Article
Multidisciplinary Sciences
Chih Chuan Shih, Jieqi Chen, Ai Shan Lee, Nicolas Bertin, Maxime Hebrard, Chiea Chuen Khor, Zheng Li, Joanna Hui Juan Tan, Wee Yang Meah, Su Qin Peh, Shi Qi Mok, Kar Seng Sim, Jianjun Liu, Ling Wang, Eleanor Wong, Jingmei Li, Aung Tin, Ching-Yu Cheng, Chew-Kiat Heng, Jian-Min Yuan, Woon-Puay Koh, Seang Mei Saw, Yechiel Friedlander, Xueling Sim, Jin Fang Chai, Yap Seng Chong, Sonia Davila, Liuh Ling Goh, Eng Sing Lee, Tien Yin Wong, Neerja Karnani, Khai Pang Leong, Khung Keong Yeo, John C. Chambers, Su Chi Lim, Rick Siow Mong Goh, Patrick Tan, Rajkumar Dorajoo
Summary: Genomic researchers are increasingly using commercial cloud service providers (CSPs) to manage data and analytics needs. However, without adequate security controls, the risk of unauthorized access to cloud-stored data may be higher. The Research Assets Provisioning and Tracking Online Repository (RAPTOR) by the Genome Institute of Singapore is a cloud-native genomics data repository and analytics platform that implements a five-safes framework to provide security and governance controls to data contributors and users, ensuring compliance with regulations.
Article
Multidisciplinary Sciences
Rui Marcalo, Sonya Neto, Miguel Pinheiro, Ana J. Rodrigues, Nuno Sousa, Manuel A. S. Santos, Paula Simao, Carla Valente, Lilia Andrade, Alda Marques, Gabriela R. Moura
Summary: This study reveals a high genetic heterogeneity for COVID-19 susceptibility and severity across global populations, and it suggests that the prognosis of patients with COPD is not related to genetic risk.
Article
Genetics & Heredity
Robin J. Hofmeister, Diogo M. Ribeiro, Simone Rubinacci, Olivier Delaneau
Summary: SHAPEIT5, a new phasing method, accurately processes large sequencing datasets and improves imputation accuracy by generating reference panels of haplotypes. The method was applied to UK Biobank data, which resulted in the identification of 549 genes with compound heterozygous loss-of-function events. The use of UK Biobank as a reference panel, coupled with SHAPEIT5 phasing, further enhances genotype imputation accuracy.
Article
Biochemical Research Methods
Kristiina Ausmees, Carl Nettelblad
Summary: The study investigates the benefits of an imputation method based on haplotype frequencies in ancient DNA analysis, showing improved accuracy and ability to capture rare variation at lower coverages. The software prophaser is optimized for parallel processing on GPUs, offering reasonable runtimes in experiments.
Editorial Material
Biochemistry & Molecular Biology
Maxwell A. Sherman
Summary: It is crucial for the biomedical community to protect the privacy of participants in genomic studies, and the accurate and efficient implementation of secure genotype imputation offers practical ways to safeguard sensitive genomic data for various bioinformatics applications.
Article
Computer Science, Artificial Intelligence
Ruiting Hao, Chengwei Weng, Xinyu Liu, Xiaorong Yang
Summary: In this paper, an iterative approach based on data augmentation method is proposed for estimating censored QRNN model. The proposed method outperforms existing ones in terms of quantile loss and prediction interval width, and can be easily adapted to different censoring types.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Computer Science, Artificial Intelligence
Ruiting Hao, Huanfeng Zheng, Xiaorong Yang
Summary: In this paper, an iterative estimation method based on the data augmentation algorithm is proposed for the censored Composite Quantile Regression Neural Network (CQRNN) model. Simulation studies and real data application show that the proposed method outperforms existing censored methods and produces results close to the uncensoring case.
APPLIED SOFT COMPUTING
(2022)
Article
Biochemistry & Molecular Biology
Zhichao Li, Xiaosen Jiang, Mingyan Fang, Yong Bai, Siyang Liu, Shujia Huang, Xin Jin
Summary: The Chinese Millionome Database (CMDB) is a database that contains low-coverage whole-genome sequencing (WGS) data from 141,431 unrelated healthy Chinese individuals, covering 9.04 million single nucleotide variants (SNV) with allele frequency information. The CMDB is the most representative and comprehensive Chinese population genome database to date, housing data from a multi-ethnic Chinese population with wide geographical distribution.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Agriculture, Multidisciplinary
Yifan Zhang, Peter J. Thorburn
Summary: Digital agriculture relies on accurate water quality data for efficient resource utilization. This paper proposes a Dual-SSIM model to impute missing time series data in sensor networks, improving the efficiency and reliability of digital agriculture applications. The model outperforms alternatives in water quality data imputation based on various evaluation metrics.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2021)
Article
Environmental Sciences
Alvaro Accion, Francisco Argueello, Dora B. Heras
Summary: A new data augmentation scheme using data imputation and matrix completion methods for segment-based classification has been proposed in this study, successfully increasing classification performance. Data imputation methods applied to multispectral imagery are shown to be a valid means of performing data augmentation, improving model generalization for high spectral resolution imagery.
Article
Multidisciplinary Sciences
Sho Hosoya, Sota Yoshikawa, Mana Sato, Kiyoshi Kikuchi
Summary: The study found that the prediction accuracy of genomic selection for standard length, body weight, and testes weight in tiger pufferfish was within an acceptable range when using 4000 or 1200 SNPs. However, predictive abilities decreased with less than 1200 SNPs due to reduced accuracy in estimating genetic relationships among individuals.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Tianyu Deng, Pengfei Zhang, Dorian Garrick, Huijiang Gao, Lixian Wang, Fuping Zhao
Summary: Genotype imputation is a crucial step prior to genome-wide association studies or genomic predictions, and its accuracy is influenced by several factors. This simulation-based study investigated the impact of factors such as target marker proportion, SNP density, genetic relationship, and imputation method. Results revealed that target marker proportion or SNP density had the greatest effect on imputation accuracy. Beagle5.1 outperformed Minimac4 in most cases, particularly when imputing from low-coverage whole-genome sequencing data. Overall, low-coverage whole-genome sequencing provided more accurate imputation compared to SNP chip data.
FRONTIERS IN GENETICS
(2022)
Article
Computer Science, Information Systems
Youmin Kim, A. F. M. Shahab Uddin, Sung-Ho Bae
Summary: The proposed method, Local Augment (LA), significantly changes the local bias property by selecting local patches in an image and applying different augmentation strategies to each patch. This approach results in more diverse augmented images, improving the network's generalizability and prediction accuracy. By collapsing the global structure of the object and creating locally diversified samples, LA helps the network learn the local bias property in a more generalized way, outperforming state-of-the-art data augmentation techniques on benchmark datasets like ImageNet and STL10.
Article
Multidisciplinary Sciences
Junhyeok An, Soojin Jang, Junehyoung Kwon, Kyohoon Jin, YoungBin Kim
Summary: In this paper, a novel image augmentation method is proposed that effectively utilizes object characteristics by mixing patches extracted from salient regions in a non-overlapping manner. The method is robust and outperforms other augmentation methods in terms of accuracy.
Article
Agriculture, Dairy & Animal Science
Maya Hiltpold, Fredi Janett, Xena Marie Mapel, Naveen Kumar Kadri, Zih-Hua Fang, Hermann Schwarzenbacher, Franz R. Seefried, Mirjam Spengeler, Ulrich Witschi, Hubert Pausch
Summary: In this study, 70,990 ejaculates from 1343 Brown Swiss bulls were examined, and it was found that two bulls produced semen with abnormally low quality, with one of them carrying a 1-bp deletion in the QRICH2 gene encoding sequence, resulting in low sperm concentration and immotile sperm with multiple morphological abnormalities. Genomic sequencing and transcriptome analysis confirmed the impact of this gene loss on sperm quality issues.
GENETICS SELECTION EVOLUTION
(2022)
Article
Genetics & Heredity
Dongyan Wu, Haitao Yang, Stacey J. Winham, Yanina Natanzon, Devin C. Koestler, Tiane Luo, Brooke L. Fridley, Ellen L. Goode, Yanbo Zhang, Yuehua Cui
JOURNAL OF HUMAN GENETICS
(2018)
Article
Multidisciplinary Sciences
Janelle R. NoeI-MacDonnell, Joseph Usset, Ellen L. Goode, Brooke L. Fridley
Article
Biochemical Research Methods
Qian Li, Janelle R. Noel-MacDonnell, Devin C. Koestler, Ellen L. Goode, Brooke L. Fridley
BMC BIOINFORMATICS
(2018)
Article
Genetics & Heredity
Lena Dolman, Angela Page, Lawrence Babb, Robert R. Freimuth, Harindra Arachchi, Chris Bizon, Matthew Brush, Marc Fiume, Melissa Haendel, David P. Hansen, Aleksandar Milosavljevic, Ronak Y. Patel, Piotr Pawliczek, Andrew D. Yates, Heidi L. Rehm
Article
Genetics & Heredity
Piotr Pawliczek, Ronak Y. Patel, Lillian R. Ashmore, Andrew R. Jackson, Chris Bizon, Tristan Nelson, Bradford Powell, Robert R. Freimuth, Natasha Strande, Neethu Shah, Sameer Paithankar, Matt W. Wright, Selina Dwight, Jimmy Zhen, Melissa Landrum, Peter McGarvey, Larry Babb, Sharon E. Plon, Aleksandar Milosavljevic
Article
Medicine, General & Internal
Iftikhar J. Kullo, Janet Olson, Xiao Fan, Merin Jose, Maya Safarova, Carmen Radecki Breitkopf, Erin Winkler, David C. Kochan, Sara Snipes, Joel E. Pacyna, Meaghan Carney, Christopher G. Chute, Jyoti Gupta, Sheethal Jose, Eric Venner, Mullai Murugan, Yunyun Jiang, Magdi Zordok, Medhat Farwati, Maraisha Philogene, Erica Smith, Gabriel Q. Shaibi, Pedro Caraballo, Robert Freimuth, Noralane M. Lindor, Richard Sharp, Stephen N. Thibodeau
MAYO CLINIC PROCEEDINGS
(2018)
Article
Multidisciplinary Sciences
Farnoosh Abbas-Aghababazadeh, Qian Li, Brooke L. Fridley
Article
Multidisciplinary Sciences
Farnoosh Abbas-Aghababazadeh, Pengcheng Lu, Brooke L. Fridley
SCIENTIFIC REPORTS
(2019)
Article
Biochemical Research Methods
Oscar E. Ospina, Christopher M. Wilson, Alex C. Soupir, Anders Berglund, Inna Smalley, Kenneth Y. Tsai, Brooke L. Fridley
Summary: Spatially resolved transcriptomics has the potential to enhance our understanding of the tumor microenvironment and improve cancer prognosis and therapies. This article introduces spatialGE, a software that offers visualizations and quantification of tumor microenvironment heterogeneity through gene expression surfaces, spatial heterogeneity statistics, spot-level cell deconvolution, and spatially informed clustering.
Article
Health Care Sciences & Services
Joseph Ross Mitchell, Phillip Szepietowski, Rachel Howard, Phillip Reisman, Jennie D. Jones, Patricia Lewis, Brooke L. Fridley, Dana E. Rollison
Summary: This study developed a BERT-based NLP system to automatically extract detailed tumor site and histology information from oncological pathology reports. The system outperformed existing algorithms in predicting ICD-O-3 codes, which could improve cancer treatment outcomes.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Xiang Liu, Bo Zhao, Timothy Shaw, Brooke L. Fridley, Derek R. Duckett, Aik Choon Tan, Mingxiang Teng
Summary: This study proposes a novel computational method for identifying differential SEs by considering the activities and positions of constituent enhancers. This method not only takes into account the overall activity changes, but also discovers four new classes of differential SEs with distinct enhancer structural alterations. Compared to existing methods, this approach shows improved identification of differential SEs and better discernment of cell-type-specific SE activity and functional interpretation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Yiqing Zhao, Matthew Brush, Chen Wang, Alex H. Wagner, Hongfang Liu, Robert R. Freimuth
Summary: In this study, a drug response phenotype terminology was proposed to represent the relationships between genetic variants and treatments. The terminology was able to cover 96% of drug response phenotypes in genetic reports. By re-analyzing genetic report context and enriching the previous pharmacogenomics knowledge model, relationships between genetic variants and treatments were revealed.
Article
Oncology
Cassandra A. Hathaway, Tianyi Wang, Mary K. Townsend, Christine Vinci, Danielle E. Jake-Schoffman, Daryoush Saeed-Vafa, Carlos Moran Segura, Jonathan V. Nguyen, Jose R. Conejo-Garcia, Brooke L. Fridley, Shelley S. Tworoger
Summary: This study found that early exposure to cigarette smoke may have a slight impact on the risk of developing ovarian cancer, as well as the systemic immunity and tumor immune response. However, no research has been conducted to evaluate the effects of cigarette smoke exposure on the ovarian tumor immune microenvironment.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2023)
Article
Oncology
Cassandra A. Hathaway, Jose R. Conejo-Garcia, Brooke L. Fridley, Bernard Rosner, Daryoush Saeed-Vafa, Carlos Moran Segura, Jonathan V. Nguyen, Jonathan L. Hecht, Naoko Sasamoto, Kathryn L. Terry, Shelley S. Tworoger, Mary K. Townsend
Summary: This study used multiplex immunofluorescence to measure immune markers in ovarian tumors and found high correlations between markers within the tumors. However, very old samples may have reduced antigenicity. These findings are important for studying immune infiltration in ovarian tumors.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2023)
Article
Pharmacology & Pharmacy
Nathan D. Seligson, Jill M. Kolesar, Benish Alam, Laura Baker, Jatinder K. Lamba, Brooke L. Fridley, Ameen A. Salahudeen, Daniel L. Hertz, J. Kevin Hicks
Summary: Precision medicine has greatly improved the clinical care for cancer patients by developing targeted therapies, identifying inherited cancer predisposition syndromes, and optimizing pharmacotherapy through pharmacogenetics. It is argued that integrating pharmacogenomics into paired germline/somatic genomic testing would be an efficient method for increasing access to pharmacogenomic testing.