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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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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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A NICER View of the Massive Pulsar PSR J0740+6620 Informed by Radio Timing and XMM-Newton Spectroscopy by Riley, Thomas E., Watts, Anna L., Ray, Paul S., Bogdanov, Slavko, Guillot, Sebastien, Morsink, Sharon M., Bilous, Anna V., Arzoumanian, Zaven, Choudhury, Devarshi, Deneva, Julia S., Gendreau, Keith C., Harding, Alice K., Ho, Wynn C. G., Lattimer, James M., Loewenstein, Michael, Ludlam, Renee M., Markwardt, Craig B., Okajima, Takashi, Prescod-Weinstein, Chanda, Remillard, Ronald A., Wolff, Michael T., Fonseca, Emmanuel, Cromartie, H. Thankful, Kerr, Matthew, Pennucci, Timothy T., Parthasarathy, Aditya, Ransom, Scott, Stairs, Ingrid, Guillemot, Lucas, Cognard, Ismael

“…We report on Bayesian estimation of the radius, mass, and hot surface regions of the massive millisecond pulsar PSR J0740+6620, conditional on pulse-profile…”
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Potku – New analysis software for heavy ion elastic recoil detection analysis by Arstila, K., Julin, J., Laitinen, M.I., Aalto, J., Konu, T., Kärkkäinen, S., Rahkonen, S., Raunio, M., Itkonen, J., Santanen, J.-P., Tuovinen, T., Sajavaara, T.

“… The software combines a Python-language graphical front-end with a C code computing back-end in a user-friendly way…”
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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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PyIOmica: longitudinal omics analysis and trend identification by Domanskyi, Sergii, Piermarocchi, Carlo, Mias, George I

“…Abstract Summary PyIOmica is an open-source Python package focusing on integrating longitudinal multiple omics datasets, characterizing and categorizing temporal trends…”
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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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Entropy, Fidelity, and Entanglement During Digitized Adiabatic Quantum Computing to Form a Greenberger-Horne-Zeilinger (GHZ) State by Jansen, Nathan D, Hunt, Katharine L C

“…) state on two IBM quantum computers and four quantum simulators by comparison with direct calculations using a Python code (version 3.12…”
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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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Enhanced deep learning model for precise nodule localization and recurrence risk prediction following curative-intent surgery for lung cancer by Park, Jihwan, Rho, Mi Jung, Moon, Mi Hyoung

“…Radical surgery is the primary treatment for early-stage resectable lung cancer, yet recurrence after curative surgery is not uncommon. Identifying patients at…”
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Nature and Diffusion of Gynecologic Cancer–Related Misinformation on Social Media: Analysis of Tweets by Chen, Liang, Wang, Xiaohui, Peng, Tai-Quan

“…Over the last two decades, the incidence and mortality rates of gynecologic cancers have increased at a constant rate in China. Gynecologic cancers have become…”
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GSEApy: a comprehensive package for performing gene set enrichment analysis in Python by Fang, Zhuoqing, Liu, Xinyuan, Peltz, Gary

“…Abstract Motivation Gene set enrichment analysis (GSEA) is a commonly used algorithm for characterizing gene expression changes…”
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VULCAN: An Open-source, Validated Chemical Kinetics Python Code for Exoplanetary Atmospheres by Tsai, Shang-Min, Lyons, James R., Grosheintz, Luc, Rimmer, Paul B., Kitzmann, Daniel, Heng, Kevin

“…We present an open-source and validated chemical kinetics code for studying hot exoplanetary atmospheres, which we name VULCAN…”
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Quantitative analysis of mitochondrial ATP synthesis by Randall, E. Benjamin, Hock, Marcus, Lopez, Rachel, Marzban, Bahador, Marshall, Collin, Beard, Daniel A.

“… Computer codes for these analyses are embedded as Python scripts in a Jupyter Book to facilitate…”
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MechElastic: A Python library for analysis of mechanical and elastic properties of bulk and 2D materials by Singh, Sobhit, Lang, Logan, Dovale-Farelo, Viviana, Herath, Uthpala, Tavadze, Pedram, Coudert, François-Xavier, Romero, Aldo H.

“…The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix (Cij…”
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scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data by Faure, Louis, Soldatov, Ruslan, Kharchenko, Peter V, Adameyko, Igor

“…Abstract Summary scFates provides an extensive toolset for the analysis of dynamic trajectories comprising tree learning, feature association testing, branch differential expression and with a…”
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pyIAST: Ideal adsorbed solution theory (IAST) Python package by Simon, Cory M., Smit, Berend, Haranczyk, Maciej

“… We present an open-source, user-friendly Python package, pyIAST, to perform IAST calculations for an arbitrary number of components…”
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PHOTONAI—A Python API for rapid machine learning model development by Leenings, Ramona, Winter, Nils Ralf, Plagwitz, Lucas, Holstein, Vincent, Ernsting, Jan, Sarink, Kelvin, Fisch, Lukas, Steenweg, Jakob, Kleine-Vennekate, Leon, Gebker, Julian, Emden, Daniel, Grotegerd, Dominik, Opel, Nils, Risse, Benjamin, Jiang, Xiaoyi, Dannlowski, Udo, Hahn, Tim

“…PHOTONAI is a high-level Python API designed to simplify and accelerate machine learning model development…”
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pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods by Behdenna, Abdelkader, Colange, Maximilien, Haziza, Julien, Gema, Aryo, Appé, Guillaume, Azencott, Chloé-Agathe, Nordor, Akpéli

“… Results In this technical note, we present a new Python implementation of ComBat and ComBat-Seq…”
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Is Multitask Deep Learning Practical for Pharma? by Ramsundar, Bharath, Liu, Bowen, Wu, Zhenqin, Verras, Andreas, Tudor, Matthew, Sheridan, Robert P, Pande, Vijay

“… Our implementation enables simple python scripts to construct, fit, and evaluate sophisticated deep models…”
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