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SHARING INFORMATION TO RECONSTRUCT PATIENT-SPECIFIC PATHWAYS IN HETEROGENEOUS DISEASES

ANTHONY GITTER, ALFREDO BRAUNSTEIN, ANDREA PAGNANI, CARLO BALDASSI, CHRISTIAN BORGS, JENNIFER CHAYES, RICCARDO ZECCHINA, ERNEST FRAENKEL
<span title="">2013</span> <i title="WORLD SCIENTIFIC"> Biocomputing 2014 </i> &nbsp;
We developed a computational approach to account for heterogeneous data when inferring signaling pathways by sharing information across the samples.  ...  Leveraging data from related tumors improves our ability to recover the disrupted pathways and reveals patient-specific pathway perturbations in breast cancer.  ...  This work was supported in part by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the US Army Research Office (the content of the information does not necessarily reflect  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789814583220_0005">doi:10.1142/9789814583220_0005</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iaz7vrj5cveajmmq5g2g6ggvdu">fatcat:iaz7vrj5cveajmmq5g2g6ggvdu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922211244/http://dspace.mit.edu/bitstream/handle/1721.1/99373/Fraenkel_Sharing%20information.pdf?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/a8/c5/a8c5f5797545bdad64b3032d3e78c61591d41c66.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789814583220_0005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

Sharing information to reconstruct patient-specific pathways in heterogeneous diseases

Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer Chayes, Riccardo Zecchina, Ernest Fraenkel
<span title="">2014</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/d4nr2uqysjfnpiksvyxq54p5bm" style="color: black;">Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</a> </i> &nbsp;
We developed a computational approach to account for heterogeneous data when inferring signaling pathways by sharing information across the samples.  ...  Leveraging data from related tumors improves our ability to recover the disrupted pathways and reveals patient-specific pathway perturbations in breast cancer.  ...  This work was supported in part by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the US Army Research Office (the content of the information does not necessarily reflect  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24297532">pmid:24297532</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3910098/">pmcid:PMC3910098</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7tsclg3dnvdwfld6eupjslodti">fatcat:7tsclg3dnvdwfld6eupjslodti</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206230056/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3910098&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/8f/5e/8f5e2a44a672dc3bdc584ff084a7259558eaf73a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910098" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients [article]

Cansu Dincer, Tugba Kaya, Ozlem Keskin, Attila Gursoy, Nurcan Tuncbag
<span title="2019-01-17">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We reconstructed patient specific networks for 290 GBM tumors.  ...  Mutation profiles of Glioblastoma (GBM) tumors are very heterogeneous which is the main challenge in the interpretation of the effects of mutations in disease.  ...  Therefore, we 396 first applied an enrichment analysis of known pathways deposited in KEGG [45] to the 397 reconstructed patient-specific pathways using Webgestalt [46].  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/523563">doi:10.1101/523563</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fxgahvkxdre5fcahhmmyqmmq4y">fatcat:fxgahvkxdre5fcahhmmyqmmq4y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200710235715/https://www.biorxiv.org/content/biorxiv/early/2019/01/17/523563.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/5c/ad/5cad7ed9878564ea35e851a40cef1cc1bf16394d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/523563"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients

Cansu Dincer, Tugba Kaya, Ozlem Keskin, Attila Gursoy, Nurcan Tuncbag, Anna R. Panchenko
<span title="2019-09-17">2019</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;
organization in patient-specific subnetworks to reduce inter-patient heterogeneity and to gain potential clinically relevant insights.  ...  We stratified the patients into five groups based on their potentially affected pathways that are revealed from the patient-specific subnetworks.  ...  Acknowledgments The results published here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1006789">doi:10.1371/journal.pcbi.1006789</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31527881">pmid:31527881</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6782092/">pmcid:PMC6782092</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/otv6lrl32vd2vpu5cos5mdlhie">fatcat:otv6lrl32vd2vpu5cos5mdlhie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191214190147/https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006789&amp;type=printable" 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/7c/48/7c480105269e4ca45b0b73078955830aa29cbd2d.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.1006789"> <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/PMC6782092" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics

A. Sottoriva, I. Spiteri, S. G. M. Piccirillo, A. Touloumis, V. P. Collins, J. C. Marioni, C. Curtis, C. Watts, S. Tavare
<span title="2013-02-14">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;
Moreover, we reconstructed the phylogeny of the fragments for each patient, identifying copy number alterations in EGFR and CDKN2A/B/p14ARF as early events, and aberrations in PDGFRA and PTEN as later  ...  Our results reveal the genome-wide architecture of intratumor variability in GB across multiple spatial scales and patient-specific patterns of cancer evolution, with consequences for treatment design.  ...  Based on these results, we propose that patient-specific dynamics of tumor heterogeneity underlie variation in response to treatment.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1219747110">doi:10.1073/pnas.1219747110</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23412337">pmid:23412337</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3593922/">pmcid:PMC3593922</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ifkegwa5uzgrhcamku44gkyhae">fatcat:ifkegwa5uzgrhcamku44gkyhae</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200213023739/https://www.pnas.org/content/pnas/110/10/4009.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/2d/a0/2da09ddfd4e9ad2f2cd2d327a5ccbf532bdd2829.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1219747110"> <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/PMC3593922" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Systems Medicine: from molecular features and models to the clinic in COPD

David Gomez-Cabrero, Jörg Menche, Isaac Cano, Imad Abugessaisa, Mercedes Huertas-Migueláñez, Akos Tenyi, Igor de Mas, Narsis A Kiani, Francesco Marabita, Francesco Falciani, Kelly Burrowes, Dieter Maier (+6 others)
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qtj6jz2xnbbxdbq73ky53i7r3u" style="color: black;">Journal of Translational Medicine</a> </i> &nbsp;
Acknowledgements We would like to thank all the members of the Synergy-COPD consortium for their support.  ...  In order to elucidate possible shared molecular origins between the disease groups and COPD, we considered their respective implicated pathways: for each disease group, we first constructed a comprehensive  ...  We considered this information to be relevant in the generation of predictive models addressing the characterization of heterogeneity in COPD.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1479-5876-12-s2-s4">doi:10.1186/1479-5876-12-s2-s4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25471042">pmid:25471042</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4255907/">pmcid:PMC4255907</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uoetb2sbwfc65hib3c42smuzhq">fatcat:uoetb2sbwfc65hib3c42smuzhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503034937/https://dash.harvard.edu/bitstream/handle/1/13581146/4255907.pdf;jsessionid=4BB7D1B78763DFEC34039BF4868CEFA4?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/49/96/49968b05b653815af8ee676f5b1d51a95e666fbd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1479-5876-12-s2-s4"> <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/PMC4255907" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Fibroblast Heterogeneity in and Its Implications for Plastic and Reconstructive Surgery: A Basic Science Review

Heather E desJardins-Park, Malini S Chinta, Deshka S Foster, Mimi R Borrelli, Abra H Shen, Derrick C Wan, Michael T Longaker
<span title="2020-06-23">2020</span> <i title="Ovid Technologies (Wolters Kluwer) - Lippincott Williams &amp; Wilkins"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/so3d2ojtzzed3gk4zznknbfe6i" style="color: black;">Plastic and Reconstructive Surgery, Global Open</a> </i> &nbsp;
to improving care of our patients.  ...  We hope this information can spur readers to consider both what questions in plastic surgery can be studied from the lens of fibroblast heterogeneity, and how these preclinical insights can be translated  ...  Bottom left: identification of fibroblast subsets involved in specific pathologies, such as scarring and fibroses, may enable those specific cells to be targeted to prevent and treat disease.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1097/gox.0000000000002927">doi:10.1097/gox.0000000000002927</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32766071">pmid:32766071</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7339369/">pmcid:PMC7339369</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/435z45asabefneon3z3bq7xng4">fatcat:435z45asabefneon3z3bq7xng4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200810202154/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7339369&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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1097/gox.0000000000002927"> <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/PMC7339369" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Clonal evolution of chemotherapy-resistant urothelial carcinoma

Bishoy M Faltas, Davide Prandi, Scott T Tagawa, Ana M Molina, David M Nanus, Cora Sternberg, Jonathan Rosenberg, Juan Miguel Mosquera, Brian Robinson, Olivier Elemento, Andrea Sboner, Himisha Beltran (+2 others)
<span title="2016-10-17">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ndd3azjmwfh45iqb6bvdfttaf4" style="color: black;">Nature Genetics</a> </i> &nbsp;
To address this question, we performed whole-exome sequencing and clonality analysis of 72 UCs including 16 matched sets of primary and advanced tumors prospectively collected before and after chemotherapy  ...  Acknowledgments We would like to thank our patients and their families for participation in this study. We would like to thank Barry Sleckman for constructive review of the manuscript.  ...  We would also like to thank Theresa Y. MacDonald, Jessica Padilla and Tarcisio Fedreizzi for technical assistance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ng.3692">doi:10.1038/ng.3692</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27749842">pmid:27749842</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5549141/">pmcid:PMC5549141</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mq5467cwmff2lcjuebxljtkosy">fatcat:mq5467cwmff2lcjuebxljtkosy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211040531/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5549141&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/74/02/74028f99b47385be74382f5843abcf0ceec471eb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ng.3692"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5549141" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Integration of Multimodal Data from Disparate Sources for Identifying Disease Subtypes

Kaiyue Zhou, Bhagya Shree Kottoori, Seeya Awadhut Munj, Zhewei Zhang, Sorin Draghici, Suzan Arslanturk
<span title="2022-02-24">2022</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j5h4zct24vcofi5scx6ttoapnq" style="color: black;">Biology</a> </i> &nbsp;
However, understanding the progression risk and differentiating long- and short-term survivors cannot be achieved by analyzing data from a single modality due to the heterogeneity of disease.  ...  ) could lead to a more accurate and robust prediction of disease progression.  ...  Using heterogeneous datasets from disparate sources often lead to data blocks with partially shared features where observations (e.g., patients) from different sources differ in terms of the feature sets  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology11030360">doi:10.3390/biology11030360</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35336734">pmid:35336734</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8945377/">pmcid:PMC8945377</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pvuyoaccnzc5djxhjfedde2e7m">fatcat:pvuyoaccnzc5djxhjfedde2e7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220502211354/https://mdpi-res.com/d_attachment/biology/biology-11-00360/article_deploy/biology-11-00360-v2.pdf?version=1646459108" 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/52/59/5259d79dc11c0e077fac33cd8d5a2b4e09260e94.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology11030360"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8945377" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications

Shuting Jin, Xiangxiang Zeng, Jiansong Fang, Jiawei Lin, Stephen Y. Chan, Serpil C. Erzurum, Feixiong Cheng
<span title="2019-11-13">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ozawiqgrzrau5mefe5bvmkr54i" style="color: black;">npj Systems Biology and Applications</a> </i> &nbsp;
: disease-miRNA, miRNA-gene, disease-gene, and the human protein-protein interactome. mpDisNet is a meta-path-based random walk to reconstruct the heterogeneous neighbors of a given node. mpDisNet uses  ...  a heterogeneous skip-gram model to solve the network representation of the nodes.  ...  ACKNOWLEDGEMENTS This work was supported by the National Heart, Lung, and Blood Institute of the National Institutes of Health under Award Number K99HL138272 and R00HL138272 to F.C.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41540-019-0115-2">doi:10.1038/s41540-019-0115-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31754458">pmid:31754458</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6853960/">pmcid:PMC6853960</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6fpfai5rgnawlou3iozu4mzhve">fatcat:6fpfai5rgnawlou3iozu4mzhve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191116035241/https://www.nature.com/articles/s41540-019-0115-2.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/32/79/3279f72d4326a434b550fcdf29bbb5f99ed6e23d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41540-019-0115-2"> <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/PMC6853960" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Network Modeling Identifies Patient-specific Pathways in Glioblastoma

Nurcan Tuncbag, Pamela Milani, Jenny L. Pokorny, Hannah Johnson, Terence T. Sio, Simona Dalin, Dennis O. Iyekegbe, Forest M. White, Jann N. Sarkaria, Ernest Fraenkel
<span title="2016-06-29">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Patient tumors are extremely heterogeneous 1,2 , and understanding this diversity is likely to be critical for determining potential therapeutic targets and patient-specific treatment strategies 1 .  ...  Using a network modeling approach, we reconstruct the altered signaling pathways from tumor-specific phosphoproteomic data and known protein-protein interactions.  ...  National Institutes of Health through grant U54CA112967, U01CA184898 and by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the US Army Research Office (the content of the information  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep28668">doi:10.1038/srep28668</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27354287">pmid:27354287</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4926112/">pmcid:PMC4926112</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dbhx4jlltvbp5g5a5bhq4tczzm">fatcat:dbhx4jlltvbp5g5a5bhq4tczzm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722181607/http://dspace.mit.edu/bitstream/handle/1721.1/106550/Network%20modeling.pdf;jsessionid=AF6ECB778F85D38830B885C77D8EB698?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/4f/ae/4fae371a3a2d8e4bed867a5cf58be2c1f845fe32.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep28668"> <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/PMC4926112" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Protein Complex, Gene, and Regulatory Modules in Cancer Heterogeneity

Nikolaos A. Papanikolaou, Athanasios G. Papavassiliou
<span title="2008-07-18">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uwxjca4bdnc5nan6667onkri6q" style="color: black;">Molecular Medicine</a> </i> &nbsp;
Reducing Heterogeneity of Pathways and Genes to Genetic and Regulatory Modules Reconstructing cancer pathways (23) addressed by genome-wide approaches is a formidable task (24, 25) .  ...  tumors with heterogeneity and robustness, and largely determine disease progression.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2119/2008-00083.papanikolaou">doi:10.2119/2008-00083.papanikolaou</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18654660">pmid:18654660</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2480613/">pmcid:PMC2480613</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z2jqehmhbnfqhmwk26fl3gtpk4">fatcat:z2jqehmhbnfqhmwk26fl3gtpk4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228120727/http://pdfs.semanticscholar.org/91c3/32c810fdd715a5d1e7d1d2fd6fe764d0b037.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/91/c3/91c332c810fdd715a5d1e7d1d2fd6fe764d0b037.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2119/2008-00083.papanikolaou"> <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/PMC2480613" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational Methods for Characterizing Cancer Mutational Heterogeneity

Fabio Vandin
<span title="2017-06-14">2017</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
We first review computational methods for studying inter-tumor heterogeneity, focusing on methods that attempt to summarize cancer heterogeneity by discovering pathways that are commonly mutated across  ...  Advances in DNA sequencing technologies have allowed the characterization of somatic mutations in a large number of cancer genomes at an unprecedented level of detail, revealing the extreme genetic heterogeneity  ...  METHODS FOR INTER-TUMOR HETEROGENEITY Several methods have been designed to characterize inter-tumor heterogeneity by identifying pathways and processes altered in a significant number of patients.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2017.00083">doi:10.3389/fgene.2017.00083</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28659971">pmid:28659971</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5469877/">pmcid:PMC5469877</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aupxbfnisfgtvpqnbj4ezw2vjy">fatcat:aupxbfnisfgtvpqnbj4ezw2vjy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305013257/http://pdfs.semanticscholar.org/cd59/e9455d7942d41e2ca9ce02a0459a3d1eae71.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/cd/59/cd59e9455d7942d41e2ca9ce02a0459a3d1eae71.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2017.00083"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5469877" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Translational Bioinformatics for Cholangiocarcinoma: Opportunities and Challenges

Fuliang Qian, Junping Guo, Zhi Jiang, Bairong Shen
<span title="">2018</span> <i title="Ivyspring International Publisher"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zpgcqgolfvchhhlqaksnc6iqlq" style="color: black;">International Journal of Biological Sciences</a> </i> &nbsp;
To promote the cross-disciplinary communication and research, we take cholangiocarcinoma as an example to review the present status and the future perspectives of the bioinformatics models applied in cancer  ...  Translational bioinformatics is becoming a driven force and a new scientific paradigm for cancer research in the era of big data.  ...  It links together the small molecules, gene expression and diseases. CMap could be used to explore the molecular pathways of a specific drug functions on a disease.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7150/ijbs.24622">doi:10.7150/ijbs.24622</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29989102">pmid:29989102</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6036745/">pmcid:PMC6036745</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ht6hva62iffe7gzrnvdho65ywy">fatcat:ht6hva62iffe7gzrnvdho65ywy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304025409/http://pdfs.semanticscholar.org/b6a6/a5f8be330ca7c4b172459490cd82f229d0b3.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/b6/a6/b6a6a5f8be330ca7c4b172459490cd82f229d0b3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7150/ijbs.24622"> <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/PMC6036745" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Integrating personalized gene expression profiles into predictive disease-associated gene pools

Jörg Menche, Emre Guney, Amitabh Sharma, Patrick J. Branigan, Matthew J. Loza, Frédéric Baribaud, Radu Dobrin, Albert-László Barabási
<span title="2017-03-13">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ozawiqgrzrau5mefe5bvmkr54i" style="color: black;">npj Systems Biology and Applications</a> </i> &nbsp;
We show that despite the high heterogeneity of the individual perturbation profiles, patients with asthma, Parkinson and Huntington's disease share a broadpool of sporadically disease-associated genes,  ...  This allows us to characterize the heterogeneity of the molecular manifestations of complex diseases by quantifying the expression-level similarities and differences among patients with the same phenotype  ...  reflect disruptions in common disease-specific pathways (Fig. 3a) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41540-017-0009-0">doi:10.1038/s41540-017-0009-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28649437">pmid:28649437</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5445628/">pmcid:PMC5445628</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lwcx7g4qfrfprnn3xynppu6gqi">fatcat:lwcx7g4qfrfprnn3xynppu6gqi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724043617/https://dash.harvard.edu/bitstream/handle/1/33490881/5445628.pdf?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/f2/e5/f2e52f94a15831d4c403224fa62c86e18306b91b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41540-017-0009-0"> <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/PMC5445628" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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