*  Olivia Martinez | Stanford Medicine Profiles
CAP Network is a virtual workspace, to support collaboration among faculty, graduate students, postdocs and staff. ... bioinformatics and genomics highlights the importance of understanding mechanisms involved in gene expression and regulation. ... are a central component of the cellular gene regulatory network. MicroRNAs (miRNAs) are a family of endogenous, small, ... CYTOKINE AND T-CELL RECEPTOR GENE-EXPRESSION AT THE SITE OF ALLOGRAFT-REJECTION 10TH ANNUAL MEETING OF THE AMERICAN SOC OF ...
  https://med.stanford.edu/profiles/olivia-martinez
*  Bioinformatics Expertise - Omicsoft Corporation
Expertise Bioinformatics, in the fields of Cancer Genomics, Immunology, and Next Generation Sequencing is integral to Omicsoft ... gene expression regulatory motifs identification and gene expression regulation networks. John has authored and co-authored ... and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis. ... Jason Lu obtained his Ph.D. in Bioinformatics from NCSU, and has worked in the field of genomics and bioinformatics for more ...
  http://www.omicsoft.com/bioinformatics-expertise/
*  IEEE Computer Society Bioinformatics Conference
... regulatory network from large scale or whole genome scale gene expression data sets. Return to Program or Index Probability ... With the rapid accumulation of gene expression data in publicly accessible databases, computational study of gene regulation ... in gene promoters with specific gene expression profiles.. A given set of genes with known expression levels under certain ... adenocarcinoma gene expression data set. The typical approach to the analysis of gene expression data is to cluster the genes; ...
  http://conferences.computer.org/bioinformatics/CSB2003/SectA.html
*  MacDevCenter.com
Another part of the problem is that many systems involve the regulation of gene expression and protein synthesis, each of which ... People have had some success in modeling specific regulatory networks in bacteria or yeast at a qualitative level, but no ... As an aside, I hope to return to the issues of "free" access to data and software within bioinformatics in the future. It is a ... The early-stage development of an embryo involves exquisite cascades of regulation. The switching on and off of genes in those ...
  http://www.macdevcenter.com/pub/a/mac/2004/08/20/bioinformatics.html?page=2
*  Julio Collado-Vides - Wikipedia
... research focuses on the regulation of gene expression in bacteria, in particular, creating a model of the regulatory network of ... His research focuses on genomics and bioinformatics. Collado-Vides studied at the National Autonomous University of Mexico, ... ISBN 9780262032391 Gene Regulation and Metabolism: Post-Genomic Computational Approaches, 2002, MIT Press (edited with Ralf ... transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)". Nucleic ...
  https://en.wikipedia.org/wiki/Julio_Collado-Vides
*  BIOTECHNO 2012
Genetics (Gene regulation; Gene expression databases; Gene pattern discovery and identification; Genetic network modeling and ... A. Bioinformatics, chemoinformatics, neuroinformatics and applications *Bioinformatics (Bioinformatics modeling; Bioinformatics ... Gene expression analysis; RNA and DNA structure and sequencing; Evolution of regulatory genomic sequences; Biological data ... Formalisms for gene regulation and expression databases; Algorithms for gene identification and pattern discovery; Techniques ...
  https://www.iaria.org/conferences2012/BIOTECHNO12.html
*  Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development |...
From plant gene regulatory grids to network dynamics. Maria Katherine Mejia-Guerra, Marcelo Pomeranz, Kengo Morohashi, Erich ... Photosynthetic control of electron transport and the regulation of gene expression. Christine H. Foyer, Jenny Neukermans, ... Evolution of proline biosynthesis: enzymology, bioinformatics, genetics, and transcriptional regulation. Yosef Fichman, ... Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes. Jigar S. Desai, Ryan C. Sartor, ...
  http://www.plantcell.org/content/19/3/731/tab-article-info
*  ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data | Garvan...
Combining this with pairwise TF-TG interactions enabled us to visualise temporal regulation of a transcriptional network. ... which would enable us to determine the topology of the transcriptional network and predict novel regulatory interactions. To ... and bioinformatics predictions. We have subsequently categorised TF-TG interactions in ORTI according to the quality of this ... Consequently, we often seek to determine the key TFs and their regulated target genes (TGs) amidst gene expression data. This ...
  https://www.garvan.org.au/research/publications/13795
*  Regulation of H19 and its encoded microRNA-675 in osteoarthritis and under anabolic and catabolic in vitro conditions
These regulatory loops serve as important motifs in gene regulatory networks and play critical roles in multiple biological ... There are many levels at which regulation of gene expression can occur, and recent evidence demonstrates the importance ofmRNA ... Briefings in Bioinformatics;Jan2015, Vol. 16 Issue 1, p45 Transcription factors (TFs) and microRNAs (miRNAs) can jointly ... OBJECTIVE: TO identify key genes associated with squamous lung cancer (SLC) through analyzing gene expression data with ...
  http://connection.ebscohost.com/c/articles/79824463/regulation-h19-encoded-microrna-675-osteoarthritis-under-anabolic-catabolic-vitro-conditions
*  Metabolites | Free Full-Text | Optimality Principles in the Regulation of Metabolic Networks | HTML
To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks need to be identified ... One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and ... whether universal design principles apply to molecular networks. ... when gene expression data is used to infer regulatory networks ... Bioinformatics 2008, 24, 2044-2050. [Google Scholar] [CrossRef]. © 2012 by the authors; licensee MDPI, Basel, Switzerland. This ...
  http://www.mdpi.com/2218-1989/2/3/529/htm
*  Reconstructing differentiation networks and their regulation from time series single-cell RNA-Seq data | RNA-Seq Blog
Genexpi - a toolset for identifying regulons and validating gene regulatory networks using time-course expression data. 2 days ... Featured RNA-Seq Job - Bioinformatics/Scientist RNA Biology (NCI). *SSBTs - sequence-based querying of terabyte scale ... Genexpi - a toolset for identifying regulons and validating gene regulatory networks using time-course expression data. 2 days ... Genexpi - a toolset for identifying regulons and validating gene regulatory networks using time-course expression data. 2 days ...
  http://www.rna-seqblog.com/reconstructing-differentiation-networks-and-their-regulation-from-time-series-single-cell-rna-seq-data/
*  Identification of key miRNA‑gene pairs in chronic lymphocytic leukemia through integrated analysis of mRNA and miRNA microarray
A miRNA‑Gene regulatory network was constructed. Bioinformatics methods could help us develop a better understanding of the ... though miRNA is also known as important in the regulation of gene expression and cancer formation. In this study, we firstly ... The miRNA-gene regulatory network. A total of 405 miRNA-Gene regulatory pairs were identified via the miRNAWalk platform. The ... 405 miRNA‑Gene regulatory pairs were identified. The miRNA‑Gene regulatory pairs contained 351 target genes of the DEMs, ...
  https://www.spandidos-publications.com/ol/15/1/361
*  Regulatory sequence - Wikipedia
C1 E1 G1 Regulator gene Regulation of gene expression Cis-acting element Gene regulatory network Operon DNA binding site ... doi:10.1038/nmeth.3065 Stepanova et al., Bioinformatics, 21(9): 1789-96, year 2005. A comparative analysis of relative ... Regulation of gene expression is an essential feature of all living organisms and viruses. In DNA, regulation of gene ... Regulation of insulin gene transcription Biochemical and Biophysical Research Communications ... ORegAnno - Open Regulatory ...
  https://en.wikipedia.org/wiki/Regulatory_sequence
*  Identification of yeast transcriptional regulation networks using multivariate random forests. - PubMed - NCBI
... condition-dependent regulatory cliques. Each regulatory clique features homogeneous gene expression profiles and common motifs ... Department of Epidemiology and Biostatistics, Center for Bioinformatics and Molecular Biostatistics, University of California, ... to relate gene expression (as derived from expression microarrays) to sequence features residing in gene promoters (as derived ... by time-course gene expression measures. An analysis of the multivariate random forest output reveals complex regulatory ...
  https://www.ncbi.nlm.nih.gov/pubmed/19543377
*  sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay...
... systematic generation of gene regulatory networks. Bioinformatics. 2009; 25(9):1205-7. doi:10.1093/bioinformatics/btp115. http ... of a network uses non-linear functions based on Michaelis-Menten and hill enzyme kinetic equations to model gene regulation ... The connection structure corresponds to the regulatory network which defines which genes control the expression of other genes ... Gene expression dataGene networkSimulation. Background. Networks provide a statistical and mathematical framework for the ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1731-8
*  FUNCTIONS AND TARGETS OF LET-7 MICRO RNAS - Patent application
... gene pathways, and gene networks. Mis-regulation or alteration of these miRNA related regulatory pathways and networks are ... precisely predict miRNA targets with bioinformatics tools alone. [0013]Correcting gene expression errors by manipulating miRNA ... gene products, and gene functions that respond to excess hsa-let-7. Gene Product Function Gene expression reduced in HepG2 & ... An aspect of the invention includes the modulation of gene expression, miRNA expression or function or mRNA expression or ...
  http://www.patentsencyclopedia.com/app/20090163430
*  CPIB » Inference of the Genetic Network Regulating Lateral Root Initiation in Arabidopsis thaliana
Regulation of gene expression is crucial for organism growth, and it is one of the challenges in systems biology to reconstruct ... the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana ... IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 (1), 50-60 ... Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on ...
  https://www.cpib.ac.uk/publications/papers/inference-of-the-genetic-network-regulating-lateral-root-initiation-in-arabidopsis-thaliana/
*  Christopher Burge Lab - Papers
2007). Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev. 21, 578-89. ... 2007). Coevolutionary Networks of Splicing cis-Regulatory Elements. PNAS 104, 18583-18588. ... 2004). Gene structure prediction using an orthologous gene of known exon-intron structure. Appl. Bioinformatics 3, 81-90. ... 2004). Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc. Natl. Acad. Sci. USA ...
  http://genes.mit.edu/burgelab/papers.html
*  NUS Postdocatoral Research Fellow in computational analysis of gene regulatory networks
Postdoctoral position to work on Gene Expression Regulation, Centre for Molecular Medicine Norway Background A 3-year ... Bioinformatics Scientist (Post-Doctoral) Position: Bioinformatics Scientist Research Area: Bioinformatics Full/Part Time: Full ... We are looking for three highly motivated postdoctoral researchers in computational analysis of gene regulatory networks ( ... Job: NUS Postdocatoral Research Fellow in computational analysis of gene regulatory networks ...
  https://www.biostars.org/p/231027/
*  SegCorr a statistical procedure for the detection of genomic regions of correlated expression | BMC Bioinformatics | Full Text
... and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data. ... Genomic neighbourhood and the regulation of gene expression. Curr Opin Cell Biol. 2010; 22(3):326-33. doi:10.1016/j.ceb.2010.04 ... Gene expression have been measured using RNA-seq. The number of genes per chromosome ranges from 293 to 1695 (with average 702 ... Integrated analysis of DNA copy number and gene expression microarray data using gene sets. BMC Bioinforma. 2009; 10:1-15. doi: ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1742-5
*  Reconstruction of xylose utilization pathway and regulons in Firmicutes | Springer for Research & Development
In addition to XylR regulation, expression of xyl genes in Bacillus is also subject to catabolite repression mediated by the ... allowed us to significantly improve the quality of gene annotations and to accurately infer metabolic and regulatory networks ... Bioinformatics analysis. (i) Genome resources and bioinformatics tools. Complete genomes of bacteria from the Firmicutes ... Candidate regulatory sites of XylR from ROK family are shown by red circles. Genes predicted by genome context analysis are ...
  https://rd.springer.com/article/10.1186/1471-2164-11-255
*  PSB 2003 Online Proceedings
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations. M. ... Gene Regulation. *Genome, Pathway, and Interaction Bioinformatics. *Informatics Approaches in Structural Genomics ... Extracting Conserved Gene Expression Motifs from Gene Expression Data. T.M. Murali, S. Kasif; Pacific Symposium on Biocomputing ... Multiclass Cancer Classification Using Gene Expression Profiling and Probabilistic Neural Networks. D.P. Berrar, C.S. Downes, W ...
  http://psb.stanford.edu/psb-online/proceedings/psb03/
*  Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers | Biology Direct | Full Text
... "gene regulatory network". Evolution of gene regulation is concerned with the evolution of the gene regulatory network [5-9]. ... Gene Expression tracks for Pou5f1. Gene expression tracks at the UCSC genome browser for the murine Pou5f1 gene. Green color ... Evolutionary Bioinformatics of Gene Regulation. Bioinformatics tools and software for estimating, analyzing and/or visualizing ... Principles of the Evolution of Gene Regulatory Networks. Evolution of gene regulatory networks for developmental processes ...
  https://0-biologydirect-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1745-6150-5-67
*  Modelling and Analysis in Bioinformatics | Tietojenkäsittelytieteen laitos
The course explores computational models for biological networks, including e.g. network motifs and gene regulation, and ... Sampsa Hautaniemi: Cancer, Genomics and Networks. Andre S. Ribeiro: Modelling, Analysis, and Validation of a Gene Regulatory ... Teemu Kivioja: Computational challenges in genome-scale measurements of gene expression and its regulation ... Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs. Bioinformatics 20(11):1746- ...
  https://www.cs.helsinki.fi/courses/582746/2016/s/k/1
*  Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers
Topics covered by the journal include, but are not limited to: bioinformatics, clinical genomics, disease genomics, epigenomics ... CircNet also provides tissue-specific circRNA expression profiles, circRNA-miRNA-gene regulatory networks, and a thorough ... CircNet generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs, and genes [58]. ... circular RNA expression profiles and bioinformatics analyses," Tumour Biology, vol. 39, no. 6, article 1010428317705850, 2017. ...
  https://www.hindawi.com/journals/ijg/2017/6218353/