Genomes and Genes
Summary: Use of sophisticated analysis tools to sort through, organize, examine, and combine large sets of information.
Publications108 found, 100 shown here
- Boscarino J, Moorman A, Rupp L, Zhou Y, Lu M, Teshale E, et al. Comparison of ICD-9 Codes for Depression and Alcohol Misuse to Survey Instruments Suggests These Codes Should Be Used with Caution. Dig Dis Sci. 2017;62:2704-2712 pubmed publisher..ICD-9 codes were limited in predicting current depression and alcohol misuse, suggesting that caution should be exercised when using ICD-9 codes to assess depression or alcohol misuse among CHC patients. ..
- Rüping S, Anguita A, Bucur A, Cirstea T, Jacobs B, Torge A. Improving the implementation of clinical decision support systems. Conf Proc IEEE Eng Med Biol Soc. 2013;2013:3214-7 pubmed publisher..This, in turn, allows to use data mining tools to automatically create hypotheses for CDS models, which reduces the manual workload in the creation of a ..
- Morrow J, Riegler M, Gilchrist A, Shearman D, Frommer M. Comprehensive transcriptome analysis of early male and female Bactrocera jarvisi embryos. BMC Genet. 2014;15 Suppl 2:S7 pubmed publisher..Our data contribute fundamental information to sex-determination research, and provide candidates for the sourcing of gene promoters for transgenic pest-management strategies of tephritid fruit flies. ..
- Xu R, Wang Q. Comparing a knowledge-driven approach to a supervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature. BMC Bioinformatics. 2015;16 Suppl 5:S6 pubmed publisher..In summary, we automatically constructed a large-scale higher-level drug phenotype relationship knowledge, which can have great potential in computational drug discovery. ..
- Glotov A, Tiys E, Vashukova E, Pakin V, Demenkov P, Saik O, et al. Molecular association of pathogenetic contributors to pre-eclampsia (pre-eclampsia associome). BMC Syst Biol. 2015;9 Suppl 2:S4 pubmed publisher..Recently, we have shown a similar result for inversely comorbid diseases. This suggests that comorbid and inversely comorbid diseases have common features concerning structural organization of associative molecular genetic networks. ..
- Madden S, Clarke C, Gaule P, Aherne S, O Donovan N, Clynes M, et al. BreastMark: an integrated approach to mining publicly available transcriptomic datasets relating to breast cancer outcome. Breast Cancer Res. 2013;15:R52 pubmed..The value of this tool will be in the preliminary assessment of putative biomarkers in breast cancer. It will be of particular use to research groups with limited bioinformatics facilities. ..
- Pafilis E, Frankild S, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou A, et al. The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. PLoS ONE. 2013;8:e65390 pubmed publisher..jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org. ..
- Chien P, Tseng Y, Hsu Y, Lai Y, Weng S. Frequency and pattern of Chinese herbal medicine prescriptions for urticaria in Taiwan during 2009: analysis of the national health insurance database. BMC Complement Altern Med. 2013;13:209 pubmed publisher..Frequent itemset mining, as applied to data mining, was used to analyse co-prescription of CHM for patients with urticaria...
- Rybinski M, Aldana Montes J. Calculating semantic relatedness for biomedical use in a knowledge-poor environment. BMC Bioinformatics. 2014;15 Suppl 14:S2 pubmed publisher..Our method improves flexibility of the existing methods without a notable loss of quality. It is a legitimate alternative to the costly construction of specialized knowledge-rich resources. ..
- Winnenburg R, Sorbello A, Ripple A, Harpaz R, Tonning J, Szarfman A, et al. Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies. J Biomed Inform. 2015;57:425-35 pubmed publisher..ADEs extracted from MEDLINE indexing are complementary to, not a replacement for, other sources. ..
- Incoronato M, Aiello M, Infante T, Cavaliere C, Grimaldi A, Mirabelli P, et al. Radiogenomic Analysis of Oncological Data: A Technical Survey. Int J Mol Sci. 2017;18: pubmed publisher..The impact of single and combined techniques will be discussed in light of their suitability in correlation and predictive studies of specific oncologic diseases. ..
- Komenda M, Karolyi M, Pokorná A, Vaitsis C. Medical and Healthcare Curriculum Exploratory Analysis. Stud Health Technol Inform. 2017;235:231-235 pubmed..The achieved results from the selected analytical issues are presented here in clear visual interpretations in an attempt to visually describe the entire medical and healthcare curriculum. ..
- Martin Sanchez F, Aguiar Pulido V, López Campos G, Peek N, Sacchi L. Secondary Use and Analysis of Big Data Collected for Patient Care. Yearb Med Inform. 2017;26:28-37 pubmed publisher..This contribution from the IMIA working group on "Data mining and Big Data analytics" focuses on the literature published during the last two years, covering the ..
- Zwierzyna M, Overington J. Classification and analysis of a large collection of in vivo bioassay descriptions. PLoS Comput Biol. 2017;13:e1005641 pubmed publisher..Finally, we combine information mined from text with curated annotations stored in ChEMBL to investigate the patterns of usage of different animal models across a range of experiments, drug classes, and disease areas. ..
- Kim Y, Yoon D, Byun J, Park H, Lee A, Kim I, et al. Extracting information from free-text electronic patient records to identify practice-based evidence of the performance of coronary stents. PLoS ONE. 2017;12:e0182889 pubmed publisher..Post surveillance of the practice based evidence in the PCI data warehouse indicated that the biodegradable-polymer DES might have a lower risk of TVR than the durable-polymer DES. ..
- Cano I, Tényi Á, Schueller C, Wolff M, Huertas Migueláñez M, Gomez Cabrero D, et al. The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research. J Transl Med. 2014;12 Suppl 2:S6 pubmed publisher..We plan to further extend the COPDKB by offering it as a repository to publish and semantically integrate data from relevant clinical trials. The COPDKB is freely available after registration at http://www.copdknowledgebase.eu. ..
- Chen L, Vallmuur K, Nayak R. Injury narrative text classification using factorization model. BMC Med Inform Decis Mak. 2015;15 Suppl 1:S5 pubmed publisher..With the selection of right dimension k, Non Negative Matrix Factorization-model method achieves 10 CV accuracy of 0.93. ..
- Alborzi S, Devignes M, Ritchie D. ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. BMC Bioinformatics. 2017;18:107 pubmed publisher..These EC-Pfam associations could be used to annotate some 58,722 protein chains in the PDB which currently lack any EC annotation. The ECDomainMiner database is publicly available at http://ecdm.loria.fr/ . ..
- Long E, Xu S, Liu Z, Wu X, Zhang X, Wang J, et al. Construction and implications of structural equation modeling network for pediatric cataract: a data mining research of rare diseases. BMC Ophthalmol. 2017;17:74 pubmed publisher..the interrelationship and the effectiveness of potential factors of pediatric cataract, for the exploration of data mining strategy in the scenarios of rare diseases...
- Hu H, Chen Y, Tang K. A novel decision-tree method for structured continuous-label classification. IEEE Trans Cybern. 2013;43:1734-46 pubmed..5 algorithm using eight real data sets. The empirical results indicate that the proposed method outperforms the C4.5 algorithm with regard to prediction accuracy, prediction specificity, and computational complexity. ..
- Li F, Zhang M, Fu G, Ji D. A neural joint model for entity and relation extraction from biomedical text. BMC Bioinformatics. 2017;18:198 pubmed publisher..In addition, parameter sharing is an alternative method for neural models to jointly process this task. Our work can facilitate the research on biomedical text mining. ..
- Lu Y, Wu Y, Liu J, Li J, Zhang P. Understanding Health Care Social Media Use From Different Stakeholder Perspectives: A Content Analysis of an Online Health Community. J Med Internet Res. 2017;19:e109 pubmed publisher..These findings could help improve social media services to facilitate diverse stakeholder engagement for health information sharing and social interaction more effectively. ..
- Drawnel F, Zhang J, Küng E, Aoyama N, Benmansour F, Araujo Del Rosario A, et al. Molecular Phenotyping Combines Molecular Information, Biological Relevance, and Patient Data to Improve Productivity of Early Drug Discovery. Cell Chem Biol. 2017;24:624-634.e3 pubmed publisher..Our results advocate for application of molecular phenotyping in early drug discovery, promoting biological relevance as a key selection criterion early in the drug development cascade. ..
- Davis F, Sutzko D, Grey S, Mansour M, Jain K, Nypaver T, et al. Predictors of surgical site infection after open lower extremity revascularization. J Vasc Surg. 2017;65:1769-1778.e3 pubmed publisher..Several patient, operative, and hospital-related risk factors that predict postoperative SSI were identified, suggesting that targeted improvements in perioperative care may decrease complications and improve vascular patient outcomes. ..
- Huang T, Chen L, Song J, Zheng M, Yang J, Zhang Z. Integrated Analysis of Multiscale Large-Scale Biological Data for Investigating Human Disease 2016. Biomed Res Int. 2016;2016:6585069 pubmed
- Takeda K, Takahashi K, Masukawa H, Shimamori Y. Influence on Learning of a Collaborative Learning Method Comprising the Jigsaw Method and Problem-based Learning (PBL). Yakugaku Zasshi. 2017;137:659-664 pubmed publisher..This finding suggests that the use of text mining to analyze qualitative data could enable teachers to evaluate the effectiveness of various methods employed to improve learning. ..
- Shah N, Tenenbaum J. The coming age of data-driven medicine: translational bioinformatics' next frontier. J Am Med Inform Assoc. 2012;19:e2-4 pubmed
- Jalali A, Buckley E, Lynch J, Schwab P, Licht D, Nataraj C. Prediction of periventricular leukomalacia occurrence in neonates after heart surgery. IEEE J Biomed Health Inform. 2014;18:1453-60 pubmed publisher..A data mining approach has been employed to generate a set of rules for classification of subjects as healthy or PVL affected...
- Loharch S, Bhutani I, Jain K, Gupta P, Sahoo D, Parkesh R. EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape. Database (Oxford). 2015;2015: pubmed publisher..EpiDBase provides comprehensive resources for further design, development and refinement of small molecule modulators of epigenetic markers. ..
- Ravikumar K, Rastegar Mojarad M, Liu H. BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. Database (Oxford). 2017;2017: pubmed publisher..There is a marked improvement by over 20% in the overall performance of the BELMiner's capability to extract BEL statement on the test set. The system is available as a REST-API at http://184.108.40.206:8484/BELXtractor/finder/...
- Yergens D, Dutton D, Fiest K. Automated Identification of National Health Survey Research Topics in the Academic Literature. Stud Health Technol Inform. 2017;235:211-215 pubmed..This study investigates, through the use of automated text data mining, an approach to identify and collate the type of academic literature being published using national health ..
- Mo T, Liu W, Ji W, Zhao J, Chen T, Ding W, et al. Biosynthetic Insights into Linaridin Natural Products from Genome Mining and Precursor Peptide Mutagenesis. ACS Chem Biol. 2017;12:1484-1488 pubmed publisher..Our results reveal valuable insights into linaridin biosynthesis and highlight the potential to explore this class of natural products by genome mining and by biosynthetic engineering studies. ..
- Gibbens N. Chief veterinary officer's update: Big data is our best shot at challenging extreme breeding. Vet Rec. 2017;181:133-134 pubmed publisher..In his latest update for Veterinary Record, Nigel Gibbens, the UK's Chief Veterinary Officer, looks back at the past year and discusses the UK's achievements and the challenges that it faces. ..
- Hassan S, Farhan M, Mangayil R, Huttunen H, Aho T. Bioprocess data mining using regularized regression and random forests. BMC Syst Biol. 2013;7 Suppl 1:S5 pubmed publisher..In this work, the applicability of regularized regression (Lasso) and random forests (RF) in bioprocess data mining was examined, and their performance was benchmarked against multiple linear regression...
- Izzo M, Mortola F, Arnulfo G, Fato M, Varesio L. A digital repository with an extensible data model for biobanking and genomic analysis management. BMC Genomics. 2014;15 Suppl 3:S3 pubmed publisher..The web interface allows the operators to easily manage, query, and annotate the files, without dealing with the technicalities of the data grid. ..
- Rinaldi F, Clematide S, Marques H, Ellendorff T, Romacker M, Rodriguez Esteban R. OntoGene web services for biomedical text mining. BMC Bioinformatics. 2014;15 Suppl 14:S6 pubmed publisher..The web services leverage a state-of-the-art platform for text mining (OntoGene) which has been tested in several community-organized evaluation challenges,with top ranked results in several of them. ..
- Larralde M, Lawson T, Weber R, Moreno P, Haug K, Rocca Serra P, et al. mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data. Bioinformatics. 2017;33:2598-2600 pubmed publisher..com/ISA-tools. Documentation is available from http://2isa.readthedocs.io/en/latest/. firstname.lastname@example.org or email@example.com. Supplementary data are available at Bioinformatics online. ..
- Milovanovic I, Busarcevic M, Trbovich A, Ivovic V, Uzelac A, Djurkovic Djakovic O. Evidence for host genetic regulation of altered lipid metabolism in experimental toxoplasmosis supported with gene data mining results. PLoS ONE. 2017;12:e0176700 pubmed publisher..We propose that the observed changes in Chl metabolism are part of the host defense response. Further insight into the lipid metabolism in T. gondii infection may provide novel targets for therapeutic agents. ..
- Blakeman K. Finding research information on the web: how to make the most of Google and other free search tools. Sci Prog. 2013;96:61-84 pubmed
- Chawla N, Davis D. Bringing big data to personalized healthcare: a patient-centered framework. J Gen Intern Med. 2013;28 Suppl 3:S660-5 pubmed..We present the foundations of work that takes a Big Data driven approach towards personalized healthcare, and demonstrate its applicability to patient-centered outcomes, meaningful use, and reducing re-admission rates. ..
- Zehir A, Benayed R, Shah R, Syed A, Middha S, Kim H, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med. 2017;23:703-713 pubmed publisher..Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible. ..
- Luo Y, Li Z, Guo H, Cao H, Song C, Guo X, et al. Predicting congenital heart defects: A comparison of three data mining methods. PLoS ONE. 2017;12:e0177811 pubmed publisher..All three models are precise enough to identify groups at high risk of CHD. They should all be considered for future investigations of other birth defects and diseases. ..
- Cremaschi P, Rovida S, Sacchi L, Lisa A, Calvi F, Montecucco A, et al. CorrelaGenes: a new tool for the interpretation of the human transcriptome. BMC Bioinformatics. 2014;15 Suppl 1:S6 pubmed publisher..expression data available in public repositories has grown exponentially in the last years, now requiring new data mining tools to transform them in information easily accessible to biologists...
- Salusso A, Zlocowski N, Mayol G, Zamponi N, RÃ³polo A. Histone methyltransferase 1 regulates the encystation process in the parasite Giardia lamblia. FEBS J. 2017;284:2396-2409 pubmed publisher..Altogether, these findings suggest that the function of HMT1 is critical for the success and timing of the encystation process, and reinforce the idea that epigenetic marks are critical for cyst formation in G. lamblia. ..
- Raja K, Subramani S, Natarajan J. A hybrid named entity tagger for tagging human proteins/genes. Int J Data Min Bioinform. 2014;10:315-28 pubmed..47, F-score of 75.77 and outperforms most of the state-of-the-art systems. However, the recall of 71.60 still remains low and leaves much room for future improvement. ..
- Zheng J, Howsmon D, Zhang B, Hahn J, McGuinness D, Hendler J, et al. Entity linking for biomedical literature. BMC Med Inform Decis Mak. 2015;15 Suppl 1:S4 pubmed publisher..By providing a small benchmark data set and identifying opportunities, we hope to stimulate discussions across natural language processing and bioinformatics and motivate others to develop techniques for this largely untapped domain. ..
- Liao V, Chen M. Efficient mining gapped sequential patterns for motifs in biological sequences. BMC Syst Biol. 2013;7 Suppl 4:S7 pubmed publisher..Biological data mining yield impact in diverse biological fields, such as discovery of co-occurring biosequences, which is important ..
- Moskalev A, Shaposhnikov M, Plyusnina E, Plyusnin S, Shostal O, Aliper A, et al. Exhaustive data mining comparison of the effects of low doses of ionizing radiation, formaldehyde and dioxins. BMC Genomics. 2014;15 Suppl 12:S5 pubmed publisher..They can also be useful in the development of new bio-sensing methods for detection of pollutants in the environment and combating the deleterious effects. ..
- Harpaz R, Odgers D, Gaskin G, DuMouchel W, Winnenburg R, Bodenreider O, et al. A time-indexed reference standard of adverse drug reactions. Sci Data. 2014;1:140043 pubmed publisherUndetected adverse drug reactions (ADRs) pose a major burden on the health system. Data mining methodologies designed to identify signals of novel ADRs are of deep importance for drug safety surveillance...
- Hakala K, Van Landeghem S, Salakoski T, Van de Peer Y, Ginter F. Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis. BMC Bioinformatics. 2015;16 Suppl 16:S3 pubmed publisher..A detailed performance and error analysis provides more insight into the relatively low recall rates. ..
- Liu J, Pan J, Wang Y, Lin D, Shen D, Yang H, et al. Component analysis of Chinese medicine and advances in fuming-washing therapy for knee osteoarthritis via unsupervised data mining methods. J Tradit Chin Med. 2013;33:686-91 pubmed..for knee osteoarthritis (KOA), and develop new fuming-washing prescriptions for KOA through unsupervised data mining methods. Chinese medicine recipes for fuming-washing therapy for KOA were collected and recorded in a database...
- Wu J, Guo W, Zhang X, Yang B, Zhang B. [Study on medication regularity of grand master of traditional Chinese medicine YAN Zheng-hua's Ostreae Concha-containing prescriptions based on data mining]. Zhongguo Zhong Yao Za Zhi. 2014;39:2762-6 pubmed
- Soldatova L, Nadis D, King R, Basu P, Haddi E, BaumlÃ© V, et al. EXACT2: the semantics of biomedical protocols. BMC Bioinformatics. 2014;15 Suppl 14:S5 pubmed publisher..It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format. ..
- Khare R, Good B, Leaman R, Su A, Lu Z. Crowdsourcing in biomedicine: challenges and opportunities. Brief Bioinform. 2016;17:23-32 pubmed publisher..Finally, we identify important emerging trends, opportunities and remaining challenges for future crowdsourcing research in biomedicine. ..
- Hetrick K, van der Donk W. Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era. Curr Opin Chem Biol. 2017;38:36-44 pubmed publisher..We also discuss a small number of the many RiPPs discovered in the years 2014-2016. ..
- Shi P, Wu T, Li P, Guo B, Fang G, Dong Y. Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD. IET Syst Biol. 2017;11:65-68 pubmed publisher..Finally, the authors compared the constructed plasmid with other successful examples in BLAST and PlasMapper software to demonstrate the rationality of the orderly logic gate. ..
- Marx P, Antal P, Bolgár B, Bagdy G, Deakin B, Juhasz G. Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression. PLoS Comput Biol. 2017;13:e1005487 pubmed publisher..The computed interactive comprehensive multimorbidity views over the diseasome are available on the web at Co=MorNet: bioinformatics.mit.bme.hu/UKBNetworks. ..
- Kumar D, Hassan M, Pattnaik N, Mohapatra N, Dixit M. Reduced expression of IQGAP2 and higher expression of IQGAP3 correlates with poor prognosis in cancers. PLoS ONE. 2017;12:e0186977 pubmed publisher..Our in-vivo (IHC) data confirmed the in-silico findings completely. Hence, IQGAP2 and IQGAP3 have potential to be used as prognostic markers or therapeutic targets in specific cancers. ..
- Zeng S, Duan L, Chen B, Li P, Liu E. Chemicalome and metabolome profiling of polymethoxylated flavonoids in Citri Reticulatae Pericarpium based on an integrated strategy combining background subtraction and modified mass defect filter in a Microsoft Excel Platform. J Chromatogr A. 2017;1508:106-120 pubmed publisher..an integrated strategy that combined background subtraction program and modified mass defect filter (MMDF) data mining in a Microsoft Excel platform for chemicalome and metabolome profiling of the polymethoxylated flavonoids (PMFs)..
- Covell D. A data mining approach for identifying pathway-gene biomarkers for predicting clinical outcome: A case study of erlotinib and sorafenib. PLoS ONE. 2017;12:e0181991 pubmed publisherA novel data mining procedure is proposed for identifying potential pathway-gene biomarkers from preclinical drug sensitivity data for predicting clinical responses to erlotinib or sorafenib...
- Kapraun D, Wambaugh J, Ring C, Tornero Velez R, Setzer R. A Method for Identifying Prevalent Chemical Combinations in the U.S. Population. Environ Health Perspect. 2017;125:087017 pubmed publisher..population. We demonstrated how FIM can be used in conjunction with biomonitoring data to narrow a large number of possible chemical combinations down to a smaller set of prevalent chemical combinations. https://doi.org/10.1289/EHP1265. ..
- Mao Y, Van Auken K, Li D, Arighi C, McQuilton P, Hayman G, et al. Overview of the gene ontology task at BioCreative IV. Database (Oxford). 2014;2014: pubmed publisher..http://www.biocreative.org/tasks/biocreative-iv/track-4-GO/. ..
- Sacchi L, Dagliati A, Segagni D, Leporati P, Chiovato L, Bellazzi R. Improving risk-stratification of Diabetes complications using temporal data mining. Conf Proc IEEE Eng Med Biol Soc. 2015;2015:2131-4 pubmed publisher..In this work we show how temporal data mining can be fruitfully exploited to improve risk stratification...