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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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PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations by Reis, Pedro B P S, Vila-Viçosa, Diogo, Rocchia, Walter, Machuqueiro, Miguel

“…The protonation of titratable residues has a significant impact on the structure and function of biomolecules, influencing many physicochemical and ADME…”
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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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ACPYPE - AnteChamber PYthon Parser interfacE by Sousa da Silva, Alan W, Vranken, Wim F

“… (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http…”
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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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AI Writes, We Analyze: The ChatGPT Python Code Saga by Rabbi, Md Fazle, Champa, Arifa, Zibran, Minhaz, Islam, Md Rakibul

“…In this study, we quantitatively analyze 1,756 AI-written Python code snippets in the DevGPT dataset and evaluate them for quality and security issues…”
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PSHRisk-Tool: A Python-Based Computational Tool for Developing Site Seismic Hazard Analysis and Failure Risk Assessment of Infrastructure by Nahar, Tahmina Tasnim, Rahman, Md Motiur, Kim, Dookie

“… vulnerable condition for the infrastructure. This python-code based tool can demonstrate the source identification, probability distribution plot of magnitude and distance…”
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mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data by Pérez-Hernández, Guillermo, Hildebrand, Peter W.

“…) for easy, one-shot analysis and representation of molecular dynamics (MD) simulation data. Building upon the widely used concept of residue-residue contact-frequencies…”
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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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WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data by Yang, Darian T, Chong, Lillian T

“… Here, we present the WEDAP Python package for simplifying the analysis of data generated from either conventional MD simulations or the weighted ensemble…”
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MDAnalysis: A toolkit for the analysis of molecular dynamics simulations by Michaud-Agrawal, Naveen, Denning, Elizabeth J., Woolf, Thomas B., Beckstein, Oliver

“…MDAnalysis is an object‐oriented library for structural and temporal analysis of molecular dynamics (MD…”
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xNose: A Test Smell Detector for C# by Paul, Partha P., Akanda, Md Tonoy, Ullah, M. Raihan, Mondal, Dipto, Chowdhury, Nazia S., Tawsif, Fazle M.

“…Test smells, similar to code smells, can negatively impact both the test code and the production code being tested…”
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Enhanced urban impervious surface land use mapping using a novel multi-sensor feature fusion method and remote sensing data by Ahmad, Muhammad Nasar, Almutlaq, Fahad, Huq, Md. Enamul, Islam, Fakhrul, Javed, Akib, Skilodimou, Hariklia D., Bathrellos, George D.

“…) and modified indices (using Landsat-8), and then classified these features using an XGBoost algorithm implemented in Python and Google Earth Engine…”
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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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RETRACTED: PSHRisk-Tool: A Python-Based Computational Tool for Developing Site Seismic Hazard Analysis and Failure Risk Assessment of Infrastructure by Nahar, Tahmina, Rahman, Md, Kim, Dookie

“… vulnerable condition for the infrastructure. This python-code based tool can demonstrate the source identification, probability distribution plot of magnitude and distance…”
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Sarkas: A Fast Pure-Python Molecular Dynamics Suite for Non-Ideal Plasmas by Silvestri, Luciano G., Stanek, Luke J., Choi, Yongjun, Murillo, Michael S., Dharuman, Gautham

“… As a matter of fact for each of these research fields we can find MD codes, open-source or proprietary, optimized for the simulation of their respective dynamical systems…”
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Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module by Pool, René, Heringa, Jaap, Hoefling, Martin, Schulz, Roland, Smith, Jeremy C., Feenstra, K. Anton

“…We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy…”
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BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories by Mukhaleva, Elizaveta, Manookian, Babgen, Chen, Hanyu, Sivaraj, Indira R, Ma, Ning, Wei, Wenyuan, Urbaniak, Konstancja, Gogoshin, Grigoriy, Bhattacharya, Supriyo, Vaidehi, Nagarajan, Rodin, Andrei S, Branciamore, Sergio

“… However, the analysis of MD simulation trajectories has not been data-driven but rather dependent on the user's prior knowledge of the systems, thus limiting the scope and utility of the MD simulations…”
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