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1 ategic searches with small seeds (~14 nt for mammalian genomes).
2 well to many genomes of large size (such as mammalian genomes).
3 , including the largest miRNA cluster in the mammalian genome.
4 has evolved an essential function(s) in the mammalian genome.
5 been considered limiting for translating the mammalian genome.
6 higher coverage than has been reported in a mammalian genome.
7 ly suggests evolutionary conservation in the mammalian genome.
8 but also in distal regulatory regions in the mammalian genome.
9 ethylation process occurs extensively in the mammalian genome.
10 sex chromosomes impacts the evolution of the mammalian genome.
11 deoxyribonucleic acid (DNA) damage from the mammalian genome.
12 s), comprising a substantial fraction of the mammalian genome.
13 regulation of transcriptional networks in a mammalian genome.
14 ing the function of all genes encoded by the mammalian genome.
15 otransposons compose a staggering 40% of the mammalian genome.
16 s (PRCs) to spread over broad regions of the mammalian genome.
17 Transposable elements make up half of the mammalian genome.
18 coding DNA occurs pervasively throughout the mammalian genome.
19 ranscriptionally silent genes throughout the mammalian genome.
20 ation is the most common modification in the mammalian genome.
21 s (ERVs), constitute a large fraction of the mammalian genome.
22 ability, but current methods do not scale to mammalian genomes.
23 rt their workflows, which is intractable for mammalian genomes.
24 ion ( approximately 20%) of total lncRNAs in mammalian genomes.
25 inducible enhancers independently in diverse mammalian genomes.
26 osine is the only form of DNA methylation in mammalian genomes.
27 locations where DNA replication initiates in mammalian genomes.
28 s the ability to engineer precise changes in mammalian genomes.
29 gnancy and reproduction from 23 high-quality mammalian genomes.
30 revalent, collectively occupying up to 5% of mammalian genomes.
31 identifying functional noncoding elements in mammalian genomes.
32 re rare in yeasts but highly likely in large mammalian genomes.
33 of 9900 proteins conserved in all sequenced mammalian genomes.
34 t of the epigenetic regulation repertoire in mammalian genomes.
35 cating the application of such approaches to mammalian genomes.
36 l to maintain homeostatic gene expression in mammalian genomes.
37 or insert transgenes at precise locations in mammalian genomes.
38 gBGC) has a major impact on the evolution of mammalian genomes.
39 ransposable elements comprise roughly 40% of mammalian genomes.
40 ution of enhancers is a universal feature of mammalian genomes.
41 i-C to create kilobase-resolution 3D maps of mammalian genomes.
42 n and higher-order chromatin organization of mammalian genomes.
43 l fraction of endogenous Dicer substrates in mammalian genomes.
44 LINE retrotransposons actively shape mammalian genomes.
45 eramide synthase, both beta-transferases, in mammalian genomes.
46 ded to minimize off-target cleavage in large mammalian genomes.
47 grading enzymes, which are largely absent in mammalian genomes.
48 ed, largely due to its low abundance in most mammalian genomes.
49 transposable elements (TEs) are abundant in mammalian genomes.
50 frequent CHR-based regulation is utilized in mammalian genomes.
51 tionships with multiple other SR proteins in mammalian genomes.
52 e analysis of all CpG island sequences in 10 mammalian genomes.
53 in a PWM, based on a multiple alignment of 5 mammalian genomes.
54 gene expression and are abundant throughout mammalian genomes.
55 of TLS and HDR across defined DNA lesions in mammalian genomes.
56 egulation of the transcriptional products of mammalian genomes.
57 lexity from simple microbial species through mammalian genomes.
58 to correctly reconstruct the phylogeny of 10 mammalian genomes.
59 plified gene families in the mouse and other mammalian genomes.
60 the extent of structural divergence between mammalian genomes.
61 y distributed, autonomous retrotransposon in mammalian genomes.
62 to their suitability for analysis of hmC in mammalian genomes.
63 ological domains are an inherent property of mammalian genomes.
64 gene regulatory regions in large and complex mammalian genomes.
65 lomeric, promoter and transcribed regions of mammalian genomes.
66 c finger proteins (KRAB-ZFPs) are encoded in mammalian genomes.
67 s, each of which has a conserved ortholog in mammalian genomes.
68 e primary driver of non-random gene order in mammalian genomes.
69 ements, constitute a substantial fraction of mammalian genomes.
70 s of ten or more genes are extremely rare in mammalian genomes.
71 aspect of the evolution of functional DNA in mammalian genomes.
72 city for guanine, a highly prevalent base in mammalian genomes.
73 d the structural and functional units of the mammalian genomes.
74 ve enabled the creation of highly contiguous mammalian genomes.
75 for understanding complex events that shape mammalian genomes.
76 peats (MIRs) are retrotransposed elements of mammalian genomes.
77 nd member of the MIF cytokine superfamily in mammalian genomes.
78 ighborhoods represent functional regulons in mammalian genomes.
79 omous non-LTR retroelement that is active in mammalian genomes.
80 RNA) elements ubiquitously spread throughout mammalian genomes.
81 mostly unmethylated within highly methylated mammalian genomes.
82 ion in the Csf1r locus in reptile, avian and mammalian genomes.
83 portant factors influencing the evolution of mammalian genomes.
84 approaches, with a focus on the analysis of mammalian genomes.
85 cles describing different approaches to edit mammalian genomes; 330 articles describing CRISPR-Cas9-m
86 nce in Man, the Functional Annotation of the Mammalian genome 5, the Genotype-Tissue Expression and t
87 mC) as a prominent DNA modification found in mammalian genomes, an emergent question has been what ro
88 constituting at least 10% of the orthologous mammalian genome and encompassing many hundreds of human
89 the annotation of functional elements in the mammalian genome and for the study of mechanisms regulat
90 n surveying the Functional Annotation of the Mammalian Genome and Gene Expression Omnibus Profiles da
91 insights into DSB resection and repair in a mammalian genome and offers a tantalizing glimpse of how
92 veals a new example of the complexity of the mammalian genome and provides novel insights into the fu
93 s as one of the major states for 5hmC in the mammalian genome and suggest that they could function in
94 EARCH-D algorithm for identifying D genes in mammalian genomes and applied it to the recently complet
95 cRNAs) are derived from thousands of loci in mammalian genomes and are frequently enriched in transpo
96 -derived sequence dominates the landscape of mammalian genomes and can modulate gene function by dysr
97 dogenous retroviruses (ERVs) are abundant in mammalian genomes and contain sequences modulating trans
98 DSBs rapidly at defined endogenous sites in mammalian genomes and enables direct assessment of repai
99 the large amount of repetitive sequences in mammalian genomes and have been linked to species-specif
100 n between promoters and enhancers in complex mammalian genomes and indicate that studying the evoluti
102 s) are transcribed from thousands of loci in mammalian genomes and might play widespread roles in gen
103 how the bacterial Cas9 protein interrogates mammalian genomes and navigates eukaryotic chromatin str
104 he two major DNA epigenetic modifications in mammalian genomes and play crucial roles in development
105 osable elements (TEs) compose nearly half of mammalian genomes and provide building blocks for cis-re
106 e define the group of CHR-regulated genes in mammalian genomes and provide evidence that the CHR is t
107 ed, hotspots occurs at thousands of genes in mammalian genomes and represents an important and dynami
108 transposons are still actively shaping some mammalian genomes and reveals an unprecedented opportuni
109 Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harbori
110 oding RNAs (ncRNAs) has expanded our view on mammalian genomes and transcriptomes, as well as their o
111 in viruses, are being identified within the mammalian genome, and that these may provide new insight
112 has not been rigorously measured across the mammalian genome, and until now little has been known ab
114 eage, a double loss seen in none of 56 other mammalian genomes, and suggests a hitherto unappreciated
115 onstitute the majority of transcripts in the mammalian genomes, and yet, their functions remain large
116 Recently, it was shown that enhancers in the mammalian genome are associated with characteristic hist
117 Our capacities to understand and manipulate mammalian genomes are accelerating at an astounding pace
119 ites and show that several mammalian and non-mammalian genomes are enriched for strong microRNA tripl
126 est scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication.
127 ate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potenti
130 omosome conformation capture have shown that mammalian genomes are partitioned into topologically ass
138 re theory." Instead, our findings depict the mammalian genome as a tapestry of mostly short homogeneo
140 s a path forward for the routine assembly of mammalian genomes at a level approaching that of the cur
141 ation is not encountered when reconstructing mammalian genomes at the synteny-block level, although t
142 d and maintained, how the 3D architecture of mammalian genomes both facilitates and constrains enhanc
143 firms widespread distribution of 5hmC in the mammalian genome but also reveals sequence bias and stra
144 ci of genetic and epigenetic lability in the mammalian genome but argue against a direct role for spe
145 (TFs) bind to thousands of DNA sequences in mammalian genomes, but most of these binding events appe
146 oding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcrip
147 bly the most abundant base lesion induced in mammalian genomes by reactive oxygen species, is repaire
153 th iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gat
154 protein (HMGCLL1) has been annotated in the Mammalian Genome Collection as a previously unidentified
165 r the former enzyme, GTK/KAT I, is listed in mammalian genome data banks as CCBL1 (cysteine conjugate
166 ltaneous editing of several sites within the mammalian genome, demonstrating easy programmability and
167 suggest that, though relatively rare in the mammalian genome, divergence in higher order chromatin s
170 Retrotransposons are highly prevalent in mammalian genomes due to their ability to amplify in plu
171 lation (APA) generate diverse transcripts in mammalian genomes during development and differentiation
173 ruses has been "horizontally transferred" to mammalian genomes during evolution, but the impact of th
174 marize CRISPR-based technologies that enable mammalian genome editing and their various applications.
175 (Pyl)CUA pair (and its derivatives) into the mammalian genome enables efficient, homogeneous incorpor
186 relatively recently has it become clear that mammalian genomes encode tens of thousands of long non-c
193 and its subsequent adaptation as a tool for mammalian genome engineering has opened up new avenues f
195 genomic locations is a significant driver of mammalian genome evolution, but these mutagenic events c
197 ifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integr
199 chanism and function of DNA demethylation in mammalian genomes, focusing particularly on how developm
200 nsidered to be functionally important in the mammalian genome for transcriptional regulation, DNA rep
206 eletions, insertions and replacements in the mammalian genome has revolutionized the field of genome
208 While the number of annotated lncRNAs in mammalian genomes has greatly expanded, studying lncRNA
214 4000 host genes that harbour an iCGI in the mammalian genome, including both previously annotated an
217 nd cohesin play critical roles in organizing mammalian genomes into topologically associating domains
227 ecent studies show that transcription of the mammalian genome is not only pervasive but also enormous
233 , and claims that almost the entirety of the mammalian genome is transcribed into functional noncodin
236 mount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin s
238 ymethylcytosine (hmC), the sixth base of the mammalian genome, is increasingly recognized as an epige
239 ished role of L1 retrotransposons in shaping mammalian genomes, it becomes an important task to track
241 RNAs (lincRNAs) have been identified in the mammalian genome, many of which have important roles in
243 t PRMT5-mediated H4R3me2s uniquely marks the mammalian genome, mostly at G + C-rich regions, and inde
244 collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequ
247 t cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell
250 ecades the compositional organization of the mammalian genome posed a formidable challenge to molecul
251 rong heterogeneity of SCU induced by gBGC in mammalian genomes precludes any optimization of the tRNA
252 he recent discovery that the human and other mammalian genomes produce thousands of long non-coding R
253 (5hmC) is a recently discovered base in the mammalian genome, produced upon oxidation of 5-methylcyt
255 s, in combination with the wealth of TSSs in mammalian genomes, provide a framework with which evolut
256 thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunit
257 anscription at multiple enhancers within the mammalian genome raises critical questions regarding whe
265 discovery of N(6)-methyladenine (N(6)-mA) in mammalian genomes suggests that it may serve as an epige
266 Our findings establish RNase H2 as a key mammalian genome surveillance enzyme required for ribonu
267 -dC (cadC) are newly discovered bases in the mammalian genome that are supposed to be substrates for
268 lly important epigenetic modification of the mammalian genome that has widespread influences on gene
269 ped for isolation of a desirable region from mammalian genomes that are enriched in autonomously repl
270 priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences.
271 ytosine (5fC) is an epigenetic nucleobase of mammalian genomes that occurs as intermediate of active
272 we identify endogenous retroviral fossils in mammalian genomes that share a unique recombinant struct
274 sociated long non-coding RNAs encoded by the mammalian genome, the Uph-Hand2 regulatory partnership o
275 Although the HNMT-like gene is absent in mammalian genomes, the activity of carnosine N-methyltra
278 Although thousands of NATs are encoded by mammalian genomes, their functions in innate immunity ar
279 is revealed cryptic nonamers in RSSs of many mammalian genomes, thus demonstrating that the V(DD)J re
281 ccessively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-f
284 some association are highly conserved across mammalian genomes, underscoring their possible biologica
285 Here we calculate 3D structures of entire mammalian genomes using data from a new chromosome confo
286 ecificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and beta-g
287 in replicating single-stranded templates in mammalian genomes, warranting prereplicative repair of t
289 omparison to the eight mglurs present in the mammalian genome, we identified 13 different mglur genes
290 and enable editing of repetitive elements of mammalian genomes, we made use of a set of dead-Cas9 bas
291 testing a human model on the nine different mammalian genomes, we provide the first evidence that k-
292 nce conservation have been appreciated since mammalian genomes were first sequenced, but the function
293 hat GeoCas9 is an effective tool for editing mammalian genomes when delivered as a ribonucleoprotein
294 among bacteria and phage and is detected in mammalian genomes, where its function is largely unexplo
295 st genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/
296 strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifac
297 roteins that compose approximately 4% of the mammalian genome whose members share a common membrane t
299 reby establishing the feasibility of in vivo mammalian genome-wide investigations to dissect tissue d
300 e in suppressing retrotransposon activity in mammalian genomes, yet there are stages of mammalian dev