Results 91 to 100 of about 474,387 (314)

Wigwams : identifying gene modules co-regulated across multiple biological conditions [PDF]

, 2014
Motivation: Identification of modules of co-regulated genes is a crucial first step towards dissecting the regulatory circuitry underlying biological processes. Co-regulated genes are likely to reveal themselves by showing tight co-expression, e.g.
Rhodes, Johanna, Jenkins, Dafyd J, Jironkin, Aleksey, Kiddle, Steven J., Beynon, Jim, Buchanan-Wollaston, Vicky, Kiddle, Steven J, Hills, Claire E., Denby, Katherine J, Denby, Katherine J., Hill, Claire, Jenkins, Dafyd J., Zhang, Peijun, Polański, Krzysztof, Kiddle, Steven, Ott, Sascha, Rhodes, Johanna; id_orcid   +16 more
core   +1 more source

Stable Gene Regulatory Network Modeling From Steady-State Data

Bioengineering, 2016
Gene regulatory networks represent an abstract mapping of gene regulations in living cells. They aim to capture dependencies among molecular entities such as transcription factors, proteins and metabolites.
Joy Edward Larvie, Mohammad Gorji Sefidmazgi, Abdollah Homaifar, Scott H. Harrison, Ali Karimoddini, Anthony Guiseppi-Elie   +5 more
doaj   +1 more source

The inferred cardiogenic gene regulatory network in the mammalian heart. [PDF]

PLoS ONE, 2014
Cardiac development is a complex, multiscale process encompassing cell fate adoption, differentiation and morphogenesis. To elucidate pathways underlying this process, a recently developed algorithm to reverse engineer gene regulatory networks was ...
Jason N Bazil, Karl D Stamm, Xing Li, Raghuram Thiagarajan, Timothy J Nelson, Aoy Tomita-Mitchell, Daniel A Beard   +6 more
doaj   +1 more source

Phosphoinositides and inositol phosphates as molecular glues

FEBS Letters, EarlyView.
Inositol phosphates (IPs) and phosphoinositides (PIPs) regulate diverse eukaryotic processes. Beyond recruiting signaling proteins or acting as structural cofactors, recent studies suggest they mediate protein–protein interactions as natural molecular glues.
Aleshia Seaton‐Terry, Alexander J. Cutright, Mong Na Claire Loi, Jessica Martin, Joseph W. Gilligan, Jakub N. Kubina, Michael J. Arambula, Susanna Tanada Palmu, Daniella Zhou, Raymond D. Blind   +9 more
wiley   +1 more source

Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes [PDF]

, 2010
<b>Method:</b> Dynamic Bayesian networks (DBNs) have been applied widely to reconstruct the structure of regulatory processes from time series data, and they have established themselves as a standard modelling tool in computational systems ...
Husmeier, D., Marco Grzegorczyk, Dirk Husmeier, Grzegorczyk, M., Husmeier, Dirk, Grzegorczyk, Marco   +5 more
core   +1 more source

D3GRN: a data driven dynamic network construction method to infer gene regulatory networks

BMC Genomics, 2019
Background To infer gene regulatory networks (GRNs) from gene-expression data is still a fundamental and challenging problem in systems biology. Several existing algorithms formulate GRNs inference as a regression problem and obtain the network with an ...
Xiang Chen, Min Li, Ruiqing Zheng, Fang-Xiang Wu, Jianxin Wang   +4 more
doaj   +1 more source

Quantitative analysis of the ThrbCRM1-centered gene regulatory network

Biology Open, 2019
Enhancer activity is determined by both the activity and occupancy of transcription factors as well as the specific sequences they bind. Experimental investigation of this dynamic requires the ability to manipulate components of the system, ideally in as
Benjamin Souferi, Mark M. Emerson
doaj   +1 more source

The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. [PDF]

PLoS Biology, 2013
Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying ...
David A Garfield, Daniel E Runcie, Courtney C Babbitt, Ralph Haygood, William J Nielsen, Gregory A Wray   +5 more
doaj   +1 more source

PARK(ing) time–How park deficiency affects the biological clock in a Drosophila model of Parkinson's disease

FEBS Letters, EarlyView.
Drosophila park mutants serve as a model for Parkinson's disease. We used this strain to investigate the connection between oxidative stress and the circadian clock mechanism. We showed that increased oxidative stress affects the physiology of pacemaker cells, disrupting their daily structural plasticity. Lack of rhythmic signaling from pacemaker cells
Kamila Zientara, Kinga Skoczek, Elzbieta Pyza, Milena Damulewicz   +3 more
wiley   +1 more source

Estimating gene regulatory networks with pandaR [PDF]

Bioinformatics, 2017
Abstract PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that begins with a model of transcription factor–target gene interactions and uses message passing to update the network model given available transcriptomic and protein–protein interaction data.
Daniel Schlauch, Joseph N. Paulson, Albert Young, Kimberly Glass, John Quackenbush   +4 more
openaire   +4 more sources