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Exploratory bioinformatics analysis reveals importance of “junk” DNA in early embryo development
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Expression of Cdx‐2 in the mouse embryo and placenta: Possible role in patterning of the extra‐embryonic membranes
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Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis‐driven science in the post‐genomic era
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Mice lacking the Obox6 homeobox gene undergo normal early embryonic development and are fertile
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Six1: A critical transcription factor in tumorigenesis
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Display of different modes of transcription by the promoters of an early embryonic gene, Zfp352, in preimplantation embryos and in somatic cells
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Establishment of trophectoderm and inner cell mass lineages in the mouse embryo
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Characterization of Gene Expression in Mouse Blastocyst Using Single-Pass Sequencing of 3995 Clones
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Generation of Two Homologous and Intronless Zinc-Finger Protein Genes, Zfp352 and Zfp353, with Different Expression Patterns by Retrotransposition
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Obox, a Family of Homeobox Genes Preferentially Expressed in Germ Cells
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Optimizing RNA-Seq Mapping with STAR
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LINEs in mice: features, families, and potential roles in early development
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Homeodomain proteins: an update
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The visual display of quantitative information
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Hesx1 enhances pluripotency by working downstream of multiple pluripotency-associated signaling pathways
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Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells
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A Role for TFIIIC Transcription Factor Complex in Genome Organization
inferredcites →https://doi.org/10.1016/j.cell.2006.07.024openalex-snapshot
Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors
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Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome
inferredcites →https://doi.org/10.1016/j.cell.2008.04.043openalex-snapshot
Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2010.10.019openalex-snapshot
Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome
inferredcites →https://doi.org/10.1016/j.cell.2011.11.058openalex-snapshot
Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
inferredcites →https://doi.org/10.1016/j.cell.2014.08.009openalex-snapshot
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
inferredcites →https://doi.org/10.1016/j.celrep.2014.03.011openalex-snapshot
Evolution of Alu Elements toward Enhancers
inferredcites →https://doi.org/10.1016/j.devcel.2004.09.004openalex-snapshot
Retrotransposons Regulate Host Genes in Mouse Oocytes and Preimplantation Embryos
inferredcites →https://doi.org/10.1016/j.devcel.2011.09.010openalex-snapshot
Conditional Deletion of MSX Homeobox Genes in the Uterus Inhibits Blastocyst Implantation by Altering Uterine Receptivity
inferredcites →https://doi.org/10.1016/j.gene.2006.09.018openalex-snapshot
Repetitive sequence environment distinguishes housekeeping genes
inferredcites →https://doi.org/10.1016/j.gene.2007.04.012openalex-snapshot
The oncogene and developmental regulator EVI1: Expression, biochemical properties, and biological functions
inferredcites →https://doi.org/10.1016/j.gene.2011.09.018openalex-snapshot
Extra-transcriptional functions of RNA Polymerase III complexes: TFIIIC as a potential global chromatin bookmark
inferredcites →https://doi.org/10.1016/j.gene.2012.02.005openalex-snapshot
Widespread occurrence of power-law distributions in inter-repeat distances shaped by genome dynamics
inferredcites →https://doi.org/10.1016/j.modgep.2005.06.003openalex-snapshot
High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization
inferredcites →https://doi.org/10.1016/j.stem.2010.03.015openalex-snapshot
Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis
inferredcites →https://doi.org/10.1016/s0166-4328(01)00297-2openalex-snapshot
Controlling the false discovery rate in behavior genetics research
inferredcites →https://doi.org/10.1016/s1079-9796(03)00159-1openalex-snapshot
The role of EVI1 in normal and leukemic cells
inferredcites →https://doi.org/10.1016/s1534-5807(03)00373-3openalex-snapshot
Dynamics of Global Gene Expression Changes during Mouse Preimplantation Development
inferredcites →https://doi.org/10.1038/332459a0openalex-snapshot
Human gene expression first occurs between the four- and eight-cell stages of preimplantation development
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/nature01262openalex-snapshot
Initial sequencing and comparative analysis of the mouse genome
inferredcites →https://doi.org/10.1038/nature06904openalex-snapshot
Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes
inferredcites →https://doi.org/10.1038/nature06908openalex-snapshot
Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
inferredcites →https://doi.org/10.1038/nature08882openalex-snapshot
Zscan4 regulates telomere elongation and genomic stability in ES cells
inferredcites →https://doi.org/10.1038/nature10006openalex-snapshot
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA
inferredcites →https://doi.org/10.1038/nature10413openalex-snapshot
Mouse genomic variation and its effect on phenotypes and gene regulation
inferredcites →https://doi.org/10.1038/nature10531openalex-snapshot
Somatic retrotransposition alters the genetic landscape of the human brain
inferredcites →https://doi.org/10.1038/nature10960openalex-snapshot
A unique regulatory phase of DNA methylation in the early mammalian embryo
inferredcites →https://doi.org/10.1038/nature11243openalex-snapshot
A map of the cis-regulatory sequences in the mouse genome
inferredcites →https://doi.org/10.1038/nature11244openalex-snapshot
Embryonic stem cell potency fluctuates with endogenous retrovirus activity
inferredcites →https://doi.org/10.1038/nature12111openalex-snapshot
The zebrafish reference genome sequence and its relationship to the human genome
inferredcites →https://doi.org/10.1038/nature12364openalex-snapshot
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
inferredcites →https://doi.org/10.1038/nature13544openalex-snapshot
The DNA methylation landscape of human early embryos
inferredcites →https://doi.org/10.1038/nature13804openalex-snapshot
Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
inferredcites →https://doi.org/10.1038/nature14308openalex-snapshot
Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
inferredcites →https://doi.org/10.1038/ncomms2966openalex-snapshot
Zscan4 restores the developmental potency of embryonic stem cells
inferredcites →https://doi.org/10.1038/ncomms4719openalex-snapshot
Klf4 and Klf5 differentially inhibit mesoderm and endoderm differentiation in embryonic stem cells
inferredcites →https://doi.org/10.1038/ncomms9207openalex-snapshot
Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development
inferredcites →https://doi.org/10.1038/ng.368openalex-snapshot
The regulated retrotransposon transcriptome of mammalian cells
inferredcites →https://doi.org/10.1038/ng.600openalex-snapshot
Transposable elements have rewired the core regulatory network of human embryonic stem cells
inferredcites →https://doi.org/10.1038/ng.917openalex-snapshot
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nprot.2012.016openalex-snapshot
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
inferredcites →https://doi.org/10.1038/nrg2072openalex-snapshot
Transposable elements and the epigenetic regulation of the genome
inferredcites →https://doi.org/10.1038/nsmb.1794openalex-snapshot
Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells
inferredcites →https://doi.org/10.1038/nsmb.2495openalex-snapshot
Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA
inferredcites →https://doi.org/10.1038/nsmb.2660openalex-snapshot
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells
inferredcites →https://doi.org/10.1038/nsmb.3066openalex-snapshot
Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly
inferredcites →https://doi.org/10.1038/sj.onc.1204039openalex-snapshot
Expression and function of Ets transcription factors in mammalian development: a regulatory network
inferredcites →https://doi.org/10.1038/sj.onc.1204044openalex-snapshot
The Ets-transcription factor family in embryonic development: lessons from the amphibian and bird
inferredcites →https://doi.org/10.1038/srep00208openalex-snapshot
Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells
inferredcites →https://doi.org/10.1073/pnas.0708366105openalex-snapshot
Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo
inferredcites →https://doi.org/10.1073/pnas.0709193104openalex-snapshot
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells
inferredcites →https://doi.org/10.1073/pnas.1321569111openalex-snapshot
Fine mapping of genome activation in bovine embryos by RNA sequencing
inferredcites →https://doi.org/10.1073/pnas.1413299111openalex-snapshot
Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential
inferredcites →https://doi.org/10.1073/pnas.92.18.8229openalex-snapshot
The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element.
inferredcites →https://doi.org/10.1073/pnas.93.18.9374openalex-snapshot
DNA sequence insertion and evolutionary variation in gene regulation.
inferredcites →https://doi.org/10.1074/jbc.270.39.22777openalex-snapshot
Identification of a New Subclass of Alu DNA Repeats Which Can Function as Estrogen Receptor-dependent Transcriptional Enhancers
inferredcites →https://doi.org/10.1074/jbc.m611814200openalex-snapshot
Oct4 and Sox2 Directly Regulate Expression of Another Pluripotency Transcription Factor, Zfp206, in Embryonic Stem Cells
inferredcites →https://doi.org/10.1083/jcb.152.3.545openalex-snapshot
Pitx2 Regulates Procollagen Lysyl Hydroxylase (Plod) Gene Expression
inferredcites →https://doi.org/10.1093/bioinformatics/bth078openalex-snapshot
Open source clustering software
inferredcites →https://doi.org/10.1093/bioinformatics/bth349openalex-snapshot
Java Treeview—extensible visualization of microarray data
inferredcites →https://doi.org/10.1093/bioinformatics/bti525openalex-snapshot
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btt744openalex-snapshot
ALEA: a toolbox for allele-specific epigenomics analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btv422openalex-snapshot
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets
inferredcites →https://doi.org/10.1093/nar/gku091openalex-snapshot
An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition
inferredcites →https://doi.org/10.1095/biolreprod.102.007906openalex-snapshot
MuERV-L Is One of the Earliest Transcribed Genes in Mouse One-Cell Embryos1
inferredcites →https://doi.org/10.1095/biolreprod.108.068478openalex-snapshot
SEBOX Is Essential for Early Embryogenesis at the Two-Cell Stage in the Mouse1
inferredcites →https://doi.org/10.1098/rsob.130035openalex-snapshot
A new role for muscle segment homeobox genes in mammalian embryonic diapause
inferredcites →https://doi.org/10.1101/gad.1803909openalex-snapshot
L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism
inferredcites →https://doi.org/10.1101/gad.1833510openalex-snapshot
Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal
inferredcites →https://doi.org/10.1101/gad.6.7.1190openalex-snapshot
Gene expression during preimplantation mouse development.
inferredcites →https://doi.org/10.1101/gr.100594.109openalex-snapshot
Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species
inferredcites →https://doi.org/10.1101/gr.157826.113openalex-snapshot
Hypothesis-generating research and predictive medicine
inferredcites →https://doi.org/10.1111/j.1474-9726.2008.00442.xopenalex-snapshot
The Human Ageing Genomic Resources: online databases and tools for biogerontologists
inferredcites →https://doi.org/10.1126/science.1058040openalex-snapshot
The Sequence of the Human Genome
inferredcites →https://doi.org/10.1126/science.1089670openalex-snapshot
Mobile Elements: Drivers of Genome Evolution
inferredcites →https://doi.org/10.1126/science.1140693openalex-snapshot
The Maternal-Zygotic Transition: Death and Birth of RNAs
inferredcites →https://doi.org/10.1126/science.1242527openalex-snapshot
Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates
inferredcites →https://doi.org/10.1126/science.1245316openalex-snapshot
Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells
inferredcites →https://doi.org/10.1126/science.338.6108.758openalex-snapshot
Transposable Elements, Epigenetics, and Genome Evolution
inferredcites →https://doi.org/10.1126/science.aad5497openalex-snapshot
Regulatory evolution of innate immunity through co-option of endogenous retroviruses
inferredcites →https://doi.org/10.1128/mcb.16.8.4495openalex-snapshot
Germ Line-Specific Expression of Intracisternal A-Particle Retrotransposons in Transgenic Mice
inferredcites →https://doi.org/10.1128/mcb.24.13.5844-5849.2004openalex-snapshot
The ETS Transcription Factor GABPα Is Essential for Early Embryogenesis
inferredcites →https://doi.org/10.1146/annurev-cellbio-100913-013027openalex-snapshot
Zygotic Genome Activation During the Maternal-to-Zygotic Transition
inferredcites →https://doi.org/10.1155/jbb/2006/71753openalex-snapshot
L1 Antisense Promoter Drives Tissue‐Specific Transcriptionof Human Genes
inferredcites →https://doi.org/10.1159/000078195openalex-snapshot
Systems biology of the 2-cell mouse embryo
inferredcites →https://doi.org/10.1159/000084979openalex-snapshot
Repbase Update, a database of eukaryotic repetitive elements
inferredcites →https://doi.org/10.1172/jci43853openalex-snapshot
Mouse ES and iPS cells can form similar definitive endoderm despite differences in imprinted genes
inferredcites →https://doi.org/10.1186/1471-2164-10-563openalex-snapshot
Alu-directed transcriptional regulation of some novel miRNAs
inferredcites →https://doi.org/10.1186/1471-2164-14-568openalex-snapshot
Global expression profiling reveals genetic programs underlying the developmental divergence between mouse and human embryogenesis
inferredcites →https://doi.org/10.1186/1471-2164-7-133openalex-snapshot
Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes
inferredcites →https://doi.org/10.1186/1471-2164-8-23openalex-snapshot
Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution
inferredcites →https://doi.org/10.1186/1745-6150-6-2openalex-snapshot
Impact of Alu repeats on the evolution of human p53 binding sites
inferredcites →https://doi.org/10.1186/gb-2004-5-10-r80openalex-snapshot
Bioconductor: open software development for computational biology and bioinformatics
inferredcites →https://doi.org/10.1186/gb-2008-9-2-r25openalex-snapshot
Do Alu repeats drive the evolution of the primate transcriptome?
inferredcites →https://doi.org/10.1186/gb-2011-12-12-236openalex-snapshot
Alu elements: know the SINEs
inferredcites →https://doi.org/10.1242/dev.054775openalex-snapshot
Klf5 regulates lineage formation in the pre-implantation mouse embryo
inferredcites →https://doi.org/10.1242/dev.064741openalex-snapshot
Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development
inferredcites →https://doi.org/10.1242/dev.095091openalex-snapshot
Identification of the zebrafish maternal and paternal transcriptomes
inferredcites →https://doi.org/10.1242/dev.127.8.1737openalex-snapshot
Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development
inferredcites →https://doi.org/10.1242/jcs.34.1.247openalex-snapshot
Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox
inferredcites →https://doi.org/10.1266/ggs.88.19openalex-snapshot
Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs
inferredcites →https://doi.org/10.1371/journal.pbio.0000074openalex-snapshot
Transcriptome Analysis of Mouse Stem Cells and Early Embryos
inferredcites →https://doi.org/10.1371/journal.pcbi.1000610openalex-snapshot
Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes
inferredcites →https://doi.org/10.1371/journal.pgen.1002384openalex-snapshot
Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1002500openalex-snapshot
Msx Homeobox Genes Critically Regulate Embryo Implantation by Controlling Paracrine Signaling between Uterine Stroma and Epithelium
inferredcites →https://doi.org/10.1371/journal.pone.0007844openalex-snapshot
Transcriptome Profiling of Human Pre-Implantation Development
inferredcites →https://doi.org/10.1371/journal.pone.0067762openalex-snapshot
Six1 Regulates MyoD Expression in Adult Muscle Progenitor Cells
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1530/rep-09-0042openalex-snapshot
Retrotransposon expression as a defining event of genome reprograming in fertilized and cloned bovine embryos
inferredcites →https://doi.org/10.2307/2347963openalex-snapshot
Applications, Basics and Computing of Exploratory Data Analysis.
inferredcites →https://doi.org/10.3346/jkms.2004.19.6.783openalex-snapshot
AluandL1Retroelements Are Correlated with the Tissue Extent and Peak Rate of Gene Expression, Respectively
inferredcites →https://doi.org/10.3390/genes2020345openalex-snapshot
Post-Transcriptional Control of Gene Expression in Mouse Early Embryo Development: A View from the Tip of the Iceberg
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