An Online Tool for Correcting Performance Measures of Electronic Phenotyping Algorithms for Verification Bias by Ajay Bhasin, Sue Bielinski, Abel N. Kho, Nicholas Larson, Laura J. Rasmussen-Torvik

“…During phenotyping algorithm validation, standard classification performance measures (i.e., sensitivity, specificity, positive predictive value, negative predictive value, and accuracy) are often employed. …”
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Computable phenotypes to identify respiratory viral infections in the All of Us research program by Bennett J. Waxse, Fausto Andres Bustos Carrillo, Tam C. Tran, Huan Mo, Emily E. Ricotta, Joshua C. Denny

“…Using laboratory results as a reference standard, phenotypes using virus-specific ICD codes and medications had variable sensitivity (8–67%) but high positive predictive value (PPV, 90–97%) for most viruses, while influenza virus and SARS-CoV-2 phenotypes had lower PPV (69–70%) that improved with the inclusion of additional ICD codes. …”
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Employing Spectral Features to Accelerate Sorghum Phenotyping Against Sap‐Feeding Aphids by Kumar Shrestha, Kantilata Thapa, Esha Kaler, Misaki Taniguchi, Scott E. Sattler, James C. Schnable, Joe Louis

“…ABSTRACT Current efforts to detect and evaluate crop resistance to insect pests are limited by traditional phenotyping methods, which are time‐consuming and highly variable. …”
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Ectopic adipose tissue: association of obesity phenotypes with integral metabolic indices of obesity by V. I. Podzolkov, A. E. Bragina, Yu. N. Rodionova, K. K. Osadchiy, M. K. Vasilchenko, Zh. M. Sizova, E. V. Mospanova, N. S. Litvinenko, I. D. Muradova, D. V. Akvitskaya

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Hyperspectral imaging combined with machine learning for high‐throughput phenotyping in winter wheat by Sehijpreet Kaur, Vijaya Gopal Kakani, Brett Carver, Diego Jarquin, Aditya Singh

“…The study was conducted with 2145 genotypes of winter wheat, and UAV‐based hyperspectral measurements were used to predict the phenotype. Reflectance measurements were taken at narrow wavelength intervals, spanning 400–2500 nm. …”
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UAV-based aerial phenotyping to assess key morphophysiological traits and yield in soybean by Lalit Pun Magar, Jeremy Sandifer, Deepak Khatri, Sudip Poudel, Anuj Chiluwal

“…The pod development to full seed stages was the best time for aerial phenotyping. Overall, UAV-derived MS images combined with LASSO regression proved to be a practical and efficient approach for large-scale soybean phenotyping and yield monitoring. …”
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Features of Intracellular Matrix State during Development and Formation of COPD Clinical Phenotypes by T. V. Tayutina, S. V. Shlyk, D. A. Kudlay, S. V. Smerdin, L. A. Shovkun, E. A. Kizhevatova, N. Yu. Nikolenko, E. D. Kampos

“…In COPD patients with MMP-2 level of 214 ng/ml, the formation of bronchitis phenotype can be predicted, while with MMP-2 level of 214 ng/ml or more, the formation of emphysema phenotype can be predicted.…”
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Phenotypic and genotypic characterization of Mycobacterium tuberculosis pyrazinamide resistance—India, 2018–2020 by Sembulingam Tamilzhalagan, Evanslin Santus Justin, Ashok Selvaraj, Karthick Venkateswaran, Arun Kumar Sivakumar, Suganthi Chittibabu, Heather P. McLaughlin, Patrick K. Moonan, Jonathan P. Smith, Sakthi Suba, Mukesh Kumar Sathya Narayanan, Christine S. Ho, Nishant Kumar, Srikanth P. Tripathy, Srikanth P. Tripathy, Siva K. Shanmugam, Patricia J. Hall-Eidson, Uma Devi Ranganathan

“…Mutations distributed across pncA correlate to 94% of PZA resistance and were the predominant drivers of phenotypic resistance; evidence generated herein substantiates sequencing the entire gene and promoter for comprehensive genotypic-based prediction of PZA resistance. …”
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Frailty index, frailty phenotype and 6-year mortality trends in the FRASNET cohort by Sarah Damanti, Sarah Damanti, Rebecca De Lorenzo, Rebecca De Lorenzo, Lorena Citterio, Laura Zagato, Elena Brioni, Cristiano Magnaghi, Marco Simonini, Maria Pia Ruggiero, Simona Santoro, Eleonora Senini, Marco Messina, Francesca Farina, Costanza Festorazzi, Giordano Vitali, Paolo Manunta, Paolo Manunta, Angelo Andrea Manfredi, Chiara Lanzani, Chiara Lanzani, Patrizia Rovere-Querini, Patrizia Rovere-Querini

“…Frailty was measured with the Frailty Index (FI) and the Frailty Phenotype (FP). Concordance was assessed using Cohen’s Kappa coefficients. …”
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Relationship Between Sepsis Phenotypes and Treatment Characteristics of Patients with Viral and Bacterial Pneumonia by I. A. Ruslyakova, E. Z. Shamsutdinova, L. B. Gaikovaya

“…Differences in sepsis phenotype between patients with viral or bacterial SCAP may stratify patients for different therapeutic management and more accurately predict potential complications and unfavorable outcome.…”
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Multi-domain rule-based phenotyping algorithms enable improved GWAS signal by Abigail Newbury, Ahmed Elhussein, Gamze Gürsoy

“…Here, we assess the impact of various rule-based phenotyping algorithms on GWAS outcomes, examining factors such as power, heritability, replicability, functional annotations, and polygenic risk score prediction accuracy across seven diseases in the UK Biobank. …”
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Cell types or cell states? An investigation of adrenergic and mesenchymal cell phenotypes in neuroblastoma by Anuraag Bukkuri, Stina Andersson, Marina S. Mazariegos, Joel S. Brown, Emma U. Hammarlund, Sofie Mohlin

“…We develop evolutionary game theoretic models predicting how the populations would respond if ADRN and MES phenotypes (1) are distinct cell types or (2) represent dynamic cell states and fit these models to the experimental data. …”
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Leveraging neuroinformatics to understand cognitive phenotypes in elite athletes through systems neuroscience by Yubin Huang, Jun Liu, Qi Yu

“…The model features a specialized embedding mechanism for disentangling latent factors and a tailored optimization strategy incorporating domain-specific priors and regularization techniques.ResultsExperimental evaluations demonstrate LCEN's superiority in predicting and interpreting cognitive phenotypes across diverse datasets, providing deeper insights into the neural underpinnings of elite performance.DiscussionThis work bridges computational modeling, neuroscience, and psychology, contributing to the broader understanding of cognitive variability in specialized populations.…”
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Metabolic Phenotype and Adipose Tissue Inflammation in Patients with Chronic Obstructive Pulmonary Disease by Peter Skyba, Jozef Ukropec, Pavol Pobeha, Barbara Ukropcova, Pavol Joppa, Timea Kurdiova, Katarina Stroffekova, Miroslav Brusik, Iwar Klimes, Ivan Tkac, Daniela Gasperikova, Ruzena Tkacova

“…Adipose tissue CD68 and TNF-α expressions predicted insulin sensitivity independently of known confounders (P=.005; P=.025; R2=0.840). …”
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Ten simple rules for the sharing of bacterial genotype-Phenotype data on antimicrobial resistance. by Leonid Chindelevitch, Maarten van Dongen, Heather Graz, Antonio Pedrotta, Anita Suresh, Swapna Uplekar, Elita Jauneikaite, Nicole Wheeler

“…We therefore present our recommendations for the publication and sharing of genotype and phenotype data on AMR, in the form of 10 simple rules. …”
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Single cell kinetics of phenotypic switching in the arabinose utilization system of E. coli. by Georg Fritz, Judith A Megerle, Sonja A Westermayer, Delia Brick, Ralf Heermann, Kirsten Jung, Joachim O Rädler, Ulrich Gerland

“…Inducible switching between phenotypes is a common strategy of bacteria to adapt to fluctuating environments. …”
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The audiological phenotype of patients with a variant in MYH9 and MYH14 genes by Seong Hoon Bae, Sun Young Joo, Seung Hyeon Jang, Sung Huhn Kim, Jae Young Choi, Dongju Won, Heon Yung Gee, Jinsei Jung

“…One MYH14 case presented with congenital hearing loss linked to a nonsense variant (p.Q25*), expanding the phenotypic spectrum of MYH14-related hearing loss. Several novel variants were identified in both genes, all of which were extremely rare and predicted to be deleterious by in silico analyses. …”
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Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer by Hari Prasad, Harshavardhan BV, Ayalur Raghu Subbalakshmi, Susmita Mandal, Mohit Kumar Jolly, Sandhya S. Visweswariah

“…The model recapitulated NHE9-induced calcium signalling and the emergence of migratory phenotypes in colorectal cancer cells. Model predictions were compared with patient data and experimental results from RNA sequencing analysis of colorectal cancer cells with stable NHE9 expression. …”
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Evaluation of familial phenotype deviation to measure the impact of de novo mutations in autism by Soo-Whee Kim, Hyeji Lee, Da Yea Song, Gang-Hee Lee, Jae Hyun Han, Jee Won Lee, Hee Jung Byun, Ji Hyun Son, Ye Rim Kim, Yoojeong Lee, Eunjoon Kim, Donna M. Werling, So Hyun Kim, Stephan J. Sanders, Hee Jeong Yoo, Joon-Yong An

“…Abstract Background The phenotypic outcomes of de novo variants (DNVs) in autism spectrum disorder (ASD) exhibit wide variability. …”
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Phenotypic Trait Acquisition Method for Tomato Plants Based on RGB-D SLAM by Penggang Wang, Yuejun He, Jiguang Zhang, Jiandong Liu, Ran Chen, Xiang Zhuang

“…Traditional manual measurements of phenotypic traits are labor-intensive and inefficient. …”
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