Filters








88 Hits in 2.3 sec

Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes

Diogo Pratas, Raquel Silva, Armando Pinho
2018 Entropy  
The last include mitochondrial DNA (mtDNA), messenger RNA (mRNA) and genomic DNA (gDNA) of seven primates.  ...  In this paper, we compare directly two information measures, the Normalized Compression Distance (NCD) and the Normalized Relative Compression (NRC).  ...  On the other hand, comparing Figure 2A with Figure 2B , we see an increase in the non-linear behaviour of the NCD, while the NRC seems to approximate to a linear behaviour.  ... 
doi:10.3390/e20060393 pmid:33265483 fatcat:ue3djnewkvhp7a47cpfjo3acva

GeCoAgent: A Conversational Agent for Empowering Genomic Data Extraction and Analysis

Pietro Crovari, Sara Pidò, Pietro Pinoli, Anna Bernasconi, Arif Canakoglu, Franca Garzotto, Stefano Ceri
2022 ACM Transactions on Computing for Healthcare  
Typical interactions require applying comparative data analysis to huge repositories of genomic information for building new knowledge, taking advantage of the latest findings in applied genomics for healthcare  ...  This work presents GeCoAgent, a big-data service for clinicians and biologists.  ...  ACKNOWLEDGEMENTS This work was supported by the ERC Advanced Grant 693174 "Data-Driven Genomic Computing (GeCo)".  ... 
doi:10.1145/3464383 fatcat:z55wpyjvhjdytkr6g53uflswyi

Stimulus-Dependent Regulation of Nuclear Ca2+ Signaling in Cardiomyocytes: A Role of Neuronal Calcium Sensor-1

Shu Nakao, Shigeo Wakabayashi, Tomoe Y. Nakamura, Derek Laver
2015 PLoS ONE  
To address these issues, we used a new region-specific fluorescent protein-based Ca 2+ indicator, GECO, together with the conventional probe Fluo-4 AM.  ...  On the other hand, receptor stimulation such as with insulin-like growth factor-1 (IGF-1) preferentially increased nuclear [Ca 2+ ] compared to cytoplasmic [Ca 2+ ].  ...  Haruka Kawakami for technical assistance of animal care. Author Contributions  ... 
doi:10.1371/journal.pone.0125050 pmid:25897502 pmcid:PMC4405540 fatcat:j55umxmypncf5nmxq6c46pkjmi

EDGAR 2.0: an enhanced software platform for comparative gene content analyses

Jochen Blom, Julian Kreis, Sebastian Spänig, Tobias Juhre, Claire Bertelli, Corinna Ernst, Alexander Goesmann
2016 Nucleic Acids Research  
Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics.  ...  By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study.  ...  ACKNOWLEDGEMENT The authors further wish to thank the Bioinformatics Core Facility (BCF) for expert technical support.  ... 
doi:10.1093/nar/gkw255 pmid:27098043 pmcid:PMC4987874 fatcat:5btj3lxjwngs5cqfuakgzestiy

Implementing a Transcription Factor Interaction Prediction System Using the GenoMetric Query Language [chapter]

Stefano Perna, Arif Canakoglu, Pietro Pinoli, Stefano Ceri, Limsoon Wong
2018 Msphere  
Novel technologies and growing interest have resulted in a large increase in the amount of data available for genomics and transcriptomics studies, both in terms of volume and contents.  ...  Notably, TICA allows investigators to upload and analyse their own ChIP-seq experiments datasets, comparing them both against ENCODE data or between themselves, achieving computation time which increases  ...  Acknowledgements This work was supported by the ERC Advanced Grant GeCo (Data-Driven Genomic Computing) (Grant No. 693174) awarded to Prof. Stefano Ceri.  ... 
doi:10.1007/978-1-4939-8561-6_6 pmid:30030804 fatcat:xho3wt27pjfxfmjaf6avma6wqa

Misoprostol regulates Bnip3 repression and alternative splicing to control cellular calcium homeostasis during hypoxic stress [article]

Jared T. Field, Matthew D. Martens, Wajihah Mughal, Yan Hai, Donald Chapman, Grant M. Hatch, Tammy L. Ivanco, William Diehl-Jones, Joseph W. Gordon
2018 bioRxiv   pre-print
The cellular response to hypoxia involves the activation of a conserved pathway for gene expression regulated by the transcription factor complex called hypoxia-inducible factor (HIF).  ...  (H) Linear motif diagram for Bnip3-FL, human BNIP3ΔExon2, and mouse Bnip3ΔExon3.  ...  (B) RT-PCR for Bnip3 isoforms comparing expression patterns between human and mouse cell lines.  ... 
doi:10.1101/313163 fatcat:5ljxsnleqrhizbnbxzl6przgra

Misoprostol regulates Bnip3 repression and alternative splicing to control cellular calcium homeostasis during hypoxic stress

Jared T. Field, Matthew D. Martens, Wajihah Mughal, Yan Hai, Donald Chapman, Grant M. Hatch, Tammy L. Ivanco, William Diehl-Jones, Joseph W. Gordon
2018 Cell Death Discovery  
The cellular response to hypoxia involves the activation of a conserved pathway for gene expression regulated by the transcription factor complex called hypoxia-inducible factor (HIF).  ...  Extracts were western blotted as indicated. i Linear motif diagram for Bnip3-FL, human BNIP3ΔExon2, and mouse Bnip3ΔExon3.  ...  Misoprostol alters the splicing of Bnip3. a RT-PCR for Bnip3-FL and Bnip3ΔExon3 in the heart of PND10 rat pups treated with misoprostol for 7 days. b RT-PCR for Bnip3 isoforms comparing expression patterns  ... 
doi:10.1038/s41420-018-0104-z pmid:30275982 pmcid:PMC6155004 fatcat:jczm6lkhnzhptlqi2odtyhs6hy

EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species

Anna Bernasconi, Luca Cilibrasi, Ruba Al Khalaf, Tommaso Alfonsi, Stefano Ceri, Pietro Pinoli, Arif Canakoglu
2021 Database: The Journal of Biological Databases and Curation  
Viral sequences are searched within ViruSurf, which stores curated metadata and amino acid changes imported from the most widely used deposition sources for viral databases (GenBank, COVID-19 Genomics  ...  The results may also be inspected by the VirusViz Web application; epitope regions are highlighted within the given viral protein, and changes can be comparatively inspected.  ...  for inspiring future developments of this research.  ... 
doi:10.1093/database/baab059 pmid:34585726 pmcid:PMC8500151 fatcat:myrikcmwwjhibc6cbtqhvgdczu

Application of Fluorescent Proteins for Functional Dissection of the Drosophila Visual System

Thomas K. Smylla, Krystina Wagner, Armin Huber
2021 International Journal of Molecular Sciences  
The Drosophila eye has been used extensively to study numerous aspects of biological systems, for example, spatio-temporal regulation of differentiation, visual signal transduction, protein trafficking  ...  genetically encoded biosensors for Ca2+ and phospholipids in vivo.  ...  An enhanced variant of R-GECO with sensitivity comparable to GCaMP6f has been successfully used in photoreceptors of transgenic flies in combination with ER-GCaMP-150 to simultaneously trace complementary  ... 
doi:10.3390/ijms22168930 pmid:34445636 pmcid:PMC8396179 fatcat:arbvrmuzsncgfmwmgp5ncczdeu

Predictive modeling of gene expression regulation

Chiara Regondi, Maddalena Fratelli, Giovanna Damia, Federica Guffanti, Monica Ganzinelli, Matteo Matteucci, Marco Masseroli
2021 BMC Bioinformatics  
Combining data from ENCODE and TCGA datasets, we built a predictive linear model for the regulation of each target gene, assessing the relationships between its expression, promoter methylation, expression  ...  Background In-depth analysis of regulation networks of genes aberrantly expressed in cancer is essential for better understanding tumors and identifying key genes that could be therapeutically targeted  ...  Fig. 4 4 Fig. 4 Network example visualizing linear regression results.  ... 
doi:10.1186/s12859-021-04481-1 pmid:34837938 pmcid:PMC8626902 fatcat:6nlib55efrf4zkvy4tp4efk5au

High Performance Integration Pipeline for Viral and Epitope Sequences

Tommaso Alfonsi, Pietro Pinoli, Arif Canakoglu
2022 BioTech  
In addition, it plays a crucial role in many analytic and visualization tools, such as ViruSurf, EpiSurf, VirusViz, and VirusLab.  ...  This pipeline made it possible to design and develop fundamental resources for any researcher interested in understanding the biological mechanisms behind the viral infection.  ...  Through them, the user can select a population of interest and explore the extracted sequences in VirusViz, visualize their amino acid or nucleotide changes aligned on the reference genome, see how they  ... 
doi:10.3390/biotech11010007 pmid:35822815 pmcid:PMC9245902 fatcat:wu3mzovf3zhzloodrzg5v2kqqq

Dual origin of relapses in retinoic-acid resistant acute promyelocytic leukemia

Jacqueline Lehmann-Che, Cécile Bally, Eric Letouzé, Caroline Berthier, Hao Yuan, Florence Jollivet, Lionel Ades, Bruno Cassinat, Pierre Hirsch, Arnaud Pigneux, Marie-Joelle Mozziconacci, Scott Kogan (+2 others)
2018 Nature Communications  
We thank the genomic platform of IUH and Integragen for sequencing, GeCo for extensive data analysis, the molecular oncology unit for preparing the samples.  ...  Bazarbachi for critical reading of the manuscript.  ...  One pair had evidence for a linear evolution (FLT3/MYC activation at both diagnosis and relapse, with mutation of NT5C2 at relapse).  ... 
doi:10.1038/s41467-018-04384-5 pmid:29795382 pmcid:PMC5967331 fatcat:wkzygaa3u5ht7nprdwlo6yydwi

Tip-link protein protocadherin 15 interacts with transmembrane channel-like proteins TMC1 and TMC2

R. Maeda, K. S. Kindt, W. Mo, C. P. Morgan, T. Erickson, H. Zhao, R. Clemens-Grisham, P. G. Barr-Gillespie, T. Nicolson
2014 Proceedings of the National Academy of Sciences of the United States of America  
of the Tmc2a N terminus results in mislocalization of Pcdh15a within hair bundles, together with a significant decrease in mechanosensitive responses, suggesting that a Pcdh15a-Tmc complex is critical for  ...  We thank Andrew Griffith for the TMC1-AcGFP and TMC2-AcGFP clones, and Ulrich Müller for the PCDH15-CD3 clone and PB811 antibody.  ...  We are also grateful for the psi7 allele of pcdh15a from Tatjana Piotrowski. This study was supported by the Howard Hughes Medical Institute  ... 
doi:10.1073/pnas.1402152111 pmid:25114259 pmcid:PMC4156717 fatcat:ddtm4m7tardwbkns7mvt2xitau

Association rule mining to identify transcription factor interactions in genomic regions

2019 Bioinformatics  
A straightforward pre-processing pipeline enables the easy extraction of input data for our approach from any set of ChIP-seq experiments.  ...  Thus, identifying functional interaction networks among these proteins is a fundamental task to understand the genome regulation framework.  ...  Funding This work was supported by the ERC Advanced Grant 693174 "Data-Driven Genomic Computing (GeCo)" and by a grant of the Italian Association for Cancer Research-AIRC to SC (IG 21663).  ... 
doi:10.1093/bioinformatics/btz687 pmid:31504203 fatcat:u2ly7sgryvbvtn673w3abd3tpy

Modelling the bioinformatics tertiary analysis research process

Sara Pidò, Pietro Crovari, Franca Garzotto
2021 BMC Bioinformatics  
The results of our research provides a reference process model for Tertiary Analysis that can be used both to analyze and to compare existing tools, or to design new tools.  ...  Background With the advancements of Next Generation Techniques, a tremendous amount of genomic information has been made available to be analyzed by means of computational methods.  ...  Acknowledgements This paper is an extension of the "in print" article "Towards an Ontology for Tertiary Bioinformatics Research Process" presented at the workshop Conceptual Modeling for Life Science during  ... 
doi:10.1186/s12859-021-04310-5 pmid:34592928 fatcat:lsfmfbuhqfandlsuavwyoe5rqu
« Previous Showing results 1 — 15 out of 88 results