Article
Biochemical Research Methods
Ahmed A. Metwally, Tom Zhang, Si Wu, Ryan Kellogg, Wenyu Zhou, Kevin Contrepois, Hua Tang, Michael Snyder
Summary: This study developed a statistical method called OmicsLonDA that robustly identifies time intervals of temporal omics biomarkers. The method uses a semi-parametric approach to model longitudinal data and infer significant time intervals based on an empirical distribution. Through testing on simulated datasets and real datasets, the method demonstrated high accuracy and sensitivity.
Article
Biotechnology & Applied Microbiology
Chan Wang, Jiyuan Hu, Martin J. Blaser, Huilin Li
Summary: In this study, a microbial trend analysis (MTA) framework was proposed for high-dimensional and phylogenetically-based longitudinal microbiome data. MTA can capture common microbial dynamic trends at the community level, examine differences in microbial dynamic trends between groups, and classify individual subjects based on their longitudinal microbial profiles. The study showed that the MTA framework is robust and effective in hypothesis testing, taxon identification, and subject classification.
Review
Biochemistry & Molecular Biology
Robert Gurke, Annika Bendes, John Bowes, Michaela Koehm, Richard M. Twyman, Anne Barton, Dirk Elewaut, Carl Goodyear, Lisa Hahnefeld, Rainer Hillenbrand, Ewan Hunter, Mark Ibberson, Vassilios Ioannidis, Sabine Kugler, Rik J. Lories, Eduard Resch, Stefan Rueping, Klaus Scholich, Jochen M. Schwenk, James C. Waddington, Phil Whitfield, Gerd Geisslinger, Oliver FitzGerald, Frank Behrens, Stephen R. Pennington
Summary: The definitive diagnosis and early treatment of immune-mediated inflammatory diseases (IMIDs) are challenging due to variable clinical manifestations. Psoriatic arthritis (PsA) is an example of such a disease. The detection of molecular biomarkers offers hope for the early diagnosis and treatment of PsA, but specific biomarkers are not yet available. By analyzing multi-omics data and integrating them with clinical assessment, it is possible to develop molecular profiles that improve the diagnosis and treatment outcomes of PsA patients.
Article
Public, Environmental & Occupational Health
Lori Post, Michael J. Boctor, Tariq Z. Issa, Charles B. Moss, Robert Leo Murphy, Chad J. Achenbach, Michael G. Ison, Danielle Resnick, Lauren Singh, Janine White, Sarah B. Welch, James F. Oehmke
Summary: The global COVID-19 pandemic has disrupted structures and communities worldwide, with varying responses across different regions. Advanced surveillance metrics are needed to help governments understand effective responses and monitor outbreaks. Canada has shown success in COVID-19 control but faces challenges in different provinces and territories, highlighting the importance of enhanced surveillance for proactive health policies.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2021)
Article
Public, Environmental & Occupational Health
Lori Post, Ramael O. Ohiomoba, Ashley Maras, Sean J. Watts, Charles B. Moss, Robert Leo Murphy, Michael G. Ison, Chad J. Achenbach, Danielle Resnick, Lauren Nadya Singh, Janine White, Azraa S. Chaudhury, Michael J. Boctor, Sarah B. Welch, James Francis Oehmke
Summary: The study aimed to provide additional surveillance metrics for tracking COVID-19 transmission more accurately in Latin America and the Caribbean. Results showed a reduction in speed, acceleration, and jerk in certain countries, but some still had high acceleration and jerk values, indicating potential concerns for the region.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2021)
Article
Medicine, Research & Experimental
Viola Melone, Annamaria Salvati, Domenico Palumbo, Giorgio Giurato, Giovanni Nassa, Francesca Rizzo, Luigi Palo, Alessandro Giordano, Mariarosaria Incoronato, Mario Vitale, Caterina Mian, Immacolata Di Biase, Stefano Cristiano, Viviana Narciso, Monica Cantile, Annabella Di Mauro, Fabiana Tatangelo, Salvatore Tafuto, Roberta Modica, Claudia Pivonello, Marco Salvatore, Annamaria Colao, Alessandro Weisz, Roberta Tarallo
Summary: By using a multi-omics approach, this study reveals the important role of ATM-dependent signaling in gastroenteropancreatic neuroendocrine tumors and medullary thyroid carcinomas. It also identifies a set of circulating miRNAs that could be potential diagnostic and prognostic biomarkers.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Health Care Sciences & Services
Lori Post, Emily Marogi, Charles B. Moss, Robert Leo Murphy, Michael G. Ison, Chad J. Achenbach, Danielle Resnick, Lauren Singh, Janine White, Michael J. Boctor, Sarah B. Welch, James Francis Oehmke
Summary: The COVID-19 pandemic has significantly impacted the Middle East and North Africa region, with factors such as falling oil prices, wealth disparities, and large refugee populations exacerbating the disease burden. This study aims to provide advanced surveillance metrics for COVID-19 transmission and found that countries with the highest cumulative caseload include Iran, Iraq, Saudi Arabia, and Israel. Dynamic public health surveillance metrics can offer valuable insights for informing policies and control efforts until an effective vaccine is developed.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2021)
Article
Health Care Sciences & Services
Lori Ann Post, Elana T. Benishay, Charles B. Moss, Robert Leo Murphy, Chad J. Achenbach, Michael G. Ison, Danielle Resnick, Lauren Nadya Singh, Janine White, Azraa S. Chaudhury, Michael J. Boctor, Sarah B. Welch, James Francis Oehmke
Summary: This study aims to provide enhanced surveillance metrics for SARS-CoV-2 transmission to better understand the risk of explosive growth in each country and identify which countries are managing the pandemic successfully. Using longitudinal trend analysis, the study tracked COVID-19 transmission rates in Central Asia, revealing increasing infection rates and a negative trend primarily due to minimal restrictions in Russia.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Peng Gao, Xiaotao Shen, Xinyue Zhang, Chao Jiang, Sai Zhang, Xin Zhou, Sophia Miryam Schussler-Fiorenza Rose, Michael Snyder
Summary: This study integrated personal exposome and internal multi-omics data to investigate the impact of exposome on individual's phenome. The results showed significant correlations between personal exposome and internal biomolecules related to immune system, kidney, and liver, highlighting the importance of studying precision health.
Article
Microbiology
Shi Huang, Tao He, Feng Yue, Xiujun Xu, Lijiang Wang, Pengfei Zhu, Fei Teng, Zheng Sun, Xiaohui Liu, Gongchao Jing, Xiaoquan Su, Lijian Jin, Jiquan Liu, Jian Xu
Summary: The research identified periodontitis-like microbiome dysbiosis in an asymptomatic suboptimal health (SoH) stage as early as 24 to 72 h after oral-hygiene pause. The SoH stage features a swift, full activation of multiple salivary cytokines but a steep synergetic decrease of plaque-derived betaine and Rothia spp. The microbial ecology during early gingivitis is highly similar to that in periodontitis under both taxonomical and functional contexts. Unexpectedly, exposures to gingivitis can accelerate over 10-fold the normal rate of oral microbiota aging.
Article
Health Care Sciences & Services
Lori Ann Post, Jasmine S. Lin, Charles B. Moss, Robert Leo Murphy, Michael G. Ison, Chad J. Achenbach, Danielle Resnick, Lauren Nadya Singh, Janine White, Michael J. Boctor, Sarah B. Welch, James Francis Oehmke
Summary: The COVID-19 pandemic has had a significant impact globally, with some countries in East Asia and the Pacific effectively controlling the virus while others still struggle. The study aims to provide advanced surveillance metrics to understand the risk of explosive growth in certain countries and those managing the pandemic successfully.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2021)
Article
Engineering, Civil
K. Raczynski, J. Dyer
Summary: Droughts often exhibit clear temporal patterns, especially in regions with defined wet or dry seasons. Recognizing and quantifying these patterns is crucial for diagnosing current and future drought probabilities, particularly in the context of climate change.
JOURNAL OF HYDROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Antoine Bodein, Marie-Pier Scott-Boyer, Olivier Perin, Kim-Anh Le Cao, Arnaud Droit
Summary: Multi-omics integration is crucial for understanding complex biological processes, but the challenge lies in interpretation. A generic approach is proposed to build hybrid multi-omics networks for predicting regulatory mechanisms and functional modules.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Environmental Sciences
Tagele Mossie Aschale, David J. Peres, Aurora Gullotta, Guido Sciuto, Antonino Cancelliere
Summary: Investigating the trends and sensitivity of reference evapotranspiration (ETo) to meteorological variables is important for water resource management and climate variability analysis. This study analyzed a 17-year dataset from a Mediterranean climate region and found a downward trend in ETo in November, as well as downward trends in solar radiation and rainfall during autumn. Other meteorological variables showed an upward trend, with specific humidity and wind speed having the highest and lowest contribution to ETo trends, respectively.
Article
Environmental Sciences
Shahfahad, Mohd Waseem Naikoo, Swapan Talukdar, Tanmoy Das, Atiqur Rahman
Summary: This study examines the trend and pattern of rainfall in Mumbai city using rainfall regionalization approach. The results show that Mumbai has two homogeneous rainfall regions with distinctive rainfall patterns. The rainfall trend is positive but not monotonic. This study may contribute to the management of water resources and urban flood mitigation in Mumbai city.
Review
Genetics & Heredity
Eren M. Veziroglu, George I. Mias
FRONTIERS IN GENETICS
(2020)
Article
Computer Science, Interdisciplinary Applications
C. Glosser, E. Lu, T. J. Bertus, C. Piermarocchi, B. Shanker
Summary: The integral-equation-based framework for solving Maxwell-Bloch systems effectively captures collective features of quantum dots, demonstrating convergence and accuracy in analyzing large ensembles of interacting quantum dots.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
George Mias, Vikas Vikram Singh, Lavida R. K. Rogers, Shuyue Xue, Minzhang Zheng, Sergii Domanskyi, Masamitsu Kanada, Carlo Piermarocchi, Jin He
Summary: Saliva omics has potential for non-invasive diagnostics and immune response monitoring. Multiple omics from saliva samples can reveal immune activation following vaccination, with mRNA results showing specificity and sensitivity to vaccination timeline compared to other omics.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Sergii Domanskyi, Alex Hakansson, Thomas Bertus, Giovanni Paternostro, Carlo Piermarocchi
Summary: This study introduces new methods for automatic cell type identification, cell anomaly quantification, and cell phenotypic landscape visualization. These methods are integrated into a software platform providing a comprehensive toolkit for scRNA-seq data analysis.
Article
Multidisciplinary Sciences
Minzhang Zheng, Sergii Domanskyi, Carlo Piermarocchi, George Mias
Summary: This paper introduces a visibility-graph-based method for building networks from time series data and detecting temporal communities within these networks. The Weighted Dual-Perspective Visibility Graph is proposed to handle unevenly sampled time series typical of biological experiments, capturing events associated with peaks and troughs. By identifying high-intensity nodes as the main stem and aggregating nodes based on proximity to this stem, temporal communities in individual signals can be effectively detected.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Yuen Gao, Natalia Duque-Wilckens, Mohammad B. Aljazi, Yan Wu, Adam J. Moeser, George I. Mias, Alfred J. Robison, Jin He
Summary: The study shows that loss of ASH1L gene in developing mouse brain can cause multiple developmental defects, core autistic-like behaviors, and impaired cognitive memory. Gene expression analyses uncover critical roles of ASH1L in regulating gene expression during neural cell development.
COMMUNICATIONS BIOLOGY
(2021)
Article
Medicine, Research & Experimental
Pin Li, Qin Li, Nilima Biswas, Hong Xin, Tanja Diemer, Lixian Liu, Lorena Perez Gutierrez, Giovanni Paternostro, Carlo Piermarocchi, Sergii Domanskyi, Ruikang K. Wang, Napoleone Ferrara
Summary: The study identified LIF as a potential therapeutic approach to prevent atrophy associated with AMD by protecting the choroid, highlighting its dual role as a mitogen for specific endothelial cells while inhibiting growth in others.
EMBO MOLECULAR MEDICINE
(2022)
Article
Oncology
Mohammad B. Aljazi, Yuen Gao, Yan Wu, George Mias, Jin He
Summary: The study reveals the critical role of ASH1L in promoting MLL-AF9-induced leukemogenesis, showing that its loss impairs the maintenance and progression of leukemia cells. The enzymatic activity of ASH1L is necessary for promoting MLL-AF9-induced leukemic transformation.
FRONTIERS IN ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Yuen Gao, Natalia Duque-Wilckens, Mohammad B. Aljazi, Adam J. Moeser, George I. Mias, Alfred J. Robison, Yi Zhang, Jin He
Summary: Recent clinical studies have shown that chromosomal 12q24.31 microdeletions are associated with autism spectrum disorder (ASD) and intellectual disability (ID). This study reveals that the gene Kdm2b, located in the chromosomal region 12q24.31, plays a critical role in maintaining neural stem cells in the mouse brain. Additionally, the Kdm2b mutation is found to induce ASD/ID-like behavioral and memory deficits.
Article
Multidisciplinary Sciences
Minzhang Zheng, Carlo Piermarocchi, George Mias
Summary: Longitudinal deep multiomics profiling holds great promise for precision health, but integrating and understanding the complexity of such data remains a challenge. In this study, an individual-focused approach was used to assess single individuals' multiomics time series and group multiple individuals based on similarity of their longitudinal deep multiomics profiles. The analysis of type 2 diabetes mellitus profiles identified individual-level immune responses and clusters of individuals with similar immune behaviors that were associated with their diabetic status.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Xing Yi Woo, Anuj Srivastava, Philip C. Mack, Joel H. Graber, Brian J. Sanderson, Michael W. Lloyd, Mandy Chen, Sergii Domanskyi, Regina Gandour-Edwards, Rebekah A. Tsai, James Keck, Mingshan Cheng, Margaret Bundy, Emily L. Jocoy, Jonathan W. Riess, William Holland, Stephen C. Grubb, James G. Peterson, Grace A. Stafford, Carolyn Paisie, Steven B. Neuhauser, R. Krishna Murthy Karuturi, Joshy George, Allen K. Simons, Margaret Chavaree, Clifford G. Tepper, Neal Goodwin, Susan D. Airhart, Primo N. Lara, Thomas H. Openshaw, Edison T. Liu, David R. Gandara, Carol J. Bult
Summary: Patient-derived xenograft models are important preclinical platforms for testing cancer therapeutics. This study describes a repository of genetically and clinically annotated lung cancer PDX models, which have been extensively characterized for histopathologic features, mutational profiles, gene expression, and copy-number aberrations. The genomic profiles of the PDX models are consistent with patient tumors, and these models serve as valuable platforms for translational cancer research.
Article
Genetics & Heredity
Shuyue Xue, Lavida R. K. Rogers, Minzhang Zheng, Jin He, Carlo Piermarocchi, George I. Mias
Summary: Differential network (DN) analysis was applied to RNA-sequencing (RNA-seq) time series datasets to investigate gene expression changes in human saliva and B cells treated with a monoclonal antibody drug. The DN method identified the activation of relevant biological pathways and revealed collective temporal behavior of gene clusters. Early and delayed responses were observed in the saliva dataset, while three temporal patterns were identified in the B cell data.
FRONTIERS IN GENETICS
(2022)
Article
Physiology
Minzhang Zheng, Jacqueline Charvat, Sara R. Zwart, Satish K. Mehta, Brian E. Crucian, Scott M. Smith, Jin He, Carlo Piermarocchi, George I. Mias
Summary: From early spaceflight to current missions, astronauts face multiple hazards that impact their health, including low gravity, high radiation, isolation, closed environment, and distance from Earth. This study provides a time-resolved assessment of the physiological impact of spaceflight on astronauts, revealing associations with bone resorption, kidney function, and immune system dysregulation.
FRONTIERS IN PHYSIOLOGY
(2023)
