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FlyBase 102—advanced approaches to interrogating FlyBase

Susan E. St. Pierre, Laura Ponting, Raymund Stefancsik, Peter McQuilton
2013 Nucleic Acids Research  
Here, we demonstrate some of our more advanced searching systems and highlight some of our new tools for searching the wealth of data on FlyBase.  ...  Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase  ...  ACKNOWLEDGEMENTS We would like to thank the PIs, curators and developers of FlyBase for their comments on the manuscript.  ... 
doi:10.1093/nar/gkt1092 pmid:24234449 pmcid:PMC3964969 fatcat:mwzvr4w5ajhn7phzqly6iwjari

In-silico definition of the Drosophila melanogaster matrisome [article]

Martin N Davis, Sally Horne-Badovinac, Alexandra Naba
2019 bioRxiv   pre-print
: The Matrisome Project, FlyBase, and GLAD.  ...  Using a similar approach, we report here that the Drosophila matrisome is composed of 641 genes.  ...  The databases Flybase, DIOPT, and Ensembl were interrogated with the full list of human and mouse matrisome and matrisome-associated gene symbols.  ... 
doi:10.1101/722868 fatcat:52ljnmqgdzgx3gzkj53efx2gvm

A genome-scale metabolic model of Drosophila melanogaster for integrative analysis of brain diseases [article]

Müberra Fatma Cesur, Kiran Patil, Tunahan Çakīr
2022 bioRxiv   pre-print
We here report a comprehensively curated genome-scale metabolic network model of Drosophila using an orthology-based approach.  ...  Overall, iDrosophila1 is promising to investigate systems-level metabolic alterations in response to genetic and environmental perturbations.  ...  Acknowledgments We would like to thank Katharina Zirngibl for providing the genome scale metabolic network of human, which was used as the template in the current study.  ... 
doi:10.1101/2022.08.22.504778 fatcat:hgxwdhp335hvzlw3tshf2shlva

The BioGRID interaction database: 2015 update

Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Rose Oughtred, Lorrie Boucher, Sven Heinicke, Daici Chen, Chris Stark, Ashton Breitkreutz, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Julie Nixon (+10 others)
2014 Nucleic Acids Research  
, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control.  ...  This interaction count represents a 50% increase compared to our previous 2013 BioGRID update.  ...  BioGRID evidence codes are periodically updated to reflect new advances in experimental methods.  ... 
doi:10.1093/nar/gku1204 pmid:25428363 pmcid:PMC4383984 fatcat:jeok6meldzhmphu3mpxqxpeoiy

Identification of Genetic Modifiers of TDP-43 Neurotoxicity in Drosophila

Lihong Zhan, Keith A. Hanson, Sang Hwa Kim, Apeksha Tare, Randal S. Tibbetts, Guy Tear
2013 PLoS ONE  
mutants in neurons is sufficient to induce neurotoxicity, paralysis, and early death.  ...  The combined findings identified pathways whose deregulation might contribute to TDP-43-induced neurotoxicity in Drosophila.  ...  Acknowledgments The authors would like to thank Andrew Peterson and Dr.  ... 
doi:10.1371/journal.pone.0057214 pmid:23468938 pmcid:PMC3584124 fatcat:hz6mcugpfbdg7b7zzrd6f2plqq

Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

E. G. King, C. M. Merkes, C. L. McNeil, S. R. Hoofer, S. Sen, K. W. Broman, A. D. Long, S. J. Macdonald
2012 Genome Research  
This work was supported by the following NIH R01 grants: RR024862 to S.J.M. and A.D.L.,  ...  ) , and the fact that low frequency variants are poorly interrogated.  ...  complement the GWAS approach.  ... 
doi:10.1101/gr.134031.111 pmid:22496517 pmcid:PMC3409269 fatcat:ykgvskalhbg6jhjwvkt23kg324

Major prospects for exploring canine vector borne diseases and novel intervention methods using 'omic technologies

Robin B Gasser, Cinzia Cantacessi, Bronwyn E Campbell, Andreas Hofmann, Domenico Otranto
2011 Parasites & Vectors  
have provided insights into CVBDs, there has been limited exploration of fundamental molecular aspects of most pathogens, their vectors, pathogen-host relationships and disease and drug resistance using advanced  ...  Tackling key biological questions employing these technologies will provide a 'systems biology' context and could lead to radically new intervention and management strategies against CVBDs.  ...  [100] [101] [102] ).  ... 
doi:10.1186/1756-3305-4-53 pmid:21489242 pmcid:PMC3095997 fatcat:ckupzypfp5frhnlm4wi5kqscbm

Rate and cost of adaptation in the Drosophila Genome [article]

Stephan Schiffels, Michael Lässig, Ville Mustonen
2014 arXiv   pre-print
Hitchhiking of deleterious alleles generates a substantial collateral cost of adaptation, leading to a fitness decline of about 30/2N per gene and per million years in the lowest-recombining regions.  ...  We would like to thank P.W. Messer for comments on an earlier version of the manuscript.  ...  St Pierre SE, Ponting L, Stefancsik R, McQuilton P, FlyBase Consortium (2014) FlyBase 102----advanced approaches to interrogating FlyBase. Nucleic Acids Res 42: D780-D788. doi:10.1093/nar/gkt1092.  ... 
arXiv:1409.1946v1 fatcat:lyx7drmgbfhotnj5ckxjkdrhsu

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Farhana R. Pinu, David J. Beale, Amy M. Paten, Konstantinos Kouremenos, Sanjay Swarup, Horst J. Schirra, David Wishart
2019 Metabolites  
Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches.  ...  We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies.  ...  Acknowledgments: The authors would like to thank the organizing committee of ANZMET 2018. Conflicts of Interest: The authors declare no conflict of interest. Metabolites 2019, 9, 76  ... 
doi:10.3390/metabo9040076 pmid:31003499 pmcid:PMC6523452 fatcat:deiwu7rgpnb3tfr7glbewoyar4

A multi-informatic description of neural differentiation in the Drosophila type-II neuroblast lineages [article]

Nigel S Michki, Ye Li, Kayvon Sanjasaz, Yimeng Zhao, Fred Y Shen, Logan A Walker, Cheng-Yu Lee, Dawen Cai
2020 bioRxiv   pre-print
In this work, we interrogated the type-II neuroblast lineages in the developing Drosophila brain using targeted single-cell mRNA sequencing.  ...  To adopt terminal neural fates, neural progenitors respond to a combination of molecular factors, the interplay between which remains difficult to untangle.  ...  FlyBase Reference Report: FlyBase, 2019-, Computation of D. melanogaster genes relevant to disease based 514 on their orthology to human "disease genes". 515 Gold, K.S., and Brand, A.H. (2014).  ... 
doi:10.1101/2020.07.02.184549 fatcat:ef2o6cn7afeofjukmpgeqz45re

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)

Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen (+7 others)
2007 BMC Bioinformatics  
To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes  ...  The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers  ...  Huang, and by the National Research Program for Genomic Medicine (NRPGM), National Science Council (Taiwan) (NSC95-3112-B-011-013-Y, Advanced Bioinformatics Core) to C. Hsu.  ... 
doi:10.1186/1471-2105-8-66 pmid:17326819 pmcid:PMC1828168 fatcat:bredj7xrcrajvbbujgmt35z6wa

Genomics, gene expression and DNA arrays

David J. Lockhart, Elizabeth A. Winzeler
2000 Nature  
Information on genomic sequence can be used experimentally with high-density DNA arrays that allow complex mixtures of RNA and DNA to be interrogated in a parallel and quantitative fashion.  ...  Experimental genomics in combination with the growing body of sequence information promise to revolutionize the way cells and cellular processes are studied.  ...  Our ability to extract knowledge from measurements of global gene expression tends to increase with time as additional information becomes available, and results can be subjected to further interrogation  ... 
doi:10.1038/35015701 pmid:10866209 fatcat:n46bsxddfjgx3gneznjvgqxfwu

Aralar Sequesters GABA into Hyperactive Mitochondria, Causing Social Behavior Deficits

Alexandros K. Kanellopoulos, Vittoria Mariano, Marco Spinazzi, Young Jae Woo, Colin McLean, Ulrike Pech, Ka Wan Li, J. Douglas Armstrong, Angela Giangrande, Patrick Callaerts, August B. Smit, Brett S. Abrahams (+3 others)
2020 Cell  
Although mitochondrial function is crucial for brain homeostasis, it remains unknown whether mitochondrial disruption contributes to social behavioral deficits.  ...  We identify the regulation of GABA availability by mitochondrial activity as a biologically relevant mechanism and demonstrate its contribution to social behavior.  ...  The index of approaches in such a complex set up (8 flies) was used to quantify behavior.  ... 
doi:10.1016/j.cell.2020.02.044 pmid:32200800 fatcat:7mpemmg7jze43imlnwgijn5zzu

Strategies for exploring TGF-β signaling in Drosophila

Aidan J. Peterson, Michael B. O'Connor
2014 Methods  
Studies rooted in classical and molecular genetic approaches continue to uncover new developmental roles for TGF-beta signaling.  ...  In addition to fleshing out how TGF-beta signaling serves the fruit fly, we anticipate that future studies will uncover new regulatory nodes and modes and will continue to advance paradigms for how TGF-beta  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1016/j.ymeth.2014.03.016 pmid:24680699 pmcid:PMC4057889 fatcat:tpvtpcsjkzgmhmrs34dxm637ia

Identifying transcriptional cis -regulatory modules in animal genomes

Kushal Suryamohan, Marc S. Halfon
2014 Wiley Interdisciplinary Reviews: Developmental Biology  
Computational methods include comparative genomics, clustering of known or predicted transcription factor binding sites, and supervised machine-learning approaches trained on known CRMs.  ...  Gene expression is regulated through the activity of transcription factors and chromatin modifying proteins acting on specific DNA sequences, referred to as cis-regulatory elements.  ...  We apologize to all those whose valuable contributions to the field we were unable to acknowledge due to space limitations.  ... 
doi:10.1002/wdev.168 pmid:25704908 pmcid:PMC4339228 fatcat:7lm4krbdfzcyxei7k2nwhg66ni
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