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The disconnect between classical biostatistics and the biological data mining community

James D Malley, Jason H Moore
2013 BioData Mining  
The situation, this disconnect between deep theory and practical methods, is unsettling.  ...  Two classics in the field are: [1] for nonparametric classification, and [2] for nonparametric regression.  ...  Acknowledgement This research was supported in part by the Intramural Research Program of the Center for Information Technology, National Institutes of Health (NIH).  ... 
doi:10.1186/1756-0381-6-12 pmid:23880104 pmcid:PMC3726458 fatcat:s7wu3qaufvhg5e5ljsrqc6msnm

On the Discordance of Metabolomics with Proteomics and Transcriptomics: Coping with Increasing Complexity in Logic, Chemistry, and Network Interactions Scientific Correspondence

A. R. Fernie, M. Stitt
2012 Plant Physiology  
Although there is sometimes an encouragingly simple relationship between changes of transcripts and proteins and changes in downstream biological functions, quite often there is a major discordance.  ...  In this scientific correspondence, we will discuss reasons for this apparent disconnect, which lie partly in technical issues and partly in the complexity and structure of metabolic networks, and then  ...  Unless this is done, most studies of metabolism will remain as stand-alone data sets that cannot be rigorously combined in databases and used for comprehensive data mining and meta-analysis.  ... 
doi:10.1104/pp.112.193235 pmid:22253257 pmcid:PMC3291261 fatcat:3nhcbdus55h55bpqwnundkmvji

Landscape Restoration: Moving from Generalities to Methodologies

2003 BioScience  
Foundation (grant DEB-0072909), the University of California, and the UC-Santa Barbara campus.  ...  We appreciate helpful comments from the Mills/Crone lab group at the University of Montana and from two anonymous reviewers.  ...  Classical methods include all analyses taught in most introductory biostatistics classes (e.g., Sokal and Rohlf 1995, Zar 1999) .  ... 
doi:10.1641/0006-3568(2003)053[0491:lrmfgt];2 fatcat:pb4enb4b6nacdptxizrmsic634

Uses and limits of empirical data in measuring and modeling human lead exposure

P Mushak
1998 Environmental Health Perspectives  
This paper examines the uses and limits of empirical data in evaluating measurement and modeling approaches to human lead exposure.  ...  Empirical and modeled datasets for lead exposure may not agree due to a) problems with the observational data or b) problems with the model; caution should be exercised before either a model or observational  ...  In other cases, communities reported by Mushak (12) as showing a relationship between mining and related waste and PbB were not mentioned by Danse et al.  ... 
doi:10.1289/ehp.98106s61467 pmid:9860906 pmcid:PMC1533425 fatcat:cugusxfqkrfbpilknazkqibhnu

A Niche for Infectious Disease in Environmental Health: Rethinking the Toxicological Paradigm

Beth J. Feingold, Leora Vegosen, Meghan Davis, Jessica Leibler, Amy Peterson, Ellen K. Silbergeld
2010 Environmental Health Perspectives  
conducted a literature review for examples of interactions between toxic agents and infectious diseases, as well as the role of these interactions as risk factors in classic "environmental" diseases.  ...  Health Sciences. data synthesis: We adapted the toxicological paradigm to guide reintegration of infectious disease into environmental health research and to identify common ground between these two fields  ...  The authors declare they have no actual or potential competing financial interests.  ... 
doi:10.1289/ehp.0901866 pmid:20385515 pmcid:PMC2920090 fatcat:jq6xtyj6gbbv3nqjeqy7jsd7re

Biomedical Informatics – A Confluence of Disciplines?

A. Hasman, E. Ammenwerth, H. Dickhaus, P. Knaup, C. Lovis, J. Mantas, V. Maojo, F. J. Martin-Sanchez, M. Musen, V. L. Patel, G. Surján, J. L. Talmon (+1 others)
2011 Methods of Information in Medicine  
Results and Conclusions: This paper contains the reflections of a number of the invited experts on the character of biomedical informatics.  ...  the sum of its supporting disciplines and c) on the position of biomedical informatics with respect to related disciplines.  ...  AH and INS combined the viewpoints into an integrated paper.  ... 
doi:10.3414/me11-06-0003 pmid:22146914 fatcat:coqtdnvi2vdmvlhdbyf5jjkyla

The 2019 Mathematical Oncology Roadmap

Russell C. Rockne, Andrea Hawkins-Daarud, Kristin R. Swanson, James P Sluka, James A. Glazier, Paul Macklin, David Hormuth, Angela M Jarrett, Ernesto Augutso Bueno da Fonseca Lima, J Oden, George Biros, Thomas E Yankeelov (+23 others)
2019 Physical Biology  
The cover art for this Roadmap was chosen as an apt metaphor for the beautiful, strange, and evolving relationship between mathematics and cancer.  ...  The dominant theme of this Roadmap is the personalization of medicine through mathematics, modelling, and simulation.  ...  McDonnell Foundation and the Ben & Catherine Ivy Foundation.  ... 
doi:10.1088/1478-3975/ab1a09 pmid:30991381 pmcid:PMC6655440 fatcat:sb4ms7zygngd3pp5xuxundp3gy

Revolution of Alzheimer Precision Neurology. Passageway of Systems Biology and Neurophysiology

Harald Hampel, Nicola Toschi, Claudio Babiloni, Filippo Baldacci, Keith L. Black, Arun L.W. Bokde, René S. Bun, Francesco Cacciola, Enrica Cavedo, Patrizia A. Chiesa, Olivier Colliot, Cristina-Maria Coman (+32 others)
2018 Journal of Alzheimer's Disease  
neurodegenerative disease (ND) populations, within the wide continuous biological and clinical spectrum of ND, applying high-throughput and Hampel et al.  ...  This translational research path is paralleled by an "omics"-based, hypothesis-free, exploratory research pathway, which will collect multimodal data from progressing asymptomatic, preclinical and clinical  ...  The vast amount of data generated will cause new challenges for data science -mainly in terms of data storage, processing, and mining.  ... 
doi:10.3233/jad-179932 pmid:29562524 pmcid:PMC6008221 fatcat:j3u6gkzfqbg47kv4o2hpkjadn4

Digital Footprints: Opportunities and Challenges for Online Social Research

Scott A. Golder, Michael W. Macy
2014 Annual Review of Sociology  
posed by "big data" and web-based experiments.  ...  invention of the telescope revolutionized the study of the heavens, so too by rendering the unmeasurable measurable, the technological revolution in mobile, Web, and Internet communications has the potential  ...  ACKNOWLEDGMENTS This research was supported by grants from the US National Science Foundation SES 1226483 and IIS 0910664, Google, and the National Research Foundation of Korea NRF-2013S1A3A2055285.  ... 
doi:10.1146/annurev-soc-071913-043145 fatcat:rozoh646wngtjdod74rbdubwfq

Learning hidden influences in large-scale dynamical social networks: A data-driven sparsity-based approach [article]

Chiara Ravazzi, Fabrizio Dabbene, Constantino Lagoa, Anton V. Proskurnikov
2020 arXiv   pre-print
Interpersonal influence estimation from empirical data is a central challenge in the study of social structures and dynamics.  ...  The term social influence refers to the behavioral change of individuals due to the interactions with others in a social system, e.g. organization, community, or society in general.  ...  Kutz, “Inferring biological networks by sparse identification of nonlinear dynamics,” IEEE Transactions on Molecular, Biological and Multi-Scale Communications, vol. 2, no. 1, pp. 52–63, 2016. [146  ... 
arXiv:2007.06713v2 fatcat:mxunepbsnrdrtavdyfdbwzohlq

On Fitting Finite Dirichlet Mixture Using ECM and MML [chapter]

Nizar Bouguila, Djemel Ziou
2005 Lecture Notes in Computer Science  
The steady-state distribution of the buffer content and related performance measures are obtained. Special cases such as Erlang, exponential and deterministic service times are discussed.  ...  The system is analysed for different active periods corresponding to the service time of an M/G/1 queue and the busy period of an M/G/1 queue.  ...  In this article we will look at the connection between data mining and statistics and some of the major tools used in data mining.  ... 
doi:10.1007/11551188_19 fatcat:gtzi5u6emvfyxea3zbklobnvom

Dynamic and Thermodynamic Models of Adaptation [article]

A.N. Gorban, T.A. Tyukina, L.I. Pokidysheva, E.V. Smirnova
2021 arXiv   pre-print
The concept of biological adaptation was closely connected to some mathematical, engineering and physical ideas from the very beginning.  ...  We explore this world of models and experiments, starting with classic works, with particular attention to the results of the last ten years and open questions.  ...  Analysis of graphs of correlations between biological traits was proposed in biostatistics in 1931 [161] .The vertices of these graphs are attributes, and the edges correspond to sufficiently strong correlations  ... 
arXiv:2103.01959v1 fatcat:za4lnanuhjelpfd6rdgfpzwqbi

Stratified medicine for mental disorders

Gunter Schumann, Elisabeth B. Binder, Arne Holte, E. Ronald de Kloet, Ketil J. Oedegaard, Trevor W. Robbins, Tom R. Walker-Tilley, Istvan Bitter, Verity J. Brown, Jan Buitelaar, Roberto Ciccocioppo, Roshan Cools (+32 others)
2014 European Neuropsychopharmacology  
Novel biomedical techniques have advanced our understanding of how the brain develops and is shaped by behaviour and  ...  There is recognition that biomedical research into the causes of mental disorders and their treatment needs to adopt new approaches to research.  ...  for data mining in hypothesis-driven and hypothesis-free experimental designs.  ... 
doi:10.1016/j.euroneuro.2013.09.010 pmid:24176673 fatcat:5u4n44l2trcydkcumhauf7l6bu


Magda Shaheen, Senait Teklehaimanot
2017 Journal of Clinical and Translational Science  
Culturally and linguistically adapted intervention that involves community and providers to increase awareness about depression and the available services/treatment among minority, immigrant, and uninsured  ...  We utilized multiple logistic regressions to determine the independent association between service use and each independent variable (demographics, health status, food security, chronic conditions, and  ...  2184 Evaluating the association among biological, social, and nutritional status on adolescent pregnancy rates, physiology and birth outcomes using electronic health records data Amanda Cheng, Caroline  ... 
doi:10.1017/cts.2017.287 fatcat:yp5uxjopfzhuzovziwsbbhl2au

Bioinformatics and statistical genomics

2008 Genomic Medicine  
Intein data obtained from InBase Intein database.  ...  The process of precise intein splicing and formation of specific peptide bonds has been exploited by researchers to develop many novel applications in the field of protein engineering, enzymology, microarray  ...  PathBuilder facilitates easy retrieval and export into community standardized data structures such as Bi-oPAX, PSI-MI and SBML.  ... 
doi:10.1007/s11568-009-9081-x pmid:19488836 pmcid:PMC2694866 fatcat:kmyq6l3qefdhpaz5zsi6eyc37m
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