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Identification of structural features in chemicals associated with cancer drug response: A systematic data-driven analysis [article]

Suleiman A Khan, Seppo Virtanen, Olli P Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski
<span title="2014-04-29">2014</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
New methods are required for integrated analyses of a large number of chemical features of drugs against the corresponding genome-wide responses of multiple cell models.  ...  The task is formulated as searching for drug response components across multiple cancers to reveal shared effects of drugs and the chemical features that may be responsible.  ...  Our goal was to uncover the big picture of relationships between chemical structure parameters and genome-wide responses, in a data-driven fashion (Fig. 1) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1312.7734v2">arXiv:1312.7734v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p2fwb325lfbvzie2t2fdser7zy">fatcat:p2fwb325lfbvzie2t2fdser7zy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200929171439/https://arxiv.org/ftp/arxiv/papers/1312/1312.7734.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/ea/a2/eaa242bb14f5439ee0dcba432de642204009db43.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1312.7734v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis

Suleiman A. Khan, Seppo Virtanen, Olli P. Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski
<span title="2014-08-22">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
New methods are required for integrated analyses of a large number of chemical features of drugs against the corresponding genome-wide responses of multiple cell models.  ...  The task is formulated as searching for drug response components across multiple cancers to reveal shared effects of drugs and the chemical features that may be responsible.  ...  Our goal was to uncover the big picture of relationships between chemical structure parameters and genome-wide responses, in a data-driven fashion (Fig. 1) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btu456">doi:10.1093/bioinformatics/btu456</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25161239">pmid:25161239</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4147909/">pmcid:PMC4147909</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hzkeopgv75dujdxjqfykdmyjzu">fatcat:hzkeopgv75dujdxjqfykdmyjzu</a> </span>
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Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

Suleiman A Khan, Ali Faisal, John Mpindi, Juuso A Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli P Kallioniemi, Krister Wennerberg, Samuel Kaski
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
space) of 1159 drugs with the microarray gene expression responses (biological space) they elicited in three cancer cell lines.  ...  As a step towards creating such computational links we developed a data-driven chemical systems biology approach to comprehensively study the relationship of 76 structural 3D-descriptors (VolSurf, chemical  ...  Systematic analysis of a network of drug effects, i.e. network pharmacology, offers great opportunities for drug design in the future [5] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-112">doi:10.1186/1471-2105-13-112</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22646858">pmid:22646858</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3532323/">pmcid:PMC3532323</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tqmbzgnou5cmfdjby3v5lpgab4">fatcat:tqmbzgnou5cmfdjby3v5lpgab4</a> </span>
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Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs [article]

Suleiman A. Khan, Ali Faisal, John Patric Mpindi, Juuso A. Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli P. Kallioniemi, Krister Wennerberg, Samuel Kaski
<span title="2011-12-27">2011</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
space) of 1159 drugs with the gene expression responses (biological space) they elicited in three cancer cell lines.  ...  As a step towards creating such computational links we developed a data-driven chemical systems biology approach to comprehensively study the relationship of 76 structural 3D-descriptors (VolSurf, chemical  ...  Systematic analysis of a network of drug effects, i.e. network pharmacology, offers great opportunities for drug design in the future [5] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1112.6015v1">arXiv:1112.6015v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h6667ffucrc2lki6pr6bzpl52m">fatcat:h6667ffucrc2lki6pr6bzpl52m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200929194232/https://arxiv.org/ftp/arxiv/papers/1112/1112.6015.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/52/3e/523e778461ea24b3dc78ec5a13b40c04617ee549.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1112.6015v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization

Muhammad Ammad-ud-din, Suleiman A. Khan, Disha Malani, Astrid Murumägi, Olli Kallioniemi, Tero Aittokallio, Samuel Kaski
<span title="2016-09-01">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Third, systematically modelling the associations between pathway-based genomic profiles and drug response with cwKBMF outperforms the existing approaches in predicting drug responses.  ...  Another widely used approach is the quantitative structureactivity relationship (QSAR) analysis which uses chemical and structural properties (often called as descriptors) of the drugs and the observed  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btw433">doi:10.1093/bioinformatics/btw433</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27587662">pmid:27587662</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/renrcnnx4je5jku6jouw7kabzm">fatcat:renrcnnx4je5jku6jouw7kabzm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210717034206/https://acris.aalto.fi/ws/portalfiles/portal/62350825/btw433.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/8b/e9/8be9fb48ebfcdeadd272ffeda110d4cc4bc2945c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btw433"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Cancer Drug Response Profile scan (CDRscan): A Deep Learning Model That Predicts Drug Effectiveness from Cancer Genomic Signature

Yoosup Chang, Hyejin Park, Hyun-Jin Yang, Seungju Lee, Kwee-Yum Lee, Tae Soon Kim, Jongsun Jung, Jae-Min Shin
<span title="2018-06-11">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Herein, we report Cancer Drug Response profile scan (CDRscan) a novel deep learning model that predicts anticancer drug responsiveness based on a large-scale drug screening assay data encompassing genomic  ...  profiles of 787 human cancer cell lines and structural profiles of 244 drugs.  ...  Acknowledgements We appreciate Ye-Bin Jung's assistance in creating the artwork in the Fig. 1 . We also thank Jon Kim for proofreading of the manuscript. Author Contributions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-018-27214-6">doi:10.1038/s41598-018-27214-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29891981">pmid:29891981</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5996063/">pmcid:PMC5996063</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/siogdemuozewbnycmetpwho6fi">fatcat:siogdemuozewbnycmetpwho6fi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209232846/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5996063&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/23/92/239237dc8aa4df5e060a148bde5910101e6f21b3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-018-27214-6"> <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/PMC5996063" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Machine learning and feature selection for drug response prediction in precision oncology applications

Mehreen Ali, Tero Aittokallio
<span title="2018-08-10">2018</span> <i title="Springer Nature America, Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lfdgv6hoqvcw7gez42d2dlp4sy" style="color: black;">Biophysical Reviews</a> </i> &nbsp;
In-depth modeling of the complex interplay among multiple omics data measured from cancer cell lines or patient tumors is providing new opportunities toward identification of tailored therapies for individual  ...  of therapy responses using multi-omics panels of response-predictive biomarkers identified through feature selection and cross-validation.  ...  drug information as drug chemical properties) in a Bayesian setting (Ammad-ud-din et al. 2016 ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12551-018-0446-z">doi:10.1007/s12551-018-0446-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30097794">pmid:30097794</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mnrzqyngmbgx5jpwpf3fa7bws4">fatcat:mnrzqyngmbgx5jpwpf3fa7bws4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429123328/https://link.springer.com/content/pdf/10.1007%2Fs12551-018-0446-z.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/3c/b0/3cb054f909511575e3ee69d3da2d3fc9ff8f43f3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12551-018-0446-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses

Zhaonan Zou, Michio Iwata, Yoshihiro Yamanishi, Shinya Oki
<span title="2022-01-24">2022</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results With the use of a computational method, we attempted to elucidate the epigenetic landscape of drug responses, in terms of transcription factors (TFs), through large-scale ChIP-seq data analyses  ...  Despite the development of several data-driven approaches for predicting chemical–disease associations, the molecular cues that organize the epigenetic landscape of drug responses remain poorly understood  ...  Shuh Narumiya and the members of Department of Drug Discovery Medicine at Kyoto University.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-022-04571-8">doi:10.1186/s12859-022-04571-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35073843">pmid:35073843</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8785570/">pmcid:PMC8785570</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6ok4w52mgzei7j65ci5cszo244">fatcat:6ok4w52mgzei7j65ci5cszo244</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220209153129/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04571-8.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/f8/7a/f87a66cd8f8ab6ab1870e38799f20d60f0677787.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-022-04571-8"> <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/PMC8785570" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

T-Cell Response [chapter]

Periasamy Selvaraj
<span title="">2011</span> <i title="Springer Berlin Heidelberg"> Encyclopedia of Cancer </i> &nbsp;
Characteristics Identification of drugs for cancer treatment in today's highly technology-driven research environment begins with understanding the biology of cancer and those molecules which can modify  ...  Through a retrospective multivariate analysis of nearly 6,000 patients with germ cell tumors, this group identified the clinical features strongly associated with prognosis: primary site of disease, the  ...  This process occurs at a time that is simultaneous with tumor promotion and is first noted as an increase in vascular permeability. Tumor associated angiogenesis is in itself a multi-step process.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-16483-5_5702">doi:10.1007/978-3-642-16483-5_5702</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q5ikc7lwvzf75ndbfafnc4fbnm">fatcat:q5ikc7lwvzf75ndbfafnc4fbnm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170920053019/https://link.springer.com/content/pdf/10.1007%2F978-3-642-16483-5_2400.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/10.1007/978-3-642-16483-5_5702"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Humoral Response Profiling Reveals Pathways to Prostate Cancer Progression

Barry S. Taylor, Manoj Pal, Jianjun Yu, Bharathi Laxman, Shanker Kalyana-Sundaram, Rong Zhao, Anjana Menon, John T. Wei, Alexey I. Nesvizhskii, Debashis Ghosh, Gilbert S. Omenn, David M. Lubman (+2 others)
<span title="2007-12-11">2007</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/63atlvwyorhorfip35rcvk6bey" style="color: black;">Molecular &amp; Cellular Proteomics</a> </i> &nbsp;
Here we examine serum humoral responses in a cohort of 34 patients with either benign prostatic hyperplasia or clinically localized prostate cancer (PCa).  ...  A supervised learning analysis of the humoral response arrays generated a parsimonious predictor having 78% sensitivity and 75% specificity in distinguishing PCa from benign prostatic hyperplasia in a  ...  Poisson for access to tissue metabolomics data, R. Mehra for help with clinical information, and X. Wang for assistance in printing protein arrays.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.m700263-mcp200">doi:10.1074/mcp.m700263-mcp200</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18077443">pmid:18077443</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/esxprk6qkzeendsnqescvodh6u">fatcat:esxprk6qkzeendsnqescvodh6u</a> </span>
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Radiogenomics and radiotherapy response modeling

Issam El Naqa, Sarah L Kerns, James Coates, Yi Luo, Corey Speers, Catharine M L West, Barry S Rosenstein, Randall K Ten Haken
<span title="2017-08-01">2017</span> <i title="IOP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zuggg3zvsfaatpw6invuoevl7a" style="color: black;">Physics in Medicine and Biology</a> </i> &nbsp;
Radiogenomics has emerged as a new field that investigates the role of genetics in treatment response to radiation therapy.  ...  Here, we provide an overview of radiogenomics starting with genotyping, data aggregation, and application of different modeling approaches based on modifying traditional radiobiological methods or application  ...  In a large individual patient data metaanalysis of over 5,000 breast and prostate cancer patients, rs1801516, a protein coding SNP in ATM, was associated with overall acute and late toxicity (Andreassen  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/1361-6560/aa7c55">doi:10.1088/1361-6560/aa7c55</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28657906">pmid:28657906</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5557376/">pmcid:PMC5557376</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ju25t6azbnaihk2fruqwcsa6me">fatcat:ju25t6azbnaihk2fruqwcsa6me</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200505191522/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5557376&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/0c/60/0c6093c0f92c8a5878eb576f45247b818824bc48.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/1361-6560/aa7c55"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> iop.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557376" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Meeting Abstracts of the BACR conference: response and resistance in cancer therapy

Tim R. Fenton, Michelle D. Garrett, Martin Michaelis, Mark N. Wass
<span title="">2018</span> <i title="OAE Publishing Inc."> Cancer Drug Resistance </i> &nbsp;
models of acquired drug resistance in cancer. he molecular analysis of tumours by highly sophisticated gene expression and sequencing methods allows the comprehensive identiication of drugable targets  ...  If untreated, RCC is associated with high rates of metastasis and high mortality, partially due to high levels of drug resistance. he novel gold-standard tyrosine kinase inhibitor, Sunitinib, targets angiogenesis  ...  describe drug response data derived from a panel of breast cancer cell lines.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.20517/cdr.2018.18">doi:10.20517/cdr.2018.18</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4jqntap6hvgadmihdqgb373qji">fatcat:4jqntap6hvgadmihdqgb373qji</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200307144734/https://kar.kent.ac.uk/73043/1/__bodiam_CUR_ecs33_My%20Files_Cancer.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/a7/15/a715515fad3de17e1f269286da598f932cb24beb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.20517/cdr.2018.18"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A systematic analysis of genomics-based modeling approaches for prediction of drug response to cytotoxic chemotherapies

Joshua D. Mannheimer, Dawn L. Duval, Ashok Prasad, Daniel L. Gustafson
<span title="2019-06-17">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rbtzjpig4jcsfbjr5yo23sjnj4" style="color: black;">BMC Medical Genomics</a> </i> &nbsp;
The availability and generation of large amounts of genomic data has led to the development of a new paradigm in cancer treatment emphasizing a precision approach at the molecular and genomic level.  ...  Statistical modeling techniques aimed at leveraging broad scale in vitro, in vivo, and clinical data for precision drug treatment has become an active area of research.  ...  Availability of data and materials The data used to generate all figures and results has been included in Additional files 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12920-019-0519-2">doi:10.1186/s12920-019-0519-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31208429">pmid:31208429</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6580596/">pmcid:PMC6580596</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bdp67kl7abcxte2n7dsjximcnu">fatcat:bdp67kl7abcxte2n7dsjximcnu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208003731/https://bmcmedgenomics.biomedcentral.com/track/pdf/10.1186/s12920-019-0519-2" 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/85/21/8521ba10b4edaa576db4e2dd751f4a7eecb20f4a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12920-019-0519-2"> <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/PMC6580596" 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 regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response [article]

Evanthia Koukouli, Dennis Wang, Frank Dondelinger, Juhyun Park
<span title="2020-06-18">2020</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Using in vitro cancer cell line dose-response and gene expression data from the Genomics of Drug Sensitivity in Cancer (GDSC) project, we build a dose-varying regression model.  ...  We highlight the dosage-dependent dynamics of the associations between the selected genes and drug response, and we perform pathway enrichment analysis to show that the selected genes play an important  ...  Acknowledgments We acknowledge Emily Chambers and the Sheffield Bioinformatics Core Facility for their assistance in GDSC2 data pre-processing. Their input to this study is greatly appreciated.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.06.18.158907">doi:10.1101/2020.06.18.158907</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qrsoknkbszaufi35jmbdepcpye">fatcat:qrsoknkbszaufi35jmbdepcpye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715011842/https://eprints.whiterose.ac.uk/172396/1/journal.pcbi.1008066.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/b5/b7/b5b78c23ac3c16a543f8310b005e32b27b534dcd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.06.18.158907"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Genetic and epigenetic determinants of inter-individual variability in responses to toxicants

Lauren Lewis, Gregory E. Crawford, Terrence S. Furey, Ivan Rusyn
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/h56zvswxpba4bhbcxgyuilgspu" style="color: black;">Current Opinion in Toxicology</a> </i> &nbsp;
It is well established that genetic variability has a major impact on susceptibility to common diseases, responses to drugs and toxicants, and influences disease-related outcomes.  ...  The appreciation that epigenetic marks also vary across the population is growing with more data becoming available from studies in humans and model organisms.  ...  While advances in sequencing technologies, statistical genetics analysis methods and clinical trial designs have shown promise for the discovery of variants associated with drug response, interpretation  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cotox.2017.08.006">doi:10.1016/j.cotox.2017.08.006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29276797">pmid:29276797</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5739339/">pmcid:PMC5739339</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cegdvjoe2vb7pmaaoyajdh43qq">fatcat:cegdvjoe2vb7pmaaoyajdh43qq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206015449/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5739339&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/c8/06/c80600c6dcd01e05d5439d406b0fb091cd3a2581.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cotox.2017.08.006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739339" 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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