Review
Oncology
Peng Jiang, Sanju Sinha, Kenneth Aldape, Sridhar Hannenhalli, Cenk Sahinalp, Eytan Ruppin
Summary: Historically, cancer research has focused on a few essential pathways and genes, but recent advances in high-throughput technologies have led to the rapid accumulation of large-scale cancer omics data. The analysis of this "big data" requires significant computational resources and has the potential to bring new insights to cancer research. The combination of big data, bioinformatics, and artificial intelligence has already made notable advances in our understanding of cancer biology and translational research. Future progress will require collaboration among data scientists, clinicians, biologists, and policymakers.
NATURE REVIEWS CANCER
(2022)
Review
Dentistry, Oral Surgery & Medicine
R. E. Schuler, A. Bugacov, J. G. Hacia, T. V. Ho, J. Iwata, L. Pearlman, B. D. Samuels, C. Williams, Z. Zhao, C. Kesselman, Y. Chai
Summary: The FaceBase Consortium is an organization established in 2009 to address the increasing data-intensive nature of dental and craniofacial research. It promotes data sharing and adheres to the FAIR principles, supporting a wide range of users. FaceBase serves as a successful model for researchers to self-curate their data. It provides research outputs and educational resources, facilitating data-intensive research and reproducibility.
JOURNAL OF DENTAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Barbara Zdrazil, Eloy Felix, Fiona Hunter, Emma J. Manners, James Blackshaw, Sybilla Corbett, Marleen de Veij, Harris Ioannidis, David Mendez Lopez, Juan F. Mosquera, Maria Paula Magarinos, Nicolas Bosc, Ricardo Arcila, Tevfik Kiziloren, Anna Gaulton, A. Patricia Bento, Melissa F. Adasme, Peter Monecke, Gregory A. Landrum, Andrew R. Leach
Summary: ChEMBL is a curated resource of bioactive molecules with drug-like properties. It has evolved significantly in size and diversity of data types over time. The inclusion of new datasets has expanded the bioactivity data available and added new features to ChEMBL.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Efi Athieniti, George M. Spyrou
Summary: The emergence of high-throughput technologies has shifted the design of translational medicine projects towards collecting and analyzing multi-omics patient samples. However, integrating these datasets poses challenges in terms of appropriate computational methods and the selection of omics types. This article aims to guide the design of multi-omics studies in translational medicine by reviewing articles that integrate multiple omics measurements, identifying objectives in translational medicine applications, describing computational methods and tools for data integration, and discussing downstream analysis and extraction of novel insights from multi-omics datasets.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Efi Athieniti, George M. Spyrou
Summary: The emergence of high-throughput technologies has changed the design of translational medicine projects, leading to the collection and integrated analysis of multi-omics patient samples. However, integrating these datasets poses computational challenges and the optimal methods for data integration are still not clear. This article aims to provide guidance on the design of multi-omics studies in translational medicine, including the selection of omics types and integration methods. It reviews articles on the integration of multiple omics measurements and identifies five objectives in translational medicine applications. The article describes common trends in omic selection for different objectives and diseases, and provides examples of computational methods and tools for data integration.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Psychology, Multidisciplinary
Katarina Blask, Lea Gerhards, Maria Jalynskij
Summary: This article proposes a curation standard for behavioral psychological research data, focusing on the needs of researchers as data providers and users. The standard includes three documentation levels covering research design, operationalization, data collection, and analysis processes, aiming to improve the efficiency of data reuse.
FRONTIERS IN PSYCHOLOGY
(2021)
Article
Geosciences, Multidisciplinary
Taylor R. R. Lee, Benjamin J. J. Phrampus, Jeffrey Obelcz
Summary: In marine geosciences, research vessels are used for data acquisition to study specific phenomena or areas of interest. Despite a plateau in ship time and active research vessels, data production in marine geosciences continues to increase. Legacy data repositories contain a large amount of data, but they are rarely curated for accessibility, resulting in inefficient use and exclusion of high-quality data. This paper discusses improvements in data acquisition, curation, and integration to align marine geosciences with the big data paradigm and addresses challenges and solutions in utilizing both new and legacy data.
FRONTIERS IN EARTH SCIENCE
(2023)
Article
Multidisciplinary Sciences
Wanda Marsolek, Sarah J. Wright, Hoa Luong, Susan M. Braxton, Jake Carlson, Sophia Lafferty-Hess
Summary: Data curation is a series of actions to ensure research data are fit for purpose and can be discovered and reused. Researchers value and find satisfaction in data curation, as it adds value to the data sharing process, is worth the effort, and increases their confidence in sharing data.
Article
Biochemistry & Molecular Biology
Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jingfa Xiao, Shun-min He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Yingke Ma, Meili Chen, Cuiping Li, Shuai Jiang, Dong Zou, Zheng Gong, Xue-tong Zhao, Yanqing Wang, Junwei Zhu, Shuhui Song, Yunchao Ling, Yiwei Wang, Jiaxin Yang, Xinhao Zhuang, Guangya Duan, Gangao Wu, Xiaoning Chen, Dongmei Tian, Zhaohua Li, Yan-ling Sun, Zhenglin Du, Lili Hao, Yuan Gao, Bixia Tang, Yadong Zhang, Hao Zhang, Zaichao Zhang, Qiheng Qian, Zhewen Zhang, Hailong Kang, Tianhao Huang, Zhiqiang Xia, Xincheng Zhou, Jin-quan Chao, Zhonghuang Wang, Jun-wei Zhu, Sisi Zhang, Weimin Tian, Wenquan Wang, Song Wu, Yue Huang, Mochen Zhang, Guoliang Wang, Xin-chang Zheng, Wenting Zong, Wei Zhao, Peiqi Xing, Rujiao Li, Zhaoqi Liu, Mingming Lu, Fengchun Yang, Jialin Mai, Qianwen Gao, Xiaowei Xu, Hongyu Kang, Li Hou, Yunfei Shang, Qiheng Qain, Jie Liu, Meiye Jiang, Congfan Bu, Jinyue Wang, Jingyao Zeng, Jiao Li, Siyu Pan, Hongen Kang, Xinxuan Liu, Shiqi Lin, Na Yuan, Peilin Jia, Xinchang Zheng, Yanling Sun, Zhuang Xiong, Fei Yang, Xu Chen, Tingting Chen, Caixia Yu, Lili Dong, Shuang Zhai, Yubin Sun, Qiancheng Chen, Xiaoyu Yang, Xin Zhang, Zhengqi Sang, Yonggang Wang, Yilin Zhao, Huanxin Chen, Li Lan, Yan-qing Wang, Anke Wang, Yaokai Jia, Xuetong Zhao, Yitong Pan, Xiaonan Liu, Rongqin Zhang, Yi Wang, Lina Ma, Xufei Teng, Lun Li, Na Li, Ying Cui, Tong Jin, Enhui Jin, Tao Zhang, Tianyi Xu, Ming Chen, Guangyi Niu, Rong Pan, Tongtong Zhu, Yuan Chu, Jian Sang, Yuanpu Zhang, Zhennan Wang, Yuan-sheng Zhang, Qiliang Yao, Xinran Zhang, Xutong Guo, Zhao Li, Lin Liu, Changrui Feng, Yuxin Qin, Wei Jing, Sicheng Luo, Tong-tong Zhu, Yuansheng Zhang, Zis-han Wu, Qianpeng Li, Pei Liu, Yongqing Sun, Zhuojing Fan, Wen-ming Zhao, Wen-Kang Shen, An-Yuan Guo, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Dan Liu, Chi Zhang, Yu Xue, Zheng Zhao, Tao Jiang, Wanying Wu, Fangqing Zhao, Xianwen Meng, Yujie Gou, Miaomiao Chen, Di Peng, Hao Luo, Feng Gao, Wanshan Ning, Wan Liu, Ruifang Cao, Guo-qing Zhang, Yuxiang Wei, Chun-Jie Liu, Gui-Yan Xie, Hao Yuan, Tianhan Su, Yong E. Zhang, Chenfen Zhou, Pengyu Wang, Yincong Zhou, Guoji Guo, Qiong Zhang, Shanshan Fu, Xiaodan Tan, Dachao Tang, Weizhi Zhang, Mei Luo, Yubin Xie, Ya-Ru Miao, Xinhe Huang, Zihao Feng, Xingyu Liao, Xin Gao, Jianxin Wang, Guiyan Xie, Chunhui Yuan, Dechang Yang, Feng Tian, Ge Gao, Wenyi Wu, Cheng Han, Qinghua Cui, Chunfu Xiao, Chuan-Yun Li, XiaoTong Luo, Qing Tang
Summary: The National Genomics Data Center (NGDC) of the China National Center for Bioinformation (CNCB) provides database resources to support global academic and industrial communities. The NGDC constantly expands and updates core database resources by archiving big data, conducting integrative analysis, and providing value-added curation. New database resources have been developed for infectious diseases and microbiology, cancer-trait association, and tropical plants. Additionally, resources for the monkeypox virus and SARS-CoV-2 have been newly constructed and regularly updated. All resources and services are publicly accessible at https://ngdc.cncb.ac.cn.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Noemi del Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal, Colin Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa Ratan, Gautam Shirodkar, Odilia Lu, Balint Meszaros, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret Duesbury, Sylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwinski, Sandra Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob
Summary: IntAct is a curated database of molecular interactions derived from scientific literature, containing over one million binary interactions curated by twelve global partners. The IMEx curation policy emphasizes fine-grained data and curation model to capture essential experimental details for interpretation of the molecular interaction data. Recently, IntAct has introduced a completely redeveloped website to present data in a more user-friendly and detailed way.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Construction & Building Technology
Duy H. Ho, Yugyung Lee, Srichakradhar Nagireddy, Charan Thota, Brent Never, Ye Wang
Summary: Local governments are increasingly using administrative data to improve performance and responsiveness to citizens' demands. However, city managers face challenges when utilizing secondary data collected at different geographic levels and time horizons. To overcome this, an inductive analytical methodology was developed to create pragmatically and analytically appropriate units of analysis. The framework, called OpenComm, harmonizes administrative and secondary data and has shown promising results in uncovering hidden patterns of city service disparity. Privacy-preserving technology is also applied to protect community privacy.
SUSTAINABLE CITIES AND SOCIETY
(2022)
Article
Computer Science, Information Systems
William R. Hogan, Elizabeth A. Shenkman, Temple Robinson, Olveen Carasquillo, Patricia S. Robinson, Rebecca Z. Essner, Jiang Bian, Gigi Lipori, Christopher Harle, Tanja Magoc, Lizabeth Manini, Tona Mendoza, Sonya White, Alex Loiacono, Jackie Hall, Dave Nelson
Summary: The OneFlorida Data Trust is a centralized research patient data repository managed by the OneFlorida Clinical Research Consortium, collecting structured electronic health record and other data on 17.2 million individuals in Florida. The Data Trust uses privacy-preserving entity resolution for patient deduplication and establishes mother-baby relationships, serving as a valuable and relatively unique research resource.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2022)
Editorial Material
Physics, Multidisciplinary
Leonida A. Gizzi, Maria Grazia Andreassi
Summary: Laser accelerators have not been able to meet the requirements for dose control and stability in biomedical applications, but an experiment has now achieved translational research with proton beams at ultrahigh dose rate.
Review
Immunology
Erica L. Katz, John E. Harris
Summary: Vitiligo is a skin disease characterized by white spots, and significant progress has been made in understanding its pathogenesis over the past 30 years through perseverance, collaboration, and open-minded discussion. Researchers have explored various possible mechanisms through innervation, microvascular anomalies, oxidative stress, defects in melanocyte adhesion, autoimmunity, somatic mosaicism, and genetics, with animal models and improved patient sample collection methods playing important roles in translational studies.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Almut Heinken, Stefania Magnusdottir, Ronan M. T. Fleming, Ines Thiele
Summary: DEMETER is a tool that can efficiently refine thousands of draft genome-scale reconstructions simultaneously, ensuring adherence to quality standards, agreement with available experimental data, and refinement of pathways based on manually refined genome annotations.
Article
Public, Environmental & Occupational Health
Abigail S. Baldridge, Jennifer A. Pacheco, Sharon A. Aufox, Kwang-Youn A. Kim, J. C. Silverstein, W. Denham, E. Hungness, Maureen E. Smith, Norrina B. Allen, Philip Greenland, Laura J. Rasmussen-Torvik
AMERICAN JOURNAL OF EPIDEMIOLOGY
(2015)
Article
Oncology
Yitan Zhu, Yanxun Xu, Donald L. Helseth, Kamalakar Gulukota, Shengjie Yang, Lorenzo L. Pesce, Riten Mitra, Peter Mueller, Subhajit Sengupta, Wentian Guo, Jonathan C. Silverstein, Ian Foster, Nigel Parsad, Kevin P. White, Yuan Ji
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2015)
Article
Surgery
Laura J. Rasmussen-Torvik, Abigail S. Baldridge, Jennifer A. Pacheco, Sharon A. Aufox, Kwang-Youn A. Kim, Jonathan C. Silverstein, Erwin W. Denham, Eric Hungness, Maureen E. Smith, Philip Greenland
Article
Oncology
Yitan Zhu, Yanxun Xu, Donald L. Helseth, Kamalakar Gulukota, Shengjie Yang, Lorenzo L. Pesce, Riten Mitra, Peter Mueller, Subhajit Sengupta, Wentian Guo, Jonathan C. Silverstein, Ian Foster, Nigel Parsad, Kevin P. White, Yuan Ji
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2015)
Article
Computer Science, Interdisciplinary Applications
Alexa T. McCray, John Glaser, Ross Koppel, Curtis P. Langlotz, Jonathan Silverstein
JOURNAL OF BIOMEDICAL INFORMATICS
(2016)
Article
Health Care Sciences & Services
Qian Cheng, Joshua Juen, Shashi Bellam, Nicholas Fulara, Deanna Close, Jonathan C. Silverstein, Bruce Schatz
TELEMEDICINE AND E-HEALTH
(2017)
Article
Health Care Sciences & Services
Qian Cheng, Joshua Juen, Shashi Bellam, Nicholas Fulara, Deanna Close, Jonathan C. Silverstein, Bruce Schatz
TELEMEDICINE AND E-HEALTH
(2017)
Article
Computer Science, Information Systems
Abel N. Kho, Denise M. Hynes, Satyender Goel, Anthony E. Solomonides, Ron Price, Bala Hota, Shannon A. Sims, Neil Bahroos, Francisco Angulo, William E. Trick, Elizabeth Tarlov, Fred D. Rachman, Andrew Hamilton, Erin O. Kaleba, Sameer Badlani, Samuel L. Volchenboum, Jonathan C. Silverstein, Jonathan N. Tobin, Michael A. Schwartz, David Levine, John B. Wong, Richard H. Kennedy, Jerry A. Krishnan, David O. Meltzer, John M. Collins, Terry Mazany
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2014)
Article
Multidisciplinary Sciences
Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Borner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Jay Shendure, Cole Trapnell, Shin Lin, Dana Jackson, Michael P. Snyder, Garry Nolan, William James Greenleaf, Yiing Lin, Sylvia Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Kun Zhang, Xin Sun, Sanjay Jain, James Hagood, Gloria Pryhuber, Peter Kharchenko, Mark Atkinson, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Amanda Posgai, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark deCaestecker, Agnes B. Fogo, Raf van de Plas, Ken Lau, Long Cai, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Julia Laskin, DongHye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Pehr Harbury, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Ziv Bar-Joseph, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma A. Akoju, Matthew Ruffalo, Nils Gehlenborg, Peter Kharchenko, Margaret Vella, Chuck McCallum, Katy Borner, Leonard E. Cross, Samuel H. Friedman, Randy Heiland, Bruce Herr, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Nicholas A. Nystrom, Jonathan C. Silverstein, Philip D. Blood, Alexander J. Ropelewski, William E. Shirey, Robin M. Scibek, Paula Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, Rahul Satija, John Marioni, Aviv Regev, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Jennifer Rood, Leslie Gaffney, Gokcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Richard Conroy, Dena Procaccini, Ananda Roy, Ajay Pillai, Marishka Brown, Zorina Galis, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth Wilder, James Anderson
Article
Health Care Sciences & Services
Noah R. Delapaz, William K. Hor, Michael Gilbert, Andrew D. La, Feiran Liang, Peihao Fan, Xiguang Qi, Xiaojiang Guo, Jian Ying, Dara Sakolsky, Levent Kirisci, Jonathan C. Silverstein, Lirong Wang
Summary: Post-traumatic stress disorder (PTSD) is a common mental disorder characterized by psychological and behavioral changes. This study aimed to investigate if certain antipsychotics could decrease the risk of suicide-related events in the PTSD population. The results suggest that lurasidone may significantly reduce suicide-related events when compared to other antipsychotics.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Health Care Sciences & Services
Oshin Miranda, Peihao Fan, Xiguang Qi, Zeshui Yu, Jian Ying, Haohan Wang, David A. Brent, Jonathan C. Silverstein, Yu Chen, Lirong Wang
Summary: By utilizing the deep-learning model DeepBiomarker in conjunction with lab tests and contribution analysis, the study effectively predicted the risk of suicide-related events in PTSD patients. The results indicated the significant role of lab tests in suicide prediction.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Biology
Katy Borner, Andreas Bueckle, Bruce W. Herr, Leonard E. Cross, Ellen M. Quardokus, Elizabeth G. Record, Yingnan Ju, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, N. Heath Patterson, Griffin M. Weber
Summary: Seventeen international consortia are collaborating on a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Software tools and user interfaces have been developed to annotate and explore the tissue data. A significant amount of tissue data has been registered and published.
COMMUNICATIONS BIOLOGY
(2022)
Article
Computer Science, Information Systems
Rumana Rashid, Susan Copelli, Jonathan C. Silverstein, Michael J. Becich
Summary: This study describes the use of REDCap by NMVB to establish a biospecimen and data sharing network. REDCap integrates honest broker activities and provides access to clinical data and biospecimens for researchers. The development of a Web Portal Query tool allows public users to discover research materials through an interactive and faceted search. This study is important for rare disease research.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2023)
Article
Neurosciences
Peihao Fan, Xiaojiang Guo, Xiguang Qi, Mallika Matharu, Ravi Patel, Dara Sakolsky, Levent Kirisci, Jonathan C. Silverstein, Lirong Wang
Article
Surgery
Matthew E. Gitelis, Adelaide Kaczynski, Torin Shear, Mark Deshur, Mohammad Beig, Meredith Sefa, Jonathan Silverstein, Michael Ujiki
AMERICAN JOURNAL OF SURGERY
(2017)
