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Genetic Network Inference Using Hierarchical Structure

Shuhei Kimura, Masato Tokuhisa, Mariko Okada-Hatakeyama
2016 Frontiers in Physiology  
We take this step using an existing method that combines a genetic network inference method with a bootstrap method.  ...  The improvement accomplished by the use of the hierarchical structure is small. However, the hierarchical structure could be used to improve the performances of many existing inference methods.  ...  The method proposed in this study, on the other hand, searches for them using multiple genetic networks inferred by the bootstrap approach.  ... 
doi:10.3389/fphys.2016.00057 pmid:26941653 pmcid:PMC4763037 fatcat:c24tq5mh6vftbgl5zwbugdfsdm

Using A Priori Knowledge after Genetic Network Inference: Integrating Multiple Kinds of Knowledge
遺伝子ネットワーク同定後の事前知識利用法: 複数の事前知識の統合

Shuhei Kimura, Koji Kitazawa, Masato Tokuhisa, Mariko Okada-Hatakeyama
2017 Chem-Bio Informatics Journal  
The framework uses a priori knowledge only to modify the genetic network that has already been inferred by the other inference method.  ...  Yet the genetic networks inferred by these methods often contain large numbers of false-positive regulations along with the true-positives.  ...  Acknowledgements This work has been supported by JSPS KAKENHI Grant Number 26330275.  ... 
doi:10.1273/cbij.17.53 fatcat:7nvzttg2gbcxphdzn2dtjegiay

Mitochondrial DNA from Prehistoric Canids Highlights Relationships Between Dogs and South-East European Wolves

Fabio Verginelli, Cristian Capelli, Valentina Coia, Marco Musiani, Mario Falchetti, Laura Ottini, Raffaele Palmirotta, Antonio Tagliacozzo, Iacopo De Grossi Mazzorin, Renato Mariani-Costantini
2005 Molecular biology and evolution  
Acknowledgments This work was supported by the Italian National Re-  ...  Networks based on the 262-bp PIC segment were also constructed by MP method using TCS version 1.13 (Clement, Posada, and Crandall 2000) , where the probability of parsimony, calculated for pairwise differences  ...  Materials and Methods Specimens and Radiocarbon Dating PIC specimens were provided by the Luigi Pigorini National Prehistoric-Ethnographic Museum (LPM), Rome, and by the Laboratory of Archaeozoology (LA  ... 
doi:10.1093/molbev/msi248 pmid:16120801 fatcat:bap7og4it5enbdcpmrbr6r2yhq

Influenza A(H7N9) virus emerged and resulted in human infections in Chongqing, southwestern China since 2017

Kun Su, Sheng Ye, Qin Li, Weijia Xie, Hongyue Yu, Li Qi, Yu Xiong, Han Zhao, Baisong Li, Hua Ling, Yun Tang, Bangzhong Xiao (+3 others)
2019 International Journal of Infectious Diseases  
Genetic sequencing and phylogenetic analysis were also conducted.  ...  This study aimed to describe the epidemiological characteristics of the first epidemic in this region. Methods: The epidemiological data of patients were collected.  ...  We gratefully acknowledge the authors, originating and submitting laboratories of the influenza A(H7N9) virus sequences from GISAID's EpiFlu Database and NIH's Genbank used in the phylogenetic analysis  ... 
doi:10.1016/j.ijid.2019.02.011 fatcat:qgzdjccwk5d7xjxvlycxsv54m4

Emergence and Evolution of H10 Subtype Influenza Viruses in Poultry in China

Chi Ma, Tommy Tsan-Yuk Lam, Yujuan Chai, Jia Wang, Xiaohui Fan, Wenshan Hong, Yu Zhang, Lifeng Li, Yongmei Liu, David K. Smith, Richard J. Webby, Joseph S. M. Peiris (+3 others)
2015 Journal of Virology  
Phylogenetic analysis of H10 and related viruses showed that the chicken H10N8 viruses were generated through multiple reassortments between H10 and N8 viruses from domestic ducks and the enzootic chicken  ...  The emergence and prevalence of H10 viruses in chickens and the occurrence of human infections provide direct evidence of the threat from the current influenza ecosystem in China.IMPORTANCEAfter the outbreak  ...  ACKNOWLEDGMENTS This study was supported by the Li Ka Shing Foundation, the Shenzhen Peacock Plan High-End Talents Program (KQTD201203), the University Grants Committee of the Hong Kong SAR (Area of Excellence  ... 
doi:10.1128/jvi.03167-14 pmid:25589662 pmcid:PMC4403437 fatcat:ezozm5dqe5cjrm7hasqs4jxsiy

Regulatory back-up circuit of medaka Wt1 co-orthologs ensures PGC maintenance

Nils Klüver, Amaury Herpin, Ingo Braasch, Julia Drieβle, Manfred Schartl
2009 Developmental Biology  
Analysis of morpholino knockdown experiments revealed functions of wt1 genes in pronephros development.  ...  Unexpectedly, by down-regulating Wt1a protein we observed wt1b expression during embryogenesis in the wildtype wt1a expression domains including somatic cells of the gonadal primordium.  ...  This work was supported by the DFG-Graduiertenkolleg 1048 (Molecular Basis of Organ Development in Vertebrates) through a PhD fellowship to NK and by a grant of the Rudolf-Virchow-Zentrum for Experimental  ... 
doi:10.1016/j.ydbio.2008.10.009 pmid:18992736 fatcat:ed2lq3iaazh2rc2ydexo4ma7eq

Climate connectivity of the bobcat in the Great Lakes region

Robby R. Marrotte, Jeff Bowman, Paul J. Wilson
2020 Ecology and Evolution  
Functional connectivity in southern Ontario is relatively low and was limited in part by the low amount of forest cover.  ...  Pathways across the Great Lakes were through the Niagara region and through the Lower Peninsula of Michigan over the Straits of Mackinac and the St. Marys River.  ...  This information can be used to infer past patterns of movements of individuals and their genes across the landscape (Holderegger & Wagner, 2008) .  ... 
doi:10.1002/ece3.6049 pmid:32128144 pmcid:PMC7042766 fatcat:k4t4xv4omvf7fhcbyaappqu6l4

The Apportionment of Total Genetic Variation by Categorical Analysis of Variance

Tsung Fei Khang, Von Bing Yap
2010 Statistical Applications in Genetics and Molecular Biology  
This method potentially challenges researchers to rethink conclusions derived from a well-known method known as the analysis of molecular variance (AMOVA).  ...  We wish to suggest the categorical analysis of variance as a means of quantifying the proportion of total genetic variation attributed to different sources of variation.  ...  The SSBR is computed by complementation. The parameters of interest can be similarly found using methods in Section 3.1.  ... 
doi:10.2202/1544-6115.1482 pmid:20196757 fatcat:vcjenou7r5c5fjrir5oneotgc4

Runx1 is required for zebrafish blood and vessel development and expression of a human RUNX1-CBF2T1 transgene advances a model for studies of leukemogenesis

Maggie L Kalev-Zylinska, Julia A Horsfield, Maria Vega C Flores, John H Postlethwait, Maria R Vitas, Andrea M Baas, Philip S Crosier, Kathryn E Crosier
2002 Development  
To further elucidate the role of RUNX1 in hematopoiesis, we cloned the zebrafish ortholog (runx1) and analyzed its function using this model system.  ...  Depletion of Runx1 with antisense morpholino oligonucleotides abrogated the development of both blood and vessels, as demonstrated by loss of circulation, incomplete development of vasculature and the  ...  Phylogenetic analysis Phylogenetic analysis was performed using the Phylogenetic Inference Package, PHYLIP 3.5 (Felsenstein, 1993) . The sequences were aligned using the ClustalW method.  ... 
pmid:11934867 fatcat:fbkb54dnmfdg7i2e4u2g5unpni

Can Religion Insure Against Aggregate Shocks to Happiness? The Case of Transition Countries

Olga Popova
2010 Social Science Research Network  
The determinants of happiness to be similar to developed coun- tries are found by studies that use a single transition country for the analysis (for instance, Russia by Veenhoven, 2001 and Graham et al  ...  Thus, the magnitudes of the e¤ects of explanatory variables on dependent variables are robust to the estimation method used.  ... 
doi:10.2139/ssrn.1699984 fatcat:7cmin3gtcrfqxnzrww4jey4jh4

Mapping Spread and Risk of Avian Influenza A (H7N9) in China

Li-Qun Fang, Xin-Lou Li, Kun Liu, Yin-Jun Li, Hong-Wu Yao, Song Liang, Yang Yang, Zi-Jian Feng, Gregory C. Gray, Wu-Chun Cao
2013 Scientific Reports  
We then collected data of agro-ecological, environmental and meteorological factors at the county level, and used boosted regression tree (BRT) models to examine the relative contribution of each factor  ...  These findings could be used to inform targeted surveillance and control efforts in both human and animal populations to reduce the risk of future human infections.  ...  Charlie Kidd of the Emerging Pathogens Institute, University of Florida, for his technical editing of the manuscript. This study was supported by a  ... 
doi:10.1038/srep02722 pmid:24072008 pmcid:PMC3784030 fatcat:nsnqofz55ncwppxejmsemipz3i

Flood Prediction Using Machine Learning Models: Literature Review

Amir Mosavi, Pinar Ozturk, Kwok-wing Chau
2018 Water  
on the various ML algorithms used in the field.  ...  This survey can be used as a guideline for hydrologists as well as climate scientists in choosing the proper ML method according to the prediction task.  ...  REVIEW 20 of Comparative performance analysis of hybrid methods of ML for short-term flood prediction, using R 2 and RMSE.  ... 
doi:10.3390/w10111536 fatcat:5ewkgi4oibbkhn7nievusbyrim

Aerobiology in High Latitudes: Evidence of Bacteria Acting as Tracer of Warm Air Mass Advection reaching Northern Antarctic Peninsula [article]

CESAR R.L. AMARAL, Alexandre Alencar, Marcelo Sampaio, Emanuele Kuhn, Vivian Pellizari, Alvaro Luiz Bertho, Jose Augusto Adler Pereira, Heitor Evangelista, Marcio Cataldo
2021 bioRxiv   pre-print
Use of satellite images combined with air mass back-trajectory analysis obtained from the NOAA/ HYSPLIT model corroborated the results.  ...  Despite the extent use of geochemical tracers to track warm air mass origin reaching the Antarctic continent, we present here evidences that microorganisms being transported by the atmosphere and deposited  ...  We also thank the CASA project and University of Maine to have provided the samplings at Detroit Plateau and measurements of the stable isotopes of oxygen.  ... 
doi:10.1101/2021.06.27.450079 fatcat:x2wbcsvno5h2ndb7dmne5h6qwm

Genetic Diversity and Population Structure of Leishmania infantum from Southeastern France: Evaluation Using Multi-Locus Microsatellite Typing

Christelle Pomares, Pierre Marty, Anne Laure Bañuls, Emmanuel Lemichez, Francine Pratlong, Benoît Faucher, Fakhri Jeddi, Sandy Moore, Grégory Michel, Srikanth Aluru, Renaud Piarroux, Mallorie Hide (+1 others)
2016 PLoS Neglected Tropical Diseases  
This study represents the most extensive population analysis of L. infantum isolates using MLMT conducted in France.  ...  A model-based analysis using STRUCTURE revealed two main populations: population A (consisting of samples primarily from the P and AM endemic areas with MON-1 and non-MON-1 strains) and population B consisting  ...  The data used in this study were processed at the GenSeq capillary electrophoresis facilities of the labex « Centre Méditerranéen de l'Environnement et de la Biodiversité », Montpellier.  ... 
doi:10.1371/journal.pntd.0004303 pmid:26808522 pmcid:PMC4726517 fatcat:cdjnkdvlbfhwhhemthkyo7ipmy

Secondary metabolism drives ecological breadth in the Xylariaceae [article]

Mario E.E. Franco, Jennifer H. Wisecaver, A. Elizabeth Arnold, Yu-Ming Ju, Jason C. Slot, Steven Ahrendt, Lillian P. Moore, Katharine E. Eastman, Kelsey Scott, Zachary Konkel, Stephen J. Mondo, Alan Kuo (+24 others)
2021 bioRxiv   pre-print
Global, large-scale surveys of phylogenetically diverse plant and lichen hosts have revealed an extremely high richness of endophytes in the Xylariales, one of the largest clades of filamentous fungi and  ...  Endophytes may produce host protective antimicrobial or insecticidal SMs, as well as compounds that facilitate symbiotic establishment through suppression or degradation of host immune response, but the  ...  ACKNOWLEDGEMENTS 845 Funding for the project was provided by the DOE JGI Large-scale Community Science Project (Grant  ... 
doi:10.1101/2021.06.01.446356 fatcat:kxb46rdbw5dybaou25abu7aamu
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