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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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2FAST2Q: a general-purpose sequence search and counting program for FASTQ files by Bravo, Afonso M., Typas, Athanasios, Veening, Jan-Willem

“… Despite 2FAST2Q being previously described as part of a CRISPRi-seq analysis pipeline, in here we further elaborate on the program's functionality, and its broader applicability and functions…”
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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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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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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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eqtools: Modular, extensible, open-source, cross-machine Python tools for working with magnetic equilibria by Chilenski, M. A., Faust, I. C., Walk, J. R.

“… in the Python programming language for handling magnetic equilibria and associated data from tokamaks…”
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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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Enhancing Monte Carlo Workflows for Nuclear Reactor Analysis with Metamodel-Driven Modeling by Kowal, Peter J., Blake, Camden E., Dominesey, Kurt A., Lefebvre, Robert A., Brown, Forrest B., Ji, Wei

“…Monte Carlo codes are essential components of many reactor physics simulation workflows as high-fidelity continuous-energy neutron transport solvers…”
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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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LIVVkit: An extensible, python‐based, land ice verification and validation toolkit for ice sheet models by Kennedy, Joseph H., Bennett, Andrew R., Evans, Katherine J., Price, Stephen, Hoffman, Matthew, Lipscomb, William H., Fyke, Jeremy, Vargo, Lauren, Boghozian, Adrianna, Norman, Matthew, Worley, Patrick H.

“…), the corresponding verification and validation (V&V) process is being coordinated through a new, robust, Python…”
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pyPheWAS: A Phenome-Disease Association Tool for Electronic Medical Record Analysis by Kerley, Cailey I., Chaganti, Shikha, Nguyen, Tin Q., Bermudez, Camilo, Cutting, Laurie E., Beason-Held, Lori L., Lasko, Thomas, Landman, Bennett A.

“… In this article, we introduce pyPheWAS , an open-source python package for conducting PheDAS and related analyses…”
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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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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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Shutdown dose rate analysis with the Shift Monte Carlo radiation transport code and modular verification workflow by Bae, Jin Whan, Kos, Bor, Biondo, Elliott

“… These features make it an attractive transport solver choice for an R2S workflow. An R2S workflow for the Shift Monte Carlo code is developed and compared to the existing Oak Ridge National Laboratory Shutdown Dose Rate Code Suite (ORCS) workflow…”
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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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The TDHF code Sky3D version 1.2 by Abhishek, Stevenson, Paul, Shi, Yue, Yüksel, Esra, Umar, A.S.

“…The Sky3D code has been widely used to describe nuclear ground states, collective vibrational excitations, and heavy-ion collisions…”
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Modeling for insight using Tools for Energy Model Optimization and Analysis (Temoa) by Hunter, Kevin, Sreepathi, Sarat, DeCarolis, Joseph F.

“…This paper introduces Tools for Energy Model Optimization and Analysis (Temoa), an open source framework for conducting energy system analysis…”
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Sensitivity analysis of thermal contact conductance modeling to inform MiniFuel irradiation capsule designs by Meehan, Nicholas A., Gorton, Jacob P., Capps, Nathan A., Brown, Nicholas R.

“…•Sensitivity analysis to identify high-impact parameters that contribute to fuel temperature variance…”
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