Filters








17 Hits in 6.4 sec

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

Marcel H Schulz, William E Devanny, Anthony Gitter, Shan Zhong, Jason Ernst, Ziv Bar-Joseph
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
In this paper we focus on the reconstruction of dynamic GRNs using time-series expression data.  ...  Conclusions: DREM 2.0 provides a unique framework for constructing and visualizing dynamic regulatory networks. DREM 2.0 can be downloaded from: www.sb.cs.cmu.edu/drem.  ...  Acknowledgements We would like to acknowledge all groups that have contributed and made available the human ChIP-Seq predictions for human as part of the ENCODE project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-6-104">doi:10.1186/1752-0509-6-104</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22897824">pmid:22897824</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3464930/">pmcid:PMC3464930</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oqi4y77cobdaxe3gd3x6jo65ca">fatcat:oqi4y77cobdaxe3gd3x6jo65ca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724212751/https://cloudfront.escholarship.org/dist/prd/content/qt8tj1r8j4/qt8tj1r8j4.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ba/75/ba753f1d4d42eeb0549476dcc925244dfc3f1636.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-6-104"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464930" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

iDREM: Interactive visualization of dynamic regulatory networks

Jun Ding, James S. Hagood, Namasivayam Ambalavanan, Naftali Kaminski, Ziv Bar-Joseph, Dina Schneidman
<span title="2018-03-14">2018</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
The Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data.  ...  data to reconstruct networks that can lead to novel hypotheses on the function and timing of regulators.  ...  In 2007, we presented the Dynamic Regulatory Events Miner (DREM) that was developed to integrate time series gene expression and static protein-DNA interaction data [15] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1006019">doi:10.1371/journal.pcbi.1006019</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29538379">pmid:29538379</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5868853/">pmcid:PMC5868853</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gfzuaeahdjeeln55mzqqbqjibe">fatcat:gfzuaeahdjeeln55mzqqbqjibe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222194934/http://pdfs.semanticscholar.org/397a/062b0a5d3575057cf56f55e681bb3fd79a15.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/39/7a/397a062b0a5d3575057cf56f55e681bb3fd79a15.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1006019"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5868853" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Reconstructing dynamic microRNA-regulated interaction networks

M. H. Schulz, K. V. Pandit, C. L. Lino Cardenas, N. Ambalavanan, N. Kaminski, Z. Bar-Joseph
<span title="2013-08-28">2013</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
We developed the MIRna Dynamic Regulatory Events Miner (mirDREM), a probabilistic modeling method that uses input-output hidden Markov models to reconstruct dynamic regulatory networks that explain how  ...  The reconstructed dynamic network correctly identified known miRNAs and transcription factors.  ...  This work was supported by National Institutes of Health Grants 1R01 GM085022 (to Z.B.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1303236110">doi:10.1073/pnas.1303236110</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23986498">pmid:23986498</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3785769/">pmcid:PMC3785769</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s6db5y6c35dwjimsorcxuwh7ne">fatcat:s6db5y6c35dwjimsorcxuwh7ne</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191204075557/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3785769&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2f/d2/2fd2b41f96277dfea8c95787917ec6681c131bee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1303236110"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785769" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency

Deborah Gérard, Florian Schmidt, Aurélien Ginolhac, Martine Schmitz, Rashi Halder, Peter Ebert, Marcel H Schulz, Thomas Sauter, Lasse Sinkkonen
<span title="2018-12-14">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Temporal data on gene expression and context-specific open chromatin states can improve identification of key transcription factors (TFs) and the gene regulatory networks (GRNs) controlling cellular differentiation  ...  Here, we delineate a general approach for data-driven and unbiased identification of key TFs and dynamic GRNs, called EPIC-DREM.  ...  The experiments presented in this paper were carried out using the HPC facilities of the University of Luxembourg (92) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1240">doi:10.1093/nar/gky1240</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30544251">pmid:30544251</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6380961/">pmcid:PMC6380961</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l7yqzxdkyrf5hg4wltkk43le3a">fatcat:l7yqzxdkyrf5hg4wltkk43le3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190923030201/http://orbilu.uni.lu/bitstream/10993/38244/1/Gerard_et_al_NAR_PUBLISHED%28gky1240%29.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/96/8b/968bfdeed1e30b2bf6aa2fa3dfd8e566d96a1ec1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1240"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380961" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Intricate genetic programs controlling dormancy in Mycobacterium tuberculosis [article]

Abrar A. Abidi, Eliza J. R. Peterson, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga
<span title="2019-07-22">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Using a comprehensive genome-wide transcription factor binding location map and insights from network topology analysis, we identified regulatory circuits that deterministically drive sequential transitions  ...  The architecture of the genetic programs explains the transcriptional dynamics underlying synchronous entry of cells into a dormant state that is primed to infect the host upon encountering favorable conditions  ...  Acknowledgements: We thank members of the Baliga (in particular Christopher Plaisier now at  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/709378">doi:10.1101/709378</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pn7bpamijjh5rmwqxvlwtxgplm">fatcat:pn7bpamijjh5rmwqxvlwtxgplm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324034815/https://www.biorxiv.org/content/biorxiv/early/2019/07/22/709378.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8c/7f/8c7fd1880ceaf5000a27be14f87ce268486ab5fe.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/709378"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Temporal epigenomic profiling identifies AHR and GLIS1 as super-enhancer controlled regulators of mesenchymal multipotency [article]

Deborah Gerard, Florian Schmidt, Aurelien Ginolhac, Martine Schmitz, Rashi Halder, Peter Ebert, Marcel H. Schulz, Thomas Sauter, Lasse Sinkkonen
<span title="2017-09-03">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Temporal data on gene expression and context-specific open chromatin states can improve identification of key transcription factors (TFs) and the gene regulatory networks (GRNs) controlling cellular differentiation  ...  Here, we delineate a general approach for data-driven and unbiased identification of key TFs and dynamic GRNs, called EPIC-DREM.  ...  DREM 2.0: Improved reconstruction of dynamic regulatory networks 15 from time-series expression data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/183988">doi:10.1101/183988</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tkq3cfemi5gm5i6r4riefgl4f4">fatcat:tkq3cfemi5gm5i6r4riefgl4f4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503190529/https://www.biorxiv.org/content/biorxiv/early/2018/03/26/183988.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/06/1d/061dfeb5086f17b330c005099748feef89bae0bb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/183988"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Eliza J.R. Peterson, Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga
<span title="2020-04-28">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5ihveavyobfs3mlzee7cjt7mfe" style="color: black;">Cell Reports</a> </i> &nbsp;
Using a comprehensive genome-wide transcription factor binding map and insights from network topology analysis, we identify regulatory circuits that deterministically drive sequential transitions across  ...  The architecture of the genetic programs explains the transcriptional dynamics underlying synchronous entry of cells into a dormant state that is primed to infect the host upon encountering favorable conditions  ...  The granuloma formation shown in the graphical abstract was adapted from Ehlers and Schaible (2013) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.celrep.2020.107577">doi:10.1016/j.celrep.2020.107577</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32348771">pmid:32348771</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7605849/">pmcid:PMC7605849</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rbuyzcj635ftdc5z7rcsdxvt4q">fatcat:rbuyzcj635ftdc5z7rcsdxvt4q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210527050718/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7605849&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e9/75/e975b70f63349030dc7a3b9d6776fbf03dd77d22.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.celrep.2020.107577"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605849" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dynamic regulatory module networks for inference of cell type-specific transcriptional networks

Alireza Fotuhi Siahpirani, Sara Knaack, Deborah Chasman, Morten Seirup, Rupa Sridharan, Ron Stewart, James Thomson, Sushmita Roy
<span title="2022-06-15">2022</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
DRMN identified known and novel regulators driving cell type-specific expression patterns demonstrating its broad applicability to examine dynamics of gene regulatory networks from linearly and hierarchically  ...  However, integrating these data to infer cell type-specific regulatory networks is a major challenge.  ...  models of gene regulation from time-series data using an Input/Output HMM approach.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.276542.121">doi:10.1101/gr.276542.121</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35705328">pmid:35705328</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fhwz4fcjnnfkbgezv2nu5f4iya">fatcat:fhwz4fcjnnfkbgezv2nu5f4iya</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220616020406/https://genome.cshlp.org/content/early/2022/06/15/gr.276542.121.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/33/59/335991c08bafc29c333b636cac2133d32cd0fd68.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.276542.121"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Reconstructing SARS-CoV-2 response signaling and regulatory networks [article]

Jun Ding, Jose Lugo-Martinez, Ye Yuan, Darrell N. Kotton, Ziv Bar-Joseph
<span title="2020-06-01">2020</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp;
Here we extend computational methods to integrate several different types of sequence, functional and interaction data to reconstruct networks and pathways activated by the virus in host cells.  ...  We identify the key proteins in these networks and further intersect them with genes differentially expressed at conditions that are known to impact viral activity.  ...  SDREM integrates time-series gene expression data with static PPIs and protein-DNA interaction to reconstruct response regulatory networks and signaling pathways. SDREM iterates between two methods.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.06.01.127589">doi:10.1101/2020.06.01.127589</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33083801">pmid:33083801</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7574259/">pmcid:PMC7574259</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bqhuyibj5nhgjn6z77aclqsiie">fatcat:bqhuyibj5nhgjn6z77aclqsiie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200715230144/https://www.biorxiv.org/content/biorxiv/early/2020/06/01/2020.06.01.127589.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/43/9d/439d828f896d5bf1cd0203872aa9ce9ecc2288a0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.06.01.127589"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7574259" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Transcriptional Dynamics of the Salicylic Acid Response and its Interplay with the Jasmonic Acid Pathway [article]

Richard Hickman, Marciel Pereira Mendes, Marcel C. Van Verk, Anja J.H. Van Dijken, Jacopo Di Sora, Katherine Denby, Corne C.M.J. Pieterse, Saskia C.M. Van Wees
<span title="2019-08-24">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Integration of our expression data with information on TF-DNA binding allowed us to generate a dynamic regulatory network model of the SA response, recovering known regulators and identifying novel ones  ...  To obtain a deep understanding of SA-mediated transcriptional reprogramming and SA/JA crosstalk, we generated a high-resolution time series of gene expression from Arabidopsis leaves treated with SA alone  ...  DREM 2.0: Improved reconstruction of dynamic regulatory networks from timeseries expression data. BMC systems biology 6, 104. Song, L., Huang, S.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/742742">doi:10.1101/742742</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vf36i5hoqjaatmwydsxbb5ii3a">fatcat:vf36i5hoqjaatmwydsxbb5ii3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200310162049/https://www.biorxiv.org/content/biorxiv/early/2019/08/24/742742.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1c/3b/1c3b4307611d115e3d339ee1c4b04db15e965b3b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/742742"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Gene network analysis of poplar root transcriptome in response to drought stress identifies a PtaJAZ3PtaRAP2.6-centered hierarchical network

Madhumita Dash, Yordan S. Yordanov, Tatyana Georgieva, Hairong Wei, Victor Busov, Keqiang Wu
<span title="2018-12-12">2018</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Using time-series transcriptomic data from poplar roots undergoing polyethylene glycol (PEG)-induced drought stress, we built a genetic network model of the involved putative molecular responses.  ...  Several lines of evidence suggest of regulatory interactions between the two superhubs. Both superhubs were significantly induced by methyl jasmonate (MeJA).  ...  DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC systems biology. 2012; 6 (1):104. 37. Gitter A, Carmi M, Barkai N, Bar-Joseph Z.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0208560">doi:10.1371/journal.pone.0208560</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30540849">pmid:30540849</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6291141/">pmcid:PMC6291141</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p7ekexcotfac5jsj674vee47bm">fatcat:p7ekexcotfac5jsj674vee47bm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428165745/https://digitalcommons.mtu.edu/cgi/viewcontent.cgi?article=1125&amp;context=forestry-fp" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/31/27/3127b584c9f8e41d0a9c7a8f098a97aaa00bf87e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0208560"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291141" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Data- and knowledge-based modeling of gene regulatory networks: an update

Jörg Linde, Sylvie Schulze, Sebastian G Henkel, Reinhard Guthke
<span title="2015-03-02">2015</span> <i title="IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t4rny7ofhfbbpidcegrtvzrniq" style="color: black;">EXCLI Journal : Experimental and Clinical Sciences</a> </i> &nbsp;
Gene regulatory network inference is a systems biology approach which predicts interactions between genes with the help of high-throughput data.  ...  Finally, we reflect the current availability of data and prior knowledge sources and give an outlook for the inference of gene regulatory networks that reflect interacting species, in particular pathogen-host  ...  Acknowledgements This work was supported by the Deutsche Forschungsgemeinschaft (DFG) CRC/Transregio 124 'Pathogenic fungi and their human host: Networks of interaction', subproject INF (JL, RG) and B3  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17179/excli2015-168">doi:10.17179/excli2015-168</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27047314">pmid:27047314</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4817425/">pmcid:PMC4817425</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lebwxkplx5grrmffprjupt4poi">fatcat:lebwxkplx5grrmffprjupt4poi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810134221/http://www.excli.de/vol14/Guthke_02032015_proof.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/24/bb/24bb14bbb80b3f82f75ded903e24826ff751afff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17179/excli2015-168"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817425" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

scQuery: a web server for comparative analysis of single-cell RNA-seq data [article]

Amir Alavi, Matthew Ruffalo, Aiyappa Parvangada, Zhilin Huang, Ziv Bar-Joseph
<span title="2018-05-16">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We extended supervised neural networks to obtain efficient and accurate representations for scRNA-seq data.  ...  We applied our pipeline to analyze data from over 500 different studies with over 300 unique cell types and show that supervised methods greatly outperform unsupervised methods for cell type identification  ...  "DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data". In: BMC systems biology 6.1, p. 104. Smith, Cynthia L et al. (2017).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/323238">doi:10.1101/323238</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lyroov3qr5g6hmu57gr6evtrky">fatcat:lyroov3qr5g6hmu57gr6evtrky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503151043/https://www.biorxiv.org/content/biorxiv/early/2018/05/31/323238.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b0/bf/b0bffae3c073c5e0765ddda231bc28e85d1e28ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/323238"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Dynamic transcriptional response of Saccharomyces cerevisiae cells to copper

Sebnem Oc, Serpil Eraslan, Betul Kirdar, Apollo-University Of Cambridge Repository
<span title="2021-01-05">2021</span>
The integration of the transcriptomic data with regulome revealed the differences in the extensive re-wiring of dynamic transcriptional organization and regulation in these strains.  ...  The analysis of data by using different clustering algorithms revealed significantly affected processes and pathways in response to a switch from copper deficient environment to elevated copper levels.  ...  Acknowledgements The authors gratefully acknowledge scholarship support provided by Technological Research Council of Turkey (TUBITAK) for S.O. through Project No. 110M692.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17863/cam.62795">doi:10.17863/cam.62795</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wc23r544svggxaxalk6d7lftu4">fatcat:wc23r544svggxaxalk6d7lftu4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210112153929/https://www.repository.cam.ac.uk/bitstream/handle/1810/315681/Dynamic%20transcriptional%20response%20of%20Saccharomyces%20cerevisiae%20cells%20to%20copper.pdf;jsessionid=45E8494AD1BF3F2D5E1F18201C5B0CD2?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/89/2f/892fab6ccaeb917512944898eb97a49f1e2d5c7e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17863/cam.62795"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Estimating Gene Regulatory Activity using Mathematical Optimization [article]

Saskia Trescher, Humboldt-Universität Zu Berlin
<span title="2020-09-28">2020</span>
Using Floræ, we are able to improve the identification of knockout and knockdown TFs in synthetic data sets.  ...  of their regulatory model, the concrete paradigm used for solving the optimization problem and the data sets used for evaluation.  ...  The methods can be categorized into those who reconstruct static gene networks using steady-state data, and those who infer dynamic networks based on time-series data to reflect temporal changes of gene  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18452/21900">doi:10.18452/21900</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b3q4rcwpmzfc3hsdj2wvkcbwly">fatcat:b3q4rcwpmzfc3hsdj2wvkcbwly</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200930045618/https://edoc.hu-berlin.de/bitstream/handle/18452/22659/dissertation_trescher_saskia.pdf;jsessionid=BD9B5B93D386F5F95129015561A3F28B?sequence=5" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/60/67/6067e7dc981a540be1fc89b5c834e66a522d6f9a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18452/21900"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 17 results