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Predicting domain-domain interactions using a parsimony approach

Katia S Guimarães, Raja Jothi, Elena Zotenko, Teresa M Przytycka
<span title="">2006</span> <i title="BMC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
We propose a novel approach to predict domain-domain interactions from a protein-protein interaction network. In our method we apply a parsimony-driven explanation of the network, where the domain interactions are inferred using linear programming optimization, and false positives in the protein network are handled by a probabilistic construction. This method outperforms previous approaches by a considerable margin. The results indicate that the parsimony principle provides a correct approach for detecting domain-domain contacts.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2006-7-11-r104">doi:10.1186/gb-2006-7-11-r104</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17094802">pmid:17094802</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1794579/">pmcid:PMC1794579</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ukrdedsil5cmvig7ps4twer624">fatcat:ukrdedsil5cmvig7ps4twer624</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427132616/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2006-7-11-r104" 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/b2/b7/b2b779ac7df5db30ab9a76bec1ff258f1d1f6115.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2006-7-11-r104"> <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/PMC1794579" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Inferring Physical Protein Contacts from Large-Scale Purification Data of Protein Complexes

Sven-Eric Schelhorn, Julián Mestre, Mario Albrecht, Elena Zotenko
<span title="2011-03-30">2011</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;
Recent large-scale data sets of protein complex purifications have provided unprecedented insights into the organization of cellular protein complexes. Several computational methods have been developed to detect co-complexed proteins in these data sets. Their common aim is the identification of biologically relevant protein complexes. However, much less is known about the network of direct physical protein contacts within the detected protein complexes. Therefore, our work investigates whether
more &raquo; ... irect physical contacts can be computationally derived by combining raw data of largescale protein complex purifications. We assess four established scoring schemes and introduce a new scoring approach that is specifically devised to infer direct physical protein contacts from protein complex purifications. The physical contacts identified by the five methods are comprehensively benchmarked against different reference sets that provide evidence for true physical contacts. Our results show that raw purification data can indeed be exploited to determine high-confidence physical protein contacts within protein complexes. In particular, our new method outperforms competing approaches at discovering physical contacts involving proteins that have been screened multiple times in purification experiments. It also excels in the analysis of recent protein purification screens of molecular chaperones and protein kinases. In contrast to previous findings, we observe that physical contacts inferred from purification experiments of protein complexes can be qualitatively comparable to binary protein interactions measured by experimental high-throughput assays such as yeast two-hybrid. This suggests that computationally derived physical contacts might complement binary protein interaction assays and guide large-scale interactome mapping projects by prioritizing putative physical contacts for further experimental screens. Molecular &
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.m110.004929">doi:10.1074/mcp.m110.004929</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21451165">pmid:21451165</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3108834/">pmcid:PMC3108834</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kugh24vllne7dlobdkpu27ozgm">fatcat:kugh24vllne7dlobdkpu27ozgm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719154133/http://www.mcponline.org/content/10/6/M110.004929.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/cf/39/cf395485432dba3594f43db3131b051e381530b4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.m110.004929"> <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/PMC3108834" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Structural footprinting in protein structure comparison: the impact of structural fragments

Elena Zotenko, Rezarta Islamaj Dogan, W John Wilbur, Dianne P O'Leary, Teresa M Przytycka
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m36qvjwuvnegpgzopqbhvg7k3e" style="color: black;">BMC Structural Biology</a> </i> &nbsp;
Recently, Zotenko et al.  ...  Even though the comparison results of Zotenko et al.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-7-53">doi:10.1186/1472-6807-7-53</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17688700">pmid:17688700</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2082327/">pmcid:PMC2082327</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3nrcmvtcnzad3dm4d7fovhfrey">fatcat:3nrcmvtcnzad3dm4d7fovhfrey</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429064943/https://bmcstructbiol.biomedcentral.com/track/pdf/10.1186/1472-6807-7-53" 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/f5/5f/f55f5ae72c64da32ed16f6679c2f54da8b453891.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-7-53"> <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/PMC2082327" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification

Elena Zotenko, Dianne P O'Leary, Teresa M Przytycka
<span title="2006-06-08">2006</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m36qvjwuvnegpgzopqbhvg7k3e" style="color: black;">BMC Structural Biology</a> </i> &nbsp;
Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein structure into a high-dimensional vector space. Once the mapping is done, the structure comparison is reduced to distance computation between corresponding vectors. As structural similarity is approximated by distance between projections, the success of any projection method depends on how well its mapping function is able
more &raquo; ... capture the salient features of protein structure. There is no agreement on what constitutes a good projection technique and the three currently known projection methods utilize very different approaches to the mapping construction, both in terms of what structural elements are included and how this information is integrated to produce a vector representation. In this paper we propose a novel projection method that uses secondary structure information to produce the mapping. First, a diverse set of spatial arrangements of triplets of secondary structure elements, a set of structural models, is automatically selected. Then, each protein structure is mapped into a high-dimensional vector of "counts" or footprint, where each count corresponds to the number of times a given structural model is observed in the structure, weighted by the precision with which the model is reproduced. We perform the first comprehensive evaluation of our method together with all other currently known projection methods. The results of our evaluation suggest that the type of structural information used by a projection method affects the ability of the method to detect structural similarity. In particular, our method that uses the spatial conformations of triplets of secondary structure elements outperforms other methods in most of the tests.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-6-12">doi:10.1186/1472-6807-6-12</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16762072">pmid:16762072</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1526735/">pmcid:PMC1526735</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bhwh6u6u3jfzhbix77sx47iu7e">fatcat:bhwh6u6u3jfzhbix77sx47iu7e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200320190222/http://www.cs.umd.edu/~oleary/reprints/j76.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/dc/04/dc044311741620db58c6a410a0175cdf9b6858a2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-6-12"> <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/PMC1526735" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations

Raja Jothi, Elena Zotenko, Asba Tasneem, Teresa M. Przytycka
<span title="2006-01-24">2006</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;
Motivation: Determining orthology relations among genes across multiple genomes is an important problem in the post-genomic era. Identifying orthologous genes can not only help predict functional annotations for newly sequenced or poorly characterized genomes, but can also help predict new protein-protein interactions. Unfortunately, determining orthology relation through computational methods is not straightforward due to the presence of paralogs. Traditional approaches have relied on pairwise
more &raquo; ... sequence comparisons to construct graphs, which were then partitioned into putative clusters of orthologous groups. These methods do not attempt to preserve the non-transitivity and hierarchic nature of the orthology relation. Results: We propose a new method, COCO-CL, for hierarchical clustering of homology relations and identification of orthologous groups of genes. Unlike previous approaches, which are based on pairwise sequence comparisons, our method explores the correlation of evolutionary histories of individual genes in a more global context. COCO-CL can be used as a semi-independent method to delineate the orthology/ paralogy relation for a refined set of homologous proteins obtained using a less-conservative clustering approach, or as a refiner that removes putative out-paralogs from clusters computed using a more inclusive approach. We analyze our clustering results manually, with support from literature and functional annotations. Since our orthology determination procedure does not employ a species tree to infer duplication events, it can be used in situations when the species tree is unknown or uncertain. Contact:
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btl009">doi:10.1093/bioinformatics/btl009</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16434444">pmid:16434444</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1620014/">pmcid:PMC1620014</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qndlgpbim5de5dahdavqscea7u">fatcat:qndlgpbim5de5dahdavqscea7u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190307200524/http://pdfs.semanticscholar.org/dc1a/0f0467dd8fb097bb9b9824ed37d4434c4aaf.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/dc/1a/dc1a0f0467dd8fb097bb9b9824ed37d4434c4aaf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btl009"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1620014" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA

Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M. Gould, Shalima S. Nair, Susan J. Clark, Clare Stirzaker
<span title="2017-04-20">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t46dy4kadfdgbm52javmafxiyy" style="color: black;">Epigenetics &amp; Chromatin</a> </i> &nbsp;
The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping the mammalian DNA methylation landscape. The gold-standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC. However, new approaches to mapping 5hmC genomewide have advanced rapidly, although it is unclear how the different methods compare
more &raquo; ... in accurately calling 5hmC. In this study, we provide a comparative analysis on brain DNA using three 5hmC genome-wide approaches, namely whole-genome bisulphite/oxidative bisulphite sequencing (WG Bis/OxBis-seq), Infinium HumanMethylation450 BeadChip arrays coupled with oxidative bisulphite (HM450K Bis/OxBis) and antibody-based immunoprecipitation and sequencing of hydroxymethylated DNA (hMeDIP-seq). We also perform loci-specific TET-assisted bisulphite sequencing (TAB-seq) for validation of candidate regions. Results: We show that whole-genome single-base resolution approaches are advantaged in providing precise 5hmC values but require high sequencing depth to accurately measure 5hmC, as this modification is commonly in low abundance in mammalian cells. HM450K arrays coupled with oxidative bisulphite provide a cost-effective representation of 5hmC distribution, at CpG sites with 5hmC levels >~10%. However, 5hmC analysis is restricted to the genomic location of the probes, which is an important consideration as 5hmC modification is commonly enriched at enhancer elements. Finally, we show that the widely used hMeDIP-seq method provides an efficient genome-wide profile of 5hmC and shows high correlation with WG Bis/OxBis-seq 5hmC distribution in brain DNA. However, in cell line DNA with low levels of 5hmC, hMeDIP-seq-enriched regions are not detected by WG Bis/OxBis or HM450K, either suggesting misinterpretation of 5hmC calls by hMeDIP or lack of sensitivity of the latter methods. Conclusions: We highlight both the advantages and caveats of three commonly used genome-wide 5hmC profiling technologies and show that interpretation of 5hmC data can be significantly influenced by the sensitivity of methods used, especially as the levels of 5hmC are low and vary in different cell types and different genomic locations.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13072-017-0123-7">doi:10.1186/s13072-017-0123-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28428825">pmid:28428825</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5397694/">pmcid:PMC5397694</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vodepdvy35ge3jtvlr3n7znfae">fatcat:vodepdvy35ge3jtvlr3n7znfae</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922223957/https://epigeneticsandchromatin.biomedcentral.com/track/pdf/10.1186/s13072-017-0123-7?site=epigeneticsandchromatin.biomedcentral.com" 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/ce/7e/ce7e98d8d01c44755e2dbbca7fb1f39b9e6a4e84.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13072-017-0123-7"> <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/PMC5397694" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis

Warwick J Locke, Elena Zotenko, Clare Stirzaker, Mark D Robinson, Rebecca A Hinshelwood, Andrew Stone, Roger R Reddel, Lily I Huschtscha, Susan J Clark
<span title="2015-05-01">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ufgz4r5quzfk7jw7p2lg3xxjwi" style="color: black;">Clinical Epigenetics</a> </i> &nbsp;
Dysregulation of the epigenome is a common event in malignancy; however, deciphering the earliest cancer-associated epigenetic events remains a challenge. Cancer epigenome studies to date have primarily utilised cancer cell lines or clinical samples, where it is difficult to identify the initial epigenetic lesions from those that occur over time. Here, we analysed the epigenome of human mammary epithelial cells (HMEC) and a matched variant cell population (vHMEC) that have spontaneously escaped
more &raquo; ... senescence and undergone partial carcinogenic transformation. Using this model of basal-like breast carcinogenesis, we provide striking new insights into the very first epigenetic changes that occur during the initial stages of malignancy. Results: The first phase of malignancy is defined by coordinated changes in the epigenome. At the chromatin level, this is embodied in long-range epigenetic deregulation, which involves the concomitant but atypical acquisition or loss of active and repressive histone modifications across large regional blocks. Changes in DNA methylation also occurs in a highly coordinated manner. We identified differentially methylated regions (DMRs) in the very earliest passages of vHMECs. Notably, we find that differential methylation targets loci regulated by key transcription factors including p53, AHR and E2F family members suggesting that epigenetic deregulation of transcription factor binding is a key event in breast carcinogenesis. Interestingly, DMRs identified in vHMEC are extensively methylated in breast cancer, with hypermethylation frequently encroaching into neighbouring regions. A subset of vHMEC DMRs exhibited a strong basal-like cancer specific hypermethylation. Conclusions: Here, we generated epigenome-wide maps of the earliest phase of breast malignancy and show long-range epigenetic deregulation and coordinated DNA hypermethylation targets loci regulated by key transcription factors. These findings support a model where induction of breast cancer occurs through epigenetic disruption of transcription factor binding leading to deregulation of cancer-associated transcriptional networks. With their stability and very early occurrence, vHMECs hypermethylated loci could serve as excellent biomarkers for the initial detection of basal breast cancer.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13148-015-0086-0">doi:10.1186/s13148-015-0086-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25960784">pmid:25960784</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4424562/">pmcid:PMC4424562</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uvdtffpx4jhwlktblhdkcgnrky">fatcat:uvdtffpx4jhwlktblhdkcgnrky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809142232/https://clinicalepigeneticsjournal.biomedcentral.com/track/pdf/10.1186/s13148-015-0086-0?site=clinicalepigeneticsjournal.biomedcentral.com" 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/ca/eb/caeb846ff05b66ad4e7ecfba1cf131bfadc35e75.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13148-015-0086-0"> <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/PMC4424562" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas

Annette M. Lim, Nicholas C. Wong, Ruth Pidsley, Elena Zotenko, June Corry, Alexander Dobrovic, Susan J. Clark, Danny Rischin, Benjamin Solomon
<span title="2016-07-18">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ufgz4r5quzfk7jw7p2lg3xxjwi" style="color: black;">Clinical Epigenetics</a> </i> &nbsp;
DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 109 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina
more &raquo; ... n450K (HM450K) array. Data pre-processing, quality control and analysis were performed using R packages. Probes mapping to SNPs, sex chromosomes and unreliable probes were accounted for prior to downstream analyses. The relationship between methylation and patient survival was examined using both agnostic approaches and feature selection. The cohort was enlarged by incorporation of 331 The Cancer Genome Atlas (TCGA) HNSCC samples, which included 91 TCGA OTSCC samples with HM450K and survival data available. Results: Given the use of FFPE-derived DNA, we defined different cohorts for separate analyses. Overall, similar results were found between cohorts. With an unsupervised approach, no distinct hypermethylated group of samples was identified and nor was a prognostic methylation profile identified. The use of multiple downstream feature selection approaches, including a linear models for microarray data (LIMMA), centroid feature selection (CFS), and recursive feature elimination (RFE) support vector machines, similarly failed to identify a significant methylation signature informative for patient prognosis or any clinicopathological data available. Furthermore, we were unable to confirm the prognostic methylation profiles or specific prognostic loci reported within the literature for HNSCC. Conclusions: With genome-scale assessment of DNA methylation using HM450K in one of the largest OTSCC cohorts to date, we were unable to identify a hypermethylated group of tumours or a prognostic methylation signature. This suggests that either DNA methylation in isolation is not likely to be of prognostic value or larger cohorts are required to identify such a biomarker for OTSCC.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13148-016-0235-0">doi:10.1186/s13148-016-0235-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27433284">pmid:27433284</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4948090/">pmcid:PMC4948090</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kqrlqvdgonbzbez6r52uk7tvgy">fatcat:kqrlqvdgonbzbez6r52uk7tvgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171014002956/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/6ac/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEzMTQ4LTAxNi0wMjM1LTAucGRm.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/c2/e1/c2e1f2236beea9930eae569e2cccda9d9da624e4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13148-016-0235-0"> <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/PMC4948090" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Replication timing shapes the cancer epigenome and the nature of chromosomal rearrangements [article]

Qian Du, Saul A Bert, Nicola J Armstrong, C Elizabeth Caldon, Jenny Z Song, Shalima S Nair, Cathryn M Gould, Phuc Loi Luu, Amanda Khoury, Wenjia Qu, Elena Zotenko, Clare Stirzaker (+1 others)
<span title="2018-01-22">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Replication timing is known to facilitate the establishment of epigenome, however, the intimate connection between DNA replication timing and changes to the genome and epigenome in cancer remain uncharted. Here, we perform Repli-Seq and integrated epigenome analysis and show that early-replicating loci are predisposed to hypermethylation and late-replicating loci to hypomethylation, enrichment of H3K27me3 and concomitant loss of H3K9me3. We find that altered replication timing domains
more &raquo; ... to long-range epigenetically deregulated regions in prostate cancer, and a subset of these domains are remarkably conserved across cancers from different tissue origins. Analyses of 214 prostate and 35 breast cancer genomes reveal that late-replicating DNA is prone to cis and early- replicating DNA to trans chromosomal rearrangements. We propose that differences in epigenetic deregulation related to spatial and temporal positioning between early and late replication potentiate the landscape of chromosomal rearrangements in cancer.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/251280">doi:10.1101/251280</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cwb7wj7z4rehhazvjkmn65p4qy">fatcat:cwb7wj7z4rehhazvjkmn65p4qy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502113827/https://www.biorxiv.org/content/biorxiv/early/2018/01/22/251280.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/67/e5/67e5f2ab6becca099e8989a34c41cde3ce097614.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/251280"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

Ruth Pidsley, Elena Zotenko, Timothy J. Peters, Mitchell G. Lawrence, Gail P. Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker, Susan J. Clark
<span title="2016-10-07">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements. Illumina have now released the MethylationEPIC (EPIC) BeadChip, with new content specifically designed to target these regions. We have used HM450 and whole-genome bisulphite sequencing (WGBS) to perform a critical evaluation of the new EPIC array platform. Results: EPIC covers over
more &raquo; ... 00 CpG sites, including >90 % of the CpGs from the HM450 and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58 % of FANTOM5 enhancers, only 7 % distal and 27 % proximal ENCODE regulatory elements are represented. Detailed comparisons of regulatory elements from EPIC and WGBS show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region. However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform. Finally, we provide an annotated list of probes whose signal could be affected by cross-hybridisation or underlying genetic variation. Conclusion: The EPIC array is a significant improvement over the HM450 array, with increased genome coverage of regulatory regions and high reproducibility and reliability, providing a valuable tool for high-throughput human methylome analyses from diverse clinical samples.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-016-1066-1">doi:10.1186/s13059-016-1066-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27717381">pmid:27717381</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5055731/">pmcid:PMC5055731</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vtx3snggljfylee4lerletuqkq">fatcat:vtx3snggljfylee4lerletuqkq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015084539/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/83b/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEzMDU5LTAxNi0xMDY2LTEucGRm.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/90/56/90565e8f8642e6271a3f13ba7e54e74884472033.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-016-1066-1"> <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/PMC5055731" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer

Andrew Stone, Elena Zotenko, Warwick J. Locke, Darren Korbie, Ewan K. A. Millar, Ruth Pidsley, Clare Stirzaker, Peter Graham, Matt Trau, Elizabeth A. Musgrove, Robert I. Nicholson, Julia M. W. Gee (+1 others)
<span title="2015-07-14">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Expression of oestrogen receptor (ESR1) determines whether a breast cancer patient receives endocrine therapy, but does not guarantee patient response. The molecular factors that define endocrine response in ESR1-positive breast cancer patients remain poorly understood. Here we characterize the DNA methylome of endocrine sensitivity and demonstrate the potential impact of differential DNA methylation on endocrine response in breast cancer. We show that DNA hypermethylation occurs predominantly
more &raquo; ... t oestrogen-responsive enhancers and is associated with reduced ESR1 binding and decreased gene expression of key regulators of ESR1 activity, thus providing a novel mechanism by which endocrine response is abated in ESR1-positive breast cancers. Conversely, we delineate that ESR1responsive enhancer hypomethylation is critical in transition from normal mammary epithelial cells to endocrine-responsive ESR1-positive cancer. Cumulatively, these novel insights highlight the potential of ESR1-responsive enhancer methylation to both predict ESR1-positive disease and stratify ESR1-positive breast cancer patients as responders to endocrine therapy.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms8758">doi:10.1038/ncomms8758</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26169690">pmid:26169690</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4510968/">pmcid:PMC4510968</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sb7qp5dw3nch3mrpynp6plfmfq">fatcat:sb7qp5dw3nch3mrpynp6plfmfq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171203193944/https://core.ac.uk/download/pdf/42524168.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/5e/17/5e17caf6977ec60fd77146eecb1e1f3317b1c34e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms8758"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510968" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality

Elena Zotenko, Julian Mestre, Dianne P. O'Leary, Teresa M. Przytycka, Burkhard Rost
<span title="2008-08-01">2008</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;
Citation: Zotenko E, Mestre J, O'Leary DP, Przytycka TM (2008) Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000140">doi:10.1371/journal.pcbi.1000140</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18670624">pmid:18670624</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2467474/">pmcid:PMC2467474</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uqyc5cxwvbfopeq3wmpmjwio7u">fatcat:uqyc5cxwvbfopeq3wmpmjwio7u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190505214450/https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000140&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/2f/fa/2ffa623068f5388cad1919ae0e853e9fffcf8cd5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000140"> <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/PMC2467474" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer

Qian Du, Saul A. Bert, Nicola J. Armstrong, C. Elizabeth Caldon, Jenny Z. Song, Shalima S. Nair, Cathryn M. Gould, Phuc-Loi Luu, Timothy Peters, Amanda Khoury, Wenjia Qu, Elena Zotenko (+2 others)
<span title="2019-01-24">2019</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are
more &raquo; ... erved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-08302-1">doi:10.1038/s41467-019-08302-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30679435">pmid:30679435</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6345877/">pmcid:PMC6345877</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xkb6e3rbbjc7pmxl5wd4oca6xq">fatcat:xkb6e3rbbjc7pmxl5wd4oca6xq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426222854/https://researchrepository.murdoch.edu.au/id/eprint/43359/1/epigenome.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/9b/0f/9b0fde3f2f68976f46245a3c03907f0f60413b23.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-08302-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345877" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity [article]

Qian Du, Grady C Smith, Phuc Loi Luu, James M Ferguson, Nicola J Armstrong, C Elizabeth Caldon, Elyssa Campbell, Shalima S Nair, Elena Zotenko, Cathryn M Gould, Michael Buckley, Dominik Kaczorowski (+8 others)
<span title="2020-10-16">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
DNA replication timing and three-dimensional (3D) genome organisation are associated with distinct epigenome patterns across large domains during differentiation and cancer progression. However, it is unclear if alternations in the epigenome, in particular cancer-associated DNA hypomethylation, can directly promote higher order genome architectural alterations. Here, we use Hi-C and single cell Repli-Seq, in the colorectal cancer DNMT1 and DNMT3B DNA methyltransferases double knockout model, to
more &raquo; ... determine the impact of DNA hypomethylation on replication timing and 3D genome organisation. First, we find that the hypomethylated cells show a striking loss of replication timing precision with gain of intra-population replication timing heterogeneity and loss of 3D genome compartmentalisation. Second, hypomethylated regions that undergo a large change in replication timing also show loss of allelic replication timing, including at cancer-related genes. Finally, we observe the striking formation of ectopic H3K4me3-H3K9me3 domains across hypomethylated regions where late replication is maintained, which we propose serve to prevent aberrant transcription and loss of genome organisation after DNA demethylation. Together, our results highlight a previously underappreciated role for DNA methylation in the maintenance of 3D genome architecture.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.15.338855">doi:10.1101/2020.10.15.338855</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x52uwmbdxfaiblzyuo7su25pem">fatcat:x52uwmbdxfaiblzyuo7su25pem</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201211081418/https://www.biorxiv.org/content/biorxiv/early/2020/10/16/2020.10.15.338855.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/d7/a6/d7a61ac3d0f7b2eb81c46ec13991128de70473a7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.15.338855"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

Phillippa C. Taberlay, Joanna Achinger-Kawecka, Aaron T.L. Lun, Fabian A. Buske, Kenneth Sabir, Cathryn M. Gould, Elena Zotenko, Saul A. Bert, Katherine A. Giles, Denis C. Bauer, Gordon K. Smyth, Clare Stirzaker (+2 others)
<span title="2016-04-06">2016</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;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.201517.115">doi:10.1101/gr.201517.115</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27053337">pmid:27053337</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4889976/">pmcid:PMC4889976</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n4ne2zmey5c4dkwiyhzws426ai">fatcat:n4ne2zmey5c4dkwiyhzws426ai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302153049/http://pdfs.semanticscholar.org/b7d3/9eff60385732b1a7acf3373e2bcf4d75ce02.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/b7/d3/b7d39eff60385732b1a7acf3373e2bcf4d75ce02.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.201517.115"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889976" 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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