ライフサイエンスコーパス: epigenomic

1 e HD-associated changes in transcription and epigenomics.

2 nd CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer.

3 ten involve multiple types of genomic and/or epigenomic abnormalities.

4 onships among different types of genomic and epigenomic abnormalities.

5 interactions, which early in life accelerate epigenomic aging, and later in adulthood unlock metaboli

6 the conventional view that tumor-associated epigenomic alterations are primarily oncogenic.

7 3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B

8 antitumour responses may also be affected by epigenomic alterations.

9 Epigenomic analyses demonstrate that EWS-FLI1, the prima

10 Integrated transcriptomic and epigenomic analyses linked glucose starvation-mediated H

11 Integrated transcriptomic and epigenomic analyses of glioblastoma initiating cells (GI

12 Epigenomic analyses of PAX8-dependent cistrome demonstra

13 we integrated transcriptomic, proteomic and epigenomic analyses of postmortem human brains to identi

14 development by performing transcriptomic and epigenomic analyses on human induced pluripotent stem ce

15 Epigenomic analyses revealed that the promoter of Indian

16 mouse genetics, unbiased transcriptomic and epigenomic analyses, and classic molecular biology and b

17 Conclusion: Using an integrative genomic and epigenomic analysis approach, we identified four major i

18 We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous b

19 An epigenomic analysis of patient-derived and de-novo gener

20 We performed transcriptomic and epigenomic analysis of the TNF response in primary human

21 In this study, we apply epigenomic analysis to characterize the transcription dy

22 Overall, our work provides an additional epigenomic anchor for the functional annotation of verte

23 ere we cross-reference human transcriptomic, epigenomic and chromatin conformation datasets.

24 This classical bisulfite reaction used for epigenomic and epitranscriptomic sequencing diverges fro

25 of the monocyte state and characterized its epigenomic and functional phenotypes, and propose a mode

26 ng unique regulatory DNA maps and integrated epigenomic and genetic analysis.

27 of TGF-beta treated MCF10A cells and related epigenomic and Hi-C data.

28 kemic effects.METHODSTo identify genomic and epigenomic and patient variables determining the intrace

29 peutic targets, we conducted parallel global epigenomic and proteomic analysis of archival formalin-f

30 acterization of the genomic, transcriptomic, epigenomic and proteomic features of the tumour and/or t

31 -exonic element from an input of over 60,000 epigenomic and transcription factor binding features.

32 ing transient polarization signals to stable epigenomic and transcriptional changes in macrophages.

33 By coupling NC-specific epigenomic and transcriptional profiling at population a

34 Integrative genome-wide epigenomic and transcriptomic analyses of platinum-sensi

35 Epigenomic and transcriptomic analyses of regions near h

36 Here we report epigenomic and transcriptomic analyses of the two main c

37 Using epigenomic and transcriptomic approaches, we sought to d

38 have generated the global histone mark based epigenomic and transcriptomic cartogram of SCC25, a repr

39 However, a systematic study of epigenomic and transcriptomic changes across tissues dur

40 ic lesion has been determined, the resulting epigenomic and transcriptomic changes driving the phenot

41 data set represents the largest multitissue epigenomic and transcriptomic data set for vertebrate ag

42 Epigenomic and transcriptomic data suggested that a larg

43 he human epigenome have yielded thousands of epigenomic and transcriptomic datasets.

44 ehensive studies have dissected the genomic, epigenomic and transcriptomic landscape of CLL.

45 Epigenomic and transcriptomic landscapes could easily di

46 uired non-coding variants, here we establish epigenomic and transcriptomic landscapes of primary OCs

47 conjunction with RNA sequencing to create an epigenomic and transcriptomic map of the developmental t

48 inference based on genomic, transcriptomic, epigenomic and/or proteomic analysis of patient samples,

49 ched cell types and tissues from the Roadmap Epigenomics and ENCODE consortia.

50 ta for 77 cell and tissue types from Roadmap Epigenomics and ENCODE, and from H3K27Ac ChIP-seq data g

51 We report microbiota, host transcriptomics, epigenomics and genetics from matched inflamed and non-i

52 omics technologies, such as transcriptomics, epigenomics and genomics, provide an unprecedented genom

53 so provides a set of methods for comparative epigenomics and integrative analysis, which we expect to

54 as led to tremendous growth in the fields of epigenomics and transcriptional biology.

55 thelia (oncogenic, developmental, metabolic, epigenomic) and tumor microenvironment (angiogenesis, ch

56 We combine genetic, epigenomic, and biochemical studies to show that HNF1A r

57 By combining GWAS, epigenomic, and chromatin conformation data, we function

58 line training models, which include genomic, epigenomic, and conservation-based features, for SV call

59 me structure underlie clonal transcriptomic, epigenomic, and histopathologic signatures in meningioma

60 se lines was investigated by transcriptomic, epigenomic, and phenotypic analyses.

61 Surprisingly, the influence of genomic, epigenomic, and transcriptomic dysregulation on the tumo

62 Integration of GWAS signals with epigenomic annotations has demonstrated that AD risk var

63 pped variants in conjunction with continuous epigenomic annotations to identify trait-cell type enric

64 nrichment of these signals in islet-specific epigenomic annotations.

65 examined plasma cells from MM using a multi-epigenomics approach and demonstrated that, when compare

66 Here we use combined transcriptomic and epigenomic approaches to find that IFN-gamma selectively

67 rare genetic variants, thereby refining the epigenomic architecture of psychiatric disorders and ena

68 s to detect epigenetic features genome-wide (epigenomic assays).

69 tep for functional studies of epigenomes and epigenomics-based precision medicine.

70 led in response to chronic exercise, but the epigenomic basis for muscle identity and adaptation rema

71 Understanding the genomic and epigenomic basis of JMML will not only greatly improve p

72 d to understand genomic, transcriptomic, and epigenomic changes and gained traction as a significant

73 ns in the mtDNA cause distinct metabolic and epigenomic changes at different heteroplasmy levels, pot

74 Lineage-specific epigenomic changes during human corticogenesis have been

75 Here, we characterized global epigenomic changes during the direct reprogramming of mo

76 Age-related epigenomic changes first spike around late-thirties with

77 ne makes it a potential device for detecting epigenomic changes in genomes.

78 cell-type specificity of transcriptomic and epigenomic changes in the brain.

79 The epigenomic changes induced by light damage include reduc

80 Here, we mapped the early and late epigenomic changes of interleukin-4 (IL-4)-induced alter

81 Yet little is known about the epigenomic changes that underlie the tumorigenic impact

82 The epigenomic changes were similar between somatic and zygo

83 Although its functional genomic and epigenomic characteristics have been extensively studied

84 Although the functional genomic and epigenomic characteristics of HepG2 are extensively stud

85 play and determine their transcriptomic and epigenomic characteristics.

86 Integrative epigenomic characterization further pinpoints a recurren

87 Using EMBLEM, we define the genetic and epigenomic clonal evolution of hematopoietic stem cells

88 eas folding of genomes at the large scale of epigenomic compartments and topologically associating do

89 Finally, single-cell epigenomics confirmed that heterogeneity among effectors

90 127 human cell types studied by the Roadmap Epigenomics Consortium.

91 We identify an epigenomic continuum representing loss of cellular ident

92 We validated these findings by using epigenomic data across major somatic tissues and sperm.

93 Quantitative comparison of epigenomic data across multiple cell types or experiment

94 c data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain l

95 vidence of correlated activity patterns from epigenomic data and physical evidence of chromatin inter

96 We analyzed transcriptomic and epigenomic data from induced pluripotent stem cell-deriv

97 these systematic functional annotations with epigenomic data improve interpretation of EOC risk varia

98 ltogether, we provide a powerful resource of epigenomic data in 25 primary DIPG samples and 5 rare no

99 shed for validated systematic integration of epigenomic data in hematopoiesis.

100 zation method, Avocado, that compresses this epigenomic data into a dense, information-rich represent

101 We use this learned representation to impute epigenomic data more accurately than previous methods, a

102 We show empirically that the epigenomic data normalized by our method, compared to ex

103 Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an

104 ntation outperform those trained directly on epigenomic data on a variety of genomics tasks.

105 Integration of transcriptomic and epigenomic data revealed that IRF4, either alone or in c

106 Thousands of epigenomic data sets have been generated in the past dec

107 arning models trained on currently available epigenomic data sets that can be applied to the remainin

108 e assembled a rich collection of genomic and epigenomic data sets, including information about transc

109 Human physiology and epigenomic data support a central role for the pancreati

110 ocate for studies combining genomic and meta-epigenomic data to better understand the mode of action

111 (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to con

112 generate high-throughput transcriptomic and epigenomic data, many computational frameworks have been

113 eq approaches, along with publicly available epigenomic data, we systematically study the genome-wide

114 ies from both single-cell transcriptomic and epigenomic data.

115 identify real biological variation from raw epigenomic data.

116 t troves of existing functional genomics and epigenomics data for K562.

117 Starting from one-dimensional genomics and epigenomics data that are available for hundreds of cell

118 With the rapid accumulation of single-cell epigenomics data, MAPLE provides a general framework for

119 urrent state of genomic, transcriptomic, and epigenomic datasets charting the development of normal h

120 pture the salient features of the integrated epigenomic datasets for deciphering the distal (non-codi

121 we ask the question "How much information do epigenomic datasets provide about human genomic function

122 We generated 268 epigenomic datasets spanning two state transitions-from

123 Our AIKYATAN suite leverages diverse epigenomic datasets that can then be modeled using CNNs

124 Analyzing epigenomic datasets with personalized and graph genomes

125 potential therapeutic targets, we performed epigenomic deconvolution on 580 HNSCC samples from the T

126 netic analysis of tumor microenvironments by epigenomic deconvolution reveals potential novel biomark

127 N = 1132) of MDD cases and controls, we used epigenomic deconvolution to perform cell type-specific m

128 acent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, a

129 s for TEs ('toxic' Y effect), and incomplete epigenomic defenses during early development can lead to

130 ions are companion resources to the matching epigenomic developmental matrix, and are available for r

131 sion, Expression quantitative trait loci and Epigenomics (DICE) cis-interactome project).

132 r iCCA subgroups with widespread genomic and epigenomic differences and prognostic implications.

133 ted variation and provides a roadmap for the epigenomic dissection of causal regulatory variation in

134 6 human isolates and observe a high level of epigenomic diversity.

135 all gastrointestinal cancers is genomic and epigenomic DNA alterations.

136 tion factor binding motifs, and across human epigenomic domains.

137 er subtly in their relative abundance across epigenomic domains.

138 comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process in

139 The challenge of successful live-animal epigenomic editing will depend on a well-informed founda

140 M9 form a pioneer complex to create a unique epigenomic environment of open chromatin, permitting cor

141 enic events and transcriptional programs and epigenomic events are important in providing the necessa

142 hich shows congruent patterns of genomic and epigenomic evolution.

143 The gene expression and epigenomic experiments performed on PV(+) neurons isolat

144 Unexpectedly, our epigenomic experiments reveal that ZBED2 is a sequence-s

145 o link mutations of a motif to changes of an epigenomic feature without assuming a linear relationshi

146 ut human genomic function?" We consider nine epigenomic features across 115 cell types and measure in

147 ts have demonstrated that cell-type specific epigenomic features can be resolved in complex tissues u

148 eural network (CNN) models on a broad set of epigenomic features collected in a single disease-releva

149 naive-like developmental, bioenergetic, and epigenomic features despite providing primed-state-susta

150 and outperforms an existing method that uses epigenomic features in GM12878.

151 , prognostic biomarkers combining genomic or epigenomic features with proteomic ones significantly ou

152 Several epigenomic features yield more information in combinatio

153 profiles of the genomic, transcriptomic, and epigenomic heterogeneity of tumor subpopulations than do

154 es several important prospects for precision epigenomics, highlights capabilities and limitations of

155 combining genomic (TP53, RB1, CYLD, AR) and epigenomic (hypo- and hypermethylation of 20 differentia

156 lood-based biomarkers including metabolites, epigenomic, immune, inflammatory, and liver function mar

157 However, our understanding of LLDT-8-induced epigenomic impact and overall regulatory changes in key

158 To understand the genomic and epigenomic impacts of somatic embryogenesis, we characte

159 ghlight the emerging role of epigenetics and epigenomics in DKD and the translational potential of ca

160 al. use single-cell transcriptomics and epigenomics in mice and human samples to delineate devel

161 cs, including genomics, transcriptomics, and epigenomics, in an aim to discover the functional and me

162 ion is essential for the transmission of the epigenomic information encoded in posttranscriptional mo

163 Mapping of epigenomic information such as chromatin accessibility,

164 rehensive transcriptomic, DNA-occupancy, and epigenomic interrogation throughout the reprogramming pr

165 Epigenomic investigation of the chromatin environment an

166 However, epigenomics is rapidly emerging as a promising conceptua

167 idates the comprehensive transcriptional and epigenomic landscape across the lifespan of memory forma

168 a unique description of the ASCP genomic and epigenomic landscape and identify candidate therapeutic

169 Here, we define epigenomic landscape during epidermal differentiation of

170 Our results suggest that the genomic and epigenomic landscape of ASCP provide new strategies for

171 we profile the genomic, transcriptomic, and epigenomic landscape of CIS in a unique patient cohort w

172 rs, and TFAP2A/B heterodimers reorganize the epigenomic landscape of progenitor cells to promote neur

173 not created de novo and instead reflect the epigenomic landscape of the cell of origin.

174 Here, we examine the mouse epigenomic landscape of Xi and assess how Xist alters ch

175 chromatin modifiers-proteins that shape the epigenomic landscape through remodeling and regulation o

176 progressive cell commitment, remodeling the epigenomic landscape to define the presumptive neural cr

177 n profiling of a liverwort genome reveals an epigenomic landscape where the major mark of development

178 sion but also an extensive remodeling of the epigenomic landscape.

179 oes not perturb the normal pregnancy-induced epigenomic landscape.

180 ermine the clinically actionable genomic and epigenomic landscapes of N/S HNSTs.RESULTSWhole-exome se

181 heterogeneity within both transcriptomic and epigenomic layers and understanding transcriptional regu

182 Examining prostate biology through an epigenomic lens is fundamental for understanding the mec

183 differences at transcriptomic, proteomic and epigenomic levels across tissues, organs, organ systems

184 level but differ at the mRNA expression and epigenomic levels, likely due to the different growth en

185 Here, we provide an overview of epigenomic mapping in the human brain and highlight find

186 This creation of 3D epigenomic maps enables a better understanding of prosta

187 egrating tissue-specific gene expression and epigenomic maps to obtain "tissue-of-action" (TOA) score

188 es genome alignments and genome-wide maps of epigenomic marks and transcription factor binding provid

189 Evaluating predictive epigenomic marks of smokers in peripheral blood may allo

190 -specific models, as well as exploring other epigenomic marks, longitudinal and diverse population st

191 e machine learning model of transcriptomics, epigenomics, metabolomics, and proteomics.

192 omics approaches, including transcriptomics, epigenomics, microbiomics, metabolomics, and proteomics,

193 d RNA (caRNA) has been proposed as a type of epigenomic modifier.

194 ncovered numerous examples of FOXA-dependent epigenomic modulation in developmental and disease proce

195 tualized them in relevant transcriptomic and epigenomic networks.

196 s between mouse and human transcriptomic and epigenomic patterns.

197 consequences of genomic, transcriptomic, and epigenomic perturbations.

198 dothelial cells of up to 157 donors and four epigenomic phenotypes in up to 44 human donors represent

199 HDACi treatment reveals unanticipated epigenomic plasticity in SCV relationships that restore

200 Chromatin is the epigenomic platform for diverse nuclear processes such a

201 types, including their cellular composition, epigenomic profiles and gene expression for constituent

202 Through integrative analysis of 11,596 epigenomic profiles and mutations from >8200 tumor-norma

203 EpiAlignment takes DNA sequence and epigenomic profiles derived by ChIP-seq from two species

204 ultaneous measurements of transcriptomic and epigenomic profiles in the same individual cells provide

205 Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in o

206 evelopmentally regulated transcriptional and epigenomic profiles specific to early heart differentiat

207 omoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter

208 terogeneity from parallel transcriptomic and epigenomic profiles.

209 ated with tissue-specific transcriptomic and epigenomic profiles.

210 powerful methods for generating genomic and epigenomic profiles.

211 egration of GWAS signals with transcriptomic/epigenomic profiling and 3D chromatin interaction data f

212 Comparative epigenomic profiling and single-cell sequencing of two r

213 We collated epigenomic profiling data for 77 cell and tissue types f

214 features, including genome-wide genomic and epigenomic profiling data.

215 CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering

216 Advances in single-cell epigenomic profiling methods are enabling high-resolutio

217 Recent genome-wide transcriptomic and epigenomic profiling of clear cell renal cell carcinoma

218 (2020) performed extensive genomic and epigenomic profiling of hematopoietic stem and progenito

219 We perform epigenomic profiling of two enhancer marks, H3K4me1 and

220 In turn, epigenomic profiling revealed gains in the histone H3 mo

221 Epigenomic profiling revealed thousands of regeneration-

222 e Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling strategy in which antibodies are bo

223 Global epigenomic profiling was accomplished by employing an As

224 igate the mechanism that causes QPD, we used epigenomic profiling, comparative genomics, and chromati

225 RUN make it the method of choice for routine epigenomic profiling.

226 nt, failing to explain the long-term, stable epigenomic programs developed.

227 vergent exercise-induced or PGC1alpha-driven epigenomic programs direct partially convergent transcri

228 cell types and tissues from the NIH Roadmap Epigenomics Project as well as 8 histone marks (with add

229 large consortia including ENCODE and Roadmap Epigenomics Project continue to generate high-throughput

230 genomes of cell-types defined by the Roadmap Epigenomics project revealed that enhancers are more dis

231 tissues and cell types in the ENCODE/Roadmap Epigenomics Project, we provide catalogs of putative tis

232 27-epigenome dataset released by the Roadmap Epigenomics project, with enrichment for enhancers found

233 tudies on the real data from the NIH Roadmap Epigenomics project.

234 and development using data from the Roadmap Epigenomics Project.

235 Thus, epigenomics promises to generate a significant amount of

236 o identify clinical, epidemiologic, genomic, epigenomic, proteomic, and microbial correlates; discove

237 logies, including genomics, transcriptomics, epigenomics, proteomics and metabolomics, have all been

238 Epigenomic regulation and lineage-specific gene expressi

239 ng an understanding of the interplay between epigenomic regulation and molecular structure.

240 Advances in understanding of epigenomic regulation of adipogenesis have revealed crit

241 scuss recent advances in transcriptional and epigenomic regulation of adipogenesis, with a focus on f

242 radual and stochastic changes in genomic and epigenomic regulation suggest the absence of any specifi

243 ng putative mechanisms of cell-type-specific epigenomic regulation.

244 identification of novel transcriptional and epigenomic regulators of adipogenesis.

245 ineage-determining transcription factors and epigenomic regulators.

246 and their interaction to transcriptional and epigenomic regulatory dynamics requires sampling over ti

247 diated by the YAP/TEAD pathway, which drives epigenomic reprogramming and EMT to counteract apoptosis

248 This suggests that epigenomic reprogramming may be a fundamental driver of

249 This epigenomic reprogramming persists long after the initial

250 Furthermore, epigenomic resources are also incorporated, especially f

251 Defined broadly, psychiatric epigenomics seeks to understand the effects of disease-a

252 Using a two-step, in vitro/in vivo epigenomic shRNA inhibition screen, we determine the chr

253 cifically designed for comparing multi-track epigenomic signals and detecting common patterns that ma

254 tin state sequences learned from multi-track epigenomic signals and to identify locally aligned chrom

255 Mechanistically, Kmt2d loss widely impairs epigenomic signals for super-enhancers/enhancers, includ

256 h iterative learning, scAI aggregates sparse epigenomic signals in similar cells learned in an unsupe

257 The interferon epigenomic signature affects ISGs and other gene sets, i

258 These data reveal a shared epigenomic signature of aging including declining naive

259 iate CTCF binding alteration as a functional epigenomic signature of cancer.

260 that interferons also induce an 'interferon epigenomic signature' by activating latent enhancers and

261 liver to accelerate acquisition of an adult epigenomic signature.

262 h which interferon signatures and interferon epigenomic signatures are generated, as well as the expr

263 teracts with sex to alter transcriptomic and epigenomic signatures in the brain will inform individua

264 ive TF target genes are marked by permissive epigenomic signatures in the naive state, indicating tha

265 nts may be characterized by leveraging local epigenomic signatures where specific transcription facto

266 As naive hPSCs share transcriptional and epigenomic signatures with trophoblast cells, it has bee

267 results suggest a causal relationship among epigenomic state, TXNIP expression, cerebral-spleen tryp

268 n unbiased fashion using gene expression and epigenomic state.

269 chine-learning analysis showed that specific epigenomic states could predict transcriptional changes

270 Here, we quantify the epigenomic status of TEs across human anatomy and develo

271 Recent epigenomic studies have revealed the unusual chromatin l

272 Epigenomic studies that use next generation sequencing e

273 from the Accessible Resource for Integrated Epigenomic Studies, a subsample of mother-child pairs fr

274 ize the importance of culture conditions for epigenomic studies, and reveal that chromatin state is a

275 expect to be broadly applicable to bacterial epigenomic studies.

276 ty-wide, integrative approach for functional epigenomic studies.

277 represent a unique opportunity for bacterial epigenomic studies.

278 e performed an integrated transcriptomic and epigenomic study of peanut-allergic children as they rea

279 bserved that 22% of tumors exhibited a novel epigenomic subtype associated with hypermethylation and

280 nse factor) phosphorylation, constituting an epigenomic switch balancing the growth in width versus l

281 limited here to genomic, transcriptomic, and epigenomic techniques) to study neurodegenerative diseas

282 e motivates the use of these high-resolution epigenomic technologies for mapping cell states and unde

283 recent development of low-input genomic and epigenomic technologies has deepened our understanding o

284 Advances in high-throughput genomic and epigenomic technologies have revealed the tremendous com

285 advances in single-cell and single-molecule epigenomic technologies now enable the study of genome r

286 cases and highlights the potential value of epigenomic testing in the routine clinical assessment of

287 cancer will involve the vigorous testing of epigenomic therapeutics.

288 results demonstrate the power of single-cell epigenomics to identify regulatory programs to uncover m

289 Here, we use single-cell epigenomics to profile chromatin state transitions in a

290 Genomic, epigenomic, transcriptomic and proteomic landscapes have

291 differences in genomic content but rather by epigenomic, transcriptomic, and proteomic heterogeneity.

292 (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteo

293 grate information from other "-omics" (e.g., epigenomics, transcriptomics as measured by RNA expressi

294 Here, we utilized a multiomics approach (epigenomics, transcriptomics, proteomics, and phosphopro

295 ace thousands of cells from cancers, linking epigenomic variability to subclonal evolution, and infer

296 fined ALL subtypes, and assessed genomic and epigenomic variants influencing folate pathway genes (mR

297 ch additionally contributed to interspecific epigenomic variation across fungi.

298 nd plants have deepened our understanding of epigenomic variation, particularly of the modified base

299 Comparative epigenomics, which subjects both epigenome and genome to

300 d landscapes of Nannochloropsis genomics and epigenomics will promote and accelerate community effort