the models of the analysis set as a function of the <i>w</i>_<i>SP</i> with which the DOPE potential has been included in the objective function... حسب Giacomo Janson (8138517)

The eVIP algorithm uses RNA-seq data to predict the function of somatic mutations. حسب Alexis M. Thornton (11068403)

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

"…</p> <p>The study identifies specific variants (L111R, R114C, D123N, G150S, and L243P) in the coding region of the GABRD gene, which are predicted as deleterious by multiple algorithms. …"

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

"…<i>(b)</i> Metabolic byproducts move the relevant unperturbed state from <b>R</b>⁰ (gray ‘x’) to (black ‘x’), which is itself a function of the current environmental conditions. …"

Python implementation of the Trajectory Adaptive Multilevel Sampling algorithm for rare events and improvements حسب Pascal Wang (10130612)

"…<div>This directory contains Python 3 scripts implementing the Trajectory Adaptive Multilevel Sampling algorithm (TAMS), a variant of Adaptive Multilevel Splitting (AMS), for the study of rare events. …"

Data_Sheet_3_Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways.csv حسب Maxim Sorokin (4379848)

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Data_Sheet_2_Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways.pdf حسب Maxim Sorokin (4379848)

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Data_Sheet_1_Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways.zip حسب Maxim Sorokin (4379848)

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Functions of most frequently mutated genes. حسب Anda Stan (18056225)

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

The proposed method for protein function prediction. حسب Seyyede Fatemeh Seyyedsalehi (10196767)

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DE genes detected by different DEA algorithms. حسب Jie Xue (417504)

"…Here, we compare 6 performance metrics on both simulated and real scRNA-seq datasets to assess the adaptability of 8 DEA approaches, with a particular emphasis on how well they function under small biological replications. Our findings suggest that DEA algorithms extended from bulk RNA-seq are still competitive under small biological replicate conditions, whereas the newly developed method DEF-scRNA-seq which is based on information entropy offers significant advantages. …"

Core genes were selected through PPI analysis based on three algorithms. حسب 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. …"

Cost functions implemented in Neuroptimus. حسب Máté Mohácsi (20469514)

The list of genes which were identified after direct merging. حسب Bahman Panahi (7323578)

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Test functions. حسب Kejia Liu (5699651)

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Significance levels of gene biomarkers. حسب Zongjin Li (38031)

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