ライフサイエンスコーパス: epigenomic

1 ween measurement and function in single-cell epigenomics.

2 represents a general strategy for structural epigenomics.

3 n order to facilitate biomedical research in epigenomics.

4 network perturbation by explaining observed epigenomic activity patterns in cancer and normal tissue

5 The novel systems-epigenomics algorithm SEPIRA will be useful to the wider

6 Using a novel systems-epigenomics algorithm, called SEPIRA, which leverages th

7 n adult male offspring that is paralleled by epigenomic alterations and inflammation in visceral whit

8 n adult male offspring that is paralleled by epigenomic alterations and inflammation in VWAT.

9 Thus, deregulated tyrosine kinase driven epigenomic alterations have profound implications in can

10 around the globe have cataloged genomic and epigenomic alterations in gliomas across ages, grades, a

11 to identify interactions between genomic and epigenomic alterations in regulating gene expression net

12 fication of groups of patients with specific epigenomic alterations might have therapeutic relevance.

13 The contribution of epigenomic alterations to tumour progression and relapse

14 Much less so in epigenomics, although the role of k-mers in chromatin or

15 However, such epigenomic analyses are limited by averaging of populati

16 Epigenomic analyses have provided significant insight in

17 Integrated transcriptomic and epigenomic analyses uncovered a PAX6/DLX5 transcriptiona

18 of comprehensive genomic, transcriptomic and epigenomic analyses, we compared benign meningiomas to a

19 Through transcriptomic and epigenomic analyses, we investigated 5-methylcytosine (5

20 ocess through integrative transcriptomic and epigenomic analyses.

21 stem enabled integrative transcriptional and epigenomic analysis across the human reprogramming timel

22 Here we employ genetic and epigenomic analysis approaches to uncover novel genomic

23 Here we report the transcriptional and epigenomic analysis of six consecutive neural progenitor

24 ton imaging, whole-genome transcriptomic and epigenomic analysis with complementary bioinformatics, u

25 cs at the single-cell level not predicted by epigenomic analysis.

26 tools and machine learning methods utilizing epigenomic and 3D genome structure data.

27 We report comprehensive epigenomic and functional analyses, including 12 millio

28 t genes by systematic mining of comparative, epigenomic and regulatory annotations.

29 kely plays an important role in facilitating epigenomic and transcriptional differences between indiv

30 we sought to address this gap by generating epigenomic and transcriptional profiles from primary hum

31 f UVR, acute UV exposure induced substantial epigenomic and transcriptomic alterations, illuminating

32 By incorporating epigenomic and transcriptomic data with genome-wide asso

33 to a complex genomic data set including the epigenomic and transcriptomic effects of Toxoplasma gond

34 total of 28 gene sets with significant joint epigenomic and transcriptomic effects on one-year lung c

35 nating a previously underappreciated role of epigenomic and transcriptomic instability in skin pathog

36 Herein, we use integrative genomic, epigenomic and transcriptomic profiling of perturbed hum

37 e 1) or after treatment (after 2 cycles) for epigenomic and transcriptomic profiling using the Infini

38 y as they become integrated with expression, epigenomic and variation data sets.

39 mDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-

40 e) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects.

41 ractively display genomics, transcriptomics, epigenomics and metagenomics data stored either locally

42 of regulatory data from the ENCODE, Roadmap Epigenomics and other consortia provides a wealth of opp

43 allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-f

44 imaging to novel neuroanatomical, molecular, epigenomic, and computational methodologies.

45 ility of activation-induced transcriptional, epigenomic, and functional changes in Treg cells.

46 e describe how integration of large genomic, epigenomic, and phenotypic datasets, including whole gen

47 is of cognitive, neuropathological, genomic, epigenomic, and transcriptomic data, we identified ENC1

48 the data with publically available genomic, epigenomic, and transcriptomic information from human cl

49 Here, we examined genomic, epigenomic, and transcriptomic profiles in human pancrea

50 rognostic values of high-throughput genomic, epigenomic, and transcriptomic profiles individually, in

51 chnology can be advanced by transcriptomics, epigenomics, and bioinformatics that inform on genetic p

52 nt of and recent advances in mouse genomics, epigenomics, and transgenics offer ever-greater potentia

53 By integrating genetic fine-mapping and epigenomic annotation data and performing promoter-repor

54 is uniformly more accurate than the Roadmap Epigenomics annotation and the improvement is substantia

55 ics across multiple traits using hundreds of epigenomic annotations.

56 sociated variants that overlap GWAS-enriched epigenomic annotations.

57 uires evaluating them with known genomic and epigenomic annotations.

58 causal enrichments among 848 tissue-specific epigenomics annotations from ENCODE/Roadmap consortium c

59 An integrative epigenomic approach revealed 10,504 differentially methy

60 We used a meta-epigenomic approach that combines DNA methylation profil

61 Here, we used a targeted epigenomic approach to address whether specific retrotra

62 We used an integrated transcriptomic and epigenomic approach to analyze chromatin accessibility,

63 We apply an integrated epigenomic approach to characterize the molecular events

64 Our comprehensive epigenomics approach to the analysis of human macrophage

65 Although current epigenomic approaches can infer function for chromatin m

66 But current epigenomic approaches largely map DNA regulatory element

67 erse neuronal types, yet we lack single-cell epigenomic assays that are able to identify and characte

68 ghlight new developments such as single-cell epigenomic assays that will help provide us with a high-

69 Here, we report the epigenomic (ATAC-seq) and transcriptomic (RNA-seq) lands

70 Epigenomics-based annotation revealed a highly dynamic r

71 verall our results reveal substantial global epigenomic change in mammalian sperm methylomes and poin

72 These data implicate large scale epigenomic change in mediating the effects of environmen

73 aling allows tumors to acquire STAT1-related epigenomic changes and augments expression of interferon

74 l approach to study the relationship between epigenomic changes and cell lineage differentiation.

75 These epigenomic changes are not only observed during aging bu

76 cascade of gene activation that necessitates epigenomic changes in chromatin structure.

77 The global epigenomic changes in H3K27ac deposition pinpoint dynami

78 that display coordinated transcriptional and epigenomic changes in the diverse vertebrates during emb

79 Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous

80 Understanding age-dependent epigenomic changes will yield key insights into how agin

81 Furthermore, SSCs in vitro maintain the epigenomic characteristics of germ cells in vivo.

82 s assays such as ChIP-seq and DNase-seq, the epigenomic characterization of a cell type is typically

83 Genomic and epigenomic classification of these lncRNAs reveals that

84 methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool

85 about their genome-wide transcriptional and epigenomic consequences.

86 To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection

87 The Roadmap Epigenomics Consortium has published whole-genome functi

88 ence Epigenome Map, generated by the Roadmap Epigenomics Consortium, contains thousands of genome-wid

89 methods, including that used by the Roadmap Epigenomics Consortium.

90 interpretation of genome-wide ROIs within an epigenomic context.

91 independently of mCG and is a highly dynamic epigenomic correlate of allele-specific gene regulation.

92 usly inferring and exploiting the underlying epigenomic correlation between traits further improved t

93 D interactions by integrative analysis of 1D epigenomic data and associate 3D contacts to functionali

94 quantitative traits using cell type-matched epigenomic data and promoter long-range interactions.

95 Our results demonstrated that epigenomic data could be used to indicate common epigeno

96 We used the public epigenomic data from human fibroblast IMR90 cell and emb

97 Epigenomic data from human tissue revealed an enhancer s

98 alternative methods, based on the available epigenomic data from the ENCODE project.

99 Integration of Sp1 modules with genomic and epigenomic data indicates epigenetic control of Sp1 targ

100 approach in a simulation study and on a real epigenomic data set from the ENCODE project.

101 Using integrative analysis of >35 epigenomic data sets from mouse and human pre- and postn

102 ty to predict CRMs while taking into account epigenomic data such as DNase I sensitivity or histone m

103 We used our epigenomic data to infer transcriptional regulatory prot

104 ningfully inform the analysis of genomic and epigenomic data to provide insights that are missed when

105 ure, to investigate >600 sets of genomic and epigenomic data with various evolutionary and biophysica

106 in interaction frequencies, genome-wide (ie, epigenomic data), in a cell line model of hematopoietic

107 We examined epigenomic data, allelic activity, motif conservation, r

108 the interpretation of ROIs with the help of epigenomic data.

109 automated parallel processing of genome-wide epigenomics data from sequencing files into a final repo

110 es that combine genetic, transcriptomics and epigenomics data to address a wide range of issues rangi

111 (CpG Shore data, THREE data and NIH Roadmap Epigenomics data), studied previously in other works.

112 pecific steps in the analysis of large-scale epigenomics data, comprehensive software solutions for t

113 act with EpiCompare by investigating Roadmap Epigenomics data, or uploading their own data for compar

114 pe and supports their integration with other epigenomics data.

115 Large epigenomic datasets are then generated, and often combin

116 nal tools has been developed utilizing these epigenomic datasets for the interpretation of genomic da

117 , we generated extensive transcriptional and epigenomic datasets from livers of mice fed these diets

118 We collected transcriptomic and epigenomic datasets from these mice using RNA-Seq and DN

119 of WGS-based fine-mapping and complementary epigenomic datasets provided evidence for causal mechani

120 onsortium, contains thousands of genome-wide epigenomic datasets that describe epigenomes of a variet

121 mes of functional/regulatory data (reference epigenomic datasets), effectively annotating the genome

122 s to whether these genes exhibit patterns of epigenomic deregulation that transcend cancer types.

123 Epigenomic divergence is often attributable to genetic v

124 s that regulate transcription, and that this epigenomic diversity is, in fact, highly plastic and sen

125 er, these maps provide new insights into the epigenomic diversity that exists between distinct plant

126 al complexity of neurons to their underlying epigenomic diversity.

127 ducted an integrative analysis that combined epigenomic elements and previous genome-wide association

128 By this approach, we found a set of distinct epigenomic elements significantly enriched or depleted i

129 Here, we perform epigenomic enhancer profiling of a cohort of more than f

130 Starting with epigenomic enrichment analysis, we discuss leading tools

131 macaque, mouse, rat, and dog-to investigate epigenomic evolution.

132 ese genes occupy highly specialized genomic, epigenomic, evolutionary and functional niches in our ge

133 serve the changes in the correlation between epigenomic features across developmental trajectories of

134 nvestigators in exploring the specificity of epigenomic features across selected tissue and cell type

135 anwhile, DeepCode reveals the superiority of epigenomic features and their dominant roles in decoding

136 However, both somatic mutagenesis and epigenomic features are highly cell-type-specific.

137 Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for dif

138 ictors of local somatic mutation density are epigenomic features derived from the most likely cell ty

139 Myriads of epigenomic features have been comprehensively profiled i

140 works and calculate the presence of specific epigenomic features in the chromatin fragments constitut

141 lasia than previously believed, and identify epigenomic features of ACF that may provide new targets

142 wealth of information about the identity and epigenomic features of its cell of origin.

143 epigenomes in order to identify regions with epigenomic features specific to certain types of tissues

144 light on endogenous sources of mutation and epigenomic features that promote genomic instability dur

145 lution needed to investigate the genomic and epigenomic features underlying meiotic crossovers.

146 re will then identify regions with specified epigenomic features, and provide a quality assessment of

147 other elements have different characteristic epigenomic features.

148 ypes and compared them to cell-type-specific epigenomic features.

149 scusses the recent advances in breast cancer epigenomics, focusing on their contribution to diagnosis

150 To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin

151 that leverages diverse types of genomic and epigenomic functional annotations in genetic risk predic

152 s such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural

153 NIH projects such as ENCODE and Roadmap Epigenomics have revealed surprising complexity in the t

154 ence epigenomes from ENCODE 2012 and Roadmap Epigenomics, incorporating regulator binding data, expan

155 helps to annotate the noncoding genome using epigenomic information across one or multiple cell types

156 Our results demonstrate the central role of epigenomic information for understanding gene regulation

157 We used epigenomic information to identify H3K27Ac peaks in HCT1

158 tes to the chromatin landscape to ensure the epigenomic integrity of dividing cells.

159 chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global st

160 and providing a resource for future cardiac epigenomic investigations.

161 lso altered in various cancers, changing the epigenomic landscape during cancer initiation and progre

162 ng chromatin assortativity, to integrate the epigenomic landscape of a specific cell type with its ch

163 10 ATRT cell lines to define the genomic and epigenomic landscape of ATRTs and identify subgroup-spec

164 etic and environmental factors affecting the epigenomic landscape of human populations over time.

165 tegrated framework of the transcriptomic and epigenomic landscape of mouse and human keratinocytes.

166 th transcription, provides the most complete epigenomic landscape of the human placenta, and will be

167 es, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development.

168 ear architecture is correlated with a unique epigenomic landscape, we performed ATAC-seq on mouse rod

169 e its response based on the lineage-specific epigenomic landscape.

170 nt, indicating a shift in transcriptomic and epigenomic landscapes during metastasis.

171 This work defines the epigenomic landscapes of rods and cones, revealing featu

172 neocortical neurons have highly distinctive epigenomic landscapes.

173 Epigenomic-led stratification can predict resistance to

174 subsets at both the transcriptomic level and epigenomic level and by single-cell RNA sequencing.

175 We review here the comparative epigenomics literature and synthesize its overarching th

176 erapies can involve extensive genomic and/or epigenomic manipulation of autologous or allogeneic cell

177 Epigenomic mapping of enhancer-associated chromatin modi

178 wards low-input DNA sequencing and mammalian epigenomic mapping of native DNA samples.

179 hold' signals represent novel loci, and that epigenomic maps are effective at discriminating true bio

180 lting large collection of haplotype-resolved epigenomic maps reveals extensive allelic biases in both

181 te information from association studies with epigenomic maps to demonstrate that enhancers significan

182 It combines multiple genome-wide epigenomic maps, and uses combinatorial and spatial mark

183 datasets, we compared the IDEAS and Roadmap Epigenomics maps.

184 role for 6mA as a gene-expression-associated epigenomic mark in eukaryotes.

185 enomic data could be used to indicate common epigenomic marks to discover additional loci with biolog

186 tic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell t

187 Using these epigenomic marks, we performed reverse prediction analys

188 r shapes, thereby capturing the structure of epigenomic marks.

189 taneous alignment and clustering of multiple epigenomic marks.

190 m covering 127 cell/tissue types and 8 major epigenomic marks.

191 w neuroimaging can help guide the search for epigenomic mechanisms in neurodevelopmental disorders.

192 Emerging single-cell epigenomic methods are being developed with the exciting

193 Identifying the cis elements that regulate epigenomic modification is critical for understanding th

194 way abrogates adult morbidity and associated epigenomic modifications of IGF-1 in a rodent model of m

195 ytokine response and be cued to long-lasting epigenomic modifications rather than by short-term pharm

196 The Cas9 nuclease has been adapted to target epigenomic modifications, but a detailed description of

197 -binding factors that establish and maintain epigenomic modifications.

198 We conclude that TERRA functions as an epigenomic modulator in trans and as an essential regula

199 ss recent discoveries about the genomics and epigenomics of adult and pediatric gliomas and highlight

200 Epigenomic organization has been proposed as a major det

201 injury, our results have highlighted a novel epigenomic pathway in which reversal of the Polycomb pat

202 anisms targeting chromatin modifications and epigenomic patterns may vary among different species.

203 ; conversely patients exhibiting normal-like epigenomic patterns were associated with regression.

204 thways help to maintain genome integrity and epigenomic patterns.

205 he prenatal period as a time of considerable epigenomic plasticity.

206 ls drive a phenotypically relevant source of epigenomic plasticity.

207 ical confidence estimates and the utility of epigenomic priors in identifying CRMs.

208 uences activity of the genome via regulating epigenomic processes.

209 ng a comprehensive collection of genome-wide epigenomic profiles across cell types and factors, along

210 Furthermore, published epigenomic profiles are not specific to H3K36me3 or meta

211 k integrating transcriptomic, genomic and/or epigenomic profiles for any given cancer sample.

212 Integrating 110 epigenomic profiles from primary GCs, normal gastric tis

213 Distinct epigenomic profiles of histone marks have been associate

214 ncing were used to create transcriptomic and epigenomic profiles of preadipocytes and skeletal muscle

215 By connecting large-scale epigenomic profiles to expression quantitative trait loc

216 acilitates the study of multiple genome-wide epigenomic profiles, considering network topology and al

217 de research database that integrates genomic/epigenomic profiles, lifestyle patterns, dietary habits,

218 These elements are characterized by distinct epigenomic profiles, such as expanded deposition of hist

219 inguish different cells types based on their epigenomic profiles, thus recapitulating important aspec

220 Epigenomic profiling also demonstrated similar patterns

221 Epigenomic profiling and genome editing revealed that AM

222 in the past, we discuss the current state of epigenomic profiling and how functional information can

223 Here, we use epigenomic profiling from human and chimpanzee cranial n

224 ew years, systematic large-scale genomic and epigenomic profiling has provided unprecedented insight

225 Epigenomic profiling of skeletal muscle and adipose prog

226 Transcriptional and epigenomic profiling revealed that IFE and HF tumor-init

227 Detailed epigenomic profiling revealed that R-loops associate wit

228 al SNPs are first evaluated by fine mapping, epigenomic profiling, and epigenome editing, and then in

229 oding, often requiring genetic fine-mapping, epigenomic profiling, and individual reporter assays to

230 cluding whole genome sequencing data, GWASs, epigenomic profiling, protein-protein interaction networ

231 (ecMRTs) using genomic, transcriptomic, and epigenomic profiling.

232 s (ecMRTs) using genomic, transcriptomic and epigenomic profiling.

233 inactivation (XCI) confounds allele-specific epigenomic profiling.

234 DNA Elements consortium and the NIH Roadmap Epigenomics Project to predict haploinsufficiency, witho

235 one modification from ENCODE and the Roadmap Epigenomics Project, as well as through in vivo analysis

236 sets from different tissues from the Roadmap Epigenomics Project, ME-Class significantly outperforms

237 e-scale epigenome mapping by the NIH Roadmap Epigenomics Project, the ENCODE Consortium and the Inter

238 ets), effectively annotating the genome with epigenomic properties.

239 The integration of imaging and epigenomics provides a general and scalable approach for

240 The epigenomic reader Brd4 is an important drug target for c

241 These findings identify Brd4 as an enhancer epigenomic reader that links active enhancers with cell

242 model RiVIERA (Risk Variant Inference using Epigenomic Reference Annotations) for inference of drive

243 Epigenomic regulation is likely to be important in the m

244 so provide a rich resource for understanding epigenomic regulation of brown adipogenesis.

245 s the recent advances in signaling-dependent epigenomic regulation of gene transcription using a few

246 Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for impr

247 circadian clock, these results delineate an epigenomic regulatory mechanism through which the circad

248 Finally, we discuss the transcriptional and epigenomic remodeling events associated with cell fate t

249 critical to peripheral nerve repair, yet the epigenomic reprograming that leads to the induction of i

250 yocytes is the result of a well-orchestrated epigenomic reprogramming and a subsequent global transcr

251 We find a striking asymmetry in epigenomic reprogramming between luminal and myoepitheli

252 NT) provides an excellent model for studying epigenomic reprogramming during mammalian development.

253 e cardiomyocyte-derived CPCs (mCPCs) display epigenomic reprogramming with many differentially-methyl

254 enomenon, and not simply a byproduct of seed epigenomic reprogramming.

255 molecular portraits of mutant-IDH1-dependent epigenomic reprogramming.

256 e a large-scale atlas of mutant-IDH1-induced epigenomic reprogramming.

257 tive relative to the 129 version, indicating epigenomic rescue.

258 Functional genomic and epigenomic research relies fundamentally on sequencing b

259 of the recent advances in cancer genomic and epigenomic research.

260 (ATAC-Seq) has become a fundamental tool of epigenomic research.

261 The development of epigenomic resources by ENCODE, the Epigenomic Roadmap a

262 ermining factors to convey a tissue-specific epigenomic rhythm that regulates metabolism tailored to

263 pment of epigenomic resources by ENCODE, the Epigenomic Roadmap and others has led to strategies that

264 ensitive Site (DHS) information from the NIH Epigenomics Roadmap to construct an improved reference D

265 We suggest that the Septin9 serum assay (Epigenomics, Seattle, Wash) not be used for screening.

266 provide important insights into genomic and epigenomic shock that occurs following hybridization and

267 n of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of e

268 NaviSE also implements an 'epigenomics signal algebra' that allows the combination

269 nation of multiple activation and repression epigenomics signals.

270 We uncover epigenomic signatures of domestication traits during cot

271 re of chromosomal compartments with distinct epigenomic signatures.

272 A link between the epigenomic state and cell division versus cell elongatio

273 ere conducted as a functional readout of the epigenomic structural changes.

274 Recent epigenomic studies defined cis-regulatory elements (REs)

275 and its association with human disease, but epigenomic studies lack a similar reference.

276 d the potential utility of this approach for epigenomic studies of brain disorders.

277 ion (ChIP) assays poses a major obstacle for epigenomic studies of low-abundance cells.

278 It is important for large-scale epigenomic studies to determine and explore the nature o

279 for tools that facilitate cell-type-specific epigenomic studies, we developed the first affinity puri

280 rming the Accessible Resource for Integrated Epigenomics Studies (ARIES)-that includes (1) peripheral

281 We performed a transcriptomic and epigenomic study in patient-derived B-cell lines to inve

282 Epigenomic subpopulations in cancer impact drug sensitiv

283 mes of ovarian cancer patients.Significance: Epigenomic targeting may improve therapeutic outcomes in

284 Incorporating epigenomic testing into the clinical research arsenal wi

285 tivity, we apply integrative and comparative epigenomics to 25 human primary cell and tissue samples.

286 Developments in epigenomics, toxicology, and therapeutic nucleic acids a

287 In order to identify novel epigenomic traits of regulatory elements, we constructed

288 Using integrative cistromic, epigenomic, transcriptomic, and interactomic analyses, w

289 We performed genomic, epigenomic, transcriptomic, and proteomic characterizati

290 ches to integrate a growing body of genomic, epigenomic, transcriptomic, and proteomic data and eluci

291 t multiple forms of molecular data (genomic, epigenomic, transcriptomic, etc) and multiple endpoints

292 The NetGestalt CRC portal includes genomic, epigenomic, transcriptomic, proteomic and clinical data

293 erent high-throughput omics datasets, namely epigenomics, transcriptomics, glycomics and metabolomics

294 e of high-throughput technologies, including epigenomics, transcriptomics, proteomics, and metabolomi

295 Epigenomic variation at the single-cell level can rapidl

296 ingly well documented, yet their patterns of epigenomic variation remain uncharacterized.

297 with regards to genomic, transcriptomic, and epigenomic variation.

298 sh MLL3/MLL4 and CBP/p300 as master enhancer epigenomic writers and suggest that enhancer-priming by

299 To understand how these epigenomic writers orchestrate enhancer landscapes in ce

300 etyltransferases CBP/p300 are major enhancer epigenomic writers.