Article
Biochemistry & Molecular Biology
Wenyue Huang, Xiaona Hu, Yanlin Ren, Minggui Song, Chuang Ma, Zhenyan Miao
Summary: The advent of high-throughput sequencing technologies has led to the production of a significant amount of omics data in plants. However, the lack of comprehensive platforms providing evolutionary annotation information and multi-species multi-omics data has hindered systematic and efficient analysis on specific genes. In order to address this issue, an advanced plant multi-omics platform, IPOP, has been established, which collects and analyzes various types of data and provides tools to facilitate evolutionary and functional analysis. This platform offers valuable insights and data for cross-species comparison and evolutionary research in the plant sciences community.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Yong Wang, Jialei Ji, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Honghao Lv
Summary: The Brassica oleracea Genome Database (BoGDB) is a platform that integrates multi-omics data for comprehensive research on B. oleracea.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Aleksandr Ianevski, Ronja M. Simonsen, Vegard Myhre, Tanel Tenson, Valentyn Oksenych, Magnar Bjoras, Denis E. Kainov
Summary: Viruses can cause outbreaks in humans and have economic and health burdens. Broad-spectrum antivirals (BSAs) and BSA-containing drug combinations (BCCs) are immediate therapeutic options for virus identification and vaccine development. DrugVirus.info 2.0 provides an integrative portal for exploration and analysis of BSAs and BCCs, expanding the database and functionality for antiviral drug development.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Qian Liu, Pingzhao Hu
Summary: In precise medicine, computational frameworks for identifying prognostic biomarkers that capture the multi-genomic and phenotypic heterogeneity of breast cancer (BC) are of great value. However, previous radiogenomic studies have suffered from data incompleteness, feature subjectivity, and low interpretability. This study proposed a novel framework for identifying radiogenomic prognostic biomarkers for BC, addressing the limitations of previous studies. The framework includes an explainable DL model for image feature extraction, a Bayesian tensor factorization for multi-genomic feature extraction, a strategy to leverage unpaired data, and mediation analysis for further interpretation. The biomarkers identified by this framework outperformed traditional baseline radiogenomic biomarkers and had guaranteed interpretability through built-in and follow-up analyses.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
Licai Huang, James P. Long, Ehsan Irajizad, James D. Doecke, Kim-Anh Do, Min Jin Ha
Summary: This study introduces a mediation analysis framework for multilevel molecular tumor profiling, which can handle various types of outcome variables and is suitable for high-throughput molecular profiling data. By analyzing kidney renal clear cell carcinoma proteogenomic data, genes that are mediated by proteins and the underlying mechanisms for various survival outcomes are identified, capturing disease-specific clinical characteristics in both short and long-term.
Review
Genetics & Heredity
Emily Swanzey, Callan O'Connor, Laura G. Reinholdt
Summary: Utilizing genetically diverse mouse cell populations for in vitro research can uncover basic properties of cellular function and identity, providing opportunities for disease modeling and validation. The genetic resolution and functional characterization provided by these panels allow for a better understanding of the impact of genetic variation on signaling networks and phenotypic diversity.
TRENDS IN GENETICS
(2021)
Review
Health Care Sciences & Services
Christen A. Khella, Gaurav A. Mehta, Rushabh N. Mehta, Michael L. Gatza
Summary: The molecular heterogeneity of cancer leads to varied disease progression and clinical outcomes. Advances in high-throughput proteogenomic profiling have identified new oncogenic drivers and biomarkers for predicting drug sensitivity, contributing to the development of more effective treatment strategies.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Immunology
Jianxin Li, Ting Han, Xin Wang, Yinchun Wang, Xuan Chen, Wangsheng Chen, Qingqiang Yang
Summary: This study developed a prognostic signature based on lymph node ratio (LNR) to predict the prognosis of patients with gastric cancer (GC) and facilitate the development of individualized treatment strategy.
JOURNAL OF IMMUNOLOGY RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xinbin Dai, Zhaohong Zhuang, Clarissa Boschiero, Yibo Dong, Patrick X. Zhao
Summary: Legumes have been contributing to human health and sustainable food production for centuries. The study of model legumes is important for deciphering key genes and pathways. The LegumeIP V3 database provides valuable data and tools for identifying important genes in non-model legume crops.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
James T. Robinson, Helga Thorvaldsdottir, Douglass Turner, Jill P. Mesirov
Summary: igv.js is a JavaScript implementation of the Integrative Genomics Viewer (IGV) that can be easily embedded into any web page with a single line of code and does not have any external dependencies. The viewer runs entirely in the web browser without the need for a backend server or data pre-processing.
Article
Biochemical Research Methods
Nathaniel Kwok, Zita Aretz, Sumiko Takao, Zheng Ser, Paolo Cifani, Alex Kentsis
Summary: Recent advances in nucleic acid sequencing and mass spectrometry proteomics have enabled genome-scale analysis of genetic variation and transcription as well as whole proteome-scale studies of protein expression. However, most proteomic studies are limited to canonical protein sequences. Here, we develop ProteomeGenerator2 (PG2), which integrates genome and transcriptome sequencing to incorporate protein variants and other non-canonical features caused by genomic and transcriptomic variation. PG2 has been benchmarked using synthetic data and analysis of human leukemia cells and can be used with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms. It is open-source and available at https://github.com/kentsisresearchgroup/ProteomeGenerator2.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Biochemical Research Methods
Mattia Forcato, Oriana Romano, Silvio Bicciato
Summary: Recent advances in single-cell technologies are providing exciting opportunities for dissecting tissue heterogeneity and investigating cell identity, fate and function. However, combining different single-cell genomic signals is computationally challenging and requires integrative analysis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Francois Rousset, Florence Depardieu, Solange Miele, Julien Dowding, Anne-Laure Laval, Erica Lieberman, Daniel Garry, Eduardo P. C. Rocha, Aude Bernheim, David Bikard
Summary: Bacteria have various genetic systems to defend against viral infection, including those within prophages. Phage satellites pose additional pressures on phages by hijacking viral elements. This study found that E. coli P2-like phages and their P4-like satellites carry genetic hotspots with anti-phage systems. These hotspots participate in inter-viral competition and shape dynamics between the bacterial host, P2-like phages, and P4-like satellites. Importantly, the anti-phage activity of satellites can benefit the helper phage during competition, turning a parasitic relationship into a mutualistic one.
CELL HOST & MICROBE
(2022)
Article
Genetics & Heredity
Edwin S. Iversen, Gary Lipton, Steven N. Hart, Kun Y. Lee, Chunling Hu, Eric C. Polley, Tina Pesaran, Amal Yussuf, Holly LaDuca, Elizabeth Chao, Rachid Karam, David E. Goldgar, Fergus J. Couch, Alvaro N. A. Monteiro
Summary: Loss-of-function variants in BRCA1 and BRCA2 genes increase the risk of breast and ovarian cancer. VarCall XT, a multifactorial approach, allows for the classification of these variants using multiple forms of genetic evidence, leading to more accurate assessment of cancer risk for patients.
NPJ GENOMIC MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Hatairat Yingtaweesittikul, Jiaxi Wu, Aanchal Mongia, Rafael Peres, Karrie Ko, Niranjan Nagarajan, Chayaporn Suphavilai
Summary: The development of CREAMMIST, an integrative database for cancer drug response, allows researchers to capture uncertainty and utilize available data for downstream analyses, providing valuable insights for cancer pharmacogenomics research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xiao Han, Yang Yang, Sujuan Liu, Yanmei Niu, Heng Shao, Li Fu
Summary: Skeletal muscle insulin resistance is closely linked to hyperglycemia and metabolic disorders. Regular exercise can enhance insulin sensitivity in skeletal muscle, and this study aimed to explore the underlying mechanisms. The results showed that SESN3 plays a crucial role in amplifying the beneficial effects of exercise on insulin sensitivity in skeletal muscle and systemic glucose levels. The SESN3/mTORC2/AKT pathway mediated the effects of exercise on skeletal muscle insulin sensitivity.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2023)
Review
Cell Biology
Baoxu Pang, Jan H. van Weerd, Feija L. Hamoen, Michael P. Snyder
Summary: Cell type- and differentiation-specific gene expression is controlled by genomic non-coding regulatory elements (NCREs), including promoters, enhancers, silencers, and insulators. Recent studies have focused on identifying and characterizing silencers, which repress gene transcription, and have highlighted their importance in homeostasis and disease. Understanding silencers has potential implications for genome research and therapeutic applications.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Endocrinology & Metabolism
Claudia H. T. Tam, Cadmon K. P. Lim, Andrea O. Y. Luk, Mai Shi, Hoi Man Cheung, Alex C. W. Ng, Heung-man Lee, Eric S. H. Lau, Baoqi Fan, Guozhi Jiang, Alice P. S. Kong, Risa Ozaki, Elaine Y. K. Chow, Ka Fai Lee, Shing Chung Siu, Grace Hui, Chiu Chi Tsang, Kam Piu Lau, Jenny Y. Y. Leung, Elaine Y. N. Cheung, Man Wo Tsang, Grace Kam, Ip Tim Lau, June K. Y. Li, Vincent T. F. Yeung, Emmy Lau, Stanley Lo, Samuel Fung, Yuk Lun Cheng, Chun Chung Chow, Xiaodan Fan, Ting Fung Chan, Kevin Y. L. Yip, Si Lok, Weichuan Yu, Stephen K. W. Tsui, Hui-Yao Lan, Cheuk Chun Szeto, Nelson L. S. Tang, Brian Tomlinson, Yu Huang, Alicia J. Jenkins, Anthony Keech, Wing-Yee So, Juliana C. N. Chan, Ronald C. W. Ma
Summary: The objective of this study was to uncover genetic determinants of coronary heart disease (CHD) in type 2 diabetes (T2D) and explore their applications. The study identified a novel variant associated with CHD and blood pressure (BP) in Chinese T2D patients, and found that this variant interacts with BP goal attainment to have divergent effects on CHD risk.
Article
Gastroenterology & Hepatology
Zhewen Xiong, Stephen Lam Chan, Jingying Zhou, Joaquim S. L. Vong, Tsz Tung Kwong, Xuezhen Zeng, Haoran Wu, Jianquan Cao, Yalin Tu, Yu Feng, Weiqin Yang, Patrick Pak-Chun Wong, Willis Wai-Yiu Si-Tou, Xiaoyu Liu, Jing Wang, Wenshu Tang, Zhixian Liang, Jiahuan Lu, Ka Man Li, Jie-Ting Low, Michael Wing-Yan Chan, Howard H. W. Leung, Anthony W. H. Chan, Ka-Fai To, Kevin Yuk-Lap Yip, Yuk Ming Dennis Lo, Joseph Jao-Yiu Sung, Alfred Sze-Lok Cheng
Summary: This study investigates the mechanisms by which tumor cells evade immune-checkpoint targeting through the activation of the PPAR gamma/VEGF-A signaling pathway, providing a strategy to counteract immunotherapeutic resistance in hepatocellular carcinoma (HCC).
Article
Oncology
Jiapei Yuan, Yang Tong, Xiaochuan Liu, Mulin Jun Li, Qiang Zhang, Yang Yang
Summary: The researchers built a versatile data portal, eaQTLdb, to explore the effects of genetic variants on enhancer activity in different cancer types. They systematically identified genetic variants, known as eaQTLs, that influence enhancer activity and linked them to cancer hallmarks and patients' overall survival. They also identified eaQTLs associated with the infiltration abundance of different immune cell types and examined their colocalization with diseases/traits GWAS signals.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Review
Biochemical Research Methods
Mohan Babu, Michael Snyder
Summary: The rise in chronic diseases has led to a cross-disciplinary approach in understanding and treating disease. Current medical care focuses on treating patients rather than preventing illness, resulting in high costs. The advancement of omics technologies and computational capabilities has allowed for precision health approaches. This review discusses the applications and challenges of multi-omics in precision health.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Item Withdrawal
Biochemical Research Methods
Rachel Marty Pyke, Dattatreya Mellacheruvu, Steven Dea, Charles W. Abbott, Simo Zhang, Nick A. Phillips, Jason Harris, Gabor Bartha, Sejal Desai, Rena McClory, John West, Michael P. Snyder, Richard Chen, Sean Michael Boyle
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Biochemical Research Methods
Rachel Marty Pyke, Datta Mellacheruvu, Steven Dea, Charles Abbott, Simo V. Zhang, Nick A. Phillips, Jason Harris, Gabor Bartha, Sejal Desai, Rena McClory, John West, Michael P. Snyder, Richard Chen, Sean Michael Boyle
Summary: The study improves the accuracy of predicting tumor-specific antigen presentation by generating immunopeptidomics data and creating the SHERPA algorithm, which has potential for important clinical applications.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Multidisciplinary Sciences
Camilo A. Espinosa, Waqasuddin Khan, Rasheda Khanam, Sayan Das, Javairia Khalid, Jesmin Pervin, Margaret P. Kasaro, Kevin Contrepois, Alan L. Chang, Thanaphong Phongpreecha, Basil Michael, Mathew Ellenberger, Usma Mehmood, Aneeta Hotwani, Ambreen Nizar, Furqan Kabir, Ronald J. Wong, Martin Becker, Eloise Berson, Anthony Culos, Davide De Francesco, Samson Mataraso, Neal Ravindra, Melan Thuraiappah, Maria Xenochristou, Ina A. Stelzer, Ivana Maric, Arup Dutta, Rubhana Raqib, Salahuddin Ahmed, Sayedur Rahman, A. S. M. Tarik Hasan, Said M. Ali, Mohamed H. Juma, Monjur Rahman, Shaki Aktar, Saikat Deb, Joan T. Price, Paul H. Wise, Virginia D. Winn, Maurice L. Druzin, Ronald S. Gibbs, Gary L. Darmstadt, Jeffrey C. Murray, Jeffrey S. A. Stringer, Brice Gaudilliere, Michael P. Snyder, Martin S. Angst, Anisur Rahman, Abdullah H. Baqui, Fyezah Jehan, Muhammad Imran Nisar, Bellington Vwalika, Sunil Sazawal, Gary M. Shaw, David K. Stevenson, Nima Aghaeepour
Summary: Preterm birth is the leading cause of death in children under five, and its complex etiologies have hindered comprehensive studies. This study used multiomic profiling and multivariate modeling to investigate the biological signatures of maternal characteristics associated with preterm birth. Machine learning models showed reliable predictive performance for preterm birth, time-to-delivery, maternal age, gravidity, and BMI. Biological correlates of time-to-delivery included fetal-associated proteins and immune proteins, while maternal age, gravidity, and BMI were correlated with specific proteins and molecules related to collagen, endothelial function, inflammation, and metabolic regulation.
Article
Multidisciplinary Sciences
Yue Wu, Shengen Shawn Hu, Ruixuan Zhang, Nick P. Goplen, Xiaochen Gao, Harish Narasimhan, Ao Shi, Yin Chen, Ying Li, Chongzhi Zang, Haidong Dong, Thomas J. Braciale, Bibo Zhu, Jie Sun
Summary: Through single cell RNA sequencing, researchers found that alveolar macrophages (AMs) from aged mice displayed senescence-like phenotypes with decreased expression of CBFB gene. These findings suggest that AMs in aged hosts demonstrate characteristics of aging cells.
Article
Biochemical Research Methods
Shaoke Lou, Mingjun Yang, Tianxiao Li, Weihao Zhao, Hannah Cevasco, Yucheng T. Yang, Mark Gerstein
Summary: By using the statistical modeling approach MLCrosstalk, the researchers identified linkages between SARS-CoV-2, human genes, miRNAs, and microbes. They found certain human genes and microbial species that are linked to SARS-CoV-2. The findings offer potential insights for developing new treatments for COVID-19.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Review
Allergy
Sayantani B. Sindher, Andrew R. Chin, Nima Aghaeepour, Lawrence Prince, Holden Maecker, Gary M. Shaw, David K. Stevenson, Kari C. Nadeau, Michael Snyder, Purvesh Khatri, Scott D. Boyd, Virginia D. Winn, Martin S. Angst, R. Sharon Chinthrajah
Summary: The prevalence of food allergy is increasing globally, causing significant safety, economic, and emotional burdens. However, identifying patients who would benefit from preventive strategies is challenging due to the heterogeneity of allergy trajectories and clinical phenotypes. Further studies are needed to investigate the molecular mechanisms that differentiate these trajectories and drive food allergy development. Omics approaches have the potential to provide insights into these mechanisms, but their application in food allergy research is still in its early stages.
FRONTIERS IN ALLERGY
(2023)
Article
Biotechnology & Applied Microbiology
Jacob Schreiber, Carles Boix, Jin Wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Scholkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y. Yip, Jeffrey P. Spence, Sanjit Singh Batra, Yun S. Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J. Seth Strattan, Bradley Bernstein, Michael Snyder, Manolis Kellis, William Stafford, Anshul Kundaje
Summary: A promising alternative to conducting comprehensive genomics experiments is to perform a subset of experiments and use computational methods to impute the remaining data. However, determining the best imputation methods and meaningful performance evaluation measures remains an open question. In this study, we address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. Our findings indicate that imputation evaluations are challenging due to distributional shifts caused by differences in data collection and processing, the amount of available data, and redundancy among performance measures. Our analyses provide insights into overcoming these challenges and offer promising directions for more robust research.
Article
Biochemistry & Molecular Biology
Jiamin Chen, Daniel Rebibo, Jianquan Cao, Simon Yat-Man Mok, Neel Patel, Po-Cheng Tseng, Zhenghao Zhang, Kevin Y. Yip
Summary: Immune checkpoint inhibitors (ICIs) have shown durable responses in cancer patients, but their efficacy varies across cancer types and individuals. To address this, a knowledgebase and web-based portal (https://iciefficacy.org/) have been developed, providing access to the latest information on ICI efficacy, including biomarkers, computational models, and evaluation results.
Article
Health Care Sciences & Services
Ashkan Dehghani Zahedani, Arvind Veluvali, Tracey McLaughlin, Nima Aghaeepour, Amir Hosseinian, Saransh Agarwal, Jingyi Ruan, Shital Tripathi, Mark Woodward, Noosheen Hashemi, Michael Snyder
Summary: The use of continuous glucose monitoring (CGM) and wearables, together with a smartphone app and personalized recommendations, can improve blood glucose levels, reduce weight, and improve dietary habits, thereby enhancing the metabolic health of individuals with and without type 2 diabetes (T2D).
NPJ DIGITAL MEDICINE
(2023)