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2018 Update on Protein-Protein Interaction Data in WormBase

Jaehyoung Cho, Christian Grove, Kimberly Van Auken, Juancarlos Chan, Sibyl Gao, Paul W. Sternberg
2018 microPublication Biology  
Protein interaction is an important data type to understand the biological function of proteins involved in the interaction, and helps researchers to deduce the biological nature of unknown proteins from the well-characterized functions of their interaction partners. High-throughput studies, coupled with the aggregation of individual experiments, provides a global 'snapshot' of the protein interactions occurring at all levels of biological processes or circumstances. This snapshot of the
more » ... tion network, the interactome, is important to understand the overall events up to the level of comparison between species or pathway simulation, or to find new factors yet undefined in the processes, or to add details to the biological processes and pathways. As of September 2018, WormBase (www.wormbase.org) (Lee et al. 2018) contains 28,279 physical protein-protein interactions for the roundworm Caenorhabditis elegans. Among these, 1500 protein-protein interactions have been curated by BioGRID as a collaboration with WormBase. Within the data set, 17,990 protein-protein interactions are unique, and 6,079 unique genes are involved in these interactions. In order to visualize the overall interaction map, a network diagram for all the unique interactions was generated by using the 'Cytoscape' program, version 3.6.1 (Shannon et al. 2003) (Figure 1A). These numbers represent a 108% increase in the number of interaction annotations since last year, 2017. These interaction data were curated from 1,251 peer-reviewed papers, which were selected from the literature by 'Textpresso Central' using automatic SVM (Support Vector Machine)-based text mining approaches (Fang et al. 2012; Müller et al. 2018) and manual verification. Compared to other databases providing C. elegans protein-protein interaction, WormBase now presents the largest data set, which has 1.72-fold more interaction annotations than IMEx (Orchard et al. 2012) and 4.51-fold more than BioGRID (Chatr-Aryamontri et al. 2017) (Figure 1B). Most significantly, WormBase [...]
doi:10.17912/micropub.biology.000074 pmid:32550373 pmcid:PMC7255808 fatcat:mratw6yixvcktivbqq2mvroya4

Vennter - An interactive analysis tool for WormBase interaction data using Venn diagrams

Jaehyoung Cho, Sibyl Gao, Lincoln Stein, Paul W Sternberg
2020 microPublication Biology  
Figure 1 : Vennter is an interactive Venn diagram tool for integrating different interaction data types as well as offering further analysis. (A) Examples of Vennter with different overlapping patterns among interaction data sets. (B) Vennter is an interactive tool providing hyperlinks to each gene page and batch analysis tools (SimpleMine and Gene-set Enrichment Analysis) for the genes selected from a specific area within the diagram (see hatched lines).
doi:10.17912/micropub.biology.000258 pmid:32550480 pmcid:PMC7251783 fatcat:efi7i5lfrbhs7ew5gadnnxau2a

Editorial for the special issue of "Computational methods for molecular imaging" for computerized medical imaging and graphics

Kuangyu Shi, Fei Gao, Nassir Navab, Julia Schnabel, Pengcheng Shi, Sibylle I. Ziegler
2017 Computerized Medical Imaging and Graphics  
Kuangyu Shi PII: S0895-6111(17)30055-1 DOI: http://dx.doi.org/doi:10.1016/j.compmedimag.2017.06.006 Reference: CMIG 1519 To appear in: Computerized Medical Imaging and Graphics Author: Fei Gao  ...  Pengcheng Shi PII: S0895-6111(17)30055-1 DOI: http://dx.doi.org/doi:10.1016/j.compmedimag.2017.06.006 Reference: CMIG 1519 To appear in: Computerized Medical Imaging and Graphics Author: Sibylle  ... 
doi:10.1016/j.compmedimag.2017.06.006 pmid:28701281 fatcat:lj5xcr47srbxvmkaklizellzzu

A single-cell transcriptome of mesenchymal stromal cells to fabricate bioactive hydroxyapatite materials for bone regeneration

Peng Guo, Xizhe Liu, Penghui Zhang, Zhongyuan He, Zhen Li, Mauro Alini, R. Geoff Richards, Sibylle Grad, Martin J. Stoddart, Guangqian Zhou, Xuenong Zou, Danny Chan (+5 others)
2021 Bioactive Materials  
Manman Gao: Conceptualization, Data curation, Writing -Conceptualization, Data curation, Writingreview & editing, Supervision, Project administration, Funding acquisition.  ...  Sibylle Grad: Conceptualization, Writingreview & editing. Martin J. Stoddart: Conceptualization, Writingreview & editing. Guangqian Zhou: Data curation, Writingreview & editing.  ... 
doi:10.1016/j.bioactmat.2021.08.009 fatcat:geg5ctincvdw7l5lfknyvqs5eu

Topological Hall Effect in Single Thick SrRuO3 Layers Induced by Defect Engineering

Changan Wang, Ching-Hao Chang, Andreas Herklotz, Chao Chen, Fabian Ganss, Ulrich Kentsch, Deyang Chen, Xingsen Gao, Yu-Jia Zeng, Olav Hellwig, Manfred Helm, Sibylle Gemming (+2 others)
2020 Advanced Electronic Materials  
The topological Hall effect (THE) has been discovered in ultrathin SrRuO3 (SRO) films, where the interface between the SRO layer and another oxide layer breaks the inversion symmetry resulting in the appearance of THE. Thus, THE only occurs in ultra-thin SRO films of several unit cells. In addition to employing a heterostructure, the inversion symmetry can be broken intrinsically in bulk SRO by introducing defects. In this study THE is observed in 60 nm thick SRO films, in which defects and
more » ... ice distortions are introduced by helium ion irradiation. The irradiated SRO films exhibit a pronounced THE in a wide temperature range from 5 K to 80 K. These observations can be attributed to the emergence of Dzyaloshinskii-Moriya interaction as a result of artificial inversion symmetry breaking associated to the lattice defect engineering. The creation and control of the THE in oxide single layers can be realized by ex situ film processing. Therefore, this work provides new insights into the THE and illustrates a promising strategy to design novel spintronics devices.
doi:10.1002/aelm.202000184 fatcat:tzsquxmtl5fzray4h53tiqksdi

WormBase 2017: molting into a new stage

Raymond Y N Lee, Kevin L Howe, Todd W Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J Chen, Paul Davis, Sibyl Gao, Christian Grove, Ranjana Kishore, Hans-Michael Muller (+18 others)
2017 Nucleic Acids Research  
WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such
more » ... s micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, Worm-Base, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.
doi:10.1093/nar/gkx998 pmid:29069413 pmcid:PMC5753391 fatcat:5rholx7nqvaurox74fnyrulgs4

WormBase 2016: expanding to enable helminth genomic research

Kevin L. Howe, Bruce J. Bolt, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Thomas Down, Sibyl Gao, Christian Grove, Todd W. Harris, Ranjana Kishore (+22 others)
2015 Nucleic Acids Research  
WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we
more » ... have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.
doi:10.1093/nar/gkv1217 pmid:26578572 pmcid:PMC4702863 fatcat:h3yxwojkojgszivof7ahs6fprq

Genome-Wide Association Study of Multiplex Schizophrenia Pedigrees

Douglas F. Levinson, Jianxin Shi, Kai Wang, Sang Oh, Brien Riley, Ann E. Pulver, Dieter B. Wildenauer, Claudine Laurent, Bryan J. Mowry, Pablo V. Gejman, Michael J. Owen, Kenneth S. Kendler (+34 others)
2012 American Journal of Psychiatry  
The authors used a genome-wide association study (GWAS) of multiply affected families to investigate the association of schizophrenia to common single-nucleotide polymorphisms (SNPs) and rare copy number variants (CNVs). The family sample included 2,461 individuals from 631 pedigrees (581 in the primary European-ancestry analyses). Association was tested for single SNPs and genetic pathways. Polygenic scores based on family study results were used to predict case-control status in the
more » ... nia Psychiatric GWAS Consortium (PGC) data set, and consistency of direction of effect with the family study was determined for top SNPs in the PGC GWAS analysis. Within-family segregation was examined for schizophrenia-associated rare CNVs. No genome-wide significant associations were observed for single SNPs or for pathways. PGC case and control subjects had significantly different genome-wide polygenic scores (computed by weighting their genotypes by log-odds ratios from the family study) (best p=10(-17), explaining 0.4% of the variance). Family study and PGC analyses had consistent directions for 37 of the 58 independent best PGC SNPs (p=0.024). The overall frequency of CNVs in regions with reported associations with schizophrenia (chromosomes 1q21.1, 15q13.3, 16p11.2, and 22q11.2 and the neurexin-1 gene [NRXN1]) was similar to previous case-control studies. NRXN1 deletions and 16p11.2 duplications (both of which were transmitted from parents) and 22q11.2 deletions (de novo in four cases) did not segregate with schizophrenia in families. Many common SNPs are likely to contribute to schizophrenia risk, with substantial overlap in genetic risk factors between multiply affected families and cases in large case-control studies. Our findings are consistent with a role for specific CNVs in disease pathogenesis, but the partial segregation of some CNVs with schizophrenia suggests that researchers should exercise caution in using them for predictive genetic testing until their effects in diverse populations have been fully studied.
doi:10.1176/appi.ajp.2012.11091423 pmid:22885689 pmcid:PMC6927206 fatcat:hzuenge6rnesdpf4iocph5csv4

Characterization of the Branched-Chain Amino Acid Aminotransferase Enzyme Family in Tomato

G. S. Maloney, A. Kochevenko, D. M. Tieman, T. Tohge, U. Krieger, D. Zamir, M. G. Taylor, A. R. Fernie, H. J. Klee
2010 Plant Physiology  
Peng-Cheng Wei, Feng Tan, Xin-Qi Gao, Xiu-Qing Zhang, Gao-Qi Wang, Heng Xu, Li-Juan Li, Jia Chen, and Xue-Chen Wang 1031 [C] Two Closely Related Genes of Arabidopsis Encode Plastidial Cytidinediphosphate  ...  Birgit Agne, Charles Andrès, Cyril Montandon, Bastien Christ, Anouk Ertan, Friederike Jung, Sibylle Infanger, Sylvain Bischof, Sacha Baginsky, and Felix Kessler 1016 DEVELOPMENT AND HORMONE ACTION [C][  ... 
doi:10.1104/pp.110.154922 pmid:20435740 pmcid:PMC2899903 fatcat:jr7nhuei4jdoxpsdtm4wsetzym

Are protons still dominant at the knee of the cosmic-ray energy spectrum?

M. Amenomori, S. Ayabe, D. Chen, S.W. Cui, Danzengluobu, L.K. Ding, X.H. Ding, C.F. Feng, Z.Y. Feng, X.Y. Gao, Q.X. Geng, H.W. Guo (+66 others)
2006 Physics Letters B  
The proton spectrum can be expressed by a single power-law function with a differential index of -3.01 ± 0.11 and -3.05 ± 0.12 based on the QGSJET+HD and SIBYLL+HD models, respectively, which are steeper  ...  Fraction of the primary cosmic-rays heavier than helium nuclei obtained by assuming the QGSJET and SIBYLL interaction models. Our results are compared with those by the KASCADE experiment (2) .  ... 
doi:10.1016/j.physletb.2005.10.048 fatcat:wfv65htmcvhlzdp25vjlunnqiq

BMC Biotechnology reviewer acknowledgement 2014

Dafne Solera
2015 BMC Biotechnology  
Bruria Funkenstein Israel Sushama Gaikwad India Junping Gao China Manuel Garrido Portugal Brigitte Gasser Austria Elena Geiser Germany Richard Gemeinhart USACorinne Hoesli CanadaDirk Hoffmeister  ...  Lefebvre FranceJean-Luc Lenormand FranceThierry Leroy FranceRandolph Lewis USA Andrea Germer Germany Ellen Goldman USA Sailaja Gopalakrishnanchettiar Sivakamiammal USA Billie Gould Canada Sibylle  ... 
doi:10.1186/s12896-015-0119-y fatcat:s6ptzxjd4ng7ra6meuwqra7yne

Simulation of winter wheat response to variable sowing dates and densities in a high-yielding environment

Sibylle Dueri, Hamish Brown, Senthold Asseng, Frank Ewert, Heidi Webber, Mike George, Rob Craigie, Jose Rafael Guarin, Diego N L Pequeno, Tommaso Stella, Mukhtar Ahmed, Phillip D Alderman (+41 others)
2022 Journal of Experimental Botany  
Crop multi-model ensembles (MME) have proven to be effective in increasing the accuracy of simulations in modelling experiments. However, the ability of a MME to capture crop response to changes in sowing dates and densities has not yet been investigated. These management interventions are some of the main levers for adapting cropping systems to climate change. Here, we explore the performance of a MME of 29 wheat crop models to predict the effect of changing sowing dates and rates on yield and
more » ... yield components, on two sites located in a high-yielding environment in New Zealand. The experiment was conducted for 6 years and provided 50 combinations of sowing date, sowing density and growing season.". We show that the MME simulates seasonal growth of wheat well under standard sowing conditions, but fails under early sowing and high sowing rates. The comparison between observed and simulated in-season fraction of intercepted photosynthetically active radiation (FIPAR) for early sown wheat shows that the MME does not capture the decrease of crop above ground biomass during winter months due to senescence. Models need to better account for tiller competition for light, nutrients and water during vegetative growth, and early tiller senescence and tiller mortality, which are exacerbated by early sowing, high sowing densities and warmer winter temperatures.
doi:10.1093/jxb/erac221 pmid:35728801 fatcat:4log5zefjvejna2w7vx7pjdg5a

SIBYL: A Method for Detecting Similar Binary Functions Using Machine Learning

Yuma MASUBUCHI, Masaki HASHIMOTO, Akira OTSUKA
2022 IEICE transactions on information and systems  
The experimental results showed that SIBYL outperforms existing research.  ...  In this paper, we propose SIBYL, a combination of Transformer and node2vec.  ...  [5] , VulSeeker by Gao et al. [6] , CA-COMPAIR by Hu et al. [7] , and Gemini by Xu et al. [8] .  ... 
doi:10.1587/transinf.2021edp7135 fatcat:o4o5fv3mzjb5zis2pmxzamltom

Page 3546 of Mathematical Reviews Vol. , Issue 2001E [page]

2001 Mathematical Reviews  
I Gao, Bin ... Gao, Fan ........ Gao, Fu Qing . Gao, Hongjun Gao, Li .. Gao, Ping Gao, Ping! Gao, Shuhong . Gao, Suixiang Gao, Tangan ... Gao, Yi-Ming Gao, Yu Bin Gao, Zongsheng Garaev, M. Z.  ...  C. . 86002 Fritzsche, Bernd ‘ite 30068 47019 Frobenius, Georg Ferdinand See * 20001 Fréberg, Ralf ..... 13017 Frolov, Sergei Anatol’evich 81130 Frolov, Sergey See Frolov, Sergei Anatolevich Fréschle, Sibylle  ... 

Cosmic-ray energy spectrum around the knee observed with the Tibet air-shower experiment

M. Amenomori, X. J. Bi, D. Chen, S. W. Cui, Danzengluobu, L. K. Ding, X. H. Ding, C. Fan, C. F. Feng, Zhaoyang Feng, Z. Y. Feng, X. Y. Gao (+72 others)
2011 Astrophysics and Space Sciences Transactions (ASTRA)  
KASCADE reported that QGSJET model explains high energy data better than SIBYLL, on the other hand, SIBYLL model is better at lower energies.  ...  (Amenomori et al., SIBYLL TRACER H.E.S.S.QGS H.E.S.S.SIB Fig. 5.  ... 
doi:10.5194/astra-7-15-2011 fatcat:ynhonlkw6nbfhnvhldfayxr7ai
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