[ { "id": "authors:0j638-jx111", "collection": "authors", "collection_id": "0j638-jx111", "cite_using_url": "https://authors.library.caltech.edu/records/0j638-jx111", "type": "article", "title": "Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease", "author": [ { "family_name": "Polonsky", "given_name": "Michal", "orcid": "0000-0003-3871-460X", "clpid": "Polonsky-Michal" }, { "family_name": "Gerhardt", "given_name": "Louisa M. S." }, { "family_name": "Yun", "given_name": "Jina", "clpid": "Yun-Chi-H-Jina" }, { "family_name": "Koppitch", "given_name": "Kari" }, { "family_name": "Col\u00f3n", "given_name": "Katsuya Lex", "orcid": "0000-0002-7347-6128", "clpid": "Col\u00f3n-Katsuya-Lex" }, { "family_name": "Amrhein", "given_name": "Henry", "orcid": "0000-0002-4264-140X", "clpid": "Amrhein-H" }, { "family_name": "Wold", "given_name": "Barbara", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Zheng", "given_name": "Shiwei" }, { "family_name": "Yuan", "given_name": "Guo-Cheng", "orcid": "0000-0002-2283-4714" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Cai", "given_name": "Long", "orcid": "0000-0002-7154-5361", "clpid": "Cai-Long" }, { "family_name": "McMahon", "given_name": "Andrew P.", "orcid": "0000-0002-3779-1729", "clpid": "McMahon-Andrew-P" } ], "abstract": "

Kidney injury disrupts the intricate renal architecture and triggers limited regeneration, together with injury-invoked inflammation and fibrosis. Deciphering the molecular pathways and cellular interactions driving these processes is challenging due to the complex tissue structure. Here, we apply single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics reveals injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predicts Clcf1-Crfl1 in a molecular interplay between persistently injured proximal tubule cells and their neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis identifies cellular microenvironments resembling early tertiary lymphoid structures and associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease.

", "doi": "10.1038/s41467-024-51186-z", "pmcid": "PMC11377535", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2024-09-05", "series_number": "1", "volume": "15", "issue": "1", "pages": "7010" }, { "id": "authors:kyjwe-n2x60", "collection": "authors", "collection_id": "kyjwe-n2x60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200618-081148283", "type": "article", "title": "The changing mouse embryo transcriptome at whole tissue and single-cell resolution", "author": [ { "family_name": "He", "given_name": "Peng", "orcid": "0000-0002-2457-3554", "clpid": "He-Peng" }, { "family_name": "Williams", "given_name": "Brian A.", "clpid": "Williams-B-A" }, { "family_name": "Trout", "given_name": "Diane", "orcid": "0000-0002-4928-5532", "clpid": "Trout-D" }, { "family_name": "Marinov", "given_name": "Georgi K.", "orcid": "0000-0003-1822-7273", "clpid": "Marinov-G-K" }, { "family_name": "Amrhein", "given_name": "Henry", "orcid": "0000-0002-4264-140X", "clpid": "Amrhein-H" }, { "family_name": "Berghella", "given_name": "Libera", "clpid": "Berghella-L" }, { "family_name": "Goh", "given_name": "Say-Tar", "clpid": "Goh-Say-Tar" }, { "family_name": "Plajzer-Frick", "given_name": "Ingrid", "clpid": "Plajzer-Frick-I" }, { "family_name": "Afzal", "given_name": "Veena", "orcid": "0000-0001-5798-4360", "clpid": "Afzal-V" }, { "family_name": "Pennacchio", "given_name": "Len A.", "orcid": "0000-0002-8748-3732", "clpid": "Pennacchio-L-A" }, { "family_name": "Dickel", "given_name": "Diane E.", "orcid": "0000-0001-5497-6824", "clpid": "Dickel-D-E" }, { "family_name": "Visel", "given_name": "Axel", "orcid": "0000-0002-4130-7784", "clpid": "Visel-A" }, { "family_name": "Ren", "given_name": "Bing", "orcid": "0000-0002-2829-1554", "clpid": "Ren-Bing" }, { "family_name": "Hardison", "given_name": "Ross C.", "orcid": "0000-0003-4084-7516", "clpid": "Hardison-R-C" }, { "family_name": "Zhang", "given_name": "Yu", "orcid": "0000-0001-8938-1927", "clpid": "Zhang-Yu" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" } ], "abstract": "During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system. Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis-element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.", "doi": "10.1038/s41586-020-2536-x", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2020-07-30", "series_number": "7818", "volume": "583", "issue": "7818", "pages": "760-767" }, { "id": "authors:0qx9m-ze404", "collection": "authors", "collection_id": "0qx9m-ze404", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181101-114159969", "type": "article", "title": "Spatiotemporal DNA methylome dynamics of the developing mouse fetus", "author": [ { "family_name": "He", "given_name": "Yupeng", "orcid": "0000-0002-8319-0510", "clpid": "He-Yupeng" }, { "family_name": "Hariharan", "given_name": "Manoj", "orcid": "0000-0002-1006-5372", "clpid": "Hariharan-M" }, { "family_name": "Gorkin", "given_name": "David U.", "orcid": "0000-0003-4944-4107", "clpid": "Gorkin-D-U" }, { "family_name": "Dickel", "given_name": "Diane E.", "orcid": "0000-0001-5497-6824", "clpid": "Dickel-D-E" }, { "family_name": "Luo", "given_name": "Chongyuan", "orcid": "0000-0002-8541-0695", "clpid": "Luo-Chongyuan" }, { "family_name": "Castanon", "given_name": "Rosa G.", "orcid": "0000-0003-1791-002X", "clpid": "Castanon-R-G" }, { "family_name": "Nery", "given_name": "Joseph R.", "orcid": "0000-0003-0153-5659", "clpid": "Nery-J-R" }, { "family_name": "Lee", "given_name": "Ah Young", "clpid": "Lee-Ah-Young" }, { "family_name": "Zhao", "given_name": "Yuan", "clpid": "Zhao-Yuan" }, { "family_name": "Huang", "given_name": "Hui", "clpid": "Huang-Hui" }, { "family_name": "Williams", "given_name": "Brian A.", "clpid": "Williams-B-A" }, { "family_name": "Trout", "given_name": "Diane", "clpid": "Trout-D" }, { "family_name": "Amrhein", "given_name": "Henry", "orcid": "0000-0002-4264-140X", "clpid": "Amrhein-H" }, { "family_name": "Fang", "given_name": "Rongxin", "orcid": "0000-0001-8746-9650", "clpid": "Fang-Rongxin" }, { "family_name": "Chen", "given_name": "Huaming", "orcid": "0000-0001-5289-7882", "clpid": "Chen-Huaming" }, { "family_name": "Li", "given_name": "Bin", "clpid": "Li-Bin" }, { "family_name": "Visel", "given_name": "Axel", "orcid": "0000-0002-4130-7784", "clpid": "Visel-A" }, { "family_name": "Pennacchio", "given_name": "Len A.", "orcid": "0000-0002-8748-3732", "clpid": "Pennacchio-L-A" }, { "family_name": "Ren", "given_name": "Bing", "orcid": "0000-0002-2829-1554", "clpid": "Ren-Bing" }, { "family_name": "Ecker", "given_name": "Joseph R.", "orcid": "0000-0001-5799-5895", "clpid": "Ecker-J-R" } ], "abstract": "Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders.", "doi": "10.1038/s41586-020-2119-x", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2020-07-30", "series_number": "7818", "volume": "583", "issue": "7818", "pages": "752-759" }, { "id": "authors:bbq8c-fbs42", "collection": "authors", "collection_id": "bbq8c-fbs42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181031-110727092", "type": "article", "title": "An atlas of dynamic chromatin landscapes in mouse fetal development", "author": [ { "family_name": "Gorkin", "given_name": "David U.", "orcid": "0000-0003-4944-4107", "clpid": "Gorkin-D-U" }, { "family_name": "Williams", "given_name": "Brian A.", "clpid": "Williams-B-A" }, { "family_name": "Trout", "given_name": "Diane", "orcid": "0000-0002-4928-5532", "clpid": "Trout-Diane" }, { "family_name": "Amrhein", "given_name": "Henry", "orcid": "0000-0002-4264-140X", "clpid": "Amrhein-H" } ], "abstract": "The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP\u2013seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC\u2013seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.", "doi": "10.1038/s41586-020-2093-3", "pmcid": "PMC7398618", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2020-07-30", "series_number": "7818", "volume": "583", "issue": "7818", "pages": "744-751" }, { "id": "authors:9mrr1-asf33", "collection": "authors", "collection_id": "9mrr1-asf33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141210-153404920", "type": "article", "title": "A comparative encyclopedia of DNA elements in the mouse genome", "author": [ { "family_name": "Yue", "given_name": "Feng", "clpid": "Yue-Feng" }, { "family_name": "Kirilusha", "given_name": "Anthony", "clpid": "Kirilusha-A" }, { "family_name": "Marinov", "given_name": "Georgi K.", "orcid": "0000-0003-1822-7273", "clpid": "Marinov-G-K" }, { "family_name": "Williams", "given_name": "Brian A.", "clpid": "Williams-B-A" }, { "family_name": "Trout", "given_name": "Diane", "clpid": "Trout-D" }, { "family_name": "Amrhein", "given_name": "Henry", "clpid": "Amrhein-H" }, { "family_name": "Fisher-Aylor", "given_name": "Katherine I.", "clpid": "Fisher-Aylor-K-I" }, { "family_name": "Antoshechkin", "given_name": "Igor", "orcid": "0000-0002-9934-3040", "clpid": "Antoshechkin-I-A" }, { "family_name": "DeSalvo", "given_name": "Gilberto", "clpid": "DeSalvo-G" }, { "family_name": "Wold", "given_name": "Barbara", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" } ], "abstract": "The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.", "doi": "10.1038/nature13992", "pmcid": "PMC4266106", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2014-11-20", "series_number": "7527", "volume": "515", "issue": "7527", "pages": "355-364" }, { "id": "authors:3cqjg-nh279", "collection": "authors", "collection_id": "3cqjg-nh279", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131003-143259486", "type": "article", "title": "The Developmental Transcriptome of the Mosquito Aedes aegypti, an Invasive Species and Major Arbovirus Vector", "author": [ { "family_name": "Akbari", "given_name": "Omar S.", "orcid": "0000-0002-6853-9884", "clpid": "Akbari-O-S" }, { "family_name": "Amrhein", "given_name": "Henry", "clpid": "Amrhein-H" }, { "family_name": "Williams", "given_name": "Brian", "clpid": "Williams-B" }, { "family_name": "DiLoreto", "given_name": "Race", "clpid": "DiLoreto-Race" }, { "family_name": "Sandler", "given_name": "Jeremy", "clpid": "Sandler-J-E" }, { "family_name": "Hay", "given_name": "Bruce A.", "clpid": "Hay-B-A" } ], "abstract": "Mosquitoes are vectors of a number of important human and animal diseases. The development of novel vector control strategies requires a thorough understanding of mosquito biology. To facilitate this, we used RNA-seq to identify novel genes and provide the first high-resolution view of the transcriptome throughout development and in response to blood feeding in a mosquito vector of human disease, Aedes aegypti, the primary vector for Dengue and yellow fever. We characterized mRNA expression at 34 distinct time points throughout Aedes development, including adult somatic and germline tissues, by using polyA+ RNA-seq. We identify a total of 14,238 novel new transcribed regions corresponding to 12,597 new loci, as well as many novel transcript isoforms of previously annotated genes. Altogether these results increase the annotated fraction of the transcribed genome into long polyA+ RNAs by more than twofold. We also identified a number of patterns of shared gene expression, as well as genes and/or exons expressed sex-specifically or sex-differentially. Expression profiles of small RNAs in ovaries, early embryos, testes, and adult male and female somatic tissues also were determined, resulting in the identification of 38 new Aedes-specific miRNAs, and ~291,000 small RNA new transcribed regions, many of which are likely to be endogenous small-interfering RNAs and Piwi-interacting RNAs. Genes of potential interest for transgene-based vector control strategies also are highlighted. Our data have been incorporated into a user-friendly genome browser located at www.Aedes.caltech.edu, with relevant links to Vectorbase (www.vectorbase.org)", "doi": "10.1534/g3.113.006742", "pmcid": "PMC3755910", "issn": "2160-1836", "publisher": "Genetics Society of America", "publication": "G3", "publication_date": "2013-09-01", "series_number": "9", "volume": "3", "issue": "9", "pages": "1493-1509" }, { "id": "authors:y869v-bnb28", "collection": "authors", "collection_id": "y869v-bnb28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130410-142632958", "type": "article", "title": "An encyclopedia of mouse DNA elements (Mouse ENCODE)", "author": [ { "family_name": "Stamatoyannopoulos", "given_name": "John A.", "clpid": "Stamatoyannopoulos-J-A" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Marinov", "given_name": "Georgi K.", "orcid": "0000-0003-1822-7273", "clpid": "Marinov-G-K" }, { "family_name": "Williams", "given_name": "Brian A.", "clpid": "Williams-B-A" }, { "family_name": "Fisher-Aylor", "given_name": "Katherine I.", "clpid": "Fisher-Aylor-K-I" }, { "family_name": "DeSalvo", "given_name": "Gilberto", "clpid": "DeSalvo-G" }, { "family_name": "Kiralusha", "given_name": "Anthony", "clpid": "Kiralusha-A" }, { "family_name": "Trout", "given_name": "Diane", "clpid": "Trout-D" }, { "family_name": "Amrhein", "given_name": "Henry", "clpid": "Amrhein-H" }, { "literal": "Mouse ENCODE Consortium" } ], "abstract": "To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.", "doi": "10.1186/gb-2012-13-8-418", "pmcid": "PMC3491367", "issn": "1465-6906", "publisher": "BioMed Central", "publication": "Genome Biology", "publication_date": "2012-08-13", "series_number": "8", "volume": "13", "issue": "8", "pages": "Art. No. 418" }, { "id": "authors:s7ycz-pbj07", "collection": "authors", "collection_id": "s7ycz-pbj07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200416-153412946", "type": "article", "title": "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)", "author": [ { "family_name": "Wold", "given_name": "Barbara", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Mortazavi", "given_name": "Ali", "orcid": "0000-0002-4259-6362", "clpid": "Mortazavi-A" }, { "family_name": "Williams", "given_name": "Brian", "clpid": "Williams-B-A" }, { "family_name": "Marinov", "given_name": "Georgi", "orcid": "0000-0003-1822-7273", "clpid": "Marinov-G-K" }, { "family_name": "Trout", "given_name": "Diane", "clpid": "Trout-D" }, { "family_name": "King", "given_name": "Brandon", "clpid": "King-B-W" }, { "family_name": "McCue", "given_name": "Kenneth", "clpid": "McCue-K-F" }, { "family_name": "Kirilusha", "given_name": "Anthony", "clpid": "Kirilusha-A" }, { "family_name": "DeSalvo", "given_name": "Gilberto", "clpid": "DeSalvo-G" }, { "family_name": "Fisher-Aylor", "given_name": "Katherine", "clpid": "Fisher-Aylor-K-I" }, { "family_name": "Amrhein", "given_name": "Henry", "clpid": "Amrhein-H" }, { "family_name": "Vielmetter", "given_name": "Jost", "clpid": "Vielmetter-J" }, { "family_name": "Pepke", "given_name": "Shirley", "clpid": "Pepke-S" }, { "literal": "ENCODE Project Consortium" } ], "abstract": "The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.", "doi": "10.1371/journal.pbio.1001046", "pmcid": "PMC3079585", "issn": "1545-7885", "publisher": "Public Library of Science", "publication": "PLoS Biology", "publication_date": "2011-04-19", "series_number": "4", "volume": "9", "issue": "4", "pages": "Art. No.e1001046" }, { "id": "authors:wtqxc-wwg73", "collection": "authors", "collection_id": "wtqxc-wwg73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110520-094733599", "type": "article", "title": "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)", "author": [ { "family_name": "Wold", "given_name": "Barbara", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Mortazavi", "given_name": "Ali", "orcid": "0000-0002-4259-6362", "clpid": "Mortazavi-A" }, { "family_name": "Williams", "given_name": "Brian", "clpid": "Williams-B-A" }, { "family_name": "Marinov", "given_name": "Georgi", "orcid": "0000-0003-1822-7273", "clpid": "Marinov-G-K" }, { "family_name": "Trout", "given_name": "Diane", "orcid": "0000-0002-4928-5532", "clpid": "Trout-D" }, { "family_name": "King", "given_name": "Brandon", "clpid": "King-B-W" }, { "family_name": "McCue", "given_name": "Kenneth", "clpid": "McCue-K-F" }, { "family_name": "Kirilusha", "given_name": "Anthony", "clpid": "Kirilusha-A" }, { "family_name": "DeSalvo", "given_name": "Gilberto", "clpid": "DeSalvo-G" }, { "family_name": "Fisher-Aylor", "given_name": "Katherine", "clpid": "Fisher-Aylor-K-I" }, { "family_name": "Amrhein", "given_name": "Henry", "clpid": "Amrhein-H" }, { "family_name": "Vielmetter", "given_name": "Jost", "clpid": "Vielmetter-J" }, { "family_name": "Pepke", "given_name": "Shirley", "clpid": "Pepke-S" }, { "literal": "ENCODE Project Consortium" } ], "abstract": "The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.", "doi": "10.1371/journal.pbio.1001046", "pmcid": "PMC3079585", "issn": "1544-9173", "publisher": "Public Library of Science", "publication": "PLoS Biology", "publication_date": "2011-04", "series_number": "4", "volume": "9", "issue": "4", "pages": "Art. No. e1001046" } ]