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The 27th annual Nucleic Acids Research database issue and molecular biology database collection

Daniel J Rigden, Xosé M Fernández
2019 Nucleic Acids Research  
The entire Database Issue is freely available online on the Nucleic Acids Research website (  ...  PATRIC and MicroScope update in microbial genomes while human and model organism genomics resources include Ensembl, Ensembl genomes and UCSC Genome Browser.  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva, especially, and the rest of the Oxford University Press team led by Joanna Ventikos for their help in compiling this issue.  ... 
doi:10.1093/nar/gkz1161 pmid:31906604 pmcid:PMC6943072 fatcat:2dx37pg3krcs5hamrlmgyb4h5e

The 2014Nucleic Acids ResearchDatabase Issue and an updated NAR online Molecular Biology Database Collection

Xosé M. Fernández-Suárez, Daniel J. Rigden, Michael Y. Galperin
2013 Nucleic Acids Research  
The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases  ...  ACKNOWLEDGEMENTS The authors thank Sir Richard Roberts and Drs Alex Bateman and David Landsman for helpful comments and Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd  ...  One of the major highlights of this issue is the block of articles on the improved annotation of human genome and detailed analysis of genome variation and its potential clinical significance.  ... 
doi:10.1093/nar/gkt1282 pmid:24316579 pmcid:PMC3965027 fatcat:e7vrx5en2bd5le7dpjvy3t7lnm

The 2016 database issue ofNucleic Acids Researchand an updated molecular biology database collection

Daniel J. Rigden, Xosé M. Fernández-Suárez, Michael Y. Galperin
2016 Nucleic Acids Research  
The NAR online Molecular Biology Database Collection, http: //, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought  ...  Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere.  ...  ACKNOWLEDGEMENTS We thank NAR Editorial Administrator Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd and Caoimhe Ní Dhónaill for their great efforts in compiling this  ... 
doi:10.1093/nar/gkv1356 pmid:26740669 pmcid:PMC4702933 fatcat:3bkogosuu5g4lduv7ne5i6h6qi

MuStARD: Deep Learning for intra- and inter-species scanning of functional genomic patterns [article]

Georgios K Georgakilas, Andrea Grioni, Konstantinos G Liakos, Eliska Malanikova, Fotis C Plessas, Panagiotis Alexiou
2019 bioRxiv   pre-print
Regions of the genome that produce different classes of functional elements also exhibit different patterns in their sequence, secondary structure, and evolutionary conservation.  ...  given set over wide genomic areas.  ...  ACKNOWLEDGEMENT We would like to acknowledge 'MetaCentrum NGI' for providing computational infrastructure necessary for running parts of the analyses presented in this study.  ... 
doi:10.1101/547679 fatcat:32rfjjvhvfadrcoswfsy5b7xgi

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

Carl Herrmann, Bram Van de Sande, Delphine Potier, Stein Aerts
2012 Nucleic Acids Research  
The field of regulatory genomics today is characterized by the generation of high-throughput data sets that capture genome-wide transcription factor (TF) binding, histone modifications, or DNAseI hypersensitive  ...  We developed i-cisTarget (where the 'i' stands for integrative), for the first time enabling the discovery of different types of enriched 'regulatory features' in a set of co-regulated sequences in one  ...  ACKNOWLEDGEMENTS The authors thank Serge Plaza, Morgane Thomas-Chollier, Klaas Vandepoele and Jacques van Helden for insightful comments on the manuscript.  ... 
doi:10.1093/nar/gks543 pmid:22718975 pmcid:PMC3424583 fatcat:7v5sidhkenewhm63jk6pcy6jyy

Tooth agenesis and orofacial clefting: genetic brothers in arms?

M. Phan, F. Conte, K. D. Khandelwal, C. W. Ockeloen, T. Bartzela, T. Kleefstra, H. van Bokhoven, M. Rubini, H. Zhou, C. E. L. Carels
2016 Human Genetics  
UCSC Genome Browser (  ...  articles (20), Duplicate removing conference reports (10) and not available articles (10) were  ... 
doi:10.1007/s00439-016-1733-z pmid:27699475 pmcid:PMC5065589 fatcat:itybajpzjjc7dgiv7cqakum66e

De novo detection of regulatory elements in the nematode Caenorhabditis elegans

Monica Celia Sleumer
The availability of high-throughput gene expression data and completely sequenced genomes from eight species of nematodes has provided an opportunity to identify novel cis-regulatory elements in the promoter  ...  We annotated 26% of the motifs as similar to known binding sequences of transcription factors from the ORegAnno, TRANSFAC and JASPAR databases.  ...  region in their genomic context via two embedded UCSC genome browser images.  ... 
doi:10.14288/1.0067459 fatcat:r4l3pw5aavhpvb6znnpkff3f2q

Integrative and Comparative Analysis of Retinoblastoma and Osteosarcoma

Nicolas Delhomme
This work was supported by grants from the Bundesministerium fr Bildung und Wissenschaft within the National Genome Research Network (NGFN2: 01GS0460, 01GR0417 and 01GR0418) and the Medical Genome Research  ...  ACKNOWLEDGEMENT The authors want to thank Felix Engel for constructive discussions during this project, Verena Fleig, Charles Girardot and Robert Weatheritt for excellent comments on the manuscript and  ...  The final breakthrough occurred when researchers realized that the oncogenes harbored by these viruses were just modified copies of genes present in every vertebrate genome.  ... 
doi:10.11588/heidok.00014910 fatcat:xx7hl6ugknaobcvdoxqnkvqzny

Development of computational systems for the study of the expression and function of miRNAs:

Παναγιώτης Θ. Αλεξίου
The need for the study of each of these fields will be discussed as well as algorithms, web servers and other tools developed to help further our understanding on the connection of microRNAs and cancer  ...  Since our knowledge and appreciation of the importance of microRNAs is increasing rapidly, the need for novel computational approaches has become evident.  ...  In addition, the positions of the binding sites on the mRNA of the target gene are graphically presented through the UCSC genome browser.  ... 
doi:10.26262/ fatcat:ycybvhtc2bfa3hddi73ikv7bea

Computational analysis of genetic variation [article]

Matthew Arnell Field, University, The Australian National, University, The Australian National
This thesis describes six publications describing components of the larger informatics framework I have developed over the last four years to address these challenges, a framework designed from the onset  ...  The second challenge is the effective prioritisation of the huge number of variants detected in each sample, a task required to reduce the large search space for causal variants down to variant lists suitable  ...  We also would like to thank Queensland Institute of Medical Research for access to the melanoma cell line generated as part of the larger Australian Melanoma Genome Project.  ... 
doi:10.25911/5d778acb1cc8f fatcat:ed7d6ogysfb6lay4dj52nkrchu

Development of Bioinformatics Tools and Workflows for the Analysis of Cell Line Data

Thibault Robin, Amos Marc Bairoch, Frédérique Lisacek
We thank Elisabeth Gasteiger for installing the tool on the ExPASy server and for enabling a Cellosaurus entry with a STR profile to be directly linked to CLASTR.  ...  Semen samples were all obtained on-site by masturbation following 2 to 7 days of sexual abstinence.  ...  In recent years, significant breakthroughs were achieved in proteomics technologies (Altelaar et al., 2012) .  ... 
doi:10.13097/archive-ouverte/unige:143042 fatcat:yspp2pj2bbho7py3m5jebbqqqm

Investigating the Role of DDK in Replication Associated Recombination

Chinnu Rose Joseph
DDK mutants not only affect the sister chromatid junctions but also the inter-homolog junctions that rely on recombination events to the homologous chromosomes.  ...  No matter how busy they were, they would always put a smile on my face through "any means" necessary. They have been a constant support both inside and outside the lab.  ...  ACKNOWLEDGEMENTS We thank Jolanda van Leeuwen for communicating the mutations in the rio1-5001 allele. Authors' contribution: M.G.I. performed most of the biological experiments.  ... 
doi:10.21954/ fatcat:fykejytb6vdgtm3goqyj6c3ydy