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Decoding the JAK-STAT Axis in Colorectal Cancer with AI-HOPE-JAK-STAT: A Conversational Artificial Intelligence Approach to Clinical–Genomic Integration by Yang, Ei-Wen, Waldrup, Brigette, Velazquez-Villarreal, Enrique

“…: AI-HOPE-JAK-STAT combines large language models (LLMs), a natural language-to-code engine, and harmonized public CRC datasets from cBioPortal…”
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Introduction to computational causal inference using reproducible Stata, R, and Python code: A tutorial by Smith, Matthew J., Mansournia, Mohammad A., Maringe, Camille, Zivich, Paul N., Cole, Stephen R., Leyrat, Clémence, Belot, Aurélien, Rachet, Bernard, Luque‐Fernandez, Miguel A.

“…The main purpose of many medical studies is to estimate the effects of a treatment or exposure on an outcome. However, it is not always possible to randomize…”
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LiPydomics: A Python Package for Comprehensive Prediction of Lipid Collision Cross Sections and Retention Times and Analysis of Ion Mobility-Mass Spectrometry-Based Lipidomics Data by Ross, Dylan H, Cho, Jang Ho, Zhang, Rutan, Hines, Kelly M, Xu, Libin

“… Existing solutions for these data analysis challenges (i.e., multivariate statistics and lipid identification…”
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Towards Effective Static Type-Error Detection for Python by Oh, Wonseok, Oh, Hakjoo

“… This empirical investigation revealed four key static-analysis features that are crucial for the effective detection of Python type errors in practice…”
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Percolation theory using Python by Malthe-Sørenssen, Anders

“… Readers will learn how to generate, analyze, and comprehend data and models, with detailed theoretical discussions complemented by accessible computer codes…”
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VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models by Parker, Christopher, Nelson, Erik, Zhang, Tongli

“… VeVaPy includes four functional modules coded in Python, and the source code is publicly available…”
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Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data by Pakkir Shah, Abzer K., Walter, Axel, Ottosson, Filip, Russo, Francesco, Navarro-Diaz, Marcelo, Boldt, Judith, Kalinski, Jarmo-Charles J., Kontou, Eftychia Eva, Elofson, James, Polyzois, Alexandros, González-Marín, Carolina, Farrell, Shane, Aggerbeck, Marie R., Pruksatrakul, Thapanee, Chan, Nathan, Wang, Yunshu, Pöchhacker, Magdalena, Brungs, Corinna, Cámara, Beatriz, Caraballo-Rodríguez, Andrés Mauricio, Cumsille, Andres, de Oliveira, Fernanda, Dührkop, Kai, El Abiead, Yasin, Geibel, Christian, Graves, Lana G., Hansen, Martin, Heuckeroth, Steffen, Knoblauch, Simon, Kostenko, Anastasiia, Kuijpers, Mirte C. M., Mildau, Kevin, Papadopoulos Lambidis, Stilianos, Portal Gomes, Paulo Wender, Schramm, Tilman, Steuer-Lodd, Karoline, Stincone, Paolo, Tayyab, Sibgha, Vitale, Giovanni Andrea, Wagner, Berenike C., Xing, Shipei, Yazzie, Marquis T., Zuffa, Simone, de Kruijff, Martinus, Beemelmanns, Christine, Link, Hannes, Mayer, Christoph, van der Hooft, Justin J. J., Damiani, Tito, Pluskal, Tomáš, Dorrestein, Pieter, Stanstrup, Jan, Schmid, Robin, Wang, Mingxun, Aron, Allegra, Ernst, Madeleine, Petras, Daniel

“… We provide explanations and code in two scripting languages (R and Python) as well…”
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KF-NIPT: K-mer and fetal fraction-based estimation of chromosomal anomaly from NIPT data by Kim, Dongin, Sohn, Ji Yeon, Cho, Jin Hee, Choi, Ji-Hye, Oh, Gwi-young, Woo, Hyun Goo

“…Background Non-Invasive Prenatal Testing (NIPT) is a technique that allows pregnant women to screen for chromosomal abnormalities in their developing fetus…”
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SNPAAMapper-Python: A highly efficient genome-wide SNP variant analysis pipeline for Next-Generation Sequencing data by Li, Chang, Ma, Kevin, Xu, Nicole, Fu, Chenjian, He, Andrew, Liu, Xiaoming, Bai, Yongsheng

“… In this study, we updated SNPAAMapper, a variant annotation pipeline by converting perl codes to python for generating annotation output with an improved computational efficiency and updated…”
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Nestedness for Dummies (NeD): A user friendly web interface for exploratory nestedness analysis by Strona, Giovanni, Galli, Paolo, Seveso, Davide, Montano, Simone, Fattorini, Simone

“…Recent theoretical advances in nestedness analysis have led to the introduction of several alternative metrics to overcome most of the problems biasing the use of matrix 'temperature' calculated…”
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Statistics Using Python by Campesato, Oswald

“…This book is designed to offer a fast-paced yet thorough introduction to essential statistical concepts using Python code samples, and aims to assist data scientists in their daily endeavors…”
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From code to reliability: Python-powered Paraconsistent Logic for alarm detection in the power gris/ Do codigo a confiabilidade: Logica Paraconsistente impulsionada por Python para a deteccao de alarmes na rede de energia by de Oliveira, Joseffe Barroso, Gino, Joao Vitor Santa Rosa, de Lima, Carlos Jose, Filho, Joao Inacio da Silva

“… This application enables the comparison of triggered alarms with the resultant logical states obtained during the analysis…”
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Statistical Analyses and Reproducible Research by Gentleman, Robert, Temple Lang, Duncan

“…It is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, and so on with the documents that describe and rely…”
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CSA-Trans: Code Structure Aware Transformer for AST by Oh, Saeyoon, Yoo, Shin

“…When applying the Transformer architecture to source code, designing a good self-attention mechanism is critical as it affects how node relationship is extracted from the Abstract Syntax Trees (ASTs) of the source code…”
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Graphical interface for automated management of motion artifact within fMRI acquisitions: INFOBAR by Anand, Manish, Diekfuss, Jed A., Slutsky-Ganesh, Alexis B., Bonnette, Scott, Grooms, Dustin R., Myer, Gregory D.

“…Independent Component Analysis-based Automatic Removal of Motion Artifacts (ICA-AROMA; Pruim et al., 2015) is a robust approach to remove brain activity related to head motion within functional magnetic resonance imaging…”
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Facilitating the Calculation of the Efficient Score Using Symbolic Computing by B. Sibley, Alexander, Li, Zhiguo, Jiang, Yu, Li, Yi-Ju, Chan, Cliburn, Allen, Andrew, Owzar, Kouros

“… In the analysis of data from high-throughput genomic assays, inference on the basis of the score usually enjoys greater stability, considerably higher computational efficiency, and lends itself…”
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lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R by Khleborodova, Asya, Gamboa-Tuz, Samuel D, Ramos, Marcel, Segata, Nicola, Waldron, Levi, Oh, Sehyun

“…Summary LEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal…”
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Share, But be Aware: Security Smells in Python Gists by Rahman, Md Rayhanur, Rahman, Akond, Williams, Laurie

“… Through static analysis, we found 13 types of security smells with 4,403 occurrences in 5,822 publicly-available Python Gists…”
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Generation of Scale-Free Assortative Networks via Newman Rewiring for Simulation of Diffusion Phenomena by Di Lucchio, Laura, Modanese, Giovanni

“…By collecting and expanding several numerical recipes developed in previous work, we implement an object-oriented Python code, based on the networkX library, for the realization of the configuration…”
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GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions by Wang, Guannan, Oh, Dong-Ha, Dassanayake, Maheshi

“…Background Functional enrichment of genes and pathways based on Gene Ontology (GO) has been widely used to describe the results of various -omics analyses…”
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